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"<>| X{?[e}>e * 32 32 True True 0 True 0 72/1 72/1 2 ImageReady 2006-08-27T23:21:21Z 2007-09-04T21:47:27Z 2007-09-04T21:47:27Z adobe:docid:imageready:7ec277b3-37bb-11db-8f2a-fe631e034311 1 image/x-photoshop 8BIM%F &VڰwMeSaZZ HotSpotID hotSpotIDlong hotSpotTypeenum HotSpotTypeNoneMeSa["MeSa]SaveLayersSettingsIncludeBackgroundboolLayerFileSavingSettingsObjcLayerFileSavingSettingsLayerFileDuplicateBehaviorenumEDuplicateFileNameBehavioroverwriteConfirmLayerFileNameCompatibilityObjcLayerFileNameCompatibilityLayerFileNameCompatibilityMacboolLayerFileNameCompatibilityUNIXbool!LayerFileNameCompatibilityWindowsboolLayerFileNameComponentsVlLsObjcFileNameComponentFileNameComponentTypeenumEFileNameComponentdocNameObjcFileNameComponentFileNameComponentTypeenumEFileNameComponent 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HTMLSettingsObjcnullAlwaysAddAltAttributebool AttributeCaselong CloseAllTagsboolEncodinglongEscapeDoubleByteURLCharsboolFileSavingSettingsObjcnull CopyBackgroundboolDuplicateFileNameBehaviorlongHtmlFileNameComponentsVlLslonglonglonglonglonglongImageSubfolderNameTEXTimages IncludeXMPboolNameCompatibilityObjcnull NameCompatMacboolNameCompatUNIXboolNameCompatWindowsboolOutputMultipleFilesboolSavingFileNameComponentsVlLs longlonglonglonglonglonglonglonglongSliceFileNameComponentsVlLslonglonglonglonglonglongUseImageSubfolderboolUseLongExtensionsboolGoLiveCompatibleboolImageMapLocationlong ImageMapTypelongIncludeCommentsboolIncludeZeroMarginsboolIndentlong LineEndingslong OutputXHTMLboolQuoteAllAttributesboolSpacersEmptyCellslongSpacersHorizontallongSpacersVerticallong StylesFormatlong TDWidthHeightlongTagCaselongUseCSSboolUseLongHTMLExtensionboolMetadataOutputSettingsObjcnull AddCustomIRboolAddEXIFboolAddXMPboolAddXMPSourceFileURIboolWriteMinimalXMPboolWriteXMPToSidecarFilesboolVersionlongD2 J8BIMnorm(Layer 28BIMluniLayer 28BIMlyidZ.8BIMlnsrlayr8BIMlspf8BIMclbl8BIMinfx8BIMknko8BIMfxrp@(8BIMlclr8BIMshpa8BIMshmd8BIMmlstnullLaIDlongZ.LaStVlLsObjcnullFXRfObjcnullHrzndoubVrtcdoub@(FrLsVlLslongKenabbool8BIMcmlsnullLyrIlongZ. layerSettingsVlLsorigFXRefPointObjcnullHrzndoubVrtcdoub@(8BIMmdyn 8BIMnorm(Layer 48BIMlfx2 nullChFXObjcnull AntAboolClr ObjcRGBCBl doub@IGrn doub@IRd doub@IDstndoub@InvrboolMd enumBlnMDfrnMpgSObjcShpCCrv VlLsObjcCrPtHrzndoubVrtcdoubObjcCrPtHrzndoub@` Vrtcdoub@oObjcCrPtHrzndoub@oVrtcdoubNm TEXTConeOpctUntF#Prc@Fblurdoub@0enabboollaglUntF#AngT@FrFXObjcnullClr ObjcRGBCBl doubGrn doubRd doubMd enumBlnMNrmlOpctUntF#Prc@YPntTenumFrFlSClrStylenumFStlOutFSz doub?enabboolGrFlObjcnull AlgnboolAnglUntF#Ang@VGradObjcGrdnClrsVlLsObjcClryClr ObjcRGBCBl doub@oQQRGrn doub@n* Rd doub@mLctnlongMdpnlong2TypeenumClryUsrSObjcClryClr ObjcRGBCBl doub@kGrn doub@iRd doub@hGGLctnlongMdpnlong/TypeenumClryUsrSObjcClryClr ObjcRGBCBl doub@gGrn doub@fTTURd doub@eLctnlong2Mdpnlong2TypeenumClryUsrSObjcClryClr ObjcRGBCBl doub@nyyGrn doub@m@ Rd doub@l&LctnlongMdpnlong2TypeenumClryUsrSGrdFenumGrdFCstSNm TEXTCustomTrnsVlLsObjcTrnSLctnlongMdpnlong2OpctlongdObjcTrnSLctnlongMdpnlong2OpctlongdMd enumBlnMNrmlOfstObjcnullHrznUntF#PrcVrtcUntF#PrcOpctUntF#Prc@YRvrsboolScl UntF#Prc@STypeenumGrdTLnr enabboolIrGlObjcnull AntAboolCkmtdoub@ Clr ObjcRGBCBl doub@oGrn doub@oRd doub@oGlwTenumBETESfBLInprUntF#Prc@PFFFFFFMd enumBlnMScrnNoseUntF#PrcOpctUntF#Prc@RShdNUntF#Prc@@xxxxxxTrnSObjcShpCCrv VlLsObjcCrPtHrzndoubVrtcdoubObjcCrPtHrzndoub@oVrtcdoub@oblurdoub@enabboolglwSenumIGSrSrcESoFiObjcnullClr ObjcRGBCBl doub@oGrn doub@*Rd doubMd enumBlnMNrmlOpctUntF#Prc@9enabboolebblObjcnullLaldUntF#Ang@>SftndoubTrnSObjcShpCCrv VlLsObjcCrPtHrzndoubVrtcdoubObjcCrPtHrzndoub@oVrtcdoub@oblurdoub@bvlDenumBESsIn bvlSenumBESlInrBbvlTenumbvlTSfBLenabboolhglCObjcRGBCBl doub@oGrn doub@oRd doub@ohglMenumBlnMScrnhglOUntF#Prc@RlaglUntF#Ang@^sdwCObjcRGBCBl doubGrn doubRd doubsdwMenumBlnMMltpsdwOUntF#Prc@RsrgRUntF#Prc@5uglgboolantialiasGlossbooluseShapebool useTextureboolmasterFXSwitchbool8BIMlrFX8BIMcmnS8BIMdsdw3x8BIMmul 8BIMisdw3x8BIMmul 8BIMoglw*8BIMscrn8BIMiglw+8BIMscrn8BIMbevlNx8BIMscrn8BIMmul 8BIMsofi"8BIMnorm @ 8BIMluniLayer 48BIMlyid N8BIMlnsrlayr8BIMffxi N8BIMlspf8BIMclbl8BIMinfx8BIMknko8BIMfxrp8BIMlclr8BIMshpa8BIMshmd 8BIMmlstXnullLaIDlong NLaStVlLsObjcnullFrLsVlLslongKLefxObjcnullChFXObjcnull AntAboolClr ObjcRGBCBl doub@IGrn doub@IRd doub@IDstndoub@InvrboolMd enumBlnMDfrnMpgSObjcShpCCrv VlLsObjcCrPtHrzndoubVrtcdoubObjcCrPtHrzndoub@` Vrtcdoub@oObjcCrPtHrzndoub@oVrtcdoubNm TEXTConeOpctUntF#Prc@Fblurdoub@0enabboollaglUntF#AngT@FrFXObjcnullClr ObjcRGBCBl doubGrn doubRd doubMd enumBlnMNrmlOpctUntF#Prc@YPntTenumFrFlSClrStylenumFStlOutFSz doub?enabboolGrFlObjcnull AlgnboolAnglUntF#Ang@VGradObjcGrdnClrsVlLsObjcClryClr ObjcRGBCBl doub@oQQRGrn doub@n* Rd doub@mLctnlongMdpnlong2TypeenumClryUsrSObjcClryClr ObjcRGBCBl doub@kGrn doub@iRd doub@hGGLctnlongMdpnlong/TypeenumClryUsrSObjcClryClr ObjcRGBCBl doub@gGrn doub@fTTURd doub@eLctnlong2Mdpnlong2TypeenumClryUsrSObjcClryClr ObjcRGBCBl doub@nyyGrn doub@m@ Rd doub@l&LctnlongMdpnlong2TypeenumClryUsrSGrdFenumGrdFCstSNm TEXTCustomTrnsVlLsObjcTrnSLctnlongMdpnlong2OpctlongdObjcTrnSLctnlongMdpnlong2OpctlongdMd enumBlnMNrmlOfstObjcnullHrznUntF#PrcVrtcUntF#PrcOpctUntF#Prc@YRvrsboolScl UntF#Prc@STypeenumGrdTLnr enabboolIrGlObjcnull AntAboolCkmtdoub@ Clr ObjcRGBCBl doub@oGrn doub@oRd doub@oGlwTenumBETESfBLInprUntF#Prc@PFFFFFFMd enumBlnMScrnNoseUntF#PrcOpctUntF#Prc@RShdNUntF#Prc@@xxxxxxTrnSObjcShpCCrv VlLsObjcCrPtHrzndoubVrtcdoubObjcCrPtHrzndoub@oVrtcdoub@oblurdoub@enabboolglwSenumIGSrSrcESoFiObjcnullClr ObjcRGBCBl doub@oGrn doub@*Rd doubMd enumBlnMNrmlOpctUntF#Prc@9enabboolebblObjcnullLaldUntF#Ang@>SftndoubTrnSObjcShpCCrv VlLsObjcCrPtHrzndoubVrtcdoubObjcCrPtHrzndoub@oVrtcdoub@oblurdoub@bvlDenumBESsIn bvlSenumBESlInrBbvlTenumbvlTSfBLenabboolhglCObjcRGBCBl doub@oGrn doub@oRd doub@ohglMenumBlnMScrnhglOUntF#Prc@RlaglUntF#Ang@^sdwCObjcRGBCBl doubGrn doubRd doubsdwMenumBlnMMltpsdwOUntF#Prc@RsrgRUntF#Prc@5uglgboolantialiasGlossbooluseShapebool useTextureboolmasterFXSwitchboolenabbool8BIMcmlsnullLyrIlong N layerSettingsVlLsorigFXRefPointObjcnullHrzndoubVrtcdoub8BIMmdyn 8BIMnorm(Layer 38BIMlfx20nullDrShObjcnull AntAboolCkmtdoubClr ObjcRGBCBl doubGrn doubRd doubDstndoub@Md enumBlnMMltpNoseUntF#PrcOpctUntF#Prc@9TrnSObjcShpCCrv VlLsObjcCrPtHrzndoubVrtcdoubObjcCrPtHrzndoub@oVrtcdoub@oblurdoub@enabboollaglUntF#Ang@^uglgbool layerConcealsboolmasterFXSwitchbool8BIMlrFX8BIMcmnS8BIMdsdw3x8BIMmul @8BIMisdw3x8BIMmul 8BIMoglw*8BIMscrn8BIMiglw+8BIMscrn8BIMbevlNx8BIMscrn8BIMmul 8BIMsofi"8BIMnorm8BIMluniLayer 38BIMlyidhL8BIMlnsrlayr8BIMlspf8BIMclbl8BIMinfx8BIMknko8BIMfxrp8BIMlclr8BIMshpa8BIMshmd8BIMmlstnullLaIDlonghLLaStVlLsObjcnullFXRfObjcnullHrzndoubVrtcdoubFrLsVlLslongKLefxObjcnullDrShObjcnull AntAboolCkmtdoubClr ObjcRGBCBl doubGrn doubRd doubDstndoub@Md enumBlnMMltpNoseUntF#PrcOpctUntF#Prc@9TrnSObjcShpCCrv VlLsObjcCrPtHrzndoubVrtcdoubObjcCrPtHrzndoub@oVrtcdoub@oblurdoub@enabboollaglUntF#Ang@^uglgbool layerConcealsboolmasterFXSwitchboolenabbool8BIMcmlsnullLyrIlonghL layerSettingsVlLsorigFXRefPointObjcnullHrzndoubVrtcdoub8BIMmdyn         ctMlq\mbNqXE1|ZctMlq\qhC5|ZctMqwa\U% |ZiwOP.`~}@N1 mZ7m~nLK- mygO}g_:mygNvg|e0* mygNvfxEtW4 mygNvfx~N;4 ctMlq\mbNqXE1|ZctMlq\qhC5|ZctMqwa\U% |ZiwOP.`~}@N1 mZ7m~nLK- mygO}g_:mygNvg|e0* mygNvfxEtW4 mygNvfx~N;4 ctMlq\mbNqXG%|ZctMlq\qhC5|ZctMqwa\U%  |ZiwOP. `~}@ N1  mZ7 m~nLK- mygO}g_: mygNvg|e0* mygNvfxEtW4 mygNvfx~N=*   @*dE0kU8OKeNJ+dF+n/r   U ZZY kU P ki H i A < z 887 y 4 ¨ 0 , 300.014 85569 } DBE l Ĩ T ~ s l   U ZZY kU P ki H i BAB  <  8  4 100 , 300//13 δ 85569 պ DCD Ū T ʯ    U ZZY kU P ki H i AAB <  8  4  0 , 200/013 ׽ 85569 ɯ DCD ӹ T Ī  8BIMPattX ,  60's flowers$d2e349e2-37ba-11db-8f2a-fe631e034311+  $ "/+*+('&+&!     Ȑatajaaaaaaataaja}ajaaaaa}aaj}aaҿ}aaaaҵaa}}at}aaaaaajataa taa}a}aaaaajajajtaa}aaajaaaaaataa}ajaa} j $$-,,+)'*,+! !    ˁˁˁˁˁˁˁˁˁˁˁˇǗ  ļǢǢěǦěǟ˔ˮĦˢ˦DZǢĪľııǷǺıĿĮǵǟĮ˔ĦǟǢǢǗǪěǦ˶˶˵˵˴˳˲˱˯ˮ˭ˬ˪˩˨˲˸˺˻˻˻˻˻˻˹˪˪˪˫˫ˬˬˬ˭˭˭˭˭ˬ˫ˁˁˁˁˁˁˁ  & %1.,-)'*-,! !    񜁜񜁜񜁜񜁜񜁜񜁜񜁜񜁜񜁜񜁜񜁜񜇜ȩ՜Ɯڜלǜ؜ȜٜɜќٜɜٜʜٜɜߠڜȜќڜǜٜƜ͜ߠٜŜٜŜĜٜ֠ϜٜМٜМߥٜϜĥٜϜ ٜΜޜߩߜߠȜ֠ȜҜќМΜ̜ʜǜŜÜߜܜڜݜĜƜȜʜ͜ϜМҜӜӜԜԜԜԜԜԜӜҜќٜٜٜٜٜٜٜٜٜڜԜڜ՜vٜ֜vٜ֜xvٜ֜v؜֜v؜xv{vלv}}v{՜vv񜶜vv񜶜vv񜵜{vxv񜵜v}vx񜴜xv{v񜳜xvv񜲜}vv񜱜}v}v{vv{񜯜vvxv񜮜vv{v{񜭜xv{v{v񜬜}vvxvx񜪜v{vvv񜩜{v}v񜨜}v}񜲜{v{񜸜{v񜺜{v񜻜vv}񜻜}vxv{vx񜻜vvv񜻜vxvv񜻜vv{v{񜻜}vvvx񜹜vv񜪜xvv񜪜vxv񜪜{vv}񜫜vv񜫜vv񜬜v}v񜬜vxv񜬜}vv{񜭜v{vx񜭜v񜭜vޜ񜭜vޜ񜭜vݜ񜬜vݜ񜫜ۜ񜁜񜁜񜁜񜁜񜁜񜁜񜁜w,  60's flowers$007e9f37-5ccb-11dc-9a94-d14c481cfae2+  $ "/+*+('&+&!     Ȑatajaaaaaaataaja}ajaaaaa}aaj}aaҿ}aaaaҵaa}}at}aaaaaajataa taa}a}aaaaajajajtaa}aaajaaaaaataa}ajaa} j $$-,,+)'*,+! !    ˁˁˁˁˁˁˁˁˁˁˁˇǗ  ļǢǢěǦěǟ˔ˮĦˢ˦DZǢĪľııǷǺıĿĮǵǟĮ˔ĦǟǢǢǗǪěǦ˶˶˵˵˴˳˲˱˯ˮ˭ˬ˪˩˨˲˸˺˻˻˻˻˻˻˹˪˪˪˫˫ˬˬˬ˭˭˭˭˭ˬ˫ˁˁˁˁˁˁˁ  & %1.,-)'*-,! !    񜁜񜁜񜁜񜁜񜁜񜁜񜁜񜁜񜁜񜁜񜁜񜇜ȩ՜Ɯڜלǜ؜ȜٜɜќٜɜٜʜٜɜߠڜȜќڜǜٜƜ͜ߠٜŜٜŜĜٜ֠ϜٜМٜМߥٜϜĥٜϜ ٜΜޜߩߜߠȜ֠ȜҜќМΜ̜ʜǜŜÜߜܜڜݜĜƜȜʜ͜ϜМҜӜӜԜԜԜԜԜԜӜҜќٜٜٜٜٜٜٜٜٜڜԜڜ՜vٜ֜vٜ֜xvٜ֜v؜֜v؜xv{vלv}}v{՜vv񜶜vv񜶜vv񜵜{vxv񜵜v}vx񜴜xv{v񜳜xvv񜲜}vv񜱜}v}v{vv{񜯜vvxv񜮜vv{v{񜭜xv{v{v񜬜}vvxvx񜪜v{vvv񜩜{v}v񜨜}v}񜲜{v{񜸜{v񜺜{v񜻜vv}񜻜}vxv{vx񜻜vvv񜻜vxvv񜻜vv{v{񜻜}vvvx񜹜vv񜪜xvv񜪜vxv񜪜{vv}񜫜vv񜫜vv񜬜v}v񜬜vxv񜬜}vv{񜭜v{vx񜭜v񜭜vޜ񜭜vޜ񜭜vݜ񜬜vݜ񜫜ۜ񜁜񜁜񜁜񜁜񜁜񜁜񜁜w8BIMTxt2: /DocumentResources << /FontSet << /Resources [ << /Resource << /StreamTag /CoolTypeFont /Identifier << /Name (Helvetica) /Type 1 >> >> >> << /Resource << /StreamTag /CoolTypeFont /Identifier << /Name (AdobeInvisFont) /Type 0 >> >> >> ] >> /MojiKumiCodeToClassSet << /Resources [ << /Resource << /Name () /Members << /ClassMappings [ << /R (55) /C 1 >> << /R (77) /C 1 >> << /R (99) /C 1 >> << /R (;;) /C 1 >> << /R (==) /C 1 >> << /R (??) /C 1 >> << /R (AA) /C 1 >> << /R (CC) /C 1 >> << /R () /C 1 >> << /R (;;) /C 1 >> << /R ([[) /C 1 >> << /R (  ) /C 1 >> << /R (  ) /C 1 >> << /R (00) /C 1 >> << /R (0 0 ) /C 1 >> << /R (0 0 ) /C 1 >> << /R (00) /C 1 >> << /R (00) /C 1 >> << /R (00) /C 1 >> << /R (66) /C 2 >> << /R (88) /C 2 >> << /R (::) /C 2 >> << /R (<<) /C 2 >> << /R (>>) /C 2 >> << /R (@@) /C 2 >> << /R (BB) /C 2 >> << /R (DD) /C 2 >> << /R ( ) /C 2 >> << /R (==) /C 2 >> << /R (]]) /C 2 >> << /R (  ) /C 2 >> << /R (  ) /C 2 >> << /R (0 0 ) /C 2 >> << /R (0 0 ) /C 2 >> << /R (0 0 ) /C 2 >> << /R (00) /C 2 >> << /R (00) /C 2 >> << /R (00) /C 2 >> << /R () /C 3 >> << /R (^^) /C 3 >> << /R (0A0A) /C 3 >> << /R (0C0C) /C 3 >> << /R (0E0E) /C 3 >> << /R (0G0G) /C 3 >> << /R (0I0I) /C 3 >> << /R (0c0c) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R () /C 4 >> << /R () /C 4 >> << /R () /C 5 >> << /R (00) /C 5 >> << /R (  ) /C 5 >> << /R () /C 6 >> << /R (00) /C 6 >> << /R ( ) /C 7 >> << /R (00) /C 7 >> << /R (  ) /C 8 >> << /R ( % &) /C 8 >> << /R () /C 9 >> << /R () /C 9 >> << /R () /C 9 >> << /R () /C 10 >> << /R () /C 10 >> << /R () /C 10 >> << /R ( 0 0) /C 10 >> << /R ( 2 4) /C 10 >> << /R (00) /C 11 >> << /R (0B0B) /C 12 >> << /R (0D0D) /C 12 >> << /R (0F0F) /C 12 >> << /R (0H0H) /C 12 >> << /R (0J0b) /C 12 >> << /R (0d0) /C 12 >> << /R (00) /C 12 >> << /R (00) /C 12 >> << /R (00) /C 12 >> << /R () /C 13 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (2 2C) /C 14 >> << /R (22) /C 14 >> << /R (22) /C 14 >> << /R (33W) /C 14 >> << /R (3q3v) /C 14 >> << /R (33) /C 14 >> << /R (N) /C 14 >> << /R (09) /C 15 >> << /R (!~) /C 16 >> << /R () /C 16 >> ] >> >> >> ] /DisplayList [ << /Resource 0 >> ] >> /MojiKumiTableSet << /Resources [ << /Resource << /Name (Photoshop6MojiKumiSet4) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 11 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 17 ] /Data << /B << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 4 16 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> ] >> << /Index 5 /Elements [ << /P [ 5 1 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 2 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 3 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 4 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 5 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 1 >> >> >> << /P [ 5 6 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 17 ] /Data << /B << /R [ 0.25 0.25 0.25 ] >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.75 0.75 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 17 ] /Data << /B << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 17 ] /Data << /B << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 9 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 9 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 9 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 9 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 10 /Elements [ << /P [ 10 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 10 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 10 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 10 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 17 /Elements [ << /P [ 17 1 ] /Data << /A << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> << /Index 18 /Elements [ << /P [ 18 1 ] /Data << /A << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> ] >> >> /PredefinedTag 2 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet3) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 11 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 17 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 4 16 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> ] >> << /Index 5 /Elements [ << /P [ 5 1 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 2 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 3 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 4 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 5 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 1 >> >> >> << /P [ 5 6 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.75 0.75 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 17 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 17 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 9 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 9 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 9 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 9 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 10 /Elements [ << /P [ 10 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 10 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 10 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 10 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 4 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet2) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 11 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 4 16 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> ] >> << /Index 5 /Elements [ << /P [ 5 1 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 2 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 3 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 4 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 5 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 1 >> >> >> << /P [ 5 6 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.75 0.75 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 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0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 3 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet1) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.0 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<< /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 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/R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] 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/Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 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/Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] 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<< /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 3 >> >> >> << /Resource << /Name (GyomatsuYakumonoZenkaku) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before 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>> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 17 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << 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0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.75 0.75 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 17 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 17 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 9 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 9 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 9 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 9 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 10 /Elements [ << /P [ 10 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 10 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 10 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 10 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 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1 >> << /R (00) /C 1 >> << /R (66) /C 2 >> << /R (88) /C 2 >> << /R (::) /C 2 >> << /R (<<) /C 2 >> << /R (>>) /C 2 >> << /R (@@) /C 2 >> << /R (BB) /C 2 >> << /R (DD) /C 2 >> << /R ( ) /C 2 >> << /R (==) /C 2 >> << /R (]]) /C 2 >> << /R (  ) /C 2 >> << /R (  ) /C 2 >> << /R (0 0 ) /C 2 >> << /R (0 0 ) /C 2 >> << /R (0 0 ) /C 2 >> << /R (00) /C 2 >> << /R (00) /C 2 >> << /R (00) /C 2 >> << /R () /C 3 >> << /R (^^) /C 3 >> << /R (0A0A) /C 3 >> << /R (0C0C) /C 3 >> << /R (0E0E) /C 3 >> << /R (0G0G) /C 3 >> << /R (0I0I) /C 3 >> << /R (0c0c) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R () /C 4 >> << /R () /C 4 >> << /R () /C 5 >> << /R (00) /C 5 >> << /R (  ) /C 5 >> << /R () /C 6 >> << /R (00) /C 6 >> << /R ( ) /C 7 >> << /R (00) /C 7 >> << /R (  ) /C 8 >> << /R ( % &) /C 8 >> << /R () /C 9 >> << /R () /C 9 >> << /R () /C 9 >> << /R () /C 10 >> << /R () /C 10 >> << /R () /C 10 >> << /R ( 0 0) /C 10 >> << /R ( 2 4) /C 10 >> << /R (00) /C 11 >> << /R (0B0B) /C 12 >> << /R (0D0D) /C 12 >> << /R (0F0F) /C 12 >> << /R (0H0H) /C 12 >> << /R (0J0b) /C 12 >> << /R (0d0) /C 12 >> << /R (00) /C 12 >> << /R (00) /C 12 >> << /R (00) /C 12 >> << /R () /C 13 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (00) /C 14 >> << /R (2 2C) /C 14 >> << /R (22) /C 14 >> << /R (22) /C 14 >> << /R (33W) /C 14 >> << /R (3q3v) /C 14 >> << /R (33) /C 14 >> << /R (N) /C 14 >> << /R (09) /C 15 >> << /R (!~) /C 16 >> << /R () /C 16 >> ] >> >> >> ] /DisplayList [ << /Resource 0 >> ] >> /MojiKumiTableSet << /Resources [ << /Resource << /Name 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/P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 4 16 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> ] >> << /Index 5 /Elements [ << /P [ 5 1 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 2 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 3 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 4 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 5 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 1 >> >> >> << /P [ 5 6 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 17 ] /Data << /B << /R [ 0.25 0.25 0.25 ] >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.75 0.75 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 17 ] /Data << /B << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 17 ] /Data << /B << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A 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/R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 17 /Elements [ << /P [ 17 1 ] /Data << /A << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> << /Index 18 /Elements [ << /P [ 18 1 ] /Data << /A << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> ] >> >> /PredefinedTag 2 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet3) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] 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<< /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 9 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 10 /Elements [ << /P [ 10 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 10 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 10 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 10 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> 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0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 4 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet2) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> 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<< /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.75 0.75 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P 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/Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 9 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 10 /Elements [ << /P [ 10 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 10 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 10 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 10 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R 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0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 3 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet1) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 9 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 10 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 11 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] 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[ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> 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/P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 1 >> >> >> << /Resource << /Name (YakumonoHankaku) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 9 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 10 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 11 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 4 16 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> ] >> << /Index 5 /Elements [ << /P [ 5 1 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 2 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 3 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 4 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 5 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 1 >> >> >> << /P [ 5 6 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 9 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 9 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 9 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 9 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 10 /Elements [ << /P [ 10 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 10 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 10 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 10 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 1 >> >> >> << /Resource << /Name (GyomatsuYakumonoHankaku) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 11 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 4 16 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> ] >> << /Index 5 /Elements [ << /P [ 5 1 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 2 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 3 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 4 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 5 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 1 >> >> >> << /P [ 5 6 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.75 0.75 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 9 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 9 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 9 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 9 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 10 /Elements [ << /P [ 10 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 10 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 10 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 10 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 3 >> >> >> << /Resource << /Name (GyomatsuYakumonoZenkaku) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 11 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 17 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P 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5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.75 0.75 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 17 ] 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<< /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 9 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 9 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 9 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 9 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 10 /Elements [ << /P [ 10 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 10 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 10 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 10 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 4 >> >> >> << /Resource << /Name (YakumonoZenkaku) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << 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ESliceTypeImg nullTEXTaltTagTEXT bgColorTypeenumESliceBGColorTypeNone bottomOutsetlongboundsObjcRct1Btomlong LeftlongRghtlong Top longcellTextTEXTcellTextIsHTMLboolgroupIDlong horzAlignenumESliceHorzAligndefault leftOutsetlongoriginenum ESliceOrigin autoGenerated rightOutsetlongsliceIDlong topOutsetlongurlTEXT vertAlignenumESliceVertAligndefault8BIM!YAdobe ImageReadyAdobe ImageReady 8.08BIM"MM*nv(1 ~2iHHImageReady2006-08-27T23:21:21Z a  8BIM$ < 32 32 True True 0 True 0 72/1 72/1 2 ImageReady 2006-08-27T23:21:21Z 2007-09-05T14:55:30Z 2007-09-05T14:55:30Z adobe:docid:imageready:7ec277b3-37bb-11db-8f2a-fe631e034311 1 image/x-photoshop 8BIM%F &VڰwMeSaZZ HotSpotID hotSpotIDlong hotSpotTypeenum 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>> << /R (??) /C 1 >> << /R (AA) /C 1 >> << /R (CC) /C 1 >> << /R () /C 1 >> << /R (;;) /C 1 >> << /R ([[) /C 1 >> << /R (  ) /C 1 >> << /R (  ) /C 1 >> << /R (00) /C 1 >> << /R (0 0 ) /C 1 >> << /R (0 0 ) /C 1 >> << /R (00) /C 1 >> << /R (00) /C 1 >> << /R (00) /C 1 >> << /R (66) /C 2 >> << /R (88) /C 2 >> << /R (::) /C 2 >> << /R (<<) /C 2 >> << /R (>>) /C 2 >> << /R (@@) /C 2 >> << /R (BB) /C 2 >> << /R (DD) /C 2 >> << /R ( ) /C 2 >> << /R (==) /C 2 >> << /R (]]) /C 2 >> << /R (  ) /C 2 >> << /R (  ) /C 2 >> << /R (0 0 ) /C 2 >> << /R (0 0 ) /C 2 >> << /R (0 0 ) /C 2 >> << /R (00) /C 2 >> << /R (00) /C 2 >> << /R (00) /C 2 >> << /R () /C 3 >> << /R (^^) /C 3 >> << /R (0A0A) /C 3 >> << /R (0C0C) /C 3 >> << /R (0E0E) /C 3 >> << /R (0G0G) /C 3 >> << /R (0I0I) /C 3 >> << /R (0c0c) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) /C 3 >> << /R (00) 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>> << /R (3q3v) /C 14 >> << /R (33) /C 14 >> << /R (N) /C 14 >> << /R (09) /C 15 >> << /R (!~) /C 16 >> << /R () /C 16 >> ] >> >> >> ] /DisplayList [ << /Resource 0 >> ] >> /MojiKumiTableSet << /Resources [ << /Resource << /Name (Photoshop6MojiKumiSet4) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << 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2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 17 /Elements [ << /P [ 17 1 ] /Data << /A << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> << /Index 18 /Elements [ << /P [ 18 1 ] /Data << /A << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> ] >> >> /PredefinedTag 2 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet3) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 11 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 17 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 4 16 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> ] >> << /Index 5 /Elements [ << /P [ 5 1 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 2 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 3 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 4 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 5 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 1 >> >> >> << /P [ 5 6 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.75 0.75 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 17 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 17 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 9 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 9 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 9 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 9 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 10 /Elements [ << /P [ 10 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 10 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 10 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 10 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 4 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet2) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 11 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 4 16 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> ] >> << /Index 5 /Elements [ << /P [ 5 1 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 2 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 3 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 4 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 5 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 1 >> >> >> << /P [ 5 6 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.75 0.75 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 9 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 9 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 9 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 9 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 10 /Elements [ << /P [ 10 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 10 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 10 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 10 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 3 >> >> >> << /Resource << /Name (Photoshop6MojiKumiSet1) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 9 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 10 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 11 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 4 16 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> ] >> << /Index 5 /Elements [ << /P [ 5 1 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 2 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 3 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 4 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 5 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 1 >> >> >> << /P [ 5 6 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 9 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 9 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 9 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 9 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 10 /Elements [ << /P [ 10 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 10 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 10 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 10 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 1 >> >> >> << /Resource << /Name (YakumonoHankaku) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 9 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 10 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 11 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 2 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> ] >> << /Index 3 /Elements [ << /P [ 3 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 3 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 3 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 3 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 4 16 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> ] >> << /Index 5 /Elements [ << /P [ 5 1 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 2 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 3 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 4 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 5 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 1 >> >> >> << /P [ 5 6 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 2 >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 9 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 9 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 9 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R [ 0.0 0.0 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<< /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 1 >> >> >> << /Resource << /Name (GyomatsuYakumonoHankaku) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] 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<< /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 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>> << /P [ 10 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 10 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 10 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 11 /Elements [ << /P [ 11 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 11 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 11 15 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> << /P [ 11 16 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 4 >> >> >> ] >> << /Index 12 /Elements [ << /P [ 12 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 12 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 12 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 12 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 12 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 12 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 13 /Elements [ << /P [ 13 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 13 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 13 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 13 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 13 15 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 13 16 ] /Data << /B << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 14 /Elements [ << /P [ 14 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 14 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 14 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 14 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 14 15 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 14 16 ] /Data << /B << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 15 /Elements [ << /P [ 15 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 15 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 15 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 15 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 15 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 15 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 15 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 15 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 16 /Elements [ << /P [ 16 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 16 3 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 4 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 16 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 16 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 16 8 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 9 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 16 10 ] /Data << /A << /R [ 0.0 0.0 0.5 ] >> >> >> << /P [ 16 12 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 16 14 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> ] >> >> /PredefinedTag 4 >> >> >> << /Resource << /Name (YakumonoZenkaku) /Members << /CodeToClass 0 /AutoTsume << /TsumeMappings [ << /Before -0.5 /Code () >> << /Before -0.5 /Code (;) >> << /Before -0.5 /Code ([) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code ( ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0 ) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /Before -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (=) >> << /After -0.5 /Code (]) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0 ) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code (0) >> << /After -0.5 /Code () >> << /After -0.5 /Code (0) >> << /After -0.5 /Code ( ) >> << /After -0.5 /Code (0) >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code () >> << /Before -0.25 /After -0.25 /Code (0) >> << /Before -0.25 /After -0.25 /Code ( ) >> ] >> /Table << /DataArray << /SparseArray [ << /Index 1 /Elements [ << /P [ 1 5 ] /Data << /A << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> ] >> << /Index 2 /Elements [ << /P [ 2 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 2 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 3 >> >> >> << /P [ 2 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 2 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 2 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 2 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P 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<< /P [ 3 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 3 15 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> << /P [ 3 16 ] /Data << /A << /R [ 0.125 0.25 0.5 ] /P 4 >> >> >> ] >> << /Index 4 /Elements [ << /P [ 4 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 4 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 4 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 4 15 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> << /P [ 4 16 ] /Data << /A << /R [ 0.125 0.25 0.25 ] /P 4 >> >> >> ] >> << /Index 5 /Elements [ << /P [ 5 1 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 2 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 3 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 4 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 5 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 1 >> >> >> << /P [ 5 6 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 7 ] /Data << /B << /R [ 0.25 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 8 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 9 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 10 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 11 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 12 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 13 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 14 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 15 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 16 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 5 17 ] /Data << /B << /R [ 0.25 0.25 0.25 ] >> >> >> ] >> << /Index 6 /Elements [ << /P [ 6 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 6 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 5 ] /Data << /B << /R [ 0.0 0.75 0.75 ] /P 1 >> >> >> << /P [ 6 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 6 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 11 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] >> >> >> << /P [ 6 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 4 >> >> >> << /P [ 6 17 ] /Data << /B << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> << /Index 7 /Elements [ << /P [ 7 1 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 3 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 4 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 5 ] /Data << /B << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 7 7 ] /Data << /B << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 7 8 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 9 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 10 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 12 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 13 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 14 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 15 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 16 ] /Data << /B << /R [ 0.0 0.5 0.5 ] /P 2 >> >> >> << /P [ 7 17 ] /Data << /B << /R [ 0.5 0.5 0.5 ] >> >> >> ] >> << /Index 8 /Elements [ << /P [ 8 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 8 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 8 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 8 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 8 15 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> << /P [ 8 16 ] /Data << /A << /R [ 0.0 0.0 0.5 ] /P 4 >> >> >> ] >> << /Index 9 /Elements [ << /P [ 9 1 ] /Data << /A << /R [ 0.0 0.5 0.5 ] /P 3 >> >> >> << /P [ 9 3 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 5 ] /Data << /A << /R [ 0.0 0.25 0.25 ] /P 1 >> >> >> << /P [ 9 7 ] /Data << /A << /R [ 0.0 0.0 0.0 ] /P 2 >> >> >> << /P [ 9 8 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 9 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 10 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 12 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 13 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 14 ] /Data << /A << /R [ 0.0 0.0 1.0 ] >> >> >> << /P [ 9 15 ] /Data << /A << /R 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0000034778 00000 n 0000034798 00000 n 0000035313 00000 n 0000035333 00000 n 0000035619 00000 n trailer <]>> startxref 49020 %%EOF figtree-1.4.3/README.md000066400000000000000000000005451277473563300144500ustar00rootroot00000000000000_FigTree_ FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST. figtree-1.4.3/WebRoot/000077500000000000000000000000001277473563300145465ustar00rootroot00000000000000figtree-1.4.3/WebRoot/META-INF/000077500000000000000000000000001277473563300157065ustar00rootroot00000000000000figtree-1.4.3/WebRoot/META-INF/MANIFEST.MF000066400000000000000000000000471277473563300173410ustar00rootroot00000000000000Manifest-Version: 1.0 Class-Path: figtree-1.4.3/WebRoot/META-INF/context.xml000066400000000000000000000000601277473563300201100ustar00rootroot00000000000000 figtree-1.4.3/WebRoot/WEB-INF/000077500000000000000000000000001277473563300155755ustar00rootroot00000000000000figtree-1.4.3/WebRoot/WEB-INF/context.xml000066400000000000000000000000571277473563300200050ustar00rootroot00000000000000 figtree-1.4.3/WebRoot/WEB-INF/jetty-web.xml000066400000000000000000000006011277473563300202260ustar00rootroot00000000000000 false figtree-1.4.3/WebRoot/WEB-INF/web.xml000066400000000000000000000007771277473563300171070ustar00rootroot00000000000000 FigTree FigTree FigTree figtree.webui.Main FigTree /figtree/* figtree-1.4.3/WebRoot/figtree.css000066400000000000000000000001261277473563300167040ustar00rootroot00000000000000.tree { background-color: #EEEEEE; } .filename { background-color: #EEAAAA; }figtree-1.4.3/build.xml000077500000000000000000000277621277473563300150270ustar00rootroot00000000000000 Build file for FigTree $Id:$ figtree-1.4.3/build_applet.xml000066400000000000000000000050751277473563300163620ustar00rootroot00000000000000 Build file for FigTreeApplet $Id:$ figtree-1.4.3/examples/000077500000000000000000000000001277473563300150035ustar00rootroot00000000000000figtree-1.4.3/examples/HA_continuous_MCC.tre000066400000000000000000021433011277473563300207630ustar00rootroot00000000000000#NEXUS Begin taxa; Dimensions ntax=190; Taxlabels A_duck_Guangdong_12_2000 A_duck_Shanghai_08_2001 A_duck_Fujian_19_2000 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A_chicken_Bantul_BBVetI_2005 A_chicken_Salatiga_BBVetI_2005 A_chicken_Yogjakarta_BBVetIX_2004 A_chicken_Wajo_BBVM_2005 A_chicken_KulonProgo_BBVetXII1_2004 A_chicken_Guangdong_178_2004 A_chicken_Guangxi_2461_2004 A_duck_Hunan_1265_2005 A_duck_Hunan_1608_2005 A_duck_Guangxi_951_2005 A_goose_Guangxi_345_2005 A_duck_Vietnam_568_2005 A_chicken_Guangxi_2448_2004 A_greyheron_HongKong_728_2004 A_greyheron_HongKong_837_2004 A_duck_Guangxi_351_2004 A_duck_Guangxi_380_2004 A_Chicken_Shantou_810_2005 A_Quail_Shantou_911_2005 A_chicken_Guangxi_604_2005 A_quail_Guangxi_575_2005 A_duck_Guangxi_793_2005 A_chicken_Guangdong_191_2004 A_duck_Hunan_182_2005 A_chicken_Hunan_999_2005 A_duck_Hunan_139_2005 A_duck_Hunan_127_2005 A_duck_Hunan_152_2005 A_duck_Hunan_157_2005 A_Duck_Fujian_1734_2005 A_chicken_jiyuan_1_2003 A_chicken_zhengzhou_1_2002 A_chicken_Yamaguchi_7_2004 A_blowfly_Kyoto_93_2004 A_chicken_Kyoto_3_2004 A_crow_Kyoto_53_2004 A_chicken_Oita_8_2004 A_crow_Osaka_102_2004 A_chicken_Guangdong_174_2004 A_turkey_Suzdalka_Nov01_2005 A_Cygnusolor_Astrakhan_Ast0523_2005 A_Cygnusolor_Astrakhan_Ast0527_2005 A_Cygnusolor_Astrakhan_Ast0524_2005 A_Cygnusolor_Astrakhan_Ast0525_2005 A_goose_Novosibirsk_4_2005 A_grebe_Novosibirsk_29_2005 A_duck_Novosibirsk_56_2005 A_barheadedgoose_Mongolia_1_2005 A_whooperswan_Mongolia_3_2005 A_whooperswan_Mongolia_4_2005 A_whooperswan_Mongolia_6_2005 A_blackheadedgoose_Qinghai_2_2005 A_blackheadedgull_Qinghai_1_2005 A_blackheadedgoose_Qinghai_1_2005 A_BarheadedGoose_Qinghai_60_2005 A_BrownheadedGull_Qinghai_3_2005 A_greatblackheadedgull_Qinghai_1_2005 A_BarheadedGoose_Qinghai_65_2005 A_BarheadedGoose_Qinghai_59_2005 A_duck_Guangdong_173_2004 A_duck_HongKong_821_2002 A_HongKong_213_2003 A_egret_HongKong_7572_2003 A_chicken_Vietnam_27_2003 A_duck_Vietnam_S654_2005 A_quail_Vietnam_36_2004 A_chicken_VietNam_DT171_2004 A_Mallardduck_Vietnam_133_2004 A_VietNam_1203_2004 A_chicken_Nakornsawan202_2004 A_chicken_NakhonSawan_Thailand_CU39_2004 A_chicken_Bangkok_Thailand_CU20_2004 A_Hanoi_30408_2005 A_chicken_Bangkok_Thailand_CU3_2004 A_chicken_Bangkok_Thailand_CU6_2004 A_crow_Bangkok_Thailand_CU35_2004 A_chicken_Kamphaengphet204_2004 A_chicken_Nakornsawan203_2004 A_chicken_Nakornsawan207_2004 A_chicken_Kamphaengphet202_2004 A_chicken_Phitsanulok204_2004 A_chicken_Phitsanulok201_2004 A_chicken_Kamphaengphet205_2004 A_duck_Uthaithani201_2004 A_chicken_Phitsanulok202_2004 A_chicken_Nakornsawan201_2004 A_chicken_Uthaithani204_2004 A_chicken_Uthaithani202_2004 A_chicken_Uthaithani203_2004 A_chicken_Uthaithani201_2004 A_chicken_Nakornsawan205_2004 A_Hatay_2004 A_duck_Nakornsawan202_2004 A_chicken_NakhonSawan_Thailand_CU13_2004 A_rollers_Bangkok_Thailand_CU26_2004 A_chicken_Nakornsawan206_2004 A_duck_Uthaithani202_2004 A_crow_Bangkok_Thailand_CU4_2004 A_chicken_NakhonSawan_Thailand_CU12_2004 A_duck_Nakornsawan201_2004 A_chicken_Nakornsawan204_2004 A_chicken_Kamphaengphet201_2004 A_chicken_Thailand_Kamphaengphet303_2005 A_chicken_Thailand_Kamphaengphet304_2005 A_chicken_Thailand_Kamphaengphet301_2005 A_chicken_Thailand_Kamphaengphet302_2005 A_chicken_Kamphaengphet206_2004 A_duck_Phitsanulok201_2004 A_chicken_Kamphaengphet203_2004 A_crow_Bangkok_Thailand_CU25_2004 A_chicken_Phitsanulok203_2004 A_duck_Phitsanulok202_2004 A_chicken_Uthaithani205_2004 A_KaljiPheasant_Bangkok_Thailand_CU18_2004 A_whitepeafowl_Bangkok_Thailand_CU29_2004 A_muscovyduck_Vietnam_MdGL_2004 A_duck_Guangxi_35_2001 A_chicken_Hebei_326_2005 A_treesparrow_Henan_2_2004 A_chicken_Hebei_718_2001 A_duck_Guangdong_01_2001 A_duck_Shanghai_13_2001 A_duck_Guangdong_22_2002 A_duck_Fujian_17_2001 A_duck_Guangxi_22_2001 A_duck_Guangxi_07_1999 A_Goose_Guangdong_1_1996 A_HongKong_514_1997 A_HongKong_485_1997 A_HongKong_483_1997 A_chicken_HongKong_258_1997 A_Chicken_HongKong_220_1997 A_HongKong_491_1997 A_HongKong_542_1997 A_HongKong_503_1997 A_Chicken_HongKong_728_1997 A_HongKong_532_1997 A_HongKong_538_1997 A_HongKong_97_1998 A_HongKong_486_1997 A_chicken_HongKong_915_1997 A_Duck_HongKong_p46_1997 A_HongKong_516_1997 A_HongKong_488_1997 A_Goose_HongKong_w355_1997 A_HongKong_507_1997 A_HongKong_156_1997 A_HongKong_481_1997 ; End; Begin trees; Translate 1 A_duck_Guangdong_12_2000, 2 A_duck_Shanghai_08_2001, 3 A_duck_Fujian_19_2000, 4 A_duck_Guangdong_07_2000, 5 A_duck_Guangdong_40_2000, 6 A_duck_Shanghai_35_2002, 7 A_duck_Shanghai_38_2001, 8 A_duck_Guangxi_53_2002, 9 A_duck_Fujian_13_2002, 10 A_duck_Fujian_01_2002, 11 A_chicken_zhoukou_2_2002, 12 A_chicken_Hebei_108_2002, 13 A_duck_Shanghai_37_2002, 14 A_duck_Yokohama_aq10_2003, 15 A_treesparrow_Henan_4_2004, 16 A_blackbird_Hunan_1_2004, 17 A_treesparrow_Henan_3_2004, 18 A_treesparrow_Henan_1_2004, 19 A_chicken_Henan_01_2004, 20 A_chicken_Guangxi_2439_2004, 21 A_duck_Guangxi_1586_2004, 22 A_duck_Guangxi_1681_2004, 23 A_duck_Guangxi_1793_2004, 24 A_duck_Guangxi_1311_2004, 25 A_goose_Guangxi_2112_2004, 26 A_goose_Guangxi_1097_2004, 27 A_duck_Guangxi_2396_2004, 28 A_goose_Guangxi_2383_2004, 29 A_goose_Guangxi_1832_2004, 30 A_duck_Guangxi_2291_2004, 31 A_duck_Guangxi_1378_2004, 32 A_goose_Guangxi_914_2004, 33 A_swine_Fujian_F1_2001, 34 A_duck_Shantou_4610_2003, 35 A_Goose_Shantou_1621_2005, 36 A_chicken_Fujian_1042_2005, 37 A_duck_Fujian_897_2005, 38 A_goose_Shantou_2216_2005, 39 A_Ck_HK_619_2002, 40 A_chicken_HongKongi_863_2002, 41 A_duck_Guangxi_50_2001, 42 A_chicken_Wonosobo_BPPV4_2003, 43 A_chicken_Bantul_BBVetI_2005, 44 A_chicken_Salatiga_BBVetI_2005, 45 A_chicken_Yogjakarta_BBVetIX_2004, 46 A_chicken_Wajo_BBVM_2005, 47 A_chicken_KulonProgo_BBVetXII1_2004, 48 A_chicken_Guangdong_178_2004, 49 A_chicken_Guangxi_2461_2004, 50 A_duck_Hunan_1265_2005, 51 A_duck_Hunan_1608_2005, 52 A_duck_Guangxi_951_2005, 53 A_goose_Guangxi_345_2005, 54 A_duck_Vietnam_568_2005, 55 A_chicken_Guangxi_2448_2004, 56 A_greyheron_HongKong_728_2004, 57 A_greyheron_HongKong_837_2004, 58 A_duck_Guangxi_351_2004, 59 A_duck_Guangxi_380_2004, 60 A_Chicken_Shantou_810_2005, 61 A_Quail_Shantou_911_2005, 62 A_chicken_Guangxi_604_2005, 63 A_quail_Guangxi_575_2005, 64 A_duck_Guangxi_793_2005, 65 A_chicken_Guangdong_191_2004, 66 A_duck_Hunan_182_2005, 67 A_chicken_Hunan_999_2005, 68 A_duck_Hunan_139_2005, 69 A_duck_Hunan_127_2005, 70 A_duck_Hunan_152_2005, 71 A_duck_Hunan_157_2005, 72 A_Duck_Fujian_1734_2005, 73 A_chicken_jiyuan_1_2003, 74 A_chicken_zhengzhou_1_2002, 75 A_chicken_Yamaguchi_7_2004, 76 A_blowfly_Kyoto_93_2004, 77 A_chicken_Kyoto_3_2004, 78 A_crow_Kyoto_53_2004, 79 A_chicken_Oita_8_2004, 80 A_crow_Osaka_102_2004, 81 A_chicken_Guangdong_174_2004, 82 A_turkey_Suzdalka_Nov01_2005, 83 A_Cygnusolor_Astrakhan_Ast0523_2005, 84 A_Cygnusolor_Astrakhan_Ast0527_2005, 85 A_Cygnusolor_Astrakhan_Ast0524_2005, 86 A_Cygnusolor_Astrakhan_Ast0525_2005, 87 A_goose_Novosibirsk_4_2005, 88 A_grebe_Novosibirsk_29_2005, 89 A_duck_Novosibirsk_56_2005, 90 A_barheadedgoose_Mongolia_1_2005, 91 A_whooperswan_Mongolia_3_2005, 92 A_whooperswan_Mongolia_4_2005, 93 A_whooperswan_Mongolia_6_2005, 94 A_blackheadedgoose_Qinghai_2_2005, 95 A_blackheadedgull_Qinghai_1_2005, 96 A_blackheadedgoose_Qinghai_1_2005, 97 A_BarheadedGoose_Qinghai_60_2005, 98 A_BrownheadedGull_Qinghai_3_2005, 99 A_greatblackheadedgull_Qinghai_1_2005, 100 A_BarheadedGoose_Qinghai_65_2005, 101 A_BarheadedGoose_Qinghai_59_2005, 102 A_duck_Guangdong_173_2004, 103 A_duck_HongKong_821_2002, 104 A_HongKong_213_2003, 105 A_egret_HongKong_7572_2003, 106 A_chicken_Vietnam_27_2003, 107 A_duck_Vietnam_S654_2005, 108 A_quail_Vietnam_36_2004, 109 A_chicken_VietNam_DT171_2004, 110 A_Mallardduck_Vietnam_133_2004, 111 A_VietNam_1203_2004, 112 A_chicken_Nakornsawan202_2004, 113 A_chicken_NakhonSawan_Thailand_CU39_2004, 114 A_chicken_Bangkok_Thailand_CU20_2004, 115 A_Hanoi_30408_2005, 116 A_chicken_Bangkok_Thailand_CU3_2004, 117 A_chicken_Bangkok_Thailand_CU6_2004, 118 A_crow_Bangkok_Thailand_CU35_2004, 119 A_chicken_Kamphaengphet204_2004, 120 A_chicken_Nakornsawan203_2004, 121 A_chicken_Nakornsawan207_2004, 122 A_chicken_Kamphaengphet202_2004, 123 A_chicken_Phitsanulok204_2004, 124 A_chicken_Phitsanulok201_2004, 125 A_chicken_Kamphaengphet205_2004, 126 A_duck_Uthaithani201_2004, 127 A_chicken_Phitsanulok202_2004, 128 A_chicken_Nakornsawan201_2004, 129 A_chicken_Uthaithani204_2004, 130 A_chicken_Uthaithani202_2004, 131 A_chicken_Uthaithani203_2004, 132 A_chicken_Uthaithani201_2004, 133 A_chicken_Nakornsawan205_2004, 134 A_Hatay_2004, 135 A_duck_Nakornsawan202_2004, 136 A_chicken_NakhonSawan_Thailand_CU13_2004, 137 A_rollers_Bangkok_Thailand_CU26_2004, 138 A_chicken_Nakornsawan206_2004, 139 A_duck_Uthaithani202_2004, 140 A_crow_Bangkok_Thailand_CU4_2004, 141 A_chicken_NakhonSawan_Thailand_CU12_2004, 142 A_duck_Nakornsawan201_2004, 143 A_chicken_Nakornsawan204_2004, 144 A_chicken_Kamphaengphet201_2004, 145 A_chicken_Thailand_Kamphaengphet303_2005, 146 A_chicken_Thailand_Kamphaengphet304_2005, 147 A_chicken_Thailand_Kamphaengphet301_2005, 148 A_chicken_Thailand_Kamphaengphet302_2005, 149 A_chicken_Kamphaengphet206_2004, 150 A_duck_Phitsanulok201_2004, 151 A_chicken_Kamphaengphet203_2004, 152 A_crow_Bangkok_Thailand_CU25_2004, 153 A_chicken_Phitsanulok203_2004, 154 A_duck_Phitsanulok202_2004, 155 A_chicken_Uthaithani205_2004, 156 A_KaljiPheasant_Bangkok_Thailand_CU18_2004, 157 A_whitepeafowl_Bangkok_Thailand_CU29_2004, 158 A_muscovyduck_Vietnam_MdGL_2004, 159 A_duck_Guangxi_35_2001, 160 A_chicken_Hebei_326_2005, 161 A_treesparrow_Henan_2_2004, 162 A_chicken_Hebei_718_2001, 163 A_duck_Guangdong_01_2001, 164 A_duck_Shanghai_13_2001, 165 A_duck_Guangdong_22_2002, 166 A_duck_Fujian_17_2001, 167 A_duck_Guangxi_22_2001, 168 A_duck_Guangxi_07_1999, 169 A_Goose_Guangdong_1_1996, 170 A_HongKong_514_1997, 171 A_HongKong_485_1997, 172 A_HongKong_483_1997, 173 A_chicken_HongKong_258_1997, 174 A_Chicken_HongKong_220_1997, 175 A_HongKong_491_1997, 176 A_HongKong_542_1997, 177 A_HongKong_503_1997, 178 A_Chicken_HongKong_728_1997, 179 A_HongKong_532_1997, 180 A_HongKong_538_1997, 181 A_HongKong_97_1998, 182 A_HongKong_486_1997, 183 A_chicken_HongKong_915_1997, 184 A_Duck_HongKong_p46_1997, 185 A_HongKong_516_1997, 186 A_HongKong_488_1997, 187 A_Goose_HongKong_w355_1997, 188 A_HongKong_507_1997, 189 A_HongKong_156_1997, 190 A_HongKong_481_1997 ; tree TREE1 = [&R] 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End; figtree-1.4.3/examples/HA_discrete_MCC.tre000066400000000000000000006732171277473563300203730ustar00rootroot00000000000000#NEXUS [Highest Log Clade Credibility: -163.96514351850752] Begin taxa; Dimensions ntax=190; Taxlabels A_Goose_Guangdong_1_1996 A_duck_Fujian_19_2000 A_duck_Guangdong_12_2000 A_duck_Shanghai_08_2001 A_duck_Shantou_4610_2003 A_duck_Guangxi_50_2001 A_Goose_Shantou_1621_2005 A_duck_Fujian_897_2005 A_chicken_Fujian_1042_2005 A_goose_Shantou_2216_2005 A_chicken_HongKongi_863_2002 A_Ck_HK_619_2002 A_chicken_jiyuan_1_2003 A_chicken_zhengzhou_1_2002 A_chicken_Bantul_BBVetI_2005 A_chicken_Salatiga_BBVetI_2005 A_chicken_Wajo_BBVM_2005 A_chicken_Yogjakarta_BBVetIX_2004 A_chicken_KulonProgo_BBVetXII1_2004 A_chicken_Wonosobo_BPPV4_2003 A_blowfly_Kyoto_93_2004 A_chicken_Kyoto_3_2004 A_crow_Kyoto_53_2004 A_crow_Osaka_102_2004 A_chicken_Yamaguchi_7_2004 A_chicken_Oita_8_2004 A_BarheadedGoose_Qinghai_59_2005 A_BarheadedGoose_Qinghai_65_2005 A_BrownheadedGull_Qinghai_3_2005 A_blackheadedgull_Qinghai_1_2005 A_blackheadedgoose_Qinghai_2_2005 A_blackheadedgoose_Qinghai_1_2005 A_BarheadedGoose_Qinghai_60_2005 A_greatblackheadedgull_Qinghai_1_2005 A_turkey_Suzdalka_Nov01_2005 A_duck_Novosibirsk_56_2005 A_grebe_Novosibirsk_29_2005 A_goose_Novosibirsk_4_2005 A_whooperswan_Mongolia_6_2005 A_whooperswan_Mongolia_3_2005 A_whooperswan_Mongolia_4_2005 A_barheadedgoose_Mongolia_1_2005 A_Cygnusolor_Astrakhan_Ast0523_2005 A_Cygnusolor_Astrakhan_Ast0524_2005 A_Cygnusolor_Astrakhan_Ast0525_2005 A_Cygnusolor_Astrakhan_Ast0527_2005 A_chicken_Guangdong_174_2004 A_Duck_Fujian_1734_2005 A_chicken_Guangxi_2461_2004 A_chicken_Guangxi_2448_2004 A_duck_Vietnam_568_2005 A_duck_Guangxi_951_2005 A_goose_Guangxi_345_2005 A_duck_Hunan_1265_2005 A_duck_Hunan_1608_2005 A_quail_Guangxi_575_2005 A_duck_Guangxi_793_2005 A_chicken_Guangxi_604_2005 A_greyheron_HongKong_728_2004 A_greyheron_HongKong_837_2004 A_duck_Guangxi_351_2004 A_duck_Guangxi_380_2004 A_Chicken_Shantou_810_2005 A_Quail_Shantou_911_2005 A_chicken_Guangdong_178_2004 A_chicken_Guangdong_191_2004 A_duck_Hunan_139_2005 A_duck_Hunan_182_2005 A_chicken_Hunan_999_2005 A_duck_Hunan_152_2005 A_duck_Hunan_157_2005 A_duck_Hunan_127_2005 A_chicken_Vietnam_27_2003 A_chicken_NakhonSawan_Thailand_CU13_2004 A_duck_Nakornsawan202_2004 A_duck_Uthaithani202_2004 A_chicken_Nakornsawan206_2004 A_chicken_Nakornsawan205_2004 A_chicken_Nakornsawan201_2004 A_chicken_Kamphaengphet205_2004 A_chicken_Phitsanulok201_2004 A_chicken_Phitsanulok202_2004 A_chicken_Phitsanulok204_2004 A_chicken_Uthaithani201_2004 A_chicken_Uthaithani203_2004 A_duck_Uthaithani201_2004 A_chicken_Uthaithani204_2004 A_chicken_Uthaithani202_2004 A_chicken_Phitsanulok203_2004 A_duck_Phitsanulok202_2004 A_chicken_Uthaithani205_2004 A_duck_Phitsanulok201_2004 A_crow_Bangkok_Thailand_CU25_2004 A_chicken_Nakornsawan204_2004 A_chicken_Kamphaengphet201_2004 A_chicken_Thailand_Kamphaengphet302_2005 A_chicken_Thailand_Kamphaengphet301_2005 A_chicken_Thailand_Kamphaengphet304_2005 A_chicken_Thailand_Kamphaengphet303_2005 A_chicken_Kamphaengphet206_2004 A_chicken_Kamphaengphet203_2004 A_duck_Nakornsawan201_2004 A_rollers_Bangkok_Thailand_CU26_2004 A_crow_Bangkok_Thailand_CU4_2004 A_chicken_Nakornsawan202_2004 A_chicken_NakhonSawan_Thailand_CU12_2004 A_chicken_Kamphaengphet202_2004 A_chicken_Kamphaengphet204_2004 A_chicken_Nakornsawan203_2004 A_chicken_Nakornsawan207_2004 A_Hatay_2004_ A_muscovyduck_Vietnam_MdGL_2004 A_duck_Vietnam_S654_2005 A_chicken_VietNam_DT171_2004 A_Mallardduck_Vietnam_133_2004 A_quail_Vietnam_36_2004 A_Hanoi_30408_2005 A_VietNam_1203_2004 A_chicken_Bangkok_Thailand_CU20_2004 A_chicken_Bangkok_Thailand_CU3_2004 A_chicken_Bangkok_Thailand_CU6_2004 A_chicken_NakhonSawan_Thailand_CU39_2004 A_crow_Bangkok_Thailand_CU35_2004 A_KaljiPheasant_Bangkok_Thailand_CU18_2004 A_whitepeafowl_Bangkok_Thailand_CU29_2004 A_duck_HongKong_821_2002 A_egret_HongKong_7572_2003 A_HongKong_213_2003 A_duck_Guangdong_173_2004 A_duck_Yokohama_aq10_2003 A_treesparrow_Henan_3_2004 A_treesparrow_Henan_1_2004 A_blackbird_Hunan_1_2004 A_treesparrow_Henan_4_2004 A_chicken_Henan_01_2004 A_swine_Fujian_F1_2001 A_goose_Guangxi_2112_2004 A_duck_Guangxi_1793_2004 A_duck_Guangxi_1311_2004 A_duck_Guangxi_2291_2004 A_goose_Guangxi_1832_2004 A_goose_Guangxi_1097_2004 A_duck_Guangxi_2396_2004 A_goose_Guangxi_2383_2004 A_duck_Guangxi_1586_2004 A_duck_Guangxi_1681_2004 A_chicken_Guangxi_2439_2004 A_duck_Guangxi_1378_2004 A_goose_Guangxi_914_2004 A_duck_Guangxi_22_2001 A_duck_Fujian_17_2001 A_duck_Guangdong_22_2002 A_duck_Guangdong_01_2001 A_chicken_Hebei_718_2001 A_duck_Guangxi_35_2001 A_chicken_Hebei_326_2005 A_treesparrow_Henan_2_2004 A_duck_Shanghai_13_2001 A_duck_Guangdong_40_2000 A_duck_Shanghai_35_2002 A_duck_Guangxi_53_2002 A_chicken_zhoukou_2_2002 A_chicken_Hebei_108_2002 A_duck_Fujian_01_2002 A_duck_Fujian_13_2002 A_duck_Shanghai_37_2002 A_duck_Shanghai_38_2001 A_duck_Guangdong_07_2000 A_duck_Guangxi_07_1999 A_chicken_HongKong_258_1997 A_HongKong_483_1997 A_Chicken_HongKong_220_1997 A_HongKong_485_1997 A_HongKong_514_1997 A_HongKong_542_1997 A_HongKong_503_1997 A_HongKong_491_1997 A_Chicken_HongKong_728_1997 A_HongKong_532_1997 A_HongKong_481_1997 A_HongKong_538_1997 A_HongKong_97_1998 A_Duck_HongKong_p46_1997 A_HongKong_488_1997 A_HongKong_516_1997 A_chicken_HongKong_915_1997 A_HongKong_486_1997 A_Goose_HongKong_w355_1997 A_HongKong_507_1997 A_HongKong_156_1997 ; End; Begin trees; Translate 1 A_Goose_Guangdong_1_1996, 2 A_duck_Fujian_19_2000, 3 A_duck_Guangdong_12_2000, 4 A_duck_Shanghai_08_2001, 5 A_duck_Shantou_4610_2003, 6 A_duck_Guangxi_50_2001, 7 A_Goose_Shantou_1621_2005, 8 A_duck_Fujian_897_2005, 9 A_chicken_Fujian_1042_2005, 10 A_goose_Shantou_2216_2005, 11 A_chicken_HongKongi_863_2002, 12 A_Ck_HK_619_2002, 13 A_chicken_jiyuan_1_2003, 14 A_chicken_zhengzhou_1_2002, 15 A_chicken_Bantul_BBVetI_2005, 16 A_chicken_Salatiga_BBVetI_2005, 17 A_chicken_Wajo_BBVM_2005, 18 A_chicken_Yogjakarta_BBVetIX_2004, 19 A_chicken_KulonProgo_BBVetXII1_2004, 20 A_chicken_Wonosobo_BPPV4_2003, 21 A_blowfly_Kyoto_93_2004, 22 A_chicken_Kyoto_3_2004, 23 A_crow_Kyoto_53_2004, 24 A_crow_Osaka_102_2004, 25 A_chicken_Yamaguchi_7_2004, 26 A_chicken_Oita_8_2004, 27 A_BarheadedGoose_Qinghai_59_2005, 28 A_BarheadedGoose_Qinghai_65_2005, 29 A_BrownheadedGull_Qinghai_3_2005, 30 A_blackheadedgull_Qinghai_1_2005, 31 A_blackheadedgoose_Qinghai_2_2005, 32 A_blackheadedgoose_Qinghai_1_2005, 33 A_BarheadedGoose_Qinghai_60_2005, 34 A_greatblackheadedgull_Qinghai_1_2005, 35 A_turkey_Suzdalka_Nov01_2005, 36 A_duck_Novosibirsk_56_2005, 37 A_grebe_Novosibirsk_29_2005, 38 A_goose_Novosibirsk_4_2005, 39 A_whooperswan_Mongolia_6_2005, 40 A_whooperswan_Mongolia_3_2005, 41 A_whooperswan_Mongolia_4_2005, 42 A_barheadedgoose_Mongolia_1_2005, 43 A_Cygnusolor_Astrakhan_Ast0523_2005, 44 A_Cygnusolor_Astrakhan_Ast0524_2005, 45 A_Cygnusolor_Astrakhan_Ast0525_2005, 46 A_Cygnusolor_Astrakhan_Ast0527_2005, 47 A_chicken_Guangdong_174_2004, 48 A_Duck_Fujian_1734_2005, 49 A_chicken_Guangxi_2461_2004, 50 A_chicken_Guangxi_2448_2004, 51 A_duck_Vietnam_568_2005, 52 A_duck_Guangxi_951_2005, 53 A_goose_Guangxi_345_2005, 54 A_duck_Hunan_1265_2005, 55 A_duck_Hunan_1608_2005, 56 A_quail_Guangxi_575_2005, 57 A_duck_Guangxi_793_2005, 58 A_chicken_Guangxi_604_2005, 59 A_greyheron_HongKong_728_2004, 60 A_greyheron_HongKong_837_2004, 61 A_duck_Guangxi_351_2004, 62 A_duck_Guangxi_380_2004, 63 A_Chicken_Shantou_810_2005, 64 A_Quail_Shantou_911_2005, 65 A_chicken_Guangdong_178_2004, 66 A_chicken_Guangdong_191_2004, 67 A_duck_Hunan_139_2005, 68 A_duck_Hunan_182_2005, 69 A_chicken_Hunan_999_2005, 70 A_duck_Hunan_152_2005, 71 A_duck_Hunan_157_2005, 72 A_duck_Hunan_127_2005, 73 A_chicken_Vietnam_27_2003, 74 A_chicken_NakhonSawan_Thailand_CU13_2004, 75 A_duck_Nakornsawan202_2004, 76 A_duck_Uthaithani202_2004, 77 A_chicken_Nakornsawan206_2004, 78 A_chicken_Nakornsawan205_2004, 79 A_chicken_Nakornsawan201_2004, 80 A_chicken_Kamphaengphet205_2004, 81 A_chicken_Phitsanulok201_2004, 82 A_chicken_Phitsanulok202_2004, 83 A_chicken_Phitsanulok204_2004, 84 A_chicken_Uthaithani201_2004, 85 A_chicken_Uthaithani203_2004, 86 A_duck_Uthaithani201_2004, 87 A_chicken_Uthaithani204_2004, 88 A_chicken_Uthaithani202_2004, 89 A_chicken_Phitsanulok203_2004, 90 A_duck_Phitsanulok202_2004, 91 A_chicken_Uthaithani205_2004, 92 A_duck_Phitsanulok201_2004, 93 A_crow_Bangkok_Thailand_CU25_2004, 94 A_chicken_Nakornsawan204_2004, 95 A_chicken_Kamphaengphet201_2004, 96 A_chicken_Thailand_Kamphaengphet302_2005, 97 A_chicken_Thailand_Kamphaengphet301_2005, 98 A_chicken_Thailand_Kamphaengphet304_2005, 99 A_chicken_Thailand_Kamphaengphet303_2005, 100 A_chicken_Kamphaengphet206_2004, 101 A_chicken_Kamphaengphet203_2004, 102 A_duck_Nakornsawan201_2004, 103 A_rollers_Bangkok_Thailand_CU26_2004, 104 A_crow_Bangkok_Thailand_CU4_2004, 105 A_chicken_Nakornsawan202_2004, 106 A_chicken_NakhonSawan_Thailand_CU12_2004, 107 A_chicken_Kamphaengphet202_2004, 108 A_chicken_Kamphaengphet204_2004, 109 A_chicken_Nakornsawan203_2004, 110 A_chicken_Nakornsawan207_2004, 111 A_Hatay_2004_, 112 A_muscovyduck_Vietnam_MdGL_2004, 113 A_duck_Vietnam_S654_2005, 114 A_chicken_VietNam_DT171_2004, 115 A_Mallardduck_Vietnam_133_2004, 116 A_quail_Vietnam_36_2004, 117 A_Hanoi_30408_2005, 118 A_VietNam_1203_2004, 119 A_chicken_Bangkok_Thailand_CU20_2004, 120 A_chicken_Bangkok_Thailand_CU3_2004, 121 A_chicken_Bangkok_Thailand_CU6_2004, 122 A_chicken_NakhonSawan_Thailand_CU39_2004, 123 A_crow_Bangkok_Thailand_CU35_2004, 124 A_KaljiPheasant_Bangkok_Thailand_CU18_2004, 125 A_whitepeafowl_Bangkok_Thailand_CU29_2004, 126 A_duck_HongKong_821_2002, 127 A_egret_HongKong_7572_2003, 128 A_HongKong_213_2003, 129 A_duck_Guangdong_173_2004, 130 A_duck_Yokohama_aq10_2003, 131 A_treesparrow_Henan_3_2004, 132 A_treesparrow_Henan_1_2004, 133 A_blackbird_Hunan_1_2004, 134 A_treesparrow_Henan_4_2004, 135 A_chicken_Henan_01_2004, 136 A_swine_Fujian_F1_2001, 137 A_goose_Guangxi_2112_2004, 138 A_duck_Guangxi_1793_2004, 139 A_duck_Guangxi_1311_2004, 140 A_duck_Guangxi_2291_2004, 141 A_goose_Guangxi_1832_2004, 142 A_goose_Guangxi_1097_2004, 143 A_duck_Guangxi_2396_2004, 144 A_goose_Guangxi_2383_2004, 145 A_duck_Guangxi_1586_2004, 146 A_duck_Guangxi_1681_2004, 147 A_chicken_Guangxi_2439_2004, 148 A_duck_Guangxi_1378_2004, 149 A_goose_Guangxi_914_2004, 150 A_duck_Guangxi_22_2001, 151 A_duck_Fujian_17_2001, 152 A_duck_Guangdong_22_2002, 153 A_duck_Guangdong_01_2001, 154 A_chicken_Hebei_718_2001, 155 A_duck_Guangxi_35_2001, 156 A_chicken_Hebei_326_2005, 157 A_treesparrow_Henan_2_2004, 158 A_duck_Shanghai_13_2001, 159 A_duck_Guangdong_40_2000, 160 A_duck_Shanghai_35_2002, 161 A_duck_Guangxi_53_2002, 162 A_chicken_zhoukou_2_2002, 163 A_chicken_Hebei_108_2002, 164 A_duck_Fujian_01_2002, 165 A_duck_Fujian_13_2002, 166 A_duck_Shanghai_37_2002, 167 A_duck_Shanghai_38_2001, 168 A_duck_Guangdong_07_2000, 169 A_duck_Guangxi_07_1999, 170 A_chicken_HongKong_258_1997, 171 A_HongKong_483_1997, 172 A_Chicken_HongKong_220_1997, 173 A_HongKong_485_1997, 174 A_HongKong_514_1997, 175 A_HongKong_542_1997, 176 A_HongKong_503_1997, 177 A_HongKong_491_1997, 178 A_Chicken_HongKong_728_1997, 179 A_HongKong_532_1997, 180 A_HongKong_481_1997, 181 A_HongKong_538_1997, 182 A_HongKong_97_1998, 183 A_Duck_HongKong_p46_1997, 184 A_HongKong_488_1997, 185 A_HongKong_516_1997, 186 A_chicken_HongKong_915_1997, 187 A_HongKong_486_1997, 188 A_Goose_HongKong_w355_1997, 189 A_HongKong_507_1997, 190 A_HongKong_156_1997 ; tree TREE1 = [&R] 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Y_ɁXh{Re)x̜V|Z*eψ q 1jx~ LV !~W F J*IENDB`figtree-1.4.3/release/Linux/scripts/000077500000000000000000000000001277473563300173735ustar00rootroot00000000000000figtree-1.4.3/release/Linux/scripts/figtree000077500000000000000000000000721277473563300207450ustar00rootroot00000000000000#!/bin/sh java -Xms64m -Xmx512m -jar lib/figtree.jar $* figtree-1.4.3/release/common/000077500000000000000000000000001277473563300160755ustar00rootroot00000000000000figtree-1.4.3/release/common/README.txt000066400000000000000000000306361277473563300176030ustar00rootroot00000000000000 FigTree v1.4.3 2006-2016 Andrew Rambaut Institute of Evolutionary Biology University of Edinburgh a.rambaut@ed.ac.uk UNIX/Linux/Mac OS X (command-line) version README Last updated: a.rambaut@ed.ac.uk - 4th October 2016 Contents: 1) INTRODUCTION 2) VERSION HISTORY 3) INSTALLATION 4) OPENING TREES 5) USING FIGTREE 6) EXPORTING RESULTS 7) SUPPORT & LINKS 8) ACKNOWLEDGMENTS ___________________________________________________________________________ 1) INTRODUCTION FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. On the other hand, I don't think there are any commercial tree drawing programs. ___________________________________________________________________________ 2) VERSION HISTORY v1.4.3 Released 4th October 2016 New features: Node shape option can now show shapes for internal or external nodes or both. Copying selected taxon labels when these are selected, subtree when branches are selected. Selecting 'reverse axis' should automatically reverse the Time Scale scale factor. Previously the user needed to set this to -1.0. When searching for text, scrolls to show highlighted tip. Bugs fixed: Issue 102: Large SVG files from figtree are broken Issue 95: Changing the origin value for the Scale Axis does not work Issue 94: The trait legend overlaps the tree. Issue 93: Command-line PDF/SVG export options not working Issue 92: Reading a file with a mix of integer and real node labels causes exception. Issue 90: Export picture cuts the top of the higest tip label Issue 79: Export of .SVG produces corrupt files v1.4.2 Released 9th July 2014 New features: New -url command line option allows reading of trees from URLs in pipelines. Bugs fixed: Issue 76: Scale axis should only show as many decimal places as necessary. Issue 75: Export PNG & JPEG produce blank images. Issue 64: Putting node bars on translates the tree to the right (now really fixed, I think). v1.4.1 Released 14th June 2014 New features: Copy selected subtrees to clipboard as NEXUS format. New graphics export options (PDF, SVG, PNG & JPEG). Control panel now scrolls and can be resized. Bugs fixed: Issue 23: Find bar opens slowly with big trees. Issue 28: Filtering should work on currently display labels. Issue 53: Option Tip Labels: "Colour By" does not render Names in colour. Issue 57: Midpoint rooting not working correctly. Issue 59: Clear Highlighting/Cartoon etc doesn't seem to work on individual branches. Issue 62: When all clades are 'collapsed', the top triangle is clipped. Issue 64: Putting node bars on translates the tree to the right. Issue 69: Import annotation causes crash. v1.4 Released 8th October 2012. New Features: Added a 'Node Shape' option which can draw circles, squares or diamonds on each node. These can be coloured and sized by attributes. Added a 'Legend' option which can produce a colour legend for any attribute/colour scheme being used. New colour scheme for discrete attributes based on a HSB colour wheel. This replaces the old fixed sequence of colours and is more customizable. Attribute values can be re-ordered. New colour scheme for continuous attributes also based on HSB. The old interpolating colour scheme is still available. Colour schemes are now selectable for particular attributes and these are saved and loaded in FigTree files. Numerous tweaks to the controls to make things more convenient. These include the reintroduction of font size spinners (in addition to font selection dialogs) and scrolling of the entire control panel when larger than the window. New zooming/expansion. The maximum extent of zooming is now proportional to the number of tips in the tree. I.e., the bigger the tree the more you can zoom in. Also added a non-linearity to zooming (starts slower). Bug Fixes: Issue 52: Significant figure spinners don't currently have an effect. Issue 51: Preference fonts initially set to first font in list Issue 50: Problem with MidPoint rooting a tree Issue 48: Taxon labels not displaying traits of nodes Issue 45: Nexus importer doesn't ignore unrecognised commands Issue 42: Collapsed clades are clipped at the top of the page Issue 39: Rerooting doesn't always work. v1.3.1 Released 21st December 2009. Bug Fixes: Re-introduced the graphic export formats that were inadvertently omitted in the previous version. Node bar panel now shows available attributes to display (bug introduced in previous version). v1.3 Released 14th December 2009. New Features: Added a 'Background' colouring option to the 'Appearance' panel so the colour under each clade can be controlled by an attribute. Added a 'Color by' option to tip, node and branch labels so the colour of the labels can be controlled by an attribute. Restored a Export to PDF option in the File menu. This uses a different library for creating PDFs from the Graphics export and doesn't require any settings (it should produce a PDF that matches the screen image). Implemented a 'QuickLook' plugin for Mac OS X. Bug Fixes: Fixed an issue with 'branch' attributes not being loaded from a NEXUS file. The tree panel now has focus when the window opens which allows direct copy/pasting of tree files. New attributes are available in the Find panel. v1.2.3 Released 10th Aug 2009. New Features: Added a 'Reverse Axis' option to the Scale Axis settings - this reverses the direction of the scale axis. Added an option to turn on and off the grid lines in the Scale Axis settings. Bug Fixes: The scale grid lines could be out of alignment with the axis. Annotation types being defined in the dialog box were not being created. v1.2.2 Released 24th Feb 2009. Bug Fixes: Exported NEWICK trees now have a terminal semi-colon. Text boxes in control panels are now editable again. Polar trees with 'Align Tip Labels' could cause the tree to go off the page. v1.2.1 Released 9th Jan 2009. New Features: Taxon, branch and node labels now have a "Font" button which can be used to set the font for these labels. Added a "Gradient" check box to the "Appearance" panel. This will try to produce gradual colour changes on the branches. Bug Fixes: Fixed a problem reloading trees with integer annotations. 'Preferences' wasn't available on Windows & Linux (it is now in the Edit menu). Now correctly exports trees 'As Displayed' (i.e., rooted or transformed). v1.2 Released 30th Nov 2008. New Features: Added a 'highlight' button which provides a block colouring for a clade. Add a continous colour gradient option to the 'Colour By' control in the Appearance panel. Use setup to activate (at present it disables the 'Width By' option. Added a 'Name' annotation that can be used to edit taxon names. It can also be used to name clades (and these are displayed for collapsed clades). Added a new drop down find panel that is activate by Find in the Edit menu or the find icon in the tool bar. Font sizes and a few other options can now be set in the 'Preferences' box. These act as defaults for new windows. Bug Fixes: Fixed a problem with branch annotations being applied to the wrong branches when the tree is re-rooted. "Colour By" colours were reversed from those suggested in the Setup dialog. The "Colour By" setup didn't work as expected if Auto-Range was turned off. Made the control palette title bars slightly thinner. v1.1.2 Released 6th Feb 2008. New Features: Added new graphics export formats using the FreeHEP library. This includes SVG, EPS, PDF and EMF along with raster formats such as GIF, PNG etc. If a tree contains 'labels' (numbers such as bootstrap values before the branch length) then the user is given the opportunity to give these an informative name. v1.1.1 Released 22nd January 2008. New Features: Added the ability to format numerical node/branch labels as percentages (and Roman numerals). Added a 'setup' button for the 'Colour by' and 'Width by' controls in the 'Appearance' palette. These allow customization of the colours and line widths. Added hotkeys for menu options. Added direct menu options for midpoint rooting and node orderings (with hotkeys). Bug Fixes: The filter (the search box on the toolbar) was not respecting the choice made in the popup menu. The search and filtering options were essentially non-functional. These now work as intended. FigTree crashed with an exception when run on certain Linux variants. FigTree crashed when displaying node/branch labels after the tree was manually re-rootd. Branch/node label choices were being lost when colouring or annotation tools were used. Removed the ugly icons from the menu options corresponding to toolbar buttons. v1.1 Released 13th January 2008. New Features: Added a collapse and a cartoon button - collapse produces a single taxon that represents the entire collapsed clade whereas cartoon creates a triangle that covers the same space as the clade. Reroot tree - select node and click reroot button in toolbar. Also select 'Midpoint root' in "Trees" control palette. Rotate nodes - select node and click rotate button in toolbar. Rescale trees - use "Time Scale" control palette (scale factor can be negative which reverses the time axis). Scale axis with grid lines - use the "Scale Axis" control palette. 'FishEye' (1-dimensional) zooming - in "Layout" control palette. Hold down the 'Control' key ('Command/Apple' key on a Mac) to change the centre of view. Improved Find dialog - can find inequalities for numerical values. Bug Fixes: Negative branch lengths are now correctly displayed rather than being transformed to unit branches. Many, other bug fixes and improvements. v1.0 Released 30th October 2006. First Released Version ___________________________________________________________________________ 3) INSTALLATION FigTree requires a Java Virtual Machine to run. Many systems will already have this installed. It requires at least version 1.5 of Java to run. The latest versions of Java can be downloaded from: If in doubt type "java -version" to see what version of java is installed (or if it is installed at all). Mac OS X version 10.4 or better (Tiger) will already have a suitable version of Java installed. I am sorry but FigTree simply doesn't run on older versions of Mac OS X. On Mac OS X and Windows, FigTree is run like any other application - double click on the application icon. On UNIX/Linux systems, you may be able to double-click on the figtree.jar file or execute the "figtree" shell script. ___________________________________________________________________________ 4) OPENING TREES Simply select "Open" from the "File" menu or on Mac, drag a suitable file onto the icon in Finder or the Dock. You can also set files with a particular extension (say, ".tree") to open in FigTree as a default by selecting "Get Info", selecting FigTree as the "Open With" application and then pressing the "Change All" button. Trees can be in NEXUS or NEWICK format. ___________________________________________________________________________ 5) USING FIGTREE At present there is no manual for using FigTree. I suggest you simply try playing with the various controls and buttons. ___________________________________________________________________________ 6) EXPORTING RESULTS To export the figure for publication or further editing in a graphics package, select "Export PDF" from the file menu to save as a PDF file. Saving the tree from within FigTree will save in NEXUS format but add special comments and a command block which will enable FigTree to keep all the settings and annotations made to the tree. Other programs (such as PAUP) should ignore these settings. You can also 'Copy and Paste' the tree into any application that accepts text (the result will be a NEXUS format tree file). ___________________________________________________________________________ 7) SUPPORT & LINKS FigTree is a new program and is not complete or bug-free. Please email me to make suggestions or report bugs: http://tree.bio.ed.ac.uk/ ___________________________________________________________________________ 8) ACKNOWLEDGMENTS Thanks to the following for assisting with the creation or testing of FigTree: Alexei Drummond Joseph Heled Philippe Lemey Tulio de Oliveira Oliver Pybus Beth Shapiro Marc Suchard figtree-1.4.3/release/common/carnivore.tree000066400000000000000000002073111277473563300207520ustar00rootroot00000000000000#NEXUS begin taxa; dimensions ntax=63; taxlabels 'Felis silvestris' 'Lynx canadensis' 'Acinonyx jubatus' 'Puma concolor' 'Neofelis nebulosa' 'Panthera pardus' 'Uncia uncia' 'Panthera tigris' 'Herpestes auropunctatus' 'Alopex lagopus' 'Vulpes vulpes' 'Canis latrans' 'Canis lupus' 'Otaria byronia' 'Arctocephalus pusillus' 'Neophoca cinerea' 'Phocarctos hookeri' 'Arctocephalus australis' 'Arctocephalus forsteri' 'Arctocephalus townsendi' 'Eumetopias jubatus' 'Zalophus californianus' 'Callorhinus ursinus' 'Odobenus rosmarus' 'Cystophora cristata' 'Phoca largha' 'Phoca vitulina' 'Phoca caspica' 'Halichoerus grypus' 'Phoca sibirica' 'Phoca hispida' 'Phoca fasciata' 'Phoca groenlandica' 'Erignathus barbatus' 'Monachus schauinslandi' 'Monachus monachus' 'Hydrurga leptonyx' 'Leptonychotes weddellii' 'Lobodon carcinophaga' 'Ommatophoca rossii' 'Mirounga angustirostris' 'Mirounga leonina' 'Taxidea taxus' 'Enhydra lutris' 'Lontra canadensis' 'Mustela vison' 'Gulo gulo' 'Martes americana' 'Martes melampus' 'Meles meles' 'Procyon lotor' 'Ailurus fulgens' 'Mephitis mephitis' 'Spilogale putorius' 'Tremarctos ornatus' 'Helarctos malayanus' 'Ursus americanus' 'Ursus thibetanus' 'Ursus arctos' 'Ursus maritimus' 'Melursus ursinus' 'Ailuropoda melanoleuca' 'Manis tetradactyla' ; end; begin trees; tree TREE1 = [&R] [&R=true]((((('Felis silvestris'[&length_range={0.1942546268646502,0.8249044947224048},rate_range={0.48713071263378177,2.254020365174967},height_median=8.881784197001252E-16,height=7.987699981389713E-16,rate_95%_HPD={0.5749728452561609,1.6050867815047987},height_95%_HPD={0.0,1.7763568394002505E-15},length=0.5455417729722768,height_range={0.0,5.329070518200751E-15},rate_median=0.777077845937059,length_median=0.5730455317442351,length_95%_HPD={0.23141104109206645,0.6853836574407342},rate=0.86368313598804]:0.5455417729722768,('Lynx canadensis'[&length_range={0.12416487760390357,0.6529903723630749},rate_range={0.5846284683483233,3.371219138161746},height_median=8.881784197001252E-16,height=7.951732352154781E-16,rate_95%_HPD={0.7193463546643171,2.137409196335331},height_95%_HPD={0.0,1.7763568394002505E-15},length=0.4288757786404431,height_range={0.0,5.329070518200751E-15},rate_median=0.9519225207058954,length_median=0.4507006930297067,length_95%_HPD={0.17998710718452576,0.5601477374580388},rate=1.0799308161855512]:0.42887577864044313,('Acinonyx jubatus'[&length_range={0.07494436962673542,0.5341230164937385},rate_range={0.7983317639133981,5.4159844533833095},height_median=8.881784197001252E-16,height=7.981483354114539E-16,rate_95%_HPD={0.8315084298655286,3.5748984382034936},height_95%_HPD={0.0,1.7763568394002505E-15},length=0.32686653867816057,height_range={0.0,5.329070518200751E-15},rate_median=1.205835707275285,length_median=0.34524797927544526,length_95%_HPD={0.09447812698815154,0.44357523744728955},rate=1.477508785345113]:0.3268665386781608,'Puma 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nebulosa'[&length_range={0.11560351155046529,0.7623080939874496},rate_range={0.6675829558306837,4.811232415894687},height_median=8.881784197001252E-16,height=8.020781319389742E-16,rate_95%_HPD={0.7121564493925345,2.7593682311154355},height_95%_HPD={0.0,1.7763568394002505E-15},length=0.5019820498059957,height_range={0.0,7.105427357601002E-15},rate_median=1.0030970324566633,length_median=0.5277239422052145,length_95%_HPD={0.16667385839883533,0.6512791360582133},rate=1.1766104840868747]:0.5019820498059958,(('Panthera pardus'[&length_range={0.051762869859318994,0.4526257508074602},rate_range={0.49368739668785994,4.349498522520932},height_median=8.881784197001252E-16,height=7.878242936866124E-16,rate_95%_HPD={0.5875710311640657,2.388298574734536},height_95%_HPD={0.0,1.7763568394002505E-15},length=0.2563323902942868,height_range={0.0,7.105427357601002E-15},rate_median=0.8882343696143651,length_median=0.26838332331163006,length_95%_HPD={0.08328714329516121,0.36665252761390743},rate=1.0514917777211554]:0.2563323902942867,'Uncia 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malayanus'[&length_range={0.056671780921654986,0.39593496399030775},rate_range={0.7366066400232067,5.4073194685537},height_median=8.881784197001252E-16,height=8.182191606141565E-16,rate_95%_HPD={0.7672469213306831,3.282567363763658},height_95%_HPD={0.0,1.7763568394002505E-15},length=0.25424859976797687,height_range={0.0,7.105427357601002E-15},rate_median=1.1078271976873055,length_median=0.2698531144226554,length_95%_HPD={0.0743802325020158,0.33530366434692355},rate=1.3306036107335022]:0.25424859976797665,('Ursus americanus'[&length_range={0.0380861229685716,0.3255177984196708},rate_range={0.7102213341486359,6.705996937902462},height_median=8.881784197001252E-16,height=8.237253162007386E-16,rate_95%_HPD={0.8214244965000586,4.418052617322139},height_95%_HPD={0.0,1.7763568394002505E-15},length=0.20415017394761925,height_range={0.0,7.105427357601002E-15},rate_median=1.205922628202683,length_median=0.2198194714528931,length_95%_HPD={0.04258650439679049,0.2725635305891527},rate=1.5788699364573795]:0.2041501739476191,'Ursus thibetanus'[&length_range={0.0380861229685716,0.3255177984196708},rate_range={0.6807971606989713,6.248711991804251},height_median=8.881784197001252E-16,height=8.237253162007386E-16,rate_95%_HPD={0.7074488133124407,3.764525369690987},height_95%_HPD={0.0,1.7763568394002505E-15},length=0.20415017394761925,height_range={0.0,7.105427357601002E-15},rate_median=1.0473342684880007,length_median=0.2198194714528931,length_95%_HPD={0.04258650439679049,0.2725635305891527},rate=1.365362625423855]:0.2041501739476191)[&rate_range={0.3235767423716544,4.743985706347473},height_median=0.21981947145289293,length=0.05009842582035721,length_median=0.048340714938301554,length_95%_HPD={0.015796672809312184,0.08261672693748287},length_range={0.009045321802461058,0.15297157817703394},height=0.20415017394761995,rate_95%_HPD={0.3762972238119764,1.6686014008151244},height_95%_HPD={0.04258650439679279,0.27256353058915384},height_range={0.038086122968572056,0.3255177984196731},rate_median=0.9778568646638055,posterior=1.0,rate=1.0406726373695616]:0.050098425820357534)[&rate_range={0.18020262115496105,3.7542124889100403},height_median=0.2698531144226557,length=0.05191223248524515,length_median=0.047862770884130434,length_95%_HPD={0.01331961795203876,0.09116527736173549},length_range={0.009412932527909007,0.22859571172663679},height=0.2542485997679775,rate_95%_HPD={0.3241684007607926,1.520467505021167},height_95%_HPD={0.07438023250201553,0.3353036643469238},height_range={0.0566717809216577,0.39593496399030936},rate_median=0.9666295895935901,posterior=1.0,rate=0.9958013573426872]:0.05191223248524496,('Ursus arctos'[&length_range={0.017525125442297132,0.14712074613610204},rate_range={0.2977262912570704,2.9605561327312255},height_median=8.881784197001252E-16,height=8.239473386034233E-16,rate_95%_HPD={0.4062268162569324,1.669806144739978},height_95%_HPD={0.0,1.7763568394002505E-15},length=0.052356339744049296,height_range={0.0,7.105427357601002E-15},rate_median=1.0278883283821343,length_median=0.05107284127203332,length_95%_HPD={0.021116306152310256,0.07738109530394484},rate=1.0742240717521638]:0.05235633974404936,'Ursus maritimus'[&length_range={0.017525125442297132,0.14712074613610204},rate_range={0.2422218780918904,2.5653318357917794},height_median=8.881784197001252E-16,height=8.239473386034233E-16,rate_95%_HPD={0.4070585242907041,1.3534607578898583},height_95%_HPD={0.0,1.7763568394002505E-15},length=0.052356339744049296,height_range={0.0,7.105427357601002E-15},rate_median=0.8577485028790036,length_median=0.05107284127203332,length_95%_HPD={0.021116306152310256,0.07738109530394484},rate=0.8845858569425434]:0.05235633974404936)[&rate_range={0.6041074722600714,5.558363489674877},height_median=0.051072841272033376,length=0.2538044925091726,length_median=0.2673686697370828,length_95%_HPD={0.07544393821245586,0.33263927869583304},length_range={0.04418040951927491,0.3881026179473701},height=0.052356339744050184,rate_95%_HPD={0.6204088898312387,2.4973054792990927},height_95%_HPD={0.021116306152311637,0.0773810953039451},height_range={0.017525125442299228,0.14712074613610238},rate_median=0.950797755990835,posterior=1.0,rate=1.1181271743586043]:0.25380449250917225)[&rate_range={0.4398205504795164,18.082500681767065},height_median=0.3195618771140163,length=0.07051918322218502,length_median=0.06825655622812082,length_95%_HPD={0.025820687158177674,0.12596252403731512},length_range={0.0029999203876463626,0.18927503361532505},height=0.30616083225322244,rate_95%_HPD={0.5031146481412838,1.7805126252462782},height_95%_HPD={0.10693472340299692,0.38696665295189714},height_range={0.07463070189014509,0.4387521823681553},rate_median=0.99302823754368,posterior=1.0,rate=1.164750686733507]:0.07051918322218598,'Melursus ursinus'[&length_range={0.08170993146197507,0.5381116370624125},rate_range={0.49282485462752107,3.6858581684399527},height_median=8.881784197001252E-16,height=8.153550716195231E-16,rate_95%_HPD={0.5444652756332219,1.5948736014471858},height_95%_HPD={0.0,1.7763568394002505E-15},length=0.3766800154754076,height_range={0.0,5.329070518200751E-15},rate_median=0.7590655639894794,length_median=0.3897530714066152,length_95%_HPD={0.16436163067873918,0.49856305596369066},rate=0.8430627795826882]:0.3766800154754076)[&rate_range={0.48224042927995836,8.262169179340372},height_median=0.3897530714066155,length=0.48977263674240823,length_median=0.5115319972486553,length_95%_HPD={0.061515180910847345,0.7343963161751148},length_range={0.05518421186280423,1.0731899751826637},height=0.3766800154754084,rate_95%_HPD={0.5036634299750277,5.092797062902273},height_95%_HPD={0.16436163067874077,0.49856305596369177},height_range={0.08170993146197514,0.5381116370624133},rate_median=0.9941534230429822,posterior=1.0,rate=1.413596362238695]:0.48977263674241156)[&rate_range={0.4483758810969421,9.196346187244139},height_median=0.9128237824544256,length=0.2503684358081066,length_median=0.24570002952119352,length_95%_HPD={0.08585627515197292,0.4323443230620374},length_range={0.01930556385037535,0.6249915794033823},height=0.86645265221782,rate_95%_HPD={0.46031606230187005,1.7949138431171898},height_95%_HPD={0.19781315428630908,1.1560867739031115},height_range={0.16492897934228168,1.4731386998205869},rate_median=0.9179917266311476,posterior=1.0,rate=1.0407649003109327]:0.25036843580810175,'Ailuropoda melanoleuca'[&length_range={0.2697293103354609,1.6915092034427415},rate_range={0.6212120022469779,4.122570813759804},height_median=8.881784197001252E-16,height=8.011900423282352E-16,rate_95%_HPD={0.6723011515004558,2.6020275268939916},height_95%_HPD={0.0,1.7763568394002505E-15},length=1.116821088025921,height_range={0.0,5.329070518200751E-15},rate_median=0.9489697805862637,length_median=1.180038393508389,length_95%_HPD={0.3542066029401125,1.4568820439182117},rate=1.1150164561614384]:1.1168210880259208)[&rate_range={0.47043822958376846,18.082500681767065},height_median=1.18003839350839,length=1.1457623690499235,length_median=1.2449957236373843,length_95%_HPD={0.05627592969750117,1.5382800471373128},length_range={0.04347362972956981,1.7868807461987415},height=1.1168210880259217,rate_95%_HPD={0.4851180688173854,6.501047445040662},height_95%_HPD={0.3542066029401134,1.4568820439182124},height_range={0.2697293103354621,1.6915092034427426},rate_median=0.7393740265689563,!hilight={8,0.0,#-26966},posterior=1.0,rate=1.4597660442308176]:1.149080217946037)[&rate_range={0.4715130760910986,15.274282375082244},height_median=2.4709866961868445,length=0.3321755154319429,length_median=0.34089894442154955,length_95%_HPD={0.029359310415752238,0.4998826793944535},length_range={0.019535987836635182,0.835275732375488},height=2.265901305971959,rate_95%_HPD={0.5069491692887603,4.681986359598772},height_95%_HPD={0.53728960835865,2.7688227082814465},height_range={0.3704591826286716,2.9571619740957886},rate_median=1.165358469289848,posterior=1.0,rate=1.6357463316825889]:0.33217551543194546)[&rate_range={0.282002972388689,18.082500681767065},height_median=2.829702887634425,length=0.35453556108335604,length_median=0.3578263911777646,length_95%_HPD={0.028224232394259363,0.5427722463342686},length_range={0.01947742417858872,0.9895426024913903},height=2.5980768214039043,rate_95%_HPD={0.2873664017053783,4.6663286779422295},height_95%_HPD={0.570999443379538,3.14557997707718},height_range={0.41848519267088236,3.4590954042356965},rate_median=1.1260631967351116,posterior=1.0,rate=1.5720202890744799]:0.3800760543442525)[&rate_range={0.09452878347074814,4.063673479096233},height_median=3.208488264337257,length=1.5008073454404418,length_median=1.1065406422693518,length_95%_HPD={7.785030438247631E-4,6.072160995397596},length_range={4.251333494713627E-4,12.178990423371898},height=2.978152875748157,rate_95%_HPD={0.1994560461842545,1.4745329485875633},height_95%_HPD={0.6080223088966168,3.5566334315081387},height_range={0.4592924976519539,3.9386748584879365},rate_median=0.9678320787010743,posterior=0.9545045495450455,rate=0.9665084685218963]:1.4072977330687713,'Manis tetradactyla'[&length_range={1.4023539196755717,12.650890198126845},rate_range={0.10524527634672674,3.8634896083646226},height_median=8.881784197001252E-16,height=8.013010535295775E-16,rate_95%_HPD={0.11437356427817318,2.6315441115819365},height_95%_HPD={0.0,1.7763568394002505E-15},length=4.377773333491872,height_range={0.0,5.329070518200751E-15},rate_median=1.170999400458316,length_median=4.30620495842443,length_95%_HPD={1.4712906370154777,6.565411602132145},rate=1.2755734947248447]:4.385450608816927)[&height_median=4.30620495842443,height=4.385450608816928,height_95%_HPD={1.471290637015478,6.565411602132147},length=0.0,height_range={1.4023539196755719,12.650890198126847},posterior=1.0]; end; begin figtree; set appearance.backgroundColour=#-1; set appearance.branchColorAttribute="rate"; set appearance.branchLineWidth=2.0; set appearance.foregroundColour=#-16777216; set appearance.selectionColour=#-2144520576; set branchLabels.displayAttribute="Branch times"; set branchLabels.fontName="sansserif"; set branchLabels.fontSize=8; set branchLabels.fontStyle=0; set branchLabels.isShown=false; set branchLabels.significantDigits=4; set layout.expansion=0; set layout.layoutType="RECTILINEAR"; set layout.zoom=0; set nodeBars.barWidth=4.0; set nodeLabels.displayAttribute="posterior"; set nodeLabels.fontName="sansserif"; set nodeLabels.fontSize=8; set nodeLabels.fontStyle=0; set nodeLabels.isShown=true; set nodeLabels.significantDigits=2; set polarLayout.alignTipLabels=false; set polarLayout.angularRange=0; set polarLayout.rootAngle=0; set polarLayout.rootLength=100; set polarLayout.showRoot=true; set radialLayout.spread=0.0; set rectilinearLayout.alignTipLabels=false; set rectilinearLayout.curvature=0; set rectilinearLayout.rootLength=100; set scale.offsetAge=0.0; set scale.rootAge=1.0; set scale.scaleFactor=1.0; set scale.scaleRoot=false; set scaleAxis.automaticScale=true; set scaleAxis.fontSize=8.0; set scaleAxis.isShown=false; set scaleAxis.lineWidth=1.0; set scaleAxis.majorTicks=1.0; set scaleAxis.origin=0.0; set scaleAxis.significantDigits=4; set scaleBar.automaticScale=true; set scaleBar.fontSize=10.0; set scaleBar.isShown=false; set scaleBar.lineWidth=1.0; set scaleBar.scaleRange=0.5; set scaleBar.significantDigits=4; set tipLabels.displayAttribute="Names"; set tipLabels.fontName="Arial"; set tipLabels.fontSize=11; set tipLabels.fontStyle=0; set tipLabels.isShown=true; set tipLabels.significantDigits=4; set trees.order=true; set trees.orderType="increasing"; set trees.rooting=false; set trees.rootingType="User Selection"; set trees.transform=false; set trees.transformType="cladogram"; end; figtree-1.4.3/release/common/influenza.tree000066400000000000000000020303141277473563300207540ustar00rootroot00000000000000#NEXUS begin taxa; dimensions ntax=687; taxlabels 'NewYork_705_1994.1' 'NewYork_758_1993.11' 'NewYork_770_1993.19' 'NewYork_760_1993.12' 'NewYork_754_1993.06' 'NewYork_756_1993.1' 'NewYork_766_1993.14' 'NewYork_771_1993.31' 'NewYork_784_1993.31' 'NewYork_803_1993.2' 'NewYork_798_1993.2' 'NewYork_797_1993.22' 'NewYork_781_1993.25' 'NewYork_769_1993.22' 'NewYork_791_1993.21' 'NewYork_757_1993.25' 'NewYork_802_1993.18' 'NewYork_764_1993.16' 'NewYork_755_1993.21' 'NewYork_775_1993.21' 'NewYork_768_1993.2' 'NewYork_801_1993.2' 'NewYork_789_1993.27' 'NewYork_773_1993.26' 'NewYork_767_1993.27' 'NewYork_571_1996.98' 'NewYork_582_1996.94' 'NewYork_596_1996.96' 'NewYork_569_1997.02' 'NewYork_603_1996.96' 'NewYork_557_1996.91' NewYork_577_1997 'NewYork_586_1996.99' 'NewYork_567_1996.95' 'NewYork_554_1996.88' 'NewYork_578_1997.01' 'NewYork_597_1997.03' 'NewYork_588_1997.01' 'NewYork_602_1996.99' 'NewYork_598_1996.98' 'NewYork_591_1996.99' 'NewYork_589_1996.98' 'NewYork_563_1996.88' 'NewYork_556_1996.9' 'NewYork_573_1996.99' 'NewYork_555_1996.99' 'NewYork_512_1998.1' 'NewYork_523_1998.11' 'NewYork_524_1998.02' 'NewYork_547_1998.01' NewYork_516_1998 'NewYork_508_1997.99' 'NewYork_544_1998.11' 'NewYork_514_1998.05' 'NewYork_509_1997.99' 'NewYork_511_1997.98' 'NewYork_504_1998.02' 'NewYork_525_1998.19' 'NewYork_530_1998.07' 'NewYork_534_1998.1' NewYork_513_1998 'NewYork_510_1998.16' 'NewYork_502_1998.23' 'NewYork_542_1998.15' 'NewYork_531_1998.16' 'NewYork_515_1997.99' 'NewYork_507_1997.98' 'NewYork_549_1998.07' 'NewYork_519_1998.14' 'NewYork_543_1998.15' 'NewYork_503_1997.93' 'NewYork_526_1998.01' 'NewYork_517_1998.02' 'NewYork_539_1998.13' 'NewYork_535_1998.19' 'NewYork_528_1998.04' 'NewYork_532_1998.07' 'NewYork_533_1998.1' 'NewYork_538_1998.12' 'NewYork_529_1998.18' 'NewYork_527_1998.22' NewYork_545_1998 'NewYork_501_1997.92' 'NewYork_536_1998.11' 'NewYork_540_1998.14' 'NewYork_550_1998.08' 'NewYork_520_1998.03' 'NewYork_506_1998.11' 'NewYork_505_1997.94' 'NewYork_522_1998.02' 'NewYork_546_1998.09' 'NewYork_548_1998.13' 'NewYork_521_1998.07' 'NewYork_315_1999.03' 'NewYork_265_1999.1' 'NewYork_250_1998.96' 'NewYork_324_1999.09' 'NewYork_287_1999.01' 'NewYork_278_1999.11' 'NewYork_263_1999.13' 'NewYork_316_1999.09' 'NewYork_458_1999.08' 'NewYork_335_1999.07' 'NewYork_456_1999.06' 'NewYork_455_1999.05' 'NewYork_251_1999.01' 'NewYork_336_1999.17' 'NewYork_154_2000.08' 'NewYork_143_1999.92' 'NewYork_151_1999.94' 'NewYork_139_1999.94' 'NewYork_183_1999.93' 'NewYork_439_2000.08' 'NewYork_437_2000.05' 'NewYork_187_2000.09' 'NewYork_181_1999.95' 'NewYork_162_2000.13' 'NewYork_180_2000.13' 'NewYork_148_2000.13' 'NewYork_171_2000.01' 'NewYork_424_1999.98' 'NewYork_150_2000.09' 'NewYork_422_1999.97' 'NewYork_142_2000.12' 'NewYork_157_1999.97' 'NewYork_438_2000.07' 'NewYork_426_1999.99' 'NewYork_173_2000.11' 'NewYork_427_2000.01' 'NewYork_153_1999.96' 'NewYork_163_1999.99' NewYork_166_2000 'NewYork_152_2000.07' 'NewYork_432_2000.03' 'NewYork_430_2000.02' 'NewYork_179_1999.92' 'NewYork_433_2000.03' 'NewYork_155_1999.95' 'NewYork_165_2000.07' NewYork_185_2000 'NewYork_147_1999.91' 'NewYork_434_2000.04' 'NewYork_189_1999.99' 'NewYork_175_2000.03' 'NewYork_164_2000.01' 'NewYork_170_2000.03' 'NewYork_188_1999.97' 'NewYork_141_1999.87' 'NewYork_160_2000.02' 'NewYork_161_1999.98' 'NewYork_431_2000.02' 'NewYork_440_2000.08' 'NewYork_178_2000.18' 'NewYork_140_2000.01' 'NewYork_176_2000.18' 'NewYork_425_1999.98' 'NewYork_421_2000.02' 'NewYork_174_2000.03' 'NewYork_429_2000.02' 'NewYork_156_2000.03' 'NewYork_158_2000.06' 'NewYork_167_2000.01' 'NewYork_168_2000.02' 'NewYork_169_2000.02' NewYork_172_2000 'NewYork_149_1999.93' 'NewYork_436_2000.04' 'NewYork_182_2000.15' NewYork_186_2000 'NewYork_184_1999.99' 'NewYork_284_1999.2' 'NewYork_337_1999.2' 'NewYork_257_1999.11' 'NewYork_322_1999.23' 'NewYork_333_1999.15' 'NewYork_285_1999.08' 'NewYork_332_1999.15' 'NewYork_194_2003.12' 'NewYork_195_2003.15' 'NewYork_197_2003.22' 'NewYork_193_2003.16' 'NewYork_301_2001.08' 'NewYork_133_2002.12' 'NewYork_413_2002.13' 'NewYork_415_2002.16' 'NewYork_403_2002.03' 'NewYork_111_2002.12' 'NewYork_120_2002.16' 'NewYork_119_2002.1' 'NewYork_108_2002.1' 'NewYork_134_2002.03' 'NewYork_130_2002.21' 'NewYork_88_2002.18' 'NewYork_136_2002.23' 'NewYork_127_2002.02' 'NewYork_77_2002.01' 'NewYork_109_2002.1' 'NewYork_C4_2002.11' 'NewYork_104_2002.07' 'NewYork_121_2002.18' 'NewYork_112_2002.1' 'NewYork_87_2002.04' 'NewYork_71_2001.91' 'NewYork_125_2002.06' 'NewYork_405_2002.04' NewYork_94_2002 'NewYork_408_2002.05' 'NewYork_115_2002.12' 'NewYork_411_2002.08' NewYork_131_2002 'NewYork_83_2001.98' 'NewYork_97_2002.14' 'NewYork_410_2002.06' 'NewYork_407_2002.04' 'NewYork_91_2002.07' 'NewYork_275_2002.03' 'NewYork_102_2002.08' 'NewYork_81_2002.16' 'NewYork_135_2002.14' 'NewYork_276_2002.2' 'NewYork_273_2002.01' 'NewYork_419_2002.07' 'NewYork_82_2002.01' 'NewYork_124_2001.93' 'NewYork_113_2002.1' 'NewYork_132_2002.09' 'NewYork_99_2002.08' 'NewYork_129_2002.14' 'NewYork_202_2003.28' 'NewYork_106_2002.07' 'NewYork_74_2002.07' 'NewYork_107_2002.06' 'NewYork_418_2002.06' 'NewYork_192_2003.12' 'NewYork_404_2002.03' 'NewYork_110_2002.1' 'NewYork_93_2002.16' 'NewYork_89_2002.05' 'NewYork_412_2002.11' 'NewYork_126_2002.18' 'NewYork_409_2002.06' 'NewYork_75_2002.14' 'NewYork_118_2002.1' 'NewYork_122_2002.24' 'NewYork_103_2002.09' 'NewYork_128_2002.09' 'NewYork_402_2002.01' 'NewYork_416_2002.18' 'NewYork_84_2002.01' 'NewYork_414_2002.14' 'NewYork_92_2002.07' 'NewYork_420_2002.1' 'NewYork_215_2003.33' 'NewYork_213_2003.33' 'NewYork_216_2003.33' 'NewYork_86_2002.18' 'NewYork_401_2001.91' 'NewYork_80_2002.01' 'NewYork_90_2002.12' 'NewYork_116_2002.1' 'NewYork_117_2002.11' 'NewYork_100_2002.08' 'NewYork_101_2002.12' 'NewYork_274_2002.18' 'NewYork_95_2002.18' 'NewYork_114_2002.19' 'NewYork_105_2002.12' 'NewYork_85_2002.02' 'NewYork_406_2002.04' 'NewYork_76_2002.05' 'NewYork_96_2002.07' 'NewYork_214_2003.33' 'NewYork_204_2003.64' 'NewYork_16_2003.88' 'NewYork_58_2003.98' 'NewYork_46_2003.96' 'NewYork_38_2003.99' 'NewYork_15_2003.88' 'NewYork_31_2004.03' 'NewYork_47_2003.97' 'NewYork_27_2003.84' 'NewYork_44_2003.96' 'NewYork_53_2003.96' 'NewYork_29_2003.97' 'NewYork_14_2003.94' 'NewYork_49_2003.98' 'NewYork_25_2003.98' 'NewYork_39_2003.95' 'NewYork_65_2004.01' 'NewYork_21_2003.92' 'NewYork_34_2003.94' 'NewYork_24_2003.94' 'NewYork_22_2003.94' 'NewYork_12_2003.97' 'NewYork_477_2003.9' 'NewYork_268_2003.93' 'NewYork_26_2003.94' 'NewYork_11_2003.85' 'NewYork_56_2003.98' 'NewYork_41_2003.96' 'NewYork_63_2004.01' 'NewYork_498_2004.05' 'NewYork_67_2004.01' 'NewYork_54_2003.96' 'NewYork_43_2003.96' 'NewYork_50_2003.96' 'NewYork_13_2003.88' 'NewYork_40_2003.95' 'NewYork_33_2004.04' 'NewYork_272_2003.93' 'NewYork_271_2003.93' 'NewYork_37_2003.95' 'NewYork_60A_2003.98' 'NewYork_42_2003.96' 'NewYork_51_2003.96' 'NewYork_1_2003.84' 'NewYork_267_2003.93' 'NewYork_8_2004.01' 'NewYork_35_2003.95' 'NewYork_36_2003.96' 'NewYork_9_2003.85' 'NewYork_19_2003.98' 'NewYork_270_2003.9' 'NewYork_28_2003.9' 'NewYork_64_2004.01' NewYork_66_2004 'NewYork_18_2003.94' 'NewYork_479_2003.88' 'NewYork_61A_2003.99' 'NewYork_10_2004.1' 'NewYork_5_2004.04' 'NewYork_20_2003.94' 'NewYork_6_2004.04' 'NewYork_62A_2003.99' 'NewYork_476_2003.98' 'NewYork_17_2003.9' 'NewYork_480_2004.05' 'NewYork_499_2004.06' 'NewYork_23_2003.98' 'NewYork_475_2003.96' 'NewYork_70_2004.04' 'NewYork_473_2003.92' 'NewYork_45_2003.96' 'NewYork_2_2003.84' 'NewYork_4_2003.96' 'NewYork_30_2003.94' 'NewYork_7_2003.85' 'NewYork_69_2004.04' 'NewYork_55_2003.96' 'NewYork_48_2003.96' 'NewYork_474_2004.02' 'NewYork_3_2003.96' 'NewYork_478_2003.91' 'NewYork_466_2004.93' 'NewYork_365_2004.98' 'NewYork_391_2005.04' 'NewYork_362_2004.96' 'NewYork_374_2005.01' 'NewYork_381_2005.01' 'NewYork_237_2004.98' 'NewYork_389_2005.03' 'NewYork_367_2005.15' 'NewYork_356_2004.94' 'NewYork_232_2004.96' 'NewYork_210_2005.15' 'NewYork_370_2004.99' 'NewYork_361_2005.11' 'NewYork_465_2005.21' 'NewYork_377_2004.99' 'NewYork_123_2004.98' 'NewYork_363_2004.98' 'NewYork_390_2005.04' 'NewYork_98_2004.87' 'NewYork_357_2005.15' 'NewYork_396_2005.19' 'NewYork_376_2005.07' 'NewYork_368_2004.88' 'NewYork_366_2004.99' 'NewYork_258_2005.07' 'NewYork_190_2004.88' 'NewYork_68_2004.87' NewYork_372_2005 'NewYork_200_2004.92' 'NewYork_354_2005.01' 'NewYork_375_2005.1' 'NewYork_191_2005.04' 'NewYork_369_2005.03' 'NewYork_393_2005.25' 'NewYork_388_2005.1' 'NewYork_245_2004.9' 'NewYork_360_2004.9' 'NewYork_351_2004.87' 'NewYork_353_2004.87' 'NewYork_355_2004.86' NewYork_386_2005 'NewYork_352_2005.03' 'NewYork_470_2004.76' 'NewYork_236_2005.01' 'NewYork_395_2005.09' 'NewYork_380_2005.01' 'NewYork_73_2004.82' 'NewYork_334_2004.99' 'NewYork_461_2005.11' 'NewYork_378_2005.03' 'NewYork_238_2005.11' NewYork_244_2005 'NewYork_359_2005.07' 'NewYork_207_2004.96' 'NewYork_364_2005.01' 'NewYork_371_2004.96' 'NewYork_467_2004.73' 'NewYork_471_2004.88' 'NewYork_319_2004.88' 'NewYork_462_2005.13' 'NewYork_500_2004.96' 'NewYork_463_2005.13' 'NewYork_464_2005.2' 'NewYork_218_2004.96' 'NewYork_385_2005.01' 'NewYork_469_2004.74' 'NewYork_468_2004.73' 'NewYork_472_2004.76' 'NewYork_379_2004.94' 'NewYork_383_2005.02' 'NewYork_384_2005.04' 'NewYork_206_2005.07' 'NewYork_394_2005.03' 'NewYork_358_2004.94' 'NewYork_392_2004.99' 'NewYork_243_2005.11' 'NewYork_382_2005.1' 'NewYork_387_2005.01' 'NewYork_373_2005.17' 'NewYork_269_2003.93' 'NewYork_32_2003.93' 'NewYork_59_2003.98' 'NewYork_52_2004.12' 'NewYork_485_2003.07' 'NewYork_203_2003.37' 'NewYork_198_2003.2' 'NewYork_196_2003.16' 'NewYork_201_2003.29' 'NewYork_199_2003.24' 'NewYork_266_1999.36' 'NewYork_137_1999.78' 'NewYork_423_1999.98' 'NewYork_435_2000.04' 'NewYork_145_1999.87' 'NewYork_138_1999.77' 'NewYork_177_1999.83' 'NewYork_428_1999.76' 'NewYork_449_1999.03' 'NewYork_323_1999.08' 'NewYork_313_1999.01' 'NewYork_224_1999.01' 'NewYork_453_1999.05' 'NewYork_254_1999.02' 'NewYork_451_1999.05' 'NewYork_454_1999.05'[&!color=#-8381639] 'NewYork_317_1999.03'[&!color=#-8381639] 'NewYork_248_1999.11'[&!color=#-8381639] 'NewYork_311_1999.18'[&!color=#-8381639] 'NewYork_457_1999.06'[&!color=#-8381639] 'NewYork_398_1999.24'[&!color=#-8381639] 'NewYork_459_1999.08'[&!color=#-8381639] 'NewYork_397_1999.11'[&!color=#-8381639] 'NewYork_262_1999.08'[&!color=#-8381639] 'NewYork_327_1999.24' 'NewYork_249_1998.96'[&!color=#-8381639] 'NewYork_331_1999.09'[&!color=#-8381639] 'NewYork_329_1999.1'[&!color=#-8381639] 'NewYork_280_1999.3'[&!color=#-8381639] 'NewYork_253_1999.25'[&!color=#-8381639] 'NewYork_320_1999.25'[&!color=#-8381639] 'NewYork_304_1999.01'[&!color=#-8381639] 'NewYork_259_1999.11' 'NewYork_314_1999.11'[&!color=#-8381639] 'NewYork_256_1999.01' 'NewYork_338_1999.12' 'NewYork_347_1999.07' 'NewYork_450_1999.04' 'NewYork_240_1999.01' 'NewYork_328_1999.01' 'NewYork_252_1999.05' 'NewYork_261_1999.29' 'NewYork_279_1999.16' 'NewYork_255_1999.13' 'NewYork_264_1999.19' 'NewYork_330_1999.01' 'NewYork_326_1999.07' 'NewYork_318_1999.11' 'NewYork_290_1999.15' 'NewYork_321_1999.06' 'NewYork_282_1999.13' 'NewYork_286_1999.23' 'NewYork_325_1999.17' 'NewYork_288_1999.17' 'NewYork_260_1999.13' 'NewYork_340_1999.08' 'NewYork_283_1999.13' 'NewYork_277_1999.04' 'NewYork_247_1998.85' 'NewYork_452_1999.05' 'NewYork_460_1999.08' 'NewYork_289_1998.94' 'NewYork_448_1998.91' 'NewYork_339_1999.13' 'NewYork_601_1996.96' 'NewYork_595_1996.98' 'NewYork_570_1996.96' 'NewYork_561_1996.99' 'NewYork_568_1996.96' 'NewYork_559_1996.92' 'NewYork_592_1996.94' 'NewYork_587_1996.9' 'NewYork_581_1997.06' 'NewYork_579_1997.02' 'NewYork_574_1996.96' 'NewYork_564_1997.02' 'NewYork_580_1996.95' 'NewYork_594_1996.9' 'NewYork_583_1997.18' 'NewYork_600_1996.99' 'NewYork_560_1997.03' 'NewYork_565_1996.94' 'NewYork_572_1996.96' 'NewYork_599_1996.98' 'NewYork_576_1997.03' 'NewYork_566_1997.06' 'NewYork_575_1996.98' 'NewYork_541_1998.21' 'NewYork_518_1998.03' 'NewYork_590_1996.96' 'NewYork_608_1996.27' 'NewYork_617_1996.23' 'NewYork_631_1996.27' 'NewYork_652_1995.93' 'NewYork_562_1996.97' 'NewYork_558_1997.03' 'NewYork_585_1997.08' 'NewYork_593_1996.96' 'NewYork_584_1997.02' 'NewYork_671_1995.03' 'NewYork_660_1995.18' 'NewYork_662_1995.04' 'NewYork_700_1995.14' 'NewYork_678_1995.07' 'NewYork_674_1995.07' 'NewYork_668_1995.15' 'NewYork_687_1995.12' 'NewYork_703_1995.08' 'NewYork_676_1995.06' 'NewYork_692_1995.06' 'NewYork_699_1995.12' 'NewYork_632_1996.18' 'NewYork_625_1996.05' 'NewYork_701_1995.16' 'NewYork_641_1996.02' 'NewYork_628_1995.96' 'NewYork_635_1996.06' 'NewYork_618_1996.01' 'NewYork_623_1996.01' 'NewYork_613_1996.04' 'NewYork_624_1996.14' 'NewYork_611_1996.01' 'NewYork_612_1995.98' 'NewYork_636_1996.07' 'NewYork_639_1995.98' 'NewYork_634_1996.95' 'NewYork_609_1995.98' 'NewYork_637_1996.06' NewYork_647_1996 'NewYork_648_1996.02' 'NewYork_622_1996.04' 'NewYork_610_1995.98' 'NewYork_606_1995.92' 'NewYork_619_1996.04' 'NewYork_783_1993.26' 'NewYork_777_1993.23' 'NewYork_761_1993.18' 'NewYork_735_1994.05' 'NewYork_716_1994.06' 'NewYork_788_1993.17' 'NewYork_702_1995.04' 'NewYork_688_1994.96' 'NewYork_698_1995.1' 'NewYork_683_1995.18' 'NewYork_682_1995.18' 'NewYork_658_1995.16' 'NewYork_696_1995.01' 'NewYork_691_1995.02' 'NewYork_685_1995.12' 'NewYork_679_1995.18' 'NewYork_663_1994.98' 'NewYork_689_1995.07' 'NewYork_677_1995.15' 'NewYork_697_1995.13' 'NewYork_693_1995.23' 'NewYork_666_1995.12' 'NewYork_675_1995.08' 'NewYork_686_1995.1' 'NewYork_681_1995.15' 'NewYork_664_1995.21' 'NewYork_665_1994.97' 'NewYork_659_1994.95' 'NewYork_661_1994.97' 'NewYork_672_1995.06' 'NewYork_690_1995.06' 'NewYork_667_1995.04' 'NewYork_670_1995.04' 'NewYork_673_1995.07' 'NewYork_684_1995.08' 'NewYork_680_1995.12' 'NewYork_695_1995.18' 'NewYork_669_1995.04' 'NewYork_657_1994.93' 'NewYork_753_1994.14' 'NewYork_746_1994.16' 'NewYork_741_1994.18' 'NewYork_710_1994.12' 'NewYork_726_1994.12' 'NewYork_733_1994.12' 'NewYork_718_1994.12' 'NewYork_725_1994.1' 'NewYork_720_1994.08' 'NewYork_707_1994.13' 'NewYork_748_1994.06' 'NewYork_738_1994.11' 'NewYork_712_1993.93' 'NewYork_711_1994.05' 'NewYork_736_1994.07' 'NewYork_719_1994.07' 'NewYork_732_1994.03' 'NewYork_737_1994.11' 'NewYork_729_1994.17' 'NewYork_728_1994.1' 'NewYork_727_1994.1' 'NewYork_654_1994.85' 'NewYork_721_1994.05' 'NewYork_730_1994.02' 'NewYork_742_1994.04' 'NewYork_743_1994.03' 'NewYork_734_1994.03' 'NewYork_704_1994.02' 'NewYork_752_1994.01' 'NewYork_747_1994.05' 'NewYork_739_1994.14' 'NewYork_717_1994.07' 'NewYork_731_1994.2' 'NewYork_744_1994.06' 'NewYork_751_1993.87' 'NewYork_722_1994.18' 'NewYork_713_1994.14' 'NewYork_708_1994.04' 'NewYork_724_1994.09' 'NewYork_740_1994.05' 'NewYork_706_1994.01' 'NewYork_655_1994.89' 'NewYork_723_1994.02' 'NewYork_715_1994.59' 'NewYork_745_1994.12' 'NewYork_750_1994.08' 'NewYork_749_1994.04' 'NewYork_709_1994.03' 'NewYork_714_1994.05' 'NewYork_786_1993.22' 'NewYork_778_1993.1' 'NewYork_779_1993.1' 'NewYork_765_1993.18' 'NewYork_787_1993.2' 'NewYork_799_1993.2' 'NewYork_792_1993.2' 'NewYork_772_1993.2' 'NewYork_762_1993.11' 'NewYork_780_1993.18' 'NewYork_785_1993.25' 'NewYork_763_1993.25' 'NewYork_774_1993.17' 'NewYork_790_1993.11' 'NewYork_795_1993.11' 'NewYork_796_1993.15' 'NewYork_800_1993.21' 'NewYork_759_1993.2' 'NewYork_776_1993.15' 'NewYork_793_1993.1' 'NewYork_782_1993.27' 'NewYork_794_1993.19' ; end; begin trees; tree TREE1 = [&R] 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end; begin figtree; set appearance.backgroundColorAttribute="height"; set appearance.backgroundColour=#-1; set appearance.branchColorAttribute="height"; set appearance.branchLineWidth=1.0; set appearance.foregroundColour=#-16777216; set appearance.selectionColour=#-2144520576; set branchLabels.colorAttribute="User Selection"; set branchLabels.displayAttribute="Branch times"; set branchLabels.fontName="sansserif"; set branchLabels.fontSize=8; set branchLabels.fontStyle=0; set branchLabels.isShown=false; set branchLabels.significantDigits=4; set layout.expansion=0; set layout.layoutType="RECTILINEAR"; set layout.zoom=0; set nodeBars.barWidth=4.0; set nodeLabels.colorAttribute="User Selection"; set nodeLabels.displayAttribute="Node ages"; set nodeLabels.fontName="sansserif"; set nodeLabels.fontSize=8; set nodeLabels.fontStyle=0; set nodeLabels.isShown=false; set nodeLabels.significantDigits=4; set polarLayout.alignTipLabels=true; set polarLayout.angularRange=31899; set polarLayout.rootAngle=0; set polarLayout.rootLength=100; set polarLayout.showRoot=true; set radialLayout.spread=0.0; set rectilinearLayout.alignTipLabels=true; set rectilinearLayout.curvature=0; set rectilinearLayout.rootLength=100; set scale.offsetAge=2005.25; set scale.rootAge=1.0; set scale.scaleFactor=-1.0; set scale.scaleRoot=false; set scaleAxis.automaticScale=true; set scaleAxis.fontSize=8.0; set scaleAxis.isShown=true; set scaleAxis.lineWidth=1.0; set scaleAxis.majorTicks=2.5; set scaleAxis.origin=0.0; set scaleAxis.reverseAxis=true; set scaleAxis.showGrid=true; set scaleAxis.significantDigits=4; set scaleBar.automaticScale=true; set scaleBar.fontSize=6.0; set scaleBar.isShown=false; set scaleBar.lineWidth=1.0; set scaleBar.scaleRange=2.0; set scaleBar.significantDigits=4; set tipLabels.colorAttribute="height"; set tipLabels.displayAttribute="Names"; set tipLabels.fontName="Arial"; set tipLabels.fontSize=6; set tipLabels.fontStyle=0; set tipLabels.isShown=true; set tipLabels.significantDigits=4; set trees.order=true; set trees.orderType="decreasing"; set trees.rooting=false; set trees.rootingType="User Selection"; set trees.transform=false; set trees.transformType="cladogram"; end; figtree-1.4.3/src/000077500000000000000000000000001277473563300137545ustar00rootroot00000000000000figtree-1.4.3/src/figtree/000077500000000000000000000000001277473563300154015ustar00rootroot00000000000000figtree-1.4.3/src/figtree/applet/000077500000000000000000000000001277473563300166665ustar00rootroot00000000000000figtree-1.4.3/src/figtree/applet/FigTreeApplet.java000077500000000000000000000140301277473563300222250ustar00rootroot00000000000000/* * FigTreeApplet.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.applet; import jebl.evolution.trees.Tree; import jebl.evolution.io.NewickImporter; import jebl.evolution.io.ImportException; import jam.controlpalettes.ControlPalette; import jam.panels.SearchPanel; import jam.panels.SearchPanelListener; import jam.panels.StatusBar; import figtree.application.FigTreeNexusImporter; import figtree.treeviewer.*; import figtree.panel.SimpleTreeViewer; import figtree.panel.FigTreePanel; import figtree.panel.SimpleControlPalette; import javax.swing.*; import java.awt.*; import java.io.*; import java.util.*; import java.net.URL; import java.net.MalformedURLException; /** * @author Andrew Rambaut * @author Alexei Drummond * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FigTreeApplet extends JApplet { private SimpleTreeViewer treeViewer; private ControlPalette controlPalette1; private ControlPalette controlPalette2; private FigTreePanel figTreePanel; private StatusBar statusBar; private SearchPanel filterPanel; private JPopupMenu filterPopup; public void init() { FigTreePanel.Style style = FigTreePanel.Style.DEFAULT; String styleParam = getParameter("style"); if (styleParam != null) { style = FigTreePanel.Style.valueOf(styleParam.trim().toUpperCase()); } treeViewer = new SimpleTreeViewer(); controlPalette1 = new SimpleControlPalette(); controlPalette2 = new SimpleControlPalette(); figTreePanel = new FigTreePanel(treeViewer, controlPalette1, controlPalette2, style); filterPopup = new JPopupMenu(); for (TreeViewer.TextSearchType searchType : TreeViewer.TextSearchType.values()) { filterPopup.add(searchType.toString()); } filterPanel = new SearchPanel("Filter", filterPopup, true); filterPanel.setOpaque(false); filterPanel.addSearchPanelListener(new SearchPanelListener() { /** * Called when the user requests a search by pressing return having * typed a search string into the text field. If the continuousUpdate * flag is true then this method is called when the user types into * the text field. * * @param searchString the user's search string */ public void searchStarted(String searchString) { int index = filterPopup.getSelectionModel().getSelectedIndex(); if (index == -1) index = 0; TreeViewer.TextSearchType searchType = TreeViewer.TextSearchType.values()[index]; treeViewer.selectTaxa("!name", searchType, searchString, false); } /** * Called when the user presses the cancel search button or presses * escape while the search is in focus. */ public void searchStopped() { treeViewer.clearSelectedTaxa(); } }); statusBar = new StatusBar(""); statusBar.setStatusProvider(treeViewer); statusBar.add(filterPanel, BorderLayout.EAST); if (style != FigTreePanel.Style.ICARUS_SMALL) { getContentPane().add(statusBar, BorderLayout.NORTH); } getContentPane().add(figTreePanel, BorderLayout.CENTER); } public void start() { String tree = getParameter("tree"); String treefile = getParameter("treefile"); if (tree != null && tree.length() > 0) { URL fileURL = null; try { fileURL = new URL(tree); BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(fileURL.openStream())); readData(bufferedReader, true); } catch (MalformedURLException e) { treeViewer.setStatusText(e.getMessage()); } catch (IOException e) { treeViewer.setStatusText(e.getMessage()); } } else if (treefile != null && treefile.length() > 0) { try { BufferedReader bufferedReader = new BufferedReader(new StringReader(treefile)); readData(bufferedReader, true); } catch (IOException e) { treeViewer.setStatusText(e.getMessage()); } } else { treeViewer.setStatusText("Tree not specified"); } } public void stop() { } protected boolean readData(Reader reader, boolean isNexus) throws IOException { java.util.List trees = new ArrayList(); try { Map settings = new HashMap(); // First of all, fully populate the settings map so that // all the settings have defaults controlPalette1.getSettings(settings); controlPalette2.getSettings(settings); if (isNexus) { FigTreeNexusImporter importer = new FigTreeNexusImporter(reader); while (importer.hasTree()) { Tree tree = importer.importNextTree(); trees.add(tree); } // Try to find a figtree block and if found, parse the settings while (true) { try { importer.findNextBlock(); if (importer.getNextBlockName().equalsIgnoreCase("FIGTREE")) { importer.parseFigTreeBlock(settings); } } catch (EOFException ex) { break; } } } else { NewickImporter importer = new NewickImporter(reader, true); while (importer.hasTree()) { Tree tree = importer.importNextTree(); trees.add(tree); } } if (trees.size() == 0) { throw new ImportException("This file contained no trees."); } treeViewer.setTrees(trees); controlPalette1.setSettings(settings); controlPalette2.setSettings(settings); } catch (ImportException ie) { JOptionPane.showMessageDialog(this, "Error reading tree file: " + ie, "Import Error", JOptionPane.ERROR_MESSAGE); return false; } return true; } } figtree-1.4.3/src/figtree/application/000077500000000000000000000000001277473563300177045ustar00rootroot00000000000000figtree-1.4.3/src/figtree/application/Arguments.java000066400000000000000000000354121277473563300225210ustar00rootroot00000000000000/* * Arguments.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application; import java.util.StringTokenizer; /** * Parses a set of command line arguments according to the given definitions. * Can parse simple switches, numerical arguments, string arguments from a list * of options and lists. * * Will generate help text automatically. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class Arguments { public static final String ARGUMENT_CHARACTER = "-"; public static class ArgumentException extends Exception { public ArgumentException() { super(); } public ArgumentException(String message) { super(message); } }; public static class Option { public Option(String label, String description) { this.label = label; this.description = description; } String label; String description; boolean isAvailable = false; }; public static class StringOption extends Option { public StringOption(String label, String tag, String description) { super(label, description); this.tag = tag; } public StringOption(String label, String[] options, boolean caseSensitive, String description) { super(label, description); this.options = options; this.caseSensitive = caseSensitive; } String[] options = null; String tag = null; boolean caseSensitive = false; String value = null; }; public static class IntegerOption extends Option { public IntegerOption(String label, String description) { super(label, description); } public IntegerOption(String label, int minValue, int maxValue, String description) { super(label, description); this.minValue = minValue; this.maxValue = maxValue; } int minValue = Integer.MIN_VALUE; int maxValue = Integer.MAX_VALUE; int value = 0; }; public static class IntegerArrayOption extends IntegerOption { public IntegerArrayOption(String label, String description) { this(label, 0, Integer.MIN_VALUE, Integer.MAX_VALUE, description); } public IntegerArrayOption(String label, int count, String description) { this(label, count, Integer.MIN_VALUE, Integer.MAX_VALUE, description); } public IntegerArrayOption(String label, int minValue, int maxValue, String description) { this(label, 0, minValue, maxValue, description); } public IntegerArrayOption(String label, int count, int minValue, int maxValue, String description) { super(label, minValue, maxValue, description); this.count = count; } int count; int[] values = null; }; public static class RealOption extends Option { public RealOption(String label, String description) { super(label, description); } public RealOption(String label, double minValue, double maxValue, String description) { super(label, description); this.minValue = minValue; this.maxValue = maxValue; } double minValue = Double.NEGATIVE_INFINITY; double maxValue = Double.POSITIVE_INFINITY; double value = 0; }; public static class RealArrayOption extends RealOption { public RealArrayOption(String label, String description) { this(label, 0, Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY, description); } public RealArrayOption(String label, int count, String description) { this(label, count, Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY, description); } public RealArrayOption(String label, double minValue, double maxValue, String description) { this(label, 0, minValue, maxValue, description); } public RealArrayOption(String label, int count, double minValue, double maxValue, String description) { super(label, minValue, maxValue, description); this.count = count; } private int count; double[] values = null; }; /** * Parse a list of arguments ready for accessing */ public Arguments(Option[] options) { this.options = options; } public Arguments(Option[] options, boolean caseSensitive) { this.options = options; this.caseSensitive = caseSensitive; } /** * Parse a list of arguments ready for accessing */ public void parseArguments(String[] arguments) throws ArgumentException { int[] optionIndex = new int[arguments.length]; for (int i = 0; i < optionIndex.length; i++) { optionIndex[i] = -1; } for (int i = 0; i < options.length; i++) { Option option = options[i]; int index = findArgument(arguments, option.label); if (index != -1) { if (optionIndex[index] != -1) { throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument"); } // the first value may be appended to the option label (e.g., '-t1.0'): String arg = arguments[index].substring(option.label.length() + 1); optionIndex[index] = i; option.isAvailable = true; if (option instanceof IntegerArrayOption) { IntegerArrayOption o = (IntegerArrayOption)option; o.values = new int[o.count]; int k = index; int j = 0; while (j < o.count) { if (arg.length() > 0) { StringTokenizer tokenizer = new StringTokenizer(arg, ",\t "); while (tokenizer.hasMoreTokens()) { String token = tokenizer.nextToken(); if (token.length() > 0) { try { o.values[j] = Integer.parseInt(token); } catch (NumberFormatException nfe) { throw new ArgumentException("Argument, " + arguments[index] + " has a bad integer value: " + token); } if (o.values[j] > o.maxValue || o.values[j] < o.minValue) { throw new ArgumentException("Argument, " + arguments[index] + " has a bad integer value: " + token); } j++; } } } k++; if (j < o.count) { if (k >= arguments.length) { throw new ArgumentException("Argument, " + arguments[index] + " is missing one or more values: expecting " + o.count + " integers"); } if (optionIndex[k] != -1) { throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument"); } arg = arguments[k]; optionIndex[k] = i; } } } else if (option instanceof IntegerOption) { IntegerOption o = (IntegerOption)option; if (arg.length() == 0) { int k = index + 1; if (k >= arguments.length) { throw new ArgumentException("Argument, " + arguments[index] + " is missing its value: expecting an integer"); } if (optionIndex[k] != -1) { throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument"); } arg = arguments[k]; optionIndex[k] = i; } try { o.value = Integer.parseInt(arg); } catch (NumberFormatException nfe) { throw new ArgumentException("Argument, " + arguments[index] + " has a bad integer value: " + arg); } if (o.value > o.maxValue || o.value < o.minValue) { throw new ArgumentException("Argument, " + arguments[index] + " has a bad integer value: " + arg); } } else if (option instanceof RealArrayOption) { RealArrayOption o = (RealArrayOption)option; o.values = new double[o.count]; int k = index; int j = 0; while (j < o.count) { if (arg.length() > 0) { StringTokenizer tokenizer = new StringTokenizer(arg, ",\t "); while (tokenizer.hasMoreTokens()) { String token = tokenizer.nextToken(); if (token.length() > 0) { try { o.values[j] = Double.parseDouble(token); } catch (NumberFormatException nfe) { throw new ArgumentException("Argument, " + arguments[index] + " has a bad real value: " + token); } if (o.values[j] > o.maxValue || o.values[j] < o.minValue) { throw new ArgumentException("Argument, " + arguments[index] + " has a bad real value: " + token); } j++; } } } k++; if (j < o.count) { if (k >= arguments.length) { throw new ArgumentException("Argument, " + arguments[index] + " is missing one or more values: expecting " + o.count + " integers"); } if (optionIndex[k] != -1) { throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument"); } arg = arguments[k]; optionIndex[k] = i; } } } else if (option instanceof RealOption) { RealOption o = (RealOption)option; if (arg.length() == 0) { int k = index + 1; if (k >= arguments.length) { throw new ArgumentException("Argument, " + arguments[index] + " is missing its value: expecting a real number"); } if (optionIndex[k] != -1) { throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument"); } arg = arguments[k]; optionIndex[k] = i; } try { o.value = Double.parseDouble(arg); } catch (NumberFormatException nfe) { throw new ArgumentException("Argument, " + arguments[index] + " has a bad real value: " + arg); } if (o.value > o.maxValue || o.value < o.minValue) { throw new ArgumentException("Argument, " + arguments[index] + " has a bad real value: " + arg); } } else if (option instanceof StringOption) { StringOption o = (StringOption)option; if (arg.length() == 0) { int k = index + 1; if (k >= arguments.length) { throw new ArgumentException("Argument, " + arguments[index] + " is missing its value: expecting a string"); } if (optionIndex[k] != -1) { throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument"); } arg = arguments[k]; optionIndex[k] = i; } o.value = arg; if (o.options != null) { boolean found = false; for (int j = 0; j < o.options.length; j++) { if (o.options[j].equals(o.value)) { found = true; break; } } if (!found) { throw new ArgumentException("Argument, " + arguments[index] + " has a bad string value: " + arg); } } } else { // is simply an Option - nothing to do... } } } int n = 0; int i = arguments.length - 1; while (i >= 0 && optionIndex[i] == -1 && !arguments[i].startsWith(ARGUMENT_CHARACTER)) { n++; i--; } leftoverArguments = new String[n]; for (i = 0; i < n; i++) { leftoverArguments[i] = arguments[arguments.length - n + i]; } for (i = 0; i < arguments.length - n; i++) { if (optionIndex[i] == -1) { throw new ArgumentException("Unrecognized argument: " + arguments[i]); } } } private int findArgument(String[] arguments, String label) { for (int i = 0; i < arguments.length; i++) { if (arguments[i].length() - 1 >= label.length()) { if (arguments[i].startsWith(ARGUMENT_CHARACTER)) { String l = arguments[i].substring(1, label.length() + 1); if ((!caseSensitive && label.equalsIgnoreCase(l)) || label.equals(l)) { return i; } } } } return -1; } /** * Does an argument with label exist? */ public boolean hasOption(String label) { int n = findOption(label); if (n == -1) { return false; } return options[n].isAvailable; } /** * Return the value of an integer option */ public int getIntegerOption(String label) { IntegerOption o = (IntegerOption)options[findOption(label)]; return o.value; } /** * Return the value of an integer array option */ public int[] getIntegerArrayOption(String label) { IntegerArrayOption o = (IntegerArrayOption)options[findOption(label)]; return o.values; } /** * Return the value of an real number option */ public double getRealOption(String label) { RealOption o = (RealOption)options[findOption(label)]; return o.value; } /** * Return the value of an real array option */ public double[] getRealArrayOption(String label) { RealArrayOption o = (RealArrayOption)options[findOption(label)]; return o.values; } /** * Return the value of an string option */ public String getStringOption(String label) { StringOption o = (StringOption)options[findOption(label)]; return o.value; } /** * Return any arguments leftover after the options */ public String[] getLeftoverArguments() { return leftoverArguments; } public void printUsage(String name, String commandLine) { System.out.print(" Usage: " + name); for (int i = 0; i < options.length; i++) { Option option = options[i]; System.out.print(" [-" + option.label); if (option instanceof IntegerArrayOption) { IntegerArrayOption o = (IntegerArrayOption)option; for (int j = 1; j <= o.count; j++) { System.out.print(" "); } System.out.print("]"); } else if (option instanceof IntegerOption) { System.out.print(" ]"); } else if (option instanceof RealArrayOption) { RealArrayOption o = (RealArrayOption)option; for (int j = 1; j <= o.count; j++) { System.out.print(" "); } System.out.print("]"); } else if (option instanceof RealOption) { System.out.print(" ]"); } else if (option instanceof StringOption) { StringOption o = (StringOption)option; if (o.options != null) { System.out.print(" <" + o.options[0]); for (int j = 1; j < o.options.length; j++) { System.out.print("|" + o.options[j]); } System.out.print(">]"); } else { System.out.print(" <" + o.tag + ">]"); } } else { System.out.print("]"); } } System.out.println(" " + commandLine); for (int i = 0; i < options.length; i++) { Option option = options[i]; System.out.println(" -" + option.label + " " + option.description); } } private int findOption(String label) { for (int i = 0; i < options.length; i++) { String l = options[i].label; if ((!caseSensitive && label.equalsIgnoreCase(l)) || label.equals(l)) { return i; } } return -1; } private Option[] options = null; private String[] leftoverArguments = null; private boolean caseSensitive = false; } figtree-1.4.3/src/figtree/application/ExportTreeDialog.java000077500000000000000000000076461277473563300240100ustar00rootroot00000000000000/* * ExportTreeDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; import java.awt.event.ItemListener; import java.awt.event.ItemEvent; /** * Dialog presenting options for exporting one or more trees from FigTree * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ExportTreeDialog { public enum Format { NEXUS("NEXUS"), NEWICK("Newick"), JSON("JSON"); Format(String name) { this.name = name; } public String toString() { return name; } private String name; } private final JDialog dialog; private final JOptionPane optionPane; private JComboBox formatCombo = null; private JCheckBox asDisplayedCheck = new JCheckBox("Save as currently displayed"); private JCheckBox allTreesCheck = new JCheckBox("Save all trees"); private JCheckBox includeFigTreeCheck = new JCheckBox("Include FigTree block (NEXUS only)"); private JCheckBox includeAnnotationsCheck = new JCheckBox("Include Annotations (NEXUS & JSON only)"); public ExportTreeDialog(JFrame frame) { OptionsPanel options = new OptionsPanel(12, 12); formatCombo = new JComboBox(Format.values()); options.addComponentWithLabel("Tree file format: ", formatCombo); options.addComponent(asDisplayedCheck); options.addComponent(allTreesCheck); options.addComponent(includeFigTreeCheck); options.addComponent(includeAnnotationsCheck); optionPane = new JOptionPane(options, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); dialog = optionPane.createDialog(frame, "Export Trees"); dialog.pack(); formatCombo.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent e) { Object item = formatCombo.getSelectedItem(); includeFigTreeCheck.setEnabled(item.equals(Format.NEXUS)); includeAnnotationsCheck.setEnabled(item.equals(Format.NEXUS) || item.equals(Format.JSON)); } }); } public int showDialog() { dialog.setVisible(true); int result = JOptionPane.CANCEL_OPTION; Integer value = (Integer)optionPane.getValue(); if (value != null && value.intValue() != -1) { result = value.intValue(); } if (result == JOptionPane.OK_OPTION) { } return result; } public Format getFormat() { return (Format)formatCombo.getSelectedItem(); } public boolean asDisplayed() { return asDisplayedCheck.isSelected(); } public boolean allTrees() { return allTreesCheck.isSelected(); } public boolean includeFigTreeBlock() { return includeFigTreeCheck.isSelected(); } public boolean includeAnnotations() { return includeAnnotationsCheck.isSelected(); } }figtree-1.4.3/src/figtree/application/FigTreeApplication.java000077500000000000000000000431011277473563300242620ustar00rootroot00000000000000/* * FigTreeApplication.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ /** * TracerApp.java * * Title: Tracer * Description: An application for analysing MCMC trace files. * @author Andrew Rambaut * @author Alexei Drummond * @version $Id$ */ package figtree.application; import com.itextpdf.text.Document; import com.itextpdf.text.DocumentException; import com.itextpdf.text.pdf.PdfContentByte; import com.itextpdf.text.pdf.PdfTemplate; import com.itextpdf.text.pdf.PdfWriter; import figtree.application.preferences.*; import figtree.treeviewer.ExtendedTreeViewer; import jam.framework.*; import jam.controlpalettes.BasicControlPalette; import jam.controlpalettes.ControlPalette; import jam.mac.Utils; import java.awt.*; import java.awt.image.BufferedImage; import java.io.*; import java.net.URL; import java.util.*; import java.util.List; import jebl.evolution.io.ImportException; import jebl.evolution.io.NewickImporter; import jebl.evolution.trees.Tree; import javax.imageio.ImageIO; import javax.swing.*; import ch.randelshofer.quaqua.QuaquaManager; import org.apache.batik.dom.GenericDOMImplementation; import org.apache.batik.svggen.SVGGraphics2D; import org.w3c.dom.DOMImplementation; /** * Application class for FigTree including main() method for invoking it. * Uses JAM Application classes to create a MultiDoc Application. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FigTreeApplication extends MultiDocApplication { public static final String VERSION = "1.4.3"; public static final String DATES = "2006-2016"; public static FigTreeApplication application; public FigTreeApplication(MenuBarFactory menuBarFactory, String nameString, String titleString, String aboutString, Icon icon, String websiteURLString, String helpURLString) { super(menuBarFactory, nameString, titleString, aboutString, icon, websiteURLString, helpURLString); // addPreferencesSection(new GeneralPreferencesSection()); addPreferencesSection(new AppearancePreferencesSection()); addPreferencesSection(new FontsPreferencesSection()); // addPreferencesSection(new AdvancedPreferencesSection()); } public DocumentFrame doOpenFile(File file) { DocumentFrame documentFrame = getUpperDocumentFrame(); if (documentFrame != null && documentFrame.getFile() == null) { documentFrame.openFile(file); return documentFrame; } else { return super.doOpenFile(file); } } public void doPaste() { } static public void createGraphic(String graphicFormat, int width, int height, String treeFileName, String graphicFileName) { try { BufferedReader bufferedReader = new BufferedReader(new FileReader(treeFileName)); String line = bufferedReader.readLine(); while (line != null && line.length() == 0) { line = bufferedReader.readLine(); } bufferedReader.close(); boolean isNexus = (line != null && line.toUpperCase().contains("#NEXUS")); Reader reader = new FileReader(treeFileName); Map settings = new HashMap(); ExtendedTreeViewer treeViewer = new ExtendedTreeViewer(); ControlPalette controlPalette = new BasicControlPalette(FigTreePanel.CONTROL_PALETTE_WIDTH, BasicControlPalette.DisplayMode.ONLY_ONE_OPEN); FigTreePanel figTreePanel = new FigTreePanel(null, treeViewer, controlPalette); // First of all, fully populate the settings map so that // all the settings have defaults controlPalette.getSettings(settings); List trees = new ArrayList(); if (isNexus) { FigTreeNexusImporter importer = new FigTreeNexusImporter(reader); trees.add(importer.importNextTree()); // Try to find a figtree block and if found, parse the settings while (true) { try { importer.findNextBlock(); if (importer.getNextBlockName().equalsIgnoreCase("FIGTREE")) { importer.parseFigTreeBlock(settings); } } catch (EOFException ex) { break; } } } else { NewickImporter importer = new NewickImporter(reader, true); trees.add(importer.importNextTree()); } if (trees.size() == 0) { throw new ImportException("This file contained no trees."); } treeViewer.setTrees(trees); controlPalette.setSettings(settings); treeViewer.getContentPane().setSize(width, height); OutputStream stream; if (graphicFileName != null) { stream = new FileOutputStream(graphicFileName); } else { stream = System.out; } GraphicFormat format = null; if (graphicFormat.equals("PDF")) { format = GraphicFormat.PDF; } else if (graphicFormat.equals("SVG")) { format = GraphicFormat.SVG; } else if (graphicFormat.equals("GIF")) { format = GraphicFormat.GIF; } else if (graphicFormat.equals("PNG")) { format = GraphicFormat.PNG; } else if (graphicFormat.equals("JPEG")) { format = GraphicFormat.JPEG; } else { throw new RuntimeException("Unknown graphic format"); } if (graphicFileName != null) { System.out.println("Creating " + graphicFormat + " graphic: " + graphicFileName); } FigTreeFrame.exportGraphics(format, treeViewer.getContentPane(), stream); } catch(ImportException ie) { throw new RuntimeException("Error writing graphic file: " + ie.getMessage()); } catch(IOException ioe) { throw new RuntimeException("Error writing graphic file: " + ioe.getMessage()); } catch (DocumentException de) { throw new RuntimeException("Error writing graphic file: " + de.getMessage()); } } public static void centreLine(String line, int pageWidth) { int n = pageWidth - line.length(); int n1 = n / 2; for (int i = 0; i < n1; i++) { System.out.print(" "); } System.out.println(line); } public static void printTitle() { System.out.println(); centreLine("FigTree v" + VERSION + ", " + DATES, 60); centreLine("Tree Figure Drawing Tool", 60); centreLine("Andrew Rambaut", 60); System.out.println(); centreLine("Institute of Evolutionary Biology", 60); centreLine("University of Edinburgh", 60); centreLine("a.rambaut@ed.ac.uk", 60); System.out.println(); centreLine("http://tree.bio.ed.ac.uk/", 60); centreLine("Uses the Java Evolutionary Biology 2 Library (JEBL2)", 60); centreLine("http://jebl2.googlecode.com/", 60); centreLine("Thanks to Alexei Drummond, Joseph Heled, Philippe Lemey, ", 60); centreLine("Tulio de Oliveira, Oliver Pybus, Beth Shapiro & Marc Suchard", 60); System.out.println(); } public static void printUsage(Arguments arguments) { arguments.printUsage("figtree", "[] []"); System.out.println(); System.out.println(" Example: figtree test.tree"); System.out.println(" Example: figtree -graphic PDF test.tree test.pdf"); System.out.println(" Example: figtree -graphic GIF -width 320 -height 320 test.tree test.gif"); System.out.println(); } private static boolean lafLoaded = false; // Main entry point static public void main(String[] args) { // There is a major issue with languages that use the comma as a decimal separator. // To ensure compatibility between programs in the package, enforce the US locale. //Locale.setDefault(Locale.US); Arguments arguments = new Arguments( new Arguments.Option[] { new Arguments.StringOption("graphic", new String[] { "PDF", "SVG", // "SWF", "PS", "EMF", "PNG", // "GIF", "JPEG" }, false, "produce a graphic with the given format"), new Arguments.IntegerOption("width", "the width of the graphic in pixels"), new Arguments.IntegerOption("height", "the height of the graphic in pixels"), new Arguments.Option("url", "the input file is a URL"), new Arguments.Option("help", "option to print this message") }); try { arguments.parseArguments(args); } catch (Arguments.ArgumentException ae) { System.out.println(); System.out.println(ae.getMessage()); System.out.println(); printTitle(); printUsage(arguments); System.exit(1); } if (arguments.hasOption("help")) { printTitle(); printUsage(arguments); System.exit(0); } if (arguments.hasOption("graphic")) { int width = 800; int height = 600; if (arguments.hasOption("width")) { width = arguments.getIntegerOption("width"); } if (arguments.hasOption("height")) { height = arguments.getIntegerOption("height"); } // command line version... String graphicFormat = arguments.getStringOption("graphic"); String[] args2 = arguments.getLeftoverArguments(); if (args2.length == 0) { // no tree file specified printTitle(); printUsage(arguments); System.exit(0); } else if (args2.length == 1) { // no graphic file specified - write to stdout createGraphic(graphicFormat, width, height, args2[0], (args2.length > 1 ? args2[1] : null)); System.exit(0); } else { printTitle(); createGraphic(graphicFormat, width, height, args2[0], (args2.length > 1 ? args2[1] : null)); System.exit(0); } } if (Utils.isMacOSX()) { if (Utils.getMacOSXMajorVersionNumber() >= 5) { System.setProperty("apple.awt.brushMetalLook","true"); } System.setProperty("apple.laf.useScreenMenuBar","true"); System.setProperty("apple.awt.draggableWindowBackground","true"); System.setProperty("apple.awt.showGrowBox","true"); System.setProperty("apple.awt.graphics.UseQuartz","true"); try { // set the Quaqua Look and Feel in the UIManager javax.swing.SwingUtilities.invokeAndWait(new Runnable() { public void run() { try { // Only override the UI's necessary for ColorChooser and // FileChooser: Set includes = new HashSet(); includes.add("ColorChooser"); includes.add("FileChooser"); includes.add("Component"); includes.add("Browser"); includes.add("Tree"); includes.add("SplitPane"); includes.add("TitledBorder"); try { QuaquaManager.setIncludedUIs(includes); } catch (java.lang.NoClassDefFoundError ncdfe) { // this is to protect against the figtree.jar being // run on Mac OS without Quaqua on the classpath } UIManager.setLookAndFeel( "ch.randelshofer.quaqua.QuaquaLookAndFeel" ); lafLoaded = true; } catch (Exception e) { } } }); } catch (Exception e) { } UIManager.put("SystemFont", new Font("Lucida Grande", Font.PLAIN, 13)); UIManager.put("SmallSystemFont", new Font("Lucida Grande", Font.PLAIN, 11)); } if (!lafLoaded) { UIManager.LookAndFeelInfo[] lafs = UIManager.getInstalledLookAndFeels(); for (UIManager.LookAndFeelInfo laf : lafs) { System.out.println(laf); } try { // set the System Look and Feel in the UIManager javax.swing.SwingUtilities.invokeAndWait(new Runnable() { public void run() { try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); // UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName()); } catch (Exception e) { e.printStackTrace(); } } }); } catch (Exception e) { e.printStackTrace(); } } java.net.URL url = FigTreeApplication.class.getResource("images/figtreeLogo.png"); Icon icon = null; if (url != null) { icon = new ImageIcon(url); } final String nameString = "FigTree"; String titleString = "" + "

" + "

FigTree

" + "

Tree Figure Drawing Tool

" + "

Version " + VERSION + "

" + "
"; String aboutString = "" + "
" + "
"+ DATES + ", Andrew Rambaut
" + "Institute of Evolutionary Biology, University of Edinburgh.
" + "http://tree.bio.ed.ac.uk/

" + "Source code available from:
" + "http://figtree.googlecode.com/

" + "Uses the Java Evolutionary Biology 2 Library (JEBL2)
" + "http://jebl2.googlecode.com/

" + "Thanks to Alexei Drummond, Joseph Heled, Philippe Lemey,
Tulio de Oliveira, Oliver Pybus, Beth Shapiro & Marc Suchard
" + "
"; String websiteURLString = "http://tree.bio.ed.ac.uk/software/figtree/"; String helpURLString = "http://tree.bio.ed.ac.uk/software/figtree/"; FigTreeApplication.application = new FigTreeApplication(new FigTreeMenuBarFactory(), nameString, titleString, aboutString, icon, websiteURLString, helpURLString); application.setDocumentFrameFactory(new DocumentFrameFactory() { public DocumentFrame createDocumentFrame(Application app, MenuBarFactory menuBarFactory) { return new FigTreeFrame(nameString + " v" + VERSION); } }); application.initialize(); boolean useURLs = arguments.hasOption("url"); String[] leftoverArguments = arguments.getLeftoverArguments(); if (leftoverArguments.length > 0) { for (String arg : leftoverArguments) { if (useURLs) { FigTreeFrame frame = (FigTreeFrame)application.doNew(); try { frame.readFromURL(new URL(arg)); } catch (IOException e) { } } else { application.doOpen(arg); } } } // if (!jam.mac.Utils.isMacOSX() && application.getUpperDocumentFrame() == null) { // // If we haven't opened any files by now, prompt for one... // application.doOpen(); // } if (application.getUpperDocumentFrame() == null) { // If we haven't opened any files by now, open a blank window... application.doNew(); } } }figtree-1.4.3/src/figtree/application/FigTreeFrame.java000077500000000000000000002147161277473563300230650ustar00rootroot00000000000000/* * FigTreeFrame.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application; import com.itextpdf.text.Document; import com.itextpdf.text.DocumentException; import com.itextpdf.text.pdf.DefaultFontMapper; import com.itextpdf.text.pdf.PdfContentByte; import com.itextpdf.text.pdf.PdfTemplate; import com.itextpdf.text.pdf.PdfWriter; import figtree.treeviewer.decorators.DiscreteColourDecorator; import figtree.treeviewer.decorators.HSBDiscreteColourDecorator; import figtree.treeviewer.painters.StatesPainter; import jebl.evolution.align.Output; import jebl.evolution.alignments.Alignment; import jebl.evolution.alignments.BasicAlignment; import jebl.evolution.graphs.Node; import jebl.evolution.io.*; import jebl.evolution.taxa.Taxon; import jebl.evolution.trees.RootedTree; import jebl.evolution.trees.Tree; import jebl.util.Attributable; import jam.controlpalettes.BasicControlPalette; import jam.controlpalettes.ControlPalette; import jam.framework.DocumentFrame; import jam.panels.*; import jam.toolbar.*; import jam.util.IconUtils; import figtree.application.menus.TreeMenuHandler; import figtree.application.menus.FigTreeFileMenuHandler; import figtree.treeviewer.*; import figtree.treeviewer.TreeSelectionListener; import figtree.treeviewer.annotations.*; import org.apache.batik.dom.GenericDOMImplementation; import org.apache.batik.svggen.SVGGraphics2D; import org.apache.batik.svggen.SVGGraphics2DIOException; import org.w3c.dom.DOMImplementation; import org.w3c.dom.Element; import javax.imageio.ImageIO; import javax.swing.*; import java.awt.*; import java.awt.geom.Rectangle2D; import java.awt.datatransfer.*; import java.awt.event.*; import java.awt.image.BufferedImage; import java.io.*; import java.net.URL; import java.text.NumberFormat; import java.util.*; import java.util.List; /** * Primary window for FigTree. The window contains a toolbar, a control panel and a panel displaying the * tree. It responds to menu commands and hot keys specific to the focused window. * @author Andrew Rambaut * @version $Id: FigTreeApplication.java 232 2014-03-02 15:47:10Z rambaut $ * * $HeadURL: https://figtree.googlecode.com/svn/trunk/src/figtree/application/FigTreeApplication.java $ * * $LastChangedBy: rambaut $ * $LastChangedDate: 2014-03-02 15:47:10 +0000 (Sun, 02 Mar 2014) $ * $LastChangedRevision: 232 $ */ public class FigTreeFrame extends DocumentFrame implements FigTreeFileMenuHandler, TreeMenuHandler { private final ExtendedTreeViewer treeViewer; private final ControlPalette controlPalette; private final FigTreePanel figTreePanel; private StatusBar statusBar; private SearchPanel filterPanel; private JPopupMenu filterPopup; public FigTreeFrame(String title) { super(); setTitle(title); setImportAction(importAction); // setImportAction(importCharactersAction); setExportAction(exportTreesAction); treeViewer = new ExtendedTreeViewer(this); controlPalette = new BasicControlPalette(200, BasicControlPalette.DisplayMode.ONLY_ONE_OPEN); figTreePanel = new FigTreePanel(this, treeViewer, controlPalette); this.addWindowFocusListener(new WindowAdapter() { public void windowGainedFocus(WindowEvent e) { treeViewer.requestFocusInWindow(); } }); } public void initializeComponents() { setSize(new java.awt.Dimension(1024, 768)); Toolbar toolBar = new Toolbar(); toolBar.setBorder(BorderFactory.createMatteBorder(0, 0, 1, 0, Color.darkGray)); toolBar.setRollover(true); toolBar.setFloatable(false); Icon rerootToolIcon = IconUtils.getIcon(this.getClass(), "images/rerootTool.png"); Icon rotateToolIcon = IconUtils.getIcon(this.getClass(), "images/rotateTool.png"); Icon cartoonNodeToolIcon = IconUtils.getIcon(this.getClass(), "images/cartoonNodeTool.png"); Icon collapseNodeToolIcon = IconUtils.getIcon(this.getClass(), "images/collapseNodeTool.png"); Icon hilightToolIcon = IconUtils.getIcon(this.getClass(), "images/hilightTool.png"); Icon annotationToolIcon = IconUtils.getIcon(this.getClass(), "images/annotationTool.png"); Icon findToolIcon = IconUtils.getIcon(this.getClass(), "images/findTool.png"); Icon infoToolIcon = IconUtils.getIcon(this.getClass(), "images/infoTool.png"); Icon statisticsToolIcon = IconUtils.getIcon(this.getClass(), "images/statisticsTool.png"); Icon settingsToolIcon = IconUtils.getIcon(this.getClass(), "images/projectTool.png"); Icon colourToolIcon = IconUtils.getIcon(this.getClass(), "images/coloursTool.png"); Icon nextIcon = IconUtils.getIcon(this.getClass(), "images/next.png"); Icon prevIcon = IconUtils.getIcon(this.getClass(), "images/prev.png"); final ToolbarAction cartoonToolbarAction = new ToolbarAction("Cartoon", CARTOON_NODE, cartoonNodeToolIcon) { public void actionPerformed(ActionEvent e){ cartoonAction.actionPerformed(e); } }; ToolbarButton cartoonToolButton = new ToolbarButton(cartoonToolbarAction, true); cartoonToolButton.setFocusable(false); toolBar.addComponent(cartoonToolButton); final ToolbarAction collapseToolbarAction = new ToolbarAction("Collapse", COLLAPSE_NODE, collapseNodeToolIcon) { public void actionPerformed(ActionEvent e){ collapseAction.actionPerformed(e); } }; ToolbarButton collapseToolButton = new ToolbarButton(collapseToolbarAction, true); collapseToolButton.setFocusable(false); toolBar.addComponent(collapseToolButton); final ToolbarAction rerootToolbarAction = new ToolbarAction("Reroot", ROOT_ON_BRANCH, rerootToolIcon) { public void actionPerformed(ActionEvent e){ rerootAction.actionPerformed(e); } }; ToolbarButton rerootToolButton = new ToolbarButton(rerootToolbarAction, true); rerootToolButton.setFocusable(false); toolBar.addComponent(rerootToolButton); final ToolbarAction rotateToolbarAction = new ToolbarAction("Rotate", ROTATE_NODE, rotateToolIcon) { public void actionPerformed(ActionEvent e){ rotateAction.actionPerformed(e); } }; ToolbarButton rotateToolButton = new ToolbarButton(rotateToolbarAction, true); rotateToolButton.setFocusable(false); toolBar.addComponent(rotateToolButton); final ToolbarAction annotateToolbarAction = new ToolbarAction("Annotate", ANNOTATE, annotationToolIcon) { public void actionPerformed(ActionEvent e){ annotateAction.actionPerformed(e); } }; ToolbarButton annotationToolButton = new ToolbarButton(annotateToolbarAction, true); annotationToolButton.setFocusable(false); toolBar.addComponent(annotationToolButton); final ToolbarAction colourToolbarAction = new ToolbarAction("Colour", COLOUR, colourToolIcon) { public void actionPerformed(ActionEvent e){ colourAction.actionPerformed(e); } }; ToolbarButton colourToolButton = new ToolbarButton(colourToolbarAction, true); colourToolButton.setFocusable(false); toolBar.addComponent(colourToolButton); final ToolbarAction hilightToolbarAction = new ToolbarAction("Hilight", HILIGHT, hilightToolIcon) { public void actionPerformed(ActionEvent e){ hilightAction.actionPerformed(e); } }; ToolbarButton hilightToolButton = new ToolbarButton(hilightToolbarAction, true); hilightToolButton.setFocusable(false); toolBar.addComponent(hilightToolButton); toolBar.addSeparator(); final ToolbarAction findToolbarAction = new ToolbarAction("Find", "Find Taxa...", findToolIcon) { public void actionPerformed(ActionEvent e){ findAction.actionPerformed(e); } }; JButton findToolButton = new ToolbarButton(findToolbarAction); findToolButton.setFocusable(false); toolBar.addComponent(findToolButton); findToolButton.setEnabled(true); // final ToolbarAction infoToolbarAction = new ToolbarAction("Get Info", "Get Info...", infoToolIcon) { // public void actionPerformed(ActionEvent e){ // getInfoAction.actionPerformed(e); // } // }; // JButton infoToolButton = new ToolbarButton(infoToolbarAction); // toolBar.addComponent(infoToolButton); // JButton settingsToolButton = new ToolbarButton( // new ToolbarAction("Statistics", "Statistics...", statisticsToolIcon) { // public void actionPerformed(ActionEvent e){ // treeViewer.showStatistics(); // } // }); // settingsToolButton.putClientProperty("Quaqua.Button.style", "toolBarRollover"); // toolBar.addComponent(settingsToolButton); // settingsToolButton.setEnabled(false); toolBar.addSeparator(); Box box1 = Box.createHorizontalBox(); final JToggleButton toggle1 = new JToggleButton("Node"); toggle1.setFocusable(false); toggle1.putClientProperty("JButton.buttonType", "segmentedTextured"); toggle1.putClientProperty("JButton.segmentPosition", "first"); toggle1.putClientProperty( "Quaqua.Button.style", "toggleWest"); final JToggleButton toggle2 = new JToggleButton("Clade"); toggle2.setFocusable(false); toggle2.putClientProperty("JButton.buttonType", "segmentedTextured"); toggle2.putClientProperty("JButton.segmentPosition", "middle"); toggle2.putClientProperty( "Quaqua.Button.style", "toggleCenter"); final JToggleButton toggle3 = new JToggleButton("Taxa"); toggle3.setFocusable(false); toggle3.putClientProperty("JButton.buttonType", "segmentedTextured"); toggle3.putClientProperty("JButton.segmentPosition", "last"); toggle3.putClientProperty( "Quaqua.Button.style", "toggleEast"); ButtonGroup buttonGroup = new ButtonGroup(); buttonGroup.add(toggle1); buttonGroup.add(toggle2); buttonGroup.add(toggle3); toggle1.setSelected(true); toggle1.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent e) { if (e.getStateChange() == ItemEvent.SELECTED) { treeViewer.setSelectionMode(TreePaneSelector.SelectionMode.NODE); } } }); toggle2.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent e) { if (e.getStateChange() == ItemEvent.SELECTED) { treeViewer.setSelectionMode(TreePaneSelector.SelectionMode.CLADE); } } }); toggle3.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent e) { if (e.getStateChange() == ItemEvent.SELECTED) { treeViewer.setSelectionMode(TreePaneSelector.SelectionMode.TAXA); } } }); box1.add(Box.createVerticalStrut(annotationToolIcon.getIconHeight())); box1.add(toggle1); box1.add(toggle2); box1.add(toggle3); toolBar.addComponent(new GenericToolbarItem("Selection Mode", "What aspect of the tree is selected when it is clicked", box1)); toolBar.addFlexibleSpace(); final ToolbarAction prevTreeToolbarAction = new ToolbarAction(null, "Previous Tree...", prevIcon) { public void actionPerformed(ActionEvent e){ if (treeViewer.isRootingOn() && treeViewer.getRootingType() == TreePane.RootingType.USER_ROOTING) { JOptionPane.showMessageDialog(FigTreeFrame.this, "Cannot switch trees when user rooting option is on.\n" + "Turn this option off to switch trees", "Unable to switch trees", JOptionPane.ERROR_MESSAGE); } else { treeViewer.showPreviousTree(); } } }; JButton prevTreeToolButton = new ToolbarButton(prevTreeToolbarAction, true); prevTreeToolButton.setFocusable(false); prevTreeToolButton.putClientProperty("JButton.buttonType", "segmentedTextured"); prevTreeToolButton.putClientProperty("JButton.segmentPosition", "first"); prevTreeToolButton.putClientProperty( "Quaqua.Button.style", "toggleWest"); final ToolbarAction nextTreeToolbarAction = new ToolbarAction(null, "Next Tree...", nextIcon) { public void actionPerformed(ActionEvent e){ if (treeViewer.isRootingOn() && treeViewer.getRootingType() == TreePane.RootingType.USER_ROOTING) { JOptionPane.showMessageDialog(FigTreeFrame.this, "Cannot switch trees when user rooting option is on.\n" + "Turn this option off to switch trees", "Unable to switch trees", JOptionPane.ERROR_MESSAGE); } else { treeViewer.showNextTree(); } } }; JButton nextTreeToolButton = new ToolbarButton(nextTreeToolbarAction, true); nextTreeToolButton.setFocusable(false); nextTreeToolButton.putClientProperty("JButton.buttonType", "segmentedTextured"); nextTreeToolButton.putClientProperty("JButton.segmentPosition", "last"); nextTreeToolButton.putClientProperty( "Quaqua.Button.style", "toggleEast"); nextTreeToolbarAction.setEnabled(treeViewer.getCurrentTreeIndex() < treeViewer.getTreeCount() - 1); prevTreeToolbarAction.setEnabled(treeViewer.getCurrentTreeIndex() > 0); Box box2 = Box.createHorizontalBox(); box2.add(Box.createVerticalStrut(annotationToolIcon.getIconHeight())); box2.add(prevTreeToolButton); box2.add(nextTreeToolButton); toolBar.addComponent(new GenericToolbarItem("Prev/Next", "Navigate through the trees", box2)); TreeViewerListener l = new TreeViewerListener() { public void treeChanged() { boolean nextTreeEnabled = treeViewer.getCurrentTreeIndex() < treeViewer.getTreeCount() - 1; nextTreeAction.setEnabled(nextTreeEnabled); nextTreeToolbarAction.setEnabled(nextTreeEnabled); boolean prevTreeEnabled = treeViewer.getCurrentTreeIndex() > 0; previousTreeAction.setEnabled(prevTreeEnabled); prevTreeToolbarAction.setEnabled(prevTreeEnabled); } public void treeSettingsChanged() { // nothing to do } }; treeViewer.addTreeViewerListener(l); l.treeChanged(); toolBar.addFlexibleSpace(); filterPopup = new JPopupMenu(); final ButtonGroup bg = new ButtonGroup(); boolean first = true; for (TreeViewer.TextSearchType searchType : TreeViewer.TextSearchType.values()) { final JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem(searchType.toString()); if (first) { menuItem.setSelected(true); first = false; } filterPopup.add(menuItem); bg.add(menuItem); } filterPanel = new SearchPanel("Filter", filterPopup, true); // filterPanel.getSearchText().requestFocus(); filterPanel.addSearchPanelListener(new SearchPanelListener() { /** * Called when the user requests a search by pressing return having * typed a search string into the text field. If the continuousUpdate * flag is true then this method is called when the user types into * the text field. * * @param searchString the user's search string */ public void searchStarted(String searchString) { Enumeration e = bg.getElements(); String value = null; while (e.hasMoreElements()) { AbstractButton button = (AbstractButton)e.nextElement(); if (button.isSelected()) { value = button.getText(); } } for (TreeViewer.TextSearchType searchType : TreeViewer.TextSearchType.values()) { if (searchType.toString().equals(value)) { treeViewer.selectTaxa(searchType, searchString, false); } } } /** * Called when the user presses the cancel search button or presses * escape while the search is in focus. */ public void searchStopped() { treeViewer.clearSelectedTaxa(); } }); JPanel panel3 = new JPanel(new FlowLayout()); panel3.add(filterPanel); toolBar.addComponent(panel3); statusBar = new StatusBar("FigTree"); statusBar.setBorder(BorderFactory.createCompoundBorder( BorderFactory.createCompoundBorder( BorderFactory.createMatteBorder(1, 0, 0, 0, Color.darkGray), BorderFactory.createMatteBorder(1, 0, 0, 0, Color.lightGray)), BorderFactory.createEmptyBorder(2, 12, 2, 12))); statusBar.setOpaque(false); statusBar.setStatusProvider(treeViewer.getStatusProvider()); JPanel topPanel = new JPanel(new BorderLayout(0,0)); topPanel.add(toolBar, BorderLayout.NORTH); getContentPane().setLayout(new java.awt.BorderLayout(0, 0)); getContentPane().add(topPanel, BorderLayout.NORTH); getContentPane().add(figTreePanel, BorderLayout.CENTER); getContentPane().add(statusBar, BorderLayout.SOUTH); TreeSelectionListener l2 = new TreeSelectionListener() { public void selectionChanged() { boolean hasSelection = treeViewer.hasSelection(); cartoonToolbarAction.setEnabled(hasSelection); cartoonAction.setEnabled(hasSelection); collapseToolbarAction.setEnabled(hasSelection); collapseAction.setEnabled(hasSelection); // clearCollapsedAction.setEnabled(hasSelection); hilightToolbarAction.setEnabled(hasSelection); hilightAction.setEnabled(hasSelection); clearHilightingAction.setEnabled(hasSelection); // midpointRootAction.setEnabled(hasSelection); rerootToolbarAction.setEnabled(hasSelection); rerootAction.setEnabled(hasSelection); clearRootingAction.setEnabled(hasSelection); rotateToolbarAction.setEnabled(hasSelection); rotateAction.setEnabled(hasSelection); // increasingNodeOrderAction.setEnabled(hasSelection); // decreasingNodeOrderAction.setEnabled(hasSelection); // clearRotationsAction.setEnabled(hasSelection); annotateToolbarAction.setEnabled(hasSelection); // annotateNodesFromTipsAction.setEnabled(hasSelection); // annotateTipsFromNodesAction.setEnabled(hasSelection); annotateAction.setEnabled(hasSelection); // clearAnnotationsAction.setEnabled(hasSelection); colourToolbarAction.setEnabled(hasSelection); colourAction.setEnabled(hasSelection); clearColouringAction.setEnabled(hasSelection); } }; treeViewer.addTreeSelectionListener(l2); l2.selectionChanged(); getCutAction().setEnabled(false); getCopyAction().setEnabled(true); getDeleteAction().setEnabled(false); getSelectAllAction().setEnabled(true); getFindAction().setEnabled(true); getZoomWindowAction().setEnabled(false); } private void defineAnnotations() { Collection definitions = treeViewer.getAnnotationDefinitions().values(); if (annotationDefinitionsDialog == null) { annotationDefinitionsDialog = new AnnotationDefinitionsDialog(this); } annotationDefinitionsDialog.showDialog(definitions); treeViewer.setAnnotationDefinitions(annotationDefinitionsDialog.getAnnotations()); treeViewer.fireAnnotationsChanged(); } private void annotateNodesFromTips() { List annotationNames = new ArrayList(); annotationNames.add("Colour"); annotationNames.addAll(treeViewer.getAnnotationDefinitions().keySet()); annotationNames.add("Name"); if (selectAnnotationDialog == null) { selectAnnotationDialog = new SelectAnnotationDialog(this); } int result = selectAnnotationDialog.showDialog(annotationNames); if (result == JOptionPane.CANCEL_OPTION || result == JOptionPane.CLOSED_OPTION) { return; } String annotationName = selectAnnotationDialog.getAnnotationName(); if (annotationName.equals("Colour")) { annotationName = "!color"; } treeViewer.annotateNodesFromTips(annotationName); setDirty(); } private void annotateTipsFromNodes() { List annotationNames = new ArrayList(); annotationNames.add("Colour"); annotationNames.addAll(treeViewer.getAnnotationDefinitions().keySet()); if (selectAnnotationDialog == null) { selectAnnotationDialog = new SelectAnnotationDialog(this); } if (selectAnnotationDialog.showDialog(annotationNames) != JOptionPane.CANCEL_OPTION) { String annotationName = selectAnnotationDialog.getAnnotationName(); if (annotationName.equals("Colour")) { annotationName = "!color"; } treeViewer.annotateTipsFromNodes(annotationName); setDirty(); } } private void cartoonSelected() { treeViewer.cartoonSelectedNodes(); } private void collapseSelected() { treeViewer.collapseSelectedNodes(); } private void hilightSelected() { Color color = JColorChooser.showDialog(this, "Select Colour", lastColor); if (color != null) { treeViewer.hilightSelectedNodes(color); setDirty(); lastColor = color; } } private void rerootTree() { Set nodes = treeViewer.getSelectedNodes(); if (nodes.size() != 1 ) { JOptionPane.showMessageDialog(this, "Exactly one branch must be selected to re-root the tree." , "Annotating Tree", JOptionPane.WARNING_MESSAGE); return; } treeViewer.rerootOnSelectedBranch(); } private void rotateTree() { treeViewer.rotateSelectedNode(); } private void annotateSelected() { treeViewer.setToolMode(TreePaneSelector.ToolMode.SELECT); List definitions = new ArrayList(); definitions.add(new AnnotationDefinition("Name", "!name", AnnotationDefinition.Type.STRING)); definitions.addAll(treeViewer.getAnnotationDefinitions().values()); if (annotationDialog == null) { annotationDialog = new AnnotationDialog(this); } Set nodes = treeViewer.getSelectedNodes(); Set tips = treeViewer.getSelectedTips(); Attributable item = null; if (nodes.size() + tips.size() == 1 ) { if (nodes.size() == 1) { item = nodes.iterator().next(); }else if (tips.size() == 1) { item = tips.iterator().next(); } } else { int result = JOptionPane.showConfirmDialog(this, "More than one node selected for annotation. This operation\n" + "may overwrite existing annotations. Do you wish to continue?" , "Annotating Tree", JOptionPane.WARNING_MESSAGE); if (result == JOptionPane.CANCEL_OPTION || result == JOptionPane.CLOSED_OPTION) { return; } } if (annotationDialog.showDialog(definitions, item) != JOptionPane.CANCEL_OPTION) { AnnotationDefinition newDefinition = annotationDialog.getDefinition(); List defs = new ArrayList(treeViewer.getAnnotationDefinitions().values()); if (!defs.contains(newDefinition)) { defs.add(newDefinition); treeViewer.setAnnotationDefinitions(defs); } String code = newDefinition.getCode(); Object value = annotationDialog.getValue(); treeViewer.annotateSelected(code, value); setDirty(); } } private void copySelectedAnnotations() { // todo This function is disabled as it is not completely implemented // treeViewer.setToolMode(TreePaneSelector.ToolMode.SELECT); // // List definitions = new ArrayList(); // definitions.add(new AnnotationDefinition("Name", "!name", AnnotationDefinition.Type.STRING)); // definitions.addAll(treeViewer.getAnnotationDefinitions().values()); // // if (copyAnnotationDialog == null) { // copyAnnotationDialog = new AnnotationDialog(this, true); // } // // Set nodes = treeViewer.getSelectedNodes(); // Set tips = treeViewer.getSelectedTips(); // // Attributable item = null; // if (nodes.size() + tips.size() == 1 ) { // if (nodes.size() == 1) { // item = nodes.iterator().next(); // }else if (tips.size() == 1) { // item = tips.iterator().next(); // } // } else { // int result = JOptionPane.showConfirmDialog(this, // "More than one node selected for annotation. This operation\n" + // "may overwrite existing annotations. Do you wish to continue?" , // "Annotating Tree", // JOptionPane.WARNING_MESSAGE); // if (result == JOptionPane.CANCEL_OPTION || result == JOptionPane.CLOSED_OPTION) { // return; // } // } // if (annotationDialog.showDialog(definitions, item) != JOptionPane.CANCEL_OPTION) { // String code = annotationDialog.getDefinition().getCode(); // String code2 = annotationDialog.getDestinationDefinition().getCode(); // // treeViewer.copySelected(code, value); // setDirty(); // } } private static Color lastColor = Color.GRAY; private void colourSelected() { treeViewer.setToolMode(TreePaneSelector.ToolMode.SELECT); Color color = JColorChooser.showDialog(this, "Select Colour", lastColor); if (color != null) { treeViewer.annotateSelected("!color", color); setDirty(); lastColor = color; } } public boolean readFromFile(File file) throws IOException { Reader reader = null; try { reader = new FileReader(file); boolean isNexus = isNexus(reader); ProgressMonitorInputStream in = new ProgressMonitorInputStream( this, "Reading " + file.getName(), new FileInputStream(file)); in.getProgressMonitor().setMillisToDecideToPopup(1000); in.getProgressMonitor().setMillisToPopup(1000); reader = new InputStreamReader(in); boolean success = readData(reader, isNexus); reader.close(); return success; } catch (IOException ioe) { if (reader != null) { reader.close(); } throw ioe; } } public boolean readFromURL(URL url) throws IOException { InputStream in = url.openStream(); Reader reader = new InputStreamReader(url.openStream()); boolean isNexus = isNexus(reader); reader.close(); reader = new InputStreamReader(url.openStream()); return readData(reader, isNexus); } private boolean isNexus(Reader reader) throws IOException { BufferedReader bufferedReader = new BufferedReader(reader); String line = bufferedReader.readLine(); while (line != null && line.length() == 0) { line = bufferedReader.readLine(); } return (line != null && line.toUpperCase().contains("#NEXUS")); } public boolean readFromString(String string) throws IOException { boolean isNexus = string.substring(0, 80).toUpperCase().contains("#NEXUS"); return readData(new StringReader(string), isNexus); } protected boolean readData(Reader reader, boolean isNexus) throws IOException { List trees = new ArrayList(); boolean hasSettings = false; try { Map settings = new HashMap(); // First of all, fully populate the settings map so that // all the settings have defaults controlPalette.getSettings(settings); if (isNexus) { FigTreeNexusImporter importer = new FigTreeNexusImporter(reader); while (importer.hasTree()) { Tree tree = importer.importNextTree(); trees.add(tree); } // Try to find a figtree block and if found, parse the settings while (true) { try { importer.findNextBlock(); if (importer.getNextBlockName().equalsIgnoreCase("FIGTREE")) { importer.parseFigTreeBlock(settings); hasSettings = true; } } catch (EOFException ex) { break; } } } else { NewickImporter importer = new NewickImporter(reader, true); while (importer.hasTree()) { Tree tree = importer.importNextTree(); trees.add(tree); } } if (trees.size() == 0) { throw new ImportException("This file contained no trees."); } checkLabelAttribute(trees); treeViewer.setTrees(trees); controlPalette.setSettings(settings); } catch (ImportException ie) { JOptionPane.showMessageDialog(this, "Error reading tree file: \n" + ie.getMessage(), "Import Error", JOptionPane.ERROR_MESSAGE); return false; } if (!hasSettings) { // If there weren't settings in the file then this wasn't a TreeDraw // created document so we don't want to be able to overwrite it without // explicit action of the user... setDirty(); clearFile(); } return true; } /** * This version loads the trees in a thread but this needs more thought in order * to tie in to the JAM framework correctly */ // protected boolean readData(final Reader reader, final boolean isNexus) { // // final JFrame frame = this; // Thread readThread = new Thread () { // public void run() { // try { // // final List trees = new ArrayList(); // // boolean hasSettings = false; // // final Map settings = new HashMap(); // // First of all, fully populate the settings map so that // // all the settings have defaults // controlPalette.getSettings(settings); // // if (isNexus) { // FigTreeNexusImporter importer = new FigTreeNexusImporter(reader); // while (importer.hasTree()) { // Tree tree = importer.importNextTree(); // trees.add(tree); // } // // Try to find a figtree block and if found, parse the settings // while (true) { // try { // importer.findNextBlock(); // if (importer.getNextBlockName().equalsIgnoreCase("FIGTREE")) { // importer.parseFigTreeBlock(settings); // hasSettings = true; // } // } catch (EOFException ex) { // break; // } // } // } else { // NewickImporter importer = new NewickImporter(reader, true); // while (importer.hasTree()) { // Tree tree = importer.importNextTree(); // trees.add(tree); // } // } // // if (trees.size() == 0) { // throw new ImportException("This file contained no trees."); // } // // final boolean hasSettings2 = hasSettings; // // EventQueue.invokeLater ( // new Runnable () { // public void run () { // treeViewer.setTrees(trees); // controlPalette.setSettings(settings); // // if (!hasSettings2) { // // If there weren't settings in the file then this wasn't a TreeDraw // // created document so we don't want to be able to overwrite it without // // explicit action of the user... // setDirty(); // clearFile(); // } // } // }); // // } catch (final ImportException ie) { // EventQueue.invokeLater ( // new Runnable () { // public void run () { // JOptionPane.showMessageDialog(frame, "Error reading tree file: " + ie.getMessage(), // "Import Error", // JOptionPane.ERROR_MESSAGE); // } // }); // } catch (final InterruptedIOException iioex) { // // The cancel dialog button was pressed - do nothing // } catch (final IOException ioex) { // EventQueue.invokeLater ( // new Runnable () { // public void run () { // JOptionPane.showMessageDialog(frame, "File I/O Error: " + ioex.getMessage(), // "File I/O Error", // JOptionPane.ERROR_MESSAGE); // } // }); // } // // } // }; // readThread.start(); // // return true; // } private void checkLabelAttribute(List trees) { boolean hasLabel = false; for (Tree tree : trees) { for (Node node : tree.getNodes()) { if (node.getAttribute("label") != null) { hasLabel = true; } } } if (hasLabel) { String labelName = null; do { labelName = JOptionPane.showInputDialog( "The node/branches of the tree are labelled\n" + "(i.e., with bootstrap values or posterior probabilities).\n\n" + "Please select a name for these values.", "label"); if (labelName == null) { labelName = "label"; } labelName = labelName.trim(); if (labelName.length() == 0) { Toolkit.getDefaultToolkit().beep(); } } while (labelName == null || labelName.length() == 0); if (!labelName.equals("label")) { for (Tree tree : trees) { for (Node node : tree.getNodes()) { Object value = node.getAttribute("label"); if (value != null) { node.removeAttribute("label"); node.setAttribute(labelName, value); } } } } } } protected boolean writeToFile(File file) throws IOException { Map settings = new TreeMap(); controlPalette.getSettings(settings); FileWriter writer = new FileWriter(file); FigTreeNexusExporter exporter = new FigTreeNexusExporter(writer, true); exporter.exportTrees(treeViewer.getTrees(), true); exporter.writeFigTreeBlock(settings); writer.close(); return true; } public final void doImport() { FileDialog dialog = new FileDialog(this, "Import Annotations File...", FileDialog.LOAD); dialog.setVisible(true); if (dialog.getFile() != null) { File file = new File(dialog.getDirectory(), dialog.getFile()); try { Map> annotations = importAnnotationsFromFile(file); treeViewer.setTaxonAnnotations(annotations); // Hack to show tips states... // String[] annotationNames = new String[annotations.keySet().size()]; // DiscreteColourDecorator[] decorators = new DiscreteColourDecorator[annotations.keySet().size()]; // // int i = 0; // for (AnnotationDefinition definition: annotations.keySet()) { // Map annotation = annotations.get(definition); // annotationNames[i] = definition.getName(); // decorators[i] = new HSBDiscreteColourDecorator(annotationNames[i], annotation.keySet()); // i++; // } // treeViewer.setTipLabelPainter(new StatesPainter(annotationNames, decorators)); } catch (FileNotFoundException fnfe) { JOptionPane.showMessageDialog(this, "Unable to open file: File not found", "Unable to open file", JOptionPane.ERROR_MESSAGE); } catch (IOException ioe) { JOptionPane.showMessageDialog(this, "Unable to read file: " + ioe.getMessage(), "Unable to read file", JOptionPane.ERROR_MESSAGE); } } } protected Map> importAnnotationsFromFile(File file) throws IOException { BufferedReader reader = new BufferedReader(new FileReader(file)); List taxa = new ArrayList(); String line = reader.readLine(); String[] labels = line.split("\t"); Map> columns = new HashMap>(); for (int i = 1; i < labels.length; i++) { columns.put(labels[i], new ArrayList()); } line = reader.readLine(); while (line != null) { String[] values = line.split("\t"); if (values.length > 0) { taxa.add(values[0]); for (int i = 1; i < values.length; i++) { if (i < labels.length) { List column = columns.get(labels[i]); column.add(values[i]); } } } line = reader.readLine(); } Map> annotations = new TreeMap>(); NumberFormat nf = NumberFormat.getInstance(); for (int i = 1; i < labels.length; i++) { List column = columns.get(labels[i]); boolean isInteger = true; boolean isNumber = true; boolean isBoolean = true; for (String valueString : column) { if (!valueString.equalsIgnoreCase("TRUE") && !valueString.equalsIgnoreCase("FALSE")) { isBoolean = false; try { double number = Double.parseDouble(valueString); if (Math.round(number) != number) { isInteger = false; } } catch (NumberFormatException pe) { isInteger = false; isNumber = false; } } } Map values = new HashMap(); AnnotationDefinition ad; int j = 0; for (String valueString : column) { Taxon taxon = Taxon.getTaxon(taxa.get(j)); if (isBoolean) { values.put(taxon, new Boolean(valueString)); } else if (isInteger) { values.put(taxon, new Integer(valueString)); } else if (isNumber) { values.put(taxon, new Double(valueString)); } else { values.put(taxon, valueString); } j++; } Set valueSet = new HashSet(values.values()); if (isBoolean) { ad = new AnnotationDefinition(labels[i], AnnotationDefinition.Type.BOOLEAN ); } else if (isInteger) { ad = new AnnotationDefinition(labels[i], AnnotationDefinition.Type.INTEGER ); } else if (isNumber) { ad = new AnnotationDefinition(labels[i], AnnotationDefinition.Type.REAL ); } else { String[] valueArray = new String[valueSet.size()]; valueSet.toArray(valueArray); ad = new AnnotationDefinition(labels[i], AnnotationDefinition.Type.STRING); //ad.setOptions(valueArray); } annotations.put(ad, values); } return annotations; } private void doImportCharacters() { FileDialog dialog = new FileDialog(this, "Import Characters File...", FileDialog.LOAD); dialog.setVisible(true); if (dialog.getFile() != null) { File file = new File(dialog.getDirectory(), dialog.getFile()); try { importCharactersFromFile(file); } catch (FileNotFoundException fnfe) { JOptionPane.showMessageDialog(this, "Unable to open file: File not found", "Unable to open file", JOptionPane.ERROR_MESSAGE); } catch (IOException ioe) { JOptionPane.showMessageDialog(this, "Unable to read file: " + ioe.getMessage(), "Unable to read file", JOptionPane.ERROR_MESSAGE); } } } protected boolean importCharactersFromFile(File file) throws FileNotFoundException, IOException { final String fileName = file.getName(); SequenceImporter importer = new NexusImporter(new FileReader(file)); try { Alignment alignment = new BasicAlignment(importer.importSequences()); treeViewer.setCharacters(alignment); } catch (ImportException ie) { JOptionPane.showMessageDialog(this, "Error reading characters file: " + ie.getMessage(), "Import Error", JOptionPane.ERROR_MESSAGE); return false; } return true; } private void doImportColourScheme() { FileDialog dialog = new FileDialog(this, "Import Colour Scheme...", FileDialog.LOAD); dialog.setVisible(true); if (dialog.getFile() != null) { File file = new File(dialog.getDirectory(), dialog.getFile()); try { importColourSchemeFromFile(file); } catch (FileNotFoundException fnfe) { JOptionPane.showMessageDialog(this, "Unable to open file: File not found", "Unable to open file", JOptionPane.ERROR_MESSAGE); } catch (IOException ioe) { JOptionPane.showMessageDialog(this, "Unable to read file: " + ioe.getMessage(), "Unable to read file", JOptionPane.ERROR_MESSAGE); } } } protected boolean importColourSchemeFromFile(File file) throws FileNotFoundException, IOException { final String fileName = file.getName(); SequenceImporter importer = new NexusImporter(new FileReader(file)); try { Alignment alignment = new BasicAlignment(importer.importSequences()); treeViewer.setCharacters(alignment); } catch (ImportException ie) { JOptionPane.showMessageDialog(this, "Error reading characters file: " + ie.getMessage(), "Import Error", JOptionPane.ERROR_MESSAGE); return false; } return true; } public final void doExport() { if (exportTreeDialog == null) { exportTreeDialog = new ExportTreeDialog(this); } if (exportTreeDialog.showDialog() == JOptionPane.OK_OPTION) { FileDialog dialog = new FileDialog(this, "Export Tree File...", FileDialog.SAVE); dialog.setVisible(true); if (dialog.getFile() != null) { File file = new File(dialog.getDirectory(), dialog.getFile()); FileWriter writer = null; try { writer = new FileWriter(file); writeTreeFile(writer, exportTreeDialog.getFormat(), exportTreeDialog.allTrees(), exportTreeDialog.asDisplayed(), exportTreeDialog.includeFigTreeBlock(), exportTreeDialog.includeAnnotations(), false); writer.close(); } catch (IOException ioe) { JOptionPane.showMessageDialog(this, "Error writing tree file: " + ioe.getMessage(), "Export Error", JOptionPane.ERROR_MESSAGE); } } } } public final void doExportGraphic(GraphicFormat format) { FileDialog dialog = new FileDialog(this, "Export " + format.getName() + " File...", FileDialog.SAVE); String name = this.getFile().getName() + "." + format.getName().toLowerCase(); dialog.setFile(name); dialog.setVisible(true); if (dialog.getFile() != null) { File file = new File(dialog.getDirectory(), dialog.getFile()); try { OutputStream stream = new FileOutputStream(file); exportGraphics(format, treeViewer.getContentPane(), stream); stream.flush(); stream.close(); } catch(DocumentException de) { JOptionPane.showMessageDialog(this, "Error writing PDF file: " + de, "Export PDF Error", JOptionPane.ERROR_MESSAGE); } catch (IOException ioe) { JOptionPane.showMessageDialog(this, "Error writing tree file: " + ioe.getMessage(), "Export Error", JOptionPane.ERROR_MESSAGE); } } } public final static void exportGraphics(GraphicFormat format, JComponent comp, OutputStream stream) throws IOException, DocumentException { switch (format) { case PNG: case GIF: case BMP: case JPEG: exportGraphicsFile(format, comp, stream); break; case EPS: throw new UnsupportedOperationException("EPS not handled"); case SVG: exportSVGFile(comp, stream); break; case PDF: exportPDFFile(comp, stream); break; default: throw new UnsupportedOperationException("Format not handled: " + format); } } private final static void exportGraphicsFile(GraphicFormat format, JComponent component, OutputStream stream) throws IOException { int imageType = BufferedImage.TYPE_INT_RGB; if (format == GraphicFormat.PNG) { // PNG allows an alpha channel imageType = BufferedImage.TYPE_INT_ARGB; } BufferedImage bi = new BufferedImage(component.getSize().width, component.getSize().height, imageType); Graphics g = bi.createGraphics(); if (format != GraphicFormat.PNG) { g.setColor(Color.WHITE); g.fillRect(0, 0, bi.getWidth(), bi.getHeight()); } component.paint(g); g.dispose(); ImageIO.write(bi, format.getName(), stream); } private final static void exportSVGFile(JComponent component, OutputStream stream) throws IOException { // Get a DOMImplementation and create an XML document DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation(); org.w3c.dom.Document document = domImpl.createDocument(null, "svg", null); // Create an instance of the SVG Generator SVGGraphics2D svgGenerator = new SVGGraphics2D(document); component.paint(svgGenerator); Element svgRoot = svgGenerator.getRoot(); Rectangle2D bounds = component.getBounds(); String viewBox = "0 0 " + bounds.getWidth() + " " + bounds.getHeight(); svgRoot.setAttributeNS(null, svgGenerator.SVG_VIEW_BOX_ATTRIBUTE, viewBox); svgRoot.setAttributeNS(null, svgGenerator.SVG_WIDTH_ATTRIBUTE, Double.toString(bounds.getWidth())); svgRoot.setAttributeNS(null, svgGenerator.SVG_HEIGHT_ATTRIBUTE, Double.toString(bounds.getHeight())); // Write svg file Writer out = new OutputStreamWriter(stream, "UTF-8"); svgGenerator.stream(svgRoot, out, true /* use css */, false /* escaped */); } public final static void exportPDFFile(JComponent component, OutputStream stream) throws DocumentException { Rectangle2D bounds = component.getBounds(); Document document = new Document(new com.itextpdf .text.Rectangle((float)bounds.getWidth(), (float)bounds.getHeight())); // step 2 PdfWriter writer; writer = PdfWriter.getInstance(document, stream); // step 3 document.open(); // step 4 PdfContentByte cb = writer.getDirectContent(); PdfTemplate tp = cb.createTemplate((float)bounds.getWidth(), (float)bounds.getHeight()); Graphics2D g2d = tp.createGraphics((float)bounds.getWidth(), (float)bounds.getHeight(), new DefaultFontMapper()); component.print(g2d); g2d.dispose(); cb.addTemplate(tp, 0, 0); document.close(); } public void doCopy() { StringWriter writer = new StringWriter(); try { if (treeViewer.getSelectionMode() == TreePaneSelector.SelectionMode.TAXA) { writeTaxa(writer); } else { writeTreeFile(writer, ExportTreeDialog.Format.NEXUS, true, false, false, true, true); } } catch (IOException e) { e.printStackTrace(); } Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard(); StringSelection selection = new StringSelection(writer.toString()); clipboard.setContents(selection, selection); } public void doPaste() { Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard(); Transferable transfer = clipboard.getContents(null); if (transfer.isDataFlavorSupported(DataFlavor.stringFlavor)) { try { String clip = (String)transfer.getTransferData(DataFlavor.stringFlavor); boolean isNexus = clip.substring(0, Math.min(80, clip.length())).toUpperCase().contains("#NEXUS"); Reader reader = new StringReader(clip); List trees = new ArrayList(); TreeImporter importer; if (isNexus) { importer = new FigTreeNexusImporter(reader); } else { importer = new NewickImporter(reader, true); } while (importer.hasTree()) { Tree tree = importer.importNextTree(); trees.add(tree); } if (trees.size() == 0) { throw new ImportException("This clipboard contained no trees."); } treeViewer.addTrees(trees); // Show the first of the new trees treeViewer.showNextTree(); setDirty(); } catch (ImportException ie) { JOptionPane.showMessageDialog(this, "Error reading trees on clipboard: " + ie.getMessage(), "Import Error", JOptionPane.ERROR_MESSAGE); } catch (IOException ioe) { JOptionPane.showMessageDialog(this, "Error reading trees on clipboard: " + ioe.getMessage(), "Import Error", JOptionPane.ERROR_MESSAGE); } catch (UnsupportedFlavorException e) { JOptionPane.showMessageDialog(this, "Clipboard data is not compatible", "Import Error", JOptionPane.ERROR_MESSAGE); } } } public void doSelectAll() { treeViewer.selectAll(); } protected void writeTaxa(Writer writer) throws IOException { PrintWriter printWriter = new PrintWriter(writer); for (Taxon taxon : treeViewer.getSelectedTaxa()) { printWriter.println(taxon.getName()); } writer.close(); } protected void writeTreeFile(Writer writer, ExportTreeDialog.Format format, boolean writeAllTrees, boolean writeAsDisplayed, boolean writeFigTreeBlock, boolean writeAnnotations, boolean writeSelectedSubtree) throws IOException { Map settings = null; if (writeFigTreeBlock) { settings = new TreeMap(); controlPalette.getSettings(settings); } List trees = new ArrayList(); if (writeSelectedSubtree) { RootedTree tree = treeViewer.getSelectedSubtree(); if (tree != null) { trees.add(tree); } } else { trees.addAll(treeViewer.getTreesAsViewed()); } if (trees.size() > 0) { switch (format) { case NEWICK: NewickExporter newickExporter = new NewickExporter(writer); newickExporter.exportTrees(trees); break; case NEXUS: FigTreeNexusExporter nexusExporter = new FigTreeNexusExporter(writer, writeAnnotations); nexusExporter.exportTrees(trees); if (settings != null) { nexusExporter.writeFigTreeBlock(settings); } break; case JSON: JSONTreeExporter jsonExporter = new JSONTreeExporter(writer, writeAnnotations); jsonExporter.exportTrees(trees); break; } } writer.close(); } public final void doFind() { if (findPanel == null) { findPanel = new FindPanel(findAllAction, null); findPanel.setOpaque(false); treeViewer.addAnnotationsListener(new AnnotationsListener() { public void annotationsChanged() { List definitions = new ArrayList( treeViewer.getAnnotationDefinitions().values()); findPanel.setup(definitions); } }); List definitions = new ArrayList( treeViewer.getAnnotationDefinitions().values()); findPanel.setup(definitions); } if (figTreePanel.getUtilityPanel() != findPanel) { figTreePanel.showUtilityPanel(findPanel); } else { figTreePanel.hideUtilityPanel(); } } public final void doFindAll() { FindPanel.Target target = findPanel.getSearchTarget(); String targetString = findPanel.getSearchTargetString(); if (findPanel.isNumericSearchType()) { TreeViewer.NumberSearchType searchType = findPanel.getNumberSearchType(); Number searchValue = findPanel.getSearchValue(); if (target == FindPanel.Target.TAXON_LABEL) { throw new IllegalArgumentException("Can't do numeric search on taxon labels"); } else if (target == FindPanel.Target.BRANCH_LENGTH) { treeViewer.selectNodes("!length", searchType, searchValue); } else if (target == FindPanel.Target.NODE_AGE) { treeViewer.selectNodes("!height", searchType, searchValue); } else if (target == FindPanel.Target.ANY_ANNOTATION) { throw new IllegalArgumentException("Can't do numeric search on all annotations"); } else { treeViewer.selectNodes(targetString, searchType, searchValue); } } else { TreeViewer.TextSearchType searchType = findPanel.getTextSearchType(); String searchText = findPanel.getSearchText(); boolean caseSensitive = findPanel.isCaseSensitive(); if (target == FindPanel.Target.TAXON_LABEL) { treeViewer.selectTaxa("!name", searchType, searchText, caseSensitive); } else if (target == FindPanel.Target.BRANCH_LENGTH) { throw new IllegalArgumentException("Can't do text search on branch lengths"); } else if (target == FindPanel.Target.NODE_AGE) { throw new IllegalArgumentException("Can't do text search on node ages"); } else if (target == FindPanel.Target.ANY_ANNOTATION) { treeViewer.selectNodes(null, searchType, searchText, caseSensitive); } else { treeViewer.selectNodes(targetString, searchType, searchText, caseSensitive); } } } public final void doFindNext() { } public final void doGetInfo() { // List definitions = treeViewer.getAnnotationDefinitions(); // JPanel panel = new FindPanel(definitions); // panel.setOpaque(false); // figTreePanel.showUtilityPanel(panel); } public JComponent getExportableComponent() { return treeViewer.getContentPane(); } @Override public Action getImportColourSchemeAction() { return importColourSchemeAction; } @Override public Action getExportColourSchemeAction() { return exportColourSchemeAction; } public Action getExportTreesAction() { return exportTreesAction; } // public Action getExportGraphicAction() { // return exportGraphicAction; // } public Action getExportPDFAction() { return exportPDFAction; } public Action getExportPNGGraphicAction() { return exportPNGGraphicAction; } public Action getExportJPEGGraphicAction() { return exportJPEGGraphicAction; } public Action getExportSVGGraphicAction() { return exportSVGAction; } public Action getNextTreeAction() { return nextTreeAction; } public Action getPreviousTreeAction() { return previousTreeAction; } public Action getCartoonAction() { return cartoonAction; } public Action getCollapseAction() { return collapseAction; } public Action getClearCollapsedAction() { return clearCollapsedAction; } public Action getMidpointRootAction() { return midpointRootAction; } public Action getRerootAction() { return rerootAction; } public Action getClearRootingAction() { return clearRootingAction; } public Action getIncreasingNodeOrderAction() { return increasingNodeOrderAction; } public Action getDecreasingNodeOrderAction() { return decreasingNodeOrderAction; } public Action getRotateAction() { return rotateAction; } public Action getClearRotationsAction() { return clearRotationsAction; } public Action getAnnotateAction() { return annotateAction; } public Action getCopyAnnotationsAction() { return copyAnnotationsAction; } public Action getAnnotateNodesFromTipsAction() { return annotateNodesFromTipsAction; } public Action getAnnotateTipsFromNodesAction() { return annotateTipsFromNodesAction; } public AbstractAction getClearAnnotationsAction() { return clearAnnotationsAction; } public AbstractAction getDefineAnnotationsAction() { return defineAnnotationsAction; } public Action getColourAction() { return colourAction; } public Action getClearColouringAction() { return clearColouringAction; } public Action getHilightAction() { return hilightAction; } public Action getClearHilightingAction() { return clearHilightingAction; } public Action getFindAction() { return findAction; } private AbstractAction importAction = new AbstractAction("Import Annotations...") { public void actionPerformed(ActionEvent ae) { doImport(); } }; private AbstractAction importCharactersAction = new AbstractAction("Import Characters...") { public void actionPerformed(ActionEvent ae) { doImportCharacters(); } }; private AbstractAction importColourSchemeAction = new AbstractAction("Import Colour Scheme...") { public void actionPerformed(ActionEvent ae) { doImportColourScheme(); } }; private AbstractAction exportColourSchemeAction = new AbstractAction("Export Colour Scheme...") { public void actionPerformed(ActionEvent ae) { // doExportColourScheme(); } }; private AbstractAction exportTreesAction = new AbstractAction("Export Trees...") { public void actionPerformed(ActionEvent ae) { doExport(); } }; // private AbstractAction exportGraphicAction = new AbstractAction("Export Graphic...") { // public void actionPerformed(ActionEvent ae) { // doExportGraphic(GraphicFormat.PNG); // } // }; private AbstractAction exportPNGGraphicAction = new AbstractAction("Export PNG...") { public void actionPerformed(ActionEvent ae) { doExportGraphic(GraphicFormat.PNG); } }; private AbstractAction exportJPEGGraphicAction = new AbstractAction("Export JPEG...") { public void actionPerformed(ActionEvent ae) { doExportGraphic(GraphicFormat.JPEG); } }; private AbstractAction exportSVGAction = new AbstractAction("Export SVG...") { public void actionPerformed(ActionEvent ae) { doExportGraphic(GraphicFormat.SVG); } }; private AbstractAction exportPDFAction = new AbstractAction("Export PDF...") { public void actionPerformed(ActionEvent ae) { doExportGraphic(GraphicFormat.PDF); } }; private AbstractAction nextTreeAction = new AbstractAction(NEXT_TREE) { public void actionPerformed(ActionEvent e){ treeViewer.showNextTree(); } }; private AbstractAction previousTreeAction = new AbstractAction(PREVIOUS_TREE) { public void actionPerformed(ActionEvent e){ treeViewer.showPreviousTree(); } }; private AbstractAction cartoonAction = new AbstractAction(CARTOON_NODE) { public void actionPerformed(ActionEvent e){ cartoonSelected(); } }; private AbstractAction collapseAction = new AbstractAction(COLLAPSE_NODE) { public void actionPerformed(ActionEvent e){ collapseSelected(); } }; private AbstractAction clearCollapsedAction = new AbstractAction(CLEAR_COLLAPSED) { public void actionPerformed(ActionEvent e){ treeViewer.clearCollapsedNodes(); } }; private AbstractAction rerootAction = new AbstractAction(ROOT_ON_BRANCH) { public void actionPerformed(ActionEvent e){ rerootTree(); } }; private AbstractAction midpointRootAction = new AbstractAction(MIDPOINT_ROOT) { public void actionPerformed(ActionEvent e){ figTreePanel.toggleMidpointRoot(); } }; private AbstractAction clearRootingAction = new AbstractAction(CLEAR_ROOTING) { public void actionPerformed(ActionEvent e){ treeViewer.clearRooting(); } }; private AbstractAction rotateAction = new AbstractAction(ROTATE_NODE) { public void actionPerformed(ActionEvent e){ rotateTree(); } }; private AbstractAction clearRotationsAction = new AbstractAction(CLEAR_ROTATIONS) { public void actionPerformed(ActionEvent e){ treeViewer.clearRotations(); } }; private AbstractAction increasingNodeOrderAction = new AbstractAction(INCREASING_NODE_ORDER) { public void actionPerformed(ActionEvent e){ figTreePanel.toggleIncreasingNodeOrder(); } }; private AbstractAction decreasingNodeOrderAction = new AbstractAction(DECREASING_NODE_ORDER) { public void actionPerformed(ActionEvent e){ figTreePanel.toggleDecreasingNodeOrder(); } }; private AbstractAction annotateAction = new AbstractAction(ANNOTATE) { public void actionPerformed(ActionEvent ae) { annotateSelected(); } }; private AbstractAction copyAnnotationsAction = new AbstractAction(COPY_ANNOTATION_VALUES) { public void actionPerformed(ActionEvent ae) { copySelectedAnnotations(); } }; private AbstractAction annotateNodesFromTipsAction = new AbstractAction(ANNOTATE_NODES_FROM_TIPS) { public void actionPerformed(ActionEvent ae) { annotateNodesFromTips(); } }; private AbstractAction annotateTipsFromNodesAction = new AbstractAction(ANNOTATE_TIPS_FROM_NODES) { public void actionPerformed(ActionEvent ae) { annotateTipsFromNodes(); } }; private AbstractAction clearAnnotationsAction = new AbstractAction(CLEAR_ANNOTATIONS) { public void actionPerformed(ActionEvent ae) { // treeViewer.clearAnnotation(); } }; private AbstractAction defineAnnotationsAction = new AbstractAction(DEFINE_ANNOTATIONS) { public void actionPerformed(ActionEvent ae) { defineAnnotations(); } }; private AbstractAction colourAction = new AbstractAction(COLOUR) { public void actionPerformed(ActionEvent ae) { colourSelected(); } }; private AbstractAction clearColouringAction = new AbstractAction(CLEAR_COLOURING) { public void actionPerformed(ActionEvent ae) { treeViewer.clearColouring(); } }; private AbstractAction hilightAction = new AbstractAction(HILIGHT) { public void actionPerformed(ActionEvent ae) { hilightSelected(); } }; private AbstractAction clearHilightingAction = new AbstractAction(CLEAR_HILIGHTING) { public void actionPerformed(ActionEvent ae) { treeViewer.clearHilighting(); } }; private AbstractAction findAction = new AbstractAction("Find...") { public void actionPerformed(ActionEvent ae) { doFind(); } }; private AbstractAction findAllAction = new AbstractAction("Find") { public void actionPerformed(ActionEvent ae) { doFindAll(); } }; // private AbstractAction findNextAction = new AbstractAction("Find Next") { // public void actionPerformed(ActionEvent ae) { // doFindNext(); // } // }; private AbstractAction getInfoAction = new AbstractAction("Get Info...") { public void actionPerformed(ActionEvent ae) { doGetInfo(); } }; private ExportTreeDialog exportTreeDialog = null; private FindPanel findPanel = null; private AnnotationDefinitionsDialog annotationDefinitionsDialog = null; private AnnotationDialog annotationDialog = null; private AnnotationDialog copyAnnotationDialog = null; private SelectAnnotationDialog selectAnnotationDialog = null; } figtree-1.4.3/src/figtree/application/FigTreeMenuBarFactory.java000077500000000000000000000033041277473563300247010ustar00rootroot00000000000000/* * FigTreeMenuBarFactory.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application; import jam.framework.*; import jam.mac.*; import figtree.application.menus.*; /** * Register all the menus used by the FigTree app. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FigTreeMenuBarFactory extends DefaultMenuBarFactory { public FigTreeMenuBarFactory() { if (jam.mac.Utils.isMacOSX()) { registerMenuFactory(new FigTreeMacFileMenuFactory()); registerMenuFactory(new MacEditMenuFactory()); registerMenuFactory(new TreeMenuFactory()); registerMenuFactory(new MacWindowMenuFactory()); registerMenuFactory(new MacHelpMenuFactory()); } else { registerMenuFactory(new FigTreeDefaultFileMenuFactory()); registerMenuFactory(new DefaultEditMenuFactory()); registerMenuFactory(new TreeMenuFactory()); registerMenuFactory(new DefaultHelpMenuFactory()); } } }figtree-1.4.3/src/figtree/application/FigTreeNexusExporter.java000077500000000000000000000043261277473563300246600ustar00rootroot00000000000000/* * FigTreeNexusExporter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application; import jebl.evolution.io.NexusExporter; import java.io.IOException; import java.io.Writer; import java.util.Map; import java.awt.*; /** * An extension of the NexusExporter from JEBL to write FigTree settings in * a FigTree block. * * @author Andrew Rambaut * @version $Id: FigTreeApplication.java 232 2014-03-02 15:47:10Z rambaut $ * * $HeadURL: https://figtree.googlecode.com/svn/trunk/src/figtree/application/FigTreeApplication.java $ * * $LastChangedBy: rambaut $ * $LastChangedDate: 2014-03-02 15:47:10 +0000 (Sun, 02 Mar 2014) $ * $LastChangedRevision: 232 $ */ public class FigTreeNexusExporter extends NexusExporter { public FigTreeNexusExporter(Writer writer, boolean writeMetaComments) { super(writer, writeMetaComments); } /** * Writes a 'FigTree' block. */ public void writeFigTreeBlock(Map settings) throws IOException { writer.println("\nbegin figtree;"); for (String key : settings.keySet()) { Object value = settings.get(key); writer.println("\tset " + key + "=" + createString(value) + ";"); } writer.println("end;\n"); } private String createString(Object value) { if (value == null) { return "null"; } if (value instanceof Color) { return "#" + Integer.toHexString(((Color)value).getRGB()).substring(2); } if (value instanceof String) { return "\"" + value + "\""; } return value.toString(); } } figtree-1.4.3/src/figtree/application/FigTreeNexusImporter.java000077500000000000000000000062111277473563300246440ustar00rootroot00000000000000/* * FigTreeNexusImporter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application; import jebl.evolution.io.ImportException; import jebl.evolution.io.NexusImporter; import java.io.IOException; import java.io.Reader; import java.util.Map; import java.awt.*; /** * An extension of the NexusImporter from JEBL to parse FigTree settings from * a FigTree block. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FigTreeNexusImporter extends NexusImporter { public FigTreeNexusImporter(Reader reader) { super(reader); } /** * Parses a 'FigTree' block. */ public void parseFigTreeBlock(Map settings) throws ImportException, IOException { readFigTreeBlock(settings); } /** * Reads a 'FigTree' block. */ private void readFigTreeBlock(Map settings) throws ImportException, IOException { String command = helper.readToken(";"); while (!command.equalsIgnoreCase("END")) { if (command.equalsIgnoreCase("SET")) { while (helper.getLastDelimiter() != ';') { String key = helper.readToken("=;"); if (helper.getLastDelimiter() != '=') { throw new ImportException("Subcommand, " + key + ", is missing a value in command, " + command + ", in FIGTREE block"); } String value = helper.readToken(";"); settings.put(key, parseValue(value)); } } else { throw new ImportException("Unknown command, " + command + ", in FIGTREE block"); } command = helper.readToken(";"); } findEndBlock(); } private Object parseValue(String value) { if (value.equalsIgnoreCase("true") || value.equalsIgnoreCase("false")) { return new Boolean(value); } if (value.startsWith("#")) { String colourValue = value.substring(1); if (colourValue.startsWith("-")) { // old style decimal numbers try { return Color.decode(colourValue); } catch (NumberFormatException nfe1) { // not a colour } } else { return Color.decode("0x" + colourValue); } } try { return Integer.parseInt(value); } catch (NumberFormatException nfe) { } try { return Double.parseDouble(value); } catch (NumberFormatException nfe) { } // Simply return it as a string... return value; } } figtree-1.4.3/src/figtree/application/FigTreePanel.java000077500000000000000000000245441277473563300230700ustar00rootroot00000000000000/* * FigTreePanel.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application; import jam.controlpalettes.ControlPalette; import jam.disclosure.SlideOpenPanel; import figtree.treeviewer.*; import figtree.treeviewer.painters.*; import javax.swing.*; import javax.swing.plaf.basic.BasicSplitPaneDivider; import javax.swing.plaf.basic.BasicSplitPaneUI; import java.awt.*; import java.lang.reflect.Field; /** * This is a panel that has a TreeViewer and a BasicControlPalette with * the default Controllers and Painters. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FigTreePanel extends JPanel { public final static int CONTROL_PALETTE_WIDTH = 200; private final static boolean SEPARATE_NODE_SHAPE_PANELS = true; public FigTreePanel(JFrame frame, final ExtendedTreeViewer treeViewer, ControlPalette controlPalette) { this.treeViewer = treeViewer; this.controlPalette = controlPalette; // the scrollpane below now has this border // controlPalette.getPanel().setBorder(BorderFactory.createMatteBorder(0, 0, 0, 1, Color.GRAY)); controlPalette.getPanel().setBackground(new Color(231, 237, 246)); controlPalette.getPanel().setOpaque(true); treeViewerController = new TreeViewerController(treeViewer); controlPalette.addController(treeViewerController); controlPalette.addController(new MultipleTreesController(treeViewer)); // This controller handles reading/writing of attribute colour schemes but doesn't presently // show any UI AttributeColourController attributeColourController = new AttributeColourController(treeViewer, frame); controlPalette.addController(attributeColourController); controlPalette.addController(new TreeAppearanceController(treeViewer, frame, attributeColourController)); treesController = new TreesController(treeViewer); controlPalette.addController(treesController); controlPalette.addController(new TimeScaleController(treeViewer)); // Create a tip label painter and its controller final BasicLabelPainter tipLabelPainter = new BasicLabelPainter(BasicLabelPainter.PainterIntent.TIP); controlPalette.addController(new LabelPainterController("Tip Labels", "tipLabels", tipLabelPainter, frame, attributeColourController, treeViewer)); treeViewer.setTipLabelPainter(tipLabelPainter); // Create a node shape painter and its controller if (SEPARATE_NODE_SHAPE_PANELS) { final NodeShapePainter tipNodeShapePainter = new NodeShapePainter(); tipNodeShapePainter.setVisible(false); controlPalette.addController(new NodeShapeController("Tip Shapes", NodeShapeController.NodeType.EXTERNAL, tipNodeShapePainter, attributeColourController, treeViewer)); treeViewer.setTipShapePainter(tipNodeShapePainter); } // Create a node label painter and its controller final BasicLabelPainter nodeLabelPainter = new BasicLabelPainter(BasicLabelPainter.PainterIntent.NODE); nodeLabelPainter.setVisible(false); controlPalette.addController(new LabelPainterController("Node Labels", "nodeLabels", nodeLabelPainter, frame, attributeColourController, treeViewer)); treeViewer.setNodeLabelPainter(nodeLabelPainter); // Create a node shape painter and its controller final NodeShapePainter nodeShapePainter = new NodeShapePainter(); nodeShapePainter.setVisible(false); controlPalette.addController(new NodeShapeController("Node Shapes", (SEPARATE_NODE_SHAPE_PANELS ? NodeShapeController.NodeType.INTERNAL : NodeShapeController.NodeType.BOTH), nodeShapePainter, attributeColourController, treeViewer)); if (!SEPARATE_NODE_SHAPE_PANELS) { treeViewer.setTipShapePainter(nodeShapePainter); } treeViewer.setNodeShapePainter(nodeShapePainter); // Create a node bar painter and its controller final NodeBarPainter nodeBarPainter = new NodeBarPainter(); nodeBarPainter.setForeground(new Color(24, 32, 228, 128)); nodeBarPainter.setVisible(false); controlPalette.addController(new NodeBarController("Node Bars", nodeBarPainter, treeViewer)); treeViewer.setNodeBarPainter(nodeBarPainter); // Create a branch label painter and its controller final BasicLabelPainter branchLabelPainter = new BasicLabelPainter(BasicLabelPainter.PainterIntent.BRANCH); branchLabelPainter.setVisible(false); controlPalette.addController(new LabelPainterController("Branch Labels", "branchLabels", branchLabelPainter, frame, attributeColourController, treeViewer)); treeViewer.setBranchLabelPainter(branchLabelPainter); // Create a scale controller final ScaleBarPainter scaleBarPainter = new ScaleBarPainter(); scaleBarPainter.setVisible(true); controlPalette.addController(new ScaleBarPainterController(scaleBarPainter, treeViewer)); treeViewer.addScalePainter(scaleBarPainter); // Create a scale axis controller final ScaleAxisPainter scaleAxisPainter = new ScaleAxisPainter(); final ScaleGridPainter scaleGridPainter = new ScaleGridPainter(); scaleAxisPainter.setVisible(false); scaleGridPainter.setVisible(false); controlPalette.addController(new ScaleAxisPainterController(scaleAxisPainter, scaleGridPainter, treeViewer)); treeViewer.addScalePainter(scaleAxisPainter); treeViewer.setScaleGridPainter(scaleGridPainter); // Create a legend controller final LegendPainter legendPainter = new LegendPainter(attributeColourController); legendPainter.setVisible(false); controlPalette.addController(new LegendPainterController(legendPainter, attributeColourController, treeViewer)); treeViewer.setLegendPainter(legendPainter); slideOpenPanel = new SlideOpenPanel(treeViewer); setLayout(new BorderLayout()); // add(slideOpenPanel, BorderLayout.CENTER); JScrollPane scrollPane = new JScrollPane(); scrollPane.setBorder(BorderFactory.createMatteBorder(0, 0, 0, 1, Color.GRAY)); scrollPane.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER); scrollPane.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS); int scrollBarWidth = scrollPane.getVerticalScrollBar().getWidth(); int controlPanelWidth = CONTROL_PALETTE_WIDTH + scrollBarWidth; controlPalette.setPreferredWidth(controlPanelWidth); scrollPane.setViewportView(controlPalette.getPanel()); // add(scrollPane, BorderLayout.WEST); JSplitPane splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, scrollPane, slideOpenPanel); splitPane.putClientProperty("Quaqua.SplitPane.style", "bar"); splitPane.setOneTouchExpandable(true); add(splitPane, BorderLayout.CENTER); int w = splitPane.getLeftComponent().getPreferredSize().width; splitPane.getLeftComponent().setMinimumSize(new Dimension(w, 0)); // splitPane.getLeftComponent().setMaximumSize(new Dimension(2 * w, 0)); // Might be possible to improve the action of the oneTouchExpandable button. Ideally would not allow // maximization of control panel, only its collapse. // BasicSplitPaneDivider bspd = ((BasicSplitPaneUI)splitPane.getUI()).getDivider(); // try { // Field rightButtonField = BasicSplitPaneDivider.class.getDeclaredField("rightButton"); // rightButtonField.setAccessible(true); // JButton rightButton = (JButton) rightButtonField.get(((BasicSplitPaneUI)splitPane.getUI()).getDivider()); // // Field leftButtonField = BasicSplitPaneDivider.class.getDeclaredField("leftButton"); // leftButtonField.setAccessible(true); // JButton leftButton = (JButton) leftButtonField.get(((BasicSplitPaneUI)splitPane.getUI()).getDivider()); // // // } catch (Exception e) { // e.printStackTrace(); // } // treeViewer.addAnnotationsListener(new AnnotationsListener() { // public void annotationsChanged() { // // tipLabelPainter.setupAttributes(treeViewer.getTrees()); // nodeLabelPainter.setupAttributes(treeViewer.getTrees()); // nodeBarPainter.setupAttributes(treeViewer.getTrees()); // branchLabelPainter.setupAttributes(treeViewer.getTrees()); // legendPainter.setupAttributes(treeViewer.getTrees()); // } // }); } public TreeViewer getTreeViewer() { return treeViewer; } public ControlPalette getControlPalette() { return controlPalette; } public void showUtilityPanel(JPanel utilityPanel) { if (utilityPanel == null) { return; } slideOpenPanel.showUtilityPanel(utilityPanel); } public void hideUtilityPanel() { slideOpenPanel.hideUtilityPanel(); } public JPanel getUtilityPanel() { return slideOpenPanel.getUtilityPanel(); } public void toggleMidpointRoot() { treesController.toggleMidpointRoot(); } public void toggleIncreasingNodeOrder() { treesController.toggleIncreasingNodeOrder(); } public void toggleDecreasingNodeOrder() { treesController.toggleDecreasingNodeOrder(); } private final TreeViewer treeViewer; private final TreeViewerController treeViewerController; private final TreesController treesController; private final ControlPalette controlPalette; private final SlideOpenPanel slideOpenPanel; } figtree-1.4.3/src/figtree/application/GraphicFormat.java000066400000000000000000000024631277473563300233020ustar00rootroot00000000000000/* * GraphicFormat.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application; /** * ${CLASS_NAME} * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public enum GraphicFormat { JPEG("JPG"), PNG("PNG"), GIF("GIF"), BMP("BMP"), EPS("EPS"), SVG("SVG"), PDF("PDF"); GraphicFormat(String name) { this.name = name; } public String getName() { return name; } @Override public String toString() { return name; } private final String name; } figtree-1.4.3/src/figtree/application/JSONTreeExporter.java000077500000000000000000000233741277473563300237050ustar00rootroot00000000000000/* * JSONTreeExporter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application; import jebl.evolution.alignments.Alignment; import jebl.evolution.distances.DistanceMatrix; import jebl.evolution.graphs.Node; import jebl.evolution.io.NexusExporter; import jebl.evolution.io.NexusImporter; import jebl.evolution.io.TreeExporter; import jebl.evolution.sequences.Sequence; import jebl.evolution.sequences.SequenceType; import jebl.evolution.taxa.Taxon; import jebl.evolution.trees.RootedTree; import jebl.evolution.trees.Tree; import jebl.evolution.trees.Utils; import jebl.util.Attributable; import java.awt.*; import java.awt.List; import java.io.IOException; import java.io.PrintWriter; import java.io.Writer; import java.util.*; /** * TreeExport to generate a tree in a JSON format. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class JSONTreeExporter implements TreeExporter { public static final String treeNameAttributeKey = "name"; public final static Set ATTRIBUTE_NAMES = new TreeSet(Arrays.asList(new String[] { "location", "host", "Hx", "Nx", "posterior", "country", "region" })); public final static String ORIGIN = "2013.34520547945"; public JSONTreeExporter(Writer writer) { this(writer, true); } /** * * @param writer where export text goes */ public JSONTreeExporter(Writer writer, boolean writeMetaComments) { this.writeMetaComments = writeMetaComments; this.writer = new PrintWriter(writer); } /** * Export a single tree * * @param tree * @throws java.io.IOException */ @Override public void exportTree(Tree tree) throws IOException { java.util.List trees = new ArrayList(); trees.add(tree); exportTrees(trees); } private void writeTrees(Collection trees) throws IOException { int indent = 0; int treeCount = 0; writer.println("{"); if (trees.size() > 1) { writer.println("\t\"trees\": ["); indent ++; } Map> attributeMap = new LinkedHashMap>(); for( Tree t : trees ) { final boolean isRooted = t instanceof RootedTree; final RootedTree rtree = isRooted ? (RootedTree)t : Utils.rootTheTree(t); for (Node node : rtree.getNodes()) { for (String name : node.getAttributeNames()) { if (ATTRIBUTE_NAMES.contains(name)) { Object valueObject = node.getAttribute(name); if (valueObject instanceof String) { Set values = attributeMap.get(name); if (values == null) { values = new TreeSet(); attributeMap.put(name, values); } String value = (String)valueObject; if (value.contains("+")) { values.add(value.split("\\+")[0]); } else { values.add(valueObject.toString()); } } } } } StringBuilder builder = new StringBuilder(); if (trees.size() > 1) { appendIndent(builder, indent); builder.append("\"tree\": {\n"); } appendIndent(builder, indent + 1); builder.append("\"root\": "); appendTree(rtree, rtree.getRootNode(), builder, indent + 1); appendAttributes(rtree, builder, indent + 1); builder.append((trees.size() == 1 || treeCount < trees.size() - 1 ? ",\n" : "\n")); if (trees.size() > 1) { appendIndent(builder, indent); builder.append((treeCount < trees.size() - 1 ? "},\n" : "}\n")); } writer.println(builder); treeCount ++; } if (trees.size() > 1) { writer.println("\t],"); } writer.println("\t\"origin\":\"" + ORIGIN + "\","); int i = 0; for (String name : attributeMap.keySet()) { Set values = attributeMap.get(name); writer.println("\t\"" + name + ".fullSet\": ["); int j = 0; for (String value : values) { writer.println("\t\t\"" + value + "\"" + (j < values.size() - 1 ? "," : "")); j++; } writer.println("\t]" + (i < attributeMap.keySet().size() - 1 ? "," : "")); i++; } writer.println("}"); } private void appendIndent(StringBuilder builder, int indent) { for (int i = 0; i < indent; i++) { builder.append('\t'); } } @Override public void exportTrees(Collection trees) throws IOException { writeTrees(trees); } final private String nameRegex = "^(\\w|-)+$"; /** * name suitable for printing - quotes if necessary * @param taxon * @param builder * @return */ private StringBuilder appendTaxonName(Taxon taxon, StringBuilder builder) { String name = taxon.getName(); if (name.contains("\"")) { name = name.replace("\"", "\\\""); } return builder.append("\"name\": \"").append(name).append("\""); } /** * Prepare for writing a tree. If a taxa block exists and is suitable for tree, * do nothing. If not, write a new taxa block. * @param tree * @param node * @param builder */ private void appendTree(RootedTree tree, Node node, StringBuilder builder, int indent) { builder.append("{\n"); if (tree.isExternal(node)) { appendIndent(builder, indent + 1); appendTaxonName(tree.getTaxon(node), builder); } else { appendIndent(builder, indent + 1); builder.append("\"children\": [\n"); java.util.List children = tree.getChildren(node); final int last = children.size() - 1; for (int i = 0; i < children.size(); i++) { appendIndent(builder, indent + 2); appendTree(tree, children.get(i), builder, indent + 2); builder.append(i == last ? 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See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application.menus; import jam.framework.*; import javax.swing.*; import java.awt.event.KeyEvent; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FigTreeDefaultFileMenuFactory implements MenuFactory { public FigTreeDefaultFileMenuFactory() { } public String getMenuName() { return "File"; } public void populateMenu(JMenu menu, AbstractFrame frame) { JMenuItem item; Application application = Application.getApplication(); menu.setMnemonic('F'); item = new JMenuItem(application.getNewAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_N, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(application.getOpenAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_O, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(frame.getSaveAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(frame.getSaveAsAction()); menu.add(item); // On Windows and Linux platforms, each window has its own menu so items which are not needed // are simply missing. In contrast, on Mac, the menu is for the application so items should // be enabled/disabled as frames come to the front. if (frame instanceof FigTreeFileMenuHandler) { Action action = frame.getImportAction(); if (action != null) { item = new JMenuItem(action); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_I, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getImportColourSchemeAction()); menu.add(item); menu.addSeparator(); } item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportTreesAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportPDFAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, MenuBarFactory.MENU_MASK + KeyEvent.ALT_MASK)); menu.add(item); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportSVGGraphicAction()); menu.add(item); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportPNGGraphicAction()); menu.add(item); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportJPEGGraphicAction()); menu.add(item); /* to be added ... */ // menu.addSeparator(); // // item = new JMenuItem(((FigTreeFileMenuHandler)frame).getImportColourSchemeAction()); // menu.add(item); // // item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportColourSchemeAction()); // menu.add(item); } else { // If the frame is not a TracerFileMenuHandler then leave out the import/export options. } menu.addSeparator(); item = new JMenuItem(frame.getPrintAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_P, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(application.getPageSetupAction()); menu.add(item); menu.addSeparator(); if (application.getRecentFileMenu() != null) { JMenu subMenu = application.getRecentFileMenu(); menu.add(subMenu); menu.addSeparator(); } item = new JMenuItem(application.getExitAction()); menu.add(item); } public int getPreferredAlignment() { return LEFT; } } figtree-1.4.3/src/figtree/application/menus/FigTreeFileMenuHandler.java000066400000000000000000000025151277473563300261510ustar00rootroot00000000000000/* * FigTreeFileMenuHandler.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application.menus; import javax.swing.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface FigTreeFileMenuHandler { Action getImportColourSchemeAction(); Action getExportColourSchemeAction(); Action getExportTreesAction(); // Action getExportGraphicAction(); Action getExportPNGGraphicAction(); Action getExportJPEGGraphicAction(); Action getExportPDFAction(); Action getExportSVGGraphicAction(); } figtree-1.4.3/src/figtree/application/menus/FigTreeMacFileMenuFactory.java000066400000000000000000000173171277473563300266320ustar00rootroot00000000000000/* * FigTreeMacFileMenuFactory.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application.menus; import jam.framework.*; import javax.swing.*; import java.awt.event.KeyEvent; import java.awt.event.ActionEvent; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FigTreeMacFileMenuFactory implements MenuFactory { public FigTreeMacFileMenuFactory() { } public String getMenuName() { return "File"; } public void populateMenu(JMenu menu, AbstractFrame frame) { Application application = Application.getApplication(); JMenuItem item; item = new JMenuItem(application.getNewAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_N, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(application.getOpenAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_O, MenuBarFactory.MENU_MASK)); menu.add(item); if (application.getRecentFileMenu() != null) { JMenu subMenu = application.getRecentFileMenu(); menu.add(subMenu); } menu.addSeparator(); if (frame != null) { item = new JMenuItem(frame.getCloseWindowAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_W, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(frame.getSaveAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(frame.getSaveAsAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, MenuBarFactory.MENU_MASK + ActionEvent.SHIFT_MASK)); menu.add(item); } else { // No frame available so create a disabled menu for the default menu bar item = new JMenuItem("Close"); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_W, MenuBarFactory.MENU_MASK)); item.setEnabled(false); menu.add(item); item = new JMenuItem("Save"); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, MenuBarFactory.MENU_MASK)); item.setEnabled(false); menu.add(item); item = new JMenuItem("Save As..."); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, MenuBarFactory.MENU_MASK + ActionEvent.SHIFT_MASK)); item.setEnabled(false); menu.add(item); } // On Windows and Linux platforms, each window has its own menu so items which are not needed // are simply missing. In contrast, on Mac, the menu is for the application so items should // be enabled/disabled as frames come to the front. if (frame instanceof FigTreeFileMenuHandler) { Action action = frame.getImportAction(); if (action != null) { item = new JMenuItem(action); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_I, MenuBarFactory.MENU_MASK)); menu.add(item); } else { item = new JMenuItem("Import Annotations..."); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_I, MenuBarFactory.MENU_MASK)); item.setEnabled(false); menu.add(item); } item = new JMenuItem(((FigTreeFileMenuHandler)frame).getImportColourSchemeAction()); menu.add(item); menu.addSeparator(); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportTreesAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportPDFAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, MenuBarFactory.MENU_MASK + KeyEvent.ALT_MASK)); menu.add(item); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportSVGGraphicAction()); menu.add(item); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportPNGGraphicAction()); menu.add(item); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportJPEGGraphicAction()); menu.add(item); /* to be added... menu.addSeparator(); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getImportColourSchemeAction()); menu.add(item); item = new JMenuItem(((FigTreeFileMenuHandler)frame).getExportColourSchemeAction()); menu.add(item); */ } else { // If the frame is not a TracerFileMenuHandler then create a dummy set of disabled menu options. // At present the only situation where this may happen is in Mac OS X when no windows // are open and the menubar is created by the hidden frame. item = new JMenuItem("Import Annotations..."); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_I, MenuBarFactory.MENU_MASK)); item.setEnabled(false); menu.add(item); menu.addSeparator(); item = new JMenuItem("Export Trees..."); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, MenuBarFactory.MENU_MASK)); item.setEnabled(false); menu.add(item); item = new JMenuItem("Export Graphic..."); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, MenuBarFactory.MENU_MASK + KeyEvent.ALT_MASK)); item.setEnabled(false); menu.add(item); item = new JMenuItem("Export PDF..."); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, MenuBarFactory.MENU_MASK + KeyEvent.SHIFT_MASK + KeyEvent.ALT_MASK)); item.setEnabled(false); menu.add(item); } menu.addSeparator(); if (frame != null) { item = new JMenuItem(frame.getPrintAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_P, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(application.getPageSetupAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_P, MenuBarFactory.MENU_MASK + ActionEvent.SHIFT_MASK)); menu.add(item); } else { // No frame available so create a disabled menu for the default menu bar item = new JMenuItem("Print..."); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_P, MenuBarFactory.MENU_MASK)); item.setEnabled(false); menu.add(item); item = new JMenuItem("Page Setup..."); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_P, MenuBarFactory.MENU_MASK + ActionEvent.SHIFT_MASK)); item.setEnabled(false); menu.add(item); } } public int getPreferredAlignment() { return LEFT; } } figtree-1.4.3/src/figtree/application/menus/TreeMenuFactory.java000077500000000000000000000220751277473563300247630ustar00rootroot00000000000000/* * TreeMenuFactory.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application.menus; import jam.framework.*; import jam.mac.Utils; import javax.swing.*; import java.awt.event.KeyEvent; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreeMenuFactory implements MenuFactory { public String getMenuName() { return "Tree"; } public void populateMenu(JMenu menu, AbstractFrame frame) { JMenuItem item; if (frame instanceof TreeMenuHandler) { item = new JMenuItem(((TreeMenuHandler)frame).getNextTreeAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_CLOSE_BRACKET, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getPreviousTreeAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_OPEN_BRACKET, MenuBarFactory.MENU_MASK)); menu.add(item); menu.addSeparator(); item = new JMenuItem(((TreeMenuHandler)frame).getCartoonAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_2, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getCollapseAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_1, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getClearCollapsedAction()); menu.add(item); menu.addSeparator(); item = new JMenuItem(((TreeMenuHandler)frame).getRerootAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_R, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getMidpointRootAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_M, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getClearRootingAction()); menu.add(item); menu.addSeparator(); item = new JMenuItem(((TreeMenuHandler)frame).getRotateAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_T, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getIncreasingNodeOrderAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_U, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getDecreasingNodeOrderAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_D, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getClearRotationsAction()); menu.add(item); menu.addSeparator(); item = new JMenuItem(((TreeMenuHandler)frame).getDefineAnnotationsAction()); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getAnnotateAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_QUOTE, MenuBarFactory.MENU_MASK)); menu.add(item); // item = new JMenuItem(((TreeMenuHandler)frame).getCopyAnnotationsAction()); // menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getAnnotateNodesFromTipsAction()); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getAnnotateTipsFromNodesAction()); menu.add(item); // item = new JMenuItem(((TreeMenuHandler)frame).getClearAnnotationsAction()); // menu.add(item); menu.addSeparator(); item = new JMenuItem(((TreeMenuHandler)frame).getColourAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_K, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getClearColouringAction()); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getHilightAction()); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_L, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(((TreeMenuHandler)frame).getClearHilightingAction()); menu.add(item); } else if (Utils.isMacOSX()) { // make a false menu (only required for Mac OS X) item = new JMenuItem(TreeMenuHandler.NEXT_TREE); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_CLOSE_BRACKET, MenuBarFactory.MENU_MASK)); item.setEnabled(false); menu.add(item); item = new JMenuItem(TreeMenuHandler.PREVIOUS_TREE); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_OPEN_BRACKET, MenuBarFactory.MENU_MASK)); item.setEnabled(false); menu.add(item); menu.addSeparator(); item = new JMenuItem(TreeMenuHandler.CARTOON_NODE); item.setEnabled(false); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_2, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(TreeMenuHandler.COLLAPSE_NODE); item.setEnabled(false); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_1, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(TreeMenuHandler.CLEAR_COLLAPSED); item.setEnabled(false); menu.add(item); menu.addSeparator(); item = new JMenuItem(TreeMenuHandler.ROOT_ON_BRANCH); item.setEnabled(false); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_R, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(TreeMenuHandler.MIDPOINT_ROOT); item.setEnabled(false); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_M, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(TreeMenuHandler.CLEAR_ROOTING); item.setEnabled(false); menu.add(item); menu.addSeparator(); item = new JMenuItem(TreeMenuHandler.ROTATE_NODE); item.setEnabled(false); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_T, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(TreeMenuHandler.INCREASING_NODE_ORDER); item.setEnabled(false); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_U, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(TreeMenuHandler.DECREASING_NODE_ORDER); item.setEnabled(false); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_D, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(TreeMenuHandler.CLEAR_ROTATIONS); item.setEnabled(false); menu.add(item); menu.addSeparator(); item = new JMenuItem(TreeMenuHandler.DEFINE_ANNOTATIONS); item.setEnabled(false); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_QUOTE, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(TreeMenuHandler.ANNOTATE); item.setEnabled(false); menu.add(item); item = new JMenuItem(TreeMenuHandler.ANNOTATE_NODES_FROM_TIPS); item.setEnabled(false); menu.add(item); item = new JMenuItem(TreeMenuHandler.ANNOTATE_TIPS_FROM_NODES); item.setEnabled(false); menu.add(item); // item = new JMenuItem(TreeMenuHandler.COPY_ANNOTATION_VALUES); // item.setEnabled(false); // menu.add(item); // item = new JMenuItem(TreeMenuHandler.CLEAR_ANNOTATIONS); // item.setEnabled(false); // menu.add(item); menu.addSeparator(); item = new JMenuItem(TreeMenuHandler.COLOUR); item.setEnabled(false); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_K, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(TreeMenuHandler.CLEAR_COLOURING); item.setEnabled(false); menu.add(item); item = new JMenuItem(TreeMenuHandler.HILIGHT); item.setEnabled(false); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_L, MenuBarFactory.MENU_MASK)); menu.add(item); item = new JMenuItem(TreeMenuHandler.CLEAR_HILIGHTING); item.setEnabled(false); menu.add(item); } } public int getPreferredAlignment() { return LEFT; } } figtree-1.4.3/src/figtree/application/menus/TreeMenuHandler.java000077500000000000000000000063121277473563300247250ustar00rootroot00000000000000/* * TreeMenuHandler.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application.menus; import javax.swing.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface TreeMenuHandler { public static final String NEXT_TREE = "Next Tree"; public static final String PREVIOUS_TREE = "Previous Tree"; public static final String CARTOON_NODE = "Draw Subtree as Cartoon"; public static final String COLLAPSE_NODE = "Draw Subtree as Collapsed"; public static final String CLEAR_COLLAPSED = "Clear Collapsed/Cartoon"; public static final String MIDPOINT_ROOT = "Midpoint Root"; public static final String ROOT_ON_BRANCH = "Root on Branch..."; public static final String CLEAR_ROTATIONS = "Clear Rotations..."; public static final String INCREASING_NODE_ORDER = "Increasing Node Order"; public static final String DECREASING_NODE_ORDER = "Decreasing Node Order"; public static final String ROTATE_NODE = "Rotate Node..."; public static final String CLEAR_ROOTING = "Clear Rooting..."; public static final String COLOUR = "Colour..."; public static final String CLEAR_COLOURING = "Clear Colouring..."; public static final String HILIGHT = "Hilight..."; public static final String CLEAR_HILIGHTING = "Clear Hilighting..."; public static final String DEFINE_ANNOTATIONS = "Define Annotations..."; public static final String ANNOTATE = "Annotate..."; public static final String COPY_ANNOTATION_VALUES = "Copy values..."; public static final String ANNOTATE_NODES_FROM_TIPS = "Annotate Nodes from Tips..."; public static final String ANNOTATE_TIPS_FROM_NODES = "Annotate Tips from Nodes..."; public static final String CLEAR_ANNOTATIONS = "Clear Annotations"; Action getNextTreeAction(); Action getPreviousTreeAction(); Action getCartoonAction(); Action getCollapseAction(); Action getClearCollapsedAction(); Action getMidpointRootAction(); Action getRerootAction(); Action getClearRootingAction(); Action getIncreasingNodeOrderAction(); Action getDecreasingNodeOrderAction(); Action getRotateAction(); Action getClearRotationsAction(); Action getColourAction(); Action getClearColouringAction(); Action getHilightAction(); Action getClearHilightingAction(); Action getDefineAnnotationsAction(); Action getAnnotateAction(); Action getCopyAnnotationsAction(); Action getAnnotateNodesFromTipsAction(); Action getAnnotateTipsFromNodesAction(); Action getClearAnnotationsAction(); } figtree-1.4.3/src/figtree/application/preferences/000077500000000000000000000000001277473563300222055ustar00rootroot00000000000000figtree-1.4.3/src/figtree/application/preferences/AdvancedPreferencesSection.java000077500000000000000000000037731277473563300303010ustar00rootroot00000000000000/* * AdvancedPreferencesSection.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application.preferences; import jam.preferences.PreferencesSection; import jam.util.IconUtils; import figtree.application.FigTreeApplication; import javax.swing.*; import java.util.prefs.Preferences; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class AdvancedPreferencesSection implements PreferencesSection { Icon projectToolIcon = IconUtils.getIcon(FigTreeApplication.class, "images/prefsAdvanced.png"); public String getTitle() { return "Advanced"; } public Icon getIcon() { return projectToolIcon; } public JPanel getPanel() { JPanel panel = new JPanel(); panel.add(new JCheckBox("Advanced preference")); return panel; } public void retrievePreferences() { Preferences prefs = Preferences.userNodeForPackage(FigTreeApplication.class); advancedCheck.setSelected(prefs.getBoolean("advanced_check", true)); } public void storePreferences() { Preferences prefs = Preferences.userNodeForPackage(FigTreeApplication.class); prefs.putBoolean("advanced_check", advancedCheck.isSelected()); } JCheckBox advancedCheck = new JCheckBox("The preferences window is not implemented yet."); } figtree-1.4.3/src/figtree/application/preferences/AppearancePreferencesSection.java000077500000000000000000000120541277473563300306230ustar00rootroot00000000000000/* * AppearancePreferencesSection.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application.preferences; import jam.panels.OptionsPanel; import jam.preferences.PreferencesSection; import jam.util.IconUtils; import figtree.application.FigTreeApplication; import figtree.treeviewer.TreeAppearanceController; import javax.swing.*; import java.awt.*; import figtree.ui.components.ColorWellButton; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class AppearancePreferencesSection implements PreferencesSection { Icon coloursToolIcon = IconUtils.getIcon(FigTreeApplication.class, "images/coloursTool.png"); public String getTitle() { return "Appearance"; } public Icon getIcon() { return coloursToolIcon; } public JPanel getPanel() { OptionsPanel optionsPanel = new OptionsPanel(12, 18); // foregroundButton = new ColorWellButton(Color.white, "Choose Foreground Colour"); // optionsPanel.addComponentWithLabel("Foreground Colour:", foregroundButton); // // backgroundButton = new ColorWellButton(Color.white, "Choose Background Colour"); // optionsPanel.addComponentWithLabel("Background Colour:", backgroundButton); selectionButton = new ColorWellButton(Color.white, "Choose Selection Colour"); optionsPanel.addComponentWithLabel("Selection Colour:", selectionButton); optionsPanel.addSeparator(); branchLineWidthSpinner = new JSpinner( new SpinnerNumberModel(1.0, 0.01, 48.0, 1.0)); optionsPanel.addComponentWithLabel("Line Weight:", branchLineWidthSpinner); optionsPanel.addFlexibleSpace(); return optionsPanel; } public void retrievePreferences() { // int foregroundRGB = TreeAppearanceController.PREFS.getInt( // TreeAppearanceController.CONTROLLER_KEY + "." + TreeAppearanceController.FOREGROUND_COLOUR_KEY, // TreeAppearanceController.DEFAULT_FOREGROUND_COLOUR.getRGB()); // int backgroundRGB = TreeAppearanceController.PREFS.getInt( // TreeAppearanceController.CONTROLLER_KEY + "." + TreeAppearanceController.BACKGROUND_COLOUR_KEY, // TreeAppearanceController.DEFAULT_BACKGROUND_COLOUR.getRGB()); int selectionRGB = TreeAppearanceController.PREFS.getInt( TreeAppearanceController.CONTROLLER_KEY + "." + TreeAppearanceController.SELECTION_COLOUR_KEY, TreeAppearanceController.DEFAULT_SELECTION_COLOUR.getRGB()); double branchLineWidth = TreeAppearanceController.PREFS.getFloat( TreeAppearanceController.CONTROLLER_KEY + "." + TreeAppearanceController.BRANCH_LINE_WIDTH_KEY, TreeAppearanceController.DEFAULT_BRANCH_LINE_WIDTH); // foregroundButton.setSelectedColor(new Color(foregroundRGB)); // backgroundButton.setSelectedColor(new Color(backgroundRGB)); selectionButton.setSelectedColor(new Color(selectionRGB)); branchLineWidthSpinner.setValue(branchLineWidth); } public void storePreferences() { // int foregroundRGB = foregroundButton.getSelectedColor().getRGB(); // int backgroundRGB = backgroundButton.getSelectedColor().getRGB(); int selectionRGB = selectionButton.getSelectedColor().getRGB(); float branchLineWidth = ((Number)branchLineWidthSpinner.getValue()).floatValue(); // TreeAppearanceController.PREFS.putInt( // TreeAppearanceController.CONTROLLER_KEY + "." + TreeAppearanceController.FOREGROUND_COLOUR_KEY, // foregroundRGB); // TreeAppearanceController.PREFS.putInt( // TreeAppearanceController.CONTROLLER_KEY + "." + TreeAppearanceController.BACKGROUND_COLOUR_KEY, // backgroundRGB); TreeAppearanceController.PREFS.putInt( TreeAppearanceController.CONTROLLER_KEY + "." + TreeAppearanceController.SELECTION_COLOUR_KEY, selectionRGB); TreeAppearanceController.PREFS.putFloat( TreeAppearanceController.CONTROLLER_KEY + "." + TreeAppearanceController.BRANCH_LINE_WIDTH_KEY, branchLineWidth); } // ColorWellButton foregroundButton; // ColorWellButton backgroundButton; ColorWellButton selectionButton; JSpinner branchLineWidthSpinner; } figtree-1.4.3/src/figtree/application/preferences/FontsPreferencesSection.java000077500000000000000000000211611277473563300276540ustar00rootroot00000000000000/* * FontsPreferencesSection.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application.preferences; import figtree.application.FigTreeApplication; import figtree.treeviewer.painters.LabelPainterController; import figtree.treeviewer.painters.ScaleBarPainterController; import figtree.ui.FontChooserPanel; import jam.panels.OptionsPanel; import jam.preferences.PreferencesSection; import jam.util.IconUtils; import javax.swing.*; import javax.swing.border.TitledBorder; import java.awt.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FontsPreferencesSection implements PreferencesSection { Icon projectToolIcon = IconUtils.getIcon(FigTreeApplication.class, "images/prefsFonts.png"); public String getTitle() { return "Fonts"; } public Icon getIcon() { return projectToolIcon; } public JPanel getPanel() { OptionsPanel optionsPanel = new OptionsPanel(12, 18); if (tipLabelFontChooser == null) { Font font = new Font( LabelPainterController.DEFAULT_FONT_NAME, LabelPainterController.DEFAULT_FONT_STYLE, LabelPainterController.DEFAULT_FONT_SIZE); tipLabelFontChooser = new FontChooserPanel(font); } JPanel panel = new JPanel(new BorderLayout()); panel.add(tipLabelFontChooser, BorderLayout.CENTER); panel.setBorder(new TitledBorder("Tip Labels")); optionsPanel.addSpanningComponent(panel); if (nodeLabelFontChooser == null) { Font font = new Font( LabelPainterController.DEFAULT_FONT_NAME, LabelPainterController.DEFAULT_FONT_STYLE, LabelPainterController.DEFAULT_FONT_SIZE); nodeLabelFontChooser = new FontChooserPanel(font); } panel = new JPanel(new BorderLayout()); panel.add(nodeLabelFontChooser, BorderLayout.CENTER); panel.setBorder(new TitledBorder("Node Labels")); optionsPanel.addSpanningComponent(panel); if (branchLabelFontChooser == null) { Font font = new Font( LabelPainterController.DEFAULT_FONT_NAME, LabelPainterController.DEFAULT_FONT_STYLE, LabelPainterController.DEFAULT_FONT_SIZE); branchLabelFontChooser = new FontChooserPanel(font); } panel = new JPanel(new BorderLayout()); panel.add(branchLabelFontChooser, BorderLayout.CENTER); panel.setBorder(new TitledBorder("Branch Labels")); optionsPanel.addSpanningComponent(panel); if (scaleLabelFontChooser == null) { Font font = new Font( LabelPainterController.DEFAULT_FONT_NAME, LabelPainterController.DEFAULT_FONT_STYLE, LabelPainterController.DEFAULT_FONT_SIZE); scaleLabelFontChooser = new FontChooserPanel(font); } panel = new JPanel(new BorderLayout()); panel.add(scaleLabelFontChooser, BorderLayout.CENTER); panel.setBorder(new TitledBorder("Scale Bar/Axis Labels")); optionsPanel.addSpanningComponent(panel); optionsPanel.addFlexibleSpace(); return optionsPanel; } public void retrievePreferences() { String name = LabelPainterController.PREFS.get("tipLabels" + "." + LabelPainterController.FONT_NAME_KEY, LabelPainterController.DEFAULT_FONT_NAME); int size = LabelPainterController.PREFS.getInt("tipLabels" + "." + LabelPainterController.FONT_SIZE_KEY, LabelPainterController.DEFAULT_FONT_SIZE); int style = LabelPainterController.PREFS.getInt("tipLabels" + "." + LabelPainterController.FONT_STYLE_KEY, LabelPainterController.DEFAULT_FONT_STYLE); Font font = new Font(name, style, size); tipLabelFontChooser.setSelectedFont(font); name = LabelPainterController.PREFS.get("nodeLabels" + "." + LabelPainterController.FONT_NAME_KEY, LabelPainterController.DEFAULT_FONT_NAME); size = LabelPainterController.PREFS.getInt("nodeLabels" + "." + LabelPainterController.FONT_SIZE_KEY, LabelPainterController.DEFAULT_FONT_SIZE); style = LabelPainterController.PREFS.getInt("nodeLabels" + "." + LabelPainterController.FONT_STYLE_KEY, LabelPainterController.DEFAULT_FONT_STYLE); font = new Font(name, style, size); nodeLabelFontChooser.setSelectedFont(font); name = LabelPainterController.PREFS.get("branchLabels" + "." + LabelPainterController.FONT_NAME_KEY, LabelPainterController.DEFAULT_FONT_NAME); size = LabelPainterController.PREFS.getInt("branchLabels" + "." + LabelPainterController.FONT_SIZE_KEY, LabelPainterController.DEFAULT_FONT_SIZE); style = LabelPainterController.PREFS.getInt("branchLabels" + "." + LabelPainterController.FONT_STYLE_KEY, LabelPainterController.DEFAULT_FONT_STYLE); font = new Font(name, style, size); branchLabelFontChooser.setSelectedFont(font); name = ScaleBarPainterController.PREFS.get(ScaleBarPainterController.CONTROLLER_KEY + "." + ScaleBarPainterController.FONT_NAME_KEY, ScaleBarPainterController.DEFAULT_FONT_NAME); size = ScaleBarPainterController.PREFS.getInt(ScaleBarPainterController.CONTROLLER_KEY + "." + ScaleBarPainterController.FONT_SIZE_KEY, ScaleBarPainterController.DEFAULT_FONT_SIZE); style = ScaleBarPainterController.PREFS.getInt(ScaleBarPainterController.CONTROLLER_KEY + "." + ScaleBarPainterController.FONT_STYLE_KEY, ScaleBarPainterController.DEFAULT_FONT_STYLE); font = new Font(name, style, size); scaleLabelFontChooser.setSelectedFont(font); } public void storePreferences() { Font font = tipLabelFontChooser.getSelectedFont(); LabelPainterController.PREFS.put("tipLabels" + "." + LabelPainterController.FONT_NAME_KEY, font.getName()); LabelPainterController.PREFS.putInt("tipLabels" + "." + LabelPainterController.FONT_SIZE_KEY, font.getSize()); LabelPainterController.PREFS.putInt("tipLabels" + "." + LabelPainterController.FONT_STYLE_KEY, font.getStyle()); font = nodeLabelFontChooser.getSelectedFont(); LabelPainterController.PREFS.put("nodeLabels" + "." + LabelPainterController.FONT_NAME_KEY, font.getName()); LabelPainterController.PREFS.putInt("nodeLabels" + "." + LabelPainterController.FONT_SIZE_KEY, font.getSize()); LabelPainterController.PREFS.putInt("nodeLabels" + "." + LabelPainterController.FONT_STYLE_KEY, font.getStyle()); font = branchLabelFontChooser.getSelectedFont(); LabelPainterController.PREFS.put("branchLabels" + "." + LabelPainterController.FONT_NAME_KEY, font.getName()); LabelPainterController.PREFS.putInt("branchLabels" + "." + LabelPainterController.FONT_SIZE_KEY, font.getSize()); LabelPainterController.PREFS.putInt("branchLabels" + "." + LabelPainterController.FONT_STYLE_KEY, font.getStyle()); font = scaleLabelFontChooser.getSelectedFont(); ScaleBarPainterController.PREFS.put(ScaleBarPainterController.CONTROLLER_KEY + "." + ScaleBarPainterController.FONT_NAME_KEY, font.getName()); ScaleBarPainterController.PREFS.putInt(ScaleBarPainterController.CONTROLLER_KEY + "." + ScaleBarPainterController.FONT_SIZE_KEY, font.getSize()); ScaleBarPainterController.PREFS.putInt(ScaleBarPainterController.CONTROLLER_KEY + "." + ScaleBarPainterController.FONT_STYLE_KEY, font.getStyle()); } FontChooserPanel tipLabelFontChooser = null; FontChooserPanel nodeLabelFontChooser = null; FontChooserPanel branchLabelFontChooser = null; FontChooserPanel scaleLabelFontChooser = null; } figtree-1.4.3/src/figtree/application/preferences/GeneralPreferencesSection.java000077500000000000000000000037311277473563300301430ustar00rootroot00000000000000/* * GeneralPreferencesSection.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.application.preferences; import jam.preferences.PreferencesSection; import jam.util.IconUtils; import figtree.application.FigTreeApplication; import javax.swing.*; import java.util.prefs.Preferences; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class GeneralPreferencesSection implements PreferencesSection { Icon projectToolIcon = IconUtils.getIcon(FigTreeApplication.class, "images/prefsGeneral.png"); public String getTitle() { return "General"; } public Icon getIcon() { return projectToolIcon; } public JPanel getPanel() { JPanel panel = new JPanel(); panel.add(generalCheck); return panel; } public void retrievePreferences() { Preferences prefs = Preferences.userNodeForPackage(FigTreeApplication.class); generalCheck.setSelected(prefs.getBoolean("general_check", true)); } public void storePreferences() { Preferences prefs = Preferences.userNodeForPackage(FigTreeApplication.class); prefs.putBoolean("general_check", generalCheck.isSelected()); } JCheckBox generalCheck = new JCheckBox("The preferences window is not implemented yet."); } figtree-1.4.3/src/figtree/panel/000077500000000000000000000000001277473563300165005ustar00rootroot00000000000000figtree-1.4.3/src/figtree/panel/FigTreePanel.java000077500000000000000000000224001277473563300216510ustar00rootroot00000000000000/* * FigTreePanel.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.panel; import jam.controlpalettes.ControlPalette; import javax.swing.*; import java.awt.*; import java.util.Set; import java.util.HashSet; import java.util.ArrayList; import figtree.treeviewer.painters.ScaleBarPainter; import figtree.treeviewer.decorators.*; import figtree.treeviewer.TreeViewer; import jebl.evolution.graphs.Node; import jebl.evolution.trees.Tree; /** * This is a panel that has a TreeViewer and a BasicControlPalette with * the default Controllers and Painters. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FigTreePanel extends JPanel { public enum Style { DEFAULT, SIMPLE, MINIMAL, ICARUS, ICARUS_SMALL } public FigTreePanel(Style style) { this(new SimpleTreeViewer(), new SimpleControlPalette(), null, style); } public FigTreePanel(final TreeViewer treeViewer, ControlPalette controlPalette1, ControlPalette controlPalette2, Style style) { this.treeViewer = treeViewer; if (controlPalette1 != null) { controlPalette1.getPanel().setBorder(BorderFactory.createMatteBorder(1, 0, 0, 0, Color.GRAY)); controlPalette1.getPanel().setBackground(new Color(231, 237, 246)); controlPalette1.getPanel().setOpaque(true); } if (controlPalette2 != null) { controlPalette2.getPanel().setBorder(BorderFactory.createMatteBorder(0, 0, 1, 0, Color.GRAY)); controlPalette2.getPanel().setBackground(new Color(231, 237, 246)); controlPalette2.getPanel().setOpaque(true); } // Create a tip label painter and its controller final SimpleLabelPainter tipLabelPainter = new SimpleLabelPainter(SimpleLabelPainter.PainterIntent.TIP); // Create a node label painter and its controller final SimpleLabelPainter nodeLabelPainter = new SimpleLabelPainter(SimpleLabelPainter.PainterIntent.NODE); nodeLabelPainter.setVisible(false); final SimpleLabelPainter branchLabelPainter = new SimpleLabelPainter(SimpleLabelPainter.PainterIntent.BRANCH); branchLabelPainter.setVisible(false); setLayout(new BorderLayout()); switch (style) { case DEFAULT: if (controlPalette1 == null) { throw new IllegalArgumentException("DEFAULT style requires a controlPalette"); } controlPalette1.addController(new TreeViewerController(treeViewer)); controlPalette1.addController(new TreeAppearanceController( treeViewer, "tipLabels", tipLabelPainter, "nodeLabels", nodeLabelPainter, "branchLabels", branchLabelPainter)); controlPalette1.addController(new TreesController(treeViewer)); controlPalette1.addController(new LabelPainterController( "tipLabels", tipLabelPainter, "nodeLabels", nodeLabelPainter, "branchLabels", branchLabelPainter, treeViewer)); break; case SIMPLE: if (controlPalette1 == null) { throw new IllegalArgumentException("SIMPLE style requires a controlPalette"); } controlPalette1.addController(new TreeViewerController(treeViewer)); controlPalette1.addController(new TreeAppearanceController( treeViewer, "tipLabels", tipLabelPainter, "nodeLabels", nodeLabelPainter, "branchLabels", branchLabelPainter, true, true)); controlPalette1.addController(new LabelPainterController( "tipLabels", tipLabelPainter, "nodeLabels", nodeLabelPainter, "branchLabels", branchLabelPainter, treeViewer)); break; case MINIMAL: break; case ICARUS: controlPalette1.addController(new TreeViewerController(treeViewer, true)); controlPalette1.addController(new TreeAppearanceController( treeViewer, "tipLabels", tipLabelPainter, "nodeLabels", nodeLabelPainter, "branchLabels", branchLabelPainter, true, false)); controlPalette1.addController(new LabelPainterController( "tipLabels", tipLabelPainter, "nodeLabels", nodeLabelPainter, "branchLabels", branchLabelPainter, treeViewer)); controlPalette1.addController(new TreesController(treeViewer)); controlPalette2.addController(new TreeColouringController(treeViewer, "Clustering:")); add(controlPalette2.getPanel(), BorderLayout.NORTH); break; case ICARUS_SMALL: controlPalette1.addController(new TreeViewerController(treeViewer, true)); controlPalette1.addController(new TreeAppearanceController( treeViewer, "tipLabels", tipLabelPainter, "nodeLabels", nodeLabelPainter, "branchLabels", branchLabelPainter, true, false)); controlPalette2.addController(new TreeColouringController(treeViewer, "Clustering:")); add(controlPalette2.getPanel(), BorderLayout.NORTH); break; } treeViewer.setTipLabelPainter(tipLabelPainter); treeViewer.setNodeLabelPainter(nodeLabelPainter); treeViewer.setBranchLabelPainter(branchLabelPainter); AttributableDecorator tipDecorator = new AttributableDecorator(); tipDecorator.setPaintAttributeName("!color"); tipDecorator.setFontAttributeName("!font"); tipLabelPainter.setTextDecorator(tipDecorator); // Create a scale bar painter and its controller final ScaleBarPainter scaleBarPainter = new ScaleBarPainter(); // controlPalette.addController(new ScaleBarPainterController(scaleBarPainter)); treeViewer.addScalePainter(scaleBarPainter); add(treeViewer, BorderLayout.CENTER); if (controlPalette1 != null) { add(controlPalette1.getPanel(), BorderLayout.SOUTH); } } public void setColourBy(String attribute) { if (attribute == null) { treeViewer.setBranchColouringDecorator(null, null); treeViewer.setBranchDecorator(null, false); } else { Set nodes = new HashSet(); for (Tree tree : treeViewer.getTrees()) { for (Node node : tree.getNodes()) { nodes.add(node); } } if (attribute != null && attribute.length() > 0) { if (attribute.endsWith("*")) { Decorator decorator = new DiscreteColourDecorator(); treeViewer.setBranchColouringDecorator(attribute.substring(0, attribute.length() - 2), decorator); treeViewer.setBranchDecorator(null, false); } else if (DiscreteColourDecorator.isDiscrete(attribute, nodes)) { Decorator decorator = new HSBDiscreteColourDecorator(attribute, nodes); treeViewer.setBranchColouringDecorator(null, null); treeViewer.setBranchDecorator(decorator, false); } else { Decorator decorator = new InterpolatingColourDecorator( new ContinuousScale(attribute, nodes), new Color(192, 16, 0), new Color(0, 0, 0), new Color(0, 16, 192)); treeViewer.setBranchColouringDecorator(null, null); treeViewer.setBranchDecorator(decorator, false); } } } } public TreeViewer getTreeViewer() { return treeViewer; } public void setTree(Tree tree) { java.util.List trees = new ArrayList(); if (tree != null) { trees.add(tree); } treeViewer.setTrees(trees); } private final TreeViewer treeViewer; }figtree-1.4.3/src/figtree/panel/LabelPainterController.java000077500000000000000000000114071277473563300237570ustar00rootroot00000000000000/* * LabelPainterController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.panel; import figtree.treeviewer.TreeViewer; import figtree.treeviewer.painters.AttributeComboHelper; import figtree.treeviewer.painters.AttributeComboHelperListener; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.util.Map; import figtree.treeviewer.painters.LabelPainter; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class LabelPainterController extends AbstractController { private static final String DISPLAY_ATTRIBUTE_KEY = "displayAttribute"; public LabelPainterController(String tipKey, final SimpleLabelPainter tipLabelPainter, String nodeKey, final SimpleLabelPainter nodeLabelPainter, String branchKey, final SimpleLabelPainter branchLabelPainter, final TreeViewer treeViewer) { this.tipKey = tipKey; this.nodeKey = nodeKey; this.branchKey = branchKey; optionsPanel = new OptionsPanel(); tipComboBox = setupComboBox("Tips: ", tipLabelPainter, treeViewer); tipComboBox.setSelectedIndex(1); nodeComboBox = setupComboBox("Nodes: ", nodeLabelPainter, treeViewer); branchComboBox = setupComboBox("Branches: ", branchLabelPainter, treeViewer); } private JComboBox setupComboBox(String title, final SimpleLabelPainter labelPainter, final TreeViewer treeViewer) { // String[] attributes = labelPainter.getAttributes(); final JComboBox displayAttributeCombo = new JComboBox(); displayAttributeCombo.addItem("None"); for (String attribute : labelPainter.getAttributes()) { displayAttributeCombo.addItem(attribute); } new AttributeComboHelper(displayAttributeCombo, treeViewer, "None", labelPainter.getIntent()); optionsPanel.addComponentWithLabel(title, displayAttributeCombo); displayAttributeCombo.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent itemEvent) { String attribute = (String)displayAttributeCombo.getSelectedItem(); if (attribute == null || attribute.equalsIgnoreCase("none")) { labelPainter.setVisible(false); } else { labelPainter.setDisplayAttribute(attribute); labelPainter.setVisible(true); } } }); return displayAttributeCombo; } public JComponent getTitleComponent() { return null; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { tipComboBox.setSelectedItem(settings.get(tipKey+"."+DISPLAY_ATTRIBUTE_KEY)); nodeComboBox.setSelectedItem(settings.get(nodeKey+"."+DISPLAY_ATTRIBUTE_KEY)); branchComboBox.setSelectedItem(settings.get(branchKey+"."+DISPLAY_ATTRIBUTE_KEY)); } public void getSettings(Map settings) { settings.put(tipKey+"."+DISPLAY_ATTRIBUTE_KEY, tipComboBox.getSelectedItem().toString()); settings.put(nodeKey+"."+DISPLAY_ATTRIBUTE_KEY, nodeComboBox.getSelectedItem().toString()); settings.put(branchKey+"."+DISPLAY_ATTRIBUTE_KEY, branchComboBox.getSelectedItem().toString()); } public String getTitle() { return ""; } private final OptionsPanel optionsPanel; private final JComboBox tipComboBox; private final JComboBox nodeComboBox; private final JComboBox branchComboBox; private final String tipKey; private final String nodeKey; private final String branchKey; }figtree-1.4.3/src/figtree/panel/ScaleBarPainterController.java000077500000000000000000000234271277473563300244210ustar00rootroot00000000000000/* * ScaleBarPainterController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.panel; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.text.NumberFormat; import java.text.DecimalFormat; import java.util.Map; import figtree.treeviewer.painters.ScaleBarPainter; import figtree.ui.components.RealNumberField; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ScaleBarPainterController extends AbstractController { private static final String SCALE_BAR_KEY = "scaleBar"; private static final String FONT_NAME_KEY = "fontName"; private static final String FONT_SIZE_KEY = "fontSize"; private static final String FONT_STYLE_KEY = "fontStyle"; private static final String NUMBER_FORMATTING_KEY = "numberFormatting"; private static final String AUTOMATIC_SCALE_KEY = "automaticScale"; private static final String SCALE_RANGE_KEY = "scaleRange"; private static final String LINE_WIDTH_KEY = "lineWidth"; private static final String SIGNIFICANT_DIGITS_KEY = "significantDigits"; // The defaults if there is nothing in the preferences private static String DEFAULT_FONT_NAME = "sansserif"; private static int DEFAULT_FONT_SIZE = 6; private static int DEFAULT_FONT_STYLE = Font.PLAIN; private static String DEFAULT_NUMBER_FORMATTING = "#.####"; private static float DEFAULT_LINE_WIDTH = 1.0f; public ScaleBarPainterController(final ScaleBarPainter scaleBarPainter) { this.scaleBarPainter = scaleBarPainter; final String defaultFontName = DEFAULT_FONT_NAME; final int defaultFontStyle = DEFAULT_FONT_STYLE; final int defaultFontSize = DEFAULT_FONT_SIZE; final String defaultNumberFormatting = DEFAULT_NUMBER_FORMATTING; float lineWidth = DEFAULT_LINE_WIDTH; scaleBarPainter.setFont(new Font(defaultFontName, defaultFontStyle, defaultFontSize)); scaleBarPainter.setNumberFormat(new DecimalFormat(defaultNumberFormatting)); scaleBarPainter.setScaleBarStroke(new BasicStroke(lineWidth, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND)); optionsPanel = new OptionsPanel(); titleCheckBox = new JCheckBox(getTitle()); titleCheckBox.setSelected(scaleBarPainter.isVisible()); autoScaleCheck = new JCheckBox("Automatic scale"); autoScaleCheck.setSelected(true); optionsPanel.addComponent(autoScaleCheck, true); scaleRangeText = new RealNumberField(0.0, Double.MAX_VALUE); scaleRangeText.setValue(0.0); final JLabel label1 = optionsPanel.addComponentWithLabel("Scale Range:", scaleRangeText, true); label1.setEnabled(false); scaleRangeText.setEnabled(false); Font font = scaleBarPainter.getFont(); fontSizeSpinner = new JSpinner(new SpinnerNumberModel(font.getSize(), 0.01, 48, 1)); final JLabel label2 = optionsPanel.addComponentWithLabel("Font Size:", fontSizeSpinner); fontSizeSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final float size = ((Double) fontSizeSpinner.getValue()).floatValue(); Font font = scaleBarPainter.getFont().deriveFont(size); scaleBarPainter.setFont(font); } }); NumberFormat format = this.scaleBarPainter.getNumberFormat(); int digits = format.getMaximumFractionDigits(); digitsSpinner = new JSpinner(new SpinnerNumberModel(digits, 2, 14, 1)); final JLabel label3 = optionsPanel.addComponentWithLabel("Significant Digits:", digitsSpinner); digitsSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final int digits = (Integer)digitsSpinner.getValue(); NumberFormat format = scaleBarPainter.getNumberFormat(); format.setMaximumFractionDigits(digits); scaleBarPainter.setNumberFormat(format); } }); lineWeightSpinner = new JSpinner(new SpinnerNumberModel(1.0, 0.01, 48.0, 1.0)); lineWeightSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { float weight = ((Double) lineWeightSpinner.getValue()).floatValue(); scaleBarPainter.setScaleBarStroke(new BasicStroke(weight, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL)); } }); final JLabel label4 = optionsPanel.addComponentWithLabel("Line Weight:", lineWeightSpinner); final boolean isSelected1 = titleCheckBox.isSelected(); final boolean isSelected2 = autoScaleCheck.isSelected(); label1.setEnabled(isSelected1 && !isSelected2); scaleRangeText.setEnabled(isSelected1 && !isSelected2); label2.setEnabled(isSelected1); fontSizeSpinner.setEnabled(isSelected1); label3.setEnabled(isSelected1); digitsSpinner.setEnabled(isSelected1); label4.setEnabled(isSelected1); lineWeightSpinner.setEnabled(isSelected1); titleCheckBox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { final boolean isSelected1 = titleCheckBox.isSelected(); final boolean isSelected2 = autoScaleCheck.isSelected(); autoScaleCheck.setEnabled(isSelected1); label1.setEnabled(isSelected1 && !isSelected2); scaleRangeText.setEnabled(isSelected1 && !isSelected2); label2.setEnabled(isSelected1); fontSizeSpinner.setEnabled(isSelected1); label3.setEnabled(isSelected1); digitsSpinner.setEnabled(isSelected1); label4.setEnabled(isSelected1); lineWeightSpinner.setEnabled(isSelected1); scaleBarPainter.setVisible(isSelected1); } }); autoScaleCheck.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { if (autoScaleCheck.isSelected()) { scaleBarPainter.setAutomaticScale(true); double range = scaleBarPainter.getScaleRange(); scaleRangeText.setValue(range); label1.setEnabled(false); scaleRangeText.setEnabled(false); } else { label1.setEnabled(true); scaleRangeText.setEnabled(true); scaleBarPainter.setAutomaticScale(false); } } }); scaleRangeText.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { Double value = scaleRangeText.getValue(); if (value != null) { scaleBarPainter.setScaleRange(value); } } }); } public JComponent getTitleComponent() { return titleCheckBox; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // force a toggle of the checkbox autoScaleCheck.setSelected(false); autoScaleCheck.setSelected(true); } public void setSettings(Map settings) { autoScaleCheck.setSelected((Boolean)settings.get(SCALE_BAR_KEY + "." + AUTOMATIC_SCALE_KEY)); scaleRangeText.setValue((Double)settings.get(SCALE_BAR_KEY + "." + SCALE_RANGE_KEY)); fontSizeSpinner.setValue((Double)settings.get(SCALE_BAR_KEY + "." + FONT_SIZE_KEY)); digitsSpinner.setValue((Integer)settings.get(SCALE_BAR_KEY + "." + SIGNIFICANT_DIGITS_KEY)); lineWeightSpinner.setValue((Double)settings.get(SCALE_BAR_KEY + "." + LINE_WIDTH_KEY)); } public void getSettings(Map settings) { settings.put(SCALE_BAR_KEY + "." + AUTOMATIC_SCALE_KEY, autoScaleCheck.isSelected()); settings.put(SCALE_BAR_KEY + "." + SCALE_RANGE_KEY, scaleRangeText.getValue()); settings.put(SCALE_BAR_KEY + "." + FONT_SIZE_KEY, fontSizeSpinner.getValue()); settings.put(SCALE_BAR_KEY + "." + SIGNIFICANT_DIGITS_KEY, digitsSpinner.getValue()); settings.put(SCALE_BAR_KEY + "." + LINE_WIDTH_KEY, lineWeightSpinner.getValue()); } private final JCheckBox titleCheckBox; private final OptionsPanel optionsPanel; private final JCheckBox autoScaleCheck; private final RealNumberField scaleRangeText; private final JSpinner fontSizeSpinner; private final JSpinner digitsSpinner; private final JSpinner lineWeightSpinner; public String getTitle() { return "Scale Bar"; } private final ScaleBarPainter scaleBarPainter; }figtree-1.4.3/src/figtree/panel/SimpleControlPalette.java000066400000000000000000000070321277473563300234560ustar00rootroot00000000000000/* * SimpleControlPalette.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.panel; import jam.controlpalettes.*; import javax.swing.*; import java.util.ArrayList; import java.util.List; import java.util.Map; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class SimpleControlPalette extends JPanel implements ControlPalette { public SimpleControlPalette() { BoxLayout layout = new BoxLayout(this, BoxLayout.LINE_AXIS); setLayout(layout); setOpaque(true); } public JPanel getPanel() { return this; } private ControllerListener controllerListener = new ControllerListener() { public void controlsChanged() { layoutControls(); } }; public void addController(Controller controller) { controllers.add(controller); controller.addControllerListener(controllerListener); setupControls(); } public void addController(int position, Controller controller) { controllers.add(position, controller); controller.addControllerListener(controllerListener); setupControls(); } public void removeController(Controller controller) { controller.removeControllerListener(controllerListener); controllers.remove(controller); setupControls(); } public int getControllerCount() { return controllers.size(); } public void fireControlsChanged() { for (ControlPaletteListener listener : listeners) { listener.controlsChanged(); } } public void addControlPaletteListener(ControlPaletteListener listener) { listeners.add(listener); } public void removeControlPaletteListener(ControlPaletteListener listener) { listeners.remove(listener); } private final List listeners = new ArrayList(); private void setupControls() { removeAll(); for (Controller controller : controllers) { add(controller.getPanel()); } } public void layoutControls() { validate(); } public void initialize() { for (Controller controller : controllers) { controller.initialize(); } } public void getSettings(Map settings) { for (Controller controller : controllers) { controller.getSettings(settings); } } public void setSettings(Map settings) { for (Controller controller : controllers) { controller.setSettings(settings); } } @Override public void setPreferredWidth(int preferredWidth) { // ignore } private List controllers = new ArrayList(); }figtree-1.4.3/src/figtree/panel/SimpleLabelPainter.java000077500000000000000000000246421277473563300230720ustar00rootroot00000000000000/* * SimpleLabelPainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.panel; import figtree.treeviewer.TreePane; import figtree.treeviewer.painters.LabelPainter; import figtree.treeviewer.decorators.Decorator; import jebl.evolution.graphs.Node; import jebl.evolution.taxa.Taxon; import jebl.evolution.trees.RootedTree; import jebl.evolution.trees.Tree; import jebl.util.Attributable; import java.awt.*; import java.awt.geom.Rectangle2D; import java.util.*; import java.util.List; /** * A simple implementation of LabelPainter that can be used to display * tip, node or branch labels. It can display, taxon names, branch lengths, * node heights or other attributeNames of nodes. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class SimpleLabelPainter extends LabelPainter { public static final String NAMES = "Names"; public static final String NODE_AGES = "Node ages"; public static final String BRANCH_LENGTHS = "Branch lengths"; public SimpleLabelPainter(PainterIntent intent) { super(intent); setupAttributes(null); if (this.displayAttribute == null) { this.displayAttribute = attributes[0]; } else { this.displayAttribute = ""; } } public void setupAttributes(Collection trees) { List attributeNames = new ArrayList(); switch (getIntent()) { case TIP: { attributeNames.add(NAMES); attributeNames.add(NODE_AGES); attributeNames.add(BRANCH_LENGTHS); break; } case NODE: { attributeNames.add(NODE_AGES); attributeNames.add(BRANCH_LENGTHS); break; } case BRANCH: { attributeNames.add(BRANCH_LENGTHS); attributeNames.add(NODE_AGES); break; } } if (trees != null) { for (Tree tree : trees) { Set nodeAttributes = new TreeSet(); if (getIntent() == PainterIntent.TIP) { for (Node node : tree.getExternalNodes()) { nodeAttributes.addAll(node.getAttributeNames()); } } else if (getIntent() == PainterIntent.NODE) { for (Node node : tree.getInternalNodes()) { nodeAttributes.addAll(node.getAttributeNames()); } } else { for (Node node : tree.getNodes()) { nodeAttributes.addAll(node.getAttributeNames()); } } for (String attributeName : nodeAttributes) { if (!attributeName.startsWith("!")) { attributeNames.add(attributeName); } } } } this.attributes = new String[attributeNames.size()]; attributeNames.toArray(this.attributes); firePainterSettingsChanged(); } public void setTreePane(TreePane treePane) { this.treePane = treePane; } public Decorator getBorderDecorator() { return borderDecorator; } public void setBorderDecorator(Decorator borderDecorator) { this.borderDecorator = borderDecorator; } public Decorator getTextDecorator() { return textDecorator; } public void setTextDecorator(Decorator textDecorator) { this.textDecorator = textDecorator; } public Set getAttributableItems() { return null; } public Tree getTree() { return treePane.getTree(); } protected String getLabel(Tree tree, Node node) { if (displayAttribute.equalsIgnoreCase(NAMES)) { Taxon taxon = tree.getTaxon(node); if (taxon != null) { if (textDecorator != null) { textDecorator.setItem(taxon); } return taxon.getName(); } else { String name = (String)node.getAttribute("name"); if (name != null) { return name; } return "unlabelled"; } } if ( tree instanceof RootedTree) { final RootedTree rtree = (RootedTree) tree; if (textDecorator != null) { textDecorator.setItem(node); } if (displayAttribute.equalsIgnoreCase(NODE_AGES) ) { return getNumberFormat().format(rtree.getHeight(node)); } else if (displayAttribute.equalsIgnoreCase(BRANCH_LENGTHS) ) { return getNumberFormat().format(rtree.getLength(node)); } } return formatValue(node.getAttribute(displayAttribute)); } private String formatValue(Object value) { if (value != null) { if (value instanceof Double) { return getNumberFormat().format(value); } else if (value instanceof Object[]) { Object[] values = (Object[])value; if (values.length == 0) return null; if (values.length == 1) return formatValue(values[0]); StringBuilder builder = new StringBuilder("["); builder.append(formatValue(values[0])); for (int i = 1; i < values.length; i++) { builder.append(","); builder.append(formatValue(values[i])); } builder.append("]"); return builder.toString(); } return value.toString(); } return null; } public Rectangle2D calibrate(Graphics2D g2, Node item) { Tree tree = treePane.getTree(); String label = getLabel(tree, item); final Font oldFont = g2.getFont(); if (textDecorator != null) { g2.setFont(textDecorator.getFont(getFont())); } else { g2.setFont(getFont()); } FontMetrics fm = g2.getFontMetrics(); preferredHeight = fm.getHeight(); preferredWidth = 0; if (label != null) { Rectangle2D rect = fm.getStringBounds(label, g2); preferredWidth = rect.getWidth(); } yOffset = (float)fm.getAscent(); g2.setFont(oldFont); return new Rectangle2D.Double(0.0, 0.0, preferredWidth, preferredHeight); } public double getPreferredWidth() { return preferredWidth; } public double getPreferredHeight() { return preferredHeight; } public double getHeightBound() { return preferredHeight + yOffset; } public void paint(Graphics2D g2, Node item, Justification justification, Rectangle2D bounds) { Tree tree = treePane.getTree(); if (TreePane.DEBUG_OUTLINE) { g2.setPaint(Color.red); g2.draw(bounds); } String label = getLabel(tree, item); Font oldFont = g2.getFont(); Paint backgroundPaint = getBackground(); Paint borderPaint = getBorderPaint(); Stroke borderStroke = getBorderStroke(); if (borderDecorator != null) { backgroundPaint = borderDecorator.getPaint(backgroundPaint); borderPaint = borderDecorator.getPaint(borderPaint); borderStroke = borderDecorator.getStroke(borderStroke); } if (backgroundPaint != null) { g2.setPaint(backgroundPaint); g2.fill(bounds); } if (borderPaint != null && borderStroke != null) { g2.setPaint(borderPaint); g2.setStroke(borderStroke); g2.draw(bounds); } if (textDecorator != null) { g2.setPaint(textDecorator.getPaint(getForeground())); g2.setFont(textDecorator.getFont(getFont())); } else { g2.setPaint(getForeground()); g2.setFont(getFont()); } if (label != null) { Rectangle2D rect = null; if (justification == Justification.CENTER || justification == Justification.RIGHT) rect = g2.getFontMetrics().getStringBounds(label, g2); float xOffset; float y = yOffset + (float) bounds.getY(); switch (justification) { case CENTER: xOffset = (float)(-rect.getWidth()/2.0); y = yOffset + (float) rect.getY(); //xOffset = (float) (bounds.getX() + (bounds.getWidth() - rect.getWidth()) / 2.0); break; case FLUSH: case LEFT: xOffset = (float) bounds.getX(); break; case RIGHT: xOffset = (float) (bounds.getX() + bounds.getWidth() - rect.getWidth()); break; default: throw new IllegalArgumentException("Unrecognized alignment enum option"); } g2.drawString(label, xOffset, y); } g2.setFont(oldFont); } public String[] getAttributes() { return attributes; } public String getDisplayAttribute() { return displayAttribute; } public void setDisplayAttribute(String displayAttribute) { this.displayAttribute = displayAttribute; firePainterChanged(); } private double preferredWidth; private double preferredHeight; private float yOffset; protected String displayAttribute; protected String[] attributes; protected TreePane treePane; private Decorator textDecorator = null; private Decorator borderDecorator = null; }figtree-1.4.3/src/figtree/panel/SimpleTreeViewer.java000066400000000000000000000057761277473563300226150ustar00rootroot00000000000000/* * SimpleTreeViewer.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ /* * ExtendedTreeViewer.java * * (c) 2002-2005 BEAST Development Core Team * * This package may be distributed under the * Lesser Gnu Public Licence (LGPL) */ package figtree.panel; import figtree.treeviewer.AnnotationsListener; import figtree.treeviewer.DefaultTreeViewer; import figtree.treeviewer.annotations.AnnotationDefinition; import jam.panels.StatusListener; import jam.panels.StatusProvider; import java.awt.*; import java.util.ArrayList; import java.util.List; /** * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class SimpleTreeViewer extends DefaultTreeViewer implements StatusProvider { /** Creates new AlignmentPanel */ public SimpleTreeViewer() { super(); // setTreesPerPage(1); setBackground(Color.white); } private List listeners = new ArrayList(); public void addAnnotationsListener(AnnotationsListener listener) { listeners.add(listener); } public void fireAnnotationsChanged() { for (AnnotationsListener listener : listeners) { listener.annotationsChanged(); } } private List annotations = null; private final Helper statusHelper = new Helper(); public void addStatusListener(StatusListener statusListener) { statusHelper.addStatusListener(statusListener); } public void removeStatusListener(StatusListener statusListener) { statusHelper.removeStatusListener(statusListener); } public void fireStatusChanged(int status, String statusText) { statusHelper.fireStatusChanged(status, statusText); } public void addOverrideProvider(StatusProvider provider) { statusHelper.addOverrideProvider(provider); } public void removeOverrideProvider(StatusProvider provider) { statusHelper.removeOverrideProvider(provider); } public void fireStatusButtonPressed() { statusHelper.fireStatusButtonPressed(); } public void statusButtonPressed() { statusHelper.statusButtonPressed(); } public int getStatus() { return statusHelper.getStatus(); } public String getStatusText() { return statusHelper.getStatusText(); } public void setStatusText(String statusText) { statusHelper.fireStatusChanged(0, statusText); } }figtree-1.4.3/src/figtree/panel/TreeAppearanceController.java000077500000000000000000000353331277473563300243000ustar00rootroot00000000000000/* * TreeAppearanceController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.panel; import jebl.evolution.trees.SortedRootedTree; import jebl.evolution.trees.Tree; import jebl.evolution.graphs.Node; import figtree.treeviewer.TreeViewer; import figtree.treeviewer.TreeViewerListener; import figtree.treeviewer.painters.LabelPainter; import figtree.treeviewer.decorators.*; import jebl.util.Attributable; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.util.*; import java.text.DecimalFormat; import java.text.NumberFormat; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreeAppearanceController extends AbstractController { private static final String CONTROLLER_TITLE = "Appearance"; private static final String CONTROLLER_KEY = "appearance"; private static final String FOREGROUND_COLOUR_KEY = "foregroundColour"; private static final String BACKGROUND_COLOUR_KEY = "backgroundColour"; private static final String SELECTION_COLOUR_KEY = "selectionColour"; private static final String BRANCH_COLOR_ATTRIBUTE_KEY = "branchColorAttribute"; private static final String BRANCH_LINE_WIDTH_KEY = "branchLineWidth"; // The defaults if there is nothing in the preferences private static Color DEFAULT_FOREGROUND_COLOUR = Color.BLACK; private static Color DEFAULT_BACKGROUND_COLOUR = Color.WHITE; private static Color DEFAULT_SELECTION_COLOUR = new Color(90, 108, 128); private static float DEFAULT_BRANCH_LINE_WIDTH = 1.0f; private static final String FONT_NAME_KEY = "fontName"; private static final String FONT_SIZE_KEY = "fontSize"; private static final String FONT_STYLE_KEY = "fontStyle"; private static final String NUMBER_FORMATTING_KEY = "numberFormatting"; private static final String DISPLAY_ATTRIBUTE_KEY = "displayAttribute"; private static final String SIGNIFICANT_DIGITS_KEY = "significantDigits"; // The defaults if there is nothing in the preferences private static String DEFAULT_FONT_NAME = "sansserif"; private static int DEFAULT_FONT_SIZE = 6; private static int DEFAULT_FONT_STYLE = Font.PLAIN; private static String DEFAULT_NUMBER_FORMATTING = "#.####"; private static String DECIMAL_NUMBER_FORMATTING = "#.####"; private static String SCIENTIFIC_NUMBER_FORMATTING = "0.###E0"; public TreeAppearanceController(final TreeViewer treeViewer, String tipKey, final LabelPainter tipLabelPainter, String nodeKey, final LabelPainter nodeLabelPainter, String branchKey, final LabelPainter branchLabelPainter) { this(treeViewer, tipKey, tipLabelPainter, nodeKey, nodeLabelPainter, branchKey, branchLabelPainter, true, false); } public TreeAppearanceController(final TreeViewer treeViewer, String tipKey, final LabelPainter tipLabelPainter, String nodeKey, final LabelPainter nodeLabelPainter, String branchKey, final LabelPainter branchLabelPainter, boolean hideColouring, boolean ordering) { this.treeViewer = treeViewer; this.hideColouring = hideColouring; final AttributableDecorator branchDecorator = new AttributableDecorator(); branchDecorator.setPaintAttributeName("!color"); branchDecorator.setStrokeAttributeName("!stroke"); treeViewer.setBranchDecorator(branchDecorator, false); int foregroundRGB = DEFAULT_FOREGROUND_COLOUR.getRGB(); int backgroundRGB = DEFAULT_BACKGROUND_COLOUR.getRGB(); int selectionRGB = DEFAULT_SELECTION_COLOUR.getRGB(); float branchLineWidth = DEFAULT_BRANCH_LINE_WIDTH; treeViewer.setForeground(new Color(foregroundRGB)); treeViewer.setBackground(new Color(backgroundRGB)); treeViewer.setSelectionColor(new Color(selectionRGB)); treeViewer.setBranchStroke(new BasicStroke(branchLineWidth, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND)); this.tipKey = tipKey; this.nodeKey = nodeKey; this.branchKey = branchKey; final String defaultFontName = DEFAULT_FONT_NAME; final int defaultFontStyle = DEFAULT_FONT_STYLE; final int defaultFontSize = DEFAULT_FONT_SIZE; final String defaultNumberFormatting = DEFAULT_NUMBER_FORMATTING; tipLabelPainter.setFont(new Font(defaultFontName, defaultFontStyle, defaultFontSize)); tipLabelPainter.setNumberFormat(new DecimalFormat(defaultNumberFormatting)); nodeLabelPainter.setFont(new Font(defaultFontName, defaultFontStyle, defaultFontSize)); nodeLabelPainter.setNumberFormat(new DecimalFormat(defaultNumberFormatting)); branchLabelPainter.setFont(new Font(defaultFontName, defaultFontStyle, defaultFontSize)); branchLabelPainter.setNumberFormat(new DecimalFormat(defaultNumberFormatting)); optionsPanel = new OptionsPanel(); if (!hideColouring) { branchColourAttributeCombo = new JComboBox(new String[] { "No attributes" }); setupAttributes(treeViewer.getTrees()); branchColourAttributeCombo.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent itemEvent) { if (branchColourAttributeCombo.getSelectedIndex() == 0) { treeViewer.setBranchColouringDecorator(null, null); treeViewer.setBranchDecorator(branchDecorator, false); } else { Set nodes = new HashSet(); for (Tree tree : treeViewer.getTrees()) { for (Node node : tree.getNodes()) { nodes.add(node); } } String attribute = (String) branchColourAttributeCombo.getSelectedItem(); if (attribute != null && attribute.length() > 0) { if (attribute.endsWith("*")) { Decorator decorator = new DiscreteColourDecorator(); treeViewer.setBranchColouringDecorator(attribute.substring(0, attribute.length() - 2), decorator); treeViewer.setBranchDecorator(null, false); } else if (DiscreteColourDecorator.isDiscrete(attribute, nodes)) { Decorator decorator = new HSBDiscreteColourDecorator(attribute, nodes); treeViewer.setBranchColouringDecorator(null, null); treeViewer.setBranchDecorator(decorator, false); } else { Decorator decorator = new InterpolatingColourDecorator( new ContinuousScale(attribute, nodes), new Color(192, 16, 0), new Color(0, 16, 192)); treeViewer.setBranchColouringDecorator(null, null); treeViewer.setBranchDecorator(decorator, false); } } } } }); optionsPanel.addComponentWithLabel("Colour by:", branchColourAttributeCombo); } else { branchColourAttributeCombo = null; } branchLineWidthSpinner = new JSpinner(new SpinnerNumberModel(1.0, 0.01, 48.0, 1.0)); branchLineWidthSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { float lineWidth = ((Double) branchLineWidthSpinner.getValue()).floatValue(); treeViewer.setBranchStroke(new BasicStroke(lineWidth, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER)); } }); optionsPanel.addComponentWithLabel("Line Weight:", branchLineWidthSpinner); Font font = tipLabelPainter.getFont(); fontSizeSpinner = new JSpinner(new SpinnerNumberModel(font.getSize(), 0.01, 48, 1)); optionsPanel.addComponentWithLabel("Font Size:", fontSizeSpinner); fontSizeSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final float size = ((Double) fontSizeSpinner.getValue()).floatValue(); Font font = tipLabelPainter.getFont().deriveFont(size); tipLabelPainter.setFont(font); font = nodeLabelPainter.getFont().deriveFont(size); nodeLabelPainter.setFont(font); font = branchLabelPainter.getFont().deriveFont(size); branchLabelPainter.setFont(font); } }); NumberFormat format = tipLabelPainter.getNumberFormat(); int digits = format.getMaximumFractionDigits(); digitsSpinner = new JSpinner(new SpinnerNumberModel(digits, 2, 14, 1)); digitsSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final int digits = (Integer)digitsSpinner.getValue(); NumberFormat format = tipLabelPainter.getNumberFormat(); format.setMaximumFractionDigits(digits); tipLabelPainter.setNumberFormat(format); format = nodeLabelPainter.getNumberFormat(); format.setMaximumFractionDigits(digits); nodeLabelPainter.setNumberFormat(format); format = branchLabelPainter.getNumberFormat(); format.setMaximumFractionDigits(digits); branchLabelPainter.setNumberFormat(format); } }); if (!hideColouring) { treeViewer.addTreeViewerListener(new TreeViewerListener() { public void treeChanged() { setupAttributes(treeViewer.getTrees()); optionsPanel.repaint(); } public void treeSettingsChanged() { // nothing to do } }); } if (ordering) { orderCombo = new JComboBox(new String[]{"Off", SortedRootedTree.BranchOrdering.INCREASING_NODE_DENSITY.toString(), SortedRootedTree.BranchOrdering.DECREASING_NODE_DENSITY.toString()}); orderCombo.setOpaque(false); orderCombo.setSelectedItem(treeViewer.isOrderBranchesOn() ? treeViewer.getBranchOrdering().ordinal() + 1 : 0); orderCombo.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent itemEvent) { if (orderCombo.getSelectedIndex() == 0) { treeViewer.setOrderBranchesOn(false); } else { treeViewer.setOrderBranchesOn(true); treeViewer.setBranchOrdering(SortedRootedTree.BranchOrdering.values()[orderCombo.getSelectedIndex() - 1]); } } }); optionsPanel.addComponentWithLabel("Order:", orderCombo); } else { orderCombo = null; } } private void setupAttributes(Collection trees) { Object selected = branchColourAttributeCombo.getSelectedItem(); branchColourAttributeCombo.removeAllItems(); branchColourAttributeCombo.addItem("User Selection"); if (trees == null) { return; } for (Tree tree : trees) { for (String name : getAttributeNames(tree.getNodes())) { branchColourAttributeCombo.addItem(name); } } branchColourAttributeCombo.setSelectedItem(selected); } private String[] getAttributeNames(Collection items) { Set attributeNames = new TreeSet(); for (Attributable item : items) { for (String name : item.getAttributeNames()) { if (!name.startsWith("!")) { Object attr = item.getAttribute(name); if (!(attr instanceof Object[])) { attributeNames.add(name); } else { boolean isColouring = true; Object[] array = (Object[])attr; boolean isIndex = true; for (Object element : array) { if (isIndex && !(element instanceof Integer) || !isIndex && !(element instanceof Double)) { isColouring = false; break; } isIndex = !isIndex; } if (isIndex) { // a colouring should finish on an index (which means isIndex should be false)... isColouring = false; } if (isColouring) { attributeNames.add(name + " *"); } } } } } String[] attributeNameArray = new String[attributeNames.size()]; attributeNames.toArray(attributeNameArray); return attributeNameArray; } public JComponent getTitleComponent() { return null; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { // These settings don't have controls yet but they will! treeViewer.setForeground((Color)settings.get(CONTROLLER_KEY + "." + FOREGROUND_COLOUR_KEY)); treeViewer.setBackground((Color)settings.get(CONTROLLER_KEY + "." + BACKGROUND_COLOUR_KEY)); treeViewer.setSelectionColor((Color)settings.get(CONTROLLER_KEY + "." + SELECTION_COLOUR_KEY)); if (branchColourAttributeCombo != null) { branchColourAttributeCombo.setSelectedItem(settings.get(CONTROLLER_KEY+"."+BRANCH_COLOR_ATTRIBUTE_KEY)); } branchLineWidthSpinner.setValue((Double)settings.get(CONTROLLER_KEY + "." + BRANCH_LINE_WIDTH_KEY)); fontSizeSpinner.setValue(((Number)settings.get(tipKey+"."+FONT_SIZE_KEY)).doubleValue()); digitsSpinner.setValue((Integer)settings.get(tipKey+"."+SIGNIFICANT_DIGITS_KEY)); } public void getSettings(Map settings) { settings.put(CONTROLLER_KEY + "." + FOREGROUND_COLOUR_KEY, treeViewer.getForeground()); settings.put(CONTROLLER_KEY + "." + BACKGROUND_COLOUR_KEY, treeViewer.getBackground()); settings.put(CONTROLLER_KEY + "." + SELECTION_COLOUR_KEY, treeViewer.getSelectionPaint()); if (branchColourAttributeCombo != null) { settings.put(CONTROLLER_KEY + "." + BRANCH_COLOR_ATTRIBUTE_KEY, branchColourAttributeCombo.getSelectedItem().toString()); } settings.put(CONTROLLER_KEY + "." + BRANCH_LINE_WIDTH_KEY, branchLineWidthSpinner.getValue()); settings.put(tipKey+"."+FONT_SIZE_KEY, fontSizeSpinner.getValue()); settings.put(tipKey+"."+SIGNIFICANT_DIGITS_KEY, digitsSpinner.getValue()); } private final OptionsPanel optionsPanel; private final JComboBox branchColourAttributeCombo; private final JSpinner branchLineWidthSpinner; private final JSpinner fontSizeSpinner; private final JSpinner digitsSpinner; private final JComboBox orderCombo; private final TreeViewer treeViewer; private final String tipKey; private final String nodeKey; private final String branchKey; private final boolean hideColouring; }figtree-1.4.3/src/figtree/panel/TreeColouringController.java000077500000000000000000000140501277473563300241730ustar00rootroot00000000000000/* * TreeColouringController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.panel; import jebl.evolution.trees.Tree; import jebl.evolution.graphs.Node; import figtree.treeviewer.TreeViewer; import figtree.treeviewer.TreeViewerListener; import figtree.treeviewer.decorators.*; import jebl.util.Attributable; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import java.awt.*; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.util.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreeColouringController extends AbstractController { private static final String CONTROLLER_KEY = "appearance"; private static final String BRANCH_COLOR_ATTRIBUTE_KEY = "branchColorAttribute"; public TreeColouringController(final TreeViewer treeViewer) { this(treeViewer, "Colour by:"); } public TreeColouringController(final TreeViewer treeViewer, String label) { final AttributableDecorator branchDecorator = new AttributableDecorator(); branchDecorator.setPaintAttributeName("!color"); branchDecorator.setStrokeAttributeName("!stroke"); treeViewer.setBranchDecorator(branchDecorator, false); optionsPanel = new OptionsPanel(); branchColourAttributeCombo = new JComboBox(new String[] { "No attributes" }); setupAttributes(treeViewer.getTrees()); branchColourAttributeCombo.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent itemEvent) { Set nodes = new HashSet(); for (Tree tree : treeViewer.getTrees()) { for (Node node : tree.getNodes()) { nodes.add(node); } } String attribute = (String) branchColourAttributeCombo.getSelectedItem(); if (attribute != null && attribute.length() > 0) { if (attribute.endsWith("*")) { Decorator decorator = new DiscreteColourDecorator(); treeViewer.setBranchColouringDecorator(attribute.substring(0, attribute.length() - 2), decorator); treeViewer.setBranchDecorator(null, false); } else if (DiscreteColourDecorator.isDiscrete(attribute, nodes)) { Decorator decorator = new HSBDiscreteColourDecorator(attribute, nodes); treeViewer.setBranchColouringDecorator(null, null); treeViewer.setBranchDecorator(decorator, false); } else { Decorator decorator = new InterpolatingColourDecorator( new ContinuousScale(attribute, nodes), new Color(192, 16, 0), new Color(0, 16, 192)); treeViewer.setBranchColouringDecorator(null, null); treeViewer.setBranchDecorator(decorator, false); } } } }); optionsPanel.addComponentWithLabel(label, branchColourAttributeCombo); treeViewer.addTreeViewerListener(new TreeViewerListener() { public void treeChanged() { setupAttributes(treeViewer.getTrees()); optionsPanel.repaint(); } public void treeSettingsChanged() { // nothing to do } }); } private void setupAttributes(Collection trees) { Object selected = branchColourAttributeCombo.getSelectedItem(); branchColourAttributeCombo.removeAllItems(); //branchColourAttributeCombo.addItem("User Selection"); if (trees == null) { return; } for (Tree tree : trees) { for (String name : getAttributeNames(tree.getNodes())) { branchColourAttributeCombo.addItem(name); } } branchColourAttributeCombo.setSelectedItem(selected); } private String[] getAttributeNames(Collection items) { Set attributeNames = new TreeSet(); for (Attributable item : items) { for (String name : item.getAttributeNames()) { if (!name.startsWith("!")) { Object attr = item.getAttribute(name); if (!(attr instanceof Object[])) { attributeNames.add(name); } else { boolean isColouring = true; Object[] array = (Object[])attr; boolean isIndex = true; for (Object element : array) { if (isIndex && !(element instanceof Integer) || !isIndex && !(element instanceof Double)) { isColouring = false; break; } isIndex = !isIndex; } if (isIndex) { // a colouring should finish on an index (which means isIndex should be false)... isColouring = false; } if (isColouring) { attributeNames.add(name + " *"); } } } } } String[] attributeNameArray = new String[attributeNames.size()]; attributeNames.toArray(attributeNameArray); return attributeNameArray; } public JComponent getTitleComponent() { return null; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { branchColourAttributeCombo.setSelectedItem(settings.get(CONTROLLER_KEY+"."+BRANCH_COLOR_ATTRIBUTE_KEY)); } public void getSettings(Map settings) { if (branchColourAttributeCombo.getSelectedItem() != null) { settings.put(CONTROLLER_KEY + "." + BRANCH_COLOR_ATTRIBUTE_KEY, branchColourAttributeCombo.getSelectedItem().toString()); } else { settings.put(CONTROLLER_KEY + "." + BRANCH_COLOR_ATTRIBUTE_KEY, "none"); } } private final OptionsPanel optionsPanel; private final JComboBox branchColourAttributeCombo; }figtree-1.4.3/src/figtree/panel/TreeLayoutController.java000077500000000000000000000056371277473563300235220ustar00rootroot00000000000000/* * TreeLayoutController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.panel; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.Map; import figtree.treeviewer.treelayouts.RectilinearTreeLayout; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreeLayoutController extends AbstractController { private static final String RECTILINEAR_LAYOUT_KEY = "rectilinearLayout"; private static final String ALIGN_TIP_LABELS_KEY = "alignTipLabels"; public TreeLayoutController(final RectilinearTreeLayout treeLayout) { titleLabel = new JLabel("Rectangular Layout"); optionsPanel = new OptionsPanel(); alignTipLabelsCheck = new JCheckBox("Align Tip Labels"); alignTipLabelsCheck.setOpaque(false); alignTipLabelsCheck.setSelected(treeLayout.isAlignTipLabels()); alignTipLabelsCheck.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { treeLayout.setAlignTipLabels(alignTipLabelsCheck.isSelected()); } }); optionsPanel.addComponent(alignTipLabelsCheck); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { alignTipLabelsCheck.setSelected((Boolean) settings.get(RECTILINEAR_LAYOUT_KEY + "." + ALIGN_TIP_LABELS_KEY)); } public void getSettings(Map settings) { settings.put(RECTILINEAR_LAYOUT_KEY + "." + ALIGN_TIP_LABELS_KEY, alignTipLabelsCheck.isSelected()); } private final JLabel titleLabel; private final OptionsPanel optionsPanel; private final JCheckBox alignTipLabelsCheck; }figtree-1.4.3/src/figtree/panel/TreeViewerController.java000077500000000000000000000210441277473563300234740ustar00rootroot00000000000000/* * TreeViewerController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.panel; import figtree.treeviewer.treelayouts.*; import figtree.treeviewer.TreeViewer; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.util.Map; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreeViewerController extends AbstractController { private static final String CONTROLLER_TITLE = "Layout"; private static final String CONTROLLER_KEY = "layout"; private static final String ZOOM_KEY = "zoom"; private static final String EXPANSION_KEY = "expansion"; // The defaults if there is nothing in the preferences private final static int MAX_ZOOM_SLIDER = 10000; private final static int DELTA_ZOOM_SLIDER = 200; public TreeViewerController(final TreeViewer treeViewer) { this(treeViewer, false); } public TreeViewerController(final TreeViewer treeViewer, boolean hideZoom) { this.treeViewer = treeViewer; this.hideZoom = hideZoom; titleLabel = new JLabel(CONTROLLER_TITLE); optionsPanel = new OptionsPanel(); rectilinearTreeLayout = new RectilinearTreeLayout(); treeLayoutController = new TreeLayoutController(rectilinearTreeLayout); if (!hideZoom) { zoomSlider = new JSlider(SwingConstants.HORIZONTAL, 0, MAX_ZOOM_SLIDER, 0); zoomSlider.setOpaque(false); zoomSlider.setAlignmentX(Component.LEFT_ALIGNMENT); // zoomSlider.setPaintTicks(true); // zoomSlider.setPaintLabels(true); zoomSlider.setValue(0); zoomSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final int value = zoomSlider.getValue(); treeViewer.setZoom(((double) value) / MAX_ZOOM_SLIDER); } }); optionsPanel.addComponentWithLabel("Zoom:", zoomSlider, true); } verticalExpansionSlider = new JSlider(SwingConstants.HORIZONTAL, 0, MAX_ZOOM_SLIDER, 0); verticalExpansionSlider.setOpaque(false); // verticalExpansionSlider.setPaintTicks(true); // verticalExpansionSlider.setPaintLabels(true); verticalExpansionSlider.setValue(0); verticalExpansionSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final int value = verticalExpansionSlider.getValue(); treeViewer.setVerticalExpansion(((double) value) / MAX_ZOOM_SLIDER); } }); verticalExpansionLabel = new JLabel("Expansion:"); optionsPanel.addComponents(verticalExpansionLabel, false, verticalExpansionSlider, true); layoutPanel = new JPanel(new BorderLayout()); layoutPanel.setOpaque(false); setTreeLayout(); setExpansion(); optionsPanel.addSpanningComponent(layoutPanel); // Set some InputMaps and ActionMaps for key strokes. The ActionMaps are set in setExpansion() // because they differ by whether vertical expansion is allowed for the current layout. // The key strokes could be obtained from preferences and set in a preference dialog box optionsPanel.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke.getKeyStroke("meta 0"), "resetZoom"); optionsPanel.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke.getKeyStroke("meta EQUALS"), "increasePrimaryZoom"); optionsPanel.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke.getKeyStroke("meta MINUS"), "decreasePrimaryZoom"); optionsPanel.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke.getKeyStroke("meta alt EQUALS"), "increaseSecondaryZoom"); optionsPanel.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke.getKeyStroke("meta alt MINUS"), "decreaseSecondaryZoom"); optionsPanel.getActionMap().put("resetZoom", resetZoomAction); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return true; } public void setColouringAttributeName(String attributeName) { rectilinearTreeLayout.setBranchColouringAttributeName(attributeName); } public void initialize() { // nothing to do } public void setSettings(Map settings) { if (!hideZoom) { zoomSlider.setValue((Integer)settings.get(CONTROLLER_KEY + "." + ZOOM_KEY)); } verticalExpansionSlider.setValue((Integer)settings.get(CONTROLLER_KEY + "." + EXPANSION_KEY)); // These controllers are internal to TreeViewerController so settings must be done here treeLayoutController.setSettings(settings); } public void getSettings(Map settings) { if (!hideZoom) { settings.put(CONTROLLER_KEY + "." + ZOOM_KEY, zoomSlider.getValue()); } settings.put(CONTROLLER_KEY + "." + EXPANSION_KEY, verticalExpansionSlider.getValue()); // These controllers are internal to TreeViewerController so settings must be done here treeLayoutController.getSettings(settings); } private void setTreeLayout() { treeViewer.setTreeLayout(rectilinearTreeLayout); setExpansion(); layoutPanel.removeAll(); layoutPanel.add(treeLayoutController.getPanel(), BorderLayout.CENTER); fireControllerChanged(); } private void setExpansion() { if (treeViewer.verticalExpansionAllowed()) { verticalExpansionLabel.setEnabled(true); verticalExpansionSlider.setEnabled(true); optionsPanel.getActionMap().put("increasePrimaryZoom", increaseVerticalExpansionAction); optionsPanel.getActionMap().put("decreasePrimaryZoom", decreaseVerticalExpansionAction); optionsPanel.getActionMap().put("increaseSecondaryZoom", increaseZoomAction); optionsPanel.getActionMap().put("decreaseSecondaryZoom", decreaseZoomAction); } else { verticalExpansionLabel.setEnabled(false); verticalExpansionSlider.setEnabled(false); optionsPanel.getActionMap().put("increasePrimaryZoom", increaseZoomAction); optionsPanel.getActionMap().put("decreasePrimaryZoom", decreaseZoomAction); optionsPanel.getActionMap().put("increaseSecondaryZoom", increaseZoomAction); optionsPanel.getActionMap().put("decreaseSecondaryZoom", decreaseZoomAction); } } private Action resetZoomAction = new AbstractAction("Reset Zoom") { public void actionPerformed(ActionEvent actionEvent) { zoomSlider.setValue(0); verticalExpansionSlider.setValue(0); } }; private Action increaseZoomAction = new AbstractAction("Zoom In") { public void actionPerformed(ActionEvent actionEvent) { zoomSlider.setValue(zoomSlider.getValue() + DELTA_ZOOM_SLIDER); } }; private Action decreaseZoomAction = new AbstractAction("Zoom In") { public void actionPerformed(ActionEvent actionEvent) { zoomSlider.setValue(zoomSlider.getValue() - DELTA_ZOOM_SLIDER); } }; private Action increaseVerticalExpansionAction = new AbstractAction("Expand Vertically") { public void actionPerformed(ActionEvent actionEvent) { verticalExpansionSlider.setValue(verticalExpansionSlider.getValue() + DELTA_ZOOM_SLIDER); } }; private Action decreaseVerticalExpansionAction = new AbstractAction("Unexpand Vertically") { public void actionPerformed(ActionEvent actionEvent) { int value = verticalExpansionSlider.getValue(); if (value > 0) { verticalExpansionSlider.setValue(value - DELTA_ZOOM_SLIDER); } else { // If the vertical expansion was zero then assume the user is trying to un-zoom zoomSlider.setValue(zoomSlider.getValue() - DELTA_ZOOM_SLIDER); } } }; private JSlider zoomSlider; private JSlider verticalExpansionSlider; private JLabel verticalExpansionLabel; private final JPanel layoutPanel; private final JLabel titleLabel; private final OptionsPanel optionsPanel; private final RectilinearTreeLayout rectilinearTreeLayout; private final TreeLayoutController treeLayoutController; private final TreeViewer treeViewer; private final boolean hideZoom; }figtree-1.4.3/src/figtree/panel/TreesController.java000077500000000000000000000175131277473563300225030ustar00rootroot00000000000000/* * TreesController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.panel; import jebl.evolution.trees.SortedRootedTree; import jebl.evolution.trees.TransformedRootedTree; import figtree.treeviewer.*; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.util.Map; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreesController extends AbstractController { private static final String CONTROLLER_TITLE = "Trees"; private static final String CONTROLLER_KEY = "trees"; private static final String TRANSFORM_KEY = "transform"; private static final String TRANSFORM_TYPE_KEY = "transformType"; private static final String ORDER_KEY = "order"; private static final String ORDER_TYPE_KEY = "orderType"; private static final String ROOTING_KEY = "rooting"; private static final String ROOTING_TYPE_KEY = "rootingType"; public TreesController(final TreeViewer treeViewer) { this(treeViewer, true, true, true); } public TreesController(final TreeViewer treeViewer, final boolean rooting, final boolean ordering, final boolean transforming) { this.treeViewer = treeViewer; titleLabel = new JLabel(CONTROLLER_TITLE); optionsPanel = new OptionsPanel(); if (rooting) { rootingCheck = new JCheckBox("Midpoint root"); rootingCheck.setOpaque(false); optionsPanel.addComponent(rootingCheck); rootingCheck.setSelected(treeViewer.isRootingOn()); rootingCheck.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { if (rootingCheck.isSelected()) { treeViewer.setRootingOn(true); treeViewer.setRootingType(TreePane.RootingType.MID_POINT); } else { treeViewer.setRootingOn(false); treeViewer.setRootingType(TreePane.RootingType.USER_ROOTING); } } }); } else { rootingCheck = null; } if (ordering) { orderCombo = new JComboBox(new String[]{"Off", SortedRootedTree.BranchOrdering.INCREASING_NODE_DENSITY.toString(), SortedRootedTree.BranchOrdering.DECREASING_NODE_DENSITY.toString()}); orderCombo.setOpaque(false); orderCombo.setSelectedItem(treeViewer.isOrderBranchesOn() ? treeViewer.getBranchOrdering().ordinal() + 1 : 0); orderCombo.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent itemEvent) { if (orderCombo.getSelectedIndex() == 0) { treeViewer.setOrderBranchesOn(false); } else { treeViewer.setOrderBranchesOn(true); treeViewer.setBranchOrdering(SortedRootedTree.BranchOrdering.values()[orderCombo.getSelectedIndex() - 1]); } } }); optionsPanel.addComponentWithLabel("Order:", orderCombo); } else { orderCombo = null; } if (transforming) { transformCombo = new JComboBox(new String[]{"Off", TransformedRootedTree.Transform.CLADOGRAM.toString(), TransformedRootedTree.Transform.PROPORTIONAL.toString(), TransformedRootedTree.Transform.EQUAL_LENGTHS.toString()}); transformCombo.setOpaque(false); transformCombo.setSelectedItem(treeViewer.isOrderBranchesOn() ? treeViewer.getBranchTransform().ordinal() + 1 : 0); transformCombo.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent itemEvent) { if (transformCombo.getSelectedIndex() == 0) { treeViewer.setTransformBranchesOn(false); } else { treeViewer.setTransformBranchesOn(true); treeViewer.setBranchTransform(TransformedRootedTree.Transform.values()[transformCombo.getSelectedIndex() - 1]); } } }); optionsPanel.addComponentWithLabel("Transform:", transformCombo); } else { transformCombo = null; } } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { } public void setSettings(Map settings) { if (((Boolean)settings.get(CONTROLLER_KEY + "." + TRANSFORM_KEY))) { String transformName = (String)settings.get(CONTROLLER_KEY + "." + TRANSFORM_TYPE_KEY); int i = 0; for (TransformedRootedTree.Transform transform : TransformedRootedTree.Transform.values()) { if (transform.toString().equalsIgnoreCase(transformName)) { transformCombo.setSelectedIndex(i); } i++; } } else { transformCombo.setSelectedIndex(0); } if (((Boolean)settings.get(CONTROLLER_KEY + "." + ORDER_KEY))) { String orderName = (String)settings.get(CONTROLLER_KEY + "." + ORDER_TYPE_KEY); int i = 0; for (SortedRootedTree.BranchOrdering order : SortedRootedTree.BranchOrdering.values()) { if (order.toString().equalsIgnoreCase(orderName)) { orderCombo.setSelectedIndex(i); } i++; } } else { orderCombo.setSelectedIndex(0); } rootingCheck.setSelected((Boolean) settings.get(CONTROLLER_KEY + "." + ROOTING_KEY)); } public void getSettings(Map settings) { settings.put(CONTROLLER_KEY + "." + TRANSFORM_KEY, false); settings.put(CONTROLLER_KEY + "." + TRANSFORM_TYPE_KEY, transformCombo.getSelectedItem().toString()); settings.put(CONTROLLER_KEY + "." + ORDER_KEY, false); settings.put(CONTROLLER_KEY + "." + ORDER_TYPE_KEY, orderCombo.getSelectedItem().toString()); settings.put(CONTROLLER_KEY + "." + ROOTING_KEY, rootingCheck.isSelected()); settings.put(CONTROLLER_KEY + "." + ROOTING_TYPE_KEY, TreePane.RootingType.MID_POINT.toString()); } private final JLabel titleLabel; private final OptionsPanel optionsPanel; private final JComboBox transformCombo; private final JComboBox orderCombo; private final JCheckBox rootingCheck; private final TreeViewer treeViewer; } figtree-1.4.3/src/figtree/treeviewer/000077500000000000000000000000001277473563300175625ustar00rootroot00000000000000figtree-1.4.3/src/figtree/treeviewer/AnnotationsController.java000077500000000000000000000055201277473563300247730ustar00rootroot00000000000000/* * AnnotationsController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.TreePane; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import figtree.treeviewer.annotations.AnnotationDefinition; import javax.swing.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.util.Map; /** * * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class AnnotationsController extends AbstractController { public AnnotationsController(final TreePane treePane) { this.treePane = treePane; titleLabel = new JLabel("Annotations"); optionsPanel = new ControllerOptionsPanel(2, 2); final JComboBox combo2 = new JComboBox(); combo2.addItem("None"); // for (AnnotationDefinition annotation : treeViewer.getAnnotationDefinitions()) { // combo2.addItem(annotation); // } combo2.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { Object item = combo2.getSelectedItem(); if (item instanceof AnnotationDefinition) { // treePane.setBranchDecorator(new AnnotationBranchDecorator((AnnotationDefinition)item)); } else { treePane.setBranchDecorator(null, false); } } }); optionsPanel.addComponentWithLabel("Node Colours:", combo2); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return true; } public void initialize() { // nothing to do } public void setSettings(Map settings) { } public void getSettings(Map settings) { } private final JLabel titleLabel; private final OptionsPanel optionsPanel; private final TreePane treePane; } figtree-1.4.3/src/figtree/treeviewer/AnnotationsListener.java000077500000000000000000000020171277473563300244330ustar00rootroot00000000000000/* * AnnotationsListener.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface AnnotationsListener { void annotationsChanged(); } figtree-1.4.3/src/figtree/treeviewer/AttributeColourController.java000077500000000000000000000347121277473563300256320ustar00rootroot00000000000000/* * AttributeColourController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.decorators.*; import jam.controlpalettes.AbstractController; import jebl.evolution.graphs.Node; import jebl.evolution.trees.Tree; import jebl.util.Attributable; import javax.swing.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.util.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class AttributeColourController extends AbstractController { public static final String CONTROLLER_KEY = "colour"; public static final String SCHEME_KEY = "scheme"; public static final String ORDER_KEY = "order"; public AttributeColourController(final TreeViewer treeViewer, final JFrame frame) { this.treeViewer = treeViewer; this.frame = frame; } public void setupControls( final JComboBox colourAttributeCombo, final JButton colourSetupButton) { if (colourSetupButton != null) { colourSetupButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { ColourDecorator decorator = null; if (colourAttributeCombo.getSelectedIndex() > 0) { String attribute = (String) colourAttributeCombo.getSelectedItem(); decorator = getDecoratorForAttribute(attribute); } if (decorator == null) { return; } boolean update = false; if (decorator instanceof DiscreteColourDecorator) { if (discreteColourScaleDialog == null) { discreteColourScaleDialog = new DiscreteColourScaleDialog(frame); } discreteColourScaleDialog.setDecorator((DiscreteColourDecorator)decorator); int result = discreteColourScaleDialog.showDialog(); if (result != JOptionPane.CANCEL_OPTION && result != JOptionPane.CLOSED_OPTION) { decorator = discreteColourScaleDialog.getDecorator(); String attribute = (String) colourAttributeCombo.getSelectedItem(); setDecoratorForAttribute(attribute, decorator); update = true; } } else if (decorator instanceof ContinuousColourDecorator) { if (continuousColourScaleDialog == null) { continuousColourScaleDialog = new ContinuousColourScaleDialog(frame); } continuousColourScaleDialog.setDecorator((ContinuousColourDecorator)decorator); int result = continuousColourScaleDialog.showDialog(); if (result != JOptionPane.CANCEL_OPTION && result != JOptionPane.CLOSED_OPTION) { decorator = continuousColourScaleDialog.getDecorator(); String attribute = (String) colourAttributeCombo.getSelectedItem(); setDecoratorForAttribute(attribute, decorator); update = true; } } else { throw new IllegalArgumentException("Unsupported decorator type"); } if (update) { if (colourAttributeCombo.getSelectedIndex() > 0) { String attribute = (String) colourAttributeCombo.getSelectedItem(); setDecoratorForAttribute(attribute, decorator); } fireControllerChanged(); } } }); colourAttributeCombo.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent itemEvent) { colourSetupButton.setEnabled(colourAttributeCombo.getSelectedIndex() > 0); } }); colourSetupButton.setEnabled(colourAttributeCombo.getSelectedIndex() > 0); } // I don't think this is required and it throws up many, many events (i.e., every time // an attribute is added to the combo. // colourAttributeCombo.addActionListener(new ActionListener() { // public void actionPerformed(ActionEvent event) { // fireControllerChanged(); // } // }); } public Decorator getColourDecorator(JComboBox colourAttributeCombo, Decorator defaultDecorator) { Decorator decorator = defaultDecorator; if (defaultDecorator == null || colourAttributeCombo.getSelectedIndex() > 0) { String attribute = (String) colourAttributeCombo.getSelectedItem(); if (attribute != null && attribute.length() > 0) { decorator = getDecoratorForAttribute(attribute); } } return decorator; } public ColourDecorator getDecoratorForAttribute(String attribute) { ColourDecorator colourDecorator = attributeDecoratorMap.get(attribute); Set items = new HashSet(); for (Tree tree : treeViewer.getTrees()) { for (Node node : tree.getNodes()) { if (node.getAttribute(attribute) != null) { items.add(node); } if (tree.getTaxon(node) != null) { items.add(tree.getTaxon(node)); } } } // if (colourDecorator == null) { if (attribute.endsWith("*")) { // todo reinstate branch colouring return null; } else if (DiscreteColourDecorator.isDiscrete(attribute, items)) { colourDecorator = new HSBDiscreteColourDecorator(attribute, items); } else { ContinuousScale scale = attributeScaleMap.get(attribute); if (scale == null) { scale = new ContinuousScale(); attributeScaleMap.put(attribute, scale); } scale.setAttributes(attribute, items); colourDecorator = new HSBContinuousColourDecorator(scale); } } else if (colourDecorator instanceof DiscreteColourDecorator) { ((DiscreteColourDecorator)colourDecorator).setAttributes(attribute, items); } else if (colourDecorator instanceof ContinuousColourDecorator) { ((ContinuousColourDecorator)colourDecorator).setAttributes(attribute, items); } return colourDecorator; } private void setDecoratorForAttribute(String attribute, ColourDecorator decorator) { attributeDecoratorMap.put(attribute, decorator); } @Override public JComponent getTitleComponent() { return null; } @Override public JPanel getPanel() { return null; } @Override public boolean isInitiallyVisible() { return false; } @Override public void initialize() { } @Override public void setSettings(Map settings) { for (String key : settings.keySet()) { if (key.trim().startsWith(CONTROLLER_KEY + "." + SCHEME_KEY)) { String value = (String)settings.get(key); if (value != null) { String[] parts = value.split(":"); if (parts.length == 2) { String attribute = parts[0]; ColourDecorator decorator = getDecoratorForAttribute(attribute); String colourSettings = parts[1]; if (colourSettings.startsWith("HSBDiscrete")) { String settingsString = colourSettings.substring("HSBDiscrete".length()); if (decorator == null || !(decorator instanceof HSBDiscreteColourDecorator)) { decorator = new HSBDiscreteColourDecorator(attribute, settingsString); } else { decorator.setup(settingsString); } } else if (colourSettings.startsWith("FixedDiscrete")) { String settingsString = colourSettings.substring("FixedDiscrete".length()); if (decorator == null || !(decorator instanceof FixedDiscreteColourDecorator)) { decorator = new FixedDiscreteColourDecorator(attribute, settingsString); } else { decorator.setup(settingsString); } } else if (colourSettings.startsWith("HSBContinuous")) { String settingsString = colourSettings.substring("HSBContinuous".length()); if (decorator == null || !(decorator instanceof HSBDiscreteColourDecorator)) { decorator = new HSBContinuousColourDecorator(attribute, settingsString); } else { decorator.setup(settingsString); } } else if (colourSettings.startsWith("InterpolatingContinuous")) { String settingsString = colourSettings.substring("InterpolatingContinuous".length()); if (decorator == null || !(decorator instanceof InterpolatingColourDecorator)) { decorator = new InterpolatingColourDecorator(attribute, settingsString); } else { decorator.setup(settingsString); } } else { // throw new IllegalArgumentException("Unrecognized colour decorator type"); } setDecoratorForAttribute(attribute, decorator); } } } else if (key.trim().startsWith(CONTROLLER_KEY + "." + ORDER_KEY)) { String value = (String)settings.get(key); if (value != null) { String[] parts = value.split(":"); if (parts.length == 2) { String attribute = parts[0]; Object[] values = parts[1].split(","); ColourDecorator decorator = getDecoratorForAttribute(attribute); if (decorator != null && decorator instanceof DiscreteColourDecorator) { ((DiscreteColourDecorator)decorator).setValuesOrder(Arrays.asList(values)); setDecoratorForAttribute(attribute, decorator); } } } } } } @Override public void getSettings(Map settings) { for (String attribute : attributeDecoratorMap.keySet()) { ColourDecorator decorator = attributeDecoratorMap.get(attribute); String colourSettings = decorator.toString(); String name = ""; if (decorator instanceof HSBDiscreteColourDecorator) { name = "HSBDiscrete"; } else if (decorator instanceof FixedDiscreteColourDecorator) { name = "FixedDiscrete"; } else if (decorator instanceof HSBContinuousColourDecorator) { name = "HSBContinuous"; } else if (decorator instanceof InterpolatingColourDecorator) { name = "InterpolatingContinuous"; } else { throw new IllegalArgumentException("Unrecognized colour decorator type"); } settings.put(CONTROLLER_KEY + "." + SCHEME_KEY + "." + flattenName(attribute), attribute + ":" + name + colourSettings); if (decorator instanceof DiscreteColourDecorator) { if (((DiscreteColourDecorator)decorator).hasReorderedValues()) { String orderString = ((DiscreteColourDecorator)decorator).getOrderString(); settings.put(CONTROLLER_KEY + "." + ORDER_KEY + "." + flattenName(attribute), attribute + ":" + orderString); } } } } private String flattenName(String name) { String flattened = name.trim().toLowerCase(); flattened.replaceAll(" ", "_"); flattened.replaceAll("\t", "_"); flattened.replaceAll("\r", "_"); return flattened; } private final TreeViewer treeViewer; private final JFrame frame; private Map attributeDecoratorMap = new HashMap(); private Map attributeScaleMap = new HashMap(); // private List attributeNames = new ArrayList(); // private boolean editingComboBox = false; private ContinuousColourScaleDialog continuousColourScaleDialog = null; private DiscreteColourScaleDialog discreteColourScaleDialog = null; // // an internal listener interface // private interface Listener { // void attributesChanged(); // } // // private void addListener(Listener listener) { // listeners.add(listener); // } // // private void fireAttributesChanged() { // for (Listener listener : listeners) { // listener.attributesChanged(); // } // // } // private final List listeners = new ArrayList(); } figtree-1.4.3/src/figtree/treeviewer/ContinuousColourScaleDialog.java000077500000000000000000000401421277473563300260530ustar00rootroot00000000000000/* * ContinuousColourScaleDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.decorators.ContinuousColourDecorator; import figtree.treeviewer.decorators.ContinuousScale; import figtree.treeviewer.decorators.HSBContinuousColourDecorator; import figtree.treeviewer.decorators.InterpolatingColourDecorator; import figtree.ui.components.ColorWellButton; import figtree.ui.components.RangeSlider; import figtree.ui.components.RealNumberField; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; import javax.swing.border.EtchedBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.HashMap; import java.util.Map; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ContinuousColourScaleDialog { private static final int SLIDER_RANGE = 1000; private static final String HSB_SPECTRUM = "HSB Spectrum"; private static final String COLOUR_GRADIENT = "Colour Gradient"; private JFrame frame; private JComboBox colourSchemeCombo = new JComboBox(new String[] { HSB_SPECTRUM, COLOUR_GRADIENT} ); CardLayout cardLayout = new CardLayout(); private final JPanel colourSchemePanel; private Map colourSchemeNamePanelMap = new HashMap(); private Map colourSchemeClassNameMap = new HashMap(); private ContinuousColourDecorator decorator; private JComponent colourDisplay; private final JCheckBox autoScaleCheck; private final JLabel fromLabel; private final RealNumberField fromNumberField; private final JLabel toLabel; private final RealNumberField toNumberField; private JDialog dialog; public ContinuousColourScaleDialog(final JFrame frame) { this.frame = frame; colourSchemeNamePanelMap.put(HSB_SPECTRUM, new HSBColourSchemePanel()); colourSchemeNamePanelMap.put(COLOUR_GRADIENT, new InterpolatingColourSchemePanel()); colourSchemeClassNameMap.put(HSBContinuousColourDecorator.class, HSB_SPECTRUM); colourSchemeClassNameMap.put(InterpolatingColourDecorator.class, COLOUR_GRADIENT); autoScaleCheck = new JCheckBox("Auto-scale range between min and max values"); fromLabel = new JLabel("Range from:"); fromNumberField = new RealNumberField(); fromNumberField.setColumns(10); toLabel = new JLabel("to:"); toNumberField = new RealNumberField(); toNumberField.setColumns(10); autoScaleCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { boolean enabled = !autoScaleCheck.isSelected(); fromLabel.setEnabled(enabled); fromNumberField.setEnabled(enabled); toLabel.setEnabled(enabled); toNumberField.setEnabled(enabled); } }); colourSchemePanel = new JPanel(cardLayout); for (String name : colourSchemeNamePanelMap.keySet()) { ColourSchemePanel panel = colourSchemeNamePanelMap.get(name); colourSchemePanel.add(panel.getPanel(), name); } colourSchemeCombo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { cardLayout.show(colourSchemePanel, colourSchemeCombo.getSelectedItem().toString()); decorator = colourSchemeNamePanelMap.get(colourSchemeCombo.getSelectedItem()).getDecorator(); colourDisplay.repaint(); dialog.pack(); } }); colourDisplay = new JComponent() { private final static int MAX_HEIGHT = 20; @Override public void paint(Graphics graphics) { ContinuousColourDecorator decorator = getDecorator(); Graphics2D g = (Graphics2D)graphics; Rectangle r = getVisibleRect(); int width = r.width; r.width = 1; ContinuousScale scale = decorator.getContinuousScale(); double v = scale.getMinValue(); double d = (scale.getMaxValue() - v) / width; for (int i = 0; i < width; i ++) { g.setColor(decorator.getColourForValue(v)); g.fill(r); r.x ++; v += d; } } @Override public Dimension getPreferredSize() { return new Dimension(super.getPreferredSize().width, MAX_HEIGHT); } }; } public int showDialog() { ContinuousColourDecorator currentDecorator = getDecorator(); final OptionsPanel options = new OptionsPanel(6, 6); JPanel panel5 = new JPanel(new BorderLayout()); panel5.add(colourDisplay, BorderLayout.CENTER); panel5.setBorder(BorderFactory.createLineBorder(Color.black, 1)); options.addSpanningComponent(panel5); options.addComponent(autoScaleCheck); JPanel panel4 = new JPanel(); panel4.setLayout(new FlowLayout()); panel4.add(fromLabel); panel4.add(fromNumberField); panel4.add(toLabel); panel4.add(toNumberField); options.addComponent(panel4); options.addComponentWithLabel("Scheme: ", colourSchemeCombo); colourSchemePanel.setBorder(BorderFactory.createBevelBorder(1)); options.addSpanningComponent(colourSchemePanel); JOptionPane optionPane = new JOptionPane(options, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); dialog = optionPane.createDialog(frame, "Setup colour range: " + currentDecorator.getAttributeName()); colourSchemeCombo.setSelectedItem(colourSchemeClassNameMap.get(decorator.getClass())); dialog.pack(); dialog.setResizable(false); dialog.setVisible(true); int result = JOptionPane.CANCEL_OPTION; Integer value = (Integer)optionPane.getValue(); if (value != null && value.intValue() != -1) { result = value.intValue(); } return result; } public void setDecorator(ContinuousColourDecorator decorator) { this.decorator = decorator; autoScaleCheck.setSelected(!decorator.getContinuousScale().isNormalize()); fromNumberField.setValue(decorator.getContinuousScale().getLowerRange()); toNumberField.setValue(decorator.getContinuousScale().getUpperRange()); for (String key : colourSchemeNamePanelMap.keySet()) { colourSchemeNamePanelMap.get(key).setDecorator(decorator); } } public ContinuousColourDecorator getDecorator() { String name = colourSchemeCombo.getSelectedItem().toString(); decorator = colourSchemeNamePanelMap.get(name).getDecorator(); decorator.getContinuousScale().setNormalize(!autoScaleCheck.isSelected()); decorator.getContinuousScale().setLowerRange(fromNumberField.getValue()); decorator.getContinuousScale().setUpperRange(toNumberField.getValue()); return decorator; } private interface ColourSchemePanel { void setDecorator(ContinuousColourDecorator decorator); ContinuousColourDecorator getDecorator(); JPanel getPanel(); String getName(); } private class HSBColourSchemePanel implements ColourSchemePanel { public HSBColourSchemePanel() { hueSlider = new RangeSlider(0, SLIDER_RANGE); saturationSlider = new RangeSlider(0, SLIDER_RANGE); brightnessSlider = new RangeSlider(0, SLIDER_RANGE); reverseHueCheck = new JCheckBox("Reverse hue spectrum"); } public void setDecorator(ContinuousColourDecorator decorator) { if (decorator instanceof HSBContinuousColourDecorator) { hsbDecorator = (HSBContinuousColourDecorator)decorator; } else { if (hsbDecorator == null) { hsbDecorator = new HSBContinuousColourDecorator(decorator.getContinuousScale()); } } hueSlider.setValue((int)(hsbDecorator.getHueLower() * SLIDER_RANGE)); hueSlider.setUpperValue((int) (hsbDecorator.getHueUpper() * SLIDER_RANGE)); saturationSlider.setValue((int)(hsbDecorator.getSaturationLower() * SLIDER_RANGE)); saturationSlider.setUpperValue((int)(hsbDecorator.getSaturationUpper() * SLIDER_RANGE)); brightnessSlider.setValue((int)(hsbDecorator.getBrightnessLower() * SLIDER_RANGE)); brightnessSlider.setUpperValue((int)(hsbDecorator.getBrightnessUpper() * SLIDER_RANGE)); reverseHueCheck.setSelected(hsbDecorator.isReverseHue()); } @Override public ContinuousColourDecorator getDecorator() { hsbDecorator.setHueLower(((float) hueSlider.getValue()) / SLIDER_RANGE); hsbDecorator.setHueUpper(((float) hueSlider.getUpperValue()) / SLIDER_RANGE); hsbDecorator.setSaturationLower(((float) saturationSlider.getValue()) / SLIDER_RANGE); hsbDecorator.setSaturationUpper(((float) saturationSlider.getUpperValue()) / SLIDER_RANGE); hsbDecorator.setBrightnessLower(((float) brightnessSlider.getValue()) / SLIDER_RANGE); hsbDecorator.setBrightnessUpper(((float) brightnessSlider.getUpperValue()) / SLIDER_RANGE); hsbDecorator.setReverseHue(reverseHueCheck.isSelected()); return hsbDecorator; } @Override public JPanel getPanel() { if (panel == null) { final OptionsPanel options = new OptionsPanel(6, 6); options.addComponentWithLabel("Hue: ", hueSlider); options.addComponentWithLabel("Saturation: ", saturationSlider); options.addComponentWithLabel("Brightness: ", brightnessSlider); options.addComponent(reverseHueCheck); ChangeListener listener = new ChangeListener() { public void stateChanged(ChangeEvent e) { getDecorator(); colourDisplay.repaint(); } }; hueSlider.addChangeListener(listener); saturationSlider.addChangeListener(listener); brightnessSlider.addChangeListener(listener); reverseHueCheck.addChangeListener(listener); panel = options; } return panel; } @Override public String getName() { return HSB_SPECTRUM; } private RangeSlider hueSlider; private RangeSlider saturationSlider; private RangeSlider brightnessSlider; private JCheckBox reverseHueCheck; private HSBContinuousColourDecorator hsbDecorator = null; private JPanel panel = null; } private class InterpolatingColourSchemePanel implements ColourSchemePanel { public InterpolatingColourSchemePanel() { middleColourCheck = new JCheckBox("through:"); fromColourButton = new ColorWellButton(InterpolatingColourDecorator.DEFAULT_COLOR_1, "Choose Start Colour"); toColourButton = new ColorWellButton(InterpolatingColourDecorator.DEFAULT_COLOR_2, "Choose End Colour"); middleColourButton = new ColorWellButton(InterpolatingColourDecorator.DEFAULT_COLOR_3, "Choose Middle Colour"); middleColourCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { middleColourButton.setEnabled(middleColourCheck.isSelected()); } }); middleColourCheck.setSelected(false); middleColourButton.setEnabled(false); } public void setDecorator(ContinuousColourDecorator decorator) { if (decorator instanceof InterpolatingColourDecorator) { this.interpolatingDecorator = (InterpolatingColourDecorator)decorator; } else { if (interpolatingDecorator == null) { interpolatingDecorator = new InterpolatingColourDecorator(decorator.getContinuousScale()); } } fromColourButton.setSelectedColor(interpolatingDecorator.getColor1()); if (interpolatingDecorator.getColor3() != null) { middleColourCheck.setSelected(true); middleColourButton.setSelectedColor(interpolatingDecorator.getColor2()); toColourButton.setSelectedColor(interpolatingDecorator.getColor3()); } else { middleColourCheck.setSelected(false); toColourButton.setSelectedColor(interpolatingDecorator.getColor2()); } } @Override public ContinuousColourDecorator getDecorator() { if (middleColourCheck.isSelected()) { interpolatingDecorator.setColours( fromColourButton.getSelectedColor(), middleColourButton.getSelectedColor(), toColourButton.getSelectedColor()); } else { interpolatingDecorator.setColours( fromColourButton.getSelectedColor(), toColourButton.getSelectedColor()); } return interpolatingDecorator; } @Override public JPanel getPanel() { if (panel == null) { final OptionsPanel options = new OptionsPanel(6, 6); JPanel panel1 = new JPanel(); panel1.setLayout(new FlowLayout()); panel1.add(new JLabel("Colour gradient from:")); panel1.add(fromColourButton); panel1.add(new JLabel("to:")); panel1.add(toColourButton); options.addComponent(panel1); JPanel panel2 = new JPanel(); panel1.setLayout(new FlowLayout()); panel1.add(middleColourCheck); panel1.add(middleColourButton); options.addComponent(panel2); this.panel = options; ChangeListener listener = new ChangeListener() { public void stateChanged(ChangeEvent e) { getDecorator(); colourDisplay.repaint(); } }; fromColourButton.addChangeListener(listener); toColourButton.addChangeListener(listener); middleColourCheck.addChangeListener(listener); middleColourButton.addChangeListener(listener); } return panel; } @Override public String getName() { return COLOUR_GRADIENT; } private ColorWellButton fromColourButton; private ColorWellButton toColourButton; private JCheckBox middleColourCheck; private ColorWellButton middleColourButton; private InterpolatingColourDecorator interpolatingDecorator = null; private JPanel panel = null; } }figtree-1.4.3/src/figtree/treeviewer/ContinuousScaleDialog.java000077500000000000000000000105431277473563300246710ustar00rootroot00000000000000/* * ContinuousScaleDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.decorators.Decorator; import figtree.ui.components.ColorWellButton; import figtree.ui.components.RealNumberField; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ @Deprecated public class ContinuousScaleDialog { public static class ScaleSettings { // continuous colour settings: public boolean autoRange = true; public double fromValue = 0.0; public double toValue = 1.0; public boolean logarithm = false; } private JFrame frame; private JCheckBox autoScaleCheck; private JLabel fromLabel; private RealNumberField fromNumberField; private JLabel toLabel; private RealNumberField toNumberField; public ContinuousScaleDialog(final JFrame frame, final ScaleSettings settings) { this.frame = frame; autoScaleCheck = new JCheckBox("Auto-scale range between min and max values"); autoScaleCheck.setSelected(settings.autoRange); fromLabel = new JLabel("Range from:"); fromNumberField = new RealNumberField(); fromNumberField.setColumns(10); fromNumberField.setValue(settings.fromValue); toLabel = new JLabel("to:"); toNumberField = new RealNumberField(); toNumberField.setColumns(10); toNumberField.setValue(settings.toValue); fromLabel.setEnabled(false); fromNumberField.setEnabled(false); toLabel.setEnabled(false); toNumberField.setEnabled(false); autoScaleCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { boolean enabled = !autoScaleCheck.isSelected(); fromLabel.setEnabled(enabled); fromNumberField.setEnabled(enabled); toLabel.setEnabled(enabled); toNumberField.setEnabled(enabled); } } ); } public int showDialog() { final OptionsPanel options = new OptionsPanel(6, 6); boolean isResizable = false; options.addComponent(autoScaleCheck); JPanel panel = new JPanel(); panel.setLayout(new FlowLayout()); panel.add(fromLabel); panel.add(fromNumberField); panel.add(toLabel); panel.add(toNumberField); options.addComponent(panel); JOptionPane optionPane = new JOptionPane(options, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); final JDialog dialog = optionPane.createDialog(frame, "Setup colour range"); dialog.pack(); dialog.setResizable(isResizable); dialog.setVisible(true); int result = JOptionPane.CANCEL_OPTION; Integer value = (Integer)optionPane.getValue(); if (value != null && value.intValue() != -1) { result = value.intValue(); } return result; } public void getSettings(ScaleSettings settings) { settings.autoRange = autoScaleCheck.isSelected(); settings.fromValue = fromNumberField.getValue(); settings.toValue = toNumberField.getValue(); } }figtree-1.4.3/src/figtree/treeviewer/ControllerOptionsPanel.java000066400000000000000000000042761277473563300251150ustar00rootroot00000000000000/* * ControllerOptionsPanel.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.text.JTextComponent; import java.awt.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ControllerOptionsPanel extends OptionsPanel { public ControllerOptionsPanel() { super(); } public ControllerOptionsPanel(int hGap, int vGap) { super(hGap, vGap); } protected void adjustComponent(JComponent comp) { setComponentLook(comp); } public static void setComponentLook(JComponent comp) { comp.putClientProperty("Quaqua.Component.visualMargin", new Insets(0,0,0,0)); Font font = UIManager.getFont("SmallSystemFont"); if (font != null) { comp.setFont(font); } comp.putClientProperty("JComponent.sizeVariant", "small"); if (comp instanceof JSpinner && font != null) { ((JSpinner.NumberEditor)((JSpinner)comp).getEditor()).getTextField().setFont(font); } if (comp instanceof JButton) { comp.putClientProperty("JButton.buttonType", "roundRect"); } if (comp instanceof JComboBox) { //comp.putClientProperty("JComboBox.isSquare", Boolean.TRUE); } if (!(comp instanceof JTextField)) { comp.setFocusable(false); } } } figtree-1.4.3/src/figtree/treeviewer/DefaultTreeViewer.java000077500000000000000000000621561277473563300240300ustar00rootroot00000000000000/* * DefaultTreeViewer.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.painters.*; import jebl.evolution.graphs.Node; import jebl.evolution.taxa.Taxon; import jebl.evolution.trees.*; import figtree.treeviewer.decorators.Decorator; import figtree.treeviewer.treelayouts.TreeLayout; import jam.panels.StatusProvider; import javax.swing.*; import java.awt.*; import java.awt.print.PageFormat; import java.awt.print.PrinterException; import java.util.*; import java.util.List; import java.util.regex.PatternSyntaxException; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class DefaultTreeViewer extends TreeViewer { private final static double ZOOM_SCALE = 0.02; private final static double VERTICAL_EXPANSION_SCALE = 0.02; private final static double ZOOM_POWER = 1.2; public DefaultTreeViewer() { this(null); } /** * Creates new TreeViewer */ public DefaultTreeViewer(JFrame frame) { this.frame = frame; setLayout(new BorderLayout()); this.treePane = new TreePane(); treePane.setAutoscrolls(true); //enable synthetic drag events treePane.addTreePaneListener(new TreePaneListener() { public void treePaneSettingsChanged() { fireTreeSettingsChanged(); } }); JScrollPane scrollPane = new JScrollPane(treePane, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS); scrollPane.setMinimumSize(new Dimension(150, 150)); scrollPane.setBorder(null); viewport = scrollPane.getViewport(); add(scrollPane, BorderLayout.CENTER); // This overrides MouseListener and MouseMotionListener to allow selection in the TreePane - // It installs itself within the constructor. treePaneSelector = new TreePaneSelector(treePane); treePaneRollOver = new TreePaneRollOver(treePane); setFocusable(true); } public void setTree(Tree tree) { trees.clear(); addTree(tree); showTree(0); } public void setTrees(Collection trees) { this.trees.clear(); for (Tree tree : trees) { addTree(tree); } showTree(0); } public void addTree(Tree tree) { this.trees.add(tree); // if (treePane.getTipLabelPainter() != null) { // treePane.getTipLabelPainter().setupAttributes(trees); // } // // if (treePane.getBranchLabelPainter() != null) { // treePane.getBranchLabelPainter().setupAttributes(trees); // } // // if (treePane.getNodeLabelPainter() != null) { // treePane.getNodeLabelPainter().setupAttributes(trees); // } // // if (treePane.getNodeBarPainter() != null) { // treePane.getNodeBarPainter().setupAttributes(trees); // } // // if (treePane.getLegendPainter() != null) { // treePane.getLegendPainter().setupAttributes(trees); // } } public void addTrees(Collection trees) { int count = getTreeCount(); for (Tree tree : trees) { addTree(tree); } showTree(count); } public List getTrees() { return trees; } public Tree getCurrentTree() { // return trees.get(currentTreeIndex); return treePane.getTree(); } public List getTreesAsViewed() { List treeAsDisplayed = new ArrayList(); for (Tree originalTree : trees) { treeAsDisplayed.add(treePane.constructTransformedTree((RootedTree)originalTree)); } return treeAsDisplayed; } public RootedTree getSelectedSubtree() { return treePane.getSelectedSubtree(); } public int getCurrentTreeIndex() { return currentTreeIndex; } public int getTreeCount() { if (trees == null) return 0; return trees.size(); } public StatusProvider getStatusProvider() { return treePaneRollOver; } public void showTree(int index) { if (isRootingOn() && getRootingType() == TreePane.RootingType.USER_ROOTING) { JOptionPane.showMessageDialog(frame, "Cannot switch trees when user rooting option is on.\n" + "Turn this option off to switch trees", "Unable to switch trees", JOptionPane.ERROR_MESSAGE); return; } Tree tree = trees.get(index); if (tree instanceof RootedTree) { treePane.setTree((RootedTree)tree); } else { treePane.setTree(Utils.rootTheTree(tree)); } currentTreeIndex = index; fireTreeChanged(); } public void showNextTree() { if (currentTreeIndex < trees.size() - 1) { showTree(currentTreeIndex + 1); } } public void showPreviousTree() { if (currentTreeIndex > 0) { showTree(currentTreeIndex - 1); } } public void setTreeLayout(TreeLayout treeLayout) { treePane.setTreeLayout(treeLayout); fireTreeSettingsChanged(); } private boolean zoomPending = false; private double zoom = 0.0; private double verticalExpansion = 0.0; public void setZoom(double zoom) { double n = Math.max(treePane.getTree().getTaxa().size(), 50); this.zoom = Math.pow(zoom * n * ZOOM_SCALE, ZOOM_POWER); // this.zoom = zoom * MAX_ZOOM; refreshZoom(); } public void setVerticalExpansion(double verticalExpansion) { double n = Math.max(treePane.getTree().getTaxa().size(), 50); this.verticalExpansion = Math.pow(verticalExpansion * n * VERTICAL_EXPANSION_SCALE, ZOOM_POWER); // this.verticalExpansion = verticalExpansion * MAX_VERTICAL_EXPANSION; refreshZoom(); } public boolean verticalExpansionAllowed() { return !treePane.maintainAspectRatio(); } public void setTimeScale(TimeScale timeScale) { treePane.setTimeScale(timeScale); } private void refreshZoom() { setZoom(zoom, zoom + verticalExpansion); } private void setZoom(double xZoom, double yZoom) { Dimension viewportSize = viewport.getViewSize(); Point position = viewport.getViewPosition(); Dimension extentSize = viewport.getExtentSize(); double w = extentSize.getWidth() * (1.0 + xZoom); double h = extentSize.getHeight() * (1.0 + yZoom); Dimension newSize = new Dimension((int) w, (int) h); treePane.setPreferredSize(newSize); double cx = position.getX() + (0.5 * extentSize.getWidth()); double cy = position.getY() + (0.5 * extentSize.getHeight()); double rx = ((double) newSize.getWidth()) / viewportSize.getWidth(); double ry = ((double) newSize.getHeight()) / viewportSize.getHeight(); double px = (cx * rx) - (extentSize.getWidth() / 2.0); double py = (cy * ry) - (extentSize.getHeight() / 2.0); Point newPosition = new Point((int) px, (int) py); viewport.setViewPosition(newPosition); treePane.revalidate(); } public boolean hasSelection() { return treePane.hasSelection(); } public Set getSelectedNodes() { return treePane.getSelectedNodes(); } public Set getSelectedTips() { return treePane.getSelectedTips(); } public Set getSelectedTaxa() { return treePane.getSelectedTaxa(); } /** * Select taxa with a search string matching the currently displayed attribute * @param searchType * @param searchString * @param caseSensitive */ public void selectTaxa(TextSearchType searchType, String searchString, boolean caseSensitive) { String attributeName = "!name"; LabelPainter lp = treePane.getTipLabelPainter(); if (lp != null && lp.isVisible() && lp.getDisplayAttribute() != null) { attributeName = lp.getDisplayAttribute(); } selectTaxa(attributeName, searchType, searchString, caseSensitive); scrollToSelectedTips(); } public void selectTaxa(String attributeName, TextSearchType searchType, String searchString, boolean caseSensitive) { if (treePane.getTree() == null) { return; } treePane.clearSelection(); String query = searchString; if (searchType != TextSearchType.REG_EX) { query = (caseSensitive ? searchString : searchString.toUpperCase()); query = query.trim(); } Tree tree = treePane.getTree(); for (Node node : tree.getExternalNodes()) { Taxon taxon = tree.getTaxon(node); if (attributeName == null) { Object target = taxon.getName(); if (matchesItem(searchType, target, query, caseSensitive)) { treePane.addSelectedTip(node); break; } for (String name : taxon.getAttributeNames()) { target = taxon.getAttribute(name); if (matchesItem(searchType, target, query, caseSensitive)) { treePane.addSelectedTip(node); break; } } } else { Object target; if (attributeName.equals("!name")) { target = taxon.getName(); } else { target = taxon.getAttribute(attributeName); if (target == null) { // if we can't find the attribute on the taxon, try the node target = node.getAttribute(attributeName); } } if (matchesItem(searchType, target, query, caseSensitive)) { treePane.addSelectedTip(node); } } } } public void selectNodes(String attributeName, TextSearchType searchType, String searchString, boolean caseSensitive) { treePane.clearSelection(); String query = searchString; if (searchType != TextSearchType.REG_EX) { query = (caseSensitive ? searchString : searchString.toUpperCase()); query = query.trim(); } Tree tree = treePane.getTree(); for (Node node : tree.getNodes()) { if (attributeName == null) { for (String name : node.getAttributeNames()) { Object target = node.getAttribute(name); if (matchesItem(searchType, target, query, caseSensitive)) { treePane.addSelectedNode(node); break; } } } else { Object target = node.getAttribute(attributeName); if (matchesItem(searchType, target, query, caseSensitive)) { treePane.addSelectedNode(node); } } } } private boolean matchesItem(TextSearchType searchType, Object object, String query, boolean caseSensitive) { if (object != null) { String target = (caseSensitive ? object.toString() : object.toString().toUpperCase()); switch (searchType) { case CONTAINS: if (target.contains(query)) { return true; } break; case STARTS_WITH: if (target.startsWith(query)) { return true; } break; case ENDS_WITH: if (target.endsWith(query)) { return true; } break; case MATCHES: if (target.equals(query)) { return true; } break; case REG_EX: try { if (target.matches(query)) { return true; } } catch (PatternSyntaxException pse) { // ignore } break; } } return false; } public void selectTaxa(String attributeName, NumberSearchType searchType, Number searchValue) { treePane.clearSelection(); RootedTree tree = treePane.getTree(); for (Node node : tree.getExternalNodes()) { Object value = null; if (attributeName.equals("!length")) { value = tree.getLength(node); } else if (attributeName.equals("!height")) { value = tree.getHeight(node); } else { Taxon taxon = tree.getTaxon(node); value = taxon.getAttribute(attributeName); } if (matchesItem(value, searchType, searchValue)) { treePane.addSelectedTip(node); } } } public void selectNodes(String attributeName, NumberSearchType searchType, Number searchValue) { treePane.clearSelection(); RootedTree tree = treePane.getTree(); for (Node node : tree.getNodes()) { Object value = null; if (attributeName.equals("!length")) { value = tree.getLength(node); } else if (attributeName.equals("!height")) { value = tree.getHeight(node); } else { value = node.getAttribute(attributeName); } if (matchesItem(value, searchType, searchValue)) { treePane.addSelectedNode(node); } } } public void selectTaxa(Collection taxonNames) { treePane.clearSelection(); RootedTree tree = treePane.getTree(); for (Node node : tree.getExternalNodes()) { Object value = null; if (taxonNames.contains(tree.getTaxon(node).getName())) { treePane.addSelectedTip(node); } } } private boolean matchesItem(Object item, NumberSearchType searchType, Number searchValue) { if (item != null && item instanceof Number) { Number value = (Number)item; switch (searchType) { case EQUALS: if (value.equals(searchValue)) { return true; } break; case EQUALS_OR_GREATER_THAN: if (value.doubleValue() >= searchValue.doubleValue()) { return true; } break; case EQUALS_OR_LESS_THAN: if (value.doubleValue() <= searchValue.doubleValue()) { return true; } break; case GREATER_THAN: if (value.doubleValue() > searchValue.doubleValue()) { return true; } break; case LESS_THAN: if (value.doubleValue() < searchValue.doubleValue()) { return true; } break; case NOT_EQUALS: if (!searchValue.equals(value)) { return true; } break; } } return false; } public void scrollToSelectedTips() { Set selectedTips = treePane.getSelectedTips(); if (selectedTips.size() > 0) { Point point = treePane.getLocationOfTip(selectedTips.iterator().next()); treePane.scrollPointToVisible(point); } } public void cartoonSelectedNodes() { treePane.cartoonSelectedNodes(); fireTreeSettingsChanged(); } public void collapseSelectedNodes() { treePane.collapseSelectedNodes(); fireTreeSettingsChanged(); } public void clearCollapsedNodes() { treePane.clearCollapsedNodes(); fireTreeSettingsChanged(); } public void hilightSelectedNodes(Color color) { treePane.hilightSelectedNodes(color); fireTreeSettingsChanged(); } public void clearHilighting() { treePane.clearHilightedNodes(); fireTreeSettingsChanged(); } public void rerootOnSelectedBranch() { treePane.rerootOnSelectedBranch(); fireTreeSettingsChanged(); } public void clearRooting() { treePane.clearRooting(); fireTreeSettingsChanged(); } public void rotateSelectedNode() { treePane.rotateSelectedNode(); fireTreeSettingsChanged(); } public void clearRotations() { treePane.clearSelectedNodeRotations(); fireTreeSettingsChanged(); } public void annotateSelectedNodes(String name, Object value) { treePane.annotateSelectedNodes(name, value); fireTreeSettingsChanged(); } public void annotateSelectedTips(String name, Object value) { treePane.annotateSelectedTips(name, value); fireTreeSettingsChanged(); } public void clearAnnotation(String name) { treePane.clearSelectedNodeAnnotation(name); treePane.clearSelectedTipAnnotation(name); fireTreeSettingsChanged(); } public void clearColouring() { treePane.clearSelectedNodeAnnotation("!color"); treePane.clearSelectedTipAnnotation("!color"); fireTreeSettingsChanged(); } public void selectAll() { if (treePaneSelector.getSelectionMode() == TreePaneSelector.SelectionMode.TAXA) { treePane.selectAllTaxa(); } else { treePane.selectAllNodes(); } } public void clearSelectedTaxa() { treePane.clearSelection(); } public void addTreeSelectionListener(TreeSelectionListener treeSelectionListener) { treePane.addTreeSelectionListener(treeSelectionListener); } public void removeTreeSelectionListener(TreeSelectionListener treeSelectionListener) { treePane.removeTreeSelectionListener(treeSelectionListener); } public TreePaneSelector.SelectionMode getSelectionMode() { return treePaneSelector.getSelectionMode(); } public void setSelectionMode(TreePaneSelector.SelectionMode selectionMode) { TreePaneSelector.SelectionMode oldSelectionMode = treePaneSelector.getSelectionMode(); if (selectionMode == oldSelectionMode) { return; } if (oldSelectionMode == TreePaneSelector.SelectionMode.TAXA) { treePane.selectNodesFromSelectedTips(); } else if (selectionMode == TreePaneSelector.SelectionMode.TAXA) { treePane.selectTipsFromSelectedNodes(); } else if (selectionMode == TreePaneSelector.SelectionMode.CLADE) { treePane.selectCladesFromSelectedNodes(); } treePaneSelector.setSelectionMode(selectionMode); } public void setDragMode(TreePaneSelector.DragMode dragMode) { treePaneSelector.setDragMode(dragMode); } // A load of delegated method calls through to treePane (which is now hidden outside the package). public void setTipLabelPainter(LabelPainter tipLabelPainter) { treePane.setTipLabelPainter(tipLabelPainter); // tipLabelPainter.setupAttributes(trees); } public void setNodeLabelPainter(LabelPainter nodeLabelPainter) { treePane.setNodeLabelPainter(nodeLabelPainter); // nodeLabelPainter.setupAttributes(trees); } public void setNodeBarPainter(NodeBarPainter nodeBarPainter) { treePane.setNodeBarPainter(nodeBarPainter); // nodeBarPainter.setupAttributes(trees); } public void setTipShapePainter(NodeShapePainter tipShapePainter) { treePane.setTipShapePainter(tipShapePainter); } public void setNodeShapePainter(NodeShapePainter nodeShapePainter) { treePane.setNodeShapePainter(nodeShapePainter); } public void setBranchLabelPainter(LabelPainter branchLabelPainter) { treePane.setBranchLabelPainter(branchLabelPainter); // branchLabelPainter.setupAttributes(trees); } public void addScalePainter(ScalePainter scalePainter) { treePane.addScalePainter(scalePainter); } public void removeScalePainter(ScalePainter scalePainter) { treePane.removeScalePainter(scalePainter); } public void setScaleGridPainter(ScaleGridPainter scaleGridPainter) { treePane.setScaleGridPainter(scaleGridPainter); } public void setLegendPainter(LegendPainter legendPainter) { treePane.setLegendPainter(legendPainter); // legendPainter.setupAttributes(trees); } public void setBranchDecorator(Decorator branchDecorator, boolean isGradient) { treePane.setBranchDecorator(branchDecorator, isGradient); } public void setBranchColouringDecorator(String branchColouringAttribute, Decorator branchColouringDecorator) { treePane.setBranchColouringDecorator(branchColouringAttribute, branchColouringDecorator); } public void setNodeBackgroundDecorator(Decorator nodeBackgroundDecorator) { treePane.setNodeBackgroundDecorator(nodeBackgroundDecorator); } public void setHilightingGradient(boolean hilightingGradient) { treePane.setHilightingGradient(hilightingGradient); } public void setSelectionColor(Color selectionColor) { treePane.setSelectionColor(selectionColor); } public Paint getSelectionPaint() { return treePane.getSelectionPaint(); } public void setBranchStroke(BasicStroke branchStroke) { treePane.setBranchStroke(branchStroke); } public boolean isTransformBranchesOn() { return treePane.isTransformBranchesOn(); } public TransformedRootedTree.Transform getBranchTransform() { return treePane.getBranchTransform(); } public void setTransformBranchesOn(boolean transformBranchesOn) { treePane.setTransformBranchesOn(transformBranchesOn); } public void setBranchTransform(TransformedRootedTree.Transform transform) { treePane.setBranchTransform(transform); } public boolean isOrderBranchesOn() { return treePane.isOrderBranchesOn(); } public SortedRootedTree.BranchOrdering getBranchOrdering() { return treePane.getBranchOrdering(); } public void setOrderBranchesOn(boolean orderBranchesOn) { treePane.setOrderBranchesOn(orderBranchesOn); } public void setBranchOrdering(SortedRootedTree.BranchOrdering branchOrdering) { treePane.setBranchOrdering(branchOrdering); } public boolean isRootingOn() { return treePane.isRootingOn(); } public TreePane.RootingType getRootingType() { return treePane.getRootingType(); } public void setRootingOn(boolean rootingOn) { treePane.setRootingOn(rootingOn); } public void setRootingType(TreePane.RootingType rootingType) { treePane.setRootingType(rootingType); } public void setToolMode(TreePaneSelector.ToolMode toolMode) { treePaneSelector.setToolMode(toolMode); } public JComponent getContentPane() { return treePane; } public void paint(Graphics g) { if( zoomPending ) { refreshZoom(); zoomPending = false; } super.paint(g); } public int print(Graphics g, PageFormat pageFormat, int pageIndex) throws PrinterException { return treePane.print(g, pageFormat, pageIndex); } public void addTreeViewerListener(TreeViewerListener listener) { listeners.add(listener); } public void removeTreeViewerListener(TreeViewerListener listener) { listeners.remove(listener); } public void fireTreeChanged() { for (TreeViewerListener listener : listeners) { listener.treeChanged(); } } public void fireTreeSettingsChanged() { for (TreeViewerListener listener : listeners) { listener.treeSettingsChanged(); } } private java.util.List listeners = new ArrayList(); private List trees = new ArrayList(); private int currentTreeIndex = 0; protected TreePane treePane; protected TreePaneSelector treePaneSelector; protected TreePaneRollOver treePaneRollOver; protected JViewport viewport; private final JFrame frame; }figtree-1.4.3/src/figtree/treeviewer/DiscreteColourScaleDialog.java000077500000000000000000000452171277473563300254570ustar00rootroot00000000000000/* * DiscreteColourScaleDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.decorators.*; import figtree.ui.components.RangeSlider; import jam.panels.OptionsPanel; import javax.activation.DataHandler; import javax.swing.*; import javax.swing.border.Border; import javax.swing.border.EmptyBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.table.DefaultTableModel; import javax.swing.table.TableCellRenderer; import java.awt.*; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.Transferable; import java.awt.dnd.DragSource; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class DiscreteColourScaleDialog { private static final int SLIDER_RANGE = 1000; private static final String HSB_SPECTRUM = "HSB Spectrum"; private static final String FIXED_COLOURS = "Fixed Colours"; private JFrame frame; private JComboBox colourSchemeCombo = new JComboBox(new String[] { HSB_SPECTRUM, FIXED_COLOURS} ); CardLayout cardLayout = new CardLayout(); private final JPanel colourSchemePanel; private Map colourSchemeNamePanelMap = new HashMap(); private Map colourSchemeClassNameMap = new HashMap(); // private DiscreteColourDecorator decorator; private java.util.List discreteValues = null; private JTable table; private ColourTableModel tableModel; private JDialog dialog; public DiscreteColourScaleDialog(final JFrame frame) { this.frame = frame; colourSchemeNamePanelMap.put(HSB_SPECTRUM, new HSBColourSchemePanel()); colourSchemeNamePanelMap.put(FIXED_COLOURS, new FixedColourSchemePanel()); colourSchemeClassNameMap.put(HSBDiscreteColourDecorator.class, HSB_SPECTRUM); colourSchemeClassNameMap.put(FixedDiscreteColourDecorator.class, FIXED_COLOURS); colourSchemePanel = new JPanel(cardLayout); for (String name : colourSchemeNamePanelMap.keySet()) { ColourSchemePanel panel = colourSchemeNamePanelMap.get(name); colourSchemePanel.add(panel.getPanel(), name); } colourSchemeCombo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { cardLayout.show(colourSchemePanel, colourSchemeCombo.getSelectedItem().toString()); // decorator = colourSchemeNamePanelMap.get(colourSchemeCombo.getSelectedItem()).getDecorator(); tableModel.fireTableDataChanged(); dialog.pack(); } }); tableModel = new ColourTableModel(); table = new JTable(tableModel); table.setDefaultRenderer(Color.class, new ColorRenderer(true)); table.setDefaultRenderer(Paint.class, new ColorRenderer(true)); table.setDragEnabled(true); table.setDropMode(DropMode.INSERT_ROWS); table.setTransferHandler(new TableRowTransferHandler(table)); table.setRowSelectionAllowed(true); table.setColumnSelectionAllowed(false); table.getColumnModel().getColumn(1).setWidth(80); table.getColumnModel().getColumn(1).setMinWidth(80); table.getColumnModel().getColumn(1).setMaxWidth(80); table.getColumnModel().getColumn(1).setResizable(false); } public int showDialog() { DiscreteColourDecorator currentDecorator = getDecorator(); final OptionsPanel options = new OptionsPanel(6, 6); // options.addSpanningComponent(new JLabel("Editing colour range for attribute: " + decorator.getAttributeName())); JScrollPane scrollPane = new JScrollPane(table); scrollPane.setMinimumSize(new Dimension(120, 120)); options.addSpanningComponent(scrollPane); options.addComponentWithLabel("Scheme: ", colourSchemeCombo); colourSchemePanel.setBorder(BorderFactory.createBevelBorder(1)); options.addSpanningComponent(colourSchemePanel); // setDecorator(currentDecorator); JOptionPane optionPane = new JOptionPane(options, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); dialog = optionPane.createDialog(frame, "Setup colour range: " + currentDecorator.getAttributeName()); colourSchemeCombo.setSelectedItem(colourSchemeClassNameMap.get(currentDecorator.getClass())); dialog.pack(); dialog.setResizable(true); dialog.setVisible(true); int result = JOptionPane.CANCEL_OPTION; Integer value = (Integer)optionPane.getValue(); if (value != null && value.intValue() != -1) { result = value.intValue(); } return result; } public void setDecorator(DiscreteColourDecorator decorator) { // this.decorator = decorator; discreteValues = new ArrayList(decorator.getValues()); for (String key : colourSchemeNamePanelMap.keySet()) { colourSchemeNamePanelMap.get(key).setDecorator(decorator); } } public DiscreteColourDecorator getDecorator() { String name = colourSchemeCombo.getSelectedItem().toString(); DiscreteColourDecorator decorator = colourSchemeNamePanelMap.get(name).getDecorator(); decorator.setValuesOrder(discreteValues); return decorator; } interface Reorderable { public void reorder(java.util.List sourceIndices, int destinationIndex); }; class ColourTableModel extends DefaultTableModel implements Reorderable { private final String[] COLUMN_NAMES = { "Value", "Colour" }; @Override public int getRowCount() { if (discreteValues == null) return 0; return discreteValues.size(); } @Override public int getColumnCount() { return 2; } @Override public String getColumnName(int column) { return COLUMN_NAMES[column]; } @Override public boolean isCellEditable(int row, int column) { return false; } @Override public Object getValueAt(int row, int column) { switch (column) { case 0: return discreteValues.get(row); case 1: DiscreteColourDecorator decorator = getDecorator(); // until the OK button is pressed the trait values are not actually // reordered so use the default colour order. return decorator.getColor(decorator.getValues().get(row)); } return null; } @Override public Class getColumnClass(int column) { if (column == 1) { return Color.class; } return String.class; } @Override public void setValueAt(Object o, int row, int column) { } @Override public void reorder(java.util.List sourceIndices, int destinationIndex) { java.util.List itemsToMove = new ArrayList(); for (int src : sourceIndices) { itemsToMove.add(discreteValues.get(src)); } for (int i = sourceIndices.size() - 1; i >= 0; i--) { int src = sourceIndices.get(i); discreteValues.remove(src); if (destinationIndex > src) { destinationIndex -= 1; } } discreteValues.addAll(destinationIndex, itemsToMove); fireTableDataChanged(); } } public class ColorRenderer extends JLabel implements TableCellRenderer { Border unselectedBorder = null; Border selectedBorder = null; boolean isBordered = true; public ColorRenderer(boolean isBordered) { this.isBordered = isBordered; setOpaque(true); //MUST do this for background to show up. } public Component getTableCellRendererComponent( JTable table, Object color, boolean isSelected, boolean hasFocus, int row, int column) { Color newColor = (Color)color; setBackground(newColor); if (isBordered) { if (isSelected) { if (selectedBorder == null) { selectedBorder = BorderFactory.createMatteBorder(2,5,2,5, table.getSelectionBackground()); } setBorder(selectedBorder); } else { if (unselectedBorder == null) { unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5, table.getBackground()); } setBorder(unselectedBorder); } } setToolTipText("RGB value: " + newColor.getRed() + ", " + newColor.getGreen() + ", " + newColor.getBlue()); return this; } } /** * Handles drag & drop row reordering */ public class TableRowTransferHandler extends TransferHandler { // private final DataFlavor localObjectFlavor = new ActivationDataFlavor(Integer.class, DataFlavor.javaJVMLocalObjectMimeType, "Integer Row Index"); private final DataFlavor localObjectFlavor = new DataFlavor(ArrayList.class, "Integer Row Index"); private JTable table = null; public TableRowTransferHandler(JTable table) { this.table = table; } @Override protected Transferable createTransferable(JComponent c) { assert (c == table); java.util.List selectedRows = new ArrayList(); for (int row : table.getSelectedRows()) { selectedRows.add(row); } return new DataHandler(selectedRows, localObjectFlavor.getMimeType()); } @Override public boolean canImport(TransferHandler.TransferSupport info) { boolean b = info.getComponent() == table && info.isDrop() && info.isDataFlavorSupported(localObjectFlavor); table.setCursor(b ? DragSource.DefaultMoveDrop : DragSource.DefaultMoveNoDrop); return b; } @Override public int getSourceActions(JComponent c) { return TransferHandler.MOVE; } @Override public boolean importData(TransferHandler.TransferSupport info) { JTable target = (JTable) info.getComponent(); JTable.DropLocation dl = (JTable.DropLocation) info.getDropLocation(); int index = dl.getRow(); int max = table.getModel().getRowCount(); if (index < 0 || index > max) index = max; target.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); try { java.util.List selectedRows = (java.util.List)info.getTransferable().getTransferData(localObjectFlavor); if (selectedRows != null && selectedRows.size() > 0) { ((Reorderable)table.getModel()).reorder(selectedRows, index); for (int row : selectedRows) { if (index > row) index--; } target.getSelectionModel().addSelectionInterval(index, index + selectedRows.size() - 1); return true; } } catch (Exception e) { e.printStackTrace(); } return false; } @Override protected void exportDone(JComponent c, Transferable t, int act) { if (act == TransferHandler.MOVE) { table.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } } private interface ColourSchemePanel { void setDecorator(DiscreteColourDecorator decorator); DiscreteColourDecorator getDecorator(); JPanel getPanel(); String getName(); } private class HSBColourSchemePanel implements ColourSchemePanel { public HSBColourSchemePanel() { hueSlider = new RangeSlider(0, SLIDER_RANGE); saturationSlider = new RangeSlider(0, SLIDER_RANGE); brightnessSlider = new RangeSlider(0, SLIDER_RANGE); } public void setDecorator(DiscreteColourDecorator decorator) { if (decorator instanceof HSBDiscreteColourDecorator) { hsbDecorator = (HSBDiscreteColourDecorator)decorator; } else { if (hsbDecorator == null) { hsbDecorator = new HSBDiscreteColourDecorator(decorator.getAttributeName()); } } settingValues = true; secondaryCountSpinnerModel.setValue(hsbDecorator.getSecondaryCount()); hueSlider.setValue((int)(hsbDecorator.getHueLower() * SLIDER_RANGE)); hueSlider.setUpperValue((int) (hsbDecorator.getHueUpper() * SLIDER_RANGE)); saturationSlider.setValue((int)(hsbDecorator.getSaturationLower() * SLIDER_RANGE)); saturationSlider.setUpperValue((int)(hsbDecorator.getSaturationUpper() * SLIDER_RANGE)); brightnessSlider.setValue((int)(hsbDecorator.getBrightnessLower() * SLIDER_RANGE)); brightnessSlider.setUpperValue((int)(hsbDecorator.getBrightnessUpper() * SLIDER_RANGE)); settingValues = false; getDecorator(); tableModel.fireTableDataChanged(); } @Override public DiscreteColourDecorator getDecorator() { hsbDecorator.setSecondaryCount(secondaryCountSpinnerModel.getNumber().intValue()); hsbDecorator.setHueLower(((float) hueSlider.getValue()) / SLIDER_RANGE); hsbDecorator.setHueUpper(((float) hueSlider.getUpperValue()) / SLIDER_RANGE); hsbDecorator.setSaturationLower(((float) saturationSlider.getValue()) / SLIDER_RANGE); hsbDecorator.setSaturationUpper(((float) saturationSlider.getUpperValue()) / SLIDER_RANGE); hsbDecorator.setBrightnessLower(((float) brightnessSlider.getValue()) / SLIDER_RANGE); hsbDecorator.setBrightnessUpper(((float) brightnessSlider.getUpperValue()) / SLIDER_RANGE); return hsbDecorator; } private boolean settingValues = false; @Override public JPanel getPanel() { if (panel == null) { final OptionsPanel options = new OptionsPanel(6, 6); options.addComponentWithLabel("Primary: ", primaryAxisCombo); options.addComponentWithLabel("Secondary count: ", secondaryCountSpinner); options.addComponentWithLabel("Hue: ", hueSlider); options.addComponentWithLabel("Saturation: ", saturationSlider); options.addComponentWithLabel("Brightness: ", brightnessSlider); primaryAxisCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { getDecorator(); tableModel.fireTableDataChanged(); } }); ChangeListener listener = new ChangeListener() { public void stateChanged(ChangeEvent e) { if (!settingValues) { getDecorator(); tableModel.fireTableDataChanged(); } } }; secondaryCountSpinner.addChangeListener(listener); hueSlider.addChangeListener(listener); saturationSlider.addChangeListener(listener); brightnessSlider.addChangeListener(listener); panel = options; } return panel; } @Override public String getName() { return HSB_SPECTRUM; } private JComboBox primaryAxisCombo = new JComboBox(HSBDiscreteColourDecorator.Axis.values()); private SpinnerNumberModel secondaryCountSpinnerModel = new SpinnerNumberModel(2, 1, 100, 1); private JSpinner secondaryCountSpinner = new JSpinner(secondaryCountSpinnerModel); private RangeSlider hueSlider; private RangeSlider saturationSlider; private RangeSlider brightnessSlider; private HSBDiscreteColourDecorator hsbDecorator = null; private JPanel panel = null; } private class FixedColourSchemePanel implements ColourSchemePanel { public FixedColourSchemePanel() { } public void setDecorator(DiscreteColourDecorator decorator) { if (decorator instanceof FixedDiscreteColourDecorator) { fixedDecorator = (FixedDiscreteColourDecorator)decorator; } else { if (fixedDecorator == null) { fixedDecorator = new FixedDiscreteColourDecorator(decorator.getAttributeName()); } } fixedDecorator.setValues(discreteValues); } @Override public DiscreteColourDecorator getDecorator() { return fixedDecorator; } @Override public JPanel getPanel() { if (panel == null) { final OptionsPanel options = new OptionsPanel(6, 6); panel = options; } return panel; } @Override public String getName() { return FIXED_COLOURS; } private FixedDiscreteColourDecorator fixedDecorator = null; private JPanel panel = null; } }figtree-1.4.3/src/figtree/treeviewer/ExtendedTreeViewer.java000077500000000000000000000206651277473563300242030ustar00rootroot00000000000000/* * ExtendedTreeViewer.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jebl.evolution.alignments.Alignment; import jebl.evolution.alignments.Pattern; import jebl.evolution.graphs.Node; import jebl.evolution.taxa.Taxon; import jebl.evolution.trees.Tree; import jebl.util.Attributable; import jam.panels.StatusListener; import jam.panels.StatusProvider; import figtree.treeviewer.annotations.AnnotationDefinition; import figtree.treeviewer.painters.CharactersPainter; import javax.swing.*; import java.awt.*; import java.util.*; import java.util.List; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ExtendedTreeViewer extends DefaultTreeViewer implements StatusProvider { public ExtendedTreeViewer() { this(null); } public ExtendedTreeViewer(JFrame frame) { super(frame); // setTreesPerPage(1); setBackground(Color.white); } public void setPattern(Pattern pattern) { if (pattern != null) { // setBranchDecorator(new ParsimonyBranchDecorator(pattern)); } else { setBranchDecorator(null, false); } } public void addTree(Tree tree) { Set names = new TreeSet(); for (Node node : tree.getNodes()) { names.addAll(node.getAttributeNames()); } for (Taxon taxon : tree.getTaxa()) { names.addAll(taxon.getAttributeNames()); } for (String name : names) { if (!name.startsWith("!")) { AnnotationDefinition annotation = getAnnotationDefinitions().get(name); Set items = new HashSet(tree.getNodes()); items.addAll(tree.getTaxa()); AnnotationDefinition.Type type = AnnotationDefinition.guessType(name, items); if (annotation == null) { annotation = new AnnotationDefinition(name, type); getAnnotationDefinitions().put(name, annotation); } else if (type != annotation.getType()){ AnnotationDefinition.Type newType = AnnotationDefinition.Type.STRING; if (type == AnnotationDefinition.Type.INTEGER && annotation.getType() == AnnotationDefinition.Type.REAL) { newType = AnnotationDefinition.Type.REAL; } if (newType != type) { annotation = new AnnotationDefinition(name, newType); getAnnotationDefinitions().put(name, annotation); } } } } super.addTree(tree); showStatus(); } public void showTree(int index) { super.showTree(index); showStatus(); } public void setCharacters(Alignment characters) { CharactersPainter painter = new CharactersPainter(characters); setTipLabelPainter(painter); } public void setTaxonAnnotations(Map> annotations) { for (AnnotationDefinition definition: annotations.keySet()) { getAnnotationDefinitions().put(definition.getName(), definition); Map annotation = annotations.get(definition); for (Taxon taxon : annotation.keySet()) { taxon.setAttribute(definition.getName(), annotation.get(taxon)); } } fireAnnotationsChanged(); } public void showStatus() { fireStatusChanged(0, "Showing tree " + Integer.toString(getCurrentTreeIndex() + 1) + " / " + getTreeCount()); } public void showInfomation() { } public void showStatistics() { } public void annotateSelected(String name, Object value) { annotateSelectedNodes(name, value); annotateSelectedTips(name, value); fireAnnotationsChanged(); } public Map getAnnotationDefinitions() { if (annotations == null) { annotations = new HashMap(); } return annotations; } public void setAnnotationDefinitions(List annotations) { if (this.annotations == null) { this.annotations = new HashMap(); } this.annotations.clear(); for (AnnotationDefinition definition : annotations) { this.annotations.put(definition.getName(), definition); } } public void annotateNodesFromTips(String annotationName) { List stateCodes = new ArrayList(); Map stateMap = new HashMap(); Tree tree = treePane.getTree(); for (Node node : tree.getExternalNodes()) { Taxon taxon = tree.getTaxon(node); Object state = taxon.getAttribute(annotationName); int index = stateCodes.indexOf(state); if (index == -1) { index = stateCodes.size(); stateCodes.add(state); } stateMap.put(taxon, index); node.setAttribute(annotationName, state); } Parsimony parsimony = new Parsimony(stateCodes.size(), stateMap); for (Node node : tree.getInternalNodes()) { Integer stateIndex = parsimony.getState(tree, node); Object state = null; if (stateIndex != null) { state = stateCodes.get(stateIndex); } node.setAttribute(annotationName, state); } fireAnnotationsChanged(); } public void annotateTipsFromNodes(String annotationName) { Tree tree = treePane.getTree(); for (Node node : tree.getExternalNodes()) { Object state = node.getAttribute(annotationName); if (state != null) { Taxon taxon = tree.getTaxon(node); taxon.setAttribute(annotationName, state); } } fireAnnotationsChanged(); } private List listeners = new ArrayList(); public void addAnnotationsListener(AnnotationsListener listener) { listeners.add(listener); } public void fireAnnotationsChanged() { for (AnnotationsListener listener : listeners) { listener.annotationsChanged(); } fireTreeChanged(); } private static Map annotations = null; private final StatusProvider.Helper statusHelper = new StatusProvider.Helper(); public void addStatusListener(StatusListener statusListener) { statusHelper.addStatusListener(statusListener); } public void removeStatusListener(StatusListener statusListener) { statusHelper.removeStatusListener(statusListener); } public void fireStatusChanged(int status, String statusText) { statusHelper.fireStatusChanged(status, statusText); } public void addOverrideProvider(StatusProvider provider) { statusHelper.addOverrideProvider(provider); } public void removeOverrideProvider(StatusProvider provider) { statusHelper.removeOverrideProvider(provider); } public void fireStatusButtonPressed() { statusHelper.fireStatusButtonPressed(); } public void statusButtonPressed() { statusHelper.statusButtonPressed(); } public int getStatus() { return statusHelper.getStatus(); } public String getStatusText() { return statusHelper.getStatusText(); } public void setStatusText(String statusText) { statusHelper.fireStatusChanged(0, statusText); } }figtree-1.4.3/src/figtree/treeviewer/FindDialog.java000077500000000000000000000150571277473563300224400ustar00rootroot00000000000000/* * FindDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.DefaultTreeViewer; import jam.panels.OptionsPanel; import figtree.treeviewer.annotations.AnnotationDefinition; import javax.swing.*; import javax.swing.border.EmptyBorder; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemListener; import java.awt.event.ItemEvent; import java.util.List; import figtree.ui.components.RealNumberField; import figtree.ui.components.WholeNumberField; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FindDialog { public enum Target { TAXON_LABEL("Taxon Label"), BRANCH_LENGTH("Branch Length"), NODE_AGE("Node Age"), ANY_ANNOTATION("Any Annotation"), ANNOTATION("Annotation"); Target(String name) { this.name = name; } public String toString() { return name; } private String name; } private JFrame frame; private JComboBox targetCombo = null; private JComboBox textSearchCombo = new JComboBox(DefaultTreeViewer.TextSearchType.values()); private JComboBox numberSearchCombo = new JComboBox(DefaultTreeViewer.NumberSearchType.values()); private AnnotationDefinition.Type type = AnnotationDefinition.Type.STRING; private JTextField searchText = new JTextField(); private RealNumberField doubleText = new RealNumberField(); private WholeNumberField integerText = new WholeNumberField(); private JCheckBox caseSensitiveCheck = new JCheckBox("Case sensitive"); private JCheckBox findAllCheck = new JCheckBox("Find all"); private int selectedTargetIndex = 0; public FindDialog(JFrame frame) { this.frame = frame; } public int showDialog(List annotations) { OptionsPanel options = new OptionsPanel(12, 12); searchText.setColumns(18); final JPanel panel = new JPanel(new BorderLayout(6,6)); targetCombo = new JComboBox(); targetCombo.addItem(Target.TAXON_LABEL); targetCombo.addItem(Target.BRANCH_LENGTH); targetCombo.addItem(Target.NODE_AGE); targetCombo.addItem(Target.ANY_ANNOTATION); for (AnnotationDefinition annotation : annotations) { targetCombo.addItem(annotation); } panel.add(targetCombo, BorderLayout.WEST); panel.add(textSearchCombo, BorderLayout.CENTER); panel.add(searchText, BorderLayout.EAST); options.addComponent(panel); options.addComponent(caseSensitiveCheck); // options.addComponent(findAllCheck); JOptionPane optionPane = new JOptionPane(options, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); final JDialog dialog = optionPane.createDialog(frame, "Find"); dialog.pack(); targetCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { Object item = targetCombo.getSelectedItem(); if (item.equals(Target.BRANCH_LENGTH) || item.equals(Target.NODE_AGE)) { type = AnnotationDefinition.Type.REAL; } else if (item instanceof AnnotationDefinition) { type = ((AnnotationDefinition) item).getType(); } else { type = AnnotationDefinition.Type.STRING; } panel.removeAll(); panel.add(targetCombo, BorderLayout.WEST); switch (type) { case INTEGER: panel.add(numberSearchCombo, BorderLayout.CENTER); panel.add(integerText, BorderLayout.EAST); integerText.setColumns(10); caseSensitiveCheck.setEnabled(false); break; case REAL: panel.add(numberSearchCombo, BorderLayout.CENTER); panel.add(doubleText, BorderLayout.EAST); doubleText.setColumns(10); caseSensitiveCheck.setEnabled(false); break; default: panel.add(textSearchCombo, BorderLayout.CENTER); panel.add(searchText, BorderLayout.EAST); caseSensitiveCheck.setEnabled(true); } dialog.pack(); } }); targetCombo.setSelectedIndex(selectedTargetIndex); dialog.setVisible(true); int result = JOptionPane.CANCEL_OPTION; Integer value = (Integer)optionPane.getValue(); if (value != null && value.intValue() != -1) { result = value.intValue(); } if (result == JOptionPane.OK_OPTION) { } return result; } public Target getSearchTarget() { // store this for next time the dialog is shown... selectedTargetIndex = targetCombo.getSelectedIndex(); Object item = targetCombo.getSelectedItem(); if (item instanceof Target) { return (Target)item; } return Target.ANNOTATION; } public String getSearchTargetString() { return targetCombo.getSelectedItem().toString(); } public boolean isNumericSearchType() { return (type == AnnotationDefinition.Type.REAL || type == AnnotationDefinition.Type.INTEGER); } public TreeViewer.TextSearchType getTextSearchType() { return (TreeViewer.TextSearchType)textSearchCombo.getSelectedItem(); } public TreeViewer.NumberSearchType getNumberSearchType() { return (TreeViewer.NumberSearchType)numberSearchCombo.getSelectedItem(); } public String getSearchText() { return searchText.getText(); } public boolean isCaseSensitive() { return caseSensitiveCheck.isSelected(); } public Number getSearchValue() { if (type == AnnotationDefinition.Type.REAL) { return doubleText.getValue(); } else if (type == AnnotationDefinition.Type.INTEGER) { return integerText.getValue(); } return null; } }figtree-1.4.3/src/figtree/treeviewer/FindPanel.java000077500000000000000000000210061277473563300222670ustar00rootroot00000000000000/* * FindPanel.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.annotations.AnnotationDefinition; import javax.swing.*; import java.awt.*; import java.awt.event.*; import java.util.List; import figtree.ui.components.RealNumberField; import figtree.ui.components.WholeNumberField; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FindPanel extends JPanel { public enum Target { TAXON_LABEL("Taxon Label"), BRANCH_LENGTH("Branch Length"), NODE_AGE("Node Age"), ANY_ANNOTATION("Any Annotation"), ANNOTATION("Annotation"); Target(String name) { this.name = name; } public String toString() { return name; } private String name; } private JComboBox targetCombo = null; private JComboBox textSearchCombo = new JComboBox(DefaultTreeViewer.TextSearchType.values()); private JComboBox numberSearchCombo = new JComboBox(DefaultTreeViewer.NumberSearchType.values()); private AnnotationDefinition.Type type = AnnotationDefinition.Type.STRING; private JTextField searchText = new JTextField(); private RealNumberField doubleText = new RealNumberField(); private WholeNumberField integerText = new WholeNumberField(); private JCheckBox caseSensitiveCheck = new JCheckBox("Case sensitive"); private int selectedTargetIndex = 0; public FindPanel(Action findAllAction, Action findNextAction) { setLayout(new BorderLayout(0,0)); Font font = UIManager.getFont("SmallSystemFont"); if (font != null) { searchText.setFont(font); } searchText.setColumns(18); final JPanel panel = new JPanel(); panel.setLayout(new BoxLayout(panel, BoxLayout.LINE_AXIS)); panel.setOpaque(false); targetCombo = new JComboBox(); targetCombo.addItem(Target.TAXON_LABEL); targetCombo.addItem(Target.BRANCH_LENGTH); targetCombo.addItem(Target.NODE_AGE); targetCombo.addItem(Target.ANY_ANNOTATION); adjustComponent(targetCombo); adjustComponent(textSearchCombo); adjustComponent(numberSearchCombo); adjustComponent(caseSensitiveCheck); panel.add(targetCombo); panel.add(textSearchCombo); panel.add(searchText); panel.add(caseSensitiveCheck); add(panel, BorderLayout.CENTER); if (findNextAction != null) { JButton nextButton = new JButton(findNextAction); adjustComponent(nextButton); panel.add(nextButton); } findAllButton = new JButton(findAllAction); adjustComponent(findAllButton); getInputMap(WHEN_IN_FOCUSED_WINDOW).put(KeyStroke.getKeyStroke(KeyEvent.VK_ENTER, 0), "doFind"); getActionMap().put("doFind", new AbstractAction() { public void actionPerformed(ActionEvent e) { findAllButton.doClick(); } }); final JPanel panel2 = new JPanel(); panel2.setLayout(new BoxLayout(panel2, BoxLayout.LINE_AXIS)); panel2.setOpaque(false); panel2.add(findAllButton); add(panel2, BorderLayout.EAST); targetCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { Object item = targetCombo.getSelectedItem(); if (item != null) { if (item.equals(Target.BRANCH_LENGTH) || item.equals(Target.NODE_AGE)) { type = AnnotationDefinition.Type.REAL; } else if (item instanceof AnnotationDefinition) { type = ((AnnotationDefinition) item).getType(); } else { type = AnnotationDefinition.Type.STRING; } panel.removeAll(); panel.add(targetCombo); switch (type) { case INTEGER: panel.add(numberSearchCombo); panel.add(integerText); integerText.setColumns(10); panel.add(caseSensitiveCheck); caseSensitiveCheck.setEnabled(false); break; case REAL: panel.add(numberSearchCombo); panel.add(doubleText); doubleText.setColumns(10); panel.add(caseSensitiveCheck); caseSensitiveCheck.setEnabled(false); break; default: panel.add(textSearchCombo); panel.add(searchText); panel.add(caseSensitiveCheck); caseSensitiveCheck.setEnabled(true); } } revalidate(); repaint(); } }); targetCombo.setSelectedIndex(selectedTargetIndex); } public void setup(List annotations) { Object item = targetCombo.getSelectedItem(); targetCombo.removeAllItems(); targetCombo.addItem(Target.TAXON_LABEL); targetCombo.addItem(Target.BRANCH_LENGTH); targetCombo.addItem(Target.NODE_AGE); for (AnnotationDefinition annotation : annotations) { targetCombo.addItem(annotation); } targetCombo.addItem(Target.ANY_ANNOTATION); targetCombo.setSelectedItem(item); } public void doFind() { findAllButton.doClick(); } protected void adjustComponent(JComponent comp) { // comp.putClientProperty("Quaqua.Component.visualMargin", new Insets(0,0,0,0)); Font font = UIManager.getFont("SmallSystemFont"); if (font != null) { comp.setFont(font); } comp.putClientProperty("JComponent.sizeVariant", "small"); if (comp instanceof JButton) { comp.putClientProperty("JButton.buttonType", "roundRect"); comp.setFocusable(false); } if (comp instanceof JComboBox) { comp.putClientProperty("JComboBox.isSquare", Boolean.TRUE); comp.setFocusable(false); } if (comp instanceof JCheckBox) { comp.setFocusable(false); } } public Target getSearchTarget() { // store this for next time the dialog is shown... selectedTargetIndex = targetCombo.getSelectedIndex(); Object item = targetCombo.getSelectedItem(); if (item instanceof Target) { return (Target)item; } return Target.ANNOTATION; } public String getSearchTargetString() { return targetCombo.getSelectedItem().toString(); } public boolean isNumericSearchType() { return (type == AnnotationDefinition.Type.REAL || type == AnnotationDefinition.Type.INTEGER); } public TreeViewer.TextSearchType getTextSearchType() { return (TreeViewer.TextSearchType)textSearchCombo.getSelectedItem(); } public TreeViewer.NumberSearchType getNumberSearchType() { return (TreeViewer.NumberSearchType)numberSearchCombo.getSelectedItem(); } public String getSearchText() { return searchText.getText(); } public boolean isCaseSensitive() { return caseSensitiveCheck.isSelected(); } public Number getSearchValue() { if (type == AnnotationDefinition.Type.REAL) { return doubleText.getValue(); } else if (type == AnnotationDefinition.Type.INTEGER) { return integerText.getValue(); } return null; } final JButton findAllButton; }figtree-1.4.3/src/figtree/treeviewer/FontDialog.java000066400000000000000000000045521277473563300224610ustar00rootroot00000000000000/* * FontDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; import java.awt.*; import figtree.treeviewer.painters.LabelPainterController; import figtree.ui.FontChooserPanel; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FontDialog { private OptionsPanel options; private final JFrame frame; private FontChooserPanel chooser = null; public FontDialog(final JFrame frame) { this.frame = frame; } public Font getFont() { return chooser.getSelectedFont(); } public int showDialog(final Font font) { options = new OptionsPanel(); if (chooser == null) { chooser = new FontChooserPanel(font); } else { chooser.setSelectedFont(font); } options.addSpanningComponent(chooser); JOptionPane optionPane = new JOptionPane(options, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); final JDialog dialog = optionPane.createDialog(frame, "Setup colour range"); dialog.pack(); dialog.setVisible(true); int result = JOptionPane.CANCEL_OPTION; Integer value = (Integer)optionPane.getValue(); if (value != null && value.intValue() != -1) { result = value.intValue(); } return result; } } figtree-1.4.3/src/figtree/treeviewer/MultiPaneTreeViewer.java000077500000000000000000000371501277473563300243360ustar00rootroot00000000000000/* * MultiPaneTreeViewer.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.painters.*; import jebl.evolution.trees.*; import jebl.evolution.graphs.Node; import figtree.treeviewer.treelayouts.TreeLayout; import figtree.treeviewer.decorators.Decorator; import javax.swing.*; import java.awt.*; import java.awt.print.*; import java.util.*; import jam.panels.StatusProvider; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class MultiPaneTreeViewer extends TreeViewer { private final static double MAX_ZOOM = 20; private final static double MAX_VERTICAL_EXPANSION = 20; /** * Creates new TreeViewer */ public MultiPaneTreeViewer() { treePanes.add(new TreePane()); setLayout(new BorderLayout()); treePanePanel = new MultiPaneTreePanel(); treePanePanel.setLayout(new BoxLayout(treePanePanel, BoxLayout.PAGE_AXIS)); JScrollPane scrollPane = new JScrollPane(treePanePanel, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS); scrollPane.setMinimumSize(new Dimension(150, 150)); scrollPane.setBorder(null); viewport = scrollPane.getViewport(); add(scrollPane, BorderLayout.CENTER); } public void setTree(Tree tree) { trees.clear(); addTree(tree); showTree(0); } public void setTrees(Collection trees) { this.trees.clear(); for (Tree tree : trees) { addTree(tree); } showTree(0); } protected void addTree(Tree tree) { this.trees.add(tree); showTree(trees.size() - 1); } public void addTrees(Collection trees) { int count = getTreeCount(); for (Tree tree : trees) { addTree(tree); } showTree(count); } public Tree getTree() { return trees.get(0); } public java.util.List getTrees() { return trees; } public int getTreesPerPage() { return treesPerPage; } public void setTreesPerPage(int treesPerPage) { this.treesPerPage = treesPerPage; if (treePanes.size() < treesPerPage) { while (treePanes.size() < treesPerPage) { treePanes.add(new TreePane()); } } else if (treePanes.size() > treesPerPage) { while (treePanes.size() > treesPerPage) { treePanes.remove(treePanes.size() - 1); } } showTree(currentTreeIndex); } private void setupTreePane(TreePane treePane) { treePane.setAutoscrolls(true); //enable synthetic drag events // This overrides MouseListener and MouseMotionListener to allow selection in the TreePane - // It installs itself within the constructor. treePaneSelector = new TreePaneSelector(treePane); } public Tree getCurrentTree() { return trees.get(currentTreeIndex); } public int getCurrentTreeIndex() { return currentTreeIndex; } public int getTreeCount() { if (trees == null) return 0; return trees.size(); } public StatusProvider getStatusProvider() { return null; } public void showTree(int index) { int i = index; for (TreePane treePane : treePanes) { if (i < trees.size()) { Tree tree = trees.get(i); if (tree instanceof RootedTree) { treePane.setTree((RootedTree)tree); } else { treePane.setTree(Utils.rootTheTree(tree)); } } else { treePane.setTree(null); } i++; } currentTreeIndex = index; treePanePanel.removeAll(); setLayout(new BoxLayout(this, BoxLayout.PAGE_AXIS)); for (TreePane treePane : treePanes) { treePanePanel.add(treePane); setupTreePane(treePane); } fireTreeChanged(); } public void showNextTree() { if (currentTreeIndex < trees.size() - 1) { showTree(currentTreeIndex + 1); } } public void showPreviousTree() { if (currentTreeIndex > 0) { showTree(currentTreeIndex - 1); } } public void setTreeLayout(TreeLayout treeLayout) { for (TreePane treePane : treePanes) { treePane.setTreeLayout(treeLayout); } } private boolean zoomPending = false; private double zoom = 0.0, verticalExpansion = 0.0; public void setZoom(double zoom) { this.zoom = zoom * MAX_ZOOM; refreshZoom(); } public void setVerticalExpansion(double verticalExpansion) { this.verticalExpansion = verticalExpansion * MAX_VERTICAL_EXPANSION; refreshZoom(); } public boolean verticalExpansionAllowed() { return !treePanes.get(0).maintainAspectRatio(); } public void setTimeScale(TimeScale timeScale) { for (TreePane treePane : treePanes) { treePane.setTimeScale(timeScale); } } private void refreshZoom() { setZoom(zoom, zoom + verticalExpansion); } private void setZoom(double xZoom, double yZoom) { Dimension viewportSize = viewport.getViewSize(); Point position = viewport.getViewPosition(); Dimension extentSize = viewport.getExtentSize(); double w = extentSize.getWidth() * (1.0 + xZoom); double h = extentSize.getHeight() * (1.0 + yZoom); Dimension newSize = new Dimension((int) w, (int) h / treesPerPage); for (TreePane treePane : treePanes) { treePane.setPreferredSize(newSize); treePane.revalidate(); } double cx = position.getX() + (0.5 * extentSize.getWidth()); double cy = position.getY() + (0.5 * extentSize.getHeight()); double rx = ((double) newSize.getWidth()) / viewportSize.getWidth(); double ry = ((double) newSize.getHeight()) / viewportSize.getHeight(); double px = (cx * rx) - (extentSize.getWidth() / 2.0); double py = (cy * ry) - (extentSize.getHeight() / 2.0); Point newPosition = new Point((int) px, (int) py); viewport.setViewPosition(newPosition); } public boolean hasSelection() { for (TreePane treePane : treePanes) { if (treePane.hasSelection()) return true; } return false; } public Set getSelectedNodes() { for (TreePane treePane : treePanes) { if (treePane.hasSelection()) return treePane.getSelectedNodes(); } return Collections.emptySet(); } public Set getSelectedTips() { for (TreePane treePane : treePanes) { if (treePane.hasSelection()) return treePane.getSelectedTips(); } return Collections.emptySet(); } public void selectTaxa(String attributeName, TextSearchType searchType, String searchString, boolean caseSensitive) { } public void selectNodes(String attribute, TextSearchType searchType, String searchString, boolean caseSensitive) { } public void selectTaxa(String attributeName, NumberSearchType searchType, Number searchValue) { } public void selectNodes(String attributeName, NumberSearchType searchType, Number searchValue) { } public void selectTaxa(final Collection taxonNames) { } public void collapseSelectedNodes() { // treePane.collapseSelectedNodes(); } public void annotateSelectedNodes(String name, Object value) { // treePane.annotateSelectedNodes(name, value); fireTreeSettingsChanged(); } public void annotateSelectedTips(String name, Object value) { // treePane.annotateSelectedTips(name, value); fireTreeSettingsChanged(); } public void selectAll() { // if (treePaneSelector.getSelectionMode() == TreePaneSelector.SelectionMode.TAXA) { // treePane.selectAllTaxa(); // } else { // treePane.selectAllNodes(); // } } public void clearSelectedTaxa() { // treePane.clearSelection(); } public void addTreeSelectionListener(TreeSelectionListener treeSelectionListener) { for (TreePane treePane : treePanes) { treePane.addTreeSelectionListener(treeSelectionListener); } } public void removeTreeSelectionListener(TreeSelectionListener treeSelectionListener) { for (TreePane treePane : treePanes) { treePane.removeTreeSelectionListener(treeSelectionListener); } } public void setSelectionMode(TreePaneSelector.SelectionMode selectionMode) { // TreePaneSelector.SelectionMode oldSelectionMode = treePaneSelector.getSelectionMode(); // // if (selectionMode == oldSelectionMode) { // return; // } // // if (oldSelectionMode == TreePaneSelector.SelectionMode.TAXA) { // treePane.selectNodesFromSelectedTips(); // } else if (selectionMode == TreePaneSelector.SelectionMode.TAXA) { // treePane.selectTipsFromSelectedNodes(); // } else if (selectionMode == TreePaneSelector.SelectionMode.CLADE) { // treePane.selectCladesFromSelectedNodes(); // } // treePaneSelector.setSelectionMode(selectionMode); } public void setDragMode(TreePaneSelector.DragMode dragMode) { treePaneSelector.setDragMode(dragMode); } // A load of deligated method calls through to treePane (which is now hidden outside the package). public void setTipLabelPainter(LabelPainter tipLabelPainter) { for (TreePane treePane : treePanes) { treePane.setTipLabelPainter(tipLabelPainter); } // tipLabelPainter.setupAttributes(trees); fireTreeSettingsChanged(); } public void setNodeLabelPainter(LabelPainter nodeLabelPainter) { for (TreePane treePane : treePanes) { treePane.setNodeLabelPainter(nodeLabelPainter); } // nodeLabelPainter.setupAttributes(trees); fireTreeSettingsChanged(); } public void setNodeBarPainter(NodeBarPainter nodeBarPainter) { for (TreePane treePane : treePanes) { treePane.setNodeBarPainter(nodeBarPainter); } // nodeBarPainter.setupAttributes(trees); fireTreeSettingsChanged(); } public void setNodeShapePainter(NodeShapePainter nodeShapePainter) { for (TreePane treePane : treePanes) { treePane.setNodeShapePainter(nodeShapePainter); } fireTreeSettingsChanged(); } public void setBranchLabelPainter(LabelPainter branchLabelPainter) { for (TreePane treePane : treePanes) { treePane.setBranchLabelPainter(branchLabelPainter); } fireTreeSettingsChanged(); } public void addScalePainter(ScalePainter scalePainter) { for (TreePane treePane : treePanes) { treePane.addScalePainter(scalePainter); } fireTreeSettingsChanged(); } public void removeScalePainter(ScalePainter scalePainter) { for (TreePane treePane : treePanes) { treePane.removeScalePainter(scalePainter); } fireTreeSettingsChanged(); } public void setScaleGridPainter(ScaleGridPainter scaleGridPainter) { for (TreePane treePane : treePanes) { treePane.setScaleGridPainter(scaleGridPainter); } fireTreeSettingsChanged(); } public void setLegendPainter(LegendPainter legendPainter) { for (TreePane treePane : treePanes) { treePane.setLegendPainter(legendPainter); } // legendPainter.setupAttributes(trees); fireTreeSettingsChanged(); } public void setBranchDecorator(Decorator branchDecorator, boolean isGradient) { for (TreePane treePane : treePanes) { treePane.setBranchDecorator(branchDecorator, isGradient); } fireTreeSettingsChanged(); } public void setBranchColouringDecorator(String branchColouringAttribute, Decorator branchColouringDecorator) { for (TreePane treePane : treePanes) { treePane.setBranchColouringDecorator(branchColouringAttribute, branchColouringDecorator); } fireTreeSettingsChanged(); } public void setNodeBackgroundDecorator(Decorator nodeBackgroundDecorator) { for (TreePane treePane : treePanes) { treePane.setNodeBackgroundDecorator(nodeBackgroundDecorator); } fireTreeSettingsChanged(); } public void setHilightingGradient(boolean hilightingGradient) { for (TreePane treePane : treePanes) { treePane.setHilightingGradient(hilightingGradient); } } public void setSelectionColor(Color selectionColor) { for (TreePane treePane : treePanes) { treePane.setSelectionColor(selectionColor); } fireTreeSettingsChanged(); } public Paint getSelectionPaint() { return treePanes.get(0).getSelectionPaint(); } public void setBranchStroke(BasicStroke branchStroke) { for (TreePane treePane : treePanes) { treePane.setBranchStroke(branchStroke); } fireTreeSettingsChanged(); } public boolean isTransformBranchesOn() { return treePanes.get(0).isTransformBranchesOn(); } public TransformedRootedTree.Transform getBranchTransform() { return treePanes.get(0).getBranchTransform(); } public void setTransformBranchesOn(boolean transformBranchesOn) { for (TreePane treePane : treePanes) { treePane.setTransformBranchesOn(transformBranchesOn); } fireTreeSettingsChanged(); } public void setBranchTransform(TransformedRootedTree.Transform transform) { for (TreePane treePane : treePanes) { treePane.setBranchTransform(transform); } fireTreeSettingsChanged(); } public boolean isOrderBranchesOn() { return treePanes.get(0).isOrderBranchesOn(); } public SortedRootedTree.BranchOrdering getBranchOrdering() { return treePanes.get(0).getBranchOrdering(); } public void setOrderBranchesOn(boolean orderBranchesOn) { for (TreePane treePane : treePanes) { treePane.setOrderBranchesOn(orderBranchesOn); } fireTreeSettingsChanged(); } public void setBranchOrdering(SortedRootedTree.BranchOrdering branchOrdering) { for (TreePane treePane : treePanes) { treePane.setBranchOrdering(branchOrdering); } fireTreeSettingsChanged(); } public boolean isRootingOn() { return treePanes.get(0).isOrderBranchesOn(); } public TreePane.RootingType getRootingType() { return treePanes.get(0).getRootingType(); } public void setRootingOn(boolean rootingOn) { for (TreePane treePane : treePanes) { treePane.setRootingOn(rootingOn); } fireTreeSettingsChanged(); } public void setRootingType(TreePane.RootingType rootingType) { for (TreePane treePane : treePanes) { treePane.setRootingType(rootingType); } fireTreeSettingsChanged(); } public JComponent getContentPane() { return treePanePanel; } public void paint(Graphics g) { if( zoomPending ) { refreshZoom(); zoomPending = false; } super.paint(g); } public int print(Graphics g, PageFormat pageFormat, int pageIndex) throws PrinterException { return treePanePanel.print(g, pageFormat, pageIndex); } public void addTreeViewerListener(TreeViewerListener listener) { listeners.add(listener); } public void removeTreeViewerListener(TreeViewerListener listener) { listeners.remove(listener); } public void fireTreeChanged() { for (TreeViewerListener listener : listeners) { listener.treeChanged(); } } public void fireTreeSettingsChanged() { for (TreeViewerListener listener : listeners) { listener.treeSettingsChanged(); } } private java.util.List listeners = new ArrayList(); private java.util.List trees = new ArrayList(); private java.util.List treePanes = new ArrayList(); private int currentTreeIndex = 0; private int treesPerPage = 1; private MultiPaneTreePanel treePanePanel; protected TreePaneSelector treePaneSelector; protected JViewport viewport; class MultiPaneTreePanel extends JPanel implements Printable { public int print(Graphics graphics, PageFormat pageFormat, int i) throws PrinterException { return 0; } } } figtree-1.4.3/src/figtree/treeviewer/MultiPaneTreeViewerController.java000077500000000000000000000071011277473563300263730ustar00rootroot00000000000000/* * MultiPaneTreeViewerController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jebl.evolution.trees.Tree; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.util.Map; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class MultiPaneTreeViewerController extends AbstractController { public MultiPaneTreeViewerController(final MultiPaneTreeViewer treeViewer) { titleLabel = new JLabel("Current Tree"); optionsPanel = new ControllerOptionsPanel(2, 2); final JLabel treeNameLabel = new JLabel("Tree 1"); final SpinnerNumberModel spinnerModel = new SpinnerNumberModel(1, 1, 1, 1); JSpinner currentTreeSpinner = new JSpinner(spinnerModel); currentTreeSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { treeViewer.showTree((Integer)spinnerModel.getValue() - 1); } }); final JComboBox treesPerPageCombo = new JComboBox(new String[] { "1", "2", "3", "4", "5", "6", "7", "8" }); treesPerPageCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { treeViewer.setTreesPerPage(treesPerPageCombo.getSelectedIndex() + 1); } }); treeViewer.addTreeViewerListener(new TreeViewerListener() { public void treeChanged() { int index = treeViewer.getCurrentTreeIndex() + 1; int treeCount = treeViewer.getTrees().size(); Tree tree = treeViewer.getCurrentTree(); spinnerModel.setValue(index); spinnerModel.setMaximum(treeCount); String name = (String)tree.getAttribute("name"); if (name != null) { treeNameLabel.setText(name); } else { treeNameLabel.setText("Tree " + index); } titleLabel.setText("Current Tree: " + index + " / " + treeCount); } public void treeSettingsChanged() { // nothing to do } }); optionsPanel.addComponentWithLabel("Name:", treeNameLabel); optionsPanel.addComponentWithLabel("Tree:", currentTreeSpinner); optionsPanel.addComponentWithLabel("Trees per page:", treesPerPageCombo); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return true; } public void initialize() { // nothing to do } public void setSettings(Map settings) { } public void getSettings(Map settings) { } private final JLabel titleLabel; private final OptionsPanel optionsPanel; } figtree-1.4.3/src/figtree/treeviewer/MultipleTreesController.java000077500000000000000000000062211277473563300252730ustar00rootroot00000000000000/* * MultipleTreesController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jebl.evolution.trees.Tree; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.util.Map; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class MultipleTreesController extends AbstractController { public MultipleTreesController(final TreeViewer treeViewer) { titleLabel = new JLabel("Current Tree"); optionsPanel = new ControllerOptionsPanel(2, 2); final JLabel treeNameLabel = new JLabel("Tree 1"); final SpinnerNumberModel spinnerModel = new SpinnerNumberModel(1, 1, 100000, 1); JSpinner currentTreeSpinner = new JSpinner(spinnerModel); currentTreeSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { treeViewer.showTree((Integer)spinnerModel.getValue() - 1); } }); treeViewer.addTreeViewerListener(new TreeViewerListener() { public void treeChanged() { int index = treeViewer.getCurrentTreeIndex() + 1; int treeCount = treeViewer.getTrees().size(); if (treeCount > 0) { Tree tree = treeViewer.getCurrentTree(); spinnerModel.setValue(index); spinnerModel.setMaximum(treeCount); String name = (String)tree.getAttribute("name"); if (name != null) { treeNameLabel.setText(name); } else { treeNameLabel.setText("Tree " + index); } titleLabel.setText("Current Tree: " + index + " / " + treeCount); } else { titleLabel.setText("No trees"); } } public void treeSettingsChanged() { // nothing to do } }); optionsPanel.addComponentWithLabel("Name:", treeNameLabel); optionsPanel.addComponentWithLabel("Tree:", currentTreeSpinner); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { } public void getSettings(Map settings) { } private final JLabel titleLabel; private final OptionsPanel optionsPanel; } figtree-1.4.3/src/figtree/treeviewer/OldContinuousColourScaleDialog.java000077500000000000000000000141771277473563300265230ustar00rootroot00000000000000/* * OldContinuousColourScaleDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.decorators.Decorator; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import figtree.ui.components.RealNumberField; import figtree.ui.components.ColorWellButton; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ @Deprecated public class OldContinuousColourScaleDialog { public static class ColourSettings { // continuous colour settings: public boolean autoRange = true; public double fromValue = 0.0; public double toValue = 1.0; public Color fromColour; public Color toColour; public Color middleColour; } private JFrame frame; private Decorator decorator; private JCheckBox autoScaleCheck; private JLabel fromLabel; private RealNumberField fromNumberField; private JLabel toLabel; private RealNumberField toNumberField; private ColorWellButton fromColourButton; private ColorWellButton toColourButton; private JCheckBox middleColourCheck; private ColorWellButton middleColourButton; public OldContinuousColourScaleDialog(final JFrame frame, final ColourSettings settings) { this.frame = frame; autoScaleCheck = new JCheckBox("Auto-scale range between min and max values"); autoScaleCheck.setSelected(settings.autoRange); fromLabel = new JLabel("Range from:"); fromNumberField = new RealNumberField(); fromNumberField.setColumns(10); fromNumberField.setValue(settings.fromValue); toLabel = new JLabel("to:"); toNumberField = new RealNumberField(); toNumberField.setColumns(10); toNumberField.setValue(settings.toValue); fromLabel.setEnabled(false); fromNumberField.setEnabled(false); toLabel.setEnabled(false); toNumberField.setEnabled(false); middleColourCheck = new JCheckBox("through:"); fromColourButton = new ColorWellButton(settings.fromColour, "Choose Start Colour"); toColourButton = new ColorWellButton(settings.toColour, "Choose End Colour"); middleColourButton = new ColorWellButton(settings.middleColour, "Choose Middle Colour"); autoScaleCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { boolean enabled = !autoScaleCheck.isSelected(); fromLabel.setEnabled(enabled); fromNumberField.setEnabled(enabled); toLabel.setEnabled(enabled); toNumberField.setEnabled(enabled); } }); middleColourCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { middleColourButton.setEnabled(middleColourCheck.isSelected()); } }); middleColourCheck.setSelected(settings.middleColour != null); middleColourButton.setEnabled(settings.middleColour != null); } public int showDialog() { final OptionsPanel options = new OptionsPanel(6, 6); boolean isResizable = false; options.addComponent(autoScaleCheck); JPanel panel = new JPanel(); panel.setLayout(new FlowLayout()); panel.add(fromLabel); panel.add(fromNumberField); panel.add(toLabel); panel.add(toNumberField); options.addComponent(panel); JPanel panel1 = new JPanel(); panel1.setLayout(new FlowLayout()); panel1.add(new JLabel("Colour gradient from:")); panel1.add(fromColourButton); panel1.add(new JLabel("to:")); panel1.add(toColourButton); options.addComponent(panel1); JPanel panel2 = new JPanel(); panel1.setLayout(new FlowLayout()); panel1.add(middleColourCheck); panel1.add(middleColourButton); options.addComponent(panel2); JOptionPane optionPane = new JOptionPane(options, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); final JDialog dialog = optionPane.createDialog(frame, "Setup colour range"); dialog.pack(); dialog.setResizable(isResizable); dialog.setVisible(true); int result = JOptionPane.CANCEL_OPTION; Integer value = (Integer)optionPane.getValue(); if (value != null && value.intValue() != -1) { result = value.intValue(); } return result; } public void getSettings(ColourSettings settings) { settings.autoRange = autoScaleCheck.isSelected(); settings.fromValue = fromNumberField.getValue(); settings.toValue = toNumberField.getValue(); settings.fromColour = fromColourButton.getSelectedColor(); settings.toColour = toColourButton.getSelectedColor(); if (middleColourCheck.isSelected()) { settings.middleColour = middleColourButton.getSelectedColor(); } else { settings.middleColour = null; } } }figtree-1.4.3/src/figtree/treeviewer/Parsimony.java000066400000000000000000000155311277473563300224130ustar00rootroot00000000000000/* * Parsimony.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jebl.evolution.graphs.Node; import jebl.evolution.taxa.Taxon; import jebl.evolution.trees.*; import java.util.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class Parsimony { private final int stateCount; private final Map stateMap; private Map stateSets = new HashMap(); private Map states = new HashMap(); // private boolean[][] union; // Must now be local to recursive function // private boolean[][] intersection; // as nodes are not guaranteed to be called in post-order private RootedTree tree = null; private List taxa; private boolean hasCalculatedSteps = false; private boolean hasRecontructedStates = false; public Parsimony(int stateCount, Map stateMap) { this.stateCount = stateCount; this.stateMap = stateMap; } /** * Returns the reconstructed character states for a given node in the tree. If this method is repeatedly * called with the same tree and patterns then only the first call will reconstruct the states and each * subsequent call will return the stored states. * * @param tree a tree object to reconstruct the characters on * @param node the node of the tree * @return an array containing the reconstructed states for this node */ public Integer getState(Tree tree, Node node) { if (tree == null) { throw new IllegalArgumentException("The tree cannot be null"); } if (!(tree instanceof RootedTree)) { throw new IllegalArgumentException("The tree must be an instance of rooted tree"); } if (this.tree == null || this.tree != tree) { this.tree = (RootedTree) tree; if (!Utils.isBinary(this.tree)) { throw new IllegalArgumentException("The Fitch algorithm can only reconstruct ancestral states on binary trees"); } initialize(); } if (!hasCalculatedSteps) { calculateSteps(this.tree); //this.tree.getRootNode()); hasCalculatedSteps = true; } if (!hasRecontructedStates) { // reconstructStates(this.tree.getRootNode(), -1); reconstructStates2(this.tree.getRootNode(), null); hasRecontructedStates = true; } return states.get(node); } private void initialize() { hasCalculatedSteps = false; hasRecontructedStates = false; for (Node node : tree.getNodes()) { boolean[] stateSet = new boolean[stateCount]; stateSets.put(node, stateSet); } } /** * This is the first pass of the Fitch algorithm. This calculates the set of states * at each node and counts the total number of siteScores (the score). If that is all that * is required then the second pass is not necessary. */ private void calculateSteps(RootedTree tree) { // nodes in pre-order final List nodes = Utils.getNodes(tree, tree.getRootNode()); // used as locals in the loop below, allocated once boolean[] union = new boolean[stateCount]; boolean[] intersection = new boolean[stateCount]; // iterate in reverse - post order. State of child is gurantted to be reasy before parent for (int k = nodes.size() - 1; k >= 0; --k) { final Node node = nodes.get(k); final boolean[] nodeStateSet = stateSets.get(node); if (tree.isExternal(node)) { boolean[] stateSet = stateSets.get(node); Taxon taxon = tree.getTaxon(node); int state = stateMap.get(taxon); stateSet[state] = true; } else { boolean first = true; for (Node child : tree.getChildren(node)) { boolean[] childStateSet = stateSets.get(child); if (first) { copyOf(childStateSet, union); copyOf(childStateSet, intersection); first = false; } else { unionOf(union, childStateSet, union); intersectionOf(intersection, childStateSet, intersection); } } if (sizeOf(intersection) > 0) { copyOf(intersection, nodeStateSet); } else { copyOf(union, nodeStateSet); } } } } /** * The second pass of the Fitch algorithm. This reconstructs the ancestral states at * each node. * * @param node * @param parentState */ private void reconstructStates(Node node, int parentState) { if (!tree.isExternal(node)) { boolean[] nodeStateSet = stateSets.get(node); Integer nodeState = null; if (parentState != -1 && nodeStateSet[parentState]) { nodeState = parentState; } else { nodeState = firstIndexOf(nodeStateSet); } for (Node child : tree.getChildren(node)) { reconstructStates(child, nodeState); } states.put(node, nodeState); } } private boolean[] reconstructStates2(Node node, boolean[] parentStateSet) { boolean[] nodeStateSet = stateSets.get(node); if (!tree.isExternal(node)) { boolean[] union = new boolean[stateCount]; boolean first = true; for (Node child : tree.getChildren(node)) { boolean[] childStateSet = reconstructStates2(child, nodeStateSet); if (first) { copyOf(childStateSet, union); first = false; } else { unionOf(union, childStateSet, union); } } if (parentStateSet != null) { boolean[] intersection = new boolean[stateCount]; intersectionOf(parentStateSet, union, intersection); if (sizeOf(intersection) > 0) { nodeStateSet = intersection; } } if (sizeOf(nodeStateSet) == 1) { states.put(node, firstIndexOf(nodeStateSet)); } } return nodeStateSet; } private static void copyOf(boolean[] s, boolean[] d) { for (int i = 0; i < d.length; i++) { d[i] = s[i]; } } private static void unionOf(boolean[] s1, boolean[] s2, boolean[] d) { for (int i = 0; i < d.length; i++) { d[i] = s1[i] || s2[i]; } } private static void intersectionOf(boolean[] s1, boolean[] s2, boolean[] d) { for (int i = 0; i < d.length; i++) { d[i] = s1[i] && s2[i]; } } private static int firstIndexOf(boolean[] s1) { for (int i = 0; i < s1.length; i++) { if (s1[i]) { return i; } } return -1; } private static int sizeOf(boolean[] s1) { int count = 0; for (int i = 0; i < s1.length; i++) { if (s1[i]) count += 1; } return count; } }figtree-1.4.3/src/figtree/treeviewer/ReRootedTree.java000066400000000000000000000653121277473563300227770ustar00rootroot00000000000000/* * ReRootedTree.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jebl.evolution.graphs.*; import jebl.evolution.taxa.Taxon; import jebl.evolution.trees.*; import jebl.util.AttributableHelper; import jebl.util.HashPair; import java.util.*; /** * A rooted tree concrete class that wraps another tree and provides a differently * rooted view of that tree. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ final public class ReRootedTree implements RootedTree { /** * Make a copy of the given unrooted tree * @param source an unrooted source tree * @param ingroupNode the node on one side of the root * @param outgroupNode the node on the other side of the root * @param ingroupBranchLength the branch length from the root to the ingroup node * @throws jebl.evolution.graphs.Graph.NoEdgeException */ public ReRootedTree(RootedTree source, Node ingroupNode, Node outgroupNode, double ingroupBranchLength) throws NoEdgeException { this.source = source; List children = new ArrayList(); Node node1 = createNodes(source, outgroupNode, ingroupNode); setLength(node1, ingroupBranchLength); children.add(node1); Node node2 = createNodes(source, ingroupNode, outgroupNode); double l = source.getEdgeLength(ingroupNode, outgroupNode); if (outgroupNode == source.getRootNode()) { // the tree is already rooted at the required location for (Node adj : source.getAdjacencies(outgroupNode)) { if (adj != ingroupNode) { l += source.getEdgeLength(outgroupNode, adj); } } } setLength(node2, Math.max(l - ingroupBranchLength, 0.0)); children.add(node2); createInternalNode(null, children); } /** * Clones the entire tree structure from the given (unrooted) Tree. * @param tree the unrooted tree * @param parent the parent node * @param child the child node */ public Node createNodes(RootedTree tree, Node parent, Node child) throws NoEdgeException { Node newNode = null; double length; if (tree.isExternal(child)) { newNode = createExternalNode(child, tree.getTaxon(child)); length = tree.getEdgeLength(parent, child); } else { List adjacencies = tree.getAdjacencies(child); if (adjacencies.size() == 2) { // this is the root node so skip over it... if (adjacencies.get(0) == parent) { newNode = createNodes(tree, child, adjacencies.get(1)); } else { newNode = createNodes(tree, child, adjacencies.get(0)); } length = tree.getEdgeLength(adjacencies.get(0), child) + tree.getEdgeLength(adjacencies.get(1), child); } else { List children = new ArrayList(); for (Node child2 : adjacencies) { if (child2 != parent) { children.add(createNodes(tree, child, child2)); } } if (tree.getParent(parent) == child) { newNode = createInternalNode(parent, children); } else { newNode = createInternalNode(child, children); } length = tree.getEdgeLength(parent, child); } } setLength(newNode, length); return newNode; } /** * Creates a new external node with the given taxon. See createInternalNode * for a description of how to use these methods. * @param source the source node * @return the created node reference */ private Node createExternalNode(Node source, Taxon taxon) { ReRootedNode node = new ReRootedNode(source, taxon); externalNodes.put(taxon, node); return node; } /** * Once a SimpleRootedTree has been created, the node stucture can be created by * calling createExternalNode and createInternalNode. First of all createExternalNode * is called giving Taxon objects for the external nodes. Then these are put into * sets and passed to createInternalNode to create a parent of these nodes. The * last node created using createInternalNode is automatically the root so when * all the nodes are created, the tree is complete. * * @param children the child nodes of this nodes * @return the created node reference */ private ReRootedNode createInternalNode(Node source, List children) { ReRootedNode node = new ReRootedNode(source, children); for (Node child : children) { ((ReRootedNode)child).setParent(node); } internalNodes.add(node); rootNode = node; return node; } public Node getSourceNode(Node node) { return ((ReRootedNode)node).source; } /** * @param node the node whose height is being set * @param height the height */ public void setHeight(Node node, double height) { lengthsKnown = false; heightsKnown = true; // If a single height of a single node is set then // assume that all nodes have heights and by extension, // branch lengths as well as these will be calculated // from the heights hasLengths = true; hasHeights = true; ((ReRootedNode)node).setHeight(height); } /** * @param node the node whose branch length (to its parent) is being set * @param length the length */ public void setLength(Node node, double length) { heightsKnown = false; lengthsKnown = true; // If a single length of a single branch is set then // assume that all branch have lengths and by extension, // node heights as well as these will be calculated // from the lengths hasLengths = true; hasHeights = true; ((ReRootedNode)node).setLength(length); } /** * @param node the node whose children are being requested. * @return the list of nodes that are the children of the given node. * The list may be empty for a terminal node (a tip). */ public List getChildren(Node node) { return new ArrayList(((ReRootedNode)node).getChildren()); } /** * @return Whether this tree has node heights available */ public boolean hasHeights() { return hasHeights; } /** * @param node the node whose height is being requested. * @return the height of the given node. The height will be * less than the parent's height and greater than it children's heights. */ public double getHeight(Node node) { if (!hasHeights) throw new IllegalArgumentException("This tree has no node heights"); if (!heightsKnown) calculateNodeHeights(); return ((ReRootedNode)node).getHeight(); } /** * @return Whether this tree has branch lengths available */ public boolean hasLengths() { return hasLengths; } /** * @param node the node whose branch length (to its parent) is being requested. * @return the length of the branch to the parent node (0.0 if the node is the root). */ public double getLength(Node node) { if (!hasLengths) throw new IllegalArgumentException("This tree has no branch lengths"); if (!lengthsKnown) calculateBranchLengths(); return ((ReRootedNode)node).getLength(); } /** * @param node the node whose parent is requested * @return the parent node of the given node, or null * if the node is the root node. */ public Node getParent(Node node) { if (!(node instanceof ReRootedNode)) { throw new IllegalArgumentException("Node, " + node.toString() + " is not an instance of SimpleRootedNode"); } return ((ReRootedNode)node).getParent(); } public Edge getParentEdge(Node node) { if (!(node instanceof ReRootedNode)) { throw new IllegalArgumentException("Node, " + node.toString() + " is not an instance of SimpleRootedNode"); } return ((ReRootedNode)node).getEdge(); } /** * The root of the tree has the largest node height of * all nodes in the tree. * * @return the root of the tree. */ public Node getRootNode() { return rootNode; } /** * @return a set of all nodes that have degree 1. * These nodes are often refered to as 'tips'. */ public Set getExternalNodes() { return new LinkedHashSet(externalNodes.values()); } /** * @return a set of all nodes that have degree 2 or more. * These nodes are often refered to as internal nodes. */ public Set getInternalNodes() { return new LinkedHashSet(internalNodes); } /** * @return the set of taxa associated with the external * nodes of this tree. The size of this set should be the * same as the size of the external nodes set. */ public Set getTaxa() { return new LinkedHashSet(externalNodes.keySet()); } /** * @param node the node whose associated taxon is being requested. * @return the taxon object associated with the given node, or null * if the node is an internal node. */ public Taxon getTaxon(Node node) { if (!(node instanceof ReRootedNode)) { throw new IllegalArgumentException("Node, " + node.toString() + " is not an instance of SimpleRootedNode. It is an instance of "+node.getClass().getName()); } return ((ReRootedNode)node).getTaxon(); } /** * @param node the node * @return true if the node is of degree 1. */ public boolean isExternal(Node node) { if (!(node instanceof ReRootedNode)) { throw new IllegalArgumentException("Node, " + node.toString() + " is not an instance of SimpleRootedNode. It is an instance of "+node.getClass().getName()); } return ((ReRootedNode)node).getChildren().size() == 0; } /** * @param taxon the taxon * @return the external node associated with the given taxon, or null * if the taxon is not a member of the taxa set associated with this tree. */ public Node getNode(Taxon taxon) { return externalNodes.get(taxon); } public void renameTaxa(Taxon from, Taxon to) { ReRootedNode node = (ReRootedNode)externalNodes.get(from); // TT: The javadoc doesn't specify whether renameTaxa() should fail or silently do nothing // if Taxon from doesn't exist. But the code already threw a NullPointerException before (bug 4824), // so it's probably ok to throw a more informative IllegalArgumentException instead. if (node == null) { throw new IllegalArgumentException("Unknown taxon " + from + "; can't rename to " + to); } node.setTaxon(to); externalNodes.remove(from); externalNodes.put(to, node); } /** * Returns a list of edges connected to this node * * @param node * @return the set of nodes that are attached by edges to the given node. */ public List getEdges(Node node) { List edges = new ArrayList(); for (Node adjNode : getAdjacencies(node)) { edges.add(((ReRootedNode)adjNode).getEdge()); } return edges; } /** * @param node * @return the set of nodes that are attached by edges to the given node. */ public List getAdjacencies(Node node) { return ((ReRootedNode)node).getAdjacencies(); } /** * Returns the Edge that connects these two nodes * * @param node1 * @param node2 * @return the edge object. * @throws jebl.evolution.graphs.Graph.NoEdgeException * if the nodes are not directly connected by an edge. */ public Edge getEdge(Node node1, Node node2) throws NoEdgeException { if (((ReRootedNode)node1).getParent() == node2) { return ((ReRootedNode)node1).getEdge(); } else if (((ReRootedNode)node2).getParent() == node1) { return ((ReRootedNode)node2).getEdge(); } else { throw new NoEdgeException(); } } /** * @param node1 * @param node2 * @return the length of the edge connecting node1 and node2. * @throws jebl.evolution.graphs.Graph.NoEdgeException * if the nodes are not directly connected by an edge. */ public double getEdgeLength(Node node1, Node node2) throws NoEdgeException { if (((ReRootedNode)node1).getParent() == node2) { if (heightsKnown) { return ((ReRootedNode)node2).getHeight() - ((ReRootedNode)node1).getHeight(); } else { return ((ReRootedNode)node1).getLength(); } } else if (((ReRootedNode)node2).getParent() == node1) { if (heightsKnown) { return ((ReRootedNode)node1).getHeight() - ((ReRootedNode)node2).getHeight(); } else { return ((ReRootedNode)node2).getLength(); } } else { throw new NoEdgeException(); } } /** * Returns an array of 2 nodes which are the nodes at either end of the edge. * * @param edge * @return an array of 2 edges */ public Node[] getNodes(Edge edge) { for (Node node : getNodes()) { if (((ReRootedNode)node).getEdge() == edge) { return new Node[] { node, ((ReRootedNode)node).getParent() }; } } return null; } /** * @return the set of all nodes in this graph. */ public Set getNodes() { Set nodes = new LinkedHashSet(internalNodes); nodes.addAll(externalNodes.values()); return nodes; } /** * @return the set of all edges in this graph. */ public Set getEdges() { Set edges = new LinkedHashSet(); for (Node node : getNodes()) { if (node != getRootNode()) { edges.add(((ReRootedNode)node).getEdge()); } } return edges; } /** * The set of external edges. This is a pretty inefficient implementation because * a new set is constructed each time this is called. * @return the set of external edges. */ public Set getExternalEdges() { Set edges = new LinkedHashSet(); for (Node node : getExternalNodes()) { edges.add(((ReRootedNode)node).getEdge()); } return edges; } /** * The set of internal edges. This is a pretty inefficient implementation because * a new set is constructed each time this is called. * @return the set of internal edges. */ public Set getInternalEdges() { Set edges = new LinkedHashSet(); for (Node node : getInternalNodes()) { if (node != getRootNode()) { edges.add(((ReRootedNode)node).getEdge()); } } return edges; } /** * @param degree the number of edges connected to a node * @return a set containing all nodes in this graph of the given degree. */ public Set getNodes(int degree) { Set nodes = new LinkedHashSet(); for (Node node : getNodes()) { // Account for no anncesstor of root, assumed by default in getDegree final int deg = node.getDegree() ; if (deg == degree) nodes.add(node); } return nodes; } /** * Set the node heights from the current branch lengths. */ private void calculateNodeHeights() { if (!lengthsKnown) { throw new IllegalArgumentException("Can't calculate node heights because branch lengths not known"); } nodeLengthsToHeights(rootNode, 0.0); double maxHeight = 0.0; for (Node externalNode : getExternalNodes()) { if (((ReRootedNode)externalNode).getHeight() > maxHeight) { maxHeight = ((ReRootedNode)externalNode).getHeight(); } } for (Node node : getNodes()) { ((ReRootedNode)node).setHeight(maxHeight - ((ReRootedNode)node).getHeight()); } heightsKnown = true; } /** * Set the node heights from the current node branch lengths. Actually * sets distance from root so the heights then need to be reversed. */ private void nodeLengthsToHeights(ReRootedNode node, double height) { double newHeight = height; if (node.getLength() > 0.0) { newHeight += node.getLength(); } node.setHeight(newHeight); for (Node child : node.getChildren()) { nodeLengthsToHeights((ReRootedNode)child, newHeight); } } /** * Calculate branch lengths from the current node heights. */ protected void calculateBranchLengths() { if (!hasLengths) { throw new IllegalArgumentException("Can't calculate branch lengths because node heights not known"); } nodeHeightsToLengths(rootNode, getHeight(rootNode)); lengthsKnown = true; } /** * Calculate branch lengths from the current node heights. */ private void nodeHeightsToLengths(ReRootedNode node, double height) { final double h = node.getHeight(); node.setLength(h >= 0 ? height - h : 1); for (Node child : node.getChildren()) { nodeHeightsToLengths((ReRootedNode)child, node.getHeight()); } } public boolean conceptuallyUnrooted() { return false; } public boolean isRoot(Node node) { return node == rootNode; } // Attributable IMPLEMENTATION public void setAttribute(String name, Object value) { source.setAttribute(name, value); } public Object getAttribute(String name) { return source.getAttribute(name); } public void removeAttribute(String name) { source.removeAttribute(name); } public Set getAttributeNames() { return source.getAttributeNames(); } public Map getAttributeMap() { return source.getAttributeMap(); } /** * Root any tree by locating the "center" of tree and adding a new root node at that point *

* for any point on the tree x let D(x) = Max{distance between x and t : for all tips t} * The "center" c is the point with the smallest distance, i.e. D(c) = min{ D(x) : x in tree } * * @param tree to root * @return rooted tree */ public static RootedTree rootTreeAtCenter(RootedTree tree) { // Method - find the pair of tips with the longest distance. It is easy to see that the center // is at the midpoint of the path between them. HashMap, Double> dists = new LinkedHashMap, Double>(); try { double maxDistance = -Double.MAX_VALUE; // node on maximal path Node current = null; // next node on maximal path Node direction = null; // locate one terminal node of longest path for (Node e : tree.getExternalNodes()) { for (Node n : tree.getAdjacencies(e)) { final double d = dist(tree, e, n, dists); if (d > maxDistance) { maxDistance = d; current = e; direction = n; } } } // traverse along maximal path to it's middle double distanceLeft = maxDistance / 2.0; while (true) { final double len = tree.getEdgeLength(current, direction); if (distanceLeft <= len) { //System.out.println(toNewick(rtree)); return new ReRootedTree(tree, current, direction, distanceLeft); } distanceLeft -= len; maxDistance = -Double.MAX_VALUE; Node next = null; for (Node n : tree.getAdjacencies(direction)) { if (n == current) continue; final double d = dist(tree, direction, n, dists); if (d > maxDistance) { maxDistance = d; next = n; } } current = direction; direction = next; } } catch (Graph.NoEdgeException e1) { return null; // serious bug, should not happen } } private static double dist(Tree tree, Node root, Node node, Map, Double> dists) throws Graph.NoEdgeException { HashPair p = new HashPair(root, node); if (dists.containsKey(p)) { return dists.get(p); } // assume positive branches double maxDist = 0; for (Node n : tree.getAdjacencies(node)) { if (n != root) { double d = dist(tree, node, n, dists); maxDist = Math.max(maxDist, d); } } double dist = tree.getEdgeLength(node, root) + maxDist; dists.put(p, dist); return dist; } // PRIVATE members private RootedTree source = null; private ReRootedNode rootNode = null; private final Set internalNodes = new LinkedHashSet(); private final Map externalNodes = new LinkedHashMap(); private boolean heightsKnown = false; private boolean lengthsKnown = false; private boolean hasHeights = false; private boolean hasLengths = false; private class ReRootedNode implements Node { public ReRootedNode(Node source, Taxon taxon) { this.source = source; this.children = Collections.unmodifiableList(new ArrayList()); this.taxon = taxon; } public ReRootedNode(Node source, List children) { this.source = source; this.children = Collections.unmodifiableList(new ArrayList(children)); this.taxon = null; } public Node getParent() { return parent; } public void setParent(Node parent) { this.parent = parent; } public List getChildren() { return children; } public double getHeight() { return height; } // height above latest tip public void setHeight(double height) { this.height = height; } // length of branch to parent public double getLength() { return length; } public void setLength(double length) { this.length = length; } public int getDegree() { return children.size() +(this==rootNode?0:1); } public void setTaxon(Taxon to) { taxon = to; } /** * returns the edge connecting this node to the parent node * @return the edge */ public Edge getEdge() { if (edge == null) { edge = new BaseEdge() { public double getLength() { return length; } }; } return edge; } /** * For a rooted tree, getting the adjacencies is not the most efficient * operation as it makes a new set containing the children and the parent. * @return the adjacaencies */ public List getAdjacencies() { List adjacencies = new ArrayList(); if (children != null) adjacencies.addAll(children); if (parent != null) adjacencies.add(parent); return adjacencies; } public Taxon getTaxon() { return taxon; } // Attributable IMPLEMENTATION public void setAttribute(String name, Object value) { if (source == null) { if (helper == null) { helper = new AttributableHelper(); } helper.setAttribute(name, value); } else { source.setAttribute(name, value); } } public Object getAttribute(String name) { if (source == null) { if (helper == null) { return null; } return helper.getAttribute(name); } return source.getAttribute(name); } public void removeAttribute(String name) { if (source == null) { if( helper != null ) { helper.removeAttribute(name); } } else { source.removeAttribute(name); } } public Set getAttributeNames() { if (source == null) { if (helper == null) { return Collections.emptySet(); } return helper.getAttributeNames(); } return source.getAttributeNames(); } public Map getAttributeMap() { if (source == null) { if (helper == null) { return Collections.emptyMap(); } return helper.getAttributeMap(); } return source.getAttributeMap(); } private final Node source; private List children; private Taxon taxon; private Node parent; private double height; private double length; private Edge edge = null; private AttributableHelper helper = null; } }figtree-1.4.3/src/figtree/treeviewer/ScaleAxis.java000077500000000000000000000526411277473563300223140ustar00rootroot00000000000000/* * ScaleAxis.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import java.text.DecimalFormat; /** * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ScaleAxis { // The minimum and maximum values of the data // These constants are used for automatic scaling to select exactly // where the axis starts and stops. static public final int AT_MAJOR_TICK=0; static public final int AT_MAJOR_TICK_PLUS=1; static public final int AT_MINOR_TICK=2; static public final int AT_MINOR_TICK_PLUS=3; static public final int AT_DATA=4; static public final int AT_ZERO=5; static public final int AT_VALUE=6; protected double minData=Double.POSITIVE_INFINITY; protected double maxData=Double.NEGATIVE_INFINITY;// The number of major ticks and minor ticks within them protected int majorTickCount; protected int minorTickCount; // calculated automatically // The prefered minimum number of ticks protected int prefMajorTickCount = 5; protected int prefMinorTickCount = 2; // set manually // Flags using the above constants protected int minAxisFlag; protected int maxAxisFlag;// The distance between major ticks and minor Ticks protected double majorTick; protected double minorTick; // calculated automatically or set by user // The value of the first and last major tick protected double minTick; protected double maxTick; // calculated automatically or set by user // The value of the beginning and end of the axis protected double minAxis; protected double maxAxis;// User defined axis range protected double minValue; protected double maxValue;// Flags to give automatic scaling and integer division protected boolean isAutomatic = true; protected boolean isAutomaticTickSpacing = true; protected boolean isDiscrete=false;// Flags to specify that the first tick and last tick should have labels. // It is up to the AxisPanel to do something about this. protected boolean labelFirst=false; protected boolean labelLast=false; protected boolean isCalibrated = false; protected DecimalFormat formatter = new DecimalFormat("0.0#######");// Used internally private double epsilon; private int fraction; static private final int UNIT=0; static private final int HALFS=1; static private final int QUARTERS=2; static private final int FIFTHS=3; /** * Empty constructor */ public ScaleAxis() { } /** * Axis flag constructor */ public ScaleAxis(int minAxisFlag, int maxAxisFlag) { setAxisFlags(minAxisFlag, maxAxisFlag); } /** * Transform a value */ public double transform(double value) { return value; // a linear transform ! } /** * Untransform a value */ public double untransform(double value) { return value; // a linear transform ! } /** * Set axis flags */ public void setAxisFlags(int minAxisFlag, int maxAxisFlag) { this.minAxisFlag = minAxisFlag; this.maxAxisFlag = maxAxisFlag; isCalibrated = false; } /** * Set preferred number of ticks */ public void setPrefNumTicks(int prefMajorTickCount, int prefMinorTickCount) { this.prefMajorTickCount = prefMajorTickCount; this.prefMinorTickCount = prefMinorTickCount; isCalibrated = false; } /** * Set integer scale */ public void setIsDiscrete(boolean isDiscrete) { this.isDiscrete = isDiscrete; isCalibrated = false; } /** * Set show label for first tick flag */ public void setLabelFirst(boolean labelFirst) { this.labelFirst = labelFirst; } /** * Set show label for last tick flag */ public void setLabelLast(boolean labelLast) { this.labelLast = labelLast; } /** * Set the formatter for the tick labels */ public void setFormatter(DecimalFormat formatter) { this.formatter = formatter; } /** * return show label for first tick flag */ public boolean getLabelFirst() { if (getMinorTickCount(-1)==0) // The first tick is a label anyway return false; else return labelFirst; } /** * return show label for last tick flag */ public boolean getLabelLast() { if (getMinorTickCount(majorTickCount-1)==0) // The last tick is a label anyway return false; else return labelLast; } /** * Manually set the axis range. Axis flags must be set to AT_VALUE for this to take effect. */ public void setManualRange(double minValue, double maxValue) { this.minValue = minValue; this.maxValue = maxValue; isCalibrated = false; } /** * Manually set the axis ticks */ public void setManualAxis(double majorTick, double minorTick) { this.majorTick = majorTick; this.minorTick = minorTick; isAutomatic = true; isAutomaticTickSpacing = false; isCalibrated = false; } /** * Manually set the axis ticks */ public void setManualAxis(double minTick, double maxTick, double majorTick, double minorTick) { this.minTick = minTick; this.maxTick = maxTick; this.majorTick = majorTick; this.minorTick = minorTick; majorTickCount = (int)((maxTick-minTick)/majorTick)+1; // Add 1 to include the last tick minorTickCount = (int)(majorTick/minorTick)-1; // Sub 1 to exclude the major tick isAutomatic=false; isAutomaticTickSpacing = false; isCalibrated = false; } /** * Set the axis to automatic calibration */ public void setAutomatic() { setAutomatic(AT_MAJOR_TICK, AT_MAJOR_TICK); } /** * Set the axis to automatic calibration */ public void setAutomatic(int minAxisFlag, int maxAxisFlag) { setAxisFlags(minAxisFlag, maxAxisFlag); isAutomatic = true; isAutomaticTickSpacing = true; isCalibrated = false; } /** * Set the range of the data */ public void setRange(double minValue, double maxValue) { if (!Double.isNaN(minValue)) { this.minData = minValue; } if (!Double.isNaN(maxValue)) { this.maxData = maxValue; } isCalibrated = false; } /** * Adds the range to the existing range, widening if neccessary */ public void addRange(double minValue, double maxValue) { if (!Double.isNaN(maxValue) && maxValue > maxData) { maxData = maxValue; } if (!Double.isNaN(minValue) && minValue < minData) { minData = minValue; } //System.err.println("addRange("+minValue +", "+maxValue+")"); //System.err.println("maxValue = "+maxData); //System.err.println("maxData = "+maxData); isCalibrated = false; } /** * A static method that uses the natural log to obtain log to base10. * This is required for the linear autoCalibrate but will also be * used by a derived class giving a log transformed axis. */ static public double log10(double inValue) { return Math.log(inValue)/Math.log(10.0); } public void calibrate() { double minValue = minData; double maxValue = maxData; if (minAxisFlag== AT_ZERO) { minValue = 0; } else if (minAxisFlag == AT_VALUE) { minValue = this.minValue; } if (maxAxisFlag== AT_ZERO) { maxValue = 0; } else if (maxAxisFlag == AT_VALUE) { maxValue = this.maxValue; } double range = maxValue - minValue; if (range < 0.0) { range = 0.0; } epsilon = range * 1.0E-10; if (isAutomatic) { // We must find the optimum minMajorTick and maxMajorTick so // that they contain the data range (minData to maxData) and // are in the right order of magnitude if (range < 1.0E-30) { if (minData < 0.0) { if (isAutomaticTickSpacing) { majorTick = Math.pow(10.0, Math.floor(log10(Math.abs(minData)))); } minTick = Math.floor(minData / majorTick) * majorTick; maxTick = 0.0; } else if (minData > 0.0) { if (isAutomaticTickSpacing) { majorTick = Math.pow(10.0, Math.floor(log10(Math.abs(minData)))); } minTick = 0.0; maxTick = Math.ceil(maxData / majorTick) * majorTick; } else { if (isAutomaticTickSpacing) { majorTick = 1.0; } minTick = -1.0; maxTick = 1.0; } if (isAutomaticTickSpacing) { minorTick = majorTick; } majorTickCount = 1; minorTickCount = 0; } else { if (isAutomaticTickSpacing) { // First find order of magnitude below the data range... majorTick = Math.pow(10.0, Math.floor(log10(range))); } calcMinTick(); calcMaxTick(); majorTickCount=(int)(maxTick-minTick/majorTick); minorTickCount=(int)(majorTick/minorTick); if (isAutomaticTickSpacing) { calcMajorTick(); calcMinorTick(); } } } minAxis = minTick; maxAxis = maxTick; handleAxisFlags(); isCalibrated=true; } /** * Calculate the optimum minimum tick. Override to change default behaviour */ public void calcMinTick() { // Find the nearest multiple of majorTick below minData if (minData == 0.0) minTick = 0; else minTick = Math.floor(minData / majorTick) * majorTick; } /** * Calculate the optimum maximum tick. Override to change default behaviour */ public void calcMaxTick() { // Find the nearest multiple of majorTick above maxData if (maxData == 0) { maxTick = 0; } else if (maxData < 0.0) { // Added so that negative values are handled correctly -- AJD maxTick = -Math.floor(-maxData / majorTick) * majorTick; } else { maxTick = Math.ceil(maxData / majorTick) * majorTick; } } /** * Calculate the optimum major tick distance. Override to change default behaviour */ public void calcMajorTick() { fraction= UNIT; // make sure that there are at least prefNumMajorTicks major ticks // by dividing up into halves, quarters, fifths or tenths double u=majorTick; double r=maxTick-minTick; majorTickCount=(int)(r/u); while (majorTickCount < prefMajorTickCount) { u=majorTick/2; // Try using halves if (!isDiscrete || u==Math.floor(u)) { // u is an integer majorTickCount=(int)(r/u); fraction= HALFS; if (majorTickCount >= prefMajorTickCount) break; } u=majorTick/4; // Try using quarters if (!isDiscrete || u==Math.floor(u)) { // u is an integer majorTickCount=(int)(r/u); fraction= QUARTERS; if (majorTickCount >= prefMajorTickCount) break; } u=majorTick/5; // Try using fifths if (!isDiscrete || u==Math.floor(u)) { // u is an integer majorTickCount=(int)(r/u); fraction= FIFTHS; if (majorTickCount >= prefMajorTickCount) break; } if (isDiscrete && (majorTick/10)!=Math.floor(majorTick/10)) { // majorTick/10 is not an integer so no point in further subdivision u=majorTick; majorTickCount=(int)(r/u); break; } majorTick/=10; // finally just divide by ten u=majorTick; // and go back to whole units majorTickCount=(int)(r/u); fraction= UNIT; } majorTick=u; if (isDiscrete && majorTick<1.0) { majorTick=1.0; majorTickCount=(int)(r/majorTick); fraction= UNIT; } majorTickCount++; // Add 1 to give the final tick // Trim down any excess major ticks either side of the data range // Epsilon allows for any inprecision in the calculation while ((minTick + majorTick - epsilon)maxData) { maxTick-=majorTick; majorTickCount--; } } /** * Calculate the optimum minor tick distance. Override to change default behaviour */ public void calcMinorTick() { minorTick=majorTick; // start with minorTick the same as majorTick double u=minorTick; double r=majorTick; minorTickCount=(int)(r/u); while (minorTickCount < prefMinorTickCount) { // if the majorTick was divided as quarters, then we can't // divide the minor ticks into halves or quarters. if (fraction!= QUARTERS) { u=minorTick/2; // Try using halves if (!isDiscrete || u==Math.floor(u)) { // u is an integer minorTickCount=(int)(r/u); if (minorTickCount>=prefMinorTickCount) break; } u=minorTick/4; // Try using quarters if (!isDiscrete || u==Math.floor(u)) { // u is an integer minorTickCount=(int)(r/u); if (minorTickCount>=prefMinorTickCount) break; } } u=minorTick/5; // Try using fifths if (!isDiscrete || u==Math.floor(u)) { // u is an integer minorTickCount=(int)(r/u); if (minorTickCount>=prefMinorTickCount) break; } if (isDiscrete && (minorTick/10)!=Math.floor(minorTick/10)) { // minorTick/10 is not an integer so no point in further subdivision u=minorTick; minorTickCount=(int)(r/u); break; } minorTick/=10; // finally just divide by ten u=minorTick; // and go back to whole units minorTickCount=(int)(r/u); } minorTick=u; minorTickCount--; } /** * Handles axis flags. Override to change default behaviour */ public void handleAxisFlags() { // Now we must honor the min/maxAxisFlag settings if (minAxisFlag== AT_MAJOR_TICK_PLUS || minAxisFlag== AT_MINOR_TICK_PLUS) { if (minAxis==minData) { majorTickCount++; minTick-=majorTick; minAxis=minTick; } } if (minAxisFlag== AT_MINOR_TICK_PLUS) { if ((minAxis+minorTick)maxData) { majorTickCount--; maxTick-=majorTick; while ((maxAxis-minorTick)>maxData) { maxAxis-=minorTick; } } } else if (maxAxisFlag== AT_MINOR_TICK) { if ((maxAxis-minorTick)>=maxData) { majorTickCount--; maxTick-=majorTick; while ((maxAxis-minorTick)>=maxData) { maxAxis-=minorTick; } } } else if (maxAxisFlag== AT_DATA) { if (maxTick>maxData) { // in case maxTick==maxData majorTickCount--; maxTick-=majorTick; } maxAxis=maxData; } else if (maxAxisFlag== AT_VALUE) { if (maxTick>maxValue) { // in case maxTick==maxValue majorTickCount--; maxTick-=majorTick; } maxAxis=maxValue; } else if (maxAxisFlag== AT_ZERO) { majorTickCount+=(int)(-maxTick/majorTick); maxTick=0; maxTick=0; } } /** * Scale a value to between 0 and 1. */ public double scaleValue(double value) { if (!isCalibrated) calibrate(); double f=(transform(value)-transform(minAxis))/(transform(maxAxis)-transform(minAxis)); return f; } /** * @return a DecimalFormat for formating the axis labels */ public DecimalFormat getFormatter() { return formatter; } /** * @return minimum range of the axis */ public double getMinAxis() { if (!isCalibrated) calibrate(); return minAxis; } /** * @return maximum range of the axis */ public double getMaxAxis() { if (!isCalibrated) calibrate(); return maxAxis; } /** * @return minimum range of the data */ public double getMinData() { return minData; } /** * @return maximum range of the data */ public double getMaxData() { return maxData; } /** * Returns the number of major tick marks along the axis */ public int getMajorTickCount() { if (!isCalibrated) calibrate(); return majorTickCount; } /** * Returns the number of minor tick marks within each major one * By default all major ticks have the same number of minor ticks * except the last which has none. */ public int getMinorTickCount(int majorTickIndex) { if (!isCalibrated) calibrate(); if (minorTick <= 0) { return 0; } if (majorTickIndex == majorTickCount-1) return (int)((maxAxis-maxTick)/minorTick); else if (majorTickIndex==-1) return (int)((minTick-minAxis)/minorTick); else return minorTickCount; } /** getMajorTick * Returns the value of the majorTickIndex'th major tick */ public double getMajorTickValue(int majorTickIndex) { if (!isCalibrated) calibrate(); return (majorTickIndex*majorTick)+minTick; } /** getMinorTick * Returns the value of the minorTickIndex'th minor tick */ public double getMinorTickValue(int minorTickIndex, int majorTickIndex) { if (!isCalibrated) calibrate(); // get minorTickIndex+1 to skip the major tick if (majorTickIndex==-1) return minTick-((minorTickIndex+1)*minorTick); else return ((minorTickIndex+1)*minorTick)+getMajorTickValue(majorTickIndex); } /** * @return the spacing between major ticks */ public double getMajorTickSpacing() { if (!isCalibrated) calibrate(); return majorTick; } /** * @return the spacing between minor ticks */ public double getMinorTickSpacing() { if (!isCalibrated) calibrate(); return minorTick; } } figtree-1.4.3/src/figtree/treeviewer/SizeScaleDialog.java000077500000000000000000000120721277473563300234340ustar00rootroot00000000000000/* * SizeScaleDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.*; import figtree.ui.components.RealNumberField; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class SizeScaleDialog { private JFrame frame; private String dimensionName; private OptionsPanel options; private JCheckBox autoScaleCheck; private JLabel fromLabel; private RealNumberField fromNumberField; private JLabel toLabel; private RealNumberField toNumberField; private RealNumberField fromSizeField; private RealNumberField toSizeField; public SizeScaleDialog(final JFrame frame, final String dimensionName, boolean autoRange, double fromValue, double toValue, final double fromWidth, final double toWidth) { this.frame = frame; this.dimensionName = dimensionName; autoScaleCheck = new JCheckBox("Auto-scale range"); autoScaleCheck.setSelected(autoRange); fromLabel = new JLabel("Range from:"); fromNumberField = new RealNumberField(); fromNumberField.setColumns(10); fromNumberField.setValue(fromValue); toLabel = new JLabel("to:"); toNumberField = new RealNumberField(); toNumberField.setColumns(10); toNumberField.setValue(toValue); fromLabel.setEnabled(false); fromNumberField.setEnabled(false); toLabel.setEnabled(false); toNumberField.setEnabled(false); fromSizeField = new RealNumberField(); fromSizeField.setColumns(4); fromSizeField.setValue(fromWidth); toSizeField = new RealNumberField(); toSizeField.setColumns(4); toSizeField.setValue(toWidth); autoScaleCheck.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { boolean enabled = !autoScaleCheck.isSelected(); fromLabel.setEnabled(enabled); fromNumberField.setEnabled(enabled); toLabel.setEnabled(enabled); toNumberField.setEnabled(enabled); } }); } public int showDialog() { options = new OptionsPanel(6, 6); options.addComponent(autoScaleCheck); JPanel panel = new JPanel(); panel.setLayout(new FlowLayout()); panel.add(fromLabel); panel.add(fromNumberField); panel.add(toLabel); panel.add(toNumberField); options.addComponent(panel); JPanel panel1 = new JPanel(); panel1.setLayout(new FlowLayout()); panel1.add(new JLabel(dimensionName + " from:")); panel1.add(fromSizeField); panel1.add(new JLabel("to:")); panel1.add(toSizeField); options.addComponent(panel1); JOptionPane optionPane = new JOptionPane(options, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); final JDialog dialog = optionPane.createDialog(frame, "Setup " + dimensionName + " scale"); dialog.pack(); autoScaleCheck.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { boolean enabled = !autoScaleCheck.isSelected(); fromLabel.setEnabled(enabled); fromNumberField.setEnabled(enabled); toLabel.setEnabled(enabled); toNumberField.setEnabled(enabled); }}); dialog.setVisible(true); int result = JOptionPane.CANCEL_OPTION; Integer value = (Integer)optionPane.getValue(); if (value != null && value.intValue() != -1) { result = value.intValue(); } return result; } public boolean getAutoRange() { return autoScaleCheck.isSelected(); } public Number getFromValue() { return fromNumberField.getValue(); } public Number getToValue() { return toNumberField.getValue(); } public Number getFromWidth() { return fromSizeField.getValue(); } public Number getToWidth() { return toSizeField.getValue(); } }figtree-1.4.3/src/figtree/treeviewer/TimeScale.java000077500000000000000000000042271277473563300223030ustar00rootroot00000000000000/* * TimeScale.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jebl.evolution.trees.RootedTree; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TimeScale { private boolean isReversed = false; public TimeScale(double rootAge) { this.rootAge = rootAge; this.scaleFactor = Double.NaN; this.offsetAge = 0.0; } public TimeScale(double scaleFactor, double offsetAge) { this.rootAge = Double.NaN; this.offsetAge = offsetAge; this.scaleFactor = scaleFactor; } public double getScaleFactor(RootedTree tree) { if (Double.isNaN(scaleFactor)) { return rootAge / tree.getHeight(tree.getRootNode()); } return scaleFactor * (isReversed ? -1.0 : 1.0); } public double getAge(double height, RootedTree tree) { return (height * getScaleFactor(tree)) + offsetAge; } public double getTime(double length, RootedTree tree) { return (length * getScaleFactor(tree)); } public double getHeight(double age, RootedTree tree) { return (age - offsetAge) / getScaleFactor(tree); } public double getLength(double time, RootedTree tree) { return (time / getScaleFactor(tree)); } public void setReversed(boolean isReversed) { this.isReversed = isReversed; } private final double rootAge; private final double offsetAge; private final double scaleFactor; } figtree-1.4.3/src/figtree/treeviewer/TimeScaleController.java000077500000000000000000000150351277473563300243460ustar00rootroot00000000000000/* * TimeScaleController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.util.Map; import java.util.prefs.Preferences; import figtree.ui.components.RealNumberField; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TimeScaleController extends AbstractController { private static final String CONTROLLER_TITLE = "Time Scale"; private static Preferences PREFS = Preferences.userNodeForPackage(TreeViewer.class); private static final String CONTROLLER_KEY = "scale"; private static final String SCALE_ROOT_KEY = "scaleRoot"; private static final String ROOT_AGE_KEY = "rootAge"; private static final String OFFSET_AGE_KEY = "offsetAge"; private static final String SCALE_FACTOR_KEY = "scaleFactor"; // The defaults if there is nothing in the preferences private static boolean DEFAULT_SCALE_ROOT = false; private static double DEFAULT_ROOT_AGE = 1.0; private static double DEFAULT_OFFSET_AGE = 0.0; private static double DEFAULT_SCALE_FACTOR = 1.0; public TimeScaleController(final TreeViewer treeViewer) { this.treeViewer = treeViewer; titleLabel = new JLabel(CONTROLLER_TITLE); final boolean scaleRoot = PREFS.getBoolean(CONTROLLER_KEY + "." + SCALE_ROOT_KEY, DEFAULT_SCALE_ROOT); final double offsetAge = PREFS.getDouble(CONTROLLER_KEY + "." + OFFSET_AGE_KEY, DEFAULT_OFFSET_AGE); final double scaleFactor = PREFS.getDouble(CONTROLLER_KEY + "." + SCALE_FACTOR_KEY, DEFAULT_SCALE_FACTOR); final double rootAge = PREFS.getDouble(CONTROLLER_KEY + "." + ROOT_AGE_KEY, DEFAULT_ROOT_AGE); optionsPanel = new ControllerOptionsPanel(2, 2); scaleFactorRadio = new JRadioButton("Scale by factor:"); scaleFactorRadio.setSelected(!scaleRoot); optionsPanel.addSpanningComponent(scaleFactorRadio); offsetAgeText = new RealNumberField(-Double.MAX_VALUE, Double.MAX_VALUE); offsetAgeText.setValue(offsetAge); final JLabel label1 = optionsPanel.addComponentWithLabel("Offset by:", offsetAgeText, true); scaleFactorText = new RealNumberField(-Double.MAX_VALUE, Double.MAX_VALUE); scaleFactorText.setValue(scaleFactor); final JLabel label2 = optionsPanel.addComponentWithLabel("Scale factor:", scaleFactorText, true); scaleRootRadio = new JRadioButton("Scale root to:"); scaleRootRadio.setSelected(scaleRoot); optionsPanel.addSpanningComponent(scaleRootRadio); rootAgeText = new RealNumberField(0.0, Double.MAX_VALUE); rootAgeText.setValue(rootAge); final JLabel label3 = optionsPanel.addComponentWithLabel("Root age:", rootAgeText, true); ButtonGroup group = new ButtonGroup(); group.add(scaleFactorRadio); group.add(scaleRootRadio); scaleFactorRadio.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { boolean selected = scaleFactorRadio.isSelected(); label1.setEnabled(selected); offsetAgeText.setEnabled(selected); label2.setEnabled(selected); scaleFactorText.setEnabled(selected); label3.setEnabled(!selected); rootAgeText.setEnabled(!selected); setTimeScale(); } }); ChangeListener listener = new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { setTimeScale(); } }; offsetAgeText.addChangeListener(listener); scaleFactorText.addChangeListener(listener); rootAgeText.addChangeListener(listener); } private void setTimeScale() { TimeScale timeScale; if (scaleFactorRadio.isSelected()) { double offset = getValue(offsetAgeText, 0.0); double scaleFactor = getValue(scaleFactorText, 1.0); timeScale = new TimeScale(scaleFactor, offset); } else { double rootAge = getValue(rootAgeText, 0.0); timeScale = new TimeScale(rootAge); } treeViewer.setTimeScale(timeScale); } private double getValue(RealNumberField field, double defaultValue) { Double value = field.getValue(); return (value != null ? value : defaultValue); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { scaleFactorRadio.setSelected(!((Boolean)settings.get(CONTROLLER_KEY + "." + SCALE_ROOT_KEY))); scaleRootRadio.setSelected(((Boolean)settings.get(CONTROLLER_KEY + "." + SCALE_ROOT_KEY))); offsetAgeText.setValue((Double)settings.get(CONTROLLER_KEY + "." + OFFSET_AGE_KEY)); scaleFactorText.setValue((Double)settings.get(CONTROLLER_KEY + "." + SCALE_FACTOR_KEY)); rootAgeText.setValue((Double)settings.get(CONTROLLER_KEY + "." + ROOT_AGE_KEY)); } public void getSettings(Map settings) { settings.put(CONTROLLER_KEY + "." + SCALE_ROOT_KEY, new Boolean(scaleRootRadio.isSelected())); settings.put(CONTROLLER_KEY + "." + OFFSET_AGE_KEY, offsetAgeText.getValue()); settings.put(CONTROLLER_KEY + "." + SCALE_FACTOR_KEY, scaleFactorText.getValue()); settings.put(CONTROLLER_KEY + "." + ROOT_AGE_KEY, rootAgeText.getValue()); } private JRadioButton scaleFactorRadio; private final RealNumberField offsetAgeText; private final RealNumberField scaleFactorText; private JRadioButton scaleRootRadio; private final RealNumberField rootAgeText; private final JLabel titleLabel; private final OptionsPanel optionsPanel; private final TreeViewer treeViewer; }figtree-1.4.3/src/figtree/treeviewer/TreeAppearanceController.java000077500000000000000000000400031277473563300253500ustar00rootroot00000000000000/* * TreeAppearanceController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.painters.AttributeComboHelper; import figtree.treeviewer.painters.AttributeComboHelperListener; import figtree.treeviewer.painters.NodeShapePainter; import jam.controlpalettes.ControllerListener; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.*; import java.util.*; import java.util.prefs.Preferences; import figtree.treeviewer.decorators.*; import jebl.evolution.trees.RootedTree; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreeAppearanceController extends AbstractController { private static final String CONTROLLER_TITLE = "Appearance"; public static Preferences PREFS = Preferences.userNodeForPackage(TreeViewer.class); public static final String CONTROLLER_KEY = "appearance"; public static final String FOREGROUND_COLOUR_KEY = "foregroundColour"; public static final String BACKGROUND_COLOUR_KEY = "backgroundColour"; public static final String SELECTION_COLOUR_KEY = "selectionColour"; public static final String BRANCH_COLOR_ATTRIBUTE_KEY = "branchColorAttribute"; public static final String BRANCH_COLOR_GRADIENT_KEY = "branchColorGradient"; public static final String HILIGHTING_GRADIENT_KEY = "hilightingGradient"; public static final String BACKGROUND_COLOR_ATTRIBUTE_KEY = "backgroundColorAttribute"; public static final String BRANCH_LINE_WIDTH_KEY = "branchLineWidth"; public static final String BRANCH_MIN_LINE_WIDTH_KEY = "branchMinLineWidth"; public static final String BRANCH_WIDTH_ATTRIBUTE_KEY = "branchWidthAttribute"; // The defaults if there is nothing in the preferences public static Color DEFAULT_FOREGROUND_COLOUR = Color.BLACK; public static Color DEFAULT_BACKGROUND_COLOUR = Color.WHITE; public static Color DEFAULT_SELECTION_COLOUR = new Color(45, 54, 128); public static float DEFAULT_BRANCH_LINE_WIDTH = 1.0f; public static final String FIXED = "Fixed"; public TreeAppearanceController(final TreeViewer treeViewer, final JFrame frame, final AttributeColourController colourController) { this.treeViewer = treeViewer; this.colourController = colourController; userBranchColourDecorator = new AttributableDecorator(); userBranchColourDecorator.setPaintAttributeName("!color"); userBranchColourDecorator.setStrokeAttributeName("!stroke"); treeViewer.setBranchDecorator(userBranchColourDecorator, false); int foregroundRGB = TreeAppearanceController.PREFS.getInt(CONTROLLER_KEY + "." + FOREGROUND_COLOUR_KEY, DEFAULT_FOREGROUND_COLOUR.getRGB()); int backgroundRGB = TreeAppearanceController.PREFS.getInt(CONTROLLER_KEY + "." + BACKGROUND_COLOUR_KEY, DEFAULT_BACKGROUND_COLOUR.getRGB()); int selectionRGB = TreeAppearanceController.PREFS.getInt(CONTROLLER_KEY + "." + SELECTION_COLOUR_KEY, DEFAULT_SELECTION_COLOUR.getRGB()); float branchLineWidth = TreeAppearanceController.PREFS.getFloat(CONTROLLER_KEY + "." + BRANCH_LINE_WIDTH_KEY, DEFAULT_BRANCH_LINE_WIDTH); treeViewer.setForeground(new Color(foregroundRGB)); treeViewer.setBackground(new Color(backgroundRGB)); treeViewer.setSelectionColor(new Color(selectionRGB)); treeViewer.setBranchStroke(new BasicStroke(branchLineWidth, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND)); titleLabel = new JLabel(CONTROLLER_TITLE); optionsPanel = new ControllerOptionsPanel(2, 0); branchWidthAttributeCombo = new JComboBox(new String[] { "No attributes" }); branchColourAttributeCombo = new JComboBox(new String[] { "No attributes" }); backgroundColourAttributeCombo = new JComboBox(new String[] { "No attributes" }); // setupAttributes(treeViewer.getTrees()); // branchColourSettings.autoRange = true; // branchColourSettings.fromValue = 0.0; // branchColourSettings.toValue = 1.0; // branchColourSettings.fromColour = new Color(0, 16, 192); // branchColourSettings.toColour = new Color(192, 16, 0); // branchColourSettings.middleColour = new Color(0, 0, 0); branchColourIsGradient = TreeAppearanceController.PREFS.getBoolean(CONTROLLER_KEY + "." + BRANCH_COLOR_GRADIENT_KEY, false); final JButton setupColourButton = new JButton("Colours"); colourController.setupControls(branchColourAttributeCombo, setupColourButton); colourController.addControllerListener(new ControllerListener() { @Override public void controlsChanged() { setupBranchDecorators(); } }); branchColourGradientCheck = new JCheckBox("Gradient"); branchColourGradientCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { branchColourIsGradient = branchColourGradientCheck.isSelected(); setupBranchDecorators(); } }); optionsPanel.addComponentWithLabel("Colour by:", branchColourAttributeCombo); final JLabel setupColourButtonLabel = optionsPanel.addComponentWithLabel("Setup:", setupColourButton); optionsPanel.addComponent(branchColourGradientCheck); optionsPanel.addSeparator(); boolean hilightingGradient = TreeAppearanceController.PREFS.getBoolean(CONTROLLER_KEY + "." + HILIGHTING_GRADIENT_KEY, false); hilightingGradientCheck = new JCheckBox("Hilight with gradient"); hilightingGradientCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { treeViewer.setHilightingGradient(hilightingGradientCheck.isSelected()); } }); optionsPanel.addComponent(hilightingGradientCheck); hilightingGradientCheck.setSelected(hilightingGradient); optionsPanel.addSeparator(); branchLineWidthSpinner = new JSpinner(new SpinnerNumberModel(1.0, 0.01, 48.0, 1.0)); optionsPanel.addComponentWithLabel("Line Weight:", branchLineWidthSpinner); optionsPanel.addComponentWithLabel("Width by:", branchWidthAttributeCombo); branchMinLineWidthSpinner = new JSpinner(new SpinnerNumberModel(0.0, 0.0, 48.0, 1.0)); final JLabel label = optionsPanel.addComponentWithLabel("Min Weight:", branchMinLineWidthSpinner); optionsPanel.addSeparator(); // backgroundColourSettings.autoRange = true; // backgroundColourSettings.fromValue = 0.0; // backgroundColourSettings.toValue = 1.0; // backgroundColourSettings.fromColour = new Color(255, 255, 255); // backgroundColourSettings.toColour = new Color(192, 16, 0); // backgroundColourSettings.middleColour = null; final JButton bgSetupColourButton = new JButton("Colours"); colourController.setupControls(backgroundColourAttributeCombo, bgSetupColourButton); colourController.addControllerListener(new ControllerListener() { @Override public void controlsChanged() { setupBranchDecorators(); } }); optionsPanel.addComponentWithLabel("Background:", backgroundColourAttributeCombo); final JLabel bgSetupColourButtonLabel = optionsPanel.addComponentWithLabel("Setup:", bgSetupColourButton); new AttributeComboHelper(branchColourAttributeCombo, treeViewer, "User selection", false, true).addListener(new AttributeComboHelperListener() { @Override public void attributeComboChanged() { boolean isSelected = branchColourAttributeCombo.getSelectedIndex() != 0; setupColourButtonLabel.setEnabled(isSelected); setupColourButton.setEnabled(isSelected); setupBranchDecorators(); } }); new AttributeComboHelper(backgroundColourAttributeCombo, treeViewer, "Default").addListener(new AttributeComboHelperListener() { @Override public void attributeComboChanged() { boolean isSelected = backgroundColourAttributeCombo.getSelectedIndex() != 0; bgSetupColourButtonLabel.setEnabled(isSelected); bgSetupColourButton.setEnabled(isSelected); setupBranchDecorators(); } }); new AttributeComboHelper(branchWidthAttributeCombo, treeViewer, FIXED, true, false).addListener(new AttributeComboHelperListener() { @Override public void attributeComboChanged() { boolean isSelected = branchColourAttributeCombo.getSelectedIndex() != 0; label.setEnabled(isSelected); branchMinLineWidthSpinner.setEnabled(isSelected); setupBranchDecorators(); } }); branchLineWidthSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { float lineWidth = ((Double) branchLineWidthSpinner.getValue()).floatValue(); treeViewer.setBranchStroke(new BasicStroke(lineWidth, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER)); setupBranchDecorators(); } }); branchMinLineWidthSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { setupBranchDecorators(); } }); } private void setupBranchDecorators() { Decorator colourDecorator = colourController.getColourDecorator(branchColourAttributeCombo, userBranchColourDecorator); // DiversityContinuousColourDecorator colourDecorator = new DiversityContinuousColourDecorator(); // colourDecorator.setTree((RootedTree)treeViewer.getCurrentTree()); // if (colourDecorator == null) { // if (attribute.endsWith("*")) { // // This is a branch colouring (i.e., the colour can change // // along the length of the branch... // treeViewer.setBranchColouringDecorator( // attribute.substring(0, attribute.length() - 2), // new DiscreteColourDecorator()); // return; // if (colourDecorator != null && colourDecorator.isGradient()) { // // At present using a gradient precludes the use of the compoundDecorator // // and thus the branch width.. // treeViewer.setBranchDecorator(colourDecorator); // return; // } CompoundDecorator compoundDecorator = new CompoundDecorator(); if (colourDecorator != null) { treeViewer.setBranchColouringDecorator(null, null); compoundDecorator.addDecorator(colourDecorator); } if (branchWidthAttributeCombo.getSelectedIndex() > 0) { String attribute = (String) branchWidthAttributeCombo.getSelectedItem(); ContinuousScale widthScale = new ContinuousScale(attribute, treeViewer.getTrees().get(0).getNodes()); double fromWidth = (Double) branchMinLineWidthSpinner.getValue(); double toWidth = (Double)branchLineWidthSpinner.getValue() + fromWidth; compoundDecorator.addDecorator(new ContinuousStrokeDecorator( widthScale, (float)fromWidth, (float)toWidth) ); } treeViewer.setBranchDecorator(compoundDecorator, branchColourIsGradient); Decorator backgroundDecorator = null; if (backgroundColourAttributeCombo.getSelectedIndex() > 1) { backgroundDecorator = colourController.getColourDecorator(backgroundColourAttributeCombo, null); } treeViewer.setNodeBackgroundDecorator(backgroundDecorator); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { // These settings don't have controls yet but they will! treeViewer.setForeground((Color)settings.get(CONTROLLER_KEY + "." + FOREGROUND_COLOUR_KEY)); treeViewer.setBackground((Color)settings.get(CONTROLLER_KEY + "." + BACKGROUND_COLOUR_KEY)); treeViewer.setSelectionColor((Color)settings.get(CONTROLLER_KEY + "." + SELECTION_COLOUR_KEY)); branchColourAttributeCombo.setSelectedItem(settings.get(CONTROLLER_KEY+"."+BRANCH_COLOR_ATTRIBUTE_KEY)); branchColourGradientCheck.setSelected((Boolean)settings.get(CONTROLLER_KEY+"."+BRANCH_COLOR_GRADIENT_KEY)); hilightingGradientCheck.setSelected((Boolean)settings.get(CONTROLLER_KEY+"."+HILIGHTING_GRADIENT_KEY)); backgroundColourAttributeCombo.setSelectedItem(settings.get(CONTROLLER_KEY + "." + BACKGROUND_COLOR_ATTRIBUTE_KEY)); branchLineWidthSpinner.setValue((Double) settings.get(CONTROLLER_KEY + "." + BRANCH_LINE_WIDTH_KEY)); branchWidthAttributeCombo.setSelectedItem(settings.get(CONTROLLER_KEY+"."+BRANCH_WIDTH_ATTRIBUTE_KEY)); branchMinLineWidthSpinner.setValue((Double) settings.get(CONTROLLER_KEY + "." + BRANCH_MIN_LINE_WIDTH_KEY)); } public void getSettings(Map settings) { // These settings don't have controls yet but they will! settings.put(CONTROLLER_KEY + "." + FOREGROUND_COLOUR_KEY, treeViewer.getForeground()); settings.put(CONTROLLER_KEY + "." + BACKGROUND_COLOUR_KEY, treeViewer.getBackground()); settings.put(CONTROLLER_KEY + "." + SELECTION_COLOUR_KEY, treeViewer.getSelectionPaint()); settings.put(CONTROLLER_KEY + "." + BRANCH_COLOR_ATTRIBUTE_KEY, branchColourAttributeCombo.getSelectedItem().toString()); settings.put(CONTROLLER_KEY + "." + BRANCH_COLOR_GRADIENT_KEY, branchColourGradientCheck.isSelected()); settings.put(CONTROLLER_KEY + "." + HILIGHTING_GRADIENT_KEY, hilightingGradientCheck.isSelected()); settings.put(CONTROLLER_KEY + "." + BACKGROUND_COLOR_ATTRIBUTE_KEY, backgroundColourAttributeCombo.getSelectedItem().toString()); settings.put(CONTROLLER_KEY + "." + BRANCH_LINE_WIDTH_KEY, branchLineWidthSpinner.getValue()); settings.put(CONTROLLER_KEY + "." + BRANCH_WIDTH_ATTRIBUTE_KEY, branchWidthAttributeCombo.getSelectedItem().toString()); settings.put(CONTROLLER_KEY + "." + BRANCH_MIN_LINE_WIDTH_KEY, branchMinLineWidthSpinner.getValue()); } private final AttributeColourController colourController; private final AttributableDecorator userBranchColourDecorator; private final JLabel titleLabel; private final OptionsPanel optionsPanel; private final JComboBox branchColourAttributeCombo; private final JCheckBox branchColourGradientCheck; private final JCheckBox hilightingGradientCheck; private final JComboBox backgroundColourAttributeCombo; private final JSpinner branchLineWidthSpinner; private final JSpinner branchMinLineWidthSpinner; private final JComboBox branchWidthAttributeCombo; private final TreeViewer treeViewer; private boolean branchColourIsGradient = false; } figtree-1.4.3/src/figtree/treeviewer/TreePane.java000077500000000000000000002526041277473563300221440ustar00rootroot00000000000000/* * TreePane.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.painters.Painter; import jebl.evolution.graphs.Node; import jebl.evolution.graphs.Graph; import jebl.evolution.taxa.Taxon; import jebl.evolution.trees.*; import figtree.treeviewer.decorators.*; import figtree.treeviewer.painters.*; import figtree.treeviewer.treelayouts.*; import javax.swing.*; import java.awt.*; import java.awt.geom.*; import java.awt.print.*; import java.util.*; import java.util.List; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreePane extends JComponent implements PainterListener, Printable { public final static boolean DEBUG_OUTLINE = false; public enum RootingType { USER_ROOTING("User Selection"), MID_POINT("Midpoint"); // LEAST_SQUARES("least squares"); RootingType(String name) { this.name = name; } public String toString() { return name; } private String name; } public final String CARTOON_ATTRIBUTE_NAME = "!cartoon"; public final String COLLAPSE_ATTRIBUTE_NAME = "!collapse"; public final String HILIGHT_ATTRIBUTE_NAME = "!hilight"; public TreePane() { } public RootedTree getTree() { return tree; } public void setTree(RootedTree tree) { if (tree != null) { this.originalTree = tree; if (!originalTree.hasLengths()) { transformBranchesOn = true; } setupTree(); } else { originalTree = null; this.tree = null; invalidate(); repaint(); } } private void recalibrate() { calibrated = false; } private void setupTree() { tree = constructTransformedTree(originalTree); recalculateCollapsedNodes(); recalibrate(); invalidate(); repaint(); } public RootedTree constructTransformedTree(RootedTree sourceTree) { RootedTree newTree = sourceTree; if (isRootingOn) { if (rootingType == RootingType.MID_POINT) { newTree = ReRootedTree.rootTreeAtCenter(newTree); } else if (rootingType == RootingType.USER_ROOTING && rootingNode != null) { Node left = newTree.getParent(rootingNode); if (left != null) { // rooting length should be [0, 1] double length = newTree.hasLengths() ? newTree.getLength(rootingNode) * rootingLength : 1.0; try { newTree = new ReRootedTree(newTree, left, rootingNode, length); } catch (Graph.NoEdgeException e) { e.printStackTrace(); } } } } if (orderBranchesOn) { newTree = new SortedRootedTree(newTree, branchOrdering); } if (transformBranchesOn || !sourceTree.hasLengths()) { newTree = new TransformedRootedTree(newTree, branchTransform); } return newTree; } public TreeLayout getTreeLayout() { return treeLayout; } public TreeLayoutCache getTreeLayoutCache() { return treeLayoutCache; } public void setTreeLayout(TreeLayout treeLayout) { this.treeLayout = treeLayout; treeLayout.setCartoonAttributeName(CARTOON_ATTRIBUTE_NAME); treeLayout.setCollapsedAttributeName(COLLAPSE_ATTRIBUTE_NAME); treeLayout.setHilightAttributeName(HILIGHT_ATTRIBUTE_NAME); treeLayout.setBranchColouringAttributeName(branchColouringAttribute); treeLayout.addTreeLayoutListener(new TreeLayoutListener() { public void treeLayoutChanged() { recalibrate(); repaint(); } }); recalibrate(); invalidate(); repaint(); } public TimeScale getTimeScale() { return timeScale; } public void setTimeScale(TimeScale timeScale) { this.timeScale = timeScale; this.timeScale.setReversed(isAxisReversed()); recalibrate(); repaint(); } public boolean isCrosshairShown() { return isCrosshairShown; } public void setCrosshairShown(boolean crosshairShown) { isCrosshairShown = crosshairShown; } public void setCursorPosition(Point point) { cursorPosition = point; if (cursorPosition != null) { double xPos = (point.getX() - treeBounds.getX()) / treeBounds.getWidth(); xPos = (xPos < 0.0 ? 0.0 : xPos > 1.0 ? 1.0 : xPos); double yPos = (point.getY() - treeBounds.getY()) / treeBounds.getHeight(); yPos = (yPos < 0.0 ? 0.0 : yPos > 1.0 ? 1.0 : yPos); treeLayout.setPointOfInterest(xPos, yPos); } } public void midpointRoot() { isRootingOn = true; rootingType = RootingType.MID_POINT; setupTree(); fireSettingsChanged(); } public void setRootLocation(Node node, double length) { RootedTree source = tree; if (tree instanceof FilteredRootedTree) { source = ((FilteredRootedTree) tree).getSource(); } if (source instanceof ReRootedTree) { rootingNode = ((ReRootedTree)source).getSourceNode(node); } else { rootingNode = node; } rootingLength = length; isRootingOn = true; rootingType = RootingType.USER_ROOTING; setupTree(); fireSettingsChanged(); } public void rotateNode(Node node) { if (node != null) { Boolean rotate = (Boolean)node.getAttribute("!rotate"); if (rotate != null) { rotate = !rotate; } else { rotate = true; } node.setAttribute("!rotate", rotate); recalibrate(); invalidate(); repaint(); } } public void clearRotation(Node node) { if (node != null) { Boolean rotate = (Boolean)node.getAttribute("!rotate"); if (rotate != null) { node.removeAttribute("!rotate"); } recalibrate(); invalidate(); repaint(); } } public void setBranchDecorator(Decorator branchDecorator, boolean isGradient) { this.branchDecorator = branchDecorator; this.branchDecoratorGradient = isGradient; repaint(); } public void setBranchColouringDecorator(String branchColouringAttribute, Decorator branchColouringDecorator) { this.branchColouringAttribute = branchColouringAttribute; treeLayout.setBranchColouringAttributeName(branchColouringAttribute); this.branchColouringDecorator = branchColouringDecorator; repaint(); } public boolean isHilightingGradient() { return hilightingGradient; } public void setHilightingGradient(boolean hilightingGradient) { this.hilightingGradient = hilightingGradient; repaint(); } public void setNodeBackgroundDecorator(Decorator nodeBackgroundDecorator) { this.nodeBackgroundDecorator = nodeBackgroundDecorator; repaint(); } public Rectangle2D getTreeBounds() { return treeBounds; } /** * This returns the scaling factor between the graphical image and the branch * lengths of the tree * * @return the tree scale */ public double getTreeScale() { return treeScale / timeScale.getScaleFactor(tree); } /** * Transform a chart co-ordinates into a drawing co-ordinates */ public double scaleOnAxis(double value) { double height = timeScale.getHeight(value, tree); if (isAxisReversed()) { return (treeBounds.getX() + treeBounds.getWidth()) - (height * treeScale); } else { return treeBounds.getX() + (height * treeScale); } } public Shape getAxisLine(double value) { if (isAxisReversed()) { value = maxTreeHeight - value; } else { value -= rootHeightOffset; } double height = timeScale.getHeight(value, tree); Shape line = treeLayout.getAxisLine(height); if (line != null) { return transform.createTransformedShape(line); } return null; } public ScaleAxis getScaleAxis() { return scaleAxis; } public double getAxisOrigin() { return axisOrigin; } public void setAxisOrigin(double axisOrigin) { this.axisOrigin = axisOrigin; recalibrate(); repaint(); } public void setAxisReversed(final boolean isAxisReversed) { this.isAxisReversed = isAxisReversed; this.timeScale.setReversed(isAxisReversed()); recalibrate(); repaint(); } public boolean isAxisReversed() { return isAxisReversed; } private void setupScaleAxis() { double minValue = timeScale.getAge(0.0, tree); double maxValue = timeScale.getAge(maxTreeHeight, tree); if (minValue < maxValue) { if (axisOrigin < minValue) { minValue = axisOrigin; } scaleAxis.setRange(minValue, maxValue); } else { if (axisOrigin > minValue) { minValue = axisOrigin; } scaleAxis.setRange(maxValue, minValue); } } public void setRootAge(double rootAge) { double rootLength = timeScale.getHeight(rootAge, tree) - tree.getHeight(tree.getRootNode()); treeLayout.setRootLength(rootLength); recalibrate(); repaint(); } public double getRootAge() { double treeHeight = tree.getHeight(tree.getRootNode()) + treeLayout.getRootLength(); return timeScale.getAge(treeHeight, tree); } public double getMajorTickSpacing() { return scaleAxis.getMajorTickSpacing(); } public double getMinorTickSpacing() { return scaleAxis.getMinorTickSpacing(); } public void setTickSpacing(double userMajorTickSpacing, double userMinorTickSpacing) { scaleAxis.setManualAxis(userMajorTickSpacing, userMinorTickSpacing); recalibrate(); repaint(); } public void setAutomaticScale() { scaleAxis.setAutomatic(); recalibrate(); repaint(); } public void painterChanged() { recalibrate(); repaint(); } public void painterSettingsChanged() { recalibrate(); repaint(); } public void attributesChanged() { recalibrate(); repaint(); } public BasicStroke getBranchStroke() { return branchLineStroke; } public void setBranchStroke(BasicStroke stroke) { branchLineStroke = stroke; float weight = stroke.getLineWidth(); selectionStroke = new BasicStroke(Math.max(weight + 4.0F, weight * 1.5F), BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND); repaint(); } public BasicStroke getCalloutStroke() { return calloutStroke; } public void setCalloutStroke(BasicStroke calloutStroke) { this.calloutStroke = calloutStroke; } public Paint getSelectionPaint() { return selectionPaint; } public void setSelectionColor(Color selectionColor) { this.selectionPaint = new Color( selectionColor.getRed(), selectionColor.getGreen(), selectionColor.getBlue(), 128); } public boolean isTransformBranchesOn() { return transformBranchesOn; } public void setTransformBranchesOn(boolean transformBranchesOn) { this.transformBranchesOn = transformBranchesOn; setupTree(); } public TransformedRootedTree.Transform getBranchTransform() { return branchTransform; } public void setBranchTransform(TransformedRootedTree.Transform branchTransform) { this.branchTransform = branchTransform; setupTree(); } public boolean isOrderBranchesOn() { return orderBranchesOn; } public void setOrderBranchesOn(boolean orderBranchesOn) { this.orderBranchesOn = orderBranchesOn; setupTree(); } public SortedRootedTree.BranchOrdering getBranchOrdering() { return branchOrdering; } public void setBranchOrdering(SortedRootedTree.BranchOrdering branchOrdering) { this.branchOrdering = branchOrdering; setupTree(); } public boolean isRootingOn() { return isRootingOn; } public RootingType getRootingType() { return rootingType; } public void setRootingOn(boolean rootingOn) { this.isRootingOn = rootingOn; setupTree(); } public void setRootingType(RootingType rootingType) { this.rootingType = rootingType; setupTree(); } public RootedTree getOriginalTree() { return originalTree; } public boolean isShowingTipCallouts() { return showingTipCallouts; } public void setShowingTipCallouts(boolean showingTipCallouts) { this.showingTipCallouts = showingTipCallouts; recalibrate(); repaint(); } public void setSelectedNode(Node selectedNode) { selectedNodes.clear(); selectedTips.clear(); addSelectedNode(selectedNode, false, false); } public void setSelectedTip(Node selectedTip) { selectedNodes.clear(); selectedTips.clear(); addSelectedTip(selectedTip, false, false); } public void setSelectedClade(Node selectedNode) { selectedNodes.clear(); selectedTips.clear(); addSelectedClade(selectedNode, false, false); } public void setSelectedTips(Node selectedNode) { selectedNodes.clear(); selectedTips.clear(); addSelectedTips(selectedNode, false); } private boolean canSelectNode(Node selectedNode) { return selectedNode != null; } public void addSelectedNode(Node selectedNode) { addSelectedNode(selectedNode, false, false); } public void addSelectedNode(Node selectedNode, boolean toggle, boolean extend) { amendNodeSelection(selectedNode, toggle, extend); fireSelectionChanged(); clearSelectionPaths(); repaint(); } public void addSelectedTip(Node selectedTip) { addSelectedTip(selectedTip, false, false); } public void addSelectedTip(Node selectedTip, boolean toggle, boolean extend) { amendNodeSelection(selectedTip, toggle, extend); selectTipsFromSelectedNodes(); fireSelectionChanged(); clearSelectionPaths(); repaint(); } public void addSelectedClade(Node selectedNode) { addSelectedClade(selectedNode, false, false); } public void addSelectedClade(Node selectedNode, boolean toggle, boolean extend) { if (canSelectNode(selectedNode)) { amendCladeSelection(selectedNode, toggle, extend); } fireSelectionChanged(); clearSelectionPaths(); repaint(); } private void amendNodeSelection(Node selectedNode, boolean toggle, boolean extend) { if ( !canSelectNode(selectedNode) ) { return; } if (extend) { Set nodeSet = new HashSet(selectedNodes); nodeSet.add(selectedNode); Node mrca = RootedTreeUtils.getCommonAncestorNode(tree, nodeSet); for (Node node : nodeSet) { while (node != null && node != mrca) { amendNodeSelection(node, false, false); node = tree.getParent(node); } } } else { if (toggle && selectedNodes.contains(selectedNode)) { selectedNodes.remove(selectedNode); } else { selectedNodes.add(selectedNode); } } } private void amendCladeSelection(Node selectedNode, boolean toggle, boolean extend) { if ( !canSelectNode(selectedNode) ) { return; } if (extend) { Set nodeSet = new HashSet(selectedNodes); nodeSet.add(selectedNode); Node mrca = RootedTreeUtils.getCommonAncestorNode(tree, nodeSet); for (Node node : nodeSet) { while (node != null && node != mrca) { amendCladeSelection(node, false, false); node = tree.getParent(node); } } } else { if (toggle && selectedNodes.contains(selectedNode)) { selectedNodes.remove(selectedNode); } else { selectedNodes.add(selectedNode); } } for (Node child : tree.getChildren(selectedNode)) { amendCladeSelection(child, toggle, false); } } public void addSelectedTips(Node selectedNode) { addSelectedTips(selectedNode, false); } public void addSelectedTips(Node selectedNode, boolean toggle) { if (selectedNode != null) { addSelectedChildTips(selectedNode, toggle); } fireSelectionChanged(); clearSelectionPaths(); repaint(); } private void addSelectedChildTips(Node selectedNode, boolean toggle) { if (tree.isExternal(selectedNode)) { if (toggle && selectedTips.contains(selectedNode)) { selectedTips.remove(selectedNode); } else { selectedTips.add(selectedNode); } } else { for (Node child : tree.getChildren(selectedNode)) { addSelectedChildTips(child, toggle); } } } public void selectCladesFromSelectedNodes() { Set nodes = new HashSet(selectedNodes); selectedNodes.clear(); for (Node node : nodes) { addSelectedClade(node, false, false); } fireSelectionChanged(); clearSelectionPaths(); repaint(); } public void selectTipsFromSelectedNodes() { for (Node node : selectedNodes) { addSelectedChildTips(node, false); } selectedNodes.clear(); fireSelectionChanged(); clearSelectionPaths(); repaint(); } public void selectNodesFromSelectedTips() { if (selectedTips.size() > 0) { Node node = RootedTreeUtils.getCommonAncestorNode(tree, selectedTips); addSelectedClade(node, false, false); } selectedTips.clear(); fireSelectionChanged(); clearSelectionPaths(); repaint(); } public void selectAllTaxa() { selectedTips.addAll(tree.getExternalNodes()); fireSelectionChanged(); clearSelectionPaths(); repaint(); } public void selectAllNodes() { selectedNodes.addAll(tree.getNodes()); fireSelectionChanged(); clearSelectionPaths(); repaint(); } public void clearSelection() { selectedNodes.clear(); selectedTips.clear(); fireSelectionChanged(); clearSelectionPaths(); repaint(); } public boolean hasSelection() { return selectedNodes.size() > 0 || selectedTips.size() > 0; } public void cartoonSelectedNodes() { cartoonSelectedNodes(tree.getRootNode()); } private void cartoonSelectedNodes(Node node) { if (!tree.isExternal(node)) { if (selectedNodes.contains(node)) { if (node.getAttribute(CARTOON_ATTRIBUTE_NAME) != null) { node.removeAttribute(CARTOON_ATTRIBUTE_NAME); } else { int tipCount = RootedTreeUtils.getTipCount(tree, node); double height = RootedTreeUtils.getMinTipHeight(tree, node); Object[] values = new Object[] { tipCount, height }; node.setAttribute(CARTOON_ATTRIBUTE_NAME, values); } recalibrate(); repaint(); } else { for (Node child : tree.getChildren(node)) { cartoonSelectedNodes(child); } } } } public void collapseSelectedNodes() { collapseSelectedNodes(tree.getRootNode()); } private void collapseSelectedNodes(Node node) { if (!tree.isExternal(node)) { if (selectedNodes.contains(node)) { if (node.getAttribute(COLLAPSE_ATTRIBUTE_NAME) != null) { node.removeAttribute(COLLAPSE_ATTRIBUTE_NAME); } else { String tipName = "collapsed"; double height = RootedTreeUtils.getMinTipHeight(tree, node); Object[] values = new Object[] { tipName, height }; node.setAttribute(COLLAPSE_ATTRIBUTE_NAME, values); } recalibrate(); repaint(); } else { for (Node child : tree.getChildren(node)) { collapseSelectedNodes(child); } } } } public void hilightSelectedNodes(Color color) { hilightSelectedNodes(tree.getRootNode(), color); } private void hilightSelectedNodes(Node node, Color color) { if (!tree.isExternal(node)) { if (selectedNodes.contains(node)) { int tipCount = RootedTreeUtils.getTipCount(tree, node); double height = RootedTreeUtils.getMinTipHeight(tree, node); Object[] values = new Object[] { tipCount, height, color }; node.setAttribute(HILIGHT_ATTRIBUTE_NAME, values); recalibrate(); repaint(); } else { for (Node child : tree.getChildren(node)) { hilightSelectedNodes(child, color); } } } } public void recalculateCollapsedNodes() { recalculateCollapsedNodes(tree.getRootNode()); } private void recalculateCollapsedNodes(Node node) { if (!tree.isExternal(node)) { if (selectedNodes.contains(node)) { if (node.getAttribute(CARTOON_ATTRIBUTE_NAME) != null) { int tipCount = RootedTreeUtils.getTipCount(tree, node); double height = RootedTreeUtils.getMinTipHeight(tree, node); Object[] values = new Object[] { tipCount, height }; node.setAttribute(CARTOON_ATTRIBUTE_NAME, values); } if (node.getAttribute(COLLAPSE_ATTRIBUTE_NAME) != null) { String tipName = "collapsed"; double height = RootedTreeUtils.getMinTipHeight(tree, node); Object[] values = new Object[] { tipName, height }; node.setAttribute(COLLAPSE_ATTRIBUTE_NAME, values); } Object[] oldValues = (Object[])node.getAttribute(HILIGHT_ATTRIBUTE_NAME); if (oldValues != null) { int tipCount = RootedTreeUtils.getTipCount(tree, node); double height = RootedTreeUtils.getMinTipHeight(tree, node); Object[] values = new Object[] { tipCount, height, oldValues[2] }; node.setAttribute(HILIGHT_ATTRIBUTE_NAME, values); } recalibrate(); repaint(); } else { for (Node child : tree.getChildren(node)) { recalculateCollapsedNodes(child); } } } } public void clearCollapsedNodes() { if (selectedNodes.size() > 0) { clearSelectedCollapsedNodes(tree.getRootNode()); } else { for (Node node : tree.getInternalNodes()){ if (node.getAttribute(COLLAPSE_ATTRIBUTE_NAME) != null) { node.removeAttribute(COLLAPSE_ATTRIBUTE_NAME); } if (node.getAttribute(CARTOON_ATTRIBUTE_NAME) != null) { node.removeAttribute(CARTOON_ATTRIBUTE_NAME); } } recalibrate(); repaint(); } } private void clearSelectedCollapsedNodes(Node node) { if (!tree.isExternal(node)) { // Although collapsed nodes could be nested, we don't go // deeper. So one 'clear collapsed' will reveal any nested // collapsed nodes. if (selectedNodes.contains(node)) { if (node.getAttribute(COLLAPSE_ATTRIBUTE_NAME) != null) { node.removeAttribute(COLLAPSE_ATTRIBUTE_NAME); } if (node.getAttribute(CARTOON_ATTRIBUTE_NAME) != null) { node.removeAttribute(CARTOON_ATTRIBUTE_NAME); } recalibrate(); repaint(); } else { for (Node child : tree.getChildren(node)) { clearSelectedCollapsedNodes(child); } } } } public void clearHilightedNodes() { if (selectedNodes.size() > 0) { clearSelectedHilightedNodes(tree.getRootNode()); } else { for (Node node : tree.getInternalNodes()){ if (node.getAttribute(HILIGHT_ATTRIBUTE_NAME) != null) { node.removeAttribute(HILIGHT_ATTRIBUTE_NAME); } } recalibrate(); repaint(); } } private void clearSelectedHilightedNodes(Node node) { if (!tree.isExternal(node)) { if (selectedNodes.size() == 0 || selectedNodes.contains(node)) { if (node.getAttribute(HILIGHT_ATTRIBUTE_NAME) != null) { node.removeAttribute(HILIGHT_ATTRIBUTE_NAME); recalibrate(); repaint(); } } for (Node child : tree.getChildren(node)) { clearSelectedHilightedNodes(child); } } } public void rerootOnSelectedBranch() { for (Node selectedNode : selectedNodes) { setRootLocation(selectedNode, 0.5); // root on the first selected branch... // Check for multiple selected branch elsewhere return; } repaint(); } public void clearRooting() { rootingNode = null; setupTree(); fireSettingsChanged(); } public void rotateSelectedNode() { for (Node selectedNode : selectedNodes) { rotateNode(selectedNode); } repaint(); } public void clearSelectedNodeRotations() { if (selectedNodes.size() > 0) { for (Node node : selectedNodes) { clearRotation(node); } } else { for (Node node : tree.getInternalNodes()) { clearRotation(node); } } repaint(); } public void annotateSelectedNodes(String name, Object value) { for (Node selectedNode : selectedNodes) { selectedNode.setAttribute(name, value); } repaint(); } public void annotateSelectedTips(String name, Object value) { for (Node selectedTip : selectedTips) { Taxon selectedTaxon = tree.getTaxon(selectedTip); // if (selectedTaxon == null) { // throw new IllegalArgumentException("missing taxon?"); // } selectedTaxon.setAttribute(name, value); } repaint(); } public void clearSelectedNodeAnnotation(String name) { for (Node selectedNode : selectedNodes) { selectedNode.removeAttribute(name); } repaint(); } public void clearSelectedTipAnnotation(String name) { for (Node selectedTip : selectedTips) { Taxon selectedTaxon = tree.getTaxon(selectedTip); selectedTaxon.removeAttribute(name); } repaint(); } /** * Return whether the two axis scales should be maintained * relative to each other * * @return a boolean */ public boolean maintainAspectRatio() { return treeLayout.maintainAspectRatio(); } public void setTipLabelPainter(LabelPainter tipLabelPainter) { tipLabelPainter.setTreePane(this); if (this.tipLabelPainter != null) { this.tipLabelPainter.removePainterListener(this); } this.tipLabelPainter = tipLabelPainter; if (this.tipLabelPainter != null) { this.tipLabelPainter.addPainterListener(this); } recalibrate(); repaint(); } public LabelPainter getTipLabelPainter() { return tipLabelPainter; } public void setNodeLabelPainter(LabelPainter nodeLabelPainter) { nodeLabelPainter.setTreePane(this); if (this.nodeLabelPainter != null) { this.nodeLabelPainter.removePainterListener(this); } this.nodeLabelPainter = nodeLabelPainter; if (this.nodeLabelPainter != null) { this.nodeLabelPainter.addPainterListener(this); } recalibrate(); repaint(); } public LabelPainter getNodeLabelPainter() { return nodeLabelPainter; } public void setBranchLabelPainter(LabelPainter branchLabelPainter) { branchLabelPainter.setTreePane(this); if (this.branchLabelPainter != null) { this.branchLabelPainter.removePainterListener(this); } this.branchLabelPainter = branchLabelPainter; if (this.branchLabelPainter != null) { this.branchLabelPainter.addPainterListener(this); } recalibrate(); repaint(); } public LabelPainter getBranchLabelPainter() { return branchLabelPainter; } public void setNodeBarPainter(NodeBarPainter nodeBarPainter) { nodeBarPainter.setTreePane(this); if (this.nodeBarPainter != null) { this.nodeBarPainter.removePainterListener(this); } this.nodeBarPainter = nodeBarPainter; if (this.nodeBarPainter != null) { this.nodeBarPainter.addPainterListener(this); } recalibrate(); repaint(); } public NodeBarPainter getNodeBarPainter() { return nodeBarPainter; } public void setTipShapePainter(NodeShapePainter tipShapePainter) { tipShapePainter.setTreePane(this); if (this.tipShapePainter != null) { this.tipShapePainter.removePainterListener(this); } this.tipShapePainter = tipShapePainter; if (this.tipShapePainter != null) { this.tipShapePainter.addPainterListener(this); } recalibrate(); repaint(); } public NodeShapePainter getTipShapePainter() { return tipShapePainter; } public void setNodeShapePainter(NodeShapePainter nodeShapePainter) { nodeShapePainter.setTreePane(this); if (this.nodeShapePainter != null) { this.nodeShapePainter.removePainterListener(this); } this.nodeShapePainter = nodeShapePainter; if (this.nodeShapePainter != null) { this.nodeShapePainter.addPainterListener(this); } recalibrate(); repaint(); } public NodeShapePainter getNodeShapePainter() { return nodeShapePainter; } public void addScalePainter(ScalePainter scalePainter) { assert scalePainter != null; scalePainter.setTreePane(this); scalePainter.addPainterListener(this); scalePainters.add(scalePainter); recalibrate(); repaint(); } public void removeScalePainter(ScalePainter scalePainter) { assert scalePainter != null; scalePainter.removePainterListener(this); scalePainters.remove(scalePainter); recalibrate(); repaint(); } public void setScaleGridPainter(ScaleGridPainter scaleGridPainter) { scaleGridPainter.setTreePane(this); if (this.scaleGridPainter != null) { this.scaleGridPainter.removePainterListener(this); } this.scaleGridPainter = scaleGridPainter; if (this.scaleGridPainter != null) { this.scaleGridPainter.addPainterListener(this); } recalibrate(); repaint(); } public void setLegendPainter(LegendPainter legendPainter) { legendPainter.setTreePane(this); legendPainter.addPainterListener(this); this.legendPainter = legendPainter; recalibrate(); repaint(); } public LegendPainter getLegendPainter() { return legendPainter; } public float getLabelSpacing() { return labelXOffset; } public void setLabelSpacing(float labelSpacing) { this.labelXOffset = labelSpacing; recalibrate(); repaint(); } public void setPreferredSize(Dimension dimension) { if (treeLayout.maintainAspectRatio()) { super.setPreferredSize(new Dimension(dimension.width, dimension.height)); } else { super.setPreferredSize(dimension); } recalibrate(); } public double getHeightAt(Graphics2D graphics2D, Point2D point) { try { point = transform.inverseTransform(point, null); } catch (NoninvertibleTransformException e) { e.printStackTrace(); } return treeLayout.getHeightOfPoint(point); } public Node getNodeAt(Graphics2D g2, Point point) { Rectangle rect = new Rectangle(point.x - 1, point.y - 1, 3, 3); rect.translate(-insets.left, -insets.top); for (Node node : tree.getExternalNodes()) { Shape taxonLabelBound = tipLabelBounds.get(node); if (taxonLabelBound != null && g2.hit(rect, taxonLabelBound, false)) { return node; } } if (transform == null) return null; for (Node node : tree.getNodes()) { Shape branchPath = transform.createTransformedShape(treeLayoutCache.getBranchPath(node)); if (branchPath != null && g2.hit(rect, branchPath, true)) { return node; } Shape collapsedShape = transform.createTransformedShape(treeLayoutCache.getCollapsedShape(node)); if (collapsedShape != null && g2.hit(rect, collapsedShape, false)) { return node; } } return null; } public Set getNodesAt(Graphics2D g2, Rectangle rect) { Set nodes = new HashSet(); for (Node node : tree.getExternalNodes()) { Shape taxonLabelBound = tipLabelBounds.get(node); if (taxonLabelBound != null && g2.hit(rect, taxonLabelBound, false)) { nodes.add(node); } } for (Node node : tree.getNodes()) { Shape branchPath = transform.createTransformedShape(treeLayoutCache.getBranchPath(node)); if (branchPath != null && g2.hit(rect, branchPath, true)) { nodes.add(node); } Shape collapsedShape = transform.createTransformedShape(treeLayoutCache.getCollapsedShape(node)); if (collapsedShape != null && g2.hit(rect, collapsedShape, false)) { nodes.add(node); } } return nodes; } public Set getSelectedNodes() { return selectedNodes; } public Set getSelectedTips() { return selectedTips; } public Set getSelectedTaxa() { Set selectedTaxa = new LinkedHashSet(); for (Node node : getSelectedTips()) { selectedTaxa.add(tree.getTaxon(node)); } return selectedTaxa; } public RootedTree getSelectedSubtree() { if (selectedNodes.size() == 0 && selectedTips.size() == 0) { // nothing selected so return the whole tree return tree; } SimpleRootedTree newTree = new SimpleRootedTree(); getSelectedSubtree(newTree, this.tree.getRootNode(), false); if (newTree.getRootNode() == null) { // no tree was constructed, most likely because only one tip was selected return null; } return newTree; } /** * Returns a new node structure within newTree that contains the subtree subtended by selected * nodes of the current tree. * @param newTree * @param node * @param isSelected * @return */ private Node getSelectedSubtree(SimpleRootedTree newTree, Node node, boolean isSelected) { Node newNode; if (tree.isExternal(node)) { if (isSelected || selectedNodes.contains(node) || selectedTips.contains(node)) { newNode = newTree.createExternalNode(tree.getTaxon(node)); newTree.setHeight(newNode, tree.getHeight(node)); for (String key : node.getAttributeNames()) { newNode.setAttribute(key, node.getAttribute(key)); } } else { newNode = null; } } else { List children = new ArrayList(); for (Node child : tree.getChildren(node)) { Node subtree = getSelectedSubtree(newTree, child, isSelected); if (subtree != null) { children.add(subtree); } } if (children.size() == 0) { if (selectedNodes.contains(node)) { // if this node was selected but none of its children then include the entire // descendent clade... newNode = getSelectedSubtree(newTree, node, true); } else { newNode = null; } } else if (children.size() == 1) { // just one child so pass it up... newNode = children.get(0); } else { newNode = newTree.createInternalNode(children); newTree.setHeight(newNode, tree.getHeight(node)); for (String key : node.getAttributeNames()) { newNode.setAttribute(key, node.getAttribute(key)); } } } return newNode; } public Rectangle2D getDragRectangle() { return dragRectangle; } public void setDragRectangle(Rectangle2D dragRectangle) { this.dragRectangle = dragRectangle; repaint(); } public void setRuler(double rulerHeight) { this.rulerHeight = rulerHeight; } public Point getLocationOfTip(Node tip) { if (tip == null) { return new Point(0,0); } Shape path = transform.createTransformedShape(treeLayoutCache.getTipLabelPath(tip)); return path.getBounds().getLocation(); } public void scrollPointToVisible(Point point) { scrollRectToVisible(new Rectangle(point.x, point.y, 0, 0)); } private final Set treeSelectionListeners = new HashSet(); public void addTreeSelectionListener(TreeSelectionListener treeSelectionListener) { treeSelectionListeners.add(treeSelectionListener); } public void removeTreeSelectionListener(TreeSelectionListener treeSelectionListener) { treeSelectionListeners.remove(treeSelectionListener); } private void fireSelectionChanged() { for (TreeSelectionListener treeSelectionListener : treeSelectionListeners) { treeSelectionListener.selectionChanged(); } } private final Set treePaneListeners = new HashSet(); public void addTreePaneListener(TreePaneListener treePaneListener) { treePaneListeners.add(treePaneListener); } public void removeTreePaneListener(TreePaneListener treePaneListener) { treePaneListeners.remove(treePaneListener); } private void fireSettingsChanged() { for (TreePaneListener treePaneListener : treePaneListeners) { treePaneListener.treePaneSettingsChanged(); } } public void paint(Graphics graphics) { if (tree == null) return; // graphics.setColor(Color.white); // Rectangle r = graphics.getClipBounds(); // if (r != null) { // graphics.fillRect(r.x, r.y, r.width, r.height); // } // final Graphics2D g2 = (Graphics2D) graphics; g2.translate(insets.left, insets.top); if (!calibrated) { calibrate(g2, getWidth(), getHeight()); } drawTree(g2, getWidth(), getHeight()); Paint oldPaint = g2.getPaint(); Stroke oldStroke = g2.getStroke(); // if (isCrosshairShown && cursorPosition != null && dragRectangle == null) { // g2.setPaint(cursorPaint); // g2.setStroke(cursorStroke); // double x = Math.max(treeBounds.getX(), // Math.min(cursorPosition.getX(), treeBounds.getX() + treeBounds.getWidth())); // double y = Math.max(treeBounds.getY(), // Math.min(cursorPosition.getY(), treeBounds.getY() + treeBounds.getHeight())); // // g2.draw(new Line2D.Double(0.0, y, getWidth(), y)); // g2.draw(new Line2D.Double(x, 0.0, x, getHeight())); // // } if (branchSelection == null) { branchSelection = new GeneralPath(); for (Node selectedNode : selectedNodes) { Shape branchPath = treeLayoutCache.getBranchPath(selectedNode); if (branchPath != null) { Shape transPath = transform.createTransformedShape(branchPath); branchSelection.append(transPath, false); } Shape collapsedShape = treeLayoutCache.getCollapsedShape(selectedNode); if (collapsedShape != null) { Shape transPath = transform.createTransformedShape(collapsedShape); branchSelection.append(transPath, false); } } } if (labelSelection == null) { labelSelection = new GeneralPath(); for (Node selectedTip : selectedTips) { Shape labelBounds = tipLabelBounds.get(selectedTip); if (labelBounds != null) { labelSelection.append(labelBounds, false); } } } g2.setPaint(selectionPaint); g2.setStroke(selectionStroke); g2.draw(branchSelection); g2.fill(labelSelection); g2.setPaint(oldPaint); g2.setStroke(oldStroke); if (dragRectangle != null) { g2.setPaint(new Color(128, 128, 128, 128)); g2.fill(dragRectangle); } } private void clearSelectionPaths() { branchSelection = null; labelSelection = null; } private GeneralPath branchSelection = null; private GeneralPath labelSelection = null; public int print(Graphics graphics, PageFormat pageFormat, int pageIndex) throws PrinterException { if (tree == null || pageIndex > 0) return NO_SUCH_PAGE; Graphics2D g2 = (Graphics2D) graphics; g2.translate(pageFormat.getImageableX(), pageFormat.getImageableY()); recalibrate(); setDoubleBuffered(false); drawTree(g2, pageFormat.getImageableWidth(), pageFormat.getImageableHeight()); setDoubleBuffered(true); recalibrate(); return PAGE_EXISTS; } public void drawTree(Graphics2D g2, double width, double height) { final RenderingHints rhints = g2.getRenderingHints(); final boolean antialiasOn = rhints.containsValue(RenderingHints.VALUE_ANTIALIAS_ON); if( ! antialiasOn ) { g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); } if (!calibrated) { calibrate(g2, width, height); } // save graphics state which draw changes so that upon exit it can be restored final AffineTransform oldTransform = g2.getTransform(); final Paint oldPaint = g2.getPaint(); final Stroke oldStroke = g2.getStroke(); final Font oldFont = g2.getFont(); if (legendPainter != null && legendPainter.isVisible()) { legendPainter.paint(g2, this, Painter.Justification.CENTER, legendBounds); } // Paint scales for (ScalePainter scalePainter : scalePainters) { if (scalePainter.isVisible()) { Rectangle2D scaleBounds = this.scaleBounds.get(scalePainter); scalePainter.paint(g2, this, Painter.Justification.CENTER, scaleBounds); } } if (scaleGridPainter != null && scaleGridPainter.isVisible()) { Rectangle2D gridBounds = new Rectangle2D.Double( treeBounds.getX(), 0.0, treeBounds.getWidth(), treeBounds.getHeight()); scaleGridPainter.paint(g2, this, null, gridBounds); } // Paint backgrounds if (nodeBackgroundDecorator != null) { for (Node node : treeLayoutCache.getNodeAreaMap().keySet() ) { Shape nodeArea = treeLayoutCache.getNodeArea(node); if (nodeArea != null) { nodeBackgroundDecorator.setItem(node); Shape transNodePath = transform.createTransformedShape(nodeArea); Paint background = new Color(0,0,0,0); background = nodeBackgroundDecorator.getPaint(background); g2.setPaint(background); g2.fill(transNodePath); // Experimental outlining - requires order of drawing to be pre-order // g2.setStroke(new BasicStroke(8, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND)); // g2.draw(transNodePath); } } } // Paint hilighted nodes for (Node node : treeLayoutCache.getHilightNodesList() ) { Object[] values = (Object[])node.getAttribute(HILIGHT_ATTRIBUTE_NAME); Shape hilightShape = treeLayoutCache.getHilightShape(node); Shape transShape = transform.createTransformedShape(hilightShape); Paint paint = ((Color)values[2]).darker(); Paint fillPaint = (Color)values[2]; Stroke stroke = new BasicStroke(0.5F); if (hilightingGradient && fillPaint != null) { fillPaint = new GradientPaint( (float)transShape.getBounds2D().getMinX(), 0.0F, Color.WHITE, (float)transShape.getBounds2D().getMaxX(), 0.0F, (Color)values[2], false); g2.setPaint(fillPaint); g2.fill(transShape); } else { if (fillPaint != null) { g2.setPaint(fillPaint); g2.fill(transShape); } if (paint != null) { g2.setPaint(paint); g2.setStroke(stroke); g2.draw(transShape); } } } if (DEBUG_OUTLINE) { g2.setPaint(Color.blue); g2.draw(treeBounds); } // Paint collapsed nodes for (Node node : treeLayoutCache.getCollapsedShapeMap().keySet() ) { Shape collapsedShape = treeLayoutCache.getCollapsedShape(node); Shape transShape = transform.createTransformedShape(collapsedShape); Paint paint = Color.BLACK; Paint fillPaint = null; Stroke stroke = branchLineStroke; if (branchDecorator != null) { branchDecorator.setItem(node); paint = branchDecorator.getPaint(paint); fillPaint = branchDecorator.getFillPaint(fillPaint); stroke = branchDecorator.getStroke(stroke); } if (fillPaint != null) { g2.setPaint(fillPaint); g2.fill(transShape); } g2.setPaint(paint); g2.setStroke(stroke); g2.draw(transShape); } // Paint branches for (Node node : treeLayoutCache.getBranchPathMap().keySet() ) { Stroke stroke = branchLineStroke; if (branchDecorator != null) { branchDecorator.setItem(node); stroke = branchDecorator.getStroke(stroke); } g2.setStroke(stroke); Object[] branchColouring = null; if (treeLayout.isShowingColouring() && branchColouringAttribute != null) { branchColouring = (Object[])node.getAttribute(branchColouringAttribute); } Shape branchPath = treeLayoutCache.getBranchPath(node); if (branchColouring != null) { PathIterator iter = branchPath.getPathIterator(transform); float[] coords1 = new float[2]; iter.currentSegment(coords1); for (int i = 0; i < branchColouring.length - 1; i+=2) { iter.next(); float[] coords2 = new float[2]; iter.currentSegment(coords2); int colour = ((Number)branchColouring[i]).intValue(); branchColouringDecorator.setItem(colour); g2.setPaint(branchColouringDecorator.getPaint(Color.BLACK)); g2.draw(new Line2D.Float(coords1[0], coords1[1], coords2[0], coords2[1])); coords1 = coords2; } // Draw the remaining branch as a path so it has proper line joins... int colour = ((Number)branchColouring[branchColouring.length - 1]).intValue(); branchColouringDecorator.setItem(colour); g2.setPaint(branchColouringDecorator.getPaint(Color.BLACK)); // Append the rest of the PathIterator to this new path... GeneralPath path = new GeneralPath(); path.moveTo(coords1[0], coords1[1]); path.append(iter, true); // and draw it... g2.draw(path); } else { Shape transPath = transform.createTransformedShape(branchPath); Paint paint = Color.BLACK; if (branchDecorator != null) { if (branchDecoratorGradient && branchDecorator.allowsGradient()) { branchDecorator.setItems(node, tree.getParent(node)); PathIterator iter = transPath.getPathIterator(null); double[] coords = new double[6]; iter.currentSegment(coords); Point2D point1 = new Point2D.Double(coords[0], coords[1]); do { iter.currentSegment(coords); iter.next(); } while (!iter.isDone()); Point2D point2 = new Point2D.Double(coords[0], coords[1]); paint = branchDecorator.getPaint(paint, point1, point2); } else { branchDecorator.setItem(node); paint = branchDecorator.getPaint(paint); } } g2.setPaint(paint); g2.draw(transPath); } } // Paint node bars if (!isTransformBranchesOn() && nodeBarPainter != null && nodeBarPainter.isVisible()) { for (Node node : nodeBars.keySet() ) { Shape nodeBar = nodeBars.get(node); nodeBar = transform.createTransformedShape(nodeBar); nodeBarPainter.paint(g2, node, NodePainter.Justification.CENTER, nodeBar); } } // Paint node shapes if (nodeShapePainter != null && nodeShapePainter.isVisible()) { for (Node node : nodePoints.keySet()) { Point2D point = nodePoints.get(node); point = transform.transform(point, null); nodeShapePainter.paint(g2, node, point, nodeShapeTransforms.get(node)); } } if (tipShapePainter != null && tipShapePainter.isVisible()) { for (Node node : tipPoints.keySet()) { Point2D point = tipPoints.get(node); point = transform.transform(point, null); tipShapePainter.paint(g2, node, point, nodeShapeTransforms.get(node)); } } // Paint tip labels if (tipLabelPainter != null && tipLabelPainter.isVisible()) { for (Node node : tipLabelTransforms.keySet()) { AffineTransform tipLabelTransform = tipLabelTransforms.get(node); Painter.Justification tipLabelJustification = tipLabelJustifications.get(node); g2.transform(tipLabelTransform); double labelWidth = tipLabelWidths.get(node); tipLabelPainter.paint(g2, node, tipLabelJustification, new Rectangle2D.Double(0.0, 0.0, labelWidth, tipLabelPainter.getPreferredHeight())); g2.setTransform(oldTransform); if (showingTipCallouts) { Shape calloutPath = transform.createTransformedShape(treeLayoutCache.getCalloutPath(node)); if (calloutPath != null) { g2.setStroke(calloutStroke); g2.draw(calloutPath); } } } } // Paint node labels if (nodeLabelPainter != null && nodeLabelPainter.isVisible()) { for (Node node : nodeLabelTransforms.keySet() ) { AffineTransform nodeTransform = nodeLabelTransforms.get(node); Painter.Justification nodeLabelJustification = nodeLabelJustifications.get(node); g2.transform(nodeTransform); nodeLabelPainter.paint(g2, node, nodeLabelJustification, new Rectangle2D.Double(0.0, 0.0, nodeLabelPainter.getPreferredWidth(), nodeLabelPainter.getPreferredHeight())); g2.setTransform(oldTransform); } } // Paint branch labels if (branchLabelPainter != null && branchLabelPainter.isVisible()) { for (Node node : branchLabelTransforms.keySet() ) { AffineTransform branchTransform = branchLabelTransforms.get(node); g2.transform(branchTransform); branchLabelPainter.calibrate(g2, node); final double preferredWidth = branchLabelPainter.getPreferredWidth(); final double preferredHeight = branchLabelPainter.getPreferredHeight(); branchLabelPainter.paint(g2, node, Painter.Justification.CENTER, new Rectangle2D.Double(0, 0, preferredWidth, preferredHeight)); g2.setTransform(oldTransform); } } g2.setStroke(oldStroke); g2.setPaint(oldPaint); g2.setFont(oldFont); } private void calibrate(Graphics2D g2, double width, double height) { // First layout the tree treeLayout.layout(tree, treeLayoutCache); maxTreeHeight = tree.getHeight(tree.getRootNode()) + treeLayout.getRootLength(); rootHeightOffset = 0.0; // First of all get the bounds for the unscaled tree treeBounds = null; // There are two sets of bounds here. The treeBounds are the bounds of the elements // that make up the actual tree. These are scaled from branch length space // The bounds are then the extra stuff that doesn't get scaled with the tree such // as labels and the like. // bounds on branches for (Shape branchPath : treeLayoutCache.getBranchPathMap().values()) { // Add the bounds of the branch path to the overall bounds final Rectangle2D branchBounds = branchPath.getBounds2D(); if (treeBounds == null) { treeBounds = branchBounds; } else { treeBounds.add(branchBounds); } } // Iterate though the callout paths for (Shape calloutPath : treeLayoutCache.getCalloutPathMap().values()) { // Get the line that represents the path for the taxon label // and add the translated bounds to the overall bounds final Rectangle2D calloutBounds = calloutPath.getBounds2D(); treeBounds.add(calloutBounds); } for (Shape collapsedShape : treeLayoutCache.getCollapsedShapeMap().values()) { // Add the bounds of the branch path to the overall bounds final Rectangle2D branchBounds = collapsedShape.getBounds2D(); if (treeBounds == null) { treeBounds = branchBounds; } else { treeBounds.add(branchBounds); } } for (Shape hilightShape : treeLayoutCache.getHilightShapeMap().values()) { // Add the bounds of the branch path to the overall bounds final Rectangle2D branchBounds = hilightShape.getBounds2D(); if (treeBounds == null) { treeBounds = branchBounds; } else { treeBounds.add(branchBounds); } } // bounds on node bars if (!isTransformBranchesOn() && nodeBarPainter != null && nodeBarPainter.isVisible()) { nodeBars.clear(); // Iterate though the nodes for (Node node : tree.getInternalNodes()) { Rectangle2D shapeBounds = nodeBarPainter.calibrate(g2, node); if (shapeBounds != null) { treeBounds.add(shapeBounds); nodeBars.put(node, nodeBarPainter.getNodeBar()); } } if (nodeBarPainter.getMaxHeight() > maxTreeHeight) { rootHeightOffset = Math.max(nodeBarPainter.getMaxHeight() - maxTreeHeight, 0.0); maxTreeHeight = nodeBarPainter.getMaxHeight(); } } // totalTreeBounds includes all the stuff which is not in a tree scale (like labels and shapes) but in // screen pixel scale. This is added to the treeBounds to make space round the edge. // add the tree bounds final Rectangle2D totalTreeBounds = treeBounds.getBounds2D(); // final Rectangle2D totalTreeBounds = new Rectangle2D.Double(0.0, 0.0,treeBounds.getWidth(),treeBounds.getHeight()); tipLabelWidths.clear(); if (tipLabelPainter != null && tipLabelPainter.isVisible()) { // calculateMaxTipLabelWidth(g2, tree.getRootNode()); // put this in a recursive function to allow for collapsed node labels calibrateTipLabels(g2, tree.getRootNode(), totalTreeBounds); } if (nodeLabelPainter != null && nodeLabelPainter.isVisible()) { // Iterate though the nodes with node labels for (Node node : treeLayoutCache.getNodeLabelPathMap().keySet()) { // Get the line that represents the path for the taxon label final Line2D labelPath = treeLayoutCache.getNodeLabelPath(node); nodeLabelPainter.calibrate(g2, node); final double labelHeight = nodeLabelPainter.getPreferredHeight(); final double labelWidth = nodeLabelPainter.getPreferredWidth(); Rectangle2D labelBounds = new Rectangle2D.Double(0.0, 0.0, labelWidth, labelHeight); // Work out how it is rotated and create a transform that matches that AffineTransform labelTransform = calculateTransform(null, labelPath, labelWidth, labelHeight, true); // and add the translated bounds to the overall bounds totalTreeBounds.add(labelTransform.createTransformedShape(labelBounds).getBounds2D()); } } if (branchLabelPainter != null && branchLabelPainter.isVisible()) { // Iterate though the nodes with branch labels for (Node node : treeLayoutCache.getBranchLabelPathMap().keySet()) { // Get the line that represents the path for the branch label final Line2D labelPath = treeLayoutCache.getBranchLabelPath(node); branchLabelPainter.calibrate(g2, node); final double labelHeight = branchLabelPainter.getHeightBound(); final double labelWidth = branchLabelPainter.getPreferredWidth(); Rectangle2D labelBounds = new Rectangle2D.Double(0.0, 0.0, labelWidth, labelHeight); // Work out how it is rotated and create a transform that matches that AffineTransform labelTransform = calculateTransform(null, labelPath, labelWidth, labelHeight, false); // and add the translated bounds to the overall bounds totalTreeBounds.add(labelTransform.createTransformedShape(labelBounds).getBounds2D()); } } // bounds on nodeShapes if (tipShapePainter != null && tipShapePainter.isVisible()) { tipPoints.clear(); // Iterate though the external nodes for (Node node : tree.getExternalNodes()) { Rectangle2D shapeBounds = tipShapePainter.calibrate(g2, node); if (shapeBounds != null) { totalTreeBounds.add(shapeBounds); // just at the centroid in here as the actual shape will be reconstructed when drawing tipPoints.put(node, new Point2D.Double(shapeBounds.getCenterX(), shapeBounds.getCenterY())); } } } if (nodeShapePainter != null && nodeShapePainter.isVisible()) { nodePoints.clear(); // Iterate though the internal nodes for (Node node : tree.getInternalNodes()) { Rectangle2D shapeBounds = nodeShapePainter.calibrate(g2, node); if (shapeBounds != null) { totalTreeBounds.add(shapeBounds); // just at the centroid in here as the actual shape will be reconstructed when drawing nodePoints.put(node, new Point2D.Double(shapeBounds.getCenterX(), shapeBounds.getCenterY())); } } } // Now rescale the scale axis setupScaleAxis(); bottomPanelBounds = new Rectangle2D.Double(); double y = totalTreeBounds.getHeight(); for (ScalePainter scalePainter : scalePainters) { if (scalePainter.isVisible()) { scalePainter.calibrate(g2, this); Rectangle2D sb = new Rectangle2D.Double( treeBounds.getX(), y, treeBounds.getWidth(), scalePainter.getPreferredHeight()); y += sb.getHeight(); bottomPanelBounds.add(sb); scaleBounds.put(scalePainter, sb); } } leftPanelBounds = new Rectangle2D.Double(); if (legendPainter != null && legendPainter.isVisible()) { legendPainter.calibrate(g2, this); final double w2 = legendPainter.getPreferredWidth(); legendBounds = new Rectangle2D.Double(0.0, 0.0, w2, height); leftPanelBounds.add(legendBounds); } final double availableW = width - insets.left - insets.right; final double availableH = height - insets.top - insets.bottom; // get the difference between the tree's bounds and the overall bounds boolean maintainAspectRatio = treeLayout.maintainAspectRatio(); double xDiff; double yDiff; if (maintainAspectRatio) { double topDiff = treeBounds.getY() - totalTreeBounds.getY(); double leftDiff = treeBounds.getX() - totalTreeBounds.getX(); double bottomDiff = (totalTreeBounds.getHeight() + totalTreeBounds.getY()) - (treeBounds.getHeight() + treeBounds.getY()); double rightDiff = (totalTreeBounds.getWidth() + totalTreeBounds.getX()) - (treeBounds.getWidth() + treeBounds.getX()); assert topDiff >= 0 && leftDiff >= 0 && bottomDiff >= 0 && rightDiff >= 0; xDiff = 2.0 * (leftDiff > rightDiff ? leftDiff : rightDiff); yDiff = 2.0 * (topDiff > bottomDiff ? topDiff : bottomDiff); } else { xDiff = totalTreeBounds.getWidth() - treeBounds.getWidth(); yDiff = totalTreeBounds.getHeight() - treeBounds.getHeight(); assert xDiff >= 0 && yDiff >= 0; } // small tree, long labels, label bounds may get larger that window, protect against that if( xDiff >= availableW ) { xDiff = Math.min(availableW, totalTreeBounds.getWidth()) - treeBounds.getWidth(); } if( yDiff >= availableH ) { yDiff = Math.min(availableH, totalTreeBounds.getHeight()) - treeBounds.getHeight(); } // Get the amount of canvas that is going to be taken up by the tree - // The rest is taken up by taxon labels which don't scale final double w = availableW - xDiff - leftPanelBounds.getWidth() - rightPanelBounds.getWidth(); final double h = availableH - yDiff - topPanelBounds.getHeight() - bottomPanelBounds.getHeight(); double xScale; double yScale; double xOffset = 0.0; double yOffset = 0.0; if (maintainAspectRatio) { // If the tree is laid out in both dimensions then we // need to find out which axis has the least space and scale // the tree to that (to keep the aspect ratio). if ((w / treeBounds.getWidth()) < (h / treeBounds.getHeight())) { xScale = w / treeBounds.getWidth(); yScale = xScale; } else { yScale = h / treeBounds.getHeight(); xScale = yScale; } treeScale = xScale; assert treeScale > 0; // and set the origin so that the center of the tree is in // the center of the canvas xOffset = ((width - (treeBounds.getWidth() * xScale)) / 2) - (treeBounds.getX() * xScale); yOffset = ((height - (treeBounds.getHeight() * yScale)) / 2) - (treeBounds.getY() * yScale); } else { // Otherwise just scale both dimensions xScale = w / treeBounds.getWidth(); yScale = h / treeBounds.getHeight(); // and set the origin in the top left corner xOffset = -treeBounds.getX() * xScale + (treeBounds.getX() - totalTreeBounds.getX()); yOffset = -treeBounds.getY() * yScale + (treeBounds.getY() - totalTreeBounds.getY()); treeScale = xScale; } assert treeScale > 0; // Create the overall transform transform = new AffineTransform(); transform.translate(xOffset + leftPanelBounds.getWidth(), yOffset + topPanelBounds.getHeight()); transform.scale(xScale, yScale); // Get the bounds for the newly scaled tree treeBounds = null; // bounds on branches for (Shape branchPath : treeLayoutCache.getBranchPathMap().values()) { // Add the bounds of the branch path to the overall bounds final Rectangle2D branchBounds = transform.createTransformedShape(branchPath).getBounds2D(); if (treeBounds == null) { treeBounds = branchBounds; } else { treeBounds.add(branchBounds); } } for (Shape collapsedShape : treeLayoutCache.getCollapsedShapeMap().values()) { // Add the bounds of the branch path to the overall bounds final Rectangle2D branchBounds = transform.createTransformedShape(collapsedShape).getBounds2D(); if (treeBounds == null) { treeBounds = branchBounds; } else { treeBounds.add(branchBounds); } } // bounds on node bars if (!isTransformBranchesOn() && nodeBarPainter != null && nodeBarPainter.isVisible()) { nodeBars.clear(); // Iterate though the nodes for (Node node : tree.getInternalNodes()) { Rectangle2D shapeBounds = nodeBarPainter.calibrate(g2, node); if (shapeBounds != null) { shapeBounds = transform.createTransformedShape(shapeBounds).getBounds2D(); treeBounds.add(shapeBounds); nodeBars.put(node, nodeBarPainter.getNodeBar()); } } } // Clear the map of individual taxon label bounds and transforms tipLabelBounds.clear(); tipLabelTransforms.clear(); tipLabelJustifications.clear(); if (tipLabelPainter != null && tipLabelPainter.isVisible()) { final double labelHeight = tipLabelPainter.getPreferredHeight(); // Iterate though the external nodes with tip labels for (Node node : treeLayoutCache.getTipLabelPathMap().keySet()) { // Get the line that represents the path for the tip label Line2D tipPath = treeLayoutCache.getTipLabelPath(node); final double labelWidth = tipLabelWidths.get(node); Rectangle2D labelBounds = new Rectangle2D.Double(0.0, 0.0, labelWidth, labelHeight); // Work out how it is rotated and create a transform that matches that AffineTransform taxonTransform = calculateTransform(transform, tipPath, labelWidth, labelHeight, true); // Store the transformed bounds in the map for use when selecting tipLabelBounds.put(node, taxonTransform.createTransformedShape(labelBounds)); // Store the transform in the map for use when drawing tipLabelTransforms.put(node, taxonTransform); // Store the alignment in the map for use when drawing final Painter.Justification just = (tipPath.getX1() < tipPath.getX2()) ? Painter.Justification.LEFT : Painter.Justification.RIGHT; tipLabelJustifications.put(node, just); } } // Clear the map of individual node label bounds and transforms nodeLabelBounds.clear(); nodeLabelTransforms.clear(); nodeLabelJustifications.clear(); if (nodeLabelPainter != null && nodeLabelPainter.isVisible()) { final double labelHeight = nodeLabelPainter.getPreferredHeight(); final double labelWidth = nodeLabelPainter.getPreferredWidth(); final Rectangle2D labelBounds = new Rectangle2D.Double(0.0, 0.0, labelWidth, labelHeight); // Iterate though the external nodes with node labels for (Node node : treeLayoutCache.getNodeLabelPathMap().keySet()) { // Get the line that represents the path for the node label final Line2D labelPath = treeLayoutCache.getNodeLabelPath(node); // Work out how it is rotated and create a transform that matches that AffineTransform labelTransform = calculateTransform(transform, labelPath, labelWidth, labelHeight, true); // Store the transformed bounds in the map for use when selecting nodeLabelBounds.put(node, labelTransform.createTransformedShape(labelBounds)); // Store the transform in the map for use when drawing nodeLabelTransforms.put(node, labelTransform); // Store the alignment in the map for use when drawing if (labelPath.getX1() < labelPath.getX2()) { nodeLabelJustifications.put(node, Painter.Justification.LEFT); } else { nodeLabelJustifications.put(node, Painter.Justification.RIGHT); } } } branchLabelBounds.clear(); branchLabelTransforms.clear(); branchLabelJustifications.clear(); if (branchLabelPainter != null && branchLabelPainter.isVisible()) { // Iterate though the external nodes with branch labels for (Node node : treeLayoutCache.getBranchLabelPathMap().keySet()) { // Get the line that represents the path for the branch label Line2D labelPath = treeLayoutCache.getBranchLabelPath(node); final double labelHeight = branchLabelPainter.getPreferredHeight(); final double labelWidth = branchLabelPainter.getPreferredWidth(); final Rectangle2D labelBounds = new Rectangle2D.Double(0.0, 0.0, labelWidth, labelHeight); final double dx = labelPath.getP2().getX() - labelPath.getP1().getX(); final double dy = labelPath.getP2().getY() - labelPath.getP1().getY(); final double branchLength = Math.sqrt(dx*dx + dy*dy); final Painter.Justification just = labelPath.getX1() < labelPath.getX2() ? Painter.Justification.LEFT : Painter.Justification.RIGHT; // Work out how it is rotated and create a transform that matches that AffineTransform labelTransform = calculateTransform(transform, labelPath, labelWidth, labelHeight, false); // move to middle of branch - since the move is before the rotation final double direction = just == Painter.Justification.RIGHT ? 1 : -1; labelTransform.translate(-direction * xScale * branchLength /2, 0); // Store the transformed bounds in the map for use when selecting branchLabelBounds.put(node, labelTransform.createTransformedShape(labelBounds)); // Store the transform in the map for use when drawing branchLabelTransforms.put(node, labelTransform); // Store the alignment in the map for use when drawing branchLabelJustifications.put(node, just); } } nodeShapeTransforms.clear(); if (nodeShapePainter != null && nodeShapePainter.isVisible()) { // Iterate though the nodes for (Node node : nodePoints.keySet()) { Line2D shapePath = getTreeLayoutCache().getNodeShapePath(node); if (shapePath != null) { nodeShapeTransforms.put(node, calculateTransform(transform, shapePath)); } } } if (tipShapePainter != null && tipShapePainter.isVisible()) { // Iterate though the nodes for (Node node : tipPoints.keySet()) { Line2D shapePath = getTreeLayoutCache().getNodeShapePath(node); if (shapePath != null) { nodeShapeTransforms.put(node, calculateTransform(transform, shapePath)); } } } y = availableH; for (ScalePainter scalePainter : scalePainters) { if (scalePainter.isVisible()) { scalePainter.calibrate(g2, this); y -= scalePainter.getPreferredHeight(); } } bottomPanelBounds = new Rectangle2D.Double(0, y, treeBounds.getWidth(), 0.0); for (ScalePainter scalePainter : scalePainters) { if (scalePainter.isVisible()) { scalePainter.calibrate(g2, this); final double h1 = scalePainter.getPreferredHeight(); Rectangle2D sb = new Rectangle2D.Double(treeBounds.getX(), y, treeBounds.getWidth(), h1); y += h1; bottomPanelBounds.add(sb); scaleBounds.put(scalePainter, sb); } } leftPanelBounds = new Rectangle2D.Double(0, 0, 0.0, 0.0); if (legendPainter != null && legendPainter.isVisible()) { legendPainter.calibrate(g2, this); final double w2 = legendPainter.getPreferredWidth(); legendBounds = new Rectangle2D.Double(0.0, 0.0, w2, availableH); leftPanelBounds.add(legendBounds); } calloutPaths.clear(); clearSelectionPaths(); calibrated = true; } // private void calculateMaxTipLabelWidth(final Graphics2D g2, final Node node) { // // if (tree.isExternal(node) || node.getAttribute(COLLAPSE_ATTRIBUTE_NAME) != null) { // tipLabelPainter.calibrate(g2, node); // double labelWidth = tipLabelPainter.getPreferredWidth(); // tipLabelWidths.put(node, labelWidth); // maxTipLabelWidth = Math.max(maxTipLabelWidth, labelWidth); // } else { // for (Node child : tree.getChildren(node)) { // calculateMaxTipLabelWidth(g2, child); // } // } // } private void calibrateTipLabels(final Graphics2D g2, final Node node, final Rectangle2D totalTreeBounds) { if (tree.isExternal(node) || node.getAttribute(COLLAPSE_ATTRIBUTE_NAME) != null) { tipLabelPainter.calibrate(g2, node); double labelWidth = tipLabelPainter.getPreferredWidth(); double labelHeight = tipLabelPainter.getPreferredHeight(); tipLabelWidths.put(node, labelWidth); Rectangle2D labelBounds = new Rectangle2D.Double(0.0, 0.0, labelWidth, labelHeight); // Get the line that represents the path for the taxon label Line2D taxonPath = treeLayoutCache.getTipLabelPath(node); if (taxonPath != null) { // Work out how it is rotated and create a transform that matches that AffineTransform taxonTransform = calculateTransform(null, taxonPath, labelWidth, labelHeight, true); // and add the translated bounds to the overall bounds totalTreeBounds.add(taxonTransform.createTransformedShape(labelBounds).getBounds2D()); } } else { for (Node child : tree.getChildren(node)) { calibrateTipLabels(g2, child, totalTreeBounds); } } } private AffineTransform calculateTransform(AffineTransform globalTransform, Line2D line, double width, double height, boolean justify) { final Point2D origin = line.getP1(); if (globalTransform != null) { globalTransform.transform(origin, origin); } // Work out how it is rotated and create a transform that matches that AffineTransform lineTransform = new AffineTransform(); final double dy = line.getY2() - line.getY1(); // efficency if( dy != 0.0 ) { final double dx = line.getX2() - line.getX1(); final double angle = dx != 0.0 ? Math.atan(dy / dx) : 0.0; lineTransform.rotate(angle, origin.getX(), origin.getY()); } // Now add a translate to the transform - if it is on the left then we need // to shift it by the entire width of the string. final double ty = origin.getY() - (height / 2.0); double tx = origin.getX(); if (justify) { if (line.getX2() > line.getX1()) { tx += labelXOffset; } else { tx -= (labelXOffset + width); } } lineTransform.translate(tx, ty); return lineTransform; } private AffineTransform calculateTransform(AffineTransform globalTransform, Line2D line) { final Point2D origin = line.getP1(); if (globalTransform != null) { globalTransform.transform(origin, origin); } // Work out how it is rotated and create a transform that matches that AffineTransform lineTransform = new AffineTransform(); final double dy = line.getY2() - line.getY1(); // efficency if( dy != 0.0 ) { final double dx = line.getX2() - line.getX1(); final double angle = dx != 0.0 ? Math.atan(dy / dx) : 0.0; lineTransform.rotate(angle, origin.getX(), origin.getY()); } return lineTransform; } // Overridden methods to recalibrate tree when bounds change public void setBounds(int x, int y, int width, int height) { recalibrate(); super.setBounds(x, y, width, height); } public void setBounds(Rectangle rectangle) { recalibrate(); super.setBounds(rectangle); } public void setSize(Dimension dimension) { recalibrate(); super.setSize(dimension); } public void setSize(int width, int height) { recalibrate(); super.setSize(width, height); } private RootedTree originalTree = null; private RootedTree tree = null; private TreeLayout treeLayout = null; private TreeLayoutCache treeLayoutCache = new TreeLayoutCache(); private boolean orderBranchesOn = false; private SortedRootedTree.BranchOrdering branchOrdering = SortedRootedTree.BranchOrdering.INCREASING_NODE_DENSITY; private boolean transformBranchesOn = false; private TransformedRootedTree.Transform branchTransform = TransformedRootedTree.Transform.CLADOGRAM; private boolean isRootingOn = false; private RootingType rootingType = RootingType.USER_ROOTING; private Node rootingNode = null; private double rootingLength = 0.01; private Rectangle2D treeBounds = new Rectangle2D.Double(); private double treeScale; private double maxTreeHeight; private double rootHeightOffset; private ScaleAxis scaleAxis = new ScaleAxis(ScaleAxis.AT_DATA, ScaleAxis.AT_DATA); private double axisOrigin = 0.0; private TimeScale timeScale = new TimeScale(1.0, 0.0); private boolean isAxisReversed = false; //private Insets insets = new Insets(0, 0, 0, 0); private Insets insets = new Insets(6, 6, 6, 6); private Set selectedNodes = new HashSet(); private Set selectedTips = new LinkedHashSet(); private double rulerHeight = -1.0; private Rectangle2D dragRectangle = null; private Point2D cursorPosition = null; private boolean isCrosshairShown = true; private Decorator branchDecorator = null; private Decorator branchColouringDecorator = null; private boolean branchDecoratorGradient = false; private String branchColouringAttribute = null; private boolean hilightingGradient = false; private Decorator nodeBackgroundDecorator = null; private float labelXOffset = 10.0F; private LabelPainter tipLabelPainter = null; //private double maxTipLabelWidth; private LabelPainter nodeLabelPainter = null; private LabelPainter branchLabelPainter = null; private NodeBarPainter nodeBarPainter = null; private NodeShapePainter nodeShapePainter = null; private NodeShapePainter tipShapePainter = null; private List scalePainters = new ArrayList(); private Map scaleBounds = new HashMap(); private ScaleGridPainter scaleGridPainter = null; private LegendPainter legendPainter = null; private Rectangle2D legendBounds = new Rectangle2D.Double(); private Rectangle2D topPanelBounds = new Rectangle2D.Double(); private Rectangle2D leftPanelBounds = new Rectangle2D.Double(); private Rectangle2D bottomPanelBounds = new Rectangle2D.Double(); private Rectangle2D rightPanelBounds = new Rectangle2D.Double(); private BasicStroke branchLineStroke = new BasicStroke(1.0F, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER); private BasicStroke calloutStroke = new BasicStroke(0.5F, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND, 1.0f, new float[]{0.5f, 2.0f}, 0.0f); private Stroke selectionStroke = new BasicStroke(6.0F, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND); private Paint selectionPaint; private Stroke cursorStroke = new BasicStroke(0.5F, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER); private Paint cursorPaint = Color.DARK_GRAY; private boolean calibrated = false; private AffineTransform transform = null; private boolean showingTipCallouts = true; private Map tipLabelTransforms = new HashMap(); private Map tipLabelBounds = new HashMap(); private Map tipLabelWidths = new HashMap(); private Map tipLabelJustifications = new HashMap(); private Map nodeLabelTransforms = new HashMap(); private Map nodeLabelBounds = new HashMap(); private Map nodeLabelJustifications = new HashMap(); private Map branchLabelTransforms = new HashMap(); private Map branchLabelBounds = new HashMap(); private Map branchLabelJustifications = new HashMap(); private Map nodeBars = new HashMap(); private Map tipPoints = new HashMap(); private Map nodePoints = new HashMap(); private Map nodeShapeTransforms = new HashMap(); private Map calloutPaths = new HashMap(); }figtree-1.4.3/src/figtree/treeviewer/TreePaneListener.java000077500000000000000000000020141277473563300236360ustar00rootroot00000000000000/* * TreePaneListener.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface TreePaneListener { void treePaneSettingsChanged(); } figtree-1.4.3/src/figtree/treeviewer/TreePaneRollOver.java000077500000000000000000000054721277473563300236300ustar00rootroot00000000000000/* * TreePaneRollOver.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jebl.evolution.graphs.Node; import jebl.evolution.trees.RootedTree; import jebl.evolution.trees.RootedTreeUtils; import jebl.util.NumberFormatter; import jam.panels.StatusPanel; import jam.panels.StatusProvider; import java.awt.*; import java.awt.event.MouseEvent; import java.awt.event.MouseMotionListener; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreePaneRollOver extends StatusProvider.Helper implements MouseMotionListener { public TreePaneRollOver(TreePane treePane) { this.treePane = treePane; treePane.addMouseMotionListener(this); } public void mouseEntered(MouseEvent mouseEvent) { } public void mouseExited(MouseEvent mouseEvent) { } public void mouseMoved(MouseEvent mouseEvent) { RootedTree tree = treePane.getTree(); if (tree != null) { Node node = treePane.getNodeAt((Graphics2D) treePane.getGraphics(), mouseEvent.getPoint()); if (node != null) { fireStatusChanged(StatusPanel.NORMAL, getNodeText(tree, node)); } else { fireStatusChanged(StatusPanel.NORMAL, getNodeText(tree, tree.getRootNode())); } } else { fireStatusChanged(StatusPanel.NORMAL, " "); } } private String getNodeText(RootedTree tree, Node node) { StringBuilder sb = new StringBuilder(); if (!tree.isExternal(node)) { int n = RootedTreeUtils.getTipCount(tree, node); sb.append(tree.isRoot(node) ? "Tree: " : "Subtree: ").append(n).append(" tips"); } else { sb.append("Tip: \"").append(tree.getTaxon(node).toString()).append("\""); } sb.append(" [height = ").append(formatter.getFormattedValue(tree.getHeight(node))); sb.append(", length = ").append(formatter.getFormattedValue(tree.getLength(node))); sb.append("]"); return sb.toString(); } public void mouseDragged(MouseEvent mouseEvent) { } private TreePane treePane; private NumberFormatter formatter = new NumberFormatter(4); ; }figtree-1.4.3/src/figtree/treeviewer/TreePaneRuler.java000077500000000000000000000050161277473563300231470ustar00rootroot00000000000000/* * TreePaneRuler.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import java.awt.*; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.Point2D; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreePaneRuler implements MouseListener, MouseMotionListener { public TreePaneRuler(TreePane treePane) { this.treePane = treePane; treePane.addMouseListener(this); treePane.addMouseMotionListener(this); } public void mouseClicked(MouseEvent mouseEvent) { // double selectedHeight = treePane.getHeightAt((Graphics2D)treePane.getGraphics(), mouseEvent.getPoint()); // if (!mouseEvent.isShiftDown()) { // treePane.clearSelection(); // } // // treePane.addSelectedHeight(isShiftDown); } public void mousePressed(MouseEvent mouseEvent) { // This is used for dragging in combination with mouseDragged // in the MouseMotionListener, below. dragPoint = new Point2D.Double(mouseEvent.getPoint().getX(), mouseEvent.getPoint().getY()); } public void mouseReleased(MouseEvent mouseEvent) { } public void mouseEntered(MouseEvent mouseEvent) { treePane.setCursor(Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR)); } public void mouseExited(MouseEvent mouseEvent) { } public void mouseMoved(MouseEvent mouseEvent) { double height = treePane.getHeightAt((Graphics2D)treePane.getGraphics(), mouseEvent.getPoint()); treePane.setRuler(height); } public void mouseDragged(MouseEvent mouseEvent) { } private TreePane treePane; private Point2D dragPoint = null; } figtree-1.4.3/src/figtree/treeviewer/TreePaneSelector.java000077500000000000000000000265511277473563300236450ustar00rootroot00000000000000/* * TreePaneSelector.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jebl.evolution.graphs.Node; import jam.mac.Utils; import java.awt.*; import java.awt.event.*; import java.awt.geom.Point2D; import java.awt.geom.Rectangle2D; import java.util.Set; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreePaneSelector implements MouseListener, MouseMotionListener, KeyListener { public enum SelectionMode { NODE, CLADE, TAXA }; public enum DragMode { SELECT, SCROLL }; public enum ToolMode { SELECT, ROOTING, CARTOONING, COLLAPSING, ROTATING, ANNOTATING, COLOURING }; public TreePaneSelector(TreePane treePane) { this.treePane = treePane; treePane.addMouseListener(this); treePane.addMouseMotionListener(this); treePane.addKeyListener(this); } public SelectionMode getSelectionMode() { return selectionMode; } public DragMode getDragMode() { return dragMode; } public void setSelectionMode(SelectionMode selectionMode) { defaultSelectionMode = selectionMode; this.selectionMode = selectionMode; } public void setDragMode(DragMode dragMode) { this.dragMode = dragMode; } public void setToolMode(ToolMode toolMode) { this.toolMode = toolMode; setupCursor(); } public boolean isCrossHairCursor() { return crossHairCursor; } public void setCrossHairCursor(boolean crossHairCursor) { this.crossHairCursor = crossHairCursor; } private void setupCursor() { if (toolMode != ToolMode.SELECT) { treePane.setCursor(java.awt.Cursor.getPredefinedCursor(java.awt.Cursor.CROSSHAIR_CURSOR)); treePane.setCrosshairShown(crossHairCursor); } else if (dragMode == DragMode.SELECT) { if (crossHairCursor) { treePane.setCursor(java.awt.Cursor.getPredefinedCursor(java.awt.Cursor.CROSSHAIR_CURSOR)); } else { treePane.setCursor(java.awt.Cursor.getPredefinedCursor(java.awt.Cursor.DEFAULT_CURSOR)); } treePane.setCrosshairShown(crossHairCursor); } else { treePane.setCursor(java.awt.Cursor.getPredefinedCursor(java.awt.Cursor.HAND_CURSOR)); treePane.setCrosshairShown(false); } treePane.repaint(); } public void mouseClicked(MouseEvent mouseEvent) { if (treePane.getTree() == null) { return; } if (toolMode == ToolMode.ROOTING) { Node node = treePane.getNodeAt((Graphics2D) treePane.getGraphics(), mouseEvent.getPoint()); if (node != null) { treePane.setRootLocation(node, 0.5); } } else if (toolMode == ToolMode.ROTATING) { Node node = treePane.getNodeAt((Graphics2D) treePane.getGraphics(), mouseEvent.getPoint()); treePane.rotateNode(node); } else if (dragMode == DragMode.SELECT) { boolean isCrossHairShown = treePane.isCrosshairShown(); treePane.setCrosshairShown(false); Node selectedNode = treePane.getNodeAt((Graphics2D) treePane.getGraphics(), mouseEvent.getPoint()); boolean extendSelection = mouseEvent.isShiftDown(); boolean invertSelection = isCommandKeyDown(mouseEvent); if (!extendSelection && !invertSelection) { treePane.clearSelection(); } SelectionMode mode = selectionMode; if (mouseEvent.isAltDown()) { if (mode == SelectionMode.NODE) { mode = SelectionMode.CLADE; } else if (mode == SelectionMode.CLADE) { mode = SelectionMode.NODE; } } switch (mode) { case NODE: treePane.addSelectedNode(selectedNode, invertSelection, extendSelection); break; case CLADE: treePane.addSelectedClade(selectedNode, invertSelection, extendSelection); break; case TAXA: treePane.addSelectedTip(selectedNode, invertSelection, extendSelection); break; default: throw new IllegalArgumentException("Unknown SelectionMode: " + selectionMode.name()); } treePane.setCrosshairShown(isCrossHairShown); } } public void mousePressed(MouseEvent mouseEvent) { treePane.requestFocus(); // This is used for dragging in combination with mouseDragged // in the MouseMotionListener, below. dragPoint = new Point2D.Double(mouseEvent.getPoint().getX(), mouseEvent.getPoint().getY()); } public void mouseReleased(MouseEvent mouseEvent) { if (treePane.getTree() == null) { return; } if (dragMode == DragMode.SELECT) { if (treePane.getDragRectangle() != null) { Set selectedNodes = treePane.getNodesAt((Graphics2D) treePane.getGraphics(), treePane.getDragRectangle().getBounds()); boolean extendSelection = mouseEvent.isShiftDown(); boolean invertSelection = isCommandKeyDown(mouseEvent); if (!extendSelection && !invertSelection) { treePane.clearSelection(); } SelectionMode mode = selectionMode; if (mouseEvent.isAltDown()) { if (mode == SelectionMode.NODE) { mode = SelectionMode.CLADE; } else if (mode == SelectionMode.CLADE) { mode = SelectionMode.NODE; } } for (Node selectedNode : selectedNodes) { switch (mode) { case NODE: treePane.addSelectedNode(selectedNode, invertSelection, extendSelection); break; case CLADE: treePane.addSelectedClade(selectedNode, invertSelection, extendSelection); break; case TAXA: treePane.addSelectedTip(selectedNode, invertSelection, extendSelection); break; default: throw new IllegalArgumentException("Unknown SelectionMode: " + selectionMode.name()); } } } } treePane.setDragRectangle(null); } public void mouseEntered(MouseEvent mouseEvent) { // treePane.requestFocusInWindow(); if (isCommandKeyDown(mouseEvent)) { treePane.setCursorPosition(mouseEvent.getPoint()); } } public void mouseExited(MouseEvent mouseEvent) { if (isCommandKeyDown(mouseEvent)) { treePane.setCursorPosition(mouseEvent.getPoint()); } } public void mouseMoved(MouseEvent mouseEvent) { if (isCommandKeyDown(mouseEvent)) { treePane.setCursorPosition(mouseEvent.getPoint()); } } /** * On Mac, check for the 'Command' key, otherwise use the 'Control' key * @param event * @return is it pressed */ private boolean isCommandKeyDown(InputEvent event) { return Utils.isMacOSX() ? event.isMetaDown() : event.isControlDown(); } /** * On Mac, check for the 'Option' key, otherwise use the 'Alt' key * @param event * @return is it pressed */ private boolean isOptionKeyDown(InputEvent event) { return event.isAltDown(); } public void mouseDragged(MouseEvent mouseEvent) { if (toolMode != ToolMode.SELECT || dragPoint == null) { return; } if (dragMode == DragMode.SCROLL) { // Calculate how far the mouse has been dragged from the point clicked in // mousePressed, above. int deltaX = (int) (mouseEvent.getX() - dragPoint.getX()); int deltaY = (int) (mouseEvent.getY() - dragPoint.getY()); // Get the currently visible window Rectangle visRect = treePane.getVisibleRect(); // Calculate how much we need to scroll if (deltaX > 0) { deltaX = visRect.x - deltaX; } else { deltaX = visRect.x + visRect.width - deltaX; } if (deltaY > 0) { deltaY = visRect.y - deltaY; } else { deltaY = visRect.y + visRect.height - deltaY; } // Scroll the visible region Rectangle r = new Rectangle(deltaX, deltaY, 1, 1); treePane.scrollRectToVisible(r); } else { double x1 = Math.min(dragPoint.getX(), mouseEvent.getPoint().getX()); double y1 = Math.min(dragPoint.getY(), mouseEvent.getPoint().getY()); double x2 = Math.max(dragPoint.getX(), mouseEvent.getPoint().getX()); double y2 = Math.max(dragPoint.getY(), mouseEvent.getPoint().getY()); treePane.setDragRectangle(new Rectangle2D.Double(x1, y1, x2 - x1, y2 - y1)); treePane.scrollPointToVisible(mouseEvent.getPoint()); } } public void keyTyped(KeyEvent event) { } public void keyPressed(KeyEvent event) { if (event.getKeyCode() == KeyEvent.VK_SPACE) { dragMode = DragMode.SCROLL; } if (isOptionKeyDown(event)) { switch (defaultSelectionMode) { case NODE: case CLADE: selectionMode = SelectionMode.TAXA; break; case TAXA: selectionMode = SelectionMode.NODE ; break; } } else { selectionMode = defaultSelectionMode; } crossHairCursor = isCommandKeyDown(event); setupCursor(); } public void keyReleased(KeyEvent event) { if (event.getKeyCode() == KeyEvent.VK_SPACE) { dragMode = DragMode.SELECT; } crossHairCursor = isCommandKeyDown(event); setupCursor(); } private TreePane treePane; private SelectionMode defaultSelectionMode = SelectionMode.NODE; private SelectionMode selectionMode = SelectionMode.NODE; private ToolMode toolMode = ToolMode.SELECT; private DragMode dragMode = DragMode.SELECT; private Point2D dragPoint = null; private boolean crossHairCursor = false; } figtree-1.4.3/src/figtree/treeviewer/TreeSelectionListener.java000077500000000000000000000020221277473563300246770ustar00rootroot00000000000000/* * TreeSelectionListener.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface TreeSelectionListener { void selectionChanged(); } figtree-1.4.3/src/figtree/treeviewer/TreeViewer.java000077500000000000000000000146721277473563300225230ustar00rootroot00000000000000/* * TreeViewer.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.painters.*; import jebl.evolution.graphs.Node; import jebl.evolution.trees.*; import figtree.treeviewer.decorators.Decorator; import figtree.treeviewer.treelayouts.TreeLayout; import javax.swing.*; import java.awt.*; import java.awt.print.Printable; import java.util.Collection; import java.util.Set; import jam.panels.StatusProvider; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public abstract class TreeViewer extends JPanel implements Printable { public abstract void setTrees(Collection trees); public abstract java.util.List getTrees(); public abstract Tree getCurrentTree(); public abstract int getCurrentTreeIndex(); public abstract int getTreeCount(); public abstract StatusProvider getStatusProvider(); public abstract void showTree(int index); public abstract void setTreeLayout(TreeLayout treeLayout); public abstract void setZoom(double zoom); public abstract void setVerticalExpansion(double verticalExpansion); public abstract boolean verticalExpansionAllowed(); public abstract void setTimeScale(TimeScale timeScale); public abstract boolean hasSelection(); public abstract Set getSelectedNodes(); public abstract Set getSelectedTips(); public abstract void selectTaxa(String attributeName, TextSearchType searchType, String searchString, boolean caseSensitive); public abstract void selectNodes(String attributeName, TextSearchType searchType, String searchString, boolean caseSensitive); public abstract void selectTaxa(String attributeName, NumberSearchType searchType, Number searchValue); public abstract void selectNodes(String attributeName, NumberSearchType searchType, Number searchValue); public abstract void selectTaxa(Collection taxonNames); public abstract void collapseSelectedNodes(); public abstract void annotateSelectedNodes(String name, Object value); public abstract void annotateSelectedTips(String name, Object value); public abstract void selectAll(); public abstract void clearSelectedTaxa(); public abstract void addTreeSelectionListener(TreeSelectionListener treeSelectionListener); public abstract void removeTreeSelectionListener(TreeSelectionListener treeSelectionListener); public abstract void setSelectionMode(TreePaneSelector.SelectionMode selectionMode); public abstract void setDragMode(TreePaneSelector.DragMode dragMode); public abstract void setTipLabelPainter(LabelPainter tipLabelPainter); public abstract void setNodeLabelPainter(LabelPainter nodeLabelPainter); public abstract void setNodeBarPainter(NodeBarPainter nodeBarPainter); public abstract void setNodeShapePainter(NodeShapePainter nodeShapePainter); public abstract void setBranchLabelPainter(LabelPainter branchLabelPainter); public abstract void addScalePainter(ScalePainter scalePainter); public abstract void removeScalePainter(ScalePainter scalePainter); public abstract void setScaleGridPainter(ScaleGridPainter scaleGridPainter); public abstract void setLegendPainter(LegendPainter legendPainter); public abstract void setBranchDecorator(Decorator branchDecorator, boolean isGradient); public abstract void setBranchColouringDecorator(String branchColouringAttribute, Decorator branchColouringDecorator); public abstract void setNodeBackgroundDecorator(Decorator nodeBackgroundDecorator); public abstract void setHilightingGradient(boolean hilightingGradient); public abstract void setSelectionColor(Color selectionColor); public abstract Paint getSelectionPaint(); public abstract void setBranchStroke(BasicStroke branchStroke); public abstract boolean isTransformBranchesOn(); public abstract TransformedRootedTree.Transform getBranchTransform(); public abstract void setTransformBranchesOn(boolean transformBranchesOn); public abstract void setBranchTransform(TransformedRootedTree.Transform transform); public abstract boolean isOrderBranchesOn(); public abstract SortedRootedTree.BranchOrdering getBranchOrdering(); public abstract void setOrderBranchesOn(boolean orderBranchesOn); public abstract void setBranchOrdering(SortedRootedTree.BranchOrdering branchOrdering); public abstract boolean isRootingOn(); public abstract TreePane.RootingType getRootingType(); public abstract void setRootingOn(boolean rootingOn); public abstract void setRootingType(TreePane.RootingType rootingType); public abstract JComponent getContentPane(); public abstract void addTreeViewerListener(TreeViewerListener listener); public abstract void removeTreeViewerListener(TreeViewerListener listener); public enum TextSearchType { CONTAINS("contains"), STARTS_WITH("starts with"), ENDS_WITH("ends with"), MATCHES("matches"), REG_EX("regular expression"); TextSearchType(String name) { this.name = name; } public String toString() { return name; } private final String name; } public enum NumberSearchType { EQUALS("equals"), NOT_EQUALS("doesn't equals"), GREATER_THAN("greater than"), EQUALS_OR_GREATER_THAN("equals or greater than"), LESS_THAN("less than"), EQUALS_OR_LESS_THAN("equals or less than"); NumberSearchType(String name) { this.name = name; } public String toString() { return name; } private final String name; } } figtree-1.4.3/src/figtree/treeviewer/TreeViewerController.java000077500000000000000000000357441277473563300245720ustar00rootroot00000000000000/* * TreeViewerController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import figtree.treeviewer.treelayouts.*; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import jam.util.IconUtils; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.Map; import java.util.prefs.Preferences; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreeViewerController extends AbstractController { public enum TreeLayoutType { RECTILINEAR("Rectangle"), POLAR("Polar"), RADIAL("Radial"); TreeLayoutType(String name) { this.name = name; } public String toString() { return name; } private final String name; } private static final String CONTROLLER_TITLE = "Layout"; private static Preferences PREFS = Preferences.userNodeForPackage(TreeViewerController.class); private static final String CONTROLLER_KEY = "layout"; private static final String LAYOUT_KEY = "layoutType"; private static final String ZOOM_KEY = "zoom"; private static final String EXPANSION_KEY = "expansion"; // The defaults if there is nothing in the preferences private static String DEFAULT_LAYOUT = TreeLayoutType.RECTILINEAR.name(); private final static int MAX_ZOOM_SLIDER = 1000; private final static int DELTA_ZOOM_SLIDER = 1; public TreeViewerController(final TreeViewer treeViewer) { this.treeViewer = treeViewer; final TreeLayoutType defaultLayout = TreeLayoutType.valueOf(PREFS.get(CONTROLLER_KEY + "." + LAYOUT_KEY, DEFAULT_LAYOUT)); titleLabel = new JLabel(CONTROLLER_TITLE); optionsPanel = new ControllerOptionsPanel(2, 2); rectilinearTreeLayout = new RectilinearTreeLayout(); rectilinearTreeLayoutController = new RectilinearTreeLayoutController(rectilinearTreeLayout); polarTreeLayout = new PolarTreeLayout(); polarTreeLayoutController = new PolarTreeLayoutController(polarTreeLayout); radialTreeLayout = new RadialTreeLayout(); radialTreeLayoutController = new RadialTreeLayoutController(radialTreeLayout); JPanel panel1 = new JPanel(); panel1.setOpaque(false); panel1.setLayout(new BoxLayout(panel1, BoxLayout.LINE_AXIS)); Icon rectangularTreeIcon = IconUtils.getIcon(this.getClass(), "images/rectangularTree.png"); Icon polarTreeIcon = IconUtils.getIcon(this.getClass(), "images/polarTree.png"); Icon radialTreeIcon = IconUtils.getIcon(this.getClass(), "images/radialTree.png"); rectangularTreeToggle = new JToggleButton(rectangularTreeIcon); polarTreeToggle = new JToggleButton(polarTreeIcon); radialTreeToggle = new JToggleButton(radialTreeIcon); rectangularTreeToggle.setToolTipText("Rectangular tree layout"); polarTreeToggle.setToolTipText("Polar tree layout"); radialTreeToggle.setToolTipText("Radial tree layout"); rectangularTreeToggle.setFocusable(false); polarTreeToggle.setFocusable(false); radialTreeToggle.setFocusable(false); rectangularTreeToggle.putClientProperty("Quaqua.Button.style", "toggleWest"); rectangularTreeToggle.putClientProperty("JButton.buttonType", "segmentedTextured"); rectangularTreeToggle.putClientProperty("JButton.segmentPosition", "first"); polarTreeToggle.putClientProperty("Quaqua.Button.style", "toggleCenter"); polarTreeToggle.putClientProperty("JButton.buttonType", "segmentedTextured"); polarTreeToggle.putClientProperty("JButton.segmentPosition", "middle"); radialTreeToggle.putClientProperty("Quaqua.Button.style", "toggleEast"); radialTreeToggle.putClientProperty("JButton.buttonType", "segmentedTextured"); radialTreeToggle.putClientProperty("JButton.segmentPosition", "last"); ButtonGroup buttonGroup = new ButtonGroup(); buttonGroup.add(rectangularTreeToggle); buttonGroup.add(polarTreeToggle); buttonGroup.add(radialTreeToggle); rectangularTreeToggle.setSelected(true); panel1.add(Box.createHorizontalGlue()); panel1.add(rectangularTreeToggle); panel1.add(polarTreeToggle); panel1.add(radialTreeToggle); panel1.add(Box.createHorizontalGlue()); optionsPanel.addSpanningComponent(panel1); zoomSlider = new JSlider(SwingConstants.HORIZONTAL, 0, MAX_ZOOM_SLIDER, 0); zoomSlider.setOpaque(false); zoomSlider.setAlignmentX(Component.LEFT_ALIGNMENT); // zoomSlider.setPaintTicks(true); // zoomSlider.setPaintLabels(true); zoomSlider.setValue(0); zoomSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final int value = zoomSlider.getValue(); treeViewer.setZoom(((double) value) / MAX_ZOOM_SLIDER); } }); optionsPanel.addComponentWithLabel("Zoom:", zoomSlider, true); verticalExpansionSlider = new JSlider(SwingConstants.HORIZONTAL, 0, MAX_ZOOM_SLIDER, 0); verticalExpansionSlider.setOpaque(false); // verticalExpansionSlider.setPaintTicks(true); // verticalExpansionSlider.setPaintLabels(true); verticalExpansionSlider.setValue(0); verticalExpansionSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final int value = verticalExpansionSlider.getValue(); treeViewer.setVerticalExpansion(((double) value) / MAX_ZOOM_SLIDER); } }); verticalExpansionLabel = new JLabel("Expansion:"); optionsPanel.addComponents(verticalExpansionLabel, false, verticalExpansionSlider, true); fishEyeSlider = new JSlider(SwingConstants.HORIZONTAL, 0, MAX_ZOOM_SLIDER, 0); fishEyeSlider.setOpaque(false); fishEyeSlider.setValue(0); fishEyeSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final double fishEye = ((double) fishEyeSlider.getValue()) / MAX_ZOOM_SLIDER; rectilinearTreeLayout.setFishEye(fishEye); polarTreeLayout.setFishEye(fishEye); radialTreeLayout.setFishEye(fishEye); } }); fishEyeLabel = new JLabel("Fish Eye:"); optionsPanel.addComponents(fishEyeLabel, false, fishEyeSlider, true); optionsPanel.addSeparator(); layoutPanel = new JPanel(new BorderLayout()); layoutPanel.setOpaque(false); setTreeLayout(defaultLayout); setExpansion(); optionsPanel.addSpanningComponent(layoutPanel); rectangularTreeToggle.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { if (rectangularTreeToggle.isSelected()) setTreeLayout(TreeLayoutType.RECTILINEAR); } }); polarTreeToggle.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { if (polarTreeToggle.isSelected()) setTreeLayout(TreeLayoutType.POLAR); } }); radialTreeToggle.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { if (radialTreeToggle.isSelected()) setTreeLayout(TreeLayoutType.RADIAL); } }); // Set some InputMaps and ActionMaps for key strokes. The ActionMaps are set in setExpansion() // because they differ by whether vertical expansion is allowed for the current layout. // The key strokes could be obtained from preferences and set in a preference dialog box optionsPanel.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke.getKeyStroke("meta 0"), "resetZoom"); optionsPanel.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke.getKeyStroke("meta EQUALS"), "increasePrimaryZoom"); optionsPanel.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke.getKeyStroke("meta MINUS"), "decreasePrimaryZoom"); optionsPanel.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke.getKeyStroke("meta alt EQUALS"), "increaseSecondaryZoom"); optionsPanel.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke.getKeyStroke("meta alt MINUS"), "decreaseSecondaryZoom"); optionsPanel.getActionMap().put("resetZoom", resetZoomAction); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return true; } public void setColouringAttributeName(String attributeName) { rectilinearTreeLayout.setBranchColouringAttributeName(attributeName); polarTreeLayout.setBranchColouringAttributeName(attributeName); radialTreeLayout.setBranchColouringAttributeName(attributeName); } public void initialize() { // nothing to do } public void setSettings(Map settings) { String treeLayoutName = (String)settings.get(CONTROLLER_KEY + "." + LAYOUT_KEY); final TreeLayoutType layout = TreeLayoutType.valueOf(treeLayoutName); switch (layout) { case RECTILINEAR: rectangularTreeToggle.setSelected(true); break; case POLAR: polarTreeToggle.setSelected(true); break; case RADIAL: radialTreeToggle.setSelected(true); break; } setTreeLayout(layout); zoomSlider.setValue((Integer)settings.get(CONTROLLER_KEY + "." + ZOOM_KEY)); verticalExpansionSlider.setValue((Integer)settings.get(CONTROLLER_KEY + "." + EXPANSION_KEY)); // These controllers are internal to TreeViewerController so settings must be done here rectilinearTreeLayoutController.setSettings(settings); polarTreeLayoutController.setSettings(settings); radialTreeLayoutController.setSettings(settings); } public void getSettings(Map settings) { if (rectangularTreeToggle.isSelected()) { settings.put(CONTROLLER_KEY + "." + LAYOUT_KEY, TreeLayoutType.RECTILINEAR.name()); } else if (polarTreeToggle.isSelected()) { settings.put(CONTROLLER_KEY + "." + LAYOUT_KEY, TreeLayoutType.POLAR.name()); } else if (radialTreeToggle.isSelected()) { settings.put(CONTROLLER_KEY + "." + LAYOUT_KEY, TreeLayoutType.RADIAL.name()); } settings.put(CONTROLLER_KEY + "." + ZOOM_KEY, zoomSlider.getValue()); settings.put(CONTROLLER_KEY + "." + EXPANSION_KEY, verticalExpansionSlider.getValue()); // These controllers are internal to TreeViewerController so settings must be done here rectilinearTreeLayoutController.getSettings(settings); polarTreeLayoutController.getSettings(settings); radialTreeLayoutController.getSettings(settings); } private void setTreeLayout(TreeLayoutType layoutType) { switch (layoutType) { case RECTILINEAR: treeViewer.setTreeLayout(rectilinearTreeLayout); setExpansion(); fishEyeLabel.setEnabled(true); fishEyeSlider.setEnabled(true); layoutPanel.removeAll(); layoutPanel.add(rectilinearTreeLayoutController.getPanel(), BorderLayout.CENTER); fireControllerChanged(); break; case POLAR: treeViewer.setTreeLayout(polarTreeLayout); setExpansion(); fishEyeLabel.setEnabled(true); fishEyeSlider.setEnabled(true); layoutPanel.removeAll(); layoutPanel.add(polarTreeLayoutController.getPanel(), BorderLayout.CENTER); fireControllerChanged(); break; case RADIAL: treeViewer.setTreeLayout(radialTreeLayout); setExpansion(); fishEyeLabel.setEnabled(false); fishEyeSlider.setEnabled(false); layoutPanel.removeAll(); layoutPanel.add(radialTreeLayoutController.getPanel(), BorderLayout.CENTER); fireControllerChanged(); break; default: new RuntimeException("Unknown TreeLayoutType: " + layoutType); } } private void setExpansion() { if (treeViewer.verticalExpansionAllowed()) { verticalExpansionLabel.setEnabled(true); verticalExpansionSlider.setEnabled(true); optionsPanel.getActionMap().put("increasePrimaryZoom", increaseVerticalExpansionAction); optionsPanel.getActionMap().put("decreasePrimaryZoom", decreaseVerticalExpansionAction); optionsPanel.getActionMap().put("increaseSecondaryZoom", increaseZoomAction); optionsPanel.getActionMap().put("decreaseSecondaryZoom", decreaseZoomAction); } else { verticalExpansionLabel.setEnabled(false); verticalExpansionSlider.setEnabled(false); optionsPanel.getActionMap().put("increasePrimaryZoom", increaseZoomAction); optionsPanel.getActionMap().put("decreasePrimaryZoom", decreaseZoomAction); optionsPanel.getActionMap().put("increaseSecondaryZoom", increaseZoomAction); optionsPanel.getActionMap().put("decreaseSecondaryZoom", decreaseZoomAction); } } private Action resetZoomAction = new AbstractAction("Reset Zoom") { public void actionPerformed(ActionEvent actionEvent) { zoomSlider.setValue(0); verticalExpansionSlider.setValue(0); } }; private Action increaseZoomAction = new AbstractAction("Zoom In") { public void actionPerformed(ActionEvent actionEvent) { zoomSlider.setValue(zoomSlider.getValue() + DELTA_ZOOM_SLIDER); } }; private Action decreaseZoomAction = new AbstractAction("Zoom In") { public void actionPerformed(ActionEvent actionEvent) { zoomSlider.setValue(zoomSlider.getValue() - DELTA_ZOOM_SLIDER); } }; private Action increaseVerticalExpansionAction = new AbstractAction("Expand Vertically") { public void actionPerformed(ActionEvent actionEvent) { verticalExpansionSlider.setValue(verticalExpansionSlider.getValue() + DELTA_ZOOM_SLIDER); } }; private Action decreaseVerticalExpansionAction = new AbstractAction("Unexpand Vertically") { public void actionPerformed(ActionEvent actionEvent) { int value = verticalExpansionSlider.getValue(); if (value > 0) { verticalExpansionSlider.setValue(value - DELTA_ZOOM_SLIDER); } else { // If the vertical expansion was zero then assume the user is trying to un-zoom zoomSlider.setValue(zoomSlider.getValue() - DELTA_ZOOM_SLIDER); } } }; private JToggleButton rectangularTreeToggle; private JToggleButton polarTreeToggle; private JToggleButton radialTreeToggle; private JSlider zoomSlider; private JSlider verticalExpansionSlider; private JLabel verticalExpansionLabel; private JSlider fishEyeSlider; private JLabel fishEyeLabel; private final JPanel layoutPanel; private final JLabel titleLabel; private final OptionsPanel optionsPanel; private final RectilinearTreeLayout rectilinearTreeLayout; private final PolarTreeLayout polarTreeLayout; private final RadialTreeLayout radialTreeLayout; private final RectilinearTreeLayoutController rectilinearTreeLayoutController; private final PolarTreeLayoutController polarTreeLayoutController; private final RadialTreeLayoutController radialTreeLayoutController; private final TreeViewer treeViewer; } figtree-1.4.3/src/figtree/treeviewer/TreeViewerListener.java000077500000000000000000000020441277473563300242170ustar00rootroot00000000000000/* * TreeViewerListener.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface TreeViewerListener { void treeChanged(); void treeSettingsChanged(); } figtree-1.4.3/src/figtree/treeviewer/TreeViewerPanel.java000077500000000000000000000147751277473563300235070ustar00rootroot00000000000000/* * TreeViewerPanel.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jebl.evolution.io.TreeImporter; import jebl.evolution.io.NexusImporter; import jebl.evolution.trees.Tree; import jam.controlpalettes.BasicControlPalette; import jam.controlpalettes.ControlPalette; import javax.swing.*; import java.awt.*; import java.io.File; import java.io.FileReader; import java.io.Reader; import java.io.BufferedReader; import figtree.treeviewer.painters.LabelPainterController; import figtree.treeviewer.painters.NodeBarController; import figtree.treeviewer.painters.NodeBarPainter; import figtree.treeviewer.painters.BasicLabelPainter; /** * This is a panel that has a TreeViewer and a BasicControlPalette with * the default Controllers and Painters. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreeViewerPanel extends JPanel { public TreeViewerPanel(JFrame frame, TreeViewer treeViewer, ControlPalette controlPalette) { this.treeViewer = treeViewer; this.controlPalette = controlPalette; controlPalette.getPanel().setBorder(BorderFactory.createMatteBorder(0, 0, 0, 1, Color.GRAY)); controlPalette.getPanel().setBackground(new Color(231, 237, 246)); controlPalette.getPanel().setOpaque(true); controlPalette.addController(new TreeViewerController(treeViewer)); // This controller handles reading/writing of attribute colour schemes but doesn't presently // show any UI AttributeColourController attributeColourController = new AttributeColourController(treeViewer, frame); controlPalette.addController(attributeColourController); controlPalette.addController(new TreeAppearanceController(treeViewer, frame, attributeColourController)); controlPalette.addController(new TreesController(treeViewer)); // Create a tip label painter and its controller BasicLabelPainter tipLabelPainter = new BasicLabelPainter(BasicLabelPainter.PainterIntent.TIP); controlPalette.addController(new LabelPainterController("Tip Labels", "tipLabels", tipLabelPainter, frame, attributeColourController, treeViewer)); treeViewer.setTipLabelPainter(tipLabelPainter); // Create a node label painter and its controller BasicLabelPainter nodeLabelPainter = new BasicLabelPainter(BasicLabelPainter.PainterIntent.NODE); nodeLabelPainter.setVisible(false); controlPalette.addController(new LabelPainterController("Node Labels", "nodeLabels", nodeLabelPainter, frame, attributeColourController, treeViewer)); treeViewer.setNodeLabelPainter(nodeLabelPainter); // Create a node shape painter and its controller NodeBarPainter nodeBarPainter = new NodeBarPainter(); nodeBarPainter.setForeground(new Color(24, 32, 228, 128)); nodeBarPainter.setVisible(false); controlPalette.addController(new NodeBarController("Node Bars", nodeBarPainter, treeViewer)); treeViewer.setNodeBarPainter(nodeBarPainter); // Create a branch label painter and its controller BasicLabelPainter branchLabelPainter = new BasicLabelPainter(BasicLabelPainter.PainterIntent.BRANCH); branchLabelPainter.setVisible(false); controlPalette.addController(new LabelPainterController("Branch Labels", "branchLabels", branchLabelPainter, frame, attributeColourController, treeViewer)); treeViewer.setBranchLabelPainter(branchLabelPainter); // Create a scale bar painter and its controller controlPalette.addController(new TimeScaleController(treeViewer)); setLayout(new BorderLayout()); add(treeViewer, BorderLayout.CENTER); JPanel leftPanel = new JPanel(new BorderLayout()); leftPanel.add(controlPalette.getPanel(), BorderLayout.NORTH); JScrollPane scrollPane = new JScrollPane(leftPanel); add(scrollPane, BorderLayout.WEST); } public TreeViewer getTreeViewer() { return treeViewer; } public ControlPalette getControlPalette() { return controlPalette; } private final TreeViewer treeViewer; private final ControlPalette controlPalette; static public void main(String[] args) { JFrame frame = new JFrame("TreeViewer Test"); TreeViewer treeViewer = new DefaultTreeViewer(frame); ControlPalette controlPalette = new BasicControlPalette(200, BasicControlPalette.DisplayMode.ONLY_ONE_OPEN); frame.getContentPane().add(new TreeViewerPanel(frame, treeViewer, controlPalette), BorderLayout.CENTER); try { File inputFile = null; if (args.length > 0) { inputFile = new File(args[0]); } if (inputFile == null) { // No input file name was given so throw up a dialog box... java.awt.FileDialog chooser = new java.awt.FileDialog(frame, "Select NEXUS Tree File", java.awt.FileDialog.LOAD); chooser.setVisible(true); inputFile = new java.io.File(chooser.getDirectory(), chooser.getFile()); chooser.dispose(); } if (inputFile == null) { throw new RuntimeException("No file specified"); } // TreeImporter importer = new NewickImporter(new FileReader(inputFile)); Reader reader = new BufferedReader(new FileReader(inputFile)); TreeImporter importer = new NexusImporter(reader); java.util.List trees = importer.importTrees(); reader.close(); treeViewer.setTrees(trees); } catch (Exception ie) { ie.printStackTrace(); System.exit(1); } frame.setSize(640, 480); frame.setVisible(true); } } figtree-1.4.3/src/figtree/treeviewer/TreesController.java000077500000000000000000000262401277473563300235620ustar00rootroot00000000000000/* * TreesController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer; import jebl.evolution.trees.SortedRootedTree; import jebl.evolution.trees.TransformedRootedTree; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.util.Map; import java.util.prefs.Preferences; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreesController extends AbstractController { private static final String CONTROLLER_TITLE = "Trees"; private static Preferences PREFS = Preferences.userNodeForPackage(TreeViewer.class); private static final String CONTROLLER_KEY = "trees"; private static final String TRANSFORM_KEY = "transform"; private static final String TRANSFORM_TYPE_KEY = "transformType"; private static final String ORDER_KEY = "order"; private static final String ORDER_TYPE_KEY = "orderType"; private static final String ROOTING_KEY = "rooting"; private static final String ROOTING_TYPE_KEY = "rootingType"; public TreesController(final TreeViewer treeViewer) { this.treeViewer = treeViewer; titleLabel = new JLabel(CONTROLLER_TITLE); optionsPanel = new ControllerOptionsPanel(2, 6); rootingCheck = new JCheckBox("Root tree"); rootingCheck.setOpaque(false); optionsPanel.addSpanningComponent(rootingCheck); rootingCheck.setSelected(treeViewer.isRootingOn()); rootingCombo = new JComboBox(TreePane.RootingType.values()); rootingCombo.setOpaque(false); rootingCombo.setSelectedItem(treeViewer.getRootingType()); rootingCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) { treeViewer.setRootingType((TreePane.RootingType) rootingCombo.getSelectedItem()); } }); final JLabel label1 = optionsPanel.addComponentWithLabel("Rooting:", rootingCombo); label1.setEnabled(rootingCheck.isSelected()); rootingCombo.setEnabled(rootingCheck.isSelected()); rootingCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { label1.setEnabled(rootingCheck.isSelected()); rootingCombo.setEnabled(rootingCheck.isSelected()); treeViewer.setRootingOn(rootingCheck.isSelected()); } }); optionsPanel.addSeparator(); orderCheck = new JCheckBox("Order nodes"); orderCheck.setOpaque(false); optionsPanel.addSpanningComponent(orderCheck); orderCheck.setSelected(treeViewer.isOrderBranchesOn()); orderCombo = new JComboBox(SortedRootedTree.BranchOrdering.values()); orderCombo.setOpaque(false); orderCombo.setSelectedItem(treeViewer.getBranchOrdering()); orderCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) { treeViewer.setBranchOrdering( (SortedRootedTree.BranchOrdering) orderCombo.getSelectedItem()); } }); final JLabel label2 = optionsPanel.addComponentWithLabel("Ordering:", orderCombo); label2.setEnabled(orderCheck.isSelected()); orderCombo.setEnabled(orderCheck.isSelected()); orderCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { label2.setEnabled(orderCheck.isSelected()); orderCombo.setEnabled(orderCheck.isSelected()); treeViewer.setOrderBranchesOn(orderCheck.isSelected()); } }); optionsPanel.addSeparator(); transformCheck = new JCheckBox("Transform branches"); transformCheck.setOpaque(false); optionsPanel.addSpanningComponent(transformCheck); transformCheck.setSelected(treeViewer.isTransformBranchesOn()); transformCombo = new JComboBox(TransformedRootedTree.Transform.values()); transformCombo.setOpaque(false); transformCombo.setSelectedItem(treeViewer.getBranchTransform()); transformCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { treeViewer.setBranchTransform( (TransformedRootedTree.Transform) transformCombo.getSelectedItem()); } }); final JLabel label3 = optionsPanel.addComponentWithLabel("Transform:", transformCombo); label3.setEnabled(transformCheck.isSelected()); transformCombo.setEnabled(transformCheck.isSelected()); transformCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final boolean selected = transformCheck.isSelected(); label3.setEnabled(selected); transformCombo.setEnabled(selected); treeViewer.setTransformBranchesOn(selected); } }); treeViewer.addTreeViewerListener(new TreeViewerListener() { public void treeChanged() { // ignore this one } // the settings may have changed programmatically - update the controls to match public void treeSettingsChanged() { rootingCheck.setSelected(treeViewer.isRootingOn()); rootingCombo.setSelectedItem(treeViewer.getRootingType()); transformCheck.setSelected(treeViewer.isTransformBranchesOn()); transformCombo.setSelectedItem(treeViewer.getBranchTransform()); orderCheck.setSelected(treeViewer.isOrderBranchesOn()); orderCombo.setSelectedItem(treeViewer.getBranchOrdering()); } }); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { treeViewer.setRootingOn(rootingCheck.isSelected()); treeViewer.setRootingType((TreePane.RootingType) rootingCombo.getSelectedItem()); treeViewer.setTransformBranchesOn(transformCheck.isSelected()); treeViewer.setBranchTransform((TransformedRootedTree.Transform) transformCombo.getSelectedItem()); treeViewer.setOrderBranchesOn(orderCheck.isSelected()); treeViewer.setBranchOrdering((SortedRootedTree.BranchOrdering) orderCombo.getSelectedItem()); } public void toggleMidpointRoot() { if (!rootingCheck.isSelected() || rootingCombo.getSelectedItem() != TreePane.RootingType.MID_POINT) { rootingCheck.setSelected(true); rootingCombo.setSelectedItem(TreePane.RootingType.MID_POINT); } else { rootingCombo.setSelectedItem(TreePane.RootingType.USER_ROOTING); } treeViewer.setRootingType((TreePane.RootingType) rootingCombo.getSelectedItem()); treeViewer.setRootingOn(rootingCheck.isSelected()); } public void toggleIncreasingNodeOrder() { if (!orderCheck.isSelected() || orderCombo.getSelectedItem() != SortedRootedTree.BranchOrdering.INCREASING_NODE_DENSITY) { orderCheck.setSelected(true); orderCombo.setSelectedItem(SortedRootedTree.BranchOrdering.INCREASING_NODE_DENSITY); } else { orderCheck.setSelected(false); } treeViewer.setBranchOrdering((SortedRootedTree.BranchOrdering) orderCombo.getSelectedItem()); treeViewer.setOrderBranchesOn(orderCheck.isSelected()); } public void toggleDecreasingNodeOrder() { if (!orderCheck.isSelected() || orderCombo.getSelectedItem() != SortedRootedTree.BranchOrdering.DECREASING_NODE_DENSITY) { orderCheck.setSelected(true); orderCombo.setSelectedItem(SortedRootedTree.BranchOrdering.DECREASING_NODE_DENSITY); } else { orderCheck.setSelected(false); } treeViewer.setBranchOrdering((SortedRootedTree.BranchOrdering) orderCombo.getSelectedItem()); treeViewer.setOrderBranchesOn(orderCheck.isSelected()); } public void setSettings(Map settings) { transformCheck.setSelected((Boolean) settings.get(CONTROLLER_KEY + "." + TRANSFORM_KEY)); String transformName = (String)settings.get(CONTROLLER_KEY + "." + TRANSFORM_TYPE_KEY); for (TransformedRootedTree.Transform transform : TransformedRootedTree.Transform.values()) { if (transform.toString().equalsIgnoreCase(transformName)) { transformCombo.setSelectedItem(transform); } } orderCheck.setSelected((Boolean) settings.get(CONTROLLER_KEY + "." + ORDER_KEY)); String orderName = (String)settings.get(CONTROLLER_KEY + "." + ORDER_TYPE_KEY); for (SortedRootedTree.BranchOrdering order : SortedRootedTree.BranchOrdering.values()) { if (order.toString().equalsIgnoreCase(orderName)) { orderCombo.setSelectedItem(order); } } rootingCheck.setSelected((Boolean) settings.get(CONTROLLER_KEY + "." + ROOTING_KEY)); String rootingName = (String)settings.get(CONTROLLER_KEY + "." + ROOTING_TYPE_KEY); for (TreePane.RootingType rooting : TreePane.RootingType.values()) { if (rooting.toString().equalsIgnoreCase(rootingName)) { rootingCombo.setSelectedItem(rooting); } } } public void getSettings(Map settings) { settings.put(CONTROLLER_KEY + "." + TRANSFORM_KEY, transformCheck.isSelected()); settings.put(CONTROLLER_KEY + "." + TRANSFORM_TYPE_KEY, transformCombo.getSelectedItem().toString()); settings.put(CONTROLLER_KEY + "." + ORDER_KEY, orderCheck.isSelected()); settings.put(CONTROLLER_KEY + "." + ORDER_TYPE_KEY, orderCombo.getSelectedItem().toString()); settings.put(CONTROLLER_KEY + "." + ROOTING_KEY, rootingCheck.isSelected()); settings.put(CONTROLLER_KEY + "." + ROOTING_TYPE_KEY, rootingCombo.getSelectedItem().toString()); } private final JLabel titleLabel; private final OptionsPanel optionsPanel; private final JCheckBox transformCheck; private final JComboBox transformCombo; private final JCheckBox orderCheck; private final JComboBox orderCombo; private final JCheckBox rootingCheck; private final JComboBox rootingCombo; private final TreeViewer treeViewer; } figtree-1.4.3/src/figtree/treeviewer/annotations/000077500000000000000000000000001277473563300221175ustar00rootroot00000000000000figtree-1.4.3/src/figtree/treeviewer/annotations/AnnotationDefinition.java000077500000000000000000000066111277473563300271140ustar00rootroot00000000000000/* * AnnotationDefinition.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.annotations; import jebl.evolution.graphs.Node; import jebl.util.Attributable; import java.util.Set; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class AnnotationDefinition implements Comparable { public enum Type { INTEGER("Integer"), REAL("Real"), STRING("String"), BOOLEAN("Boolean"), RANGE("Range"); Type(String name) { this.name = name; } public String toString() { return name; } private String name; }; public AnnotationDefinition(String name, Type type) { this.name = name; this.code = null; this.type = type; } public AnnotationDefinition(String name, String code, Type type) { this.name = name; this.code = code; this.type = type; } public String toString() { return name; } public String getName() { return name; } public void setName(String name) { this.name = name; } public String getCode() { if (code == null) { return name; } return code; } public void setCode(String code) { this.code = code; } public Type getType() { return type; } public void setType(Type type) { this.type = type; } public static Type guessType(final String name, final Set items) { boolean isInteger = true; boolean isNumber = true; boolean isBoolean = true; for (Attributable item: items) { Object value = item.getAttribute(name); if (value != null) { if (value instanceof Number) { isBoolean = false; if (value instanceof Double || value instanceof Float) { isInteger = false; } } else { isInteger = false; isNumber = false; if (!(value instanceof Boolean)) { isBoolean = false; } } } } if (isInteger) { return Type.INTEGER; } else if (isNumber) { return Type.REAL; } else if (isBoolean) { return Type.BOOLEAN; } return Type.STRING; } public int compareTo(AnnotationDefinition o) { return toString().compareTo(o.toString()); } private String name; private String code; private Type type; } figtree-1.4.3/src/figtree/treeviewer/annotations/AnnotationDefinitionsDialog.java000077500000000000000000000137251277473563300304230ustar00rootroot00000000000000/* * AnnotationDefinitionsDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.annotations; import jam.panels.ActionPanel; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; import javax.swing.event.ListSelectionEvent; import javax.swing.event.ListSelectionListener; import javax.swing.table.AbstractTableModel; import java.awt.*; import java.awt.event.ActionEvent; import java.util.*; import java.util.List; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class AnnotationDefinitionsDialog { private JFrame frame; public AnnotationDefinitionsDialog(JFrame frame) { this.frame = frame; } public void showDialog(Collection annotations) { this.annotations.clear(); this.annotations.addAll(annotations); OptionsPanel options = new OptionsPanel(); JPanel panel = new JPanel(new BorderLayout()); annotationTableModel = new AnnotationTableModel(); table = new JTable(annotationTableModel); table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); table.getSelectionModel().addListSelectionListener(new ListSelectionListener() { public void valueChanged(ListSelectionEvent evt) { selectionChanged(); } }); JScrollPane scrollPane = new JScrollPane(table, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); panel.add(scrollPane, BorderLayout.CENTER); ActionPanel actionPanel = new ActionPanel(true); actionPanel.setAddAction(addAnnotationAction); actionPanel.setRemoveAction(removeAnnotationAction); actionPanel.setActionAction(editAnnotationAction); panel.add(actionPanel, BorderLayout.SOUTH); options.addSpanningComponent(panel); JOptionPane optionPane = new JOptionPane(options, JOptionPane.PLAIN_MESSAGE, JOptionPane.DEFAULT_OPTION, null, new String[] { "Done" }, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); final JDialog dialog = optionPane.createDialog(frame, "Annotation Definitions"); dialog.pack(); selectionChanged(); dialog.setVisible(true); } private void selectionChanged() { int row = table.getSelectedRow(); if (row < 0) { removeAnnotationAction.setEnabled(false); } else { removeAnnotationAction.setEnabled(true); } } public List getAnnotations() { return annotations; } int labelCount = 1; private void addAnnotation() { AnnotationDefinition definition = new AnnotationDefinition("Label" + labelCount, AnnotationDefinition.Type.INTEGER); doDefineAnnotation(definition); } private void removeAnnotation() { int row = table.getSelectedRow(); if (row < 0) return; annotations.remove(row); annotationTableModel.fireTableDataChanged(); } private void editAnnotation() { int row = table.getSelectedRow(); if (row < 0) return; AnnotationDefinition definition = annotations.get(row); doDefineAnnotation(definition); } private void doDefineAnnotation(AnnotationDefinition definition) { if (defineAnnotationDialog == null) { defineAnnotationDialog = new DefineAnnotationDialog(frame); } int result = defineAnnotationDialog.showDialog(definition); if (result == JOptionPane.OK_OPTION) { annotations.add(definition); labelCount++; } annotationTableModel.fireTableDataChanged(); } private List annotations = new ArrayList(); private AnnotationTableModel annotationTableModel; class AnnotationTableModel extends AbstractTableModel { final String[] columnNames = {"Label", "Type"}; public int getColumnCount() { return columnNames.length; } public int getRowCount() { return annotations.size(); } public String getColumnName(int col) { return columnNames[col]; } public Object getValueAt(int row, int col) { if (col == 0) { return annotations.get(row).getName(); } else { return annotations.get(row).getType(); } } public void setValueAt(Object value, int row, int col) { } public Class getColumnClass(int c) { return getValueAt(0, c).getClass(); } public boolean isCellEditable(int row, int col) { return false; } }; private AbstractAction addAnnotationAction = new AbstractAction() { public void actionPerformed(ActionEvent ae) { addAnnotation(); } }; private AbstractAction removeAnnotationAction = new AbstractAction() { public void actionPerformed(ActionEvent ae) { removeAnnotation(); } }; private AbstractAction editAnnotationAction = new AbstractAction() { public void actionPerformed(ActionEvent ae) { editAnnotation(); } }; private JTable table; private DefineAnnotationDialog defineAnnotationDialog = null; }figtree-1.4.3/src/figtree/treeviewer/annotations/AnnotationDialog.java000077500000000000000000000177651277473563300262370ustar00rootroot00000000000000/* * AnnotationDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.annotations; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; import java.awt.event.*; import java.util.*; import jebl.util.Attributable; import figtree.ui.components.WholeNumberField; import figtree.ui.components.RealNumberField; import figtree.treeviewer.ExtendedTreeViewer; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class AnnotationDialog { public final static String CREATE_NEW = "Create new..."; private JFrame frame; private OptionsPanel options; private JComboBox annotationCombo; private Attributable item; private List definitions; private JComponent component = null; private JComponent component2 = null; AnnotationDefinition definition = null; public AnnotationDialog(JFrame frame) { this.frame = frame; } public int showDialog(List definitions, Attributable item) { this.definitions = definitions; this.item = item; options = new OptionsPanel(6, 6); annotationCombo = new JComboBox(definitions.toArray()); // todo This requires a bit more work so has been disabled for now... // annotationCombo.addItem(CREATE_NEW); annotationCombo.setSelectedIndex(0); setupOptionsPanel(); JOptionPane optionPane = new JOptionPane(options, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); final JDialog dialog = optionPane.createDialog(frame, "Annotate Selection"); dialog.pack(); annotationCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { setupOptionsPanel(); dialog.pack(); }}); dialog.setVisible(true); int result = JOptionPane.CANCEL_OPTION; Integer value = (Integer)optionPane.getValue(); if (value != null && value.intValue() != -1) { result = value.intValue(); } return result; } private void setupOptionsPanel() { definition = getDefinition(); options.removeAll(); options.addComponentWithLabel("Annotation:", annotationCombo); if (definition == null) { // Create new has been selected final JTextField nameField = new JTextField(); nameField.setColumns(24); options.addComponentWithLabel("Name:", nameField); final JComboBox typeCombo = new JComboBox(new Object[] { AnnotationDefinition.Type.INTEGER, AnnotationDefinition.Type.REAL, AnnotationDefinition.Type.STRING, AnnotationDefinition.Type.BOOLEAN, AnnotationDefinition.Type.RANGE }); options.addComponentWithLabel("Type:", typeCombo); typeCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { definition = new AnnotationDefinition(nameField.getText(), (AnnotationDefinition.Type)typeCombo.getSelectedItem()); setupValues(); }}); typeCombo.setSelectedIndex(0); } else { setupValues(); } } private void setupValues() { Object value = null; if (item != null) { value = item.getAttribute(definition.getCode()); } component2 = null; switch (definition.getType()) { case BOOLEAN: component = new JComboBox(new String[] { "True", "False" }); if (value != null) { ((JComboBox)component).setSelectedIndex(value.equals(Boolean.TRUE) ? 0 : 1); } options.addComponentWithLabel("Value:", component); break; case INTEGER: component = new WholeNumberField(); options.addComponentWithLabel("Value:", component); ((WholeNumberField)component).setColumns(12); if (value != null) { ((WholeNumberField)component).setValue((Integer)value); } break; case REAL: component = new RealNumberField(); options.addComponentWithLabel("Value:", component); ((RealNumberField)component).setColumns(12); if (value != null) { ((RealNumberField)component).setValue((Double)value); } break; case STRING: component = new JTextField(); options.addComponentWithLabel("Value:", component); ((JTextField)component).setColumns(20); if (value != null) { ((JTextField)component).setText((String)value); } break; case RANGE: component = new RealNumberField(); ((RealNumberField)component).setColumns(12); options.addComponentWithLabel("Lower:", component); component2 = new RealNumberField(); ((RealNumberField)component2).setColumns(12); options.addComponentWithLabel("Upper:", component2); if (value != null) { ((RealNumberField)component).setValue((Double)((Object[])value)[0]); ((RealNumberField)component2).setValue((Double)((Object[])value)[1]); } break; default: throw new IllegalArgumentException("Unrecognised enum value"); } // if (definition.getValues() != null) { // valuesCombo = new JComboBox(definition.getValues()); // options.addComponentWithLabel("Value:", valuesCombo); // } } public AnnotationDefinition getDefinition() { if (annotationCombo.getSelectedItem().equals(CREATE_NEW)) { return null; } return (AnnotationDefinition)annotationCombo.getSelectedItem(); } public Object getValue() { AnnotationDefinition definition = getDefinition(); switch (definition.getType()) { case BOOLEAN: return new Boolean(((JComboBox)component).getSelectedItem().toString()); case INTEGER: return ((WholeNumberField)component).getValue(); case REAL: return ((RealNumberField)component).getValue(); case STRING: String value = ((JTextField)component).getText().trim(); if (value.length() == 0) { return null; } return value; case RANGE: double lower = ((RealNumberField)component).getValue(); double upper = ((RealNumberField)component2).getValue(); return new Double[] { lower, upper }; default: throw new IllegalArgumentException("Unrecognised enum value"); } } }figtree-1.4.3/src/figtree/treeviewer/annotations/DefineAnnotationDialog.java000077500000000000000000000052551277473563300273410ustar00rootroot00000000000000/* * DefineAnnotationDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.annotations; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class DefineAnnotationDialog { private JFrame frame; public DefineAnnotationDialog(JFrame frame) { this.frame = frame; } public int showDialog(AnnotationDefinition definition) { OptionsPanel options = new OptionsPanel(6, 6); JTextField nameField = new JTextField(definition.getName()); nameField.setColumns(32); options.addComponentWithLabel("Name:", nameField); JComboBox typeCombo = new JComboBox(new Object[] { AnnotationDefinition.Type.INTEGER, AnnotationDefinition.Type.REAL, AnnotationDefinition.Type.STRING, AnnotationDefinition.Type.BOOLEAN, AnnotationDefinition.Type.RANGE }); typeCombo.setSelectedItem(definition.getType()); options.addComponentWithLabel("Type:", typeCombo); JOptionPane optionPane = new JOptionPane(options, JOptionPane.PLAIN_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); final JDialog dialog = optionPane.createDialog(frame, "Annotation Definitions"); dialog.pack(); dialog.setVisible(true); int result = JOptionPane.CANCEL_OPTION; Integer value = (Integer)optionPane.getValue(); if (value != null && value.intValue() != -1) { result = value.intValue(); } if (result == JOptionPane.OK_OPTION) { definition.setName(nameField.getText()); definition.setType((AnnotationDefinition.Type)typeCombo.getSelectedItem()); } return result; } }figtree-1.4.3/src/figtree/treeviewer/annotations/SelectAnnotationDialog.java000066400000000000000000000046661277473563300273700ustar00rootroot00000000000000/* * SelectAnnotationDialog.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.annotations; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; import java.util.List; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class SelectAnnotationDialog { private JFrame frame; private OptionsPanel options; private JComboBox annotationCombo; public SelectAnnotationDialog(JFrame frame) { this.frame = frame; } public int showDialog(List annotationNames) { options = new OptionsPanel(6, 6); annotationCombo = new JComboBox(annotationNames.toArray()); annotationCombo.setSelectedIndex(0); setupOptionsPanel(); JOptionPane optionPane = new JOptionPane(options, JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION, null, null, null); optionPane.setBorder(new EmptyBorder(12, 12, 12, 12)); final JDialog dialog = optionPane.createDialog(frame, "Select Annotation"); dialog.pack(); dialog.setVisible(true); int result = JOptionPane.CANCEL_OPTION; Integer value = (Integer)optionPane.getValue(); if (value != null && value.intValue() != -1) { result = value.intValue(); } return result; } private void setupOptionsPanel() { options.removeAll(); options.addComponentWithLabel("Annotation:", annotationCombo); } public String getAnnotationName() { return (String)annotationCombo.getSelectedItem(); } }figtree-1.4.3/src/figtree/treeviewer/decorators/000077500000000000000000000000001277473563300217275ustar00rootroot00000000000000figtree-1.4.3/src/figtree/treeviewer/decorators/AttributableDecorator.java000077500000000000000000000136471277473563300270750ustar00rootroot00000000000000/* * AttributableDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.util.Attributable; import java.awt.*; import java.awt.geom.Point2D; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class AttributableDecorator implements Decorator { // Decorator INTERFACE public Paint getPaint(Paint paint) { if (this.paint == null) return paint; return this.paint; } @Override public boolean allowsGradient() { return true; } public Paint getFillPaint(Paint paint) { if (this.fillPaint == null) return paint; return this.fillPaint; } public Paint getPaint(Paint paint, Point2D point1, Point2D point2) { if (colour1 != null && colour2 != null) { return new GradientPaint(point1, colour1, point2, colour2, false); } else { return paint; } } public Paint getFillPaint(Paint paint, Point2D point1, Point2D point2) { if (fillColour1 != null && fillColour2 != null) { return new GradientPaint(point1, fillColour1, point2, fillColour2, false); } else { return paint; } } public Stroke getStroke(Stroke stroke) { if (this.stroke == null) return stroke; return this.stroke; } public Font getFont(Font font) { if (this.font == null) return font; return this.font; } public boolean isGradient() { return isGradient; } public void setGradient(final boolean gradient) { isGradient = gradient; } @Override public void setItem(Attributable item, Attributable fallbackItem) { setAttributableItem(item != null ? item: fallbackItem); } public void setItem(Object item) { if (item instanceof Attributable) { setAttributableItem((Attributable)item); } } public void setItems(final Object item1, final Object item2) { if (item2 == null) { setItem(item1); return; } if (item1 == null) { setItem(item2); return; } if (item1 instanceof Attributable) { setAttributableItem((Attributable)item1); } if (item2 instanceof Attributable && paintAttributeName != null) { colour2 = getColorAttribute(((Attributable)item2).getAttribute(paintAttributeName)); if (colour2 != null) { fillColour2 = colour2.brighter(); } else { fillColour2 = null; } } } // Public methods public String getFontAttributeName() { return fontAttributeName; } public void setFontAttributeName(String fontAttributeName) { this.fontAttributeName = fontAttributeName; } public String getPaintAttributeName() { return paintAttributeName; } public void setPaintAttributeName(String paintAttributeName) { this.paintAttributeName = paintAttributeName; } public String getStrokeAttributeName() { return strokeAttributeName; } public void setStrokeAttributeName(String strokeAttributeName) { this.strokeAttributeName = strokeAttributeName; } // Private methods private void setAttributableItem(Attributable item) { if (paintAttributeName != null) { colour1 = getColorAttribute(item.getAttribute(paintAttributeName)); if (colour1 != null) { fillColour1 = colour1.brighter(); paint = colour1; fillPaint = fillColour1; // fillPaint = new Color(color.getRed(), color.getGreen(), color.getBlue(), color.getAlpha() / 2); } else { fillColour1 = null; paint = null; fillPaint = null; } } if (fontAttributeName != null) { font = getFontAttribute(item.getAttribute(fontAttributeName)); } if (strokeAttributeName != null) { stroke = getStrokeAttribute(item.getAttribute(strokeAttributeName)); } } private Color getColorAttribute(Object value) { if (value != null) { if (value instanceof Color) { return (Color)value; } try { return Color.decode(value.toString()); } catch (NumberFormatException nfe) { // } } return null; } private Font getFontAttribute(Object value) { if (value != null) { return Font.decode(value.toString()); } return null; } private Stroke getStrokeAttribute(Object value) { return null; } private String paintAttributeName = null; private String fontAttributeName = null; private String strokeAttributeName = null; private Paint paint = null; private Paint fillPaint = null; private Font font = null; private Stroke stroke = null; private boolean isGradient; private Color colour1 = null; private Color colour2 = null; private Color fillColour1 = null; private Color fillColour2 = null; } figtree-1.4.3/src/figtree/treeviewer/decorators/ColourDecorator.java000077500000000000000000000154611277473563300257120ustar00rootroot00000000000000/* * ColourDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.evolution.graphs.Node; import jebl.evolution.taxa.Taxon; import jebl.util.Attributable; import java.awt.*; import java.awt.geom.Point2D; import java.util.*; import java.util.List; /** * This decorator takes an attribute name and a set of attibutable Objects. * Colours are given to each individual value. * * If the data take more values than colors, then they will wrap around * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public abstract class ColourDecorator implements Decorator { public ColourDecorator(String attributeName) { this.attributeName = attributeName; } public ColourDecorator(String attributeName, Set items) { setAttributes(attributeName, items); } public abstract void setup(String settings); @Override public boolean allowsGradient() { return true; } public void setAttributes(String attributeName, Set items) { this.attributeName = attributeName; } // Decorator INTERFACE public Paint getPaint(Paint paint) { if (this.paint == null) return paint; return this.paint; } public Paint getFillPaint(Paint paint) { if (this.fillPaint == null) return paint; return fillPaint; } public Paint getPaint(Paint paint, Point2D point1, Point2D point2) { if (colour1 != null && colour2 != null) { return new GradientPaint(point1, colour1, point2, colour2, false); } else { return getPaint(paint); } } public Paint getFillPaint(Paint paint, Point2D point1, Point2D point2) { if (fillColour1 != null && fillColour2 != null) { return new GradientPaint(point1, fillColour1, point2, fillColour2, false); } else { return getFillPaint(paint); } } public String getAttributeName() { return attributeName; } public Stroke getStroke(Stroke stroke) { return stroke; } public Font getFont(Font font) { return font; } public void setItem(Attributable item, Attributable fallbackItem) { setAttributableItem(item, fallbackItem); } public void setItem(Object item) { if (item instanceof Attributable) { setAttributableItem((Attributable)item, null); } else { paint = getColourForValue(item); } } public void setItems(Object item1, Object item2) { colour1 = null; colour2 = null; if (item2 == null) { setItem(item1); return; } if (item1 == null) { setItem(item2); return; } Object value1 = item1; if (item1 instanceof Attributable) { value1 = ((Attributable)item1).getAttribute(getAttributeName()); } if (value1 != null) { colour1 = getColourForValue(value1); paint = colour1; } Object value2 = item2; if (item2 instanceof Attributable) { value2 = ((Attributable)item2).getAttribute(getAttributeName()); } if (value2 != null) { colour2 = getColourForValue(value2); paint = colour2; } fillColour1 = null; if (colour1 != null) { fillColour1 = getLighterColour(colour1); } fillColour2 = null; if (colour2 != null) { fillColour2 = getLighterColour(colour2); } } public static boolean isDiscrete(String attributeName, Set items) { // First collect the set of all attribute values Set values = new HashSet(); for (Attributable item : items) { Object value = item.getAttribute(attributeName); if (value != null) { values.add(value); } } boolean isNumber = true; boolean isInteger = true; for (Object value : values) { if (value instanceof Number) { if (((Number)value).doubleValue() != ((Number)value).intValue()) { isInteger = false; } } else { isNumber = false; } } if (isNumber && !isInteger) return false; return true; } public static boolean isNumerical(String attributeName, Set items) { // First collect the set of all attribute values Set values = new HashSet(); for (Attributable item : items) { Object value = item.getAttribute(attributeName); if (value != null) { values.add(value); } } boolean isNumber = true; for (Object value : values) { if (!(value instanceof Number)) { isNumber = false; } } return isNumber; } // Private methods private void setAttributableItem(Attributable item, Attributable fallbackItem) { Object value = item.getAttribute(attributeName); if (value == null && fallbackItem != null) { value = fallbackItem.getAttribute(attributeName); } paint = null; Color colour = getColourForValue(value); if (colour != null) { paint = colour; fillPaint = getLighterColour(colour); } else { paint = null; fillPaint = null; } } protected abstract Color getColourForValue(Object value); protected Color getLighterColour(Color color) { return new Color(color.getRed(), color.getGreen(), color.getBlue(), color.getAlpha() / 2); } private String attributeName = null; protected Paint paint = null; protected Paint fillPaint = null; protected Color colour1 = null; protected Color colour2 = null; protected Color fillColour1 = null; protected Color fillColour2 = null; } figtree-1.4.3/src/figtree/treeviewer/decorators/CompoundDecorator.java000077500000000000000000000067121277473563300262320ustar00rootroot00000000000000/* * CompoundDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.util.Attributable; import java.awt.*; import java.awt.geom.Point2D; import java.util.HashSet; import java.util.Set; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class CompoundDecorator implements Decorator { public void addDecorator(Decorator decorator) { decorators.add(decorator); } public boolean allowsGradient() { for (Decorator decorator : decorators) { if (decorator.allowsGradient()) { return true; } } return false; } @Override public void setItem(Attributable item, Attributable fallbackItem) { for (Decorator decorator : decorators) { decorator.setItem(item, fallbackItem); } } public void setItem(Object item) { for (Decorator decorator : decorators) { decorator.setItem(item); } } public void setItems(final Object item1, final Object item2) { for (Decorator decorator : decorators) { if (decorator.allowsGradient()) { decorator.setItems(item1, item2); return; } } } public Paint getPaint(Paint paint) { Paint p = paint; for (Decorator decorator : decorators) { p = decorator.getPaint(p); } return p; } public Paint getPaint(final Paint paint, final Point2D point1, final Point2D point2) { for (Decorator decorator : decorators) { if (decorator.allowsGradient()) { return decorator.getPaint(paint, point1, point2); } } return null; } public Paint getFillPaint(Paint paint) { Paint p = paint; for (Decorator decorator : decorators) { p = decorator.getFillPaint(p); } return p; } public Paint getFillPaint(final Paint paint, final Point2D point1, final Point2D point2) { for (Decorator decorator : decorators) { if (decorator.allowsGradient()) { return decorator.getFillPaint(paint, point1, point2); } } return null; } public Stroke getStroke(Stroke stroke) { Stroke s = stroke; for (Decorator decorator : decorators) { s = decorator.getStroke(s); } return s; } public Font getFont(Font font) { Font f = font; for (Decorator decorator : decorators) { f = decorator.getFont(f); } return f; } private Set decorators = new HashSet(); } figtree-1.4.3/src/figtree/treeviewer/decorators/ContinuousColourDecorator.java000077500000000000000000000044701277473563300277770ustar00rootroot00000000000000/* * ContinuousColourDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.util.Attributable; import java.awt.*; import java.awt.geom.Point2D; import java.util.Set; /** * This decorator takes an attribute name and a set of attibutable Objects. It * autodetects the type of attributes and then provides a colouring scheme for them * based on a gradient between color1 & color2. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public abstract class ContinuousColourDecorator extends ColourDecorator { public ContinuousColourDecorator(String attributeName) { super(attributeName); } public ContinuousColourDecorator(ContinuousScale continuousScale ) { super(continuousScale.getAttributeName()); this.continuousScale = continuousScale; } public void setAttributes(String attributeName, Set items) { super.setAttributes(attributeName, items); continuousScale.setAttributes(attributeName, items); } public ContinuousScale getContinuousScale() { return continuousScale; } public void setContinuousScale(ContinuousScale continuousScale) { this.continuousScale = continuousScale; } @Override public Color getColourForValue(Object value) { return getColourForScaledValue(continuousScale.getValue(value)); } // Private methods protected abstract Color getColourForScaledValue(double value); private ContinuousScale continuousScale; } figtree-1.4.3/src/figtree/treeviewer/decorators/ContinuousScale.java000077500000000000000000000167221277473563300257230ustar00rootroot00000000000000/* * ContinuousScale.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.util.Attributable; import java.util.Set; import java.util.TreeSet; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ContinuousScale { /** * constructor that sets options from a string * @param settings */ public ContinuousScale(String settings) { if (settings.startsWith("{")) { settings = settings.substring(1, settings.length()); } if (settings.endsWith("}")) { settings = settings.substring(0, settings.length() - 1); } String[] parts = settings.split("[, ]+"); if (parts.length != 4) { throw new IllegalArgumentException("ContinousScale settings string not in correct format"); } try { normalize = Boolean.parseBoolean(parts[0]); logarithm = Boolean.parseBoolean(parts[1]); lowerRange = Double.parseDouble(parts[2]); upperRange = Double.parseDouble(parts[3]); } catch (NumberFormatException nfe) { throw new IllegalArgumentException("ContinousScale settings string not in correct format"); } } public ContinuousScale() { this(false, 0.0, 0.0, false); } public ContinuousScale(boolean normalize, double lowerRange, double upperRange, boolean logarithm) { this.normalize = normalize; this.lowerRange = lowerRange; this.upperRange = upperRange; this.logarithm = logarithm; } public ContinuousScale(String attributeName, Set items) { this(); setAttributes(attributeName, items); } public void setAttributes(String attributeName, Set items) { this.attributeName = attributeName; // First collect the set of all attribute values Set values = new TreeSet(); boolean isNumber = true; // Find the range of numbers for (Attributable item : items) { Object value = item.getAttribute(attributeName); if (value != null) { double realValue = -1.0; if (value instanceof Boolean) { realValue = ((Boolean)value ? 1 : 0); } else if (value instanceof Number) { realValue = ((Number)value).doubleValue(); } else if (value instanceof String) { // it is a string but it could still code for // a boolean, integer or real if (value.toString().equalsIgnoreCase("true")) { realValue = 1; } else if (value.toString().equalsIgnoreCase("false")) { realValue = 0; } else { try { realValue = Double.parseDouble(value.toString()); } catch(NumberFormatException nfe) { isNumber = false; } } } if (isNumber) { if (realValue < minValue) { minValue = realValue; } if (realValue > maxValue) { maxValue = realValue; } } values.add(realValue); } } if (!isNumber) { throw new NumberFormatException("One or more values for this attribute are not numbers"); } if (normalize && minValue < 0 && maxValue > 0) { // if normalizing, and some are negative, assume we are normalizing with 0 at 0.5 minValue = - maxValue; } if (logarithm) { if (minValue <= 0.0) { throw new NumberFormatException("One or more values for this attribute are negative or zero under a log scale"); } minValue = Math.log(minValue); maxValue = Math.log(maxValue); } } public double getValue(Attributable item) { return getValue(item.getAttribute(attributeName)); } public double getValue(Object value) { if (value != null) { double number = 0.0; if (value instanceof Number) { number = ((Number)value).doubleValue(); } else { number = Double.parseDouble(value.toString()); } return scaleValue(number); } return Double.NaN; } /** * Scales the value to a range 0,1 based on the current settings * @param value * @return */ public double scaleValue(double value) { if (logarithm) { value = Math.log(value); } double min = getMinValue(); double max = getMaxValue(); return ((value - min)/(max - min)); } public String getAttributeName() { return attributeName; } public boolean isNormalize() { return normalize; } public void setNormalize(boolean normalize) { this.normalize = normalize; } public boolean isLogarithm() { return logarithm; } public void setLogarithm(boolean logarithm) { this.logarithm = logarithm; } public double getLowerRange() { return lowerRange; } public void setLowerRange(double lowerRange) { this.lowerRange = lowerRange; } public double getUpperRange() { return upperRange; } public void setUpperRange(double upperRange) { this.upperRange = upperRange; } public double getMinValue() { double min = minValue; if (normalize && lowerRange < minValue) { min = lowerRange; } return min; } public double getMaxValue() { double max = maxValue; if (normalize && upperRange > maxValue) { max = upperRange; } return max; } @Override public String toString() { StringBuilder sb = new StringBuilder(); sb.append("{"); sb.append(normalize); sb.append(","); sb.append(logarithm); sb.append(","); sb.append(lowerRange); sb.append(","); sb.append(upperRange); sb.append("}"); return sb.toString(); } private boolean normalize; private boolean logarithm; private double lowerRange; private double upperRange; private String attributeName = null; private double minValue = Double.MAX_VALUE; private double maxValue = Double.MIN_VALUE; } figtree-1.4.3/src/figtree/treeviewer/decorators/ContinuousStrokeDecorator.java000077500000000000000000000064721277473563300300070ustar00rootroot00000000000000/* * ContinuousStrokeDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.util.Attributable; import java.awt.*; import java.awt.geom.Point2D; /** * This decorator takes an attribute name and a set of attibutable Objects. It * autodetects the type of attributes and then provides a colouring scheme for them * based on a gradient between color1 & color2. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ContinuousStrokeDecorator implements Decorator { public ContinuousStrokeDecorator(ContinuousScale continuousScale, float minWidth, float maxWidth) throws NumberFormatException { this.continuousScale = continuousScale; this.minWidth = minWidth; this.maxWidth = maxWidth; } @Override public boolean allowsGradient() { return false; } // Decorator INTERFACE public Paint getPaint(Paint paint) { return paint; } public Paint getPaint(final Paint paint, final Point2D point1, final Point2D point2) { throw new UnsupportedOperationException("This decorator doesn't support gradients"); } public Paint getFillPaint(Paint paint) { return paint; } public Paint getFillPaint(final Paint paint, final Point2D point1, final Point2D point2) { throw new UnsupportedOperationException("This decorator doesn't support gradients"); } public Stroke getStroke(Stroke stroke) { if (this.stroke == null) { return stroke; } return this.stroke; } public Font getFont(Font font) { return font; } public boolean isGradient() { return false; } public void setItem(Attributable item, Attributable fallbackItem) { setAttributableItem((Attributable)item); } public void setItem(Object item) { if (item instanceof Attributable) { setAttributableItem((Attributable)item); } } public void setItems(final Object item1, final Object item2) { throw new UnsupportedOperationException("This decorator doesn't support gradients"); } // Private methods private void setAttributableItem(Attributable item) { double value = continuousScale.getValue(item); if (!Double.isNaN(value)) { stroke = new BasicStroke((float)((value * (maxWidth - minWidth)) + minWidth)); } else { stroke = null; } } public ContinuousScale getContinuousScale() { return continuousScale; } private final ContinuousScale continuousScale; private final float minWidth; private final float maxWidth; private Stroke stroke = null; }figtree-1.4.3/src/figtree/treeviewer/decorators/CustomDiscreteColourDecorator.java000066400000000000000000000104401277473563300305550ustar00rootroot00000000000000/* * FixedDiscreteColourDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.util.Attributable; import java.awt.*; import java.util.ArrayList; import java.util.Set; /** * A special class for customized colour schemes for various projects. * Not generally for public use. * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class CustomDiscreteColourDecorator extends DiscreteColourDecorator { public CustomDiscreteColourDecorator(String attributeName) { super(attributeName); setupColours(); } public CustomDiscreteColourDecorator(String attributeName, String settings) { super(attributeName); setup(settings); } public CustomDiscreteColourDecorator(String attributeName, Set items) { super(attributeName, items); setupColours(); } /** * Set up from a settings string * @param settings */ public void setup(String settings) { if (!settings.startsWith("{") || !settings.endsWith("}")) { throw new IllegalArgumentException("FixedDiscreteColourDecorator settings string not in correct format"); } String[] parts = settings.substring(1, settings.length() - 1).split("[, ]+"); if (parts.length != 8) { throw new IllegalArgumentException("FixedDiscreteColourDecorator settings string not in correct format"); } try { } catch (NumberFormatException nfe) { throw new IllegalArgumentException("FixedDiscreteColourDecorator settings string not in correct format"); } catch (IllegalArgumentException iae) { throw new IllegalArgumentException("FixedDiscreteColourDecorator settings string not in correct format"); } } protected void setupColours() { java.util.List values = new ArrayList(); values.add("AC1"); values.add("AC10"); values.add("AC11"); values.add("AC12"); values.add("AC13"); values.add("AC14"); values.add("AC2"); values.add("AC3"); values.add("AC4"); values.add("AC5"); values.add("AC6"); values.add("AC7"); values.add("AC8"); values.add("AC9"); Color[] airCommunities = new Color[] { new Color(0.879F, 0.261F, 0.262F), // AC1 new Color(0.917F, 0.58F, 0.322F), // AC10 new Color(0.64F, 0.46F, 0.28F), // AC11 new Color(0.599F, 0.772F, 0.513F), // AC12 new Color(0.551F, 0.242F, 0.598F), // AC13 new Color(0.43F, 0.674F, 0.744F), // AC14 new Color(0.816F, 0.765F, 0.376F), // AC2 new Color(0.26F, 0.141F, 0.632F), // AC3 new Color(0.242F, 0.445F, 0.718F), // AC4 new Color(0.592F, 0.669F, 0.295F), // AC5 new Color(0.791F, 0.27F, 0.146F), // AC6 new Color(0.359F, 0.425F, 0.833F), // AC7 new Color(0.374F, 0.623F, 0.505F), // AC8 new Color(0.785F, 0.585F, 0.209F) // AC9 }; setColourMap(values, airCommunities); } /** * Create a string representation suitable for writing to a text file * @return the string */ @Override public String toString() { StringBuilder sb = new StringBuilder(); sb.append("{"); sb.append("FIXED"); sb.append("}"); return sb.toString(); } } figtree-1.4.3/src/figtree/treeviewer/decorators/Decorator.java000077500000000000000000000035461277473563300245270ustar00rootroot00000000000000/* * Decorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.evolution.taxa.Taxon; import jebl.util.Attributable; import java.awt.*; import java.awt.geom.Point2D; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface Decorator { boolean allowsGradient(); void setItem(Attributable item, Attributable fallbackItem); void setItem(Object item); void setItems(Object item1, Object item2); Paint getPaint(Paint paint); /** * Get stroke paint for a gradient between two point in colour scale * @param paint * @param point1 * @param point2 * @return */ Paint getPaint(Paint paint, Point2D point1, Point2D point2); Paint getFillPaint(Paint paint); /** * Get fill paint for a gradient between two point in colour scale * @param paint * @param point1 * @param point2 * @return */ Paint getFillPaint(Paint paint, Point2D point1, Point2D point2); Stroke getStroke(Stroke stroke); Font getFont(Font font); } figtree-1.4.3/src/figtree/treeviewer/decorators/DiscreteColourDecorator.java000077500000000000000000000141221277473563300273660ustar00rootroot00000000000000/* * DiscreteColourDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.util.Attributable; import java.awt.*; import java.awt.geom.Point2D; import java.util.*; import java.util.List; /** * This decorator takes an attribute name and a set of attibutable Objects. * Colours are given to each individual value. * * If the data take more values than colors, then they will wrap around * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class DiscreteColourDecorator extends ColourDecorator { public static Color[] DEFAULT_PAINTS = new Color[] { new Color(64,35,225), new Color(229,35,60), new Color(255,174,34), new Color(86,255,34), new Color(35,141,148), new Color(146,35,142), new Color(255,90,34), new Color(239,255,34), Color.DARK_GRAY, new Color(160,146,241), new Color(243,146,158), new Color(255,215,145), new Color(171,255,145), new Color(146,199,202), new Color(201,146,199), new Color(255,173,145), new Color(248,255,145), Color.LIGHT_GRAY, new Color(32,18,113), new Color(115,18,30), new Color(128,87,17), new Color(43,128,17), new Color(18,71,74), new Color(73,18,71), new Color(128,45,17), new Color(120,128,17) }; public DiscreteColourDecorator() { super(null); colours = DEFAULT_PAINTS; } public DiscreteColourDecorator(String attributeName) { super(attributeName); } public DiscreteColourDecorator(String attributeName, Set items) { super(attributeName, items); } @Override public void setup(String settings) { throw new UnsupportedOperationException("setup from string not implemented"); } public void setAttributes(String attributeName, Set items) { super.setAttributes(attributeName, items); // First collect the set of all attribute values Set sortedValues = new TreeSet(); Set unsortedValues = new HashSet(); for (Attributable item : items) { Object value = item.getAttribute(attributeName); if (value != null) { if (value instanceof Comparable) { sortedValues.add(value); } else { unsortedValues.add(value); } } } if (values == null) { values = new ArrayList(sortedValues); values.addAll(unsortedValues); } else { // if there is already a values array, only add the new values // to maintain the order that may have been edited by the user. for (Object value : sortedValues) { if (!values.contains(value)) { values.add(value); } } for (Object value : unsortedValues) { if (!values.contains(value)) { values.add(value); } } } setupColours(); } public List getValues() { return values; } public void setValues(Collection values) { this.values = new ArrayList(values); setupColours(); } protected void setupColours() { setColourMap(values, DEFAULT_PAINTS); } public Color getColor(Object value) { return (Color)colours[orderMap.get(value)]; } protected void setColourMap(Collection values, Color[] colours) { if (values == null) { return; } orderMap = new TreeMap(); this.colours = colours; this.values = new ArrayList(values); // now create a paint map for these values int i = 0; for (Object value : this.values) { orderMap.put(value, i); i = (i + 1) % colours.length; } } protected Color getColourForValue(Object value) { int index = -1; if (value != null) { if (orderMap != null && orderMap.size() > 0) { index = orderMap.get(value); } else if (value instanceof Number) { index = ((Number)value).intValue() % colours.length; } } if (index == -1) { return null; } return colours[index]; } public void setValuesOrder(List discreteValues) { values = discreteValues; hasReorderedValues = true; } public boolean hasReorderedValues() { return hasReorderedValues; } public String getOrderString() { StringBuilder sb = new StringBuilder(); boolean first = true; for (Object value : values) { if (!first) { sb.append(","); } else { first = false; } sb.append(value); } return sb.toString(); } private List values; private Map orderMap; private Color[] colours; private boolean hasReorderedValues = false; } figtree-1.4.3/src/figtree/treeviewer/decorators/DiversityContinuousColourDecorator.java000077500000000000000000000207061277473563300317020ustar00rootroot00000000000000/* * DiversityContinuousColourDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.evolution.graphs.Node; import jebl.evolution.trees.RootedTree; import jebl.evolution.trees.Tree; import jebl.util.Attributable; import java.awt.*; /** * This draws a continuous colour spectrum to show diversity across the tree. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class DiversityContinuousColourDecorator extends ColourDecorator { public DiversityContinuousColourDecorator() throws NumberFormatException { super(null); } public DiversityContinuousColourDecorator(String attribute, String settings) { super(attribute); setup(settings); } public void setup(String settings) { if (!settings.startsWith("{") || !settings.endsWith("}")) { throw new IllegalArgumentException("DiversityContinuousColourDecorator settings string not in correct format"); } String[] parts1 = settings.substring(1, settings.length() - 1).split("}[, ]+"); if (parts1.length != 2) { throw new IllegalArgumentException("DiversityContinuousColourDecorator settings string not in correct format"); } String[] parts2 = parts1[1].split("[, ]+"); if (parts2.length != 7) { throw new IllegalArgumentException("DiversityContinuousColourDecorator settings string not in correct format"); } try { hueLower = Float.parseFloat(parts2[0]); hueUpper = Float.parseFloat(parts2[1]); saturationLower = Float.parseFloat(parts2[2]); saturationUpper = Float.parseFloat(parts2[3]); brightnessLower = Float.parseFloat(parts2[4]); brightnessUpper = Float.parseFloat(parts2[5]); reverseHue = Boolean.parseBoolean(parts2[6]); } catch (NumberFormatException nfe) { throw new IllegalArgumentException("HSBContinuousColourDecorator settings string not in correct format"); } catch (IllegalArgumentException iae) { throw new IllegalArgumentException("HSBContinuousColourDecorator settings string not in correct format"); } } public void setup(float hueUpper, float hueLower, float saturationUpper, float saturationLower, float brightnessUpper, float brightnessLower, boolean reverseHue) { this.hueUpper = hueUpper; this.hueLower = hueLower; this.saturationUpper = saturationUpper; this.saturationLower = saturationLower; this.brightnessUpper = brightnessUpper; this.brightnessLower = brightnessLower; this.reverseHue = reverseHue; } public void setTree(RootedTree tree) { this.tree = tree; double[] maxValue = { 0 }; traverseTree((RootedTree)tree, ((RootedTree) tree).getRootNode(), 0.0, 1.0, maxValue); for (Node node : tree.getNodes()) { double value = (Double)node.getAttribute("@hue"); node.setAttribute("@hue", value / maxValue[0]); } } private double traverseTree(RootedTree tree, Node node, double lower, double upper, double[] maxValue) { double value; if (tree.isExternal(node)) { value = (upper + lower) / 2; } else { value = 0.0; double range = upper - lower; int n = tree.getChildren(node).size(); double[] counts = new double[n]; int i = 0; double count = 0.0; for (Node child : tree.getChildren(node)) { double c = countTips(tree, child); count += c; counts[i] = c; i++; } double l = lower; i = 0; for (Node child : tree.getChildren(node)) { double prop = range * (counts[i] / count); double u = l + prop; value += traverseTree(tree, child, l, u, maxValue); l = u; i++; } value /= n; } // value *= tree.getLength(node); node.setAttribute("@hue", value); if (value > maxValue[0]) { maxValue[0] = value; } return value; } private double countTips(RootedTree tree, Node node) { double count; if (tree.isExternal(node)) { count = 1; } else { count = 0; for (Node child : tree.getChildren(node)) { count += countTips(tree, child); } } return count; } @Override public void setItem(Object item) { if (item instanceof Attributable) { hue = (Double)((Attributable) item).getAttribute("@hue"); paint = getColourForValue(item); } } @Override protected Color getColourForValue(Object value) { return Color.getHSBColor(getHue((float)hue), getSaturation((float)0.5), getBrightness((float)0.5)); } private float getHue(float value) { if (reverseHue) { return hueUpper - ((hueUpper - hueLower) * value); } return ((hueUpper - hueLower) * value) + hueLower; } private float getSaturation(float value) { return ((saturationUpper - saturationLower) * value) + saturationLower; } private float getBrightness(float value) { return ((brightnessUpper - brightnessLower) * value) + brightnessLower; } public float getHueUpper() { return hueUpper; } public void setHueUpper(float hueUpper) { this.hueUpper = hueUpper; } public float getHueLower() { return hueLower; } public void setHueLower(float hueLower) { this.hueLower = hueLower; } public float getSaturationUpper() { return saturationUpper; } public void setSaturationUpper(float saturationUpper) { this.saturationUpper = saturationUpper; } public float getSaturationLower() { return saturationLower; } public void setSaturationLower(float saturationLower) { this.saturationLower = saturationLower; } public float getBrightnessUpper() { return brightnessUpper; } public void setBrightnessUpper(float brightnessUpper) { this.brightnessUpper = brightnessUpper; } public float getBrightnessLower() { return brightnessLower; } public void setBrightnessLower(float brightnessLower) { this.brightnessLower = brightnessLower; } public boolean isReverseHue() { return reverseHue; } public void setReverseHue(boolean reverseHue) { this.reverseHue = reverseHue; } /** * Create a string representation suitable for writing to a text file * @return the string */ @Override public String toString() { StringBuilder sb = new StringBuilder(); sb.append("{"); sb.append(hueLower); sb.append(","); sb.append(hueUpper); sb.append(","); sb.append(saturationLower); sb.append(","); sb.append(saturationUpper); sb.append(","); sb.append(brightnessLower); sb.append(","); sb.append(brightnessUpper); sb.append(","); sb.append(reverseHue); sb.append("}"); return sb.toString(); } private RootedTree tree; private double hue; private float hueUpper = 1.0F; private float hueLower = 0.0F; private float saturationUpper = 0.6F; private float saturationLower = 0.6F; private float brightnessUpper = 0.8F; private float brightnessLower = 0.4F; private boolean reverseHue = false; } figtree-1.4.3/src/figtree/treeviewer/decorators/FixedDiscreteColourDecorator.java000066400000000000000000000056251277473563300303530ustar00rootroot00000000000000/* * FixedDiscreteColourDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.util.Attributable; import java.awt.*; import java.util.ArrayList; import java.util.Set; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FixedDiscreteColourDecorator extends DiscreteColourDecorator { public FixedDiscreteColourDecorator(String attributeName) { super(attributeName); setupColours(); } public FixedDiscreteColourDecorator(String attributeName, String settings) { super(attributeName); setup(settings); } public FixedDiscreteColourDecorator(String attributeName, Set items) { super(attributeName, items); setupColours(); } /** * Set up from a settings string * @param settings */ public void setup(String settings) { if (!settings.startsWith("{") || !settings.endsWith("}")) { throw new IllegalArgumentException("FixedDiscreteColourDecorator settings string not in correct format"); } // String[] parts = settings.substring(1, settings.length() - 1).split("[, ]+"); // if (parts.length != 8) { // throw new IllegalArgumentException("FixedDiscreteColourDecorator settings string not in correct format"); // } // // try { // } catch (NumberFormatException nfe) { // throw new IllegalArgumentException("FixedDiscreteColourDecorator settings string not in correct format"); // } catch (IllegalArgumentException iae) { // throw new IllegalArgumentException("FixedDiscreteColourDecorator settings string not in correct format"); // } } protected void setupColours() { setColourMap(getValues(), DEFAULT_PAINTS); } /** * Create a string representation suitable for writing to a text file * @return the string */ @Override public String toString() { StringBuilder sb = new StringBuilder(); sb.append("{"); sb.append("FIXED"); sb.append("}"); return sb.toString(); } } figtree-1.4.3/src/figtree/treeviewer/decorators/HSBContinuousColourDecorator.java000077500000000000000000000151121277473563300303270ustar00rootroot00000000000000/* * HSBContinuousColourDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.util.Attributable; import java.awt.*; import java.awt.geom.Point2D; /** * This decorator takes an attribute name and a set of attibutable Objects. It * autodetects the type of attributes and then provides a colouring scheme for them * based on a gradient between color1 & color2. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class HSBContinuousColourDecorator extends ContinuousColourDecorator { public HSBContinuousColourDecorator(String attribute, String settings) { super(attribute); setup(settings); } public HSBContinuousColourDecorator(ContinuousScale continuousScale) throws NumberFormatException { super(continuousScale); } public void setup(String settings) { if (!settings.startsWith("{") || !settings.endsWith("}")) { throw new IllegalArgumentException("HSBContinuousColourDecorator settings string not in correct format"); } String[] parts1 = settings.substring(1, settings.length() - 1).split("}[, ]+"); if (parts1.length != 2) { throw new IllegalArgumentException("HSBContinuousColourDecorator settings string not in correct format"); } String[] parts2 = parts1[1].split("[, ]+"); if (parts2.length != 7) { throw new IllegalArgumentException("HSBContinuousColourDecorator settings string not in correct format"); } try { setContinuousScale(new ContinuousScale(parts1[0])); hueLower = Float.parseFloat(parts2[0]); hueUpper = Float.parseFloat(parts2[1]); saturationLower = Float.parseFloat(parts2[2]); saturationUpper = Float.parseFloat(parts2[3]); brightnessLower = Float.parseFloat(parts2[4]); brightnessUpper = Float.parseFloat(parts2[5]); reverseHue = Boolean.parseBoolean(parts2[6]); } catch (NumberFormatException nfe) { throw new IllegalArgumentException("HSBContinuousColourDecorator settings string not in correct format"); } catch (IllegalArgumentException iae) { throw new IllegalArgumentException("HSBContinuousColourDecorator settings string not in correct format"); } } public void setup(float hueUpper, float hueLower, float saturationUpper, float saturationLower, float brightnessUpper, float brightnessLower, boolean reverseHue) { this.hueUpper = hueUpper; this.hueLower = hueLower; this.saturationUpper = saturationUpper; this.saturationLower = saturationLower; this.brightnessUpper = brightnessUpper; this.brightnessLower = brightnessLower; this.reverseHue = reverseHue; } protected Color getColourForScaledValue(double value) { if (!Double.isNaN(value)) { return Color.getHSBColor(getHue((float)value), getSaturation((float)value), getBrightness((float)value)); } else { return null; } } private float getHue(float value) { if (reverseHue) { return hueUpper - ((hueUpper - hueLower) * value); } return ((hueUpper - hueLower) * value) + hueLower; } private float getSaturation(float value) { return ((saturationUpper - saturationLower) * value) + saturationLower; } private float getBrightness(float value) { return ((brightnessUpper - brightnessLower) * value) + brightnessLower; } public float getHueUpper() { return hueUpper; } public void setHueUpper(float hueUpper) { this.hueUpper = hueUpper; } public float getHueLower() { return hueLower; } public void setHueLower(float hueLower) { this.hueLower = hueLower; } public float getSaturationUpper() { return saturationUpper; } public void setSaturationUpper(float saturationUpper) { this.saturationUpper = saturationUpper; } public float getSaturationLower() { return saturationLower; } public void setSaturationLower(float saturationLower) { this.saturationLower = saturationLower; } public float getBrightnessUpper() { return brightnessUpper; } public void setBrightnessUpper(float brightnessUpper) { this.brightnessUpper = brightnessUpper; } public float getBrightnessLower() { return brightnessLower; } public void setBrightnessLower(float brightnessLower) { this.brightnessLower = brightnessLower; } public boolean isReverseHue() { return reverseHue; } public void setReverseHue(boolean reverseHue) { this.reverseHue = reverseHue; } /** * Create a string representation suitable for writing to a text file * @return the string */ @Override public String toString() { StringBuilder sb = new StringBuilder(); sb.append("{"); sb.append(getContinuousScale().toString()); sb.append(","); sb.append(hueLower); sb.append(","); sb.append(hueUpper); sb.append(","); sb.append(saturationLower); sb.append(","); sb.append(saturationUpper); sb.append(","); sb.append(brightnessLower); sb.append(","); sb.append(brightnessUpper); sb.append(","); sb.append(reverseHue); sb.append("}"); return sb.toString(); } private float hueUpper = 1.0F; private float hueLower = 0.0F; private float saturationUpper = 0.6F; private float saturationLower = 0.6F; private float brightnessUpper = 0.8F; private float brightnessLower = 0.4F; private boolean reverseHue = false; } figtree-1.4.3/src/figtree/treeviewer/decorators/HSBDiscreteColourDecorator.java000066400000000000000000000213571277473563300277300ustar00rootroot00000000000000/* * HSBDiscreteColourDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.util.Attributable; import java.awt.*; import java.util.Set; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class HSBDiscreteColourDecorator extends DiscreteColourDecorator { public enum Axis { HUE, SATURATION, BRIGHTNESS; @Override public String toString() { return super.toString().toLowerCase(); } } public HSBDiscreteColourDecorator(String attributeName) { super(attributeName); } public HSBDiscreteColourDecorator(String attributeName, String settings) { super(attributeName); setup(settings); } public HSBDiscreteColourDecorator(String attributeName, Set items) { super(attributeName, items); setupColours(); } /** * Set up from a settings string * @param settings */ public void setup(String settings) { if (!settings.startsWith("{") || !settings.endsWith("}")) { throw new IllegalArgumentException("HSBDiscreteColourDecorator settings string not in correct format"); } String[] parts = settings.substring(1, settings.length() - 1).split("[, ]+"); if (parts.length != 8) { throw new IllegalArgumentException("HSBDiscreteColourDecorator settings string not in correct format"); } try { primaryAxis = Axis.valueOf(parts[0].toUpperCase()); secondaryCount = Integer.parseInt(parts[1]); hueLower = Float.parseFloat(parts[2]); hueUpper = Float.parseFloat(parts[3]); saturationLower = Float.parseFloat(parts[4]); saturationUpper = Float.parseFloat(parts[5]); brightnessLower = Float.parseFloat(parts[6]); brightnessUpper = Float.parseFloat(parts[7]); } catch (NumberFormatException nfe) { throw new IllegalArgumentException("HSBDiscreteColourDecorator settings string not in correct format"); } catch (IllegalArgumentException iae) { throw new IllegalArgumentException("HSBDiscreteColourDecorator settings string not in correct format"); } } public void setup(int secondaryCount, float hueLower, float hueUpper, float saturationLower, float saturationUpper, float brightnessLower, float brightnessUpper, Axis primaryAxis) { this.secondaryCount = secondaryCount; this.hueUpper = hueUpper; this.hueLower = hueLower; this.saturationUpper = saturationUpper; this.saturationLower = saturationLower; this.brightnessUpper = brightnessUpper; this.brightnessLower = brightnessLower; this.primaryAxis = primaryAxis; setupColours(); } protected void setupColours() { if (getValues() == null) { return; } if (secondaryCount == 0) { return; } int valueCount = getValues().size(); int primaryCount = valueCount / secondaryCount; if (valueCount % secondaryCount > 0) { primaryCount += secondaryCount - (valueCount % secondaryCount); } Color[] paints = new Color[primaryCount * secondaryCount]; float hDelta = (hueUpper - hueLower) / (primaryAxis == Axis.HUE ? primaryCount : secondaryCount); float bDelta = (brightnessUpper - brightnessLower) / (primaryAxis == Axis.BRIGHTNESS ? primaryCount : secondaryCount); float sDelta = (saturationUpper - saturationLower) / (primaryAxis == Axis.SATURATION ? primaryCount : secondaryCount); float hue = hueLower; float brightness = brightnessUpper; float saturation = saturationLower; int k = 0; for (int i = 0; i < primaryCount; i++) { switch (primaryAxis) { case HUE: saturation = saturationLower; brightness = brightnessUpper; break; case SATURATION: hue = hueLower; brightness = brightnessUpper; break; case BRIGHTNESS: hue = hueLower; saturation = saturationLower; break; } for (int j = 0; j < secondaryCount; j++) { paints[k] = Color.getHSBColor(hue, saturation, brightness); switch (primaryAxis) { case HUE: saturation += sDelta; brightness -= bDelta; break; case SATURATION: hue += hDelta; brightness -= bDelta; break; case BRIGHTNESS: hue += hDelta; saturation += sDelta; break; } k++; } switch (primaryAxis) { case HUE: hue += hDelta; break; case SATURATION: saturation += sDelta; break; case BRIGHTNESS: brightness -= bDelta; break; } } setColourMap(getValues(), paints); } public void setSecondaryCount(int secondaryCount) { this.secondaryCount = secondaryCount; setupColours(); } public void setHueUpper(float hueUpper) { this.hueUpper = hueUpper; setupColours(); } public void setHueLower(float hueLower) { this.hueLower = hueLower; setupColours(); } public void setSaturationUpper(float saturationUpper) { this.saturationUpper = saturationUpper; setupColours(); } public void setSaturationLower(float saturationLower) { this.saturationLower = saturationLower; setupColours(); } public void setBrightnessUpper(float brightnessUpper) { this.brightnessUpper = brightnessUpper; setupColours(); } public void setBrightnessLower(float brightnessLower) { this.brightnessLower = brightnessLower; setupColours(); } public void setPrimaryAxis(Axis primaryAxis) { this.primaryAxis = primaryAxis; setupColours(); } public int getSecondaryCount() { return secondaryCount; } public float getHueUpper() { return hueUpper; } public float getHueLower() { return hueLower; } public float getSaturationUpper() { return saturationUpper; } public float getSaturationLower() { return saturationLower; } public float getBrightnessUpper() { return brightnessUpper; } public float getBrightnessLower() { return brightnessLower; } public Axis getPrimaryAxis() { return primaryAxis; } /** * Create a string representation suitable for writing to a text file * @return the string */ @Override public String toString() { StringBuilder sb = new StringBuilder(); sb.append("{"); sb.append(primaryAxis); sb.append(","); sb.append(secondaryCount); sb.append(","); sb.append(hueLower); sb.append(","); sb.append(hueUpper); sb.append(","); sb.append(saturationLower); sb.append(","); sb.append(saturationUpper); sb.append(","); sb.append(brightnessLower); sb.append(","); sb.append(brightnessUpper); sb.append("}"); return sb.toString(); } private Axis primaryAxis = Axis.HUE; private int secondaryCount = 1; private float hueUpper = 1.0F; private float hueLower = 0.0F; private float saturationUpper = 0.6F; private float saturationLower = 0.6F; private float brightnessUpper = 0.8F; private float brightnessLower = 0.4F; } figtree-1.4.3/src/figtree/treeviewer/decorators/InterpolatingColourDecorator.java000077500000000000000000000164611277473563300304530ustar00rootroot00000000000000/* * InterpolatingColourDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.util.Attributable; import java.awt.*; import java.util.Set; /** * This decorator takes an attribute name and a set of attibutable Objects. It * autodetects the type of attributes and then provides a colouring scheme for them * based on a gradient between color1 & color2. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class InterpolatingColourDecorator extends ContinuousColourDecorator { public static final Color DEFAULT_COLOR_1 = Color.getHSBColor(0.01F, 0.7F, 0.85F); public static final Color DEFAULT_COLOR_2 = Color.getHSBColor(0.63F, 0.7F, 0.85F); public static final Color DEFAULT_COLOR_3 = Color.BLACK; public InterpolatingColourDecorator(String attribute, String settings) { super(attribute); setup(settings); } public InterpolatingColourDecorator(ContinuousScale continuousScale) throws NumberFormatException { super(continuousScale); setColours(DEFAULT_COLOR_1, DEFAULT_COLOR_2); } public InterpolatingColourDecorator(ContinuousScale continuousScale, Color color1, Color color2) throws NumberFormatException { super(continuousScale); setColours(color1, color2); } public InterpolatingColourDecorator(ContinuousScale continuousScale, Color color1, Color color2, Color color3) throws NumberFormatException { super(continuousScale); setColours(color1, color2, color3); } public void setColours(Color color1, Color color2) { this.color1 = new float[4]; color1.getRGBComponents(this.color1); this.color2 = new float[4]; color2.getRGBComponents(this.color2); this.color3 = null; } public void setColours(Color color1, Color color2, Color color3) { this.color1 = new float[4]; color1.getRGBComponents(this.color1); this.color2 = new float[4]; color2.getRGBComponents(this.color2); this.color3 = new float[4]; color3.getRGBComponents(this.color3); } public Color getColor1() { if (color1 == null) { return null; } return new Color(color1[0], color1[1], color1[2], color1[3]); } public Color getColor2() { if (color2 == null) { return null; } return new Color(color2[0], color2[1], color2[2], color2[3]); } public Color getColor3() { if (color3 == null) { return null; } return new Color(color3[0], color3[1], color3[2], color3[3]); } // Private methods public Color getColourForScaledValue(double value) { if (!Double.isNaN(value)) { if (color3 != null) { if (value < 0.5) { float p = (float)value * 2; float q = 1.0F - p; return new Color( color2[0] * p + color1[0] * q, color2[1] * p + color1[1] * q, color2[2] * p + color1[2] * q, color2[3] * p + color1[3] * q); } else { float p = (float)(value - 0.5) * 2; float q = 1.0F - p; return new Color( color3[0] * p + color2[0] * q, color3[1] * p + color2[1] * q, color3[2] * p + color2[2] * q, color3[3] * p + color2[3] * q); } } else { float p = (float)value; float q = 1.0F - p; return new Color( color2[0] * p + color1[0] * q, color2[1] * p + color1[1] * q, color2[2] * p + color1[2] * q, color2[3] * p + color1[3] * q); } } else { return null; } } private float[] color1; private float[] color2; private float[] color3; @Override public void setup(String settings) { if (!settings.startsWith("{") || !settings.endsWith("}")) { throw new IllegalArgumentException("InterpolatingColourDecorator settings string not in correct format"); } String[] parts1 = settings.substring(1, settings.length() - 1).split("}[, ]+"); if (parts1.length != 2) { throw new IllegalArgumentException("InterpolatingColourDecorator settings string not in correct format"); } String[] parts2 = parts1[1].split("[, ]+"); if (parts2.length != 2 && parts2.length != 3) { throw new IllegalArgumentException("InterpolatingColourDecorator settings string not in correct format"); } try { setContinuousScale(new ContinuousScale(parts1[0])); if (parts2.length == 3) { setColours(parseColor(parts2[0]), parseColor(parts2[1]), parseColor(parts2[2])); } else { setColours(parseColor(parts2[0]), parseColor(parts2[1])); } } catch (NumberFormatException nfe) { throw new IllegalArgumentException("InterpolatingColourDecorator settings string not in correct format"); } catch (IllegalArgumentException iae) { throw new IllegalArgumentException("InterpolatingColourDecorator settings string not in correct format"); } } private Color parseColor(String value) { if (value.startsWith("#")) { try { return Color.decode(value.substring(1)); } catch (NumberFormatException nfe) { } } return null; } /** * Create a string representation suitable for writing to a text file * @return the string */ @Override public String toString() { StringBuilder sb = new StringBuilder(); sb.append("{"); sb.append(getContinuousScale().toString()); sb.append(",#"); sb.append(new Color(color1[0], color1[1], color1[2], color1[3]).getRGB()); sb.append(",#"); sb.append(new Color(color2[0], color2[1], color2[2], color2[3]).getRGB()); if (color3 != null) { sb.append(",#"); sb.append(new Color(color3[0], color3[1], color3[2], color3[3]).getRGB()); } sb.append("}"); return sb.toString(); } } figtree-1.4.3/src/figtree/treeviewer/decorators/ParsimonyBranchDecorator.java000077500000000000000000000124311277473563300275400ustar00rootroot00000000000000/* * ParsimonyBranchDecorator.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.decorators; import jebl.evolution.trees.Tree; import jebl.evolution.graphs.Node; import jebl.evolution.alignments.Pattern; import jebl.evolution.parsimony.ParsimonyCriterion; import jebl.evolution.parsimony.FitchParsimony; import jebl.evolution.sequences.State; import jebl.evolution.sequences.Nucleotides; import jebl.evolution.sequences.SequenceType; import jebl.evolution.sequences.AminoAcids; import java.util.ArrayList; import java.util.List; import java.awt.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ParsimonyBranchDecorator { public ParsimonyBranchDecorator(Pattern pattern) { List patterns = new ArrayList(); patterns.add(pattern); parsimony = new FitchParsimony(patterns, true); if (pattern.getSequenceType() == SequenceType.NUCLEOTIDE) { paints = new Paint[Nucleotides.getStateCount()]; paints[Nucleotides.A_STATE.getIndex()] = Color.RED; paints[Nucleotides.C_STATE.getIndex()] = Color.BLUE; paints[Nucleotides.G_STATE.getIndex()] = Color.BLACK; paints[Nucleotides.T_STATE.getIndex()] = Color.GREEN; paints[Nucleotides.R_STATE.getIndex()] = Color.MAGENTA; paints[Nucleotides.Y_STATE.getIndex()] = Color.DARK_GRAY; paints[Nucleotides.M_STATE.getIndex()] = Color.DARK_GRAY; paints[Nucleotides.W_STATE.getIndex()] = Color.DARK_GRAY; paints[Nucleotides.S_STATE.getIndex()] = Color.DARK_GRAY; paints[Nucleotides.K_STATE.getIndex()] = Color.DARK_GRAY; paints[Nucleotides.B_STATE.getIndex()] = Color.DARK_GRAY; paints[Nucleotides.D_STATE.getIndex()] = Color.DARK_GRAY; paints[Nucleotides.H_STATE.getIndex()] = Color.DARK_GRAY; paints[Nucleotides.V_STATE.getIndex()] = Color.DARK_GRAY; paints[Nucleotides.N_STATE.getIndex()] = Color.GRAY; paints[Nucleotides.UNKNOWN_STATE.getIndex()] = Color.GRAY; paints[Nucleotides.GAP_STATE.getIndex()] = Color.GRAY; } else if (pattern.getSequenceType() == SequenceType.AMINO_ACID) { paints = new Paint[AminoAcids.getStateCount()]; paints[AminoAcids.A_STATE.getIndex()] = new Color(204, 255, 255); paints[AminoAcids.C_STATE.getIndex()] = new Color(0, 255, 255); paints[AminoAcids.D_STATE.getIndex()] = new Color(255, 204, 153); paints[AminoAcids.E_STATE.getIndex()] = new Color(255, 204, 0); paints[AminoAcids.F_STATE.getIndex()] = new Color(0, 204, 255); paints[AminoAcids.G_STATE.getIndex()] = new Color(0, 255, 0); paints[AminoAcids.H_STATE.getIndex()] = new Color(255, 255, 153); paints[AminoAcids.I_STATE.getIndex()] = new Color(0, 0, 128); paints[AminoAcids.K_STATE.getIndex()] = new Color(198, 66, 0); paints[AminoAcids.L_STATE.getIndex()] = new Color(51, 102, 255); paints[AminoAcids.M_STATE.getIndex()] = new Color(153, 204, 255); paints[AminoAcids.N_STATE.getIndex()] = new Color(255, 153, 0); paints[AminoAcids.P_STATE.getIndex()] = new Color(255, 255, 0); paints[AminoAcids.Q_STATE.getIndex()] = new Color(255, 102, 0); paints[AminoAcids.R_STATE.getIndex()] = new Color(230, 6, 6); paints[AminoAcids.S_STATE.getIndex()] = new Color(204, 255, 153); paints[AminoAcids.T_STATE.getIndex()] = new Color(0, 255, 153); paints[AminoAcids.V_STATE.getIndex()] = new Color(0, 0, 255); paints[AminoAcids.W_STATE.getIndex()] = new Color(204, 153, 255); paints[AminoAcids.Y_STATE.getIndex()] = new Color(204, 255, 204); paints[AminoAcids.B_STATE.getIndex()] = Color.DARK_GRAY; paints[AminoAcids.Z_STATE.getIndex()] = Color.DARK_GRAY; paints[AminoAcids.X_STATE.getIndex()] = Color.GRAY; paints[AminoAcids.UNKNOWN_STATE.getIndex()] = Color.GRAY; paints[AminoAcids.STOP_STATE.getIndex()] = Color.GRAY; paints[AminoAcids.GAP_STATE.getIndex()] = Color.GRAY; } else { throw new IllegalArgumentException("Unsupported sequence type"); } } public Paint getBranchPaint(Tree tree, Node node) { State[] states = parsimony.getStates(tree, node); return paints[states[0].getIndex()]; } private final ParsimonyCriterion parsimony; private final Paint[] paints; }figtree-1.4.3/src/figtree/treeviewer/images/000077500000000000000000000000001277473563300210275ustar00rootroot00000000000000figtree-1.4.3/src/figtree/treeviewer/images/polarTree.png000077500000000000000000000006411277473563300234760ustar00rootroot00000000000000PNG  IHDRagAMAOX2tEXtSoftwareAdobe ImageReadyqe<3IDATxڤ=H@$ڂ XEAts, CWtRWEM(EkBBա"W^ېjh~ݓ; nSط:h(+(bھưI ;̺]E\q(B_`YO#235̶]BKě^u,Ohj=*<%'U݄8ZDĽHPCUos60+F8j4aIENDB`figtree-1.4.3/src/figtree/treeviewer/images/radialTree.png000077500000000000000000000005371277473563300236210ustar00rootroot00000000000000PNG  IHDRagAMAOX2tEXtSoftwareAdobe ImageReadyqe<IDATxb` q dddd?!؁ ,0$@ Xa*P@1?0 3( CH6BX 8&x\} tvP4ZC_H/@4<>t=@ @"1[C &N=@lCH m- ēAaFh`gBS̠6\  k3<̉IENDB`figtree-1.4.3/src/figtree/treeviewer/images/rectangularTree.png000077500000000000000000000006571277473563300246770ustar00rootroot00000000000000PNG  IHDRagAMAOX2tEXtSoftwareAdobe ImageReadyqe<AIDATxڌ=KAsqR!U XjaiecF"`Y I#V`.30rs8ٻwι$Ijym8/g`Y>A7ZpB 2)lh D uMwk> ^C18-4 ^Td g闕PGtzF* b5{, }`&~{s} RhKf!Xi)ѭ޵YZ*%D[[:\+#hLRfXJFhp^0e1/<2êf*Wf{ 8IENDB`figtree-1.4.3/src/figtree/treeviewer/painters/000077500000000000000000000000001277473563300214075ustar00rootroot00000000000000figtree-1.4.3/src/figtree/treeviewer/painters/AbstractPainter.java000077500000000000000000000035031277473563300253440ustar00rootroot00000000000000/* * AbstractPainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import java.util.ArrayList; import java.util.List; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public abstract class AbstractPainter implements Painter { public void addPainterListener(PainterListener listener) { listeners.add(listener); } public void removePainterListener(PainterListener listener) { listeners.remove(listener); } public void firePainterChanged() { for (PainterListener listener : listeners) { listener.painterChanged(); } } public void firePainterSettingsChanged() { for (PainterListener listener : listeners) { listener.painterSettingsChanged(); } } public void fireAttributesChanged() { for (PainterListener listener : listeners) { listener.attributesChanged(); } } private final List listeners = new ArrayList(); } figtree-1.4.3/src/figtree/treeviewer/painters/AttributeComboHelper.java000066400000000000000000000264601277473563300263450ustar00rootroot00000000000000/* * AttributeComboHelper.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.TreeViewer; import figtree.treeviewer.TreeViewerListener; import figtree.treeviewer.decorators.ColourDecorator; import jebl.evolution.graphs.Node; import jebl.evolution.taxa.Taxon; import jebl.evolution.trees.Tree; import jebl.util.Attributable; import javax.swing.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class AttributeComboHelper { public AttributeComboHelper(final JComboBox attributeComboBox, final TreeViewer treeViewer) { this(attributeComboBox, treeViewer, null, null, false, false); } public AttributeComboHelper(final JComboBox attributeComboBox, final TreeViewer treeViewer, final String defaultOption) { this(attributeComboBox, treeViewer, defaultOption, null, false, false); } public AttributeComboHelper(final JComboBox attributeComboBox, final TreeViewer treeViewer, final String defaultOption, final LabelPainter.PainterIntent intent) { this(attributeComboBox, treeViewer, defaultOption, intent, false, false); } public AttributeComboHelper(final JComboBox attributeComboBox, final TreeViewer treeViewer, final String defaultOption, final boolean numericalOnly, final boolean includeLineageColourings) { this(attributeComboBox, treeViewer, defaultOption, null, numericalOnly, includeLineageColourings); } public AttributeComboHelper(final JComboBox attributeComboBox, final TreeViewer treeViewer, final LabelPainter.PainterIntent intent) { this(attributeComboBox, treeViewer, null, intent, false, false); } public AttributeComboHelper(final JComboBox attributeComboBox, final TreeViewer treeViewer, final LabelPainter.PainterIntent intent, final boolean numericalOnly) { this(attributeComboBox, treeViewer, null, intent, numericalOnly, false); } public AttributeComboHelper(final JComboBox attributeComboBox, final TreeViewer treeViewer, final String defaultOption, final LabelPainter.PainterIntent intent, final boolean numericalOnly, final boolean includeLineageColourings) { treeViewer.addTreeViewerListener(new TreeViewerListener() { public void treeChanged() { List trees = treeViewer.getTrees(); Object selected = attributeComboBox.getSelectedItem(); addingItems = true; attributeComboBox.removeAllItems(); if (defaultOption != null) { attributeComboBox.addItem(defaultOption); } if (trees == null) { return; } List names = new ArrayList(); if (intent != null || numericalOnly) { getAttributeNames(names, trees, intent, numericalOnly); } else { getAttributeNames(names, trees, includeLineageColourings); } for (String name : names) { attributeComboBox.addItem(name); } addingItems = false; if (selected != null) { attributeComboBox.setSelectedItem(selected); } } public void treeSettingsChanged() { // nothing to do } }); attributeComboBox.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { if (!addingItems) { fireAttributeSelectionChanged(); } } }); } public static void getAttributeNames(List attributeNames, Collection trees, LabelPainter.PainterIntent intent, boolean numericalOnly) { Set nodeAttributes = new TreeSet(); if (trees != null) { for (Tree tree : trees) { if (intent == LabelPainter.PainterIntent.TIP) { for (Node node : tree.getExternalNodes()) { nodeAttributes.addAll(node.getAttributeNames()); } for (Taxon taxon : tree.getTaxa()) { nodeAttributes.addAll(taxon.getAttributeNames()); } } else if (intent == LabelPainter.PainterIntent.NODE) { for (Node node : tree.getInternalNodes()) { nodeAttributes.addAll(node.getAttributeNames()); } } else if (intent == LabelPainter.PainterIntent.RANGE) { for (Node node : tree.getInternalNodes()) { for (String name : node.getAttributeNames()) { Object attr = node.getAttribute(name); if (attr instanceof Object[]) { Object[] array = (Object[])attr; if (array.length == 2 && array[0] instanceof Number && array[1] instanceof Number) { nodeAttributes.add(name); } } } } } else { for (Node node : tree.getNodes()) { for (String key : node.getAttributeMap().keySet()) { nodeAttributes.add(key); } } } } } if (numericalOnly) { Set continuousNodeAttributes = new TreeSet(); for (String nodeAttributeName : nodeAttributes) { boolean isNumerical = true; for (Tree tree : trees) { if (!ColourDecorator.isNumerical(nodeAttributeName, tree.getNodes())) { isNumerical = false; } } if (isNumerical) { continuousNodeAttributes.add(nodeAttributeName); } } nodeAttributes = continuousNodeAttributes; } if (intent != null) { switch( intent ) { case TIP: { attributeNames.add(LabelPainter.NAMES); attributeNames.add(LabelPainter.NODE_AGES); attributeNames.add(LabelPainter.NODE_HEIGHTS); attributeNames.add(LabelPainter.BRANCH_TIMES); attributeNames.add(LabelPainter.BRANCH_LENGTHS); break; } case NODE: { if (nodeAttributes.contains("!name")) { attributeNames.add(LabelPainter.NAMES); } attributeNames.add(LabelPainter.NODE_AGES); attributeNames.add(LabelPainter.NODE_HEIGHTS); attributeNames.add(LabelPainter.BRANCH_TIMES); attributeNames.add(LabelPainter.BRANCH_LENGTHS); break; } case BRANCH: { if (nodeAttributes.contains("!name")) { attributeNames.add(LabelPainter.NAMES); } attributeNames.add(LabelPainter.BRANCH_TIMES); attributeNames.add(LabelPainter.BRANCH_LENGTHS); attributeNames.add(LabelPainter.NODE_AGES); attributeNames.add(LabelPainter.NODE_HEIGHTS); break; } } } for (String attributeName : nodeAttributes) { if (!attributeName.startsWith("!")) { attributeNames.add(attributeName); } } } private static void getAttributeNames(List attributeNames, Collection trees, final boolean includeLineageColourings) { for (Tree tree : trees) { Set attributes = new TreeSet(); for (Attributable item : tree.getNodes()) { for (String name : item.getAttributeNames()) { if (!name.startsWith("!")) { Object attr = item.getAttribute(name); if (!(attr instanceof Object[])) { attributes.add(name); } else { boolean isColouring = true; Object[] array = (Object[])attr; boolean isIndex = true; for (Object element : array) { if (isIndex && !(element instanceof Integer) || !isIndex && !(element instanceof Double)) { isColouring = false; break; } isIndex = !isIndex; } if (isIndex) { // a colouring should finish on an index (which means isIndex should be false)... isColouring = false; } if (isColouring && includeLineageColourings) { attributes.add(name + " *"); } } } } } attributeNames.addAll(attributes); } } public void addListener(AttributeComboHelperListener listener) { listeners.add(listener); } private void fireAttributeSelectionChanged() { for (AttributeComboHelperListener listener : listeners) { listener.attributeComboChanged(); } } private final List listeners = new ArrayList(); private boolean addingItems = false; } figtree-1.4.3/src/figtree/treeviewer/painters/AttributeComboHelperListener.java000066400000000000000000000020551277473563300300450ustar00rootroot00000000000000/* * AttributeComboHelperListener.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface AttributeComboHelperListener { void attributeComboChanged(); } figtree-1.4.3/src/figtree/treeviewer/painters/BasicLabelPainter.java000077500000000000000000000242171277473563300255670ustar00rootroot00000000000000/* * BasicLabelPainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.TimeScale; import figtree.treeviewer.TreePane; import figtree.treeviewer.decorators.*; import jebl.evolution.graphs.Node; import jebl.evolution.taxa.Taxon; import jebl.evolution.trees.RootedTree; import jebl.evolution.trees.Tree; import jebl.util.Attributable; import java.awt.*; import java.awt.geom.Rectangle2D; import java.util.*; import java.util.List; /** * A simple implementation of LabelPainter that can be used to display * tip, node or branch labels. It can display, taxon names, branch lengths, * node heights or other attributeNames of nodes. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class BasicLabelPainter extends LabelPainter { public BasicLabelPainter(PainterIntent intent) { super(intent); this.displayAttribute = ""; } public void setTreePane(TreePane treePane) { this.treePane = treePane; } public Decorator getBorderDecorator() { return borderDecorator; } public void setBorderDecorator(Decorator borderDecorator) { this.borderDecorator = borderDecorator; firePainterSettingsChanged(); } public Decorator getTextDecorator() { return textDecorator; } public void setTextDecorator(Decorator textDecorator) { this.textDecorator = textDecorator; firePainterSettingsChanged(); } public Tree getTree() { return treePane.getTree(); } protected String getLabel(Tree tree, Node node) { if (displayAttribute.equalsIgnoreCase(NAMES)) { if (getIntent() == PainterIntent.TIP) { Taxon taxon = tree.getTaxon(node); if (taxon != null) { if (textDecorator != null) { textDecorator.setItem(taxon); } String name = (String)taxon.getAttribute("!name"); if (name != null) { return name; } return taxon.getName(); } else { String name = (String)node.getAttribute("!name"); if (name != null) { return name; } return null; } } else { String name = (String)node.getAttribute("!name"); if (name != null) { return name; } return null; } } if ( tree instanceof RootedTree) { final RootedTree rtree = (RootedTree) tree; if (textDecorator != null) { textDecorator.setItem(node); } if (displayAttribute.equalsIgnoreCase(NODE_AGES) ) { TimeScale timeScale = treePane.getTimeScale(); double age = timeScale.getAge(rtree.getHeight(node), rtree); return getNumberFormat().format(age); } else if (displayAttribute.equalsIgnoreCase(NODE_HEIGHTS) ) { return getNumberFormat().format(rtree.getHeight(node)); } else if (displayAttribute.equalsIgnoreCase(BRANCH_TIMES) ) { TimeScale timeScale = treePane.getTimeScale(); double time = timeScale.getTime(rtree.getLength(node), rtree); return getNumberFormat().format(time); } else if (displayAttribute.equalsIgnoreCase(BRANCH_LENGTHS) ) { return getNumberFormat().format(rtree.getLength(node)); } } Object value = null; if (getIntent() == PainterIntent.TIP) { Taxon taxon = tree.getTaxon(node); if (taxon != null) { value = taxon.getAttribute(displayAttribute); } else { value = node.getAttribute(displayAttribute); } } if (value == null) { value = node.getAttribute(displayAttribute); } return formatValue(value); } private String formatValue(Object value) { if (value != null) { if (value instanceof Double) { return getNumberFormat().format(value); } else if (value instanceof Object[]) { Object[] values = (Object[])value; if (values.length == 0) return null; if (values.length == 1) return formatValue(values[0]); StringBuilder builder = new StringBuilder("["); builder.append(formatValue(values[0])); for (int i = 1; i < values.length; i++) { builder.append(","); builder.append(formatValue(values[i])); } builder.append("]"); return builder.toString(); } return value.toString(); } return null; } public Rectangle2D calibrate(Graphics2D g2, Node item) { Tree tree = treePane.getTree(); String label = getLabel(tree, item); final Font oldFont = g2.getFont(); if (textDecorator != null) { g2.setFont(textDecorator.getFont(getFont())); } else { g2.setFont(getFont()); } FontMetrics fm = g2.getFontMetrics(); preferredHeight = fm.getHeight(); preferredWidth = 0; if (label != null) { Rectangle2D rect = fm.getStringBounds(label, g2); preferredWidth = rect.getWidth(); } yOffset = (float)fm.getAscent(); g2.setFont(oldFont); return new Rectangle2D.Double(0.0, 0.0, preferredWidth, preferredHeight); } public double getPreferredWidth() { return preferredWidth; } public double getPreferredHeight() { return preferredHeight; } public double getHeightBound() { return preferredHeight + yOffset; } public void paint(Graphics2D g2, Node item, Justification justification, Rectangle2D bounds) { Tree tree = treePane.getTree(); if (TreePane.DEBUG_OUTLINE) { g2.setPaint(Color.red); g2.draw(bounds); } String label = getLabel(tree, item); Font oldFont = g2.getFont(); Paint backgroundPaint = getBackground(); Paint borderPaint = getBorderPaint(); Stroke borderStroke = getBorderStroke(); if (borderDecorator != null) { backgroundPaint = borderDecorator.getPaint(backgroundPaint); borderPaint = borderDecorator.getPaint(borderPaint); borderStroke = borderDecorator.getStroke(borderStroke); } if (backgroundPaint != null) { g2.setPaint(backgroundPaint); g2.fill(bounds); } if (borderPaint != null && borderStroke != null) { g2.setPaint(borderPaint); g2.setStroke(borderStroke); g2.draw(bounds); } if (textDecorator != null) { // this is a bit of a hack to detect whether we should be getting the // colour attribute from the taxon, or some other attribute from the // node: if (getIntent() == PainterIntent.TIP) { textDecorator.setItem(tree.getTaxon(item), (Node)item); } else { textDecorator.setItem(item); } g2.setPaint(textDecorator.getPaint(getForeground())); g2.setFont(textDecorator.getFont(getFont())); } else { g2.setPaint(getForeground()); g2.setFont(getFont()); } if (label != null) { Rectangle2D rect = g2.getFontMetrics().getStringBounds(label, g2); float xOffset; float y = yOffset + (float) bounds.getY(); switch (justification) { case CENTER: xOffset = (float)(-rect.getWidth()/2.0); y = yOffset + (float) rect.getY(); //xOffset = (float) (bounds.getX() + (bounds.getWidth() - rect.getWidth()) / 2.0); break; case FLUSH: case LEFT: xOffset = (float) bounds.getX(); break; case RIGHT: xOffset = (float) (bounds.getX() + bounds.getWidth() - rect.getWidth()); break; default: throw new IllegalArgumentException("Unrecognized alignment enum option"); } g2.drawString(label, xOffset, y); } g2.setFont(oldFont); } public String getDisplayAttribute() { if (displayAttribute.equalsIgnoreCase(NAMES) || displayAttribute.equalsIgnoreCase(NODE_AGES) || displayAttribute.equalsIgnoreCase(NODE_HEIGHTS) || displayAttribute.equalsIgnoreCase(BRANCH_TIMES) || displayAttribute.equalsIgnoreCase(BRANCH_LENGTHS)) { return null; } return displayAttribute; } public void setDisplayAttribute(String displayAttribute) { this.displayAttribute = displayAttribute; firePainterChanged(); } private double preferredWidth; private double preferredHeight; private float yOffset; protected String displayAttribute; protected TreePane treePane; private Decorator textDecorator = null; private Decorator borderDecorator = null; } figtree-1.4.3/src/figtree/treeviewer/painters/CharactersPainter.java000077500000000000000000000147101277473563300256620ustar00rootroot00000000000000/* * CharactersPainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import jebl.evolution.alignments.Alignment; import jebl.evolution.graphs.Node; import jebl.evolution.sequences.AminoAcids; import jebl.evolution.sequences.Sequence; import jebl.evolution.trees.Tree; import figtree.treeviewer.painters.BasicLabelPainter; import java.awt.*; import java.awt.geom.Rectangle2D; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class CharactersPainter extends BasicLabelPainter { public CharactersPainter(Alignment characters) { super(BasicLabelPainter.PainterIntent.TIP); this.characters = characters; paints[AminoAcids.A_STATE.getIndex()] = new Color(204, 255, 255); paints[AminoAcids.C_STATE.getIndex()] = new Color(0, 255, 255); paints[AminoAcids.D_STATE.getIndex()] = new Color(255, 204, 153); paints[AminoAcids.E_STATE.getIndex()] = new Color(255, 204, 0); paints[AminoAcids.F_STATE.getIndex()] = new Color(0, 204, 255); paints[AminoAcids.G_STATE.getIndex()] = new Color(0, 255, 0); paints[AminoAcids.H_STATE.getIndex()] = new Color(255, 255, 153); paints[AminoAcids.I_STATE.getIndex()] = new Color(0, 0, 128); paints[AminoAcids.K_STATE.getIndex()] = new Color(198, 66, 0); paints[AminoAcids.L_STATE.getIndex()] = new Color(51, 102, 255); paints[AminoAcids.M_STATE.getIndex()] = new Color(153, 204, 255); paints[AminoAcids.N_STATE.getIndex()] = new Color(255, 153, 0); paints[AminoAcids.P_STATE.getIndex()] = new Color(255, 255, 0); paints[AminoAcids.Q_STATE.getIndex()] = new Color(255, 102, 0); paints[AminoAcids.R_STATE.getIndex()] = new Color(230, 6, 6); paints[AminoAcids.S_STATE.getIndex()] = new Color(204, 255, 153); paints[AminoAcids.T_STATE.getIndex()] = new Color(0, 255, 153); paints[AminoAcids.V_STATE.getIndex()] = new Color(0, 0, 255); paints[AminoAcids.W_STATE.getIndex()] = new Color(204, 153, 255); paints[AminoAcids.Y_STATE.getIndex()] = new Color(204, 255, 204); paints[AminoAcids.B_STATE.getIndex()] = Color.DARK_GRAY; paints[AminoAcids.Z_STATE.getIndex()] = Color.DARK_GRAY; paints[AminoAcids.X_STATE.getIndex()] = Color.GRAY; paints[AminoAcids.UNKNOWN_STATE.getIndex()] = Color.GRAY; paints[AminoAcids.STOP_STATE.getIndex()] = Color.GRAY; paints[AminoAcids.GAP_STATE.getIndex()] = Color.GRAY; }; public Rectangle2D calibrate(Graphics2D g2, Node node) { super.calibrate(g2, node); int siteCount = characters.getSiteCount(); blockSize = super.getPreferredHeight() / 2; blockGap = blockSize / 2; width = (siteCount * (blockSize + blockGap)) + blockGap + blockGap; return new Rectangle2D.Double(0.0, 0.0, getPreferredWidth(), getPreferredHeight()); } public double getPreferredWidth() { return super.getPreferredWidth() + width; } public void paint(Graphics2D g2, Node node, Justification justification, Rectangle2D bounds) { Tree tree = getTree(); Stroke oldStroke = g2.getStroke(); Paint oldPaint = g2.getPaint(); float yOffset = (float)getPreferredHeight() / 2; switch (justification) { case FLUSH: case LEFT: { super.paint(g2, node, justification, new Rectangle2D.Double(bounds.getX() + width, bounds.getY(), bounds.getWidth() - width, bounds.getHeight())); Sequence sequence = characters.getSequence(tree.getTaxon(node)); if (sequence != null) { double x = blockGap; for (int state : sequence.getStateIndices()) { if (state != AminoAcids.GAP_STATE.getIndex()) { // Now create a bounds for the label Rectangle2D block = new Rectangle2D.Double( x, yOffset - (blockSize / 2.0), blockSize, blockSize); g2.setPaint(getStatePaint(state)); g2.fill(block); } x += blockSize + blockGap; } } } break; case RIGHT: { super.paint(g2, node, justification, new Rectangle2D.Double(bounds.getX(), bounds.getY(), bounds.getWidth() - width, bounds.getHeight())); Sequence sequence = characters.getSequence(tree.getTaxon(node)); if (sequence != null) { double x = getPreferredWidth() - blockGap - blockSize; for (int state : sequence.getStateIndices()) { // Now create a bounds for the label Rectangle2D block = new Rectangle2D.Double( x, yOffset - (blockSize / 2.0), blockSize, blockSize); g2.setPaint(getStatePaint(state)); g2.fill(block); x -= (blockSize + blockGap); } } } break; default: throw new IllegalArgumentException("Unrecognized alignment enum option"); } g2.setStroke(oldStroke); g2.setPaint(oldPaint); } private Alignment characters = null; private double width; private double blockSize = 6; private double blockGap = 2; Paint[] paints = new Paint[AminoAcids.getStateCount()]; public Paint getStatePaint(int stateIndex) { return paints[stateIndex]; } } figtree-1.4.3/src/figtree/treeviewer/painters/LabelPainter.java000077500000000000000000000066601277473563300246270ustar00rootroot00000000000000/* * LabelPainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import com.sun.tools.corba.se.idl.InterfaceEntry; import jebl.evolution.trees.Tree; import jebl.util.Attributable; import java.awt.*; import java.text.NumberFormat; import java.util.Collection; import java.util.Set; import figtree.treeviewer.decorators.Decorator; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public abstract class LabelPainter extends AbstractPainter { public static final String NAMES = "Names"; public static final String NODE_AGES = "Node ages"; public static final String NODE_HEIGHTS = "Node heights (raw)"; public static final String BRANCH_TIMES = "Branch times"; public static final String BRANCH_LENGTHS = "Branch lengths (raw)"; public enum PainterIntent { NODE, BRANCH, TIP, RANGE }; protected LabelPainter(PainterIntent intent) { this.intent = intent; } // Abstract public abstract String getDisplayAttribute(); public abstract void setDisplayAttribute(String displayAttribute); public abstract void setTextDecorator(Decorator textDecorator); // Getters public Paint getForeground() { return foreground; } public Paint getBackground() { return background; } public Paint getBorderPaint() { return borderPaint; } public Stroke getBorderStroke() { return borderStroke; } public Font getFont() { return font; } public NumberFormat getNumberFormat() { return numberFormat; } public boolean isVisible() { return visible; } // Setters public void setBackground(Paint background) { this.background = background; firePainterChanged(); } public void setBorder(Paint borderPaint, Stroke borderStroke) { this.borderPaint = borderPaint; this.borderStroke = borderStroke; firePainterChanged(); } public void setFont(Font font) { this.font = font; firePainterChanged(); } public void setForeground(Paint foreground) { this.foreground = foreground; firePainterChanged(); } public void setNumberFormat(NumberFormat numberFormat) { this.numberFormat = numberFormat; firePainterChanged(); } public void setVisible(boolean visible) { this.visible = visible; firePainterChanged(); } public PainterIntent getIntent() { return intent; } private Paint foreground = Color.BLACK; private Paint background = null; private Paint borderPaint = null; private Stroke borderStroke = null; private Font font; private boolean visible = true; private NumberFormat numberFormat = null; private final PainterIntent intent; } figtree-1.4.3/src/figtree/treeviewer/painters/LabelPainterController.java000077500000000000000000000316101277473563300266640ustar00rootroot00000000000000/* * LabelPainterController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.ui.PercentFormat; import figtree.ui.RomanFormat; import jam.controlpalettes.AbstractController; import jam.controlpalettes.ControllerListener; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.*; import java.text.DecimalFormat; import java.text.NumberFormat; import java.util.*; import java.util.prefs.Preferences; import figtree.treeviewer.*; import figtree.treeviewer.decorators.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class LabelPainterController extends AbstractController { public static Preferences PREFS = Preferences.userNodeForPackage(TreeViewer.class); private static final String USER_SELECTION = "User Selection"; public static final String FONT_NAME_KEY = "fontName"; public static final String FONT_SIZE_KEY = "fontSize"; public static final String FONT_STYLE_KEY = "fontStyle"; public static final String COLOR_ATTRIBUTE_KEY = "colorAttribute"; public static final String NUMBER_FORMATTING_KEY = "numberFormatting"; public static final String DISPLAY_ATTRIBUTE_KEY = "displayAttribute"; public static final String SIGNIFICANT_DIGITS_KEY = "significantDigits"; // The defaults if there is nothing in the preferences public static String DEFAULT_FONT_NAME = "sansserif"; public static int DEFAULT_FONT_SIZE = 8; public static int DEFAULT_FONT_STYLE = Font.PLAIN; public static String DECIMAL_NUMBER_FORMATTING = "#.####"; public static String SCIENTIFIC_NUMBER_FORMATTING = "0.###E0"; public static int DEFAULT_SIGNIFICANT_DIGITS = 2; public static String DEFAULT_NUMBER_FORMATTING = DECIMAL_NUMBER_FORMATTING; public LabelPainterController(String title, String key, final LabelPainter labelPainter, final JFrame frame, final AttributeColourController colourController, final TreeViewer treeViewer) { this.title = title; this.key = key; this.labelPainter = labelPainter; LabelPainter.PainterIntent intent = labelPainter.getIntent(); userLabelDecorator = new AttributableDecorator(); userLabelDecorator.setPaintAttributeName("!color"); userLabelDecorator.setFontAttributeName("!font"); labelPainter.setTextDecorator(userLabelDecorator); final String defaultFontName = PREFS.get(key + "." + FONT_NAME_KEY, DEFAULT_FONT_NAME); final int defaultFontStyle = PREFS.getInt(key + "." + FONT_STYLE_KEY, DEFAULT_FONT_STYLE); final int defaultFontSize = PREFS.getInt(key + "." + FONT_SIZE_KEY, DEFAULT_FONT_SIZE); final int defaultSignificantDigits = PREFS.getInt(key + "." + SIGNIFICANT_DIGITS_KEY, DEFAULT_SIGNIFICANT_DIGITS); final String defaultNumberFormatting = PREFS.get(key + "." + NUMBER_FORMATTING_KEY, DEFAULT_NUMBER_FORMATTING); labelPainter.setFont(new Font(defaultFontName, defaultFontStyle, defaultFontSize)); labelPainter.setNumberFormat(new DecimalFormat(defaultNumberFormatting)); optionsPanel = new ControllerOptionsPanel(2, 2); titleCheckBox = new JCheckBox(getTitle()); titleCheckBox.setSelected(labelPainter.isVisible()); displayAttributeCombo = new JComboBox(new String[] { "No attributes" }); new AttributeComboHelper(displayAttributeCombo, treeViewer, intent).addListener(new AttributeComboHelperListener() { @Override public void attributeComboChanged() { String attribute = (String) displayAttributeCombo.getSelectedItem(); labelPainter.setDisplayAttribute(attribute); } }); colourAttributeCombo = new JComboBox(new String[] { "No attributes" }); new AttributeComboHelper(colourAttributeCombo, treeViewer, "User selection", intent).addListener(new AttributeComboHelperListener() { @Override public void attributeComboChanged() { String attribute = (String) colourAttributeCombo.getSelectedItem(); setupLabelDecorator(); } }); final JButton setupColourButton = new JButton("Colour"); this.colourController = colourController; colourController.setupControls(colourAttributeCombo, setupColourButton); colourController.addControllerListener(new ControllerListener() { @Override public void controlsChanged() { setupLabelDecorator(); } }); final JButton fontButton = new JButton(new AbstractAction("Font") { public void actionPerformed(ActionEvent e) { final Font font = labelPainter.getFont(); if (fontDialog == null) { fontDialog = new FontDialog(frame); } int result = fontDialog.showDialog(font); if (result != JOptionPane.CANCEL_OPTION) { labelPainter.setFont(fontDialog.getFont()); } } }); Font font = labelPainter.getFont(); fontSizeSpinner = new JSpinner(new SpinnerNumberModel(font.getSize(), 0.01, 48, 1)); fontSizeSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final float size = ((Double) fontSizeSpinner.getValue()).floatValue(); Font font = labelPainter.getFont().deriveFont(size); labelPainter.setFont(font); } }); JPanel panel = new JPanel(); panel.setOpaque(false); panel.setLayout(new BoxLayout(panel, BoxLayout.LINE_AXIS)); ControllerOptionsPanel.setComponentLook(setupColourButton); ControllerOptionsPanel.setComponentLook(fontButton); panel.add(setupColourButton); panel.add(fontButton); NumberFormat format = labelPainter.getNumberFormat(); int digits = format.getMaximumFractionDigits(); numericalFormatCombo = new JComboBox(new String[] { "Decimal", "Scientific", "Percent", "Roman"}); numericalFormatCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { String formatType = (String) numericalFormatCombo.getSelectedItem(); final int digits = (Integer) digitsSpinner.getValue(); NumberFormat format = null; if (formatType.equals("Decimal")) { format = new DecimalFormat(DECIMAL_NUMBER_FORMATTING); } else if (formatType.equals("Scientific")) { format = new DecimalFormat(SCIENTIFIC_NUMBER_FORMATTING); } else if (formatType.equals("Percent")) { format = new PercentFormat(); } else if (formatType.equals("Roman")) { format = new RomanFormat(); } format.setMaximumFractionDigits(digits); labelPainter.setNumberFormat(format); } }); digitsSpinner = new JSpinner(new SpinnerNumberModel(digits, defaultSignificantDigits, 14, 1)); digitsSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final int digits = (Integer)digitsSpinner.getValue(); NumberFormat format = labelPainter.getNumberFormat(); format.setMaximumFractionDigits(digits); labelPainter.setNumberFormat(format); } }); // labelPainter.addPainterListener(new PainterListener() { // public void painterChanged() { // // } // public void painterSettingsChanged() { // } // public void attributesChanged() { // setupAttributes(); // } // }); final JLabel label1 = optionsPanel.addComponentWithLabel("Display:", displayAttributeCombo); final JLabel label2 = optionsPanel.addComponentWithLabel("Colour by:", colourAttributeCombo); final JLabel label3 = optionsPanel.addComponentWithLabel("Font Size:", fontSizeSpinner); final JLabel label4 = optionsPanel.addComponentWithLabel("Setup:", panel); final JLabel label5 = optionsPanel.addComponentWithLabel("Format:", numericalFormatCombo); final JLabel label6 = optionsPanel.addComponentWithLabel("Sig. Digits:", digitsSpinner); addComponent(label1); addComponent(displayAttributeCombo); addComponent(label2); addComponent(colourAttributeCombo); addComponent(label3); addComponent(setupColourButton); addComponent(fontButton); addComponent(label4); addComponent(fontSizeSpinner); addComponent(label5); addComponent(numericalFormatCombo); addComponent(label6); addComponent(digitsSpinner); enableComponents(titleCheckBox.isSelected()); titleCheckBox.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { enableComponents(titleCheckBox.isSelected()); labelPainter.setVisible(titleCheckBox.isSelected()); } }); } private void setupLabelDecorator() { Decorator colourDecorator = colourController.getColourDecorator(colourAttributeCombo, userLabelDecorator); CompoundDecorator compoundDecorator = new CompoundDecorator(); compoundDecorator.addDecorator(colourDecorator); AttributableDecorator fontDecorator = new AttributableDecorator(); userLabelDecorator.setFontAttributeName("!font"); compoundDecorator.addDecorator(fontDecorator); labelPainter.setTextDecorator(compoundDecorator); } public JComponent getTitleComponent() { return titleCheckBox; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { titleCheckBox.setSelected((Boolean) settings.get(key + "." + IS_SHOWN)); displayAttributeCombo.setSelectedItem(settings.get(key + "." + DISPLAY_ATTRIBUTE_KEY)); colourAttributeCombo.setSelectedItem(settings.get(key + "." + COLOR_ATTRIBUTE_KEY)); String name = (String)settings.get(key + "." + FONT_NAME_KEY); int size = ((Number)settings.get(key + "." + FONT_SIZE_KEY)).intValue(); int style = (Integer)settings.get(key + "." + FONT_STYLE_KEY); labelPainter.setFont(new Font(name, style, size)); digitsSpinner.setValue((Integer) settings.get(key + "." + SIGNIFICANT_DIGITS_KEY)); } public void getSettings(Map settings) { settings.put(key+"."+IS_SHOWN, titleCheckBox.isSelected()); settings.put(key+"."+DISPLAY_ATTRIBUTE_KEY, displayAttributeCombo.getSelectedItem().toString()); settings.put(key+"."+COLOR_ATTRIBUTE_KEY, colourAttributeCombo.getSelectedItem().toString()); Font font = labelPainter.getFont(); settings.put(key+"."+FONT_NAME_KEY, font.getName()); settings.put(key+"."+FONT_SIZE_KEY, font.getSize()); settings.put(key+"."+FONT_STYLE_KEY, font.getStyle()); settings.put(key+"."+SIGNIFICANT_DIGITS_KEY, digitsSpinner.getValue()); } public String getTitle() { return title; } private final AttributeColourController colourController; private final JCheckBox titleCheckBox; private final OptionsPanel optionsPanel; private final JComboBox displayAttributeCombo; private final JSpinner fontSizeSpinner; private FontDialog fontDialog = null; private final JComboBox numericalFormatCombo; private final JSpinner digitsSpinner; private final String title; private final String key; private final LabelPainter labelPainter; private final AttributableDecorator userLabelDecorator; private final JComboBox colourAttributeCombo; } figtree-1.4.3/src/figtree/treeviewer/painters/LegendPainter.java000077500000000000000000000207471277473563300250100ustar00rootroot00000000000000/* * LegendPainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.AttributeColourController; import figtree.treeviewer.TreePane; import figtree.treeviewer.decorators.*; import jam.controlpalettes.ControlPalette; import java.awt.*; import java.awt.geom.Line2D; import java.awt.geom.Rectangle2D; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class LegendPainter extends LabelPainter implements ScalePainter { public final static int CONTINUOUS_LENGTH = 320; public LegendPainter(AttributeColourController attributeColourController) { super(null); this.attributeColourController = attributeColourController; } public void setTreePane(TreePane treePane) { this.treePane = treePane; } public Decorator getBorderDecorator() { return borderDecorator; } public void setBorderDecorator(Decorator borderDecorator) { this.borderDecorator = borderDecorator; firePainterSettingsChanged(); } public Decorator getTextDecorator() { return textDecorator; } public void setTextDecorator(Decorator textDecorator) { this.textDecorator = textDecorator; firePainterSettingsChanged(); } public Rectangle2D calibrate(Graphics2D g2, TreePane treePane) { final Font oldFont = g2.getFont(); if (textDecorator != null) { g2.setFont(textDecorator.getFont(getFont())); } else { g2.setFont(getFont()); } FontMetrics fm = g2.getFontMetrics(); preferredHeight = fm.getHeight(); preferredWidth = 0; if (colourDecorator instanceof DiscreteColourDecorator) { for (Object value : ((DiscreteColourDecorator)colourDecorator).getValues()) { Rectangle2D rect = fm.getStringBounds(value.toString(), g2); if (rect.getWidth() > preferredWidth) { preferredWidth = rect.getWidth(); } } } else if (colourDecorator instanceof ContinuousColourDecorator){ // draw a continuous legend ContinuousScale scale = ((ContinuousColourDecorator)colourDecorator).getContinuousScale(); double min = scale.getMinValue(); double max = scale.getMaxValue(); Rectangle2D rect = g2.getFontMetrics().getStringBounds(getNumberFormat().format(max), g2); if (rect.getWidth() > preferredWidth) { preferredWidth = rect.getWidth(); } rect = g2.getFontMetrics().getStringBounds(getNumberFormat().format(min), g2); if (rect.getWidth() > preferredWidth) { preferredWidth = rect.getWidth(); } } else if (colourDecorator != null) { throw new IllegalArgumentException("Unrecognized ColourDecorator class"); } g2.setFont(oldFont); preferredWidth += insets.left + insets.right + fm.getHeight() * 2; return new Rectangle2D.Double(0.0, 0.0, preferredWidth, preferredHeight); } public void paint(Graphics2D g2, TreePane treePane, Justification justification, Rectangle2D bounds) { if (colourDecorator == null) { return; } String attribute = colourDecorator.getAttributeName(); if (TreePane.DEBUG_OUTLINE) { g2.setPaint(Color.red); g2.draw(bounds); } Font oldFont = g2.getFont(); Paint oldPaint = g2.getPaint(); Stroke oldStroke = g2.getStroke(); if (getBackground() != null) { g2.setPaint(getBackground()); g2.fill(bounds); } if (getBorderPaint() != null && getBorderStroke() != null) { g2.setPaint(getBorderPaint()); g2.setStroke(getBorderStroke()); g2.draw(bounds); } g2.setFont(getFont()); Rectangle2D labelBounds = g2.getFontMetrics().getStringBounds("ty", g2); // vertical inset float y = (float)(insets.top); float yOffset = (float)g2.getFontMetrics().getAscent(); float xOffset1 = (float)(insets.left); float yDelta = (float)labelBounds.getHeight() * 1.5F; float xOffset2 = (float)(insets.left + labelBounds.getHeight() * 2); g2.setPaint(Color.BLACK); g2.drawString(attribute, xOffset1, y + yOffset); y += yDelta; if (colourDecorator instanceof DiscreteColourDecorator) { for (Object value : ((DiscreteColourDecorator)colourDecorator).getValues()) { g2.setPaint(((DiscreteColourDecorator)colourDecorator).getColor(value)); Rectangle2D rect = new Rectangle2D.Double(xOffset1, y, labelBounds.getHeight(), labelBounds.getHeight()); g2.fill(rect); g2.drawString(value.toString(), xOffset2, y + yOffset); y += yDelta; } } else if (colourDecorator instanceof ContinuousColourDecorator){ // draw a continuous legend ContinuousScale scale = ((ContinuousColourDecorator)colourDecorator).getContinuousScale(); double min = scale.getMinValue(); double max = scale.getMaxValue(); double delta = (max - min) / CONTINUOUS_LENGTH; final String label = "0.0"; labelBounds = g2.getFontMetrics().getStringBounds(label, g2); float y0 = y; double v = max; for (int i = 0; i < CONTINUOUS_LENGTH; i++) { g2.setPaint(((ContinuousColourDecorator)colourDecorator).getColourForValue(v)); Rectangle2D rect = new Rectangle2D.Double(xOffset1, y, labelBounds.getHeight(), 1); g2.fill(rect); y += 1; v -= delta; } g2.setPaint(Color.BLACK); g2.drawString(getNumberFormat().format(max), xOffset2, y0 + (yOffset / 2)); g2.drawString(getNumberFormat().format(min), xOffset2, y + (yOffset / 2)); Line2D line = new Line2D.Double(xOffset1, y0, xOffset1 + labelBounds.getHeight() * 1.25, y0); g2.draw(line); line = new Line2D.Double(xOffset1, y, xOffset1 + labelBounds.getHeight() * 1.25, y); g2.draw(line); line = new Line2D.Double(xOffset1, y0, xOffset1, y); g2.draw(line); } else { throw new IllegalArgumentException("Unrecognized ColourDecorator class"); } g2.setFont(oldFont); g2.setPaint(oldPaint); g2.setStroke(oldStroke); } public double getPreferredWidth() { return preferredWidth; } public double getPreferredHeight() { return preferredHeight; } public double getHeightBound() { return preferredHeight; } public void setColourDecorator(ColourDecorator colourDecorator) { this.colourDecorator = colourDecorator; firePainterChanged(); } public void setControlPalette(ControlPalette controlPalette) { // nothing to do } protected ColourDecorator colourDecorator; private double preferredHeight; private double preferredWidth; protected final AttributeColourController attributeColourController; protected TreePane treePane; private Decorator textDecorator = null; private Decorator borderDecorator = null; private Insets insets = new Insets(8, 8, 8, 8); @Override public String getDisplayAttribute() { throw new UnsupportedOperationException("getDisplayAttribute not implmented"); } @Override public void setDisplayAttribute(String displayAttribute) { throw new UnsupportedOperationException("setDisplayAttribute not implmented - use setColourDecorator directly"); } }figtree-1.4.3/src/figtree/treeviewer/painters/LegendPainterController.java000077500000000000000000000250501277473563300270440ustar00rootroot00000000000000/* * LegendPainterController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.AttributeColourController; import figtree.treeviewer.ControllerOptionsPanel; import figtree.treeviewer.TreeViewer; import figtree.treeviewer.decorators.ColourDecorator; import figtree.ui.PercentFormat; import figtree.ui.RomanFormat; import jam.controlpalettes.AbstractController; import jam.controlpalettes.ControllerListener; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.text.DecimalFormat; import java.text.NumberFormat; import java.util.*; import java.util.prefs.Preferences; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class LegendPainterController extends AbstractController { public static Preferences PREFS = Preferences.userNodeForPackage(TreeViewer.class); public static final String CONTROLLER_KEY = "legend"; public static final String FONT_NAME_KEY = "fontName"; public static final String FONT_SIZE_KEY = "fontSize"; public static final String FONT_STYLE_KEY = "fontStyle"; public static final String ATTRIBUTE_KEY = "attribute"; public static final String NUMBER_FORMATTING_KEY = "numberFormatting"; public static final String SIGNIFICANT_DIGITS_KEY = "significantDigits"; // The defaults if there is nothing in the preferences public static String DEFAULT_FONT_NAME = "sansserif"; public static int DEFAULT_FONT_SIZE = 10; public static int DEFAULT_FONT_STYLE = Font.PLAIN; public static String DEFAULT_ATTRIBUTE_KEY = ""; public static String DECIMAL_NUMBER_FORMATTING = "#.####"; public static String SCIENTIFIC_NUMBER_FORMATTING = "0.###E0"; public static int DEFAULT_SIGNIFICANT_DIGITS = 2; public static String DEFAULT_NUMBER_FORMATTING = DECIMAL_NUMBER_FORMATTING; public LegendPainterController(final LegendPainter legendPainter, final AttributeColourController colourController, final TreeViewer treeViewer) { final String defaultFontName = PREFS.get(CONTROLLER_KEY + "." + FONT_NAME_KEY, DEFAULT_FONT_NAME); final int defaultFontStyle = PREFS.getInt(CONTROLLER_KEY + "." + FONT_STYLE_KEY, DEFAULT_FONT_STYLE); final int defaultFontSize = PREFS.getInt(CONTROLLER_KEY + "." + FONT_SIZE_KEY, DEFAULT_FONT_SIZE); final int defaultSignificantDigits = PREFS.getInt(CONTROLLER_KEY + "." + SIGNIFICANT_DIGITS_KEY, DEFAULT_SIGNIFICANT_DIGITS); final String defaultNumberFormatting = PREFS.get(CONTROLLER_KEY + "." + NUMBER_FORMATTING_KEY, DEFAULT_NUMBER_FORMATTING); final String attribute = PREFS.get(CONTROLLER_KEY + "." + ATTRIBUTE_KEY, DEFAULT_ATTRIBUTE_KEY); legendPainter.setFont(new Font(defaultFontName, defaultFontStyle, defaultFontSize)); // legendPainter.setDisplayAttribute(attribute); legendPainter.setNumberFormat(new DecimalFormat(defaultNumberFormatting)); optionsPanel = new ControllerOptionsPanel(2, 2); titleCheckBox = new JCheckBox(getTitle()); titleCheckBox.setSelected(legendPainter.isVisible()); attributeCombo = new JComboBox(); new AttributeComboHelper(attributeCombo, treeViewer).addListener(new AttributeComboHelperListener() { @Override public void attributeComboChanged() { ColourDecorator colourDecorator = (ColourDecorator)colourController.getColourDecorator(attributeCombo, null); legendPainter.setColourDecorator(colourDecorator); } }); colourController.setupControls(attributeCombo, null); colourController.addControllerListener(new ControllerListener() { @Override public void controlsChanged() { ColourDecorator colourDecorator = (ColourDecorator)colourController.getColourDecorator(attributeCombo, null); legendPainter.setColourDecorator(colourDecorator); } }); // attributeCombo.addActionListener(new ActionListener() { // public void actionPerformed(ActionEvent event) { // legendPainter.setDisplayAttribute((String) attributeCombo.getSelectedItem()); // } // }); Font font = legendPainter.getFont(); fontSizeSpinner = new JSpinner(new SpinnerNumberModel(font.getSize(), 0.01, 48, 1)); fontSizeSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final float size = ((Double) fontSizeSpinner.getValue()).floatValue(); Font font = legendPainter.getFont().deriveFont(size); legendPainter.setFont(font); } }); NumberFormat format = legendPainter.getNumberFormat(); int digits = format.getMaximumFractionDigits(); numericalFormatCombo = new JComboBox(new String[] { "Decimal", "Scientific", "Percent", "Roman"}); numericalFormatCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { String formatType = (String) numericalFormatCombo.getSelectedItem(); final int digits = (Integer) digitsSpinner.getValue(); NumberFormat format = null; if (formatType.equals("Decimal")) { format = new DecimalFormat(DECIMAL_NUMBER_FORMATTING); } else if (formatType.equals("Scientific")) { format = new DecimalFormat(SCIENTIFIC_NUMBER_FORMATTING); } else if (formatType.equals("Percent")) { format = new PercentFormat(); } else if (formatType.equals("Roman")) { format = new RomanFormat(); } format.setMaximumFractionDigits(digits); legendPainter.setNumberFormat(format); } }); digitsSpinner = new JSpinner(new SpinnerNumberModel(digits, defaultSignificantDigits, 14, 1)); digitsSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final int digits = (Integer)digitsSpinner.getValue(); NumberFormat format = legendPainter.getNumberFormat(); format.setMaximumFractionDigits(digits); legendPainter.setNumberFormat(format); } }); final JLabel label1 = optionsPanel.addComponentWithLabel("Attribute:", attributeCombo); final JLabel label2 = optionsPanel.addComponentWithLabel("Font Size:", fontSizeSpinner); final JLabel label3 = optionsPanel.addComponentWithLabel("Format:", numericalFormatCombo); final JLabel label4 = optionsPanel.addComponentWithLabel("Sig. Digits:", digitsSpinner); addComponent(label1); addComponent(attributeCombo); addComponent(label2); addComponent(fontSizeSpinner); addComponent(label3); addComponent(numericalFormatCombo); addComponent(label4); addComponent(digitsSpinner); enableComponents(titleCheckBox.isSelected()); titleCheckBox.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent changeEvent) { enableComponents(titleCheckBox.isSelected()); legendPainter.setVisible(titleCheckBox.isSelected()); } }); // autoScaleCheck.addActionListener(new ActionListener() { // @Override // public void actionPerformed(ActionEvent actionEvent) { // public void stateChanged(ChangeEvent changeEvent) { // if (autoScaleCheck.isSelected()) { // scaleBarPainter.setAutomaticScale(true); // double range = scaleBarPainter.getScaleRange(); // scaleRangeText.setValue(range); // label1.setEnabled(false); // scaleRangeText.setEnabled(false); // } else { // label1.setEnabled(true); // scaleRangeText.setEnabled(true); // scaleBarPainter.setAutomaticScale(false); // } // } // }); } public JComponent getTitleComponent() { return titleCheckBox; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { } public void setSettings(Map settings) { titleCheckBox.setSelected((Boolean) settings.get(CONTROLLER_KEY + "." + IS_SHOWN)); attributeCombo.setSelectedItem((String) settings.get(CONTROLLER_KEY + "." + ATTRIBUTE_KEY)); fontSizeSpinner.setValue((Double)settings.get(CONTROLLER_KEY + "." + FONT_SIZE_KEY)); digitsSpinner.setValue((Integer) settings.get(CONTROLLER_KEY + "." + SIGNIFICANT_DIGITS_KEY)); } public void getSettings(Map settings) { settings.put(CONTROLLER_KEY + "." + IS_SHOWN, titleCheckBox.isSelected()); settings.put(CONTROLLER_KEY + "." + ATTRIBUTE_KEY, attributeCombo.getSelectedItem()); settings.put(CONTROLLER_KEY + "." + FONT_SIZE_KEY, fontSizeSpinner.getValue()); settings.put(CONTROLLER_KEY + "." + SIGNIFICANT_DIGITS_KEY, digitsSpinner.getValue()); } private final JCheckBox titleCheckBox; private final OptionsPanel optionsPanel; private final JComboBox attributeCombo; private final JSpinner fontSizeSpinner; private final JComboBox numericalFormatCombo; private final JSpinner digitsSpinner; public String getTitle() { return "Legend"; } } figtree-1.4.3/src/figtree/treeviewer/painters/NodeBarController.java000077500000000000000000000124221277473563300256340ustar00rootroot00000000000000/* * NodeBarController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.TreeViewer; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeListener; import javax.swing.event.ChangeEvent; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemListener; import java.awt.event.ItemEvent; import java.awt.*; import java.util.*; import java.util.prefs.Preferences; import figtree.treeviewer.ControllerOptionsPanel; import jebl.util.Attributable; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class NodeBarController extends AbstractController { private static Preferences PREFS = Preferences.userNodeForPackage(TreeViewer.class); private static final String NODE_BARS_KEY = "nodeBars"; public static final String DISPLAY_ATTRIBUTE_KEY = "displayAttribute"; private static final String BAR_WIDTH_KEY = "barWidth"; private static float DEFAULT_BAR_WIDTH = 4.0f; public NodeBarController(String title, final NodeBarPainter nodeBarPainter, final TreeViewer treeViewer) { this.title = title; this.nodeBarPainter = nodeBarPainter; final float defaultBarWidth = PREFS.getFloat(BAR_WIDTH_KEY, DEFAULT_BAR_WIDTH); optionsPanel = new ControllerOptionsPanel(2, 2); titleCheckBox = new JCheckBox(getTitle()); titleCheckBox.setSelected(this.nodeBarPainter.isVisible()); displayAttributeCombo = new JComboBox(); new AttributeComboHelper(displayAttributeCombo, treeViewer, LabelPainter.PainterIntent.RANGE).addListener(new AttributeComboHelperListener() { @Override public void attributeComboChanged() { String attribute = (String) displayAttributeCombo.getSelectedItem(); nodeBarPainter.setDisplayAttribute(attribute); } }); barWidthSpinner = new JSpinner(new SpinnerNumberModel(defaultBarWidth, 0.01, 48.0, 1.0)); barWidthSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { float lineWidth = ((Double) barWidthSpinner.getValue()).floatValue(); nodeBarPainter.setStroke(new BasicStroke(lineWidth, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL)); } }); nodeBarPainter.setStroke(new BasicStroke(defaultBarWidth, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL)); final JLabel label1 = optionsPanel.addComponentWithLabel("Display:", displayAttributeCombo); final JLabel label2 = optionsPanel.addComponentWithLabel("Bar Width:", barWidthSpinner); addComponent(label1); addComponent(displayAttributeCombo); addComponent(label2); addComponent(barWidthSpinner); enableComponents(titleCheckBox.isSelected()); titleCheckBox.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { enableComponents(titleCheckBox.isSelected()); nodeBarPainter.setVisible(titleCheckBox.isSelected()); } }); } public JComponent getTitleComponent() { return titleCheckBox; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { titleCheckBox.setSelected((Boolean) settings.get(NODE_BARS_KEY + "." + IS_SHOWN)); displayAttributeCombo.setSelectedItem((String) settings.get(NODE_BARS_KEY + "." + DISPLAY_ATTRIBUTE_KEY)); barWidthSpinner.setValue((Double)settings.get(NODE_BARS_KEY + "." + BAR_WIDTH_KEY)); } public void getSettings(Map settings) { settings.put(NODE_BARS_KEY + "." + IS_SHOWN, titleCheckBox.isSelected()); settings.put(NODE_BARS_KEY + "." + DISPLAY_ATTRIBUTE_KEY, displayAttributeCombo.getSelectedItem()); settings.put(NODE_BARS_KEY + "." + BAR_WIDTH_KEY, barWidthSpinner.getValue()); } private final JCheckBox titleCheckBox; private final OptionsPanel optionsPanel; private JComboBox displayAttributeCombo; public String getTitle() { return title; } private final String title; private final NodeBarPainter nodeBarPainter; private final JSpinner barWidthSpinner; } figtree-1.4.3/src/figtree/treeviewer/painters/NodeBarPainter.java000077500000000000000000000110551277473563300251140ustar00rootroot00000000000000/* * NodeBarPainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.TreePane; import jebl.evolution.graphs.Node; import jebl.evolution.trees.RootedTree; import jebl.evolution.trees.Tree; import java.awt.*; import java.awt.geom.Line2D; import java.awt.geom.Rectangle2D; import java.util.Collection; import java.util.TreeSet; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class NodeBarPainter extends NodePainter { public NodeBarPainter() { } public void setTreePane(TreePane treePane) { this.treePane = treePane; } public Line2D getNodeBar() { return nodeBar; } public Rectangle2D calibrate(Graphics2D g2, Node node) { RootedTree tree = treePane.getTree(); nodeBar = null; maxHeight = 0.0; Line2D barPath = treePane.getTreeLayoutCache().getNodeShapePath(node); if (barPath != null) { double height = tree.getHeight(node); double upper = height; double lower = height; boolean hasBar = false; Object[] values = (Object[])node.getAttribute(displayAttribute); if (values != null) { Object value = values[0]; if (value != null ) { if (value instanceof Number) { lower = ((Number)value).doubleValue(); } else { lower = Double.parseDouble(value.toString()); } hasBar = true; } else { // todo - warn the user somehow? } value = values[1]; if (value != null ) { if (value instanceof Number) { upper = ((Number)value).doubleValue(); } else { upper = Double.parseDouble(value.toString()); } hasBar = true; } else { // todo - warn the user somehow? } } if (hasBar) { if (upper > maxHeight) { maxHeight = upper; } // x1,y1 is the node point double x1 = barPath.getX1(); double y1 = barPath.getY1(); // x2,y2 is 1.0 units higher than the node double x2 = barPath.getX2(); double y2 = barPath.getY2(); // dx,dy is the change in x,y for one unit of height double dx = x2 - x1; double dy = y2 - y1; double h1 = lower - height; double h2 = upper - height; nodeBar = new Line2D.Double( x1 + (dx * h1), y1 + (dy * h1), x1 + (dx * h2), y1 + (dy * h2)); } } if (nodeBar == null) { return null; } return nodeBar.getBounds2D(); } public double getPreferredWidth() { return 1.0; } public double getPreferredHeight() { return 1.0; } public double getHeightBound() { return 1.0; } /** * The bounds define the shape of the nodeBar so just draw it * @param g2 * @param node * @param justification * @param barShape */ public void paint(Graphics2D g2, Node node, Justification justification, Shape barShape) { if (barShape != null) { Stroke stroke = getStroke(); Shape strokedOutline = stroke.createStrokedShape(barShape); g2.setPaint(getForeground()); g2.fill(strokedOutline); g2.setPaint(Color.black); g2.setStroke(new BasicStroke(0.5F)); g2.draw(strokedOutline); } } /** * The bounds define the shape of the nodeBar so just draw it * @param g2 * @param node * @param justification * @param bounds */ public void paint(Graphics2D g2, Node node, Justification justification, Rectangle2D bounds) { throw new UnsupportedOperationException("This version of paint is not used in NodeBarPainter"); } public String getDisplayAttributeName() { return displayAttribute; } public void setDisplayAttribute(String displayAttribute) { this.displayAttribute = displayAttribute; firePainterChanged(); } public double getMaxHeight() { return maxHeight; } private String displayAttribute = null; private TreePane treePane; private Line2D nodeBar = null; private double maxHeight; } figtree-1.4.3/src/figtree/treeviewer/painters/NodePainter.java000077500000000000000000000047401277473563300244720ustar00rootroot00000000000000/* * NodePainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import jebl.evolution.graphs.Node; import java.awt.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public abstract class NodePainter extends AbstractPainter { protected NodePainter() { } // Getters public Stroke getStroke() { return stroke; } public Paint getForeground() { return foreground; } public Paint getBackground() { return background; } public Paint getBorderPaint() { return borderPaint; } public Stroke getBorderStroke() { return borderStroke; } public boolean isVisible() { return visible; } // Setters public void setStroke(Stroke stroke) { this.stroke = stroke; firePainterChanged(); } public void setBackground(Paint background) { this.background = background; firePainterChanged(); } public void setBorder(Paint borderPaint, Stroke borderStroke) { this.borderPaint = borderPaint; this.borderStroke = borderStroke; firePainterChanged(); } public void setForeground(Paint foreground) { this.foreground = foreground; firePainterChanged(); } public void setVisible(boolean visible) { this.visible = visible; firePainterChanged(); } private Stroke stroke = new BasicStroke(1.0F, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL); private Paint foreground = Color.BLACK; private Paint background = null; private Paint borderPaint = null; private Stroke borderStroke = null; private boolean visible = true; } figtree-1.4.3/src/figtree/treeviewer/painters/NodeShapeController.java000077500000000000000000000342011277473563300261670ustar00rootroot00000000000000/* * NodeShapeController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.AttributeColourController; import figtree.treeviewer.TreeViewer; import figtree.treeviewer.decorators.Decorator; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.Map; import java.util.prefs.Preferences; import figtree.treeviewer.ControllerOptionsPanel; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class NodeShapeController extends AbstractController { public enum NodeType { INTERNAL, EXTERNAL, BOTH } private static Preferences PREFS = Preferences.userNodeForPackage(TreeViewer.class); private static final String IS_EXTERNAL = "isExternal"; private static final String IS_INTERNAL = "isInternal"; private static final String NODE_SHAPE_KEY = "nodeShape"; public static final String SHAPE_TYPE_KEY = "shapeType"; public static final String SCALE_TYPE_KEY = "scaleType"; public static final String SIZE_ATTRIBUTE_KEY = "sizeAttribute"; public static final String COLOUR_ATTRIBUTE_KEY = "colourAttribute"; private static final String SHAPE_SIZE_KEY = "size"; private static final String SHAPE_MIN_SIZE_KEY = "minSize"; public NodeShapeController(final String title, final NodeType type, final NodeShapePainter nodeShapePainter, final AttributeColourController colourController, final TreeViewer treeViewer) { this.title = title; this.type = type; final float defaultShapeSize = PREFS.getFloat(SHAPE_SIZE_KEY, (float)NodeShapePainter.MAX_SIZE); optionsPanel = new ControllerOptionsPanel(2, 2); titleCheckBox = new JCheckBox(getTitle()); titleCheckBox.setSelected(nodeShapePainter.isVisible()); titleCheckBox.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final boolean selected = titleCheckBox.isSelected(); nodeShapePainter.setVisible(selected); } }); final ControllerOptionsPanel nodeCheckPanel; if (type == NodeType.BOTH) { externalNodeCheck = new JCheckBox("external"); internalNodeCheck = new JCheckBox("internal"); ActionListener listener = new ActionListener() { public void actionPerformed(ActionEvent event) { nodeShapePainter.setNodeType(externalNodeCheck.isSelected(), internalNodeCheck.isSelected()); } }; externalNodeCheck.addActionListener(listener); internalNodeCheck.addActionListener(listener); nodeCheckPanel = new ControllerOptionsPanel(2, 2); nodeCheckPanel.setBorder(BorderFactory.createEmptyBorder()); nodeCheckPanel.addSpanningComponent(externalNodeCheck); nodeCheckPanel.addSpanningComponent(internalNodeCheck); externalNodeCheck.setSelected(nodeShapePainter.isExternal()); internalNodeCheck.setSelected(nodeShapePainter.isInternal()); } else { nodeCheckPanel = null; externalNodeCheck = null; internalNodeCheck = null; if (type == NodeType.EXTERNAL) { nodeShapePainter.setNodeType(true, false); } else if (type == NodeType.INTERNAL) { nodeShapePainter.setNodeType(false, true); } } shapeTypeCombo = new JComboBox(NodeShapePainter.ShapeType.values()); shapeTypeCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { nodeShapePainter.setShapeType((NodeShapePainter.ShapeType) shapeTypeCombo.getSelectedItem()); } }); scaleTypeCombo = new JComboBox(NodeShapePainter.ScaleType.values()); scaleTypeCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { nodeShapePainter.setScaleType((NodeShapePainter.ScaleType) scaleTypeCombo.getSelectedItem()); } }); sizeAttributeCombo = new JComboBox(); // AttributeComboHelper & listener set after other controls are created... colourAttributeCombo = new JComboBox(); JButton setupColourButton = new JButton("Colour"); colourController.setupControls(colourAttributeCombo, setupColourButton); shapeSizeSpinner = new JSpinner(new SpinnerNumberModel(defaultShapeSize, 0.0, 100.0, 1.0)); shapeSizeSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { double shapeSize = ((Double)shapeSizeSpinner.getValue()); nodeShapePainter.setMaxSize(shapeSize); } }); shapeMinSizeSpinner = new JSpinner(new SpinnerNumberModel(10.0, 0.0, 100.0, 1.0)); shapeMinSizeSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { double minSize = ((Double)shapeMinSizeSpinner.getValue()); nodeShapePainter.setMinSize(minSize); } }); outlineStrokeCombo = new JComboBox(new String[] {"None", "0.25", "0.5", "1.0", "2.0", "3.0", "4.0", "5.0"}); outlineStrokeCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { nodeShapePainter.setOutline((outlineStrokeCombo.getSelectedIndex() == 0 ? 0.0f : Float.parseFloat(outlineStrokeCombo.getSelectedItem().toString())), (Paint)outlinePaintCombo.getSelectedItem() ); } }); final Paint[] outlinePaints = {Color.black, Color.white}; outlinePaintCombo = new JComboBox(new String[] {"black", "white"}); outlinePaintCombo.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent event) { nodeShapePainter.setOutline((outlineStrokeCombo.getSelectedIndex() == 0 ? 0.0f : Float.parseFloat(outlineStrokeCombo.getSelectedItem().toString())), outlinePaints[outlinePaintCombo.getSelectedIndex()] ); } }); final JLabel label8; if (type == NodeType.BOTH) { label8 = optionsPanel.addComponentWithLabel("Show:", nodeCheckPanel); } else { label8 = null; } final JLabel label1 = optionsPanel.addComponentWithLabel("Shape:", shapeTypeCombo); final JLabel label2 = optionsPanel.addComponentWithLabel("Max size:", shapeSizeSpinner); final JLabel label3 = optionsPanel.addComponentWithLabel("Size by:", sizeAttributeCombo); final JLabel label4 = optionsPanel.addComponentWithLabel("Min size:", shapeMinSizeSpinner); final JLabel label5 = optionsPanel.addComponentWithLabel("Using:", scaleTypeCombo); optionsPanel.addSeparator(); final JLabel label6 = optionsPanel.addComponentWithLabel("Colour by:", colourAttributeCombo); final JLabel label7 = optionsPanel.addComponentWithLabel("Setup:", setupColourButton); final JLabel label9 = optionsPanel.addComponentWithLabel("Outline width:", outlineStrokeCombo); final JLabel label10 = optionsPanel.addComponentWithLabel("Outline colour:", outlinePaintCombo); new AttributeComboHelper(colourAttributeCombo, treeViewer, "User selection").addListener(new AttributeComboHelperListener() { @Override public void attributeComboChanged() { Decorator colourDecorator = colourController.getColourDecorator(colourAttributeCombo, null); nodeShapePainter.setColourDecorator(colourDecorator); } }); new AttributeComboHelper(sizeAttributeCombo, treeViewer, NodeShapePainter.FIXED, true, false).addListener(new AttributeComboHelperListener() { @Override public void attributeComboChanged() { String attribute = (String) sizeAttributeCombo.getSelectedItem(); nodeShapePainter.setSizeAttribute(attribute); if (attribute != null) { boolean isSelected = !attribute.equals(NodeShapePainter.FIXED); label4.setEnabled(isSelected); shapeMinSizeSpinner.setEnabled(isSelected); label5.setEnabled(isSelected); scaleTypeCombo.setEnabled(isSelected); } } }); // only needed if we want to change the options depending on // the choice of shapeTypeCombo // shapeTypeCombo.addActionListener(new ActionListener() { // public void actionPerformed(ActionEvent event) { // setupOptions(); // optionsPanel.validate(); // } // }); addComponent(label1); addComponent(shapeTypeCombo); if (type == NodeType.BOTH) { addComponent(label8); addComponent(externalNodeCheck); addComponent(internalNodeCheck); } addComponent(label2); addComponent(shapeSizeSpinner); addComponent(label3); addComponent(sizeAttributeCombo); addComponent(label4); addComponent(shapeMinSizeSpinner); addComponent(label5); addComponent(scaleTypeCombo); addComponent(label6); addComponent(colourAttributeCombo); addComponent(label7); addComponent(setupColourButton); addComponent(label9); addComponent(outlineStrokeCombo); addComponent(label10); addComponent(outlinePaintCombo); enableComponents(titleCheckBox.isSelected()); titleCheckBox.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { enableComponents(titleCheckBox.isSelected()); } }); } private void setupOptions() { // optionsPanel.removeAll(); fireControllerChanged(); } public JComponent getTitleComponent() { return titleCheckBox; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { String key = NODE_SHAPE_KEY + (type == NodeType.INTERNAL ? "Internal" : (type == NodeType.EXTERNAL ? "External" : "")); titleCheckBox.setSelected((Boolean)settings.get(key + "." + IS_SHOWN)); if (type == NodeType.BOTH) { externalNodeCheck.setSelected((Boolean) settings.get(key + "." + IS_EXTERNAL)); internalNodeCheck.setSelected((Boolean) settings.get(key + "." + IS_INTERNAL)); } shapeTypeCombo.setSelectedItem((NodeShapePainter.ShapeType.valueOf(settings.get(key + "." + SHAPE_TYPE_KEY).toString().toUpperCase()))); scaleTypeCombo.setSelectedItem((NodeShapePainter.ScaleType.valueOf(settings.get(key + "." + SCALE_TYPE_KEY).toString().toUpperCase()))); colourAttributeCombo.setSelectedItem((String) settings.get(key + "." + COLOUR_ATTRIBUTE_KEY)); sizeAttributeCombo.setSelectedItem((String) settings.get(key + "." + SIZE_ATTRIBUTE_KEY)); shapeSizeSpinner.setValue((Double)settings.get(key + "." + SHAPE_SIZE_KEY)); shapeMinSizeSpinner.setValue((Double) settings.get(key + "." + SHAPE_MIN_SIZE_KEY)); } public void getSettings(Map settings) { String key = NODE_SHAPE_KEY + (type == NodeType.INTERNAL ? "Internal" : (type == NodeType.EXTERNAL ? "External" : "")); settings.put(key + "." + IS_SHOWN, titleCheckBox.isSelected()); if (type == NodeType.BOTH) { settings.put(key + "." + IS_EXTERNAL, externalNodeCheck.isSelected()); settings.put(key + "." + IS_INTERNAL, internalNodeCheck.isSelected()); } settings.put(key + "." + SHAPE_TYPE_KEY, shapeTypeCombo.getSelectedItem()); settings.put(key + "." + SCALE_TYPE_KEY, scaleTypeCombo.getSelectedItem()); settings.put(key + "." + COLOUR_ATTRIBUTE_KEY, colourAttributeCombo.getSelectedItem()); settings.put(key + "." + SIZE_ATTRIBUTE_KEY, sizeAttributeCombo.getSelectedItem()); settings.put(key + "." + SHAPE_SIZE_KEY, shapeSizeSpinner.getValue()); settings.put(key + "." + SHAPE_MIN_SIZE_KEY, shapeMinSizeSpinner.getValue()); } private final JCheckBox titleCheckBox; private final OptionsPanel optionsPanel; private final JCheckBox externalNodeCheck; private final JCheckBox internalNodeCheck; private final JComboBox shapeTypeCombo; private final JComboBox scaleTypeCombo; private final JComboBox sizeAttributeCombo; private final JComboBox colourAttributeCombo; private final JSpinner shapeSizeSpinner; private final JSpinner shapeMinSizeSpinner; private final JComboBox outlineStrokeCombo; private final JComboBox outlinePaintCombo; public String getTitle() { return title; } private final String title; private final NodeType type; } figtree-1.4.3/src/figtree/treeviewer/painters/NodeShapePainter.java000077500000000000000000000174601277473563300254560ustar00rootroot00000000000000/* * NodeShapePainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.TreePane; import figtree.treeviewer.decorators.ContinuousScale; import figtree.treeviewer.decorators.Decorator; import jebl.evolution.graphs.Node; import java.awt.*; import java.awt.geom.*; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class NodeShapePainter extends NodePainter { public static final String FIXED = "Fixed"; public static final double MAX_SIZE = 4.0; public static final double MIN_SIZE = 0.0; public enum ShapeType { CIRCLE("Circle"), RECTANGLE("Rectangle"), DIAMOND("Diamond"); ShapeType(String name) { this.name = name; } public String getName() { return name; } public String toString() { return name; } private final String name; } public enum ScaleType { WIDTH("Width"), AREA("Area"); ScaleType(String name) { this.name = name; } public String getName() { return name; } public String toString() { return name; } private final String name; } public NodeShapePainter() { } public void setTreePane(TreePane treePane) { this.treePane = treePane; } public Rectangle2D calibrate(Graphics2D g2, Node node) { Line2D shapePath = treePane.getTreeLayoutCache().getNodeShapePath(node); if (shapePath != null) { double x1 = shapePath.getX1(); double y1 = shapePath.getY1(); Shape nodeShape = createNodeShape(node, x1, y1); if (nodeShape != null) { return nodeShape.getBounds2D(); } } return null; } public void setShapeType(ShapeType shapeType) { this.shapeType = shapeType; firePainterChanged(); } public void setScaleType(ScaleType scaleType) { this.scaleType = scaleType; firePainterChanged(); } public void setNodeType(boolean external, boolean internal) { this.external = external; this.internal = internal; firePainterChanged(); } public boolean isExternal() { return external; } public boolean isInternal() { return internal; } public double getPreferredWidth() { return 1.0; } public double getPreferredHeight() { return 1.0; } public double getHeightBound() { return 1.0; } /** * The bounds define the shapeType of the nodeBar so just draw it * @param g2 * @param node */ public void paint(Graphics2D g2, Node node, Point2D point, AffineTransform transform) { Shape nodeShape = createNodeShape(node, point.getX(), point.getY()); nodeShape = transform.createTransformedShape(nodeShape); Paint paint = getForeground(); if (colourDecorator != null) { colourDecorator.setItem(node); paint = colourDecorator.getPaint(paint); } g2.setPaint(paint); g2.fill(nodeShape); if (outlineStroke > 0.0F) { g2.setPaint(outlinePaint); g2.setStroke(new BasicStroke(outlineStroke)); g2.draw(nodeShape); } } /** * The bounds define the shapeType of the nodeBar so just draw it * @param g2 * @param node * @param justification * @param bounds */ public void paint(Graphics2D g2, Node node, Justification justification, Rectangle2D bounds) { throw new UnsupportedOperationException("This version of paint is not used in NodeShapePainter"); } public void setMaxSize(double maxSize) { this.maxSize = maxSize; firePainterChanged(); } public void setMinSize(double minSize) { this.minSize = minSize; firePainterChanged(); } public void setSizeAttribute(String sizeAttribute) { this.sizeAttribute = sizeAttribute; sizeScale = new ContinuousScale(sizeAttribute, treePane.getTree().getNodes()); firePainterChanged(); } public void setColourDecorator(Decorator colourDecorator) { this.colourDecorator = colourDecorator; firePainterChanged(); } public void setOutline(final float outlineStroke, final Paint outlinePaint) { this.outlineStroke = outlineStroke; this.outlinePaint = outlinePaint; firePainterChanged(); } private Shape createNodeShape(Node node, double x, double y) { double size = maxSize; if (sizeAttribute != null && !sizeAttribute.equals(FIXED)) { Object valueObject = node.getAttribute(sizeAttribute); double value = sizeScale.getValue(valueObject); if (scaleType == ScaleType.AREA) { double minArea = getShapeArea(minSize); double maxArea = getShapeArea(maxSize + minSize); size = getShapeWidth(((maxArea - minArea) * value) + minArea); } else { size = minSize + (maxSize * value); } } if (size > 0.0) { switch (shapeType) { case CIRCLE: return new Ellipse2D.Double(x - (size * 0.5), y - (size * 0.5), size, size); case RECTANGLE: return new Rectangle2D.Double(x - (size * 0.5), y - (size * 0.5), size, size); case DIAMOND: Shape shape = new Rectangle2D.Double(x - (size * 0.5), y - (size * 0.5), size, size); return AffineTransform.getRotateInstance(Math.PI / 4.0, x, y).createTransformedShape(shape); } throw new IllegalArgumentException("Unknown node shapeType type"); } return null; } private double getShapeArea(double width) { switch (shapeType) { case CIRCLE: double radius = width * 0.5; return Math.PI * radius * radius; case RECTANGLE: case DIAMOND: return width * width; } throw new IllegalArgumentException("Unknown node shapeType type"); } private double getShapeWidth(double area) { switch (shapeType) { case CIRCLE: return 2.0 * Math.sqrt(area / Math.PI); case RECTANGLE: case DIAMOND: return Math.sqrt(area); } throw new IllegalArgumentException("Unknown node shapeType type"); } private double maxSize = MAX_SIZE; private double minSize = MIN_SIZE; private ShapeType shapeType = ShapeType.CIRCLE; private ScaleType scaleType = ScaleType.WIDTH; private String sizeAttribute = null; private boolean external = true; private boolean internal = true; private Decorator colourDecorator = null; private ContinuousScale sizeScale = null; private float outlineStroke = 0.5f; private Paint outlinePaint = Color.black; private TreePane treePane; } figtree-1.4.3/src/figtree/treeviewer/painters/Painter.java000077500000000000000000000046251277473563300236660ustar00rootroot00000000000000/* * Painter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.TreePane; import java.awt.*; import java.awt.geom.Rectangle2D; /** * A painter draws a particular decoration onto the tree within a * rectangle. * * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface Painter { public enum Orientation { TOP, LEFT, BOTTOM, RIGHT } public enum Justification { FLUSH, LEFT, RIGHT, CENTER } /** * Called when the painter is installed in a TreePane. Gives the * painter a handle on the TreePane so that it get additional * information. * @param treePane */ void setTreePane(TreePane treePane); /** * If this is false then the painter should not be displayed. * @return is visible? */ boolean isVisible(); /** * Called to calibrate the painters for a given graphics context. This should * work out the preferred width and height (perhaps for the current font). * @param g2 * @param item */ Rectangle2D calibrate(Graphics2D g2, T item); /** * Called to actually paint into the current graphics context. The painter should * respect the bounds. * @param g2 * @param item * @param justification * @param bounds */ void paint(Graphics2D g2, T item, Justification justification, Rectangle2D bounds); double getPreferredWidth(); double getPreferredHeight(); double getHeightBound(); void addPainterListener(PainterListener listener); void removePainterListener(PainterListener listener); } figtree-1.4.3/src/figtree/treeviewer/painters/PainterListener.java000077500000000000000000000021201277473563300253600ustar00rootroot00000000000000/* * PainterListener.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface PainterListener { void painterChanged(); void painterSettingsChanged(); void attributesChanged(); } figtree-1.4.3/src/figtree/treeviewer/painters/ScaleAxisPainter.java000077500000000000000000000230021277473563300254510ustar00rootroot00000000000000/* * ScaleAxisPainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.ScaleAxis; import figtree.treeviewer.TreePane; import figtree.treeviewer.decorators.Decorator; import figtree.treeviewer.treelayouts.RectilinearTreeLayout; import figtree.treeviewer.treelayouts.RadialTreeLayout; import jebl.evolution.trees.Tree; import jebl.util.Attributable; import jam.controlpalettes.ControlPalette; import java.awt.*; import java.awt.geom.Line2D; import java.awt.geom.Rectangle2D; import java.text.NumberFormat; import java.util.Collection; import java.util.Set; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ScaleAxisPainter extends LabelPainter implements ScalePainter { private double majorTickSpacing = 1.0; private double minorTickSpacing = 0.5; public ScaleAxisPainter() { super(null); } public void setTreePane(TreePane treePane) { this.treePane = treePane; } public void setAutomatic(boolean automatic) { if (automatic) { treePane.setAutomaticScale(); majorTickSpacing = treePane.getMajorTickSpacing(); minorTickSpacing = treePane.getMinorTickSpacing(); } else { treePane.setTickSpacing(majorTickSpacing, minorTickSpacing); } } public void setAxisReversed(final boolean isAxisReversed) { treePane.setAxisReversed(isAxisReversed); } public void setAxisSpacing(double majorTickSpacing, double minorTickSpacing) { treePane.setTickSpacing(majorTickSpacing, minorTickSpacing); } public double getAxisOrigin() { return 0.0; } public void setAxisOrigin(double axisOrigin) { // } public double getMajorTickSpacing() { return majorTickSpacing; } public double getMinorTickSpacing() { return minorTickSpacing; } public Rectangle2D calibrate(Graphics2D g2, TreePane treePane) { Font oldFont = g2.getFont(); g2.setFont(getFont()); FontMetrics fm = g2.getFontMetrics(); double labelHeight = fm.getHeight(); preferredWidth = treePane.getTreeBounds().getWidth(); preferredHeight = labelHeight + topMargin + bottomMargin + scaleBarStroke.getLineWidth() + majorTickSize; if (!(treePane.getTreeLayout() instanceof RectilinearTreeLayout)) { // if the tree layout is not rectilinear, we are not going to display // an axis at the moment so make the height 0. preferredHeight = 0.0; } tickLabelOffset = (float) (fm.getAscent() + topMargin + bottomMargin + majorTickSize) + scaleBarStroke.getLineWidth(); g2.setFont(oldFont); return new Rectangle2D.Double(0.0, 0.0, preferredWidth, preferredHeight); } public void paint(Graphics2D g2, TreePane treePane, Justification justification, Rectangle2D bounds) { Font oldFont = g2.getFont(); Paint oldPaint = g2.getPaint(); Stroke oldStroke = g2.getStroke(); if (TreePane.DEBUG_OUTLINE) { g2.setPaint(Color.red); g2.draw(bounds); } if (treePane.getTreeLayout() instanceof RadialTreeLayout) { // Unless the layout is the rectilinear or polar one, the grid won't make sense... return; } if (getBackground() != null) { g2.setPaint(getBackground()); g2.fill(bounds); } if (getBorderPaint() != null && getBorderStroke() != null) { g2.setPaint(getBorderPaint()); g2.setStroke(getBorderStroke()); g2.draw(bounds); } g2.setFont(getFont()); g2.setPaint(getForeground()); g2.setStroke(getScaleBarStroke()); paintAxis(g2, bounds); g2.setFont(oldFont); g2.setPaint(oldPaint); g2.setStroke(oldStroke); } /** * Get the maximum width of the labels of an axis * @param g2 * @return */ protected double getMaxTickLabelWidth(Graphics2D g2) { String label; double width; double maxWidth = 0; ScaleAxis axis = treePane.getScaleAxis(); if (axis.getLabelFirst()) { // Draw first minor tick as a major one (with a label) label = axis.getFormatter().format(axis.getMinorTickValue(0, -1)); width = g2.getFontMetrics().stringWidth(label); if (maxWidth < width) maxWidth = width; } int n = axis.getMajorTickCount(); for (int i = 0; i < n; i++) { label = axis.getFormatter().format(axis.getMajorTickValue(i)); width = g2.getFontMetrics().stringWidth(label); if (maxWidth < width) maxWidth = width; } if (axis.getLabelLast()) { // Draw first minor tick as a major one (with a label) label = axis.getFormatter().format(axis.getMinorTickValue(0, n - 1)); width = g2.getFontMetrics().stringWidth(label); if (maxWidth < width) maxWidth = width; } return maxWidth; } protected void paintAxis(Graphics2D g2, Rectangle2D axisBounds) { ScaleAxis axis = treePane.getScaleAxis(); g2.setPaint(getForeground()); g2.setStroke(getScaleBarStroke()); double minX = treePane.scaleOnAxis(axis.getMinAxis()); double maxX = treePane.scaleOnAxis(axis.getMaxAxis()); Line2D line = new Line2D.Double(minX, axisBounds.getY() + topMargin, maxX, axisBounds.getY() + topMargin); g2.draw(line); int n1 = axis.getMajorTickCount(); int n2, i, j; n2 = axis.getMinorTickCount(-1); if (axis.getLabelFirst()) { // Draw first minor tick as a major one (with a label) paintMajorTick(g2, axisBounds, axis, axis.getMinorTickValue(0, -1)); for (j = 1; j < n2; j++) { paintMinorTick(g2, axisBounds, axis.getMinorTickValue(j, -1)); } } else { for (j = 0; j < n2; j++) { paintMinorTick(g2, axisBounds, axis.getMinorTickValue(j, -1)); } } for (i = 0; i < n1; i++) { paintMajorTick(g2, axisBounds, axis, axis.getMajorTickValue(i)); n2 = axis.getMinorTickCount(i); if (i == (n1-1) && axis.getLabelLast()) { // Draw last minor tick as a major one paintMajorTick(g2, axisBounds, axis, axis.getMinorTickValue(0, i)); for (j = 1; j < n2; j++) { paintMinorTick(g2, axisBounds, axis.getMinorTickValue(j, i)); } } else { for (j = 0; j < n2; j++) { paintMinorTick(g2, axisBounds, axis.getMinorTickValue(j, i)); } } } } protected void paintMajorTick(Graphics2D g2, Rectangle2D axisBounds, ScaleAxis axis, double value) { g2.setPaint(getForeground()); g2.setStroke(getScaleBarStroke()); // String label = axis.getFormatter().format(value); String label = getNumberFormat().format(value); double pos = treePane.scaleOnAxis(value); Line2D line = new Line2D.Double(pos, axisBounds.getMinY() + topMargin, pos, axisBounds.getMinY() + majorTickSize + topMargin); g2.draw(line); g2.setPaint(getForeground()); double width = g2.getFontMetrics().stringWidth(label); g2.drawString(label, (float)(pos - (width / 2)), (float)(axisBounds.getMinY() + tickLabelOffset + topMargin)); } protected void paintMinorTick(Graphics2D g2, Rectangle2D axisBounds, double value) { g2.setPaint(getForeground()); g2.setStroke(getScaleBarStroke()); double pos = treePane.scaleOnAxis(value); Line2D line = new Line2D.Double(pos, axisBounds.getMinY() + topMargin, pos, axisBounds.getMinY() + minorTickSize + topMargin); g2.draw(line); } public double getPreferredWidth() { return preferredWidth; } public double getPreferredHeight() { return preferredHeight; } public double getHeightBound() { return preferredHeight + tickLabelOffset; } public BasicStroke getScaleBarStroke() { return scaleBarStroke; } public void setScaleBarStroke(BasicStroke scaleBarStroke) { this.scaleBarStroke = scaleBarStroke; firePainterChanged(); } public void setControlPalette(ControlPalette controlPalette) { // nothing to do } public String[] getAttributes() { return new String[0]; } public void setupAttributes(Collection trees) { // nothing to do... } @Override public String getDisplayAttribute() { throw new UnsupportedOperationException("getDisplayAttribute not implmented"); } public void setDisplayAttribute(String displayAttribute) { throw new UnsupportedOperationException("setDisplayAttribute not implemented in ScaleAxisPainter"); } public void setTextDecorator(Decorator textDecorator) { } public Set getAttributableItems() { return null; } private BasicStroke scaleBarStroke = new BasicStroke(1.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL); private double topMargin = 4.0; private double bottomMargin = 4.0; private double majorTickSize = 5.0; private double minorTickSize = 2.0; private double tickLabelOffset = 4.0; private double preferredHeight; private double preferredWidth; protected TreePane treePane; } figtree-1.4.3/src/figtree/treeviewer/painters/ScaleAxisPainterController.java000077500000000000000000000364421277473563300275310ustar00rootroot00000000000000/* * ScaleAxisPainterController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.TreeViewerListener; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.text.DecimalFormat; import java.text.NumberFormat; import java.util.Map; import java.util.prefs.Preferences; import figtree.treeviewer.ControllerOptionsPanel; import figtree.treeviewer.TreeViewer; import figtree.ui.components.RealNumberField; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ScaleAxisPainterController extends AbstractController { private static Preferences PREFS = Preferences.userNodeForPackage(TreeViewer.class); private static final String SCALE_AXIS_KEY = "scaleAxis"; private static final String FONT_NAME_KEY = "fontName"; private static final String FONT_SIZE_KEY = "fontSize"; private static final String FONT_STYLE_KEY = "fontStyle"; private static final String NUMBER_FORMATTING_KEY = "numberFormatting"; private static final String REVERSE_AXIS_KEY = "reverseAxis"; private static final String SHOW_GRID_KEY = "showGrid"; private static final String AUTOMATIC_SCALE_KEY = "automaticScale"; private static final String MINOR_TICKS_KEY = "minorTicks"; private static final String MAJOR_TICKS_KEY = "majorTicks"; private static final String ORIGIN_KEY = "origin"; private static final String LINE_WIDTH_KEY = "lineWidth"; // private static final String SIGNIFICANT_DIGITS_KEY = "significantDigits"; // The defaults if there is nothing in the preferences private static String DEFAULT_FONT_NAME = "sansserif"; private static int DEFAULT_FONT_SIZE = 8; private static int DEFAULT_FONT_STYLE = Font.PLAIN; private static String DEFAULT_NUMBER_FORMATTING = "#.####"; private static float DEFAULT_LINE_WIDTH = 1.0f; public ScaleAxisPainterController(final ScaleAxisPainter scaleAxisPainter, final ScaleGridPainter scaleGridPainter, final TreeViewer treeViewer) { this.scaleAxisPainter = scaleAxisPainter; this.scaleGridPainter = scaleGridPainter; final String defaultFontName = PREFS.get(FONT_NAME_KEY, DEFAULT_FONT_NAME); final int defaultFontStyle = PREFS.getInt(FONT_SIZE_KEY, DEFAULT_FONT_STYLE); final int defaultFontSize = PREFS.getInt(FONT_STYLE_KEY, DEFAULT_FONT_SIZE); final String defaultNumberFormatting = PREFS.get(NUMBER_FORMATTING_KEY, DEFAULT_NUMBER_FORMATTING); float lineWidth = PREFS.getFloat(LINE_WIDTH_KEY, DEFAULT_LINE_WIDTH); scaleAxisPainter.setFont(new Font(defaultFontName, defaultFontStyle, defaultFontSize)); scaleAxisPainter.setNumberFormat(new DecimalFormat(defaultNumberFormatting)); scaleAxisPainter.setScaleBarStroke(new BasicStroke(lineWidth, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND)); optionsPanel = new ControllerOptionsPanel(2, 2); titleCheckBox = new JCheckBox(getTitle()); titleCheckBox.setSelected(scaleAxisPainter.isVisible()); reverseAxisCheck = new JCheckBox("Reverse axis"); reverseAxisCheck.setSelected(false); showGridCheck = new JCheckBox("Show grid"); showGridCheck.setSelected(true); optionsPanel.addSpanningComponent(showGridCheck); autoScaleCheck = new JCheckBox("Automatic scale"); autoScaleCheck.setSelected(true); majorTicksText = new RealNumberField(); majorTicksText.setValue(1.0); minorTicksText = new RealNumberField(); minorTicksText.setValue(0.5); originText = new RealNumberField(); originText.setValue(0.0); Font font = scaleAxisPainter.getFont(); fontSizeSpinner = new JSpinner(new SpinnerNumberModel(font.getSize(), 0.01, 48, 1)); fontSizeSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final float size = ((Double) fontSizeSpinner.getValue()).floatValue(); Font font = scaleAxisPainter.getFont().deriveFont(size); scaleAxisPainter.setFont(font); } }); // NumberFormat format = this.scaleAxisPainter.getNumberFormat(); // int digits = format.getMaximumFractionDigits(); // digitsSpinner = new JSpinner(new SpinnerNumberModel(digits, 2, 14, 1)); // final JLabel label5 = optionsPanel.addComponentWithLabel("Sig. Digits:", digitsSpinner); // // digitsSpinner.addChangeListener(new ChangeListener() { // public void stateChanged(ChangeEvent changeEvent) { // final int digits = (Integer)digitsSpinner.getValue(); // NumberFormat format = scaleAxisPainter.getNumberFormat(); // format.setMaximumFractionDigits(digits); // scaleAxisPainter.setNumberFormat(format); // } // }); lineWeightSpinner = new JSpinner(new SpinnerNumberModel(1.0, 0.01, 48.0, 1.0)); lineWeightSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { float weight = ((Double) lineWeightSpinner.getValue()).floatValue(); scaleAxisPainter.setScaleBarStroke(new BasicStroke(weight, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL)); } }); final JLabel label6 = optionsPanel.addComponentWithLabel("Line Weight:", lineWeightSpinner); optionsPanel.addSpanningComponent(reverseAxisCheck); optionsPanel.addSpanningComponent(autoScaleCheck); final JLabel label1 = optionsPanel.addComponentWithLabel("Label spacing:", majorTicksText, true); final JLabel label2 = optionsPanel.addComponentWithLabel("Tick spacing:", minorTicksText, true); final JLabel label3 = optionsPanel.addComponentWithLabel("Origin value:", originText, true); final JLabel label4 = optionsPanel.addComponentWithLabel("Font Size:", fontSizeSpinner); final boolean isSelected1 = titleCheckBox.isSelected(); final boolean isSelected2 = autoScaleCheck.isSelected(); showGridCheck.setEnabled(isSelected1); reverseAxisCheck.setEnabled(isSelected1); autoScaleCheck.setEnabled(isSelected1); label1.setEnabled(isSelected1 && !isSelected2); majorTicksText.setEnabled(isSelected1 && !isSelected2); label2.setEnabled(isSelected1 && !isSelected2); minorTicksText.setEnabled(isSelected1 && !isSelected2); label3.setEnabled(isSelected1 && !isSelected2); originText.setEnabled(isSelected1 && !isSelected2); label4.setEnabled(isSelected1); fontSizeSpinner.setEnabled(isSelected1); // label5.setEnabled(isSelected1); // digitsSpinner.setEnabled(isSelected1); label6.setEnabled(isSelected1); lineWeightSpinner.setEnabled(isSelected1); titleCheckBox.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final boolean isSelected1 = titleCheckBox.isSelected(); final boolean isSelected2 = autoScaleCheck.isSelected(); showGridCheck.setEnabled(isSelected1); reverseAxisCheck.setEnabled(isSelected1); autoScaleCheck.setEnabled(isSelected1); label1.setEnabled(isSelected1 && !isSelected2); majorTicksText.setEnabled(isSelected1 && !isSelected2); label2.setEnabled(isSelected1 && !isSelected2); minorTicksText.setEnabled(isSelected1 && !isSelected2); label3.setEnabled(isSelected1 && !isSelected2); originText.setEnabled(isSelected1 && !isSelected2); label4.setEnabled(isSelected1); fontSizeSpinner.setEnabled(isSelected1); // label5.setEnabled(isSelected1); // digitsSpinner.setEnabled(isSelected1); label6.setEnabled(isSelected1); lineWeightSpinner.setEnabled(isSelected1); scaleAxisPainter.setVisible(isSelected1); scaleGridPainter.setVisible(isSelected1); } }); reverseAxisCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { scaleAxisPainter.setAxisReversed(reverseAxisCheck.isSelected()); } }); showGridCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { scaleGridPainter.setVisible(showGridCheck.isSelected()); } }); autoScaleCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { if (autoScaleCheck.isSelected()) { scaleAxisPainter.setAutomatic(true); majorTicksText.setValue(scaleAxisPainter.getMajorTickSpacing()); minorTicksText.setValue(scaleAxisPainter.getMinorTickSpacing()); originText.setValue(scaleAxisPainter.getAxisOrigin()); label1.setEnabled(false); majorTicksText.setEnabled(false); label2.setEnabled(false); minorTicksText.setEnabled(false); label3.setEnabled(false); originText.setEnabled(false); } else { label1.setEnabled(true); minorTicksText.setEnabled(true); label2.setEnabled(true); majorTicksText.setEnabled(true); label3.setEnabled(true); originText.setEnabled(true); double majorTickSpacing = getValue(majorTicksText, 1.0); double minorTickSpacing = getValue(minorTicksText, 0.5); double originValue = getValue(originText, 0.0); scaleAxisPainter.setAutomatic(false); scaleAxisPainter.setAxisSpacing(majorTickSpacing, minorTickSpacing); scaleAxisPainter.setAxisOrigin(originValue); } } }); ChangeListener listener = new ChangeListener() { @Override public void stateChanged(ChangeEvent changeEvent) { if (!autoScaleCheck.isSelected()) { double majorTickSpacing = getValue(majorTicksText, 1.0); double minorTickSpacing = getValue(minorTicksText, 0.5); scaleAxisPainter.setAxisSpacing(majorTickSpacing, minorTickSpacing); } } }; minorTicksText.addChangeListener(listener); majorTicksText.addChangeListener(listener); originText.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { if (!autoScaleCheck.isSelected()) { double originValue = getValue(originText, 0.0); scaleAxisPainter.setAxisOrigin(originValue); } } }); treeViewer.addTreeViewerListener(new TreeViewerListener() { public void treeChanged() { scaleAxisPainter.firePainterChanged(); } public void treeSettingsChanged() { // nothing to do } }); } private double getValue(RealNumberField field, double defaultValue) { Double value = field.getValue(); return (value != null ? value : defaultValue); } public JComponent getTitleComponent() { return titleCheckBox; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // force a toggle of the checkbox autoScaleCheck.setSelected(false); autoScaleCheck.setSelected(true); } public void setSettings(Map settings) { titleCheckBox.setSelected((Boolean)settings.get(SCALE_AXIS_KEY + "." + IS_SHOWN)); reverseAxisCheck.setSelected((Boolean)settings.get(SCALE_AXIS_KEY + "." + REVERSE_AXIS_KEY)); showGridCheck.setSelected((Boolean)settings.get(SCALE_AXIS_KEY + "." + SHOW_GRID_KEY)); minorTicksText.setValue((Double)settings.get(SCALE_AXIS_KEY + "." + MINOR_TICKS_KEY)); majorTicksText.setValue((Double)settings.get(SCALE_AXIS_KEY + "." + MAJOR_TICKS_KEY)); originText.setValue((Double)settings.get(SCALE_AXIS_KEY + "." + ORIGIN_KEY)); autoScaleCheck.setSelected((Boolean)settings.get(SCALE_AXIS_KEY + "." + AUTOMATIC_SCALE_KEY)); // scaleAxisPainter.setAutomaticScale(autoScaleCheck.isSelected()); fontSizeSpinner.setValue((Double)settings.get(SCALE_AXIS_KEY + "." + FONT_SIZE_KEY)); // digitsSpinner.setValue((Integer)settings.get(SCALE_AXIS_KEY + "." + SIGNIFICANT_DIGITS_KEY)); lineWeightSpinner.setValue((Double)settings.get(SCALE_AXIS_KEY + "." + LINE_WIDTH_KEY)); } public void getSettings(Map settings) { settings.put(SCALE_AXIS_KEY + "." + IS_SHOWN, titleCheckBox.isSelected()); settings.put(SCALE_AXIS_KEY + "." + REVERSE_AXIS_KEY, reverseAxisCheck.isSelected()); settings.put(SCALE_AXIS_KEY + "." + SHOW_GRID_KEY, showGridCheck.isSelected()); settings.put(SCALE_AXIS_KEY + "." + AUTOMATIC_SCALE_KEY, autoScaleCheck.isSelected()); settings.put(SCALE_AXIS_KEY + "." + MINOR_TICKS_KEY, minorTicksText.getValue()); settings.put(SCALE_AXIS_KEY + "." + MAJOR_TICKS_KEY, majorTicksText.getValue()); settings.put(SCALE_AXIS_KEY + "." + ORIGIN_KEY, originText.getValue()); settings.put(SCALE_AXIS_KEY + "." + FONT_SIZE_KEY, fontSizeSpinner.getValue()); // settings.put(SCALE_AXIS_KEY + "." + SIGNIFICANT_DIGITS_KEY, digitsSpinner.getValue()); settings.put(SCALE_AXIS_KEY + "." + LINE_WIDTH_KEY, lineWeightSpinner.getValue()); } private final JCheckBox titleCheckBox; private final OptionsPanel optionsPanel; private final JCheckBox reverseAxisCheck; private final JCheckBox showGridCheck; private final JCheckBox autoScaleCheck; private final RealNumberField minorTicksText; private final RealNumberField majorTicksText; private final RealNumberField originText; private final JSpinner fontSizeSpinner; // private final JSpinner digitsSpinner; private final JSpinner lineWeightSpinner; public String getTitle() { return "Scale Axis"; } private final ScaleAxisPainter scaleAxisPainter; private final ScaleGridPainter scaleGridPainter; }figtree-1.4.3/src/figtree/treeviewer/painters/ScaleBarPainter.java000077500000000000000000000171411277473563300252600ustar00rootroot00000000000000/* * ScaleBarPainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.*; import figtree.treeviewer.decorators.Decorator; import jebl.evolution.trees.RootedTree; import jebl.evolution.trees.Tree; import jebl.util.Attributable; import jam.controlpalettes.ControlPalette; import java.awt.*; import java.awt.geom.Line2D; import java.awt.geom.Rectangle2D; import java.util.Collection; import java.util.Set; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ScaleBarPainter extends LabelPainter implements ScalePainter { public enum ScaleBarType { BAR, AXIS } public ScaleBarPainter() { this(0.0); } public ScaleBarPainter(double scaleRange) { super(null); this.scaleRange = scaleRange; type = ScaleBarType.BAR; } public void setTreePane(TreePane treePane) { this.treePane = treePane; } public Rectangle2D calibrate(Graphics2D g2, TreePane treePane) { Font oldFont = g2.getFont(); g2.setFont(getFont()); FontMetrics fm = g2.getFontMetrics(); double labelHeight = fm.getHeight(); preferredWidth = treePane.getTreeScale() * scaleRange; preferredHeight = labelHeight + topMargin + bottomMargin + scaleBarStroke.getLineWidth(); yOffset = (float) (fm.getAscent() + topMargin + bottomMargin) + scaleBarStroke.getLineWidth(); g2.setFont(oldFont); return new Rectangle2D.Double(0.0, 0.0, preferredWidth, preferredHeight); } public void paint(Graphics2D g2, TreePane treePane, Justification justification, Rectangle2D bounds) { Font oldFont = g2.getFont(); Paint oldPaint = g2.getPaint(); Stroke oldStroke = g2.getStroke(); if (getBackground() != null) { g2.setPaint(getBackground()); g2.fill(bounds); } if (getBorderPaint() != null && getBorderStroke() != null) { g2.setPaint(getBorderPaint()); g2.setStroke(getBorderStroke()); g2.draw(bounds); } g2.setFont(getFont()); // we don't need accuracy but a nice short number final String label = Double.toString(scaleRange); Rectangle2D rect = g2.getFontMetrics().getStringBounds(label, g2); double x1, x2; float xOffset; switch (justification) { case CENTER: xOffset = (float) (bounds.getX() + (bounds.getWidth() - rect.getWidth()) / 2.0); x1 = (bounds.getX() + (bounds.getWidth() - preferredWidth) / 2.0); x2 = x1 + preferredWidth; break; case FLUSH: case LEFT: xOffset = (float) bounds.getX(); x1 = bounds.getX(); x2 = x1 + preferredWidth; break; case RIGHT: xOffset = (float) (bounds.getX() + bounds.getWidth() - rect.getWidth()); x2 = bounds.getX() + bounds.getWidth(); x1 = x2 - preferredWidth; break; default: throw new IllegalArgumentException("Unrecognized alignment enum option"); } g2.setPaint(getForeground()); g2.setStroke(getScaleBarStroke()); g2.draw(new Line2D.Double(x1, bounds.getY() + topMargin, x2, bounds.getY() + topMargin)); g2.drawString(label, xOffset, yOffset + (float) bounds.getY()); g2.setFont(oldFont); g2.setPaint(oldPaint); g2.setStroke(oldStroke); } public double getPreferredWidth() { return preferredWidth; } public double getPreferredHeight() { return preferredHeight; } public double getHeightBound() { return preferredHeight + yOffset; } public ScaleBarType getType() { return type; } public void setType(ScaleBarType type) { this.type = type; firePainterChanged(); } public BasicStroke getScaleBarStroke() { return scaleBarStroke; } public void setScaleBarStroke(BasicStroke scaleBarStroke) { this.scaleBarStroke = scaleBarStroke; firePainterChanged(); } public double getScaleRange() { return scaleRange; } public void setScaleRange(double scaleRange) { this.userScaleRange = scaleRange; calculateScaleRange(); firePainterChanged(); } public void setAutomaticScale(boolean automaticScale) { this.automaticScale = automaticScale; calculateScaleRange(); firePainterChanged(); } public void setControlPalette(ControlPalette controlPalette) { // nothing to do } public void calculateScaleRange() { if( !automaticScale && userScaleRange != 0.0 ) { scaleRange = userScaleRange; } else { RootedTree tree = treePane.getTree(); if (tree != null) { final double treeHeight = tree.getHeight(tree.getRootNode()); if( treeHeight == 0.0 ) { scaleRange = 0.0; } else { double low = treeHeight / 10.0; double b = -(Math.ceil(Math.log10(low)) - 1); for(int n = 0; n < 3; ++n) { double factor = Math.pow(10, b); double x = ((int)(low * factor) + 1)/factor; if( n == 2 || x < treeHeight / 5.0 ) { scaleRange = x; break; } ++b; } } } } } public String[] getAttributes() { return new String[0]; } public void setupAttributes(Collection trees) { // nothing to do... } @Override public String getDisplayAttribute() { throw new UnsupportedOperationException("getDisplayAttribute not implmented"); } public void setDisplayAttribute(String displayAttribute) { throw new UnsupportedOperationException("setDisplayAttribute not implemented in ScaleBarPainter"); } public void setTextDecorator(Decorator textDecorator) { } public Set getAttributableItems() { return null; } private BasicStroke scaleBarStroke = new BasicStroke(1.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL); private ScaleBarType type = ScaleBarType.BAR; private ScaleAxis axis = new ScaleAxis(ScaleAxis.AT_DATA, ScaleAxis.AT_DATA); private double scaleRange; private double topMargin = 4.0; private double bottomMargin = 4.0; private double userScaleRange = 0.0; private boolean automaticScale = true; private double preferredHeight; private double preferredWidth; private float yOffset; protected TreePane treePane; }figtree-1.4.3/src/figtree/treeviewer/painters/ScaleBarPainterController.java000077500000000000000000000253451277473563300273310ustar00rootroot00000000000000/* * ScaleBarPainterController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.TreeViewerListener; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.text.NumberFormat; import java.text.DecimalFormat; import java.util.Map; import java.util.prefs.Preferences; import figtree.treeviewer.ControllerOptionsPanel; import figtree.treeviewer.TreeViewer; import figtree.ui.components.RealNumberField; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ScaleBarPainterController extends AbstractController { public static Preferences PREFS = Preferences.userNodeForPackage(TreeViewer.class); public static final String CONTROLLER_KEY = "scaleBar"; public static final String FONT_NAME_KEY = "fontName"; public static final String FONT_SIZE_KEY = "fontSize"; public static final String FONT_STYLE_KEY = "fontStyle"; public static final String NUMBER_FORMATTING_KEY = "numberFormatting"; public static final String AUTOMATIC_SCALE_KEY = "automaticScale"; public static final String SCALE_RANGE_KEY = "scaleRange"; public static final String LINE_WIDTH_KEY = "lineWidth"; // public static final String SIGNIFICANT_DIGITS_KEY = "significantDigits"; // The defaults if there is nothing in the preferences public static String DEFAULT_FONT_NAME = "sansserif"; public static int DEFAULT_FONT_SIZE = 10; public static int DEFAULT_FONT_STYLE = Font.PLAIN; public static String DEFAULT_NUMBER_FORMATTING = "#.####"; public static float DEFAULT_LINE_WIDTH = 1.0f; public ScaleBarPainterController(final ScaleBarPainter scaleBarPainter, final TreeViewer treeViewer) { this.scaleBarPainter = scaleBarPainter; final String defaultFontName = PREFS.get(CONTROLLER_KEY + "." + FONT_NAME_KEY, DEFAULT_FONT_NAME); final int defaultFontStyle = PREFS.getInt(CONTROLLER_KEY + "." + FONT_STYLE_KEY, DEFAULT_FONT_STYLE); final int defaultFontSize = PREFS.getInt(CONTROLLER_KEY + "." + FONT_SIZE_KEY, DEFAULT_FONT_SIZE); final String defaultNumberFormatting = PREFS.get(CONTROLLER_KEY + "." + NUMBER_FORMATTING_KEY, DEFAULT_NUMBER_FORMATTING); float lineWidth = PREFS.getFloat(LINE_WIDTH_KEY, DEFAULT_LINE_WIDTH); scaleBarPainter.setFont(new Font(defaultFontName, defaultFontStyle, defaultFontSize)); scaleBarPainter.setNumberFormat(new DecimalFormat(defaultNumberFormatting)); scaleBarPainter.setScaleBarStroke(new BasicStroke(lineWidth, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND)); optionsPanel = new ControllerOptionsPanel(2, 2); titleCheckBox = new JCheckBox(getTitle()); titleCheckBox.setSelected(scaleBarPainter.isVisible()); autoScaleCheck = new JCheckBox("Automatic scale"); autoScaleCheck.setSelected(true); optionsPanel.addSpanningComponent(autoScaleCheck); scaleRangeText = new RealNumberField(0.0, Double.MAX_VALUE); scaleRangeText.setValue(0.0); final JLabel label1 = optionsPanel.addComponentWithLabel("Scale Range:", scaleRangeText, true); label1.setEnabled(false); scaleRangeText.setEnabled(false); Font font = scaleBarPainter.getFont(); fontSizeSpinner = new JSpinner(new SpinnerNumberModel(font.getSize(), 0.01, 48, 1)); final JLabel label2 = optionsPanel.addComponentWithLabel("Font Size:", fontSizeSpinner); fontSizeSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final float size = ((Double) fontSizeSpinner.getValue()).floatValue(); Font font = scaleBarPainter.getFont().deriveFont(size); scaleBarPainter.setFont(font); } }); // NumberFormat format = this.scaleBarPainter.getNumberFormat(); // int digits = format.getMaximumFractionDigits(); // digitsSpinner = new JSpinner(new SpinnerNumberModel(digits, 2, 14, 1)); // final JLabel label3 = optionsPanel.addComponentWithLabel("Sig. Digits:", digitsSpinner); // // digitsSpinner.addChangeListener(new ChangeListener() { // public void stateChanged(ChangeEvent changeEvent) { // final int digits = (Integer)digitsSpinner.getValue(); // NumberFormat format = scaleBarPainter.getNumberFormat(); // format.setMaximumFractionDigits(digits); // scaleBarPainter.setNumberFormat(format); // } // }); lineWeightSpinner = new JSpinner(new SpinnerNumberModel(1.0, 0.01, 48.0, 1.0)); lineWeightSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { float weight = ((Double) lineWeightSpinner.getValue()).floatValue(); scaleBarPainter.setScaleBarStroke(new BasicStroke(weight, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL)); } }); final JLabel label4 = optionsPanel.addComponentWithLabel("Line Weight:", lineWeightSpinner); final boolean isSelected1 = titleCheckBox.isSelected(); final boolean isSelected2 = autoScaleCheck.isSelected(); label1.setEnabled(isSelected1 && !isSelected2); scaleRangeText.setEnabled(isSelected1 && !isSelected2); label2.setEnabled(isSelected1); fontSizeSpinner.setEnabled(isSelected1); // label3.setEnabled(isSelected1); // digitsSpinner.setEnabled(isSelected1); label4.setEnabled(isSelected1); lineWeightSpinner.setEnabled(isSelected1); titleCheckBox.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final boolean isSelected1 = titleCheckBox.isSelected(); final boolean isSelected2 = autoScaleCheck.isSelected(); autoScaleCheck.setEnabled(isSelected1); label1.setEnabled(isSelected1 && !isSelected2); scaleRangeText.setEnabled(isSelected1 && !isSelected2); label2.setEnabled(isSelected1); fontSizeSpinner.setEnabled(isSelected1); // label3.setEnabled(isSelected1); // digitsSpinner.setEnabled(isSelected1); label4.setEnabled(isSelected1); lineWeightSpinner.setEnabled(isSelected1); scaleBarPainter.setVisible(isSelected1); } }); autoScaleCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { if (autoScaleCheck.isSelected()) { scaleBarPainter.setAutomaticScale(true); double range = scaleBarPainter.getScaleRange(); scaleRangeText.setValue(range); label1.setEnabled(false); scaleRangeText.setEnabled(false); } else { label1.setEnabled(true); scaleRangeText.setEnabled(true); scaleBarPainter.setAutomaticScale(false); } } }); scaleRangeText.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { Double value = scaleRangeText.getValue(); if (value != null) { scaleBarPainter.setScaleRange(value); } } }); treeViewer.addTreeViewerListener(new TreeViewerListener() { public void treeChanged() { scaleBarPainter.calculateScaleRange(); scaleBarPainter.firePainterChanged(); } public void treeSettingsChanged() { // nothing to do } }); } public JComponent getTitleComponent() { return titleCheckBox; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // force a toggle of the checkbox autoScaleCheck.setSelected(false); autoScaleCheck.setSelected(true); } public void setSettings(Map settings) { titleCheckBox.setSelected((Boolean)settings.get(CONTROLLER_KEY + "." + IS_SHOWN)); autoScaleCheck.setSelected((Boolean)settings.get(CONTROLLER_KEY + "." + AUTOMATIC_SCALE_KEY)); scaleRangeText.setValue((Double)settings.get(CONTROLLER_KEY + "." + SCALE_RANGE_KEY)); fontSizeSpinner.setValue((Double)settings.get(CONTROLLER_KEY + "." + FONT_SIZE_KEY)); // digitsSpinner.setValue((Integer)settings.get(CONTROLLER_KEY + "." + SIGNIFICANT_DIGITS_KEY)); lineWeightSpinner.setValue((Double)settings.get(CONTROLLER_KEY + "." + LINE_WIDTH_KEY)); } public void getSettings(Map settings) { settings.put(CONTROLLER_KEY + "." + IS_SHOWN, titleCheckBox.isSelected()); settings.put(CONTROLLER_KEY + "." + AUTOMATIC_SCALE_KEY, autoScaleCheck.isSelected()); settings.put(CONTROLLER_KEY + "." + SCALE_RANGE_KEY, scaleRangeText.getValue()); settings.put(CONTROLLER_KEY + "." + FONT_SIZE_KEY, fontSizeSpinner.getValue()); // settings.put(CONTROLLER_KEY + "." + SIGNIFICANT_DIGITS_KEY, digitsSpinner.getValue()); settings.put(CONTROLLER_KEY + "." + LINE_WIDTH_KEY, lineWeightSpinner.getValue()); } private final JCheckBox titleCheckBox; private final OptionsPanel optionsPanel; private final JCheckBox autoScaleCheck; private final RealNumberField scaleRangeText; private final JSpinner fontSizeSpinner; // private final JSpinner digitsSpinner; private final JSpinner lineWeightSpinner; public String getTitle() { return "Scale Bar"; } private final ScaleBarPainter scaleBarPainter; } figtree-1.4.3/src/figtree/treeviewer/painters/ScaleGridPainter.java000077500000000000000000000132631277473563300254420ustar00rootroot00000000000000/* * ScaleGridPainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.ScaleAxis; import figtree.treeviewer.TreePane; import figtree.treeviewer.decorators.Decorator; import figtree.treeviewer.treelayouts.RadialTreeLayout; import jebl.evolution.trees.Tree; import jebl.util.Attributable; import jam.controlpalettes.ControlPalette; import java.awt.*; import java.awt.geom.Rectangle2D; import java.util.Collection; import java.util.Set; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class ScaleGridPainter extends LabelPainter implements ScalePainter { public ScaleGridPainter() { super(null); } public void setTreePane(TreePane treePane) { this.treePane = treePane; } public Rectangle2D calibrate(Graphics2D g2, TreePane treePane) { preferredWidth = treePane.getTreeBounds().getWidth(); preferredHeight = treePane.getTreeBounds().getHeight(); return new Rectangle2D.Double(0.0, 0.0, preferredWidth, preferredHeight); } public void paint(Graphics2D g2, TreePane treePane, Justification justification, Rectangle2D bounds) { Paint oldPaint = g2.getPaint(); Stroke oldStroke = g2.getStroke(); if (TreePane.DEBUG_OUTLINE) { g2.setPaint(Color.blue); g2.draw(bounds); } if (treePane.getTreeLayout() instanceof RadialTreeLayout) { // Unless the layout is the rectilinear or polar one, the grid won't make sense... return; } if (getBackground() != null) { g2.setPaint(getBackground()); g2.fill(bounds); } if (getBorderPaint() != null && getBorderStroke() != null) { g2.setPaint(getBorderPaint()); g2.setStroke(getBorderStroke()); g2.draw(bounds); } paintAxis(g2, bounds); g2.setPaint(oldPaint); g2.setStroke(oldStroke); } protected void paintAxis(Graphics2D g2, Rectangle2D axisBounds) { ScaleAxis axis = treePane.getScaleAxis(); g2.setPaint(getForeground()); int n1 = axis.getMajorTickCount(); int n2, i, j; n2 = axis.getMinorTickCount(-1); if (axis.getLabelFirst()) { // Draw first minor tick as a major one (with a label) paintMajorLine(g2, axisBounds, axis, axis.getMinorTickValue(0, -1)); for (j = 1; j < n2; j++) { paintMinorLine(g2, axisBounds, axis.getMinorTickValue(j, -1)); } } else { for (j = 0; j < n2; j++) { paintMinorLine(g2, axisBounds, axis.getMinorTickValue(j, -1)); } } for (i = 0; i < n1; i++) { paintMajorLine(g2, axisBounds, axis, axis.getMajorTickValue(i)); n2 = axis.getMinorTickCount(i); if (i == (n1-1) && axis.getLabelLast()) { // Draw last minor tick as a major one paintMajorLine(g2, axisBounds, axis, axis.getMinorTickValue(0, i)); for (j = 1; j < n2; j++) { paintMinorLine(g2, axisBounds, axis.getMinorTickValue(j, i)); } } else { for (j = 0; j < n2; j++) { paintMinorLine(g2, axisBounds, axis.getMinorTickValue(j, i)); } } } } protected void paintMajorLine(Graphics2D g2, Rectangle2D axisBounds, ScaleAxis axis, double value) { g2.setStroke(getMajorStroke()); Shape line = treePane.getAxisLine(value); g2.draw(line); } protected void paintMinorLine(Graphics2D g2, Rectangle2D axisBounds, double value) { g2.setStroke(getMinorStroke()); Shape line = treePane.getAxisLine(value); g2.draw(line); } public double getPreferredWidth() { return preferredWidth; } public double getPreferredHeight() { return preferredHeight; } public double getHeightBound() { return preferredHeight; } public BasicStroke getMajorStroke() { return majorStroke; } public void setMajorStroke(BasicStroke majorStroke) { this.majorStroke = majorStroke; firePainterChanged(); } public BasicStroke getMinorStroke() { return minorStroke; } public void setMinorStroke(BasicStroke minorStroke) { this.minorStroke = minorStroke; firePainterChanged(); } public void setControlPalette(ControlPalette controlPalette) { // nothing to do } public String[] getAttributes() { return new String[0]; } public void setupAttributes(Collection trees) { // nothing to do... } @Override public String getDisplayAttribute() { throw new UnsupportedOperationException("getDisplayAttribute not implmented"); } public void setDisplayAttribute(String displayAttribute) { throw new UnsupportedOperationException("setDisplayAttribute not implemented in ScaleGridPainter"); } public void setTextDecorator(Decorator textDecorator) { } public Set getAttributableItems() { return null; } private BasicStroke majorStroke = new BasicStroke(0.5f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL); private BasicStroke minorStroke = new BasicStroke(0.25f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL); private double preferredHeight; private double preferredWidth; protected TreePane treePane; }figtree-1.4.3/src/figtree/treeviewer/painters/ScalePainter.java000077500000000000000000000020511277473563300246250ustar00rootroot00000000000000/* * ScalePainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import figtree.treeviewer.TreePane; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface ScalePainter extends Painter{ } figtree-1.4.3/src/figtree/treeviewer/painters/StatesPainter.java000077500000000000000000000124341277473563300250470ustar00rootroot00000000000000/* * StatesPainter.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.painters; import jebl.evolution.graphs.Node; import jebl.evolution.trees.Tree; import figtree.treeviewer.decorators.DiscreteColourDecorator; import java.awt.*; import java.awt.geom.Rectangle2D; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class StatesPainter extends BasicLabelPainter { public StatesPainter(String[] annotationNames, DiscreteColourDecorator[] decorators) { super(PainterIntent.TIP); this.annotationNames = annotationNames; this.decorators = decorators; } public Rectangle2D calibrate(Graphics2D g2, Node node) { super.calibrate(g2, node); int siteCount = annotationNames.length; // blockSize = super.getPreferredHeight() / 2; // blockGap = blockSize / 2; blockSize = super.getPreferredHeight() * 0.8; blockGap = 1; width = (siteCount * (blockSize + blockGap)) + blockGap + blockGap; return new Rectangle2D.Double(0.0, 0.0, getPreferredWidth(), getPreferredHeight()); } public double getPreferredWidth() { return super.getPreferredWidth() + width; } public void paint(Graphics2D g2, Node node, Justification justification, Rectangle2D bounds) { Tree tree = getTree(); Stroke oldStroke = g2.getStroke(); Paint oldPaint = g2.getPaint(); float yOffset = (float)getPreferredHeight() / 2; switch (justification) { case FLUSH: case LEFT: { super.paint(g2, node, justification, new Rectangle2D.Double(bounds.getX() + width, bounds.getY(), bounds.getWidth() - width, bounds.getHeight())); double x = blockGap; int i = 0; for (String name: annotationNames) { Object item = tree.getTaxon(node).getAttribute(name); if (item != null) { decorators[i].setItem(item); int state = ((Number)item).intValue(); // Now create a bounds for the label Rectangle2D block = new Rectangle2D.Double( x, yOffset - (blockSize / 2.0), blockSize, blockSize); g2.setPaint(decorators[i].getPaint(Color.white)); g2.fill(block); g2.setPaint(Color.white); g2.setFont(new Font("helvetica", Font.PLAIN, 9)); FontMetrics fm = g2.getFontMetrics(); g2.drawString(Integer.toString(state), (float)(x+1), (float)(yOffset - (blockSize / 2.0) + fm.getAscent() + 1)); g2.setPaint(Color.black); g2.setFont(new Font("helvetica", Font.PLAIN, 9)); g2.drawString(Integer.toString(state), (float)x, (float)(yOffset - (blockSize / 2.0) + fm.getAscent())); } x += blockSize + blockGap; i++; } } break; case RIGHT: { super.paint(g2, node, justification, new Rectangle2D.Double(bounds.getX(), bounds.getY(), bounds.getWidth() - width, bounds.getHeight())); int i = 0; for (String name: annotationNames) { double x = getPreferredWidth() - blockGap - blockSize; Object item = tree.getTaxon(node).getAttribute(name); if (item != null) { decorators[i].setItem(item); // Now create a bounds for the label Rectangle2D block = new Rectangle2D.Double( x, yOffset - (blockSize / 2.0), blockSize, blockSize); g2.setPaint(decorators[i].getPaint(Color.white)); g2.fill(block); x -= (blockSize + blockGap); i++; } } } break; default: throw new IllegalArgumentException("Unrecognized alignment enum option"); } g2.setStroke(oldStroke); g2.setPaint(oldPaint); } private String[] annotationNames = null; private DiscreteColourDecorator[] decorators; private double width; private double blockSize = 8; private double blockGap = 2; }figtree-1.4.3/src/figtree/treeviewer/treelayouts/000077500000000000000000000000001277473563300221425ustar00rootroot00000000000000figtree-1.4.3/src/figtree/treeviewer/treelayouts/AbstractTreeLayout.java000077500000000000000000000063641277473563300266020ustar00rootroot00000000000000/* * AbstractTreeLayout.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.treelayouts; import java.util.HashSet; import java.util.Set; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public abstract class AbstractTreeLayout implements TreeLayout { private double rootLength = 0.0; public double getRootLength() { return rootLength; } public void setRootLength(double rootLength) { this.rootLength = rootLength; fireTreeLayoutChanged(); } public void addTreeLayoutListener(TreeLayoutListener listener) { listeners.add(listener); } public void removeTreeLayoutListener(TreeLayoutListener listener) { listeners.remove(listener); } protected void fireTreeLayoutChanged() { for (TreeLayoutListener listener : listeners) { listener.treeLayoutChanged(); } } public String getBranchColouringAttributeName() { return branchColouringAttribute; } public void setBranchColouringAttributeName(String branchColouringAttribute) { this.branchColouringAttribute = branchColouringAttribute; fireTreeLayoutChanged(); } public String getCartoonAttributeName() { return cartoonAttributeName; } public void setCartoonAttributeName(String cartoonAttributeName) { this.cartoonAttributeName = cartoonAttributeName; fireTreeLayoutChanged(); } public boolean isShowingCartoonTipLabels() { return showingCartoonTipLabels; } public void setShowingCartoonTipLabels(boolean showingCartoonTipLabels) { this.showingCartoonTipLabels = showingCartoonTipLabels; fireTreeLayoutChanged(); } public String getCollapsedAttributeName() { return collapsedAttributeName; } public void setCollapsedAttributeName(String collapsedAttributeName) { this.collapsedAttributeName = collapsedAttributeName; fireTreeLayoutChanged(); } public String getHilightAttributeName() { return hilightAttributeName; } public void setHilightAttributeName(String hilightAttributeName) { this.hilightAttributeName = hilightAttributeName; fireTreeLayoutChanged(); } private Set listeners = new HashSet(); protected String branchColouringAttribute = null; protected String cartoonAttributeName = null; protected boolean showingCartoonTipLabels = true; protected String collapsedAttributeName = null; protected String hilightAttributeName = null; } figtree-1.4.3/src/figtree/treeviewer/treelayouts/PolarTreeLayout.java000077500000000000000000000672401277473563300261140ustar00rootroot00000000000000/* * PolarTreeLayout.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.treelayouts; import jebl.evolution.graphs.Node; import jebl.evolution.trees.RootedTree; import java.awt.*; import java.awt.geom.*; import java.util.List; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class PolarTreeLayout extends AbstractTreeLayout { private double rootAngle = 180.0; private double rootLengthProportion = 0.01; private double angularRange = 360.0; private double fishEye = 0.0; private double pointOfInterest = 0.5; private int tipCount = 0; private double totalRootLength = 0.0; private boolean showingRootBranch = true; private TipLabelPosition tipLabelPosition = TipLabelPosition.FLUSH; private double yPosition; private double yIncrement; private double maxXPosition; public enum TipLabelPosition { FLUSH, RADIAL, HORIZONTAL } public AxisType getXAxisType() { return AxisType.CONTINUOUS; } public AxisType getYAxisType() { return AxisType.CONTINUOUS; } public boolean maintainAspectRatio() { return true; } public void setFishEye(double fishEye) { this.fishEye = fishEye; fireTreeLayoutChanged(); } public void setPointOfInterest(double x, double y) { this.pointOfInterest = getPolarAngle(x, y); fireTreeLayoutChanged(); } public double getHeightOfPoint(Point2D point) { throw new UnsupportedOperationException("Method getHeightOfPoint() is not supported in this TreeLayout"); } public Shape getAxisLine(double height) { double x = height; return new Ellipse2D.Double(-x, -x, x * 2.0, x * 2.0); } public Shape getHeightArea(double height1, double height2) { Area area1 = new Area(new Ellipse2D.Double(0.0, 0.0, height2 * 2.0, height2 * 2.0)); Area area2 = new Area(new Ellipse2D.Double(0.0, 0.0, height1 * 2.0, height1 * 2.0)); area1.subtract(area2); return area1; } public double getRootAngle() { return rootAngle; } public double getAngularRange() { return angularRange; } public boolean isShowingRootBranch() { return showingRootBranch; } public double getTotalRootLength() { return totalRootLength; } public double getRootLengthProportion() { return rootLengthProportion; } public TipLabelPosition getTipLabelPosition() { return tipLabelPosition; } public void setRootAngle(double rootAngle) { this.rootAngle = rootAngle; constant = rootAngle - ((360.0 - angularRange) * 0.5); fireTreeLayoutChanged(); } public void setAngularRange(double angularRange) { this.angularRange = angularRange; constant = rootAngle - ((360.0 - angularRange) * 0.5); fireTreeLayoutChanged(); } public void setShowingRootBranch(boolean showingRootBranch) { this.showingRootBranch = showingRootBranch; fireTreeLayoutChanged(); } public void setRootLengthProportion(double rootLengthProportion) { this.rootLengthProportion = rootLengthProportion; fireTreeLayoutChanged(); } public void setTipLabelPosition(TipLabelPosition tipLabelPosition) { this.tipLabelPosition = tipLabelPosition; fireTreeLayoutChanged(); } public boolean isShowingColouring() { return (branchColouringAttribute != null); } public void layout(RootedTree tree, TreeLayoutCache cache) { cache.clear(); Node root = tree.getRootNode(); double totalRootLength = (rootLengthProportion * tree.getHeight(root)) * 10.0; maxXPosition = 0.0; getMaxXPosition(tree, root, totalRootLength); yPosition = 0.0; tipCount = tree.getExternalNodes().size(); yIncrement = 1.0 / tipCount; final Point2D rootPoint = constructNode(tree, root, 0.0, totalRootLength, /*new Area(),*/ cache); // constructNodeAreas(tree, root, new Area(), cache); if (showingRootBranch) { // construct a root branch line final double y = rootPoint.getY(); Line2D line = new Line2D.Double(transform(0.0, y), transform(rootPoint.getX(), y)); // add the line to the map of branch paths cache.branchPaths.put(root, line); } } private Point2D constructNode(RootedTree tree, Node node, double xParent, double xPosition, /*final Area parentNodeArea,*/ TreeLayoutCache cache) { Point2D nodePoint; if (hilightAttributeName != null && node.getAttribute(hilightAttributeName) != null) { constructHilight(tree, node, xParent, xPosition, cache); } if (!tree.isExternal(node)) { if (collapsedAttributeName != null && node.getAttribute(collapsedAttributeName) != null) { nodePoint = constructCollapsedNode(tree, node, xPosition, cache); } else if (cartoonAttributeName != null && node.getAttribute(cartoonAttributeName) != null) { nodePoint = constructCartoonNode(tree, node, xPosition, cache); } else { double yPos = 0.0; List childList = tree.getChildren(node); Node[] children = new Node[childList.size()]; Point2D[] childPoints = new Point2D[childList.size()]; boolean rotate = false; if (node.getAttribute("!rotate") != null && ((Boolean)node.getAttribute("!rotate"))) { rotate = true; } // Area[] childAreas = new Area[childList.size()]; for (int i = 0; i < childList.size(); i++) { int index = i; if (rotate) { index = childList.size() - i - 1; } children[i] = childList.get(index); final double length = tree.getLength(children[i]); // childAreas[i] = new Area(); childPoints[i] = constructNode(tree, children[i], xPosition, xPosition + length, cache); // parentNodeArea.add(childAreas[i]); yPos += childPoints[i].getY(); } // the y-position of the node is the average of the child nodes yPos /= childList.size(); nodePoint = new Point2D.Double(xPosition, yPos); Point2D transformedNodePoint = transform(nodePoint); final double start = getAngle(yPos); // GeneralPath nodeAreaPath = new GeneralPath(); double firstChildAngle = 0; for (int i = 0; i < childList.size(); i++) { int index = i; if (rotate) { index = childList.size() - i - 1; } GeneralPath branchPath = new GeneralPath(); final Point2D transformedChildPoint = transform(childPoints[i]); final Point2D transformedShoulderPoint = transform( nodePoint.getX(), childPoints[i].getY()); // if (i == 0) { // nodeAreaPath.moveTo( // (float) transformedShoulderPoint.getX(), // (float) transformedShoulderPoint.getY()); // final Point2D transformedPoint2 = transform( // maxXPosition, childPoints[i].getY()); // nodeAreaPath.lineTo( // (float) transformedPoint2.getX(), // (float) transformedPoint2.getY()); // firstChildAngle = getAngle(childPoints[i].getY()); // } Object[] colouring = null; if (branchColouringAttribute != null) { colouring = (Object[])children[i].getAttribute(branchColouringAttribute); } if (colouring != null) { // If there is a colouring, then we break the path up into // segments. This should allow use to iterate along the segments // and colour them as we draw them. float nodeHeight = (float) tree.getHeight(node); float childHeight = (float) tree.getHeight(children[i]); double x1 = childPoints[i].getX(); double x0 = nodePoint.getX(); branchPath.moveTo( (float) transformedChildPoint.getX(), (float) transformedChildPoint.getY()); float x = (float)x1; for (int j = 0; j < colouring.length - 1; j+=2) { // double height = ((Number)colouring[j+1]).doubleValue(); // double p = (height - childHeight) / (nodeHeight - childHeight); float interval = ((Number)colouring[j+1]).floatValue(); float p = interval / (nodeHeight - childHeight); x -= ((x1 - x0) * p); final Point2D transformedPoint = transform(x, childPoints[index].getY()); branchPath.lineTo( (float) transformedPoint.getX(), (float) transformedPoint.getY()); } branchPath.lineTo( (float) transformedShoulderPoint.getX(), (float) transformedShoulderPoint.getY()); } else { branchPath.moveTo( (float) transformedChildPoint.getX(), (float) transformedChildPoint.getY()); branchPath.lineTo( (float) transformedShoulderPoint.getX(), (float) transformedShoulderPoint.getY()); } final double finish = getAngle(childPoints[index].getY()); Arc2D arc = new Arc2D.Double(); arc.setArcByCenter(0.0, 0.0, nodePoint.getX(), finish, start - finish, Arc2D.OPEN); branchPath.append(arc, true); // if (i == childList.size() - 1) { // Arc2D arc2 = new Arc2D.Double(); // arc2.setArcByCenter(0.0, 0.0, maxXPosition, firstChildAngle, finish - firstChildAngle, Arc2D.OPEN); // nodeAreaPath.append(arc2, true); // // nodeAreaPath.lineTo( // (float) transformedShoulderPoint.getX(), // (float) transformedShoulderPoint.getY()); // // Arc2D arc3 = new Arc2D.Double(); // arc3.setArcByCenter(0.0, 0.0, nodePoint.getX(), finish, firstChildAngle - finish, Arc2D.OPEN); // nodeAreaPath.append(arc3, true); // } // add the branchPath to the map of branch paths cache.branchPaths.put(children[i], branchPath); final double x3 = (nodePoint.getX() + childPoints[index].getX()) / 2; Line2D branchLabelPath = new Line2D.Double( transform(x3 - 1.0, childPoints[index].getY()), transform(x3 + 1.0, childPoints[index].getY())); cache.branchLabelPaths.put(children[i], branchLabelPath); } // nodeAreaPath.closePath(); // // Area nodeArea = new Area(nodeAreaPath); // parentNodeArea.add(nodeArea); // // for (Area childArea : childAreas) { // nodeArea.subtract(childArea); // } // // cache.nodeAreas.put(node, nodeArea); Line2D nodeLabelPath = new Line2D.Double( transform(nodePoint.getX(), yPos), transform(nodePoint.getX() + 1.0, yPos)); cache.nodeLabelPaths.put(node, nodeLabelPath); Line2D nodeShapePath = new Line2D.Double( transform(nodePoint.getX(), yPos), transform(nodePoint.getX() - 1.0, yPos)); cache.nodeShapePaths.put(node, nodeShapePath); // add the node point to the map of node points cache.nodePoints.put(node, transformedNodePoint); } } else { nodePoint = new Point2D.Double(xPosition, yPosition); Point2D transformedNodePoint = transform(nodePoint); Line2D tipLabelPath; if (tipLabelPosition == TipLabelPosition.FLUSH) { tipLabelPath = new Line2D.Double(transformedNodePoint, transform(xPosition + 1.0, yPosition)); } else if (tipLabelPosition == TipLabelPosition.RADIAL) { tipLabelPath = new Line2D.Double(transform(maxXPosition, yPosition), transform(maxXPosition + 1.0, yPosition)); Line2D calloutPath = new Line2D.Double(transformedNodePoint, transform(maxXPosition, yPosition)); cache.calloutPaths.put(node, calloutPath); } else if (tipLabelPosition == TipLabelPosition.HORIZONTAL) { // this option disabled in getControls (JH) throw new UnsupportedOperationException("Not implemented yet"); } else { // this is a bug throw new IllegalArgumentException("Unrecognized enum value"); } cache.tipLabelPaths.put(node, tipLabelPath); Line2D nodeShapePath = new Line2D.Double( transform(nodePoint.getX(), yPosition), transform(nodePoint.getX() - 1.0, yPosition)); cache.nodeShapePaths.put(node, nodeShapePath); yPosition += yIncrement; // add the node point to the map of node points cache.nodePoints.put(node, transformedNodePoint); } return nodePoint; } private void constructNodeAreas(final RootedTree tree, final Node node, final Area parentNodeArea, TreeLayoutCache cache) { if (!tree.isExternal(node)) { List children = tree.getChildren(node); boolean rotate = false; if (node.getAttribute("!rotate") != null && ((Boolean)node.getAttribute("!rotate"))) { rotate = true; } int index = (rotate ? children.size() - 1 : 0); Node child1 = children.get(index); Area childArea1 = new Area(); constructNodeAreas(tree, child1, childArea1, cache); index = (rotate ? 0 : children.size() - 1); Node child2 = children.get(index); Area childArea2 = new Area(); constructNodeAreas(tree, child2, childArea2, cache); GeneralPath nodePath = new GeneralPath(); PathIterator pi1 = cache.getBranchPath(child1).getPathIterator(null); nodePath.append(pi1, false); // start point // final float x0 = (float) branchBounds1.getX(); // final float y0 = (float) (branchBounds1.getY() + branchBounds1.getHeight()); // nodePath.moveTo(x0, y0); // // final float y1 = (float) branchBounds1.getY(); // nodePath.lineTo(x0, y1); // // nodePath.lineTo(maxXPosition, y1); // // final float y2 = (float) (branchBounds2.getY() + branchBounds2.getHeight()); // nodePath.lineTo(maxXPosition, y2); // // nodePath.lineTo(x0, y2); // // nodePath.lineTo(x0, y0); // nodePath.closePath(); // // Area nodeArea = new Area(nodePath); // // parentNodeArea.add(nodeArea); // parentNodeArea.add(childArea1); // parentNodeArea.add(childArea2); // // nodeArea.subtract(childArea1); // nodeArea.subtract(childArea2); // // cache.nodeAreas.put(node, nodeArea); } } private Point2D constructCartoonNode(RootedTree tree, Node node, double xPosition, TreeLayoutCache cache) { Point2D nodePoint; Object[] values = (Object[])node.getAttribute(cartoonAttributeName); int tipCount = (Integer)values[0]; double tipHeight = (Double)values[1]; double height = tree.getHeight(node); double maxXPos = xPosition + height - tipHeight; double minYPos = yPosition; yPosition += yIncrement * (tipCount - 1); double maxYPos = yPosition; yPosition += yIncrement; // the y-position of the node is the average of the child nodes double yPos = (maxYPos + minYPos) / 2; nodePoint = new Point2D.Double(xPosition, yPos); Point2D transformedNodePoint0 = transform(nodePoint); Point2D transformedNodePoint1 = transform(new Point2D.Double(maxXPos, minYPos)); Point2D transformedNodePoint2 = transform(new Point2D.Double(maxXPos, maxYPos)); GeneralPath collapsedShape = new GeneralPath(); collapsedShape.moveTo((float)transformedNodePoint0.getX(), (float)transformedNodePoint0.getY()); collapsedShape.lineTo((float)transformedNodePoint1.getX(), (float)transformedNodePoint1.getY()); final double start = getAngle(maxYPos); final double finish = getAngle(minYPos); Arc2D arc = new Arc2D.Double(); arc.setArcByCenter(0.0, 0.0, maxXPos, finish, start - finish, Arc2D.OPEN); collapsedShape.append(arc, true); collapsedShape.closePath(); // add the collapsedShape to the map of branch paths cache.collapsedShapes.put(node, collapsedShape); Line2D nodeLabelPath = new Line2D.Double( transform(nodePoint.getX(), yPos), transform(nodePoint.getX() + 1.0, yPos)); cache.nodeLabelPaths.put(node, nodeLabelPath); Line2D nodeBarPath = new Line2D.Double( transform(nodePoint.getX(), yPos), transform(nodePoint.getX() - 1.0, yPos)); cache.nodeShapePaths.put(node, nodeBarPath); if (showingCartoonTipLabels) { constructCartoonTipLabelPaths(tree, node, maxXPos, new double[] { minYPos }, cache); } // add the node point to the map of node points cache.nodePoints.put(node, transformedNodePoint0); return nodePoint; } private void constructCartoonTipLabelPaths(RootedTree tree, Node node, double xPosition, double[] yPosition, TreeLayoutCache cache) { if (!tree.isExternal(node)) { for (Node child : tree.getChildren(node)) { constructCartoonTipLabelPaths(tree, child, xPosition, yPosition, cache); } } else { Point2D nodePoint = new Point2D.Double(xPosition, yPosition[0]); Point2D transformedNodePoint = transform(nodePoint); Line2D tipLabelPath; if (tipLabelPosition == TipLabelPosition.FLUSH) { tipLabelPath = new Line2D.Double(transformedNodePoint, transform(xPosition + 1.0, yPosition[0])); } else if (tipLabelPosition == TipLabelPosition.RADIAL) { tipLabelPath = new Line2D.Double(transform(maxXPosition, yPosition[0]), transform(maxXPosition + 1.0, yPosition[0])); Line2D calloutPath = new Line2D.Double(transformedNodePoint, transform(maxXPosition, yPosition[0])); cache.calloutPaths.put(node, calloutPath); } else if (tipLabelPosition == TipLabelPosition.HORIZONTAL) { // this option disabled in getControls (JH) throw new UnsupportedOperationException("Not implemented yet"); } else { // this is a bug throw new IllegalArgumentException("Unrecognized enum value"); } cache.tipLabelPaths.put(node, tipLabelPath); yPosition[0] += yIncrement; } } private Point2D constructCollapsedNode(RootedTree tree, Node node, double xPosition, TreeLayoutCache cache) { Point2D nodePoint; Object[] values = (Object[])node.getAttribute(collapsedAttributeName); //String tipName = (String)values[0]; double tipHeight = (Double)values[1]; double height = tree.getHeight(node); double maxXPos = xPosition + height - tipHeight; double minYPos = yPosition - (yIncrement * 0.5); double maxYPos = minYPos + yIncrement; yPosition += yIncrement; // the y-position of the node is the average of the child nodes double yPos = (maxYPos + minYPos) / 2; nodePoint = new Point2D.Double(xPosition, yPos); Point2D transformedNodePoint0 = transform(nodePoint); Point2D transformedNodePoint1 = transform(new Point2D.Double(maxXPos, minYPos)); GeneralPath collapsedShape = new GeneralPath(); collapsedShape.moveTo((float)transformedNodePoint0.getX(), (float)transformedNodePoint0.getY()); collapsedShape.lineTo((float)transformedNodePoint1.getX(), (float)transformedNodePoint1.getY()); final double start = getAngle(maxYPos); final double finish = getAngle(minYPos); Arc2D arc = new Arc2D.Double(); arc.setArcByCenter(0.0, 0.0, maxXPos, finish, start - finish, Arc2D.OPEN); collapsedShape.append(arc, true); collapsedShape.closePath(); // add the collapsedShape to the map of branch paths cache.collapsedShapes.put(node, collapsedShape); Line2D nodeLabelPath = new Line2D.Double( transform(nodePoint.getX(), yPos), transform(nodePoint.getX() + 1.0, yPos)); cache.nodeLabelPaths.put(node, nodeLabelPath); Line2D nodeBarPath = new Line2D.Double( transform(nodePoint.getX(), yPos), transform(nodePoint.getX() - 1.0, yPos)); cache.nodeShapePaths.put(node, nodeBarPath); Point2D transformedNodePoint = transform(maxXPos, yPos); Line2D tipLabelPath; if (tipLabelPosition == TipLabelPosition.FLUSH) { tipLabelPath = new Line2D.Double(transformedNodePoint, transform(maxXPos + 1.0, yPos)); } else if (tipLabelPosition == TipLabelPosition.RADIAL) { tipLabelPath = new Line2D.Double(transform(maxXPosition, yPos), transform(maxXPosition + 1.0, yPos)); Line2D calloutPath = new Line2D.Double(transformedNodePoint, transform(maxXPosition, yPos)); cache.calloutPaths.put(node, calloutPath); } else if (tipLabelPosition == TipLabelPosition.HORIZONTAL) { // this option disabled in getControls (JH) throw new UnsupportedOperationException("Not implemented yet"); } else { // this is a bug throw new IllegalArgumentException("Unrecognized enum value"); } cache.tipLabelPaths.put(node, tipLabelPath); // add the node point to the map of node points cache.nodePoints.put(node, transformedNodePoint0); return nodePoint; } private void constructHilight(RootedTree tree, Node node, double xParent, double xPosition, TreeLayoutCache cache) { Object[] values = (Object[])node.getAttribute(hilightAttributeName); int tipCount = (Integer)values[0]; double tipHeight = (Double)values[1]; double height = tree.getHeight(node); GeneralPath hilightShape = new GeneralPath(); double x0 = ((xPosition + xParent) / 2.0); double x1 = (xPosition + height /*- tipHeight*/); double y0 = yPosition - (yIncrement / 2); double y1 = yPosition + (yIncrement * tipCount) - (yIncrement / 2); Point2D p1 = transform(new Point2D.Double(x0, y0)); Point2D p2 = transform(new Point2D.Double(x1, y0)); Point2D p3 = transform(new Point2D.Double(x1, y1)); Point2D p4 = transform(new Point2D.Double(x0, y1)); final double start = getAngle(y0); final double finish = getAngle(y1); hilightShape.moveTo((float)p1.getX(), (float)p1.getY()); hilightShape.lineTo((float)p2.getX(), (float)p2.getY()); Arc2D arc = new Arc2D.Double(); arc.setArcByCenter(0.0, 0.0, x1, start, finish - start, Arc2D.OPEN); hilightShape.append(arc, true); hilightShape.lineTo((float)p3.getX(), (float)p3.getY()); arc = new Arc2D.Double(); arc.setArcByCenter(0.0, 0.0, x0, finish, start - finish, Arc2D.OPEN); hilightShape.append(arc, true); hilightShape.closePath(); // add the collapsedShape to the map of branch paths cache.hilightNodes.add(node); cache.hilightShapes.put(node, hilightShape); } private void getMaxXPosition(RootedTree tree, Node node, double xPosition) { if (!tree.isExternal(node)) { List children = tree.getChildren(node); for (Node child : children) { final double length = tree.getLength(child); getMaxXPosition(tree, child, xPosition + length); } } else { if (xPosition > maxXPosition) { maxXPosition = xPosition; } } } /** * Polar transform * * @param point * @return the point in polar space */ private Point2D transform(Point2D point) { return transform(point.getX(), point.getY()); } /** * Polar transform * * @param h the hypotenuse * @param a the angle * @return the point in euclidean space */ private Point2D transform(double h, double a) { double r = - Math.toRadians(getAngle(a)); return new Point2D.Double(h * Math.cos(r), h * Math.sin(r)); } private double constant; /** * Polar angle for an x, y coordinate * * @param x * @param y * @return the angle */ private double getPolarAngle(double x, double y) { double r = Math.toDegrees(Math.atan(y/x)); return (constant - r) / angularRange; } /** * The angle in degrees given by a 0, 1 proportion of the circle * @param y * @return */ private double getAngle(double y) { if (fishEye == 0.0) { return constant - (y * angularRange); } double scale = 1.0 / (fishEye * tipCount); double dist = pointOfInterest - y; double min = 1.0 - (pointOfInterest / (scale + pointOfInterest)); double max = 1.0 - ((pointOfInterest - 1.0) / (scale - (pointOfInterest - 1.0))); double c = 1.0 - (dist < 0 ? (dist / (scale - dist)) : (dist / (scale + dist))); double tY = (c - min) / (max - min); return rootAngle - ((360.0 - angularRange) * 0.5) - (tY * angularRange); } } figtree-1.4.3/src/figtree/treeviewer/treelayouts/PolarTreeLayoutController.java000077500000000000000000000172511277473563300301550ustar00rootroot00000000000000/* * PolarTreeLayoutController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.treelayouts; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.Map; import figtree.treeviewer.ControllerOptionsPanel; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class PolarTreeLayoutController extends AbstractController { private static final String POLAR_LAYOUT_KEY = "polarLayout"; private static final String ROOT_ANGLE_KEY = "rootAngle"; private static final String ANGULAR_RANGE_KEY = "angularRange"; private static final String ROOT_LENGTH_KEY = "rootLength"; private static final String SHOW_ROOT_KEY = "showRoot"; private static final String ALIGN_TIP_LABELS_KEY = "alignTipLabels"; public PolarTreeLayoutController(final PolarTreeLayout treeLayout) { this.treeLayout = treeLayout; titleLabel = new JLabel("Polar Layout"); optionsPanel = new ControllerOptionsPanel(0, 0); rootAngleSlider = new JSlider(SwingConstants.HORIZONTAL, 0, 360000, 0); rootAngleSlider.setOpaque(false); rootAngleSlider.setValue((int) ((180.0 - (treeLayout.getRootAngle()) * 1000))); //rootAngleSlider.setMajorTickSpacing(rootAngleSlider.getMaximum() / 5); // rootAngleSlider.setPaintTicks(true); rootAngleSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { double value = 180 + (rootAngleSlider.getValue() / 1000.0); treeLayout.setRootAngle(value % 360); } }); optionsPanel.addComponentWithLabel("Root Angle:", rootAngleSlider, true); angularRangeSlider = new JSlider(SwingConstants.HORIZONTAL, 0, 360000, 0); angularRangeSlider.setOpaque(false); angularRangeSlider.setValue((int) ((360.0 - (treeLayout.getAngularRange()) * 1000.0))); //angularRangeSlider.setMajorTickSpacing(angularRangeSlider.getMaximum() / 5); // angularRangeSlider.setPaintTicks(true); angularRangeSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { double value = 360.0 - (angularRangeSlider.getValue() / 1000.0); treeLayout.setAngularRange(value); } }); optionsPanel.addComponentWithLabel("Angle Range:", angularRangeSlider, true); final int sliderMax = 10000; rootLengthSlider = new JSlider(SwingConstants.HORIZONTAL, 0, sliderMax, 0); rootLengthSlider.setOpaque(false); rootLengthSlider.setValue((int) (treeLayout.getRootLengthProportion() * sliderMax)); //rootLengthSlider.setMajorTickSpacing(rootLengthSlider.getMaximum() / 5); // rootLengthSlider.setPaintTicks(true); rootLengthSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { double value = rootLengthSlider.getValue(); treeLayout.setRootLengthProportion(value / sliderMax); } }); optionsPanel.addComponentWithLabel("Root Length:", rootLengthSlider, true); showRootCheck = new JCheckBox("Show Root"); showRootCheck.setOpaque(false); optionsPanel.addComponent(showRootCheck); showRootCheck.setSelected(treeLayout.isShowingRootBranch()); showRootCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { treeLayout.setShowingRootBranch(showRootCheck.isSelected()); } }); // labelPositionCombo = new JComboBox(); // for (PolarTreeLayout.TipLabelPosition position : PolarTreeLayout.TipLabelPosition.values()) { // if (position != PolarTreeLayout.TipLabelPosition.HORIZONTAL) // not implemented yet // labelPositionCombo.addItem(position); // } // labelPositionCombo.setSelectedItem(treeLayout.getTipLabelPosition()); // labelPositionCombo.addActionListener(new ActionListener() { // public void actionPerformed(ActionEvent event) { // treeLayout.setTipLabelPosition((PolarTreeLayout.TipLabelPosition) labelPositionCombo.getSelectedItem()); // // } // }); // optionsPanel.addComponentWithLabel("Label Position:", labelPositionCombo); alignTipLabelsCheck = new JCheckBox("Align Tip Labels"); alignTipLabelsCheck.setOpaque(false); alignTipLabelsCheck.setSelected(treeLayout.getTipLabelPosition() == PolarTreeLayout.TipLabelPosition.RADIAL); alignTipLabelsCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { treeLayout.setTipLabelPosition(alignTipLabelsCheck.isSelected() ? PolarTreeLayout.TipLabelPosition.RADIAL : PolarTreeLayout.TipLabelPosition.FLUSH); } }); optionsPanel.addSpanningComponent(alignTipLabelsCheck); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { rootAngleSlider.setValue((Integer) settings.get(POLAR_LAYOUT_KEY + "." + ROOT_ANGLE_KEY)); angularRangeSlider.setValue((Integer) settings.get(POLAR_LAYOUT_KEY + "." + ANGULAR_RANGE_KEY)); rootLengthSlider.setValue((Integer) settings.get(POLAR_LAYOUT_KEY + "." + ROOT_LENGTH_KEY)); showRootCheck.setSelected((Boolean) settings.get(POLAR_LAYOUT_KEY + "." + SHOW_ROOT_KEY)); alignTipLabelsCheck.setSelected((Boolean) settings.get(POLAR_LAYOUT_KEY + "." + ALIGN_TIP_LABELS_KEY)); } public void getSettings(Map settings) { settings.put(POLAR_LAYOUT_KEY + "." + ROOT_ANGLE_KEY, rootAngleSlider.getValue()); settings.put(POLAR_LAYOUT_KEY + "." + ANGULAR_RANGE_KEY, angularRangeSlider.getValue()); settings.put(POLAR_LAYOUT_KEY + "." + ROOT_LENGTH_KEY, rootLengthSlider.getValue()); settings.put(POLAR_LAYOUT_KEY + "." + SHOW_ROOT_KEY, showRootCheck.isSelected()); settings.put(POLAR_LAYOUT_KEY + "." + ALIGN_TIP_LABELS_KEY, alignTipLabelsCheck.isSelected()); } private final JLabel titleLabel; private final OptionsPanel optionsPanel; private final JSlider rootAngleSlider; private final JSlider rootLengthSlider; private final JSlider angularRangeSlider; //private final JComboBox labelPositionCombo; private final JCheckBox alignTipLabelsCheck; private final JCheckBox showRootCheck; private final PolarTreeLayout treeLayout; }figtree-1.4.3/src/figtree/treeviewer/treelayouts/RadialTreeLayout.java000077500000000000000000000263301277473563300262260ustar00rootroot00000000000000/* * RadialTreeLayout.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.treelayouts; import jebl.evolution.graphs.Graph; import jebl.evolution.graphs.Node; import jebl.evolution.trees.RootedTree; import java.awt.*; import java.awt.geom.*; import java.util.List; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class RadialTreeLayout extends AbstractTreeLayout { private double spread = 0.0; public AxisType getXAxisType() { return AxisType.CONTINUOUS; } public AxisType getYAxisType() { return AxisType.CONTINUOUS; } public boolean isShowingRootBranch() { return false; } public double getTotalRootLength() { return 0.0; } public void setFishEye(double fishEye) { // do nothing } public void setPointOfInterest(double x, double y) { // do nothing } public boolean isShowingColouring() { return (branchColouringAttribute != null); } public boolean maintainAspectRatio() { return true; } public double getHeightOfPoint(Point2D point) { throw new UnsupportedOperationException("Method getHeightOfPoint() is not supported in this TreeLayout"); } public Line2D getAxisLine(double height) { throw new UnsupportedOperationException("Method getHeightLine() is not supported in this TreeLayout"); } public Shape getHeightArea(double height1, double height2) { throw new UnsupportedOperationException("Method getHeightArea() is not supported in this TreeLayout"); } public double getSpread() { return spread; } public void setSpread(double spread) { this.spread = spread; fireTreeLayoutChanged(); } public void layout(RootedTree tree, TreeLayoutCache cache) { cache.clear(); try { final Node root = tree.getRootNode(); constructNode(tree, root, 0.0, Math.PI * 2, 0.0, 0.0, 0.0, cache); // Haven't been able to make these look nice.... // constructNodeAreas(tree, root, new Area(), cache); } catch (Graph.NoEdgeException e) { e.printStackTrace(); } } private Point2D constructNode(RootedTree tree, Node node, double angleStart, double angleFinish, double xPosition, double yPosition, double length, TreeLayoutCache cache) throws Graph.NoEdgeException { final double branchAngle = (angleStart + angleFinish) / 2.0; final double directionX = Math.cos(branchAngle); final double directionY = Math.sin(branchAngle); Point2D nodePoint = new Point2D.Double(xPosition + (length * directionX), yPosition + (length * directionY)); // System.out.println("Node: " + Utils.DEBUGsubTreeRep(tree, node) + " at " + nodePoint); if (!tree.isExternal(node)) { // Not too clear how to do hilighting for radial trees so leave it out... // if (hilightAttributeName != null && node.getAttribute(hilightAttributeName) != null) { // constructHilight(tree, node, angleStart, angleFinish, xPosition, yPosition, length, cache); // } List children = tree.getChildren(node); int[] leafCounts = new int[children.size()]; int sumLeafCount = 0; int i = 0; for (Node child : children) { leafCounts[i] = jebl.evolution.trees.Utils.getExternalNodeCount(tree, child); sumLeafCount += leafCounts[i]; i++; } double span = (angleFinish - angleStart); if (!tree.isRoot(node)) { span *= 1.0 + (spread / 10.0); angleStart = branchAngle - (span / 2.0); angleFinish = branchAngle + (span / 2.0); } double a2 = angleStart; boolean rotate = false; if (node.getAttribute("!rotate") != null && ((Boolean)node.getAttribute("!rotate"))) { rotate = true; } for(i = 0; i < children.size(); ++i) { int index = i; if (rotate) { index = children.size() - i - 1; } Node child = children.get(index); final double childLength = tree.getLength(child); double a1 = a2; a2 = a1 + (span * leafCounts[index] / sumLeafCount); Point2D childPoint = constructNode(tree, child, a1, a2, nodePoint.getX(), nodePoint.getY(), childLength, cache); Line2D branchLine = new Line2D.Double( childPoint.getX(), childPoint.getY(), nodePoint.getX(), nodePoint.getY() ); Object[] colouring = null; if (branchColouringAttribute != null) { colouring = (Object[])child.getAttribute(branchColouringAttribute); } if (colouring != null) { // If there is a colouring, then we break the path up into // segments. This should allow use to iterate along the segments // and colour them as we draw them. float nodeHeight = (float) tree.getHeight(node); float childHeight = (float) tree.getHeight(child); float x1 = (float)childPoint.getX(); float y1 = (float)childPoint.getY(); float x0 = (float)nodePoint.getX(); float y0 = (float)nodePoint.getY(); GeneralPath branchPath = new GeneralPath(); // to help this, we are going to draw the branch backwards branchPath.moveTo(x1, y1); float interval = 0.0F; for (int j = 0; j < colouring.length - 1; j+=2) { // float height = ((Number)colouring[j+1]).floatValue(); // float p = (height - childHeight) / (nodeHeight - childHeight); interval += ((Number)colouring[j+1]).floatValue(); float p = interval / (nodeHeight - childHeight); float x = x1 + ((x0 - x1) * p); float y = y1 + ((y0 - y1) * p); branchPath.lineTo(x, y); } branchPath.lineTo(x0, y0); // add the branchPath to the map of branch paths cache.branchPaths.put(child, branchPath); } else { // add the branchLine to the map of branch paths cache.branchPaths.put(child, branchLine); } cache.branchLabelPaths.put(child, (Line2D)branchLine.clone()); } Point2D nodeLabelPoint = new Point2D.Double(xPosition + ((length + 1.0) * directionX), yPosition + ((length + 1.0) * directionY)); Line2D nodeLabelPath = new Line2D.Double(nodePoint, nodeLabelPoint); cache.nodeLabelPaths.put(node, nodeLabelPath); } else { Point2D taxonPoint = new Point2D.Double(xPosition + ((length + 1.0) * directionX), yPosition + ((length + 1.0) * directionY)); Line2D taxonLabelPath = new Line2D.Double(nodePoint, taxonPoint); cache.tipLabelPaths.put(node, taxonLabelPath); } Point2D nodeShapePoint = new Point2D.Double(xPosition + ((length - 1.0) * directionX), yPosition + ((length - 1.0) * directionY)); Line2D nodeShapePath = new Line2D.Double(nodePoint, nodeShapePoint); cache.nodeShapePaths.put(node, nodeShapePath); // add the node point to the map of node points cache.nodePoints.put(node, nodePoint); return nodePoint; } private void constructNodeAreas(final RootedTree tree, final Node node, final Area parentNodeArea, TreeLayoutCache cache) { if (!tree.isExternal(node)) { List children = tree.getChildren(node); boolean rotate = false; if (node.getAttribute("!rotate") != null && ((Boolean)node.getAttribute("!rotate"))) { rotate = true; } int index = (rotate ? children.size() - 1 : 0); Node child1 = children.get(index); Area childArea1 = new Area(); constructNodeAreas(tree, child1, childArea1, cache); index = (rotate ? 0 : children.size() - 1); Node child2 = children.get(index); Area childArea2 = new Area(); constructNodeAreas(tree, child2, childArea2, cache); GeneralPath nodePath = new GeneralPath(); Line2D line1 = (Line2D)cache.getBranchPath(child1); Line2D line2 = (Line2D)cache.getBranchPath(child2); nodePath.moveTo(line2.getX1(), line2.getY1()); nodePath.lineTo(line2.getX2(), line2.getY2()); nodePath.lineTo(line1.getX1(), line1.getY1()); nodePath.closePath(); Area nodeArea = new Area(nodePath); parentNodeArea.add(nodeArea); parentNodeArea.add(childArea1); parentNodeArea.add(childArea2); nodeArea.subtract(childArea1); nodeArea.subtract(childArea2); cache.nodeAreas.put(node, nodeArea); } } private void constructHilight(RootedTree tree, Node node, double angleStart, double angleFinish, double xPosition, double yPosition, double length, TreeLayoutCache cache) { Object[] values = (Object[])node.getAttribute(hilightAttributeName); int tipCount = (Integer)values[0]; double tipHeight = (Double)values[1]; double height = tree.getHeight(node); GeneralPath hilightShape = new GeneralPath(); final double branchAngle = (angleStart + angleFinish) / 2.0; float x0 = (float)(xPosition + (0.5 * length * Math.cos(branchAngle))); float y0 = (float)(yPosition + (0.5 * length * Math.sin(branchAngle))); float x1 = (float)(x0 + (tipHeight * Math.cos(angleStart))); float y1 = (float)(y0 + (tipHeight * Math.sin(angleStart))); float x2 = (float)(x0 + (tipHeight * Math.cos(angleFinish))); float y2 = (float)(y0 + (tipHeight * Math.sin(angleFinish))); hilightShape.moveTo(x0, y0); hilightShape.lineTo(x1, y1); hilightShape.lineTo(x2, y2); hilightShape.lineTo(x0, y0); hilightShape.closePath(); // add the collapsedShape to the map of branch paths cache.hilightNodes.add(node); cache.hilightShapes.put(node, hilightShape); } }figtree-1.4.3/src/figtree/treeviewer/treelayouts/RadialTreeLayoutController.java000077500000000000000000000063241277473563300302730ustar00rootroot00000000000000/* * RadialTreeLayoutController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.treelayouts; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeListener; import javax.swing.event.ChangeEvent; import java.util.Map; import figtree.treeviewer.ControllerOptionsPanel; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class RadialTreeLayoutController extends AbstractController { private static final String RADIAL_LAYOUT_KEY = "radialLayout"; private static final String SPREAD_KEY = "spread"; public RadialTreeLayoutController(final RadialTreeLayout treeLayout) { this.treeLayout = treeLayout; titleLabel = new JLabel("Radial Layout"); optionsPanel = new ControllerOptionsPanel(0, 0); // final int sliderMax = 100; // final JSlider spreadSlider = new JSlider(SwingConstants.HORIZONTAL, 0, sliderMax, 0); // spreadSlider.setValue((int)(treeLayout.getSpread() * sliderMax / 2.0)); // // spreadSlider.addChangeListener(new ChangeListener() { // public void stateChanged(ChangeEvent changeEvent) { // double value = spreadSlider.getValue(); // treeLayout.setSpread((value / sliderMax)); // } // }); // optionsPanel.addComponentWithLabel("Spread:", spreadSlider, true); double spread = treeLayout.getSpread(); spreadSpinner = new JSpinner(new SpinnerNumberModel(spread, 0, 100, 1)); optionsPanel.addComponentWithLabel("Spread:", spreadSpinner, true); spreadSpinner.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { final double spread = (Double)spreadSpinner.getValue(); treeLayout.setSpread(spread / 100.0); } }); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { spreadSpinner.setValue((Double) settings.get(RADIAL_LAYOUT_KEY + "." + SPREAD_KEY)); } public void getSettings(Map settings) { settings.put(RADIAL_LAYOUT_KEY + "." + SPREAD_KEY, spreadSpinner.getValue()); } private final JLabel titleLabel; private final OptionsPanel optionsPanel; private final JSpinner spreadSpinner; private final RadialTreeLayout treeLayout; } figtree-1.4.3/src/figtree/treeviewer/treelayouts/RectilinearTreeLayout.java000077500000000000000000000540731277473563300273000ustar00rootroot00000000000000/* * RectilinearTreeLayout.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.treelayouts; import jebl.evolution.graphs.Node; import jebl.evolution.trees.RootedTree; import java.awt.*; import java.awt.geom.*; import java.util.List; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class RectilinearTreeLayout extends AbstractTreeLayout { private double curvature = 0.0; private boolean alignTipLabels = false; private double fishEye = 0.0; private double pointOfInterest = 0.5; private int tipCount = 0; private double rootLengthProportion = 0.01; private double yPosition; private double yIncrement; private double maxXPosition; public AxisType getXAxisType() { return AxisType.CONTINUOUS; } public AxisType getYAxisType() { return AxisType.DISCRETE; } public boolean isShowingRootBranch() { return true; } public boolean maintainAspectRatio() { return false; } public double getRootLengthProportion() { return rootLengthProportion; } public void setRootLengthProportion(double rootLengthProportion) { this.rootLengthProportion = rootLengthProportion; fireTreeLayoutChanged(); } public double getHeightOfPoint(Point2D point) { return point.getX(); } public Shape getAxisLine(double height) { double x = height; double y1 = 0.0; double y2 = 1.0; return new Line2D.Double(x, y1, x, y2); } public Shape getHeightArea(double height1, double height2) { double x = height1; double y = 0.0; double w = Math.abs(height2 - height1); double h = 1.0; return new Rectangle2D.Double(x, y, w, h); } public boolean isAlignTipLabels() { return alignTipLabels; } public double getCurvature() { return curvature; } public double getFishEye() { return fishEye; } public double getPointOfInterest() { return pointOfInterest; } public void setAlignTipLabels(boolean alignTipLabels) { this.alignTipLabels = alignTipLabels; fireTreeLayoutChanged(); } public void setCurvature(double curvature) { this.curvature = curvature; fireTreeLayoutChanged(); } public void setFishEye(double fishEye) { this.fishEye = fishEye; fireTreeLayoutChanged(); } public void setPointOfInterest(double x, double y) { this.pointOfInterest = y; fireTreeLayoutChanged(); } public boolean isShowingColouring() { return (branchColouringAttribute != null && curvature == 0.0); } public void layout(RootedTree tree, TreeLayoutCache cache) { cache.clear(); maxXPosition = 0.0; yPosition = 0.0; tipCount = tree.getExternalNodes().size(); yIncrement = 1.0 / (tipCount - 1); Node root = tree.getRootNode(); setRootLength(rootLengthProportion * tree.getHeight(root)); maxXPosition = 0.0; getMaxXPosition(tree, root, getRootLength()); Point2D rootPoint = constructNode(tree, root, 0.0, getRootLength(), cache); constructNodeAreas(tree, root, new Area(), cache); // construct a root branch line double ty = transformY(rootPoint.getY()); Line2D line = new Line2D.Double(0.0, ty, rootPoint.getX(), ty); // add the line to the map of branch paths cache.branchPaths.put(root, line); } private Point2D constructNode(final RootedTree tree, final Node node, final double xParent, final double xPosition, TreeLayoutCache cache) { Point2D nodePoint; if (hilightAttributeName != null && node.getAttribute(hilightAttributeName) != null) { constructHilight(tree, node, xParent, xPosition, cache); } if (!tree.isExternal(node)) { if (collapsedAttributeName != null && node.getAttribute(collapsedAttributeName) != null) { nodePoint = constructCollapsedNode(tree, node, xPosition, cache); } else if (cartoonAttributeName != null && node.getAttribute(cartoonAttributeName) != null) { nodePoint = constructCartoonNode(tree, node, xPosition, cache); } else { double yPos = 0.0; List children = tree.getChildren(node); boolean rotate = false; if (node.getAttribute("!rotate") != null && ((Boolean)node.getAttribute("!rotate"))) { rotate = true; } for (int i = 0; i < children.size(); i++) { int index = i; if (rotate) { index = children.size() - i - 1; } Node child = children.get(index); double length = tree.getLength(child); Point2D childPoint = constructNode(tree, child, xPosition, xPosition + length, cache); yPos += childPoint.getY(); } // the y-position of the node is the average of the child nodes yPos /= children.size(); nodePoint = new Point2D.Double(xPosition, yPos); final double ty = transformY(yPos); // start point final float x0 = (float) nodePoint.getX(); final float y0 = (float) ty; for (Node child : children) { Point2D childPoint = cache.nodePoints.get(child); GeneralPath branchPath = new GeneralPath(); // end point final float x1 = (float) childPoint.getX(); final float y1 = (float) transformY(childPoint.getY()); if (curvature == 0.0) { Object[] colouring = null; if (branchColouringAttribute != null) { colouring = (Object[])child.getAttribute(branchColouringAttribute); } if (colouring != null) { // If there is a colouring, then we break the path up into // segments. This should allow us to iterate along the segments // and colour them as we draw them. float nodeHeight = (float) tree.getHeight(node); float childHeight = (float) tree.getHeight(child); // to help this, we are going to draw the branch backwards branchPath.moveTo(x1, y1); float x = x1; for (int i = 0; i < colouring.length - 1; i+=2) { // float height = ((Number)colouring[i+1]).floatValue(); // float p = (height - childHeight) / (nodeHeight - childHeight); float interval = ((Number)colouring[i+1]).floatValue(); float p = interval / (nodeHeight - childHeight); x -= ((x1 - x0) * p); branchPath.lineTo(x, y1); } branchPath.lineTo(x0, y1); branchPath.lineTo(x0, y0); } else { branchPath.moveTo(x1, y1); branchPath.lineTo(x0, y1); branchPath.lineTo(x0, y0); } } else if (curvature == 1.0) { // The extreme is to use a triangular look branchPath.moveTo(x0, y0); branchPath.lineTo(x1, y1); } else { // if the curvature is on then we simply don't // do tree colouring - I just can't be bothered to // implement it (and it would probably be confusing anyway). float x2 = x1 - ((x1 - x0) * (float) (1.0 - curvature)); float y2 = y0 + ((y1 - y0) * (float) (1.0 - curvature)); branchPath.moveTo(x1, y1); branchPath.lineTo(x2, y1); branchPath.quadTo(x0, y1, x0, y2); branchPath.lineTo(x0, y0); } // add the branchPath to the map of branch paths cache.branchPaths.put(child, branchPath); double x3 = (nodePoint.getX() + childPoint.getX()) / 2; Line2D branchLabelPath = new Line2D.Double( x3 - 1.0, y1, x3 + 1.0, y1); cache.branchLabelPaths.put(child, branchLabelPath); } Line2D nodeLabelPath = new Line2D.Double( nodePoint.getX(), ty, nodePoint.getX() + 1.0, ty); cache.nodeLabelPaths.put(node, nodeLabelPath); Line2D nodeShapePath = new Line2D.Double( nodePoint.getX(), ty, nodePoint.getX() - 1.0, ty); cache.nodeShapePaths.put(node, nodeShapePath); } } else { nodePoint = new Point2D.Double(xPosition, yPosition); double ty = transformY(yPosition); Line2D tipLabelPath; if (alignTipLabels) { tipLabelPath = new Line2D.Double( maxXPosition, ty, maxXPosition + 1.0, ty); Line2D calloutPath = new Line2D.Double( nodePoint.getX(), ty, maxXPosition, ty); cache.calloutPaths.put(node, calloutPath); } else { tipLabelPath = new Line2D.Double( nodePoint.getX(), ty, nodePoint.getX() + 1.0, ty); } cache.tipLabelPaths.put(node, tipLabelPath); Line2D nodeShapePath = new Line2D.Double( nodePoint.getX(), ty, nodePoint.getX() - 1.0, ty); cache.nodeShapePaths.put(node, nodeShapePath); yPosition += yIncrement; } // add the node point to the map of node points cache.nodePoints.put(node, nodePoint); return nodePoint; } private void constructNodeAreas(final RootedTree tree, final Node node, final Area parentNodeArea, TreeLayoutCache cache) { if (!tree.isExternal(node) && (collapsedAttributeName == null || node.getAttribute(collapsedAttributeName) == null) && (cartoonAttributeName == null || node.getAttribute(cartoonAttributeName) == null)) { List children = tree.getChildren(node); boolean rotate = false; if (node.getAttribute("!rotate") != null && ((Boolean)node.getAttribute("!rotate"))) { rotate = true; } int index = (rotate ? children.size() - 1 : 0); Node child1 = children.get(index); Area childArea1 = new Area(); constructNodeAreas(tree, child1, childArea1, cache); Rectangle2D branchBounds1 = cache.getBranchPath(child1).getBounds2D(); index = (rotate ? 0 : children.size() - 1); Node child2 = children.get(index); Area childArea2 = new Area(); constructNodeAreas(tree, child2, childArea2, cache); Rectangle2D branchBounds2 = cache.getBranchPath(child2).getBounds2D(); GeneralPath nodePath = new GeneralPath(); // start point final float x0 = (float) branchBounds1.getX(); final float y0 = (float) (branchBounds1.getY() + branchBounds1.getHeight()); nodePath.moveTo(x0, y0); if (curvature == 0.0) { final float y1 = (float) branchBounds1.getY(); nodePath.lineTo(x0, y1); nodePath.lineTo((float)maxXPosition, y1); final float y2 = (float) (branchBounds2.getY() + branchBounds2.getHeight()); nodePath.lineTo((float)maxXPosition, y2); nodePath.lineTo(x0, y2); } else if (curvature == 1.0) { // The extreme is to use a triangular look final float x1 = (float) (branchBounds1.getX() + branchBounds1.getWidth()); final float y1 = (float) branchBounds1.getY(); nodePath.lineTo(x1, y1); nodePath.lineTo((float)maxXPosition, y1); final float y2 = (float) (branchBounds2.getY() + branchBounds2.getHeight()); nodePath.lineTo((float)maxXPosition, y2); final float x2 = (float) (branchBounds2.getX() + branchBounds2.getWidth()); nodePath.lineTo(x2, y2); } else { final float x1 = (float) (branchBounds1.getX() + branchBounds1.getWidth()); final float y1 = (float) branchBounds1.getY(); float x2 = x1 - ((x1 - x0) * (float) (1.0 - curvature)); float y2 = y0 - ((y0 - y1) * (float) (1.0 - curvature)); nodePath.lineTo(x0, y2); nodePath.quadTo(x0, y1, x2, y1); nodePath.lineTo((float)maxXPosition, y1); final float y3 = (float) (branchBounds2.getY() + branchBounds2.getHeight()); nodePath.lineTo((float)maxXPosition, y3); final float x3 = (float) (branchBounds2.getX() + branchBounds2.getWidth()); final float x4 = x3 - ((x3 - x0) * (float) (1.0 - curvature)); final float y4 = y0 + ((y3 - y0) * (float) (1.0 - curvature)); nodePath.lineTo(x4, y3); nodePath.quadTo(x0, y3, x0, y4); } nodePath.lineTo(x0, y0); nodePath.closePath(); Area nodeArea = new Area(nodePath); parentNodeArea.add(nodeArea); parentNodeArea.add(childArea1); parentNodeArea.add(childArea2); nodeArea.subtract(childArea1); nodeArea.subtract(childArea2); cache.nodeAreas.put(node, nodeArea); } } private Point2D constructCartoonNode(RootedTree tree, Node node, double xPosition, TreeLayoutCache cache) { Point2D nodePoint; Object[] values = (Object[])node.getAttribute(cartoonAttributeName); int tipCount = (Integer)values[0]; double tipHeight = (Double)values[1]; double height = tree.getHeight(node); double maxXPos = xPosition + height - tipHeight; double minYPos = yPosition; yPosition += yIncrement * (tipCount - 1); double maxYPos = yPosition; yPosition += yIncrement; // the y-position of the node is the average of the child nodes double yPos = (maxYPos + minYPos) / 2; nodePoint = new Point2D.Double(xPosition, yPos); GeneralPath collapsedShape = new GeneralPath(); // start point float x0 = (float)nodePoint.getX(); float y0 = (float)transformY(nodePoint.getY()); // end point float x1 = (float)maxXPos; float y1 = (float)transformY(minYPos); float y2 = (float)transformY(maxYPos); collapsedShape.moveTo(x0, y0); collapsedShape.lineTo(x1, y1); collapsedShape.lineTo(x1, y2); collapsedShape.closePath(); // add the collapsedShape to the map of branch paths cache.collapsedShapes.put(node, collapsedShape); Line2D nodeLabelPath = new Line2D.Double( nodePoint.getX(), y0, nodePoint.getX() + 1.0, y0); cache.nodeLabelPaths.put(node, nodeLabelPath); Line2D nodeBarPath = new Line2D.Double( nodePoint.getX(), y0, nodePoint.getX() - 1.0, y0); cache.nodeShapePaths.put(node, nodeBarPath); if (showingCartoonTipLabels) { constructCartoonTipLabelPaths(tree, node, maxXPos, new double[] { minYPos }, cache); } return nodePoint; } private void constructCartoonTipLabelPaths(RootedTree tree, Node node, double xPosition, double[] yPosition, TreeLayoutCache cache) { if (!tree.isExternal(node)) { for (Node child : tree.getChildren(node)) { constructCartoonTipLabelPaths(tree, child, xPosition, yPosition, cache); } } else { Point2D nodePoint = new Point2D.Double(xPosition, yPosition[0]); double x0 = nodePoint.getX(); double y0 = transformY(nodePoint.getY()); Line2D tipLabelPath; if (alignTipLabels) { tipLabelPath = new Line2D.Double(maxXPosition, y0, maxXPosition + 1.0, y0); Line2D calloutPath = new Line2D.Double(x0, y0, maxXPosition, y0); cache.calloutPaths.put(node, calloutPath); } else { tipLabelPath = new Line2D.Double(x0, y0, x0 + 1.0, y0); } cache.tipLabelPaths.put(node, tipLabelPath); yPosition[0] += yIncrement; } } private Point2D constructCollapsedNode(RootedTree tree, Node node, double xPosition, TreeLayoutCache cache) { Point2D nodePoint; Object[] values = (Object[])node.getAttribute(collapsedAttributeName); double tipHeight = (Double)values[1]; double height = tree.getHeight(node); double maxXPos = xPosition + height - tipHeight; double minYPos = yPosition - (yIncrement * 0.5); double maxYPos = minYPos + yIncrement; yPosition += yIncrement; // the y-position of the node is the average of the child nodes double yPos = (maxYPos + minYPos) / 2; nodePoint = new Point2D.Double(xPosition, yPos); double ty = transformY(yPos); GeneralPath collapsedShape = new GeneralPath(); // start point float x0 = (float)nodePoint.getX(); float y0 = (float)ty; // end point float x1 = (float)maxXPos; float y1 = (float)transformY(minYPos); float y2 = (float)transformY(maxYPos); collapsedShape.moveTo(x0, y0); collapsedShape.lineTo(x1, y1); collapsedShape.lineTo(x1, y2); collapsedShape.closePath(); // add the collapsedShape to the map of branch paths cache.collapsedShapes.put(node, collapsedShape); Line2D nodeLabelPath = new Line2D.Double(xPosition, ty, xPosition + 1.0, ty); cache.nodeLabelPaths.put(node, nodeLabelPath); Line2D nodeBarPath = new Line2D.Double(xPosition, ty, xPosition - 1.0, ty); cache.nodeShapePaths.put(node, nodeBarPath); Line2D tipLabelPath; if (alignTipLabels) { tipLabelPath = new Line2D.Double( maxXPosition, ty, maxXPosition + 1.0, ty); Line2D calloutPath = new Line2D.Double( maxXPos, ty, maxXPosition, ty); cache.calloutPaths.put(node, calloutPath); } else { tipLabelPath = new Line2D.Double(maxXPos, ty, maxXPos + 1.0, ty); } cache.tipLabelPaths.put(node, tipLabelPath); return nodePoint; } private void constructHilight(RootedTree tree, Node node, double xParent, double xPosition, TreeLayoutCache cache) { Object[] values = (Object[])node.getAttribute(hilightAttributeName); int tipCount = (Integer)values[0]; double tipHeight = (Double)values[1]; double height = tree.getHeight(node); GeneralPath hilightShape = new GeneralPath(); float x0 = (float)((xPosition + xParent) / 2.0); float x1 = (float)(xPosition + height /*- tipHeight*/); double tmp = yPosition - (yIncrement / 2); float y0 = (float)transformY(tmp); float y1 = (float)transformY(tmp + (yIncrement * tipCount)); hilightShape.moveTo(x0, y0); hilightShape.lineTo(x1, y0); hilightShape.lineTo(x1, y1); hilightShape.lineTo(x0, y1); hilightShape.closePath(); // add the collapsedShape to the map of branch paths cache.hilightNodes.add(node); cache.hilightShapes.put(node, hilightShape); } private void getMaxXPosition(RootedTree tree, Node node, double xPosition) { if (!tree.isExternal(node)) { List children = tree.getChildren(node); for (Node child : children) { double length = tree.getLength(child); getMaxXPosition(tree, child, xPosition + length); } } else { if (xPosition > maxXPosition) { maxXPosition = xPosition; } } } private double transformY(double y) { if (fishEye == 0.0) { return y; } double scale = 1.0 / (fishEye * tipCount); double dist = pointOfInterest - y; double min = 1.0 - (pointOfInterest / (scale + pointOfInterest)); double max = 1.0 - ((pointOfInterest - 1.0) / (scale - (pointOfInterest - 1.0))); double c = 1.0 - (dist < 0 ? (dist / (scale - dist)) : (dist / (scale + dist))); return (c - min) / (max - min); } }figtree-1.4.3/src/figtree/treeviewer/treelayouts/RectilinearTreeLayoutController.java000077500000000000000000000120651277473563300313370ustar00rootroot00000000000000/* * RectilinearTreeLayoutController.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.treelayouts; import jam.controlpalettes.AbstractController; import jam.panels.OptionsPanel; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.Map; import figtree.treeviewer.ControllerOptionsPanel; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class RectilinearTreeLayoutController extends AbstractController { private static final String RECTILINEAR_LAYOUT_KEY = "rectilinearLayout"; private static final String ROOT_LENGTH_KEY = "rootLength"; private static final String CURVATURE_KEY = "curvature"; private static final String ALIGN_TIP_LABELS_KEY = "alignTipLabels"; public RectilinearTreeLayoutController(final RectilinearTreeLayout treeLayout) { this.treeLayout = treeLayout; titleLabel = new JLabel("Rectangular Layout"); optionsPanel = new ControllerOptionsPanel(0, 0); final int sliderMax = 10000; rootLengthSlider = new JSlider(SwingConstants.HORIZONTAL, 0, sliderMax, 0); rootLengthSlider.setOpaque(false); rootLengthSlider.setValue((int) (treeLayout.getRootLengthProportion() * sliderMax)); //rootLengthSlider.setMajorTickSpacing(rootLengthSlider.getMaximum() / 5); // rootLengthSlider.setPaintTicks(true); rootLengthSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { double value = rootLengthSlider.getValue(); treeLayout.setRootLengthProportion(value / sliderMax); } }); optionsPanel.addComponentWithLabel("Root Length:", rootLengthSlider, true); curvatureSlider = new JSlider(SwingConstants.HORIZONTAL, 0, sliderMax, 0); curvatureSlider.setOpaque(false); curvatureSlider.setValue((int) (treeLayout.getCurvature() * sliderMax)); //curvatureSlider.setMajorTickSpacing(curvatureSlider.getMaximum() / 5); // curvatureSlider.setPaintTicks(true); curvatureSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { double value = curvatureSlider.getValue(); treeLayout.setCurvature(value / sliderMax); } }); optionsPanel.addComponentWithLabel("Curvature:", curvatureSlider, true); alignTipLabelsCheck = new JCheckBox("Align Tip Labels"); alignTipLabelsCheck.setOpaque(false); alignTipLabelsCheck.setSelected(treeLayout.isAlignTipLabels()); alignTipLabelsCheck.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent changeEvent) { treeLayout.setAlignTipLabels(alignTipLabelsCheck.isSelected()); } }); optionsPanel.addSpanningComponent(alignTipLabelsCheck); } public JComponent getTitleComponent() { return titleLabel; } public JPanel getPanel() { return optionsPanel; } public boolean isInitiallyVisible() { return false; } public void initialize() { // nothing to do } public void setSettings(Map settings) { rootLengthSlider.setValue((Integer) settings.get(RECTILINEAR_LAYOUT_KEY + "." + ROOT_LENGTH_KEY)); curvatureSlider.setValue((Integer) settings.get(RECTILINEAR_LAYOUT_KEY + "." + CURVATURE_KEY)); alignTipLabelsCheck.setSelected((Boolean) settings.get(RECTILINEAR_LAYOUT_KEY + "." + ALIGN_TIP_LABELS_KEY)); } public void getSettings(Map settings) { settings.put(RECTILINEAR_LAYOUT_KEY + "." + ROOT_LENGTH_KEY, rootLengthSlider.getValue()); settings.put(RECTILINEAR_LAYOUT_KEY + "." + CURVATURE_KEY, curvatureSlider.getValue()); settings.put(RECTILINEAR_LAYOUT_KEY + "." + ALIGN_TIP_LABELS_KEY, alignTipLabelsCheck.isSelected()); } private final JLabel titleLabel; private final OptionsPanel optionsPanel; private final JSlider rootLengthSlider; private final JSlider curvatureSlider; private final JCheckBox alignTipLabelsCheck; private final RectilinearTreeLayout treeLayout; } figtree-1.4.3/src/figtree/treeviewer/treelayouts/TreeLayout.java000077500000000000000000000066401277473563300251130ustar00rootroot00000000000000/* * TreeLayout.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.treelayouts; import jebl.evolution.trees.RootedTree; import java.awt.*; import java.awt.geom.Point2D; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface TreeLayout { public enum AxisType { CONTINUOUS, DISCRETE } void layout(RootedTree tree, TreeLayoutCache cache); /** * Add a listener for this layout * * @param listener */ void addTreeLayoutListener(TreeLayoutListener listener); /** * Remove a listener from this layout * * @param listener */ void removeTreeLayoutListener(TreeLayoutListener listener); /** * Return whether the x axis is continuous or discrete * * @return the axis type */ AxisType getXAxisType(); /** * Return whether the y axis is continuous or discrete * * @return the axis type */ AxisType getYAxisType(); /** * Return whether this layout displays a root branch * @return showing root branch? */ boolean isShowingRootBranch(); double getRootLength(); void setRootLength(double rootLength); /** * Return whether this layout is showing a branch colouring * @return showing colouring? */ boolean isShowingColouring(); void setFishEye(double fishEye); void setPointOfInterest(double x, double y); /** * Return whether the two axis scales should be maintained * relative to each other * * @return a boolean */ boolean maintainAspectRatio(); double getHeightOfPoint(Point2D point); /** * Return a line that defines a particular height. Some layouts * won't be able to produce this and may throw an UnsupportedOperationException. * * @param height * @return the line */ Shape getAxisLine(double height); /** * Return a shape that defines a particular height interval. Some layouts * won't be able to produce this and may throw an UnsupportedOperationException. * * @param height1 * @param height2 * @return the area */ Shape getHeightArea(double height1, double height2); String getBranchColouringAttributeName(); void setBranchColouringAttributeName(String colouringAttributeName); String getCartoonAttributeName(); void setCartoonAttributeName(String cartoonAttributeName); String getCollapsedAttributeName(); void setCollapsedAttributeName(String collapsedAttributeName); String getHilightAttributeName(); void setHilightAttributeName(String hilightAttributeName); } figtree-1.4.3/src/figtree/treeviewer/treelayouts/TreeLayoutCache.java000077500000000000000000000101321277473563300260260ustar00rootroot00000000000000/* * TreeLayoutCache.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.treelayouts; import jebl.evolution.graphs.Node; import java.awt.*; import java.awt.geom.Line2D; import java.awt.geom.Point2D; import java.util.*; import java.util.List; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class TreeLayoutCache { public Point2D getNodePoint(Node node) { return nodePoints.get(node); } public Map getNodePointMap() { return nodePoints; } public Shape getBranchPath(Node node) { return branchPaths.get(node); } public Map getBranchPathMap() { return branchPaths; } public Shape getNodeArea(Node node) { return nodeAreas.get(node); } public Map getNodeAreaMap() { return nodeAreas; } public Shape getCollapsedShape(Node node) { return collapsedShapes.get(node); } public Map getCollapsedShapeMap() { return collapsedShapes; } public List getHilightNodesList() { return hilightNodes; } public Shape getHilightShape(Node node) { return hilightShapes.get(node); } public Map getHilightShapeMap() { return hilightShapes; } public Line2D getTipLabelPath(Node node) { return tipLabelPaths.get(node); } public Map getTipLabelPathMap() { return tipLabelPaths; } public Line2D getBranchLabelPath(Node node) { return branchLabelPaths.get(node); } public Map getBranchLabelPathMap() { return branchLabelPaths; } public Line2D getNodeLabelPath(Node node) { return nodeLabelPaths.get(node); } public Map getNodeLabelPathMap() { return nodeLabelPaths; } public Line2D getNodeShapePath(Node node) { return nodeShapePaths.get(node); } public Map getNodeShapePathMap() { return nodeShapePaths; } public Shape getCalloutPath(Node node) { return calloutPaths.get(node); } public Map getCalloutPathMap() { return calloutPaths; } public void clear() { nodePoints.clear(); branchPaths.clear(); nodeAreas.clear(); collapsedShapes.clear(); hilightNodes.clear(); hilightShapes.clear(); tipLabelPaths.clear(); branchLabelPaths.clear(); nodeLabelPaths.clear(); nodeShapePaths.clear(); calloutPaths.clear(); } protected Map nodePoints = new HashMap(); protected Map branchPaths = new HashMap(); protected Map nodeAreas = new HashMap(); protected Map collapsedShapes = new HashMap(); protected List hilightNodes = new ArrayList(); protected Map hilightShapes = new HashMap(); protected Map tipLabelPaths = new HashMap(); protected Map branchLabelPaths = new HashMap(); protected Map nodeLabelPaths = new HashMap(); protected Map nodeShapePaths = new HashMap(); protected Map calloutPaths = new HashMap(); } figtree-1.4.3/src/figtree/treeviewer/treelayouts/TreeLayoutListener.java000077500000000000000000000020321277473563300266100ustar00rootroot00000000000000/* * TreeLayoutListener.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.treeviewer.treelayouts; /** * @author Andrew Rambaut * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public interface TreeLayoutListener { void treeLayoutChanged(); } figtree-1.4.3/src/figtree/ui/000077500000000000000000000000001277473563300160165ustar00rootroot00000000000000figtree-1.4.3/src/figtree/ui/FontChooserPanel.java000066400000000000000000000151211277473563300220720ustar00rootroot00000000000000/* ======================================================================== * JCommon : a free general purpose class library for the Java(tm) platform * ======================================================================== * * (C) Copyright 2000-2005, by Object Refinery Limited and Contributors. * * Project Info: http://www.jfree.org/jcommon/index.html * * This library is free software; you can redistribute it and/or modify it * under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or * (at your option) any later version. * * This library is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public * License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this library; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, * USA. * * [Java is a trademark or registered trademark of Sun Microsystems, Inc. * in the United States and other countries.] * * --------------------- * FontChooserPanel.java * --------------------- * (C) Copyright 2000-2004, by Object Refinery Limited. * * Original Author: David Gilbert (for Object Refinery Limited); * Contributor(s): Arnaud Lelievre; */ package figtree.ui; import java.awt.BorderLayout; import java.awt.Font; import java.awt.GraphicsEnvironment; import java.awt.GridLayout; import javax.swing.*; /** * A panel for choosing a font from the available system fonts * * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class FontChooserPanel extends JPanel { /** The font sizes that can be selected. */ public static final String[] SIZES = {"6", "8", "9", "10", "11", "12", "14", "16", "18", "20", "22", "24", "28", "36", "48", "72"}; /** The list of fonts. */ private JComboBox fontlist; /** The list of sizes. */ private JComboBox sizelist; /** The checkbox that indicates whether the font is bold. */ private JCheckBox boldCheck; /** The checkbox that indicates whether or not the font is italic. */ private JCheckBox italicCheck; /** * Standard constructor - builds a FontChooserPanel initialised with the specified font. * * @param font the initial font to display. */ public FontChooserPanel(final Font font) { final GraphicsEnvironment g = GraphicsEnvironment.getLocalGraphicsEnvironment(); final String[] fonts = g.getAvailableFontFamilyNames(); setLayout(new BorderLayout()); final JPanel leftPanel = new JPanel(new GridLayout(2, 1)); fontlist = new JComboBox(fonts); adjustComponent(fontlist); sizelist = new JComboBox(SIZES); adjustComponent(sizelist); leftPanel.add(fontlist); final JPanel sizePanel = new JPanel(new BorderLayout(3, 0)); final JLabel label = new JLabel("Size:"); adjustComponent(label); label.setHorizontalAlignment(JLabel.RIGHT); sizePanel.add(label, BorderLayout.CENTER); sizePanel.add(sizelist, BorderLayout.EAST); leftPanel.add(sizePanel); final JPanel rightPanel = new JPanel(new GridLayout(2, 1)); boldCheck = new JCheckBox("Bold"); adjustComponent(boldCheck); italicCheck = new JCheckBox("Italic"); adjustComponent(italicCheck); rightPanel.add(boldCheck); rightPanel.add(italicCheck); add(leftPanel, BorderLayout.CENTER); add(rightPanel, BorderLayout.EAST); setSelectedFont(font); } /** * Returns a Font object representing the selection in the panel. * * @return the font. */ public Font getSelectedFont() { return new Font(getSelectedName(), getSelectedStyle(), getSelectedSize()); } /** * Returns the selected name. * * @return the name. */ public String getSelectedName() { return (String) this.fontlist.getSelectedItem(); } /** * Returns the selected style. * * @return the style. */ public int getSelectedStyle() { if (this.boldCheck.isSelected() && this.italicCheck.isSelected()) { return Font.BOLD + Font.ITALIC; } if (this.boldCheck.isSelected()) { return Font.BOLD; } if (this.italicCheck.isSelected()) { return Font.ITALIC; } else { return Font.PLAIN; } } /** * Returns the selected size. * * @return the size. */ public int getSelectedSize() { final String selected = (String) this.sizelist.getSelectedItem(); if (selected != null) { return Integer.parseInt(selected); } else { return 10; } } /** * Initializes the contents of the dialog from the given font * object. * * @param font the font from which to read the properties. */ public void setSelectedFont (final Font font) { if (font == null) { throw new NullPointerException(); } this.boldCheck.setSelected(font.isBold()); this.italicCheck.setSelected(font.isItalic()); final String fontName = font.getName(); ListModel model = this.fontlist.getModel(); for (int i = 0; i < model.getSize(); i++) { if (fontName.equals(model.getElementAt(i))) { this.fontlist.setSelectedIndex(i); break; } } final String fontSize = String.valueOf(font.getSize()); model = this.sizelist.getModel(); for (int i = 0; i < model.getSize(); i++) { if (fontSize.equals(model.getElementAt(i))) { this.sizelist.setSelectedIndex(i); break; } } } protected void adjustComponent(JComponent comp) { // comp.putClientProperty("Quaqua.Component.visualMargin", new Insets(0,0,0,0)); Font font = UIManager.getFont("SmallSystemFont"); if (font != null) { comp.setFont(font); } comp.putClientProperty("JComponent.sizeVariant", "small"); if (comp instanceof JButton) { comp.putClientProperty("JButton.buttonType", "roundRect"); } if (comp instanceof JComboBox) { //comp.putClientProperty("JComboBox.isSquare", Boolean.TRUE); } } } figtree-1.4.3/src/figtree/ui/PercentFormat.java000077500000000000000000000141101277473563300214320ustar00rootroot00000000000000/* * PercentFormat.java * * Copyright (C) 2006-2014 Andrew Rambaut * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */ package figtree.ui; import java.text.*; /** * This NumberFormat converts numbers to and from percent notation. * Once an instance has been created, the format and parse methods may be used * as defined in java.text.NumberFormat. * * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class PercentFormat extends NumberFormat { private final NumberFormat nf; public PercentFormat() { this.nf = new DecimalFormat(); } /** * Returns the maximum number of digits allowed in the fraction portion of a * number. * * @see #setMaximumFractionDigits */ @Override public int getMaximumFractionDigits() { return nf.getMaximumFractionDigits(); } /** * Returns the maximum number of digits allowed in the integer portion of a * number. * * @see #setMaximumIntegerDigits */ @Override public int getMaximumIntegerDigits() { return nf.getMaximumIntegerDigits(); } /** * Returns the minimum number of digits allowed in the fraction portion of a * number. * * @see #setMinimumFractionDigits */ @Override public int getMinimumFractionDigits() { return nf.getMinimumFractionDigits(); } /** * Returns the minimum number of digits allowed in the integer portion of a * number. * * @see #setMinimumIntegerDigits */ @Override public int getMinimumIntegerDigits() { return nf.getMinimumIntegerDigits(); } /** * Sets the maximum number of digits allowed in the fraction portion of a * number. maximumFractionDigits must be >= minimumFractionDigits. If the * new value for maximumFractionDigits is less than the current value * of minimumFractionDigits, then minimumFractionDigits will also be set to * the new value. * * @param newValue the maximum number of fraction digits to be shown; if * less than zero, then zero is used. The concrete subclass may enforce an * upper limit to this value appropriate to the numeric type being formatted. * @see #getMaximumFractionDigits */ @Override public void setMaximumFractionDigits(int newValue) { nf.setMaximumFractionDigits(newValue); } /** * Sets the minimum number of digits allowed in the integer portion of a * number. minimumIntegerDigits must be <= maximumIntegerDigits. If the * new value for minimumIntegerDigits exceeds the current value * of maximumIntegerDigits, then maximumIntegerDigits will also be set to * the new value * * @param newValue the minimum number of integer digits to be shown; if * less than zero, then zero is used. The concrete subclass may enforce an * upper limit to this value appropriate to the numeric type being formatted. * @see #getMinimumIntegerDigits */ @Override public void setMinimumIntegerDigits(int newValue) { nf.setMinimumIntegerDigits(newValue); } /** * Sets the minimum number of digits allowed in the fraction portion of a * number. minimumFractionDigits must be <= maximumFractionDigits. If the * new value for minimumFractionDigits exceeds the current value * of maximumFractionDigits, then maximumIntegerDigits will also be set to * the new value * * @param newValue the minimum number of fraction digits to be shown; if * less than zero, then zero is used. The concrete subclass may enforce an * upper limit to this value appropriate to the numeric type being formatted. * @see #getMinimumFractionDigits */ @Override public void setMinimumFractionDigits(int newValue) { nf.setMinimumFractionDigits(newValue); } /** * Sets the maximum number of digits allowed in the integer portion of a * number. maximumIntegerDigits must be >= minimumIntegerDigits. If the * new value for maximumIntegerDigits is less than the current value * of minimumIntegerDigits, then minimumIntegerDigits will also be set to * the new value. * * @param newValue the maximum number of integer digits to be shown; if * less than zero, then zero is used. The concrete subclass may enforce an * upper limit to this value appropriate to the numeric type being formatted. * @see #getMaximumIntegerDigits */ @Override public void setMaximumIntegerDigits(int newValue) { nf.setMaximumIntegerDigits(newValue); } /** * Specialization of format. * * @see java.text.Format#format */ public StringBuffer format(double number, StringBuffer toAppendTo, FieldPosition pos) { return nf.format(number * 100.0, toAppendTo, pos).append("%"); } /** * Specialization of format. * * @see java.text.Format#format */ public StringBuffer format(long number, StringBuffer toAppendTo, FieldPosition pos) { return nf.format(number * 100, toAppendTo, pos).append("%"); } /** * @see java.text.Format#parseObject */ public Number parse(String source, ParsePosition parsePosition) { return nf.parse(source, parsePosition).doubleValue() / 100.0; } }figtree-1.4.3/src/figtree/ui/RomanFormat.java000077500000000000000000000152651277473563300211220ustar00rootroot00000000000000/* RomanFormat.java (5.1k) is a Java class for converting to/from Roman numerals. Whilst there are a number of styles for writing Roman numerals (several of which are implemented in the above code), there appears to be a simple algorithm that can correctly parse almost any 'reasonable'-looking Roman number (sufficiently simple that I'm inclined to treat it as a test for whether a number is valid or not). All this code is licensed under a BSD-like license. http://www.hawaga.org.uk/ben/tech/roman.html */ package figtree.ui; import java.text.*; /** * This NumberFormat converts long integers to and from Roman Numeral notation. * Once an instance has been created, the format and parse methods may be used * as defined in java.text.NumberFormat. * * @author Ben Clifford * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class RomanFormat extends NumberFormat { /** This method returns null. I have found no meaningful translation of floating point numbers to Roman numerals, however the NumberFormat method requires that it is implemented. Perhaps should just cast the double to a long and format accordingly. */ public StringBuffer format(double n, StringBuffer a, FieldPosition p) { return format((long)n, a, p); } /** This nested class is used to map Roman symbols onto their numerical values. Used in the Roman class. */ public static class SymTab { /** Roman symbol */ char symbol; /** Numerical value */ long value; /** Constructor to build a SymTab from supplied symbol and value @param s Roman symbol @param v Numerical value */ public SymTab(char s, long v) { this.symbol=s; this.value=v; } }; /** This table maps individual Roman symbols onto their numerical values.
Unfortunately, JavaDoc JDK 1.1 does not create documentation for the inner class Roman.SymTab, so the reader cannot see the definition. */ public static RomanFormat.SymTab syms[]= { new RomanFormat.SymTab('M',1000), new RomanFormat.SymTab('D',500), new RomanFormat.SymTab('C',100), new RomanFormat.SymTab('L',50), new RomanFormat.SymTab('X',10), new RomanFormat.SymTab('V',5), new RomanFormat.SymTab('I',1) }; /** This method converts a Roman Numeral string to a long integer. It does not check that the string is in the correct format - for some incorrectly formatted numbers, i.e. iix, it will produce a number. For others, it will throw an exception. @param text string of Roman Numerals @param parsePosition the place to start parsing @return A Long object containing the parsed Roman numeral */ public Number parse(String text, ParsePosition parsePosition) { String s = text.substring(parsePosition.getIndex()); long tot=0,max=0; char ch[]=s.toUpperCase().toCharArray(); int i,p; for(p=ch.length-1;p>=0;p--) { for(i=0;i=max) tot+= (max = syms[i].value); else tot-= syms[i].value; } } } // say that we parsed the whole string parsePosition.setIndex(s.length()); return new Long(tot); } /** This method converts a Roman Numeral string to a long integer. It does not check that the string is in the correct format - for some incorrectly formatted numbers, i.e. iix, it will produce a number. For others, it will throw an exception. @param s string of Roman Numerals @return The integer representation of the Numerals */ public static long toLong(String s) { long tot=0,max=0; char ch[]=s.toUpperCase().toCharArray(); int i,p; for(p=ch.length-1;p>=0;p--) { for(i=0;i=max) tot+= (max = syms[i].value); else tot-= syms[i].value; } } } return tot; }; /** This method converts the supplied long into capitalised Roman numerals.
BUG: the method does not take account of the FieldPosition p parameter. @param n The number to be converted into Roman numerals @param s The StringBuffer into which the output is to be placed. @return The StringBuffer s */ public StringBuffer format(long n, StringBuffer s, FieldPosition p) { int i; while(n>0) { for(i=0;i0 && shift0) { for(i=0;i0 && shift 0) { tickSpacing = minorTickSpacing; } else if (majorTickSpacing > 0) { tickSpacing = majorTickSpacing; } if (tickSpacing != 0) { // If it's not on a tick, change the value if ((upperValue - slider.getMinimum()) % tickSpacing != 0) { float temp = (float)(upperValue - slider.getMinimum()) / (float)tickSpacing; int whichTick = Math.round(temp); snappedValue = slider.getMinimum() + (whichTick * tickSpacing); } if (snappedValue != upperValue) { slider.setExtent(snappedValue - slider.getValue()); } } } // Calculate upper thumb location. The thumb is centered over its // value on the track. if (slider.getOrientation() == JSlider.HORIZONTAL) { int upperPosition = xPositionForValue(slider.getValue() + slider.getExtent()); // upperThumbRect.x = upperPosition - (upperThumbRect.width / 2); // upperThumbRect.y = trackRect.y; upperThumbRect.x = upperPosition - (upperThumbRect.width / 2); upperThumbRect.y = trackRect.y; } else { int upperPosition = yPositionForValue(slider.getValue() + slider.getExtent()); upperThumbRect.x = trackRect.x; upperThumbRect.y = upperPosition - (upperThumbRect.height / 2); } } /** * Returns the size of a thumb. */ @Override protected Dimension getThumbSize() { return new Dimension(12, 12); } /** * Paints the slider. The selected thumb is always painted on top of the * other thumb. */ @Override public void paint(Graphics g, JComponent c) { super.paint(g, c); Rectangle clipRect = g.getClipBounds(); if (upperThumbSelected) { // Paint lower thumb first, then upper thumb. if (clipRect.intersects(thumbRect)) { paintLowerThumb(g); } if (clipRect.intersects(upperThumbRect)) { paintUpperThumb(g); } } else { // Paint upper thumb first, then lower thumb. if (clipRect.intersects(upperThumbRect)) { paintUpperThumb(g); } if (clipRect.intersects(thumbRect)) { paintLowerThumb(g); } } } /** * Paints the track. */ @Override public void paintTrack(Graphics g) { // Draw track. super.paintTrack(g); Rectangle trackBounds = trackRect; if (slider.getOrientation() == JSlider.HORIZONTAL) { // Determine position of selected range by moving from the middle // of one thumb to the other. int lowerX = thumbRect.x + (thumbRect.width / 2); int upperX = upperThumbRect.x + (upperThumbRect.width / 2); // Determine track position. int cy = (trackBounds.height / 2) - 2; // Save color and shift position. Color oldColor = g.getColor(); g.translate(trackBounds.x, trackBounds.y + cy); // Draw selected range. g.setColor(rangeColor); for (int y = 0; y <= 3; y++) { g.drawLine(lowerX - trackBounds.x, y, upperX - trackBounds.x, y); } // Restore position and color. g.translate(-trackBounds.x, -(trackBounds.y + cy)); g.setColor(oldColor); } else { // Determine position of selected range by moving from the middle // of one thumb to the other. int lowerY = thumbRect.x + (thumbRect.width / 2); int upperY = upperThumbRect.x + (upperThumbRect.width / 2); // Determine track position. int cx = (trackBounds.width / 2) - 2; // Save color and shift position. Color oldColor = g.getColor(); g.translate(trackBounds.x + cx, trackBounds.y); // Draw selected range. g.setColor(rangeColor); for (int x = 0; x <= 3; x++) { g.drawLine(x, lowerY - trackBounds.y, x, upperY - trackBounds.y); } // Restore position and color. g.translate(-(trackBounds.x + cx), -trackBounds.y); g.setColor(oldColor); } } /** * Overrides superclass method to do nothing. Thumb painting is handled * within the paint() method. */ @Override public void paintThumb(Graphics g) { // Do nothing. } /** * Paints the thumb for the lower value using the specified graphics object. */ private void paintLowerThumb(Graphics g) { Rectangle knobBounds = thumbRect; int w = knobBounds.width; int h = knobBounds.height; // Create graphics copy. Graphics2D g2d = (Graphics2D) g.create(); // Create default thumb shape. Shape thumbShape = createThumbShape(w - 1, h - 1, false); // Draw thumb. g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2d.translate(knobBounds.x, knobBounds.y); g2d.setColor(Color.LIGHT_GRAY); g2d.fill(thumbShape); g2d.setColor(Color.GRAY); g2d.draw(thumbShape); // Dispose graphics. g2d.dispose(); } /** * Paints the thumb for the upper value using the specified graphics object. */ private void paintUpperThumb(Graphics g) { Rectangle knobBounds = upperThumbRect; int w = knobBounds.width; int h = knobBounds.height; // Create graphics copy. Graphics2D g2d = (Graphics2D) g.create(); // Create default thumb shape. Shape thumbShape = createThumbShape(w - 1, h - 1, true); // Draw thumb. g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2d.translate(knobBounds.x, knobBounds.y); g2d.setColor(Color.LIGHT_GRAY); g2d.fill(thumbShape); g2d.setColor(Color.GRAY); g2d.draw(thumbShape); // Dispose graphics. g2d.dispose(); } /** * Returns a Shape representing a thumb. */ private Shape createThumbShape(int width, int height, boolean upper) { // Use circular shape. // Ellipse2D shape = new Ellipse2D.Double(0, 0, width, height); // return shape; Path2D path = new Path2D.Float(); if (slider.getOrientation() == JSlider.HORIZONTAL) { float d = 0.5F * width; path.moveTo(d, 0); path.lineTo((upper ? width : 0.0), d); path.lineTo((upper ? width : 0.0), height); path.lineTo(0.5 * width, height); } else { float d = 0.5F * height; path.moveTo(0, d); path.lineTo(d, (upper ? height : 0.0)); path.lineTo(width, (upper ? height : 0.0)); path.lineTo(height, 0.5 * height); } path.closePath(); return path; } /** * Sets the location of the upper thumb, and repaints the slider. This is * called when the upper thumb is dragged to repaint the slider. The * setThumbLocation() method performs the same task for the * lower thumb. */ private void setUpperThumbLocation(int x, int y) { Rectangle upperUnionRect = new Rectangle(); upperUnionRect.setBounds(upperThumbRect); upperThumbRect.setLocation(x, y); SwingUtilities.computeUnion(upperThumbRect.x, upperThumbRect.y, upperThumbRect.width, upperThumbRect.height, upperUnionRect); slider.repaint(upperUnionRect.x, upperUnionRect.y, upperUnionRect.width, upperUnionRect.height); } /** * Moves the selected thumb in the specified direction by a block increment. * This method is called when the user presses the Page Up or Down keys. */ public void scrollByBlock(int direction) { synchronized (slider) { int blockIncrement = (slider.getMaximum() - slider.getMinimum()) / 10; if (blockIncrement <= 0 && slider.getMaximum() > slider.getMinimum()) { blockIncrement = 1; } int delta = blockIncrement * ((direction > 0) ? POSITIVE_SCROLL : NEGATIVE_SCROLL); if (upperThumbSelected) { int oldValue = ((RangeSlider) slider).getUpperValue(); ((RangeSlider) slider).setUpperValue(oldValue + delta); } else { int oldValue = slider.getValue(); slider.setValue(oldValue + delta); } } } /** * Moves the selected thumb in the specified direction by a unit increment. * This method is called when the user presses one of the arrow keys. */ public void scrollByUnit(int direction) { synchronized (slider) { int delta = 1 * ((direction > 0) ? POSITIVE_SCROLL : NEGATIVE_SCROLL); if (upperThumbSelected) { int oldValue = ((RangeSlider) slider).getUpperValue(); ((RangeSlider) slider).setUpperValue(oldValue + delta); } else { int oldValue = slider.getValue(); slider.setValue(oldValue + delta); } } } /** * Listener to handle model change events. This calculates the thumb * locations and repaints the slider if the value change is not caused by * dragging a thumb. */ public class ChangeHandler implements ChangeListener { public void stateChanged(ChangeEvent arg0) { if (!lowerDragging && !upperDragging) { calculateThumbLocation(); slider.repaint(); } } } /** * Listener to handle mouse movements in the slider track. */ public class RangeTrackListener extends TrackListener { @Override public void mousePressed(MouseEvent e) { if (!slider.isEnabled()) { return; } currentMouseX = e.getX(); currentMouseY = e.getY(); if (slider.isRequestFocusEnabled()) { slider.requestFocus(); } // Determine which thumb is pressed. If the upper thumb is // selected (last one dragged), then check its position first; // otherwise check the position of the lower thumb first. // if (upperThumbSelected) { // if (upperThumbRect.contains(currentMouseX, currentMouseY)) { // upperPressed = true; // } else if (thumbRect.contains(currentMouseX, currentMouseY)) { // lowerPressed = true; // } // } else { // if (thumbRect.contains(currentMouseX, currentMouseY)) { // lowerPressed = true; // } else if (upperThumbRect.contains(currentMouseX, currentMouseY)) { // upperPressed = true; // } // } // Determine which thumb is pressed. First check against the upper // slider rects top half... boolean lowerPressed = false; boolean upperPressed = false; Rectangle urect = new Rectangle(upperThumbRect); Rectangle lrect = new Rectangle(thumbRect); if (slider.getOrientation() == JSlider.HORIZONTAL) { urect.width = (int)Math.round(0.5 * urect.width); urect.x += urect.width; lrect.width = urect.width; } else { urect.height = (int)Math.round(0.5 * urect.height); urect.y += urect.height; lrect.height = urect.height; } if (urect.contains(currentMouseX, currentMouseY)) { upperPressed = true; } else if (lrect.contains(currentMouseX, currentMouseY)) { lowerPressed = true; } // Handle lower thumb pressed. if (lowerPressed) { switch (slider.getOrientation()) { case JSlider.VERTICAL: offset = currentMouseY - thumbRect.y; break; case JSlider.HORIZONTAL: offset = currentMouseX - thumbRect.x; break; } upperThumbSelected = false; lowerDragging = true; return; } lowerDragging = false; // Handle upper thumb pressed. if (upperPressed) { switch (slider.getOrientation()) { case JSlider.VERTICAL: offset = currentMouseY - upperThumbRect.y; break; case JSlider.HORIZONTAL: offset = currentMouseX - upperThumbRect.x; break; } upperThumbSelected = true; upperDragging = true; return; } upperDragging = false; } @Override public void mouseReleased(MouseEvent e) { lowerDragging = false; upperDragging = false; slider.setValueIsAdjusting(false); super.mouseReleased(e); } @Override public void mouseDragged(MouseEvent e) { if (!slider.isEnabled()) { return; } currentMouseX = e.getX(); currentMouseY = e.getY(); if (lowerDragging) { slider.setValueIsAdjusting(true); moveLowerThumb(); } else if (upperDragging) { slider.setValueIsAdjusting(true); moveUpperThumb(); } } @Override public boolean shouldScroll(int direction) { return false; } /** * Moves the location of the lower thumb, and sets its corresponding * value in the slider. */ private void moveLowerThumb() { int thumbMiddle = 0; switch (slider.getOrientation()) { case JSlider.VERTICAL: int halfThumbHeight = thumbRect.height / 2; int thumbTop = currentMouseY - offset; int trackTop = trackRect.y; int trackBottom = trackRect.y + (trackRect.height - 1); int vMax = yPositionForValue(slider.getValue() + slider.getExtent()); // Apply bounds to thumb position. if (drawInverted()) { trackBottom = vMax; } else { trackTop = vMax; } thumbTop = Math.max(thumbTop, trackTop - halfThumbHeight); thumbTop = Math.min(thumbTop, trackBottom - halfThumbHeight); setThumbLocation(thumbRect.x, thumbTop); // Update slider value. thumbMiddle = thumbTop + halfThumbHeight; slider.setValue(valueForYPosition(thumbMiddle)); break; case JSlider.HORIZONTAL: int halfThumbWidth = thumbRect.width / 2; int thumbLeft = currentMouseX - offset; int trackLeft = trackRect.x; int trackRight = trackRect.x + (trackRect.width - 1); int hMax = xPositionForValue(slider.getValue() + slider.getExtent()); // Apply bounds to thumb position. if (drawInverted()) { trackLeft = hMax; } else { trackRight = hMax; } thumbLeft = Math.max(thumbLeft, trackLeft - halfThumbWidth); thumbLeft = Math.min(thumbLeft, trackRight - halfThumbWidth); setThumbLocation(thumbLeft, thumbRect.y); // Update slider value. thumbMiddle = thumbLeft + halfThumbWidth; slider.setValue(valueForXPosition(thumbMiddle)); break; default: return; } } /** * Moves the location of the upper thumb, and sets its corresponding * value in the slider. */ private void moveUpperThumb() { int thumbMiddle = 0; switch (slider.getOrientation()) { case JSlider.VERTICAL: int halfThumbHeight = thumbRect.height / 2; int thumbTop = currentMouseY - offset; int trackTop = trackRect.y; int trackBottom = trackRect.y + (trackRect.height - 1); int vMin = yPositionForValue(slider.getValue()); // Apply bounds to thumb position. if (drawInverted()) { trackTop = vMin; } else { trackBottom = vMin; } thumbTop = Math.max(thumbTop, trackTop - halfThumbHeight); thumbTop = Math.min(thumbTop, trackBottom - halfThumbHeight); setUpperThumbLocation(thumbRect.x, thumbTop); // Update slider extent. thumbMiddle = thumbTop + halfThumbHeight; slider.setExtent(valueForYPosition(thumbMiddle) - slider.getValue()); break; case JSlider.HORIZONTAL: int halfThumbWidth = thumbRect.width / 2; int thumbLeft = currentMouseX - offset; int trackLeft = trackRect.x; int trackRight = trackRect.x + (trackRect.width - 1); int hMin = xPositionForValue(slider.getValue()); // Apply bounds to thumb position. if (drawInverted()) { trackRight = hMin; } else { trackLeft = hMin; } thumbLeft = Math.max(thumbLeft, trackLeft - halfThumbWidth); thumbLeft = Math.min(thumbLeft, trackRight - halfThumbWidth); setUpperThumbLocation(thumbLeft, thumbRect.y); // Update slider extent. thumbMiddle = thumbLeft + halfThumbWidth; slider.setExtent(valueForXPosition(thumbMiddle) - slider.getValue()); break; default: return; } } } } figtree-1.4.3/src/figtree/ui/components/RealNumberField.java000066400000000000000000000157221277473563300240550ustar00rootroot00000000000000/* * The contents of this file are subject to the BT "ZEUS" Open Source * Licence (L77741), Version 1.0 (the "Licence"); you may not use this file * except in compliance with the Licence. You may obtain a copy of the Licence * from $ZEUS_INSTALL/licence.html or alternatively from * http://www.labs.bt.com/projects/agents/zeus/licence.htm * * Except as stated in Clause 7 of the Licence, software distributed under the * Licence is distributed WITHOUT WARRANTY OF ANY KIND, either express or * implied. See the Licence for the specific language governing rights and * limitations under the Licence. * * The Original Code is within the package zeus.*. * The Initial Developer of the Original Code is British Telecommunications * public limited company, whose registered office is at 81 Newgate Street, * London, EC1A 7AJ, England. Portions created by British Telecommunications * public limited company are Copyright 1996-9. All Rights Reserved. * * THIS NOTICE MUST BE INCLUDED ON ANY COPY OF THIS FILE */ package figtree.ui.components; import javax.swing.*; import javax.swing.event.*; import javax.swing.text.AttributeSet; import javax.swing.text.BadLocationException; import javax.swing.text.Document; import javax.swing.text.PlainDocument; import java.awt.*; import java.awt.event.FocusEvent; import java.awt.event.FocusListener; /** * * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class RealNumberField extends JTextField implements FocusListener, DocumentListener { protected static char MINUS = '-'; protected static char PERIOD = '.'; protected EventListenerList changeListeners = new EventListenerList(); protected double min; protected double max; protected boolean range_check = false; protected boolean range_checked = false; public RealNumberField() { super(); } public RealNumberField(double min, double max) { this(); this.min = min; this.max = max; range_check = true; this.addFocusListener(this); } public void focusGained(FocusEvent evt) { } public void focusLost(FocusEvent evt) { if (range_check && !range_checked) { range_checked = true; try { double value = (Double.valueOf(getText())).doubleValue(); if (value < min || value > max) { errorMsg(); return; } } catch (NumberFormatException e) { errorMsg(); return; } } } public void setText(Double obj) { setText(obj.toString()); } public void setText(Integer obj) { setText(obj.toString()); } public void setText(Long obj) { setText(obj.toString()); } protected void errorMsg() { JOptionPane.showMessageDialog(this, "Illegal entry\nValue must be between " + min + " and " + max + " inclusive", "Error", JOptionPane.ERROR_MESSAGE); } public void setRange(double min, double max) { this.min = min; this.max = max; range_check = true; } public void setValue(double value) { if (range_check) { if (value < min || value > max) { errorMsg(); return; } } setText(Double.toString(value)); } public Double getValue() { try { return new Double(getText()); } catch (NumberFormatException e) { return null; } } public Double getValue(double def) { try { return new Double(getText()); } catch (NumberFormatException e) { return new Double(def); } } protected Document createDefaultModel() { Document doc = new RealNumberFieldDocument(); doc.addDocumentListener(this); return doc; } public void insertUpdate(DocumentEvent e) { range_checked = false; fireChanged(); } public void removeUpdate(DocumentEvent e) { range_checked = false; fireChanged(); } public void changedUpdate(DocumentEvent e) { range_checked = false; fireChanged(); } static char[] numberSet = { '0', '1', '2', '3', '4', '5', '6', '7', '8', '9' }; class RealNumberFieldDocument extends PlainDocument { public void insertString(int offs, String str, AttributeSet a) throws BadLocationException { if (str == null) return; str = str.trim(); int length = getLength(); String buf = getText(0, offs) + str + getText(offs, length - offs); buf = buf.trim().toUpperCase(); char[] array = buf.toCharArray(); if (array.length > 0) { if (array[0] != MINUS && !member(array[0], numberSet) && array[0] != PERIOD) { Toolkit.getDefaultToolkit().beep(); return; } } boolean period_found = (array.length > 0 && array[0] == PERIOD); boolean exponent_found = false; int exponent_index = -1; boolean exponent_sign_found = false; for (int i = 1; i < array.length; i++) { if (!member(array[i], numberSet)) { if (!period_found && array[i] == PERIOD) { period_found = true; } else if (!exponent_found && array[i] == 'E') { exponent_found = true; exponent_index = i; } else if (exponent_found && i == (exponent_index + 1) && !exponent_sign_found && array[i] == '-') { exponent_sign_found = true; } else { Toolkit.getDefaultToolkit().beep(); return; } } } super.insertString(offs, str, a); } } static boolean member(char item, char[] array) { for (int i = 0; i < array.length; i++) if (array[i] == item) return true; return false; } //------------------------------------------------------------------------ // Event Methods //------------------------------------------------------------------------ public void addChangeListener(ChangeListener x) { changeListeners.add(ChangeListener.class, x); } public void removeChangeListener(ChangeListener x) { changeListeners.remove(ChangeListener.class, x); } protected void fireChanged() { ChangeEvent c = new ChangeEvent(this); Object[] listeners = changeListeners.getListenerList(); for (int i = listeners.length - 2; i >= 0; i -= 2) { if (listeners[i] == ChangeListener.class) { ChangeListener cl = (ChangeListener) listeners[i + 1]; cl.stateChanged(c); } } } } figtree-1.4.3/src/figtree/ui/components/WholeNumberField.java000066400000000000000000000134561277473563300242520ustar00rootroot00000000000000/* * The contents of this file are subject to the BT "ZEUS" Open Source * Licence (L77741), Version 1.0 (the "Licence"); you may not use this file * except in compliance with the Licence. You may obtain a copy of the Licence * from $ZEUS_INSTALL/licence.html or alternatively from * http://www.labs.bt.com/projects/agents/zeus/licence.htm * * Except as stated in Clause 7 of the Licence, software distributed under the * Licence is distributed WITHOUT WARRANTY OF ANY KIND, either express or * implied. See the Licence for the specific language governing rights and * limitations under the Licence. * * The Original Code is within the package zeus.*. * The Initial Developer of the Original Code is British Telecommunications * public limited company, whose registered office is at 81 Newgate Street, * London, EC1A 7AJ, England. Portions created by British Telecommunications * public limited company are Copyright 1996-9. All Rights Reserved. * * THIS NOTICE MUST BE INCLUDED ON ANY COPY OF THIS FILE */ package figtree.ui.components; import javax.swing.*; import javax.swing.event.*; import javax.swing.text.AttributeSet; import javax.swing.text.BadLocationException; import javax.swing.text.Document; import javax.swing.text.PlainDocument; import java.awt.*; import java.awt.event.FocusEvent; import java.awt.event.FocusListener; /** * * @version $Id$ * * $HeadURL$ * * $LastChangedBy$ * $LastChangedDate$ * $LastChangedRevision$ */ public class WholeNumberField extends JTextField implements FocusListener, DocumentListener { protected static char MINUS_CHAR = '-'; protected EventListenerList changeListeners = new EventListenerList(); protected int min; protected int max; protected boolean range_check = false; protected boolean range_checked = false; public WholeNumberField() { super(); } public WholeNumberField(int min, int max) { this(); this.min = min; this.max = max; range_check = true; this.addFocusListener(this); } public void focusGained(FocusEvent evt) { } public void focusLost(FocusEvent evt) { if (range_check && !range_checked) { range_checked = true; try { int value = (Integer.valueOf(getText())).intValue(); if (value < min || value > max) { errorMsg(); return; } } catch (NumberFormatException e) { errorMsg(); return; } } } public void setText(Integer obj) { setText(obj.toString()); } protected void errorMsg() { JOptionPane.showMessageDialog(this, "Illegal entry\nValue must be between " + min + " and " + max + " inclusive", "Error", JOptionPane.ERROR_MESSAGE); } public void setValue(int value) { if (range_check) { if (value < min || value > max) { errorMsg(); return; } } setText(Integer.toString(value)); } public Integer getValue() { try { return new Integer(getText()); } catch (NumberFormatException e) { return null; } } public Integer getValue(int default_value) { Integer value = getValue(); if (value == null) return new Integer(default_value); else return value; } protected Document createDefaultModel() { Document doc = new WholeNumberFieldDocument(); doc.addDocumentListener(this); return doc; } public void insertUpdate(DocumentEvent e) { range_checked = false; fireChanged(); } public void removeUpdate(DocumentEvent e) { range_checked = false; fireChanged(); } public void changedUpdate(DocumentEvent e) { range_checked = false; fireChanged(); } static char[] numberSet = { '0', '1', '2', '3', '4', '5', '6', '7', '8', '9' }; class WholeNumberFieldDocument extends PlainDocument { public void insertString(int offs, String str, AttributeSet a) throws BadLocationException { if (str == null) return; str = str.trim(); String buf = getText(0, offs) + str; char[] array = buf.toCharArray(); if (array.length > 0) { if (array[0] != MINUS_CHAR && !member(array[0], numberSet)) { Toolkit.getDefaultToolkit().beep(); return; } } for (int i = 1; i < array.length; i++) { if (!member(array[i], numberSet)) { Toolkit.getDefaultToolkit().beep(); return; } } super.insertString(offs, str, a); } } static boolean member(char item, char[] array) { for (int i = 0; i < array.length; i++) if (array[i] == item) return true; return false; } //------------------------------------------------------------------------ // Event Methods //------------------------------------------------------------------------ public void addChangeListener(ChangeListener x) { changeListeners.add(ChangeListener.class, x); } public void removeChangeListener(ChangeListener x) { changeListeners.remove(ChangeListener.class, x); } protected void fireChanged() { ChangeEvent c = new ChangeEvent(this); Object[] listeners = changeListeners.getListenerList(); for (int i = listeners.length - 2; i >= 0; i -= 2) { if (listeners[i] == ChangeListener.class) { ChangeListener cl = (ChangeListener) listeners[i + 1]; cl.stateChanged(c); } } } } figtree-1.4.3/src/figtree/webui/000077500000000000000000000000001277473563300165145ustar00rootroot00000000000000figtree-1.4.3/src/figtree/webui/FigTreeWebApplication.java000066400000000000000000000233631277473563300235350ustar00rootroot00000000000000package figtree.webui; import java.awt.BasicStroke; import java.awt.Font; import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; import java.io.Reader; import java.text.DecimalFormat; import java.util.ArrayList; import java.util.List; import jebl.evolution.io.ImportException; import jebl.evolution.io.NewickImporter; import jebl.evolution.trees.RootedTree; import jebl.evolution.trees.SortedRootedTree; import jebl.evolution.trees.TransformedRootedTree; import jebl.evolution.trees.Tree; import eu.webtoolkit.jwt.AlignmentFlag; import eu.webtoolkit.jwt.Signal; import eu.webtoolkit.jwt.Signal1.Listener; import eu.webtoolkit.jwt.WApplication; import eu.webtoolkit.jwt.WBoxLayout; import eu.webtoolkit.jwt.WCheckBox; import eu.webtoolkit.jwt.WComboBox; import eu.webtoolkit.jwt.WContainerWidget; import eu.webtoolkit.jwt.WEnvironment; import eu.webtoolkit.jwt.WFormWidget; import eu.webtoolkit.jwt.WHBoxLayout; import eu.webtoolkit.jwt.WIntValidator; import eu.webtoolkit.jwt.WLabel; import eu.webtoolkit.jwt.WLength; import eu.webtoolkit.jwt.WSpinBox; import eu.webtoolkit.jwt.WVBoxLayout; import figtree.application.FigTreeNexusImporter; import figtree.panel.SimpleLabelPainter; import figtree.treeviewer.TreePane; import figtree.treeviewer.treelayouts.PolarTreeLayout; import figtree.treeviewer.treelayouts.RadialTreeLayout; import figtree.treeviewer.treelayouts.RectilinearTreeLayout; public class FigTreeWebApplication extends WApplication { private TreeWidget treeWidget; private SimpleLabelPainter tipPainter; private SimpleLabelPainter nodePainter; private SimpleLabelPainter branchPainter; public FigTreeWebApplication(WEnvironment env) { super(env); setTitle("FigTree"); useStyleSheet("figtree.css"); WVBoxLayout layout = new WVBoxLayout(getRoot()); FileUploadWidget uploadWidget = new FileUploadWidget(); uploadWidget.fileUploaded().addListener(this, new Listener() { @Override public void trigger(String path) { readFile(path); } }); layout.addWidget(uploadWidget); layout.addWidget(treeWidget = new TreeWidget(), 1); treeWidget.setStyleClass("tree"); readFile("/etc/figtree/example.tree"); treeWidget.getTreePane().setTipLabelPainter (tipPainter = new SimpleLabelPainter(SimpleLabelPainter.PainterIntent.TIP)); treeWidget.getTreePane().setNodeLabelPainter (nodePainter = new SimpleLabelPainter(SimpleLabelPainter.PainterIntent.NODE)); treeWidget.getTreePane().setBranchLabelPainter (branchPainter = new SimpleLabelPainter(SimpleLabelPainter.PainterIntent.BRANCH)); createControls(layout); } private void readFile(String path) { try { FileReader reader = new FileReader(path); readData(reader, true); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } private void createControls(WVBoxLayout layout) { WHBoxLayout controlsLayout = new WHBoxLayout(); layout.addLayout(controlsLayout, 0, AlignmentFlag.AlignJustify, AlignmentFlag.AlignTop); WVBoxLayout column = new WVBoxLayout(); controlsLayout.addLayout(column, 0, AlignmentFlag.AlignJustify, AlignmentFlag.AlignMiddle); WComboBox box = new WComboBox(); addField(column, "Layout: ", box, AlignmentFlag.AlignLeft); box.addItem("Rectilinear"); box.addItem("Radial"); box.addItem("Polar"); box.activated().addListener(this, new Listener() { @Override public void trigger(Integer choice) { switch (choice) { case 0: treeWidget.getTreePane().setTreeLayout(new RectilinearTreeLayout()); break; case 1: treeWidget.getTreePane().setTreeLayout(new RadialTreeLayout()); break; case 2: treeWidget.getTreePane().setTreeLayout(new PolarTreeLayout()); } } }); column = new WVBoxLayout(); controlsLayout.addLayout(column, 0, AlignmentFlag.AlignJustify, AlignmentFlag.AlignMiddle); WSpinBox spinBox = new WSpinBox(); spinBox.setValue(2); spinBox.setRange(0, 48); spinBox.setMaxLength(3); addField(column, "Line Weight: ", spinBox, AlignmentFlag.AlignRight); spinBox.valueChanged().addListener(this, new Listener() { @Override public void trigger(Double value) { treeWidget.getTreePane().setBranchStroke(new BasicStroke(value.floatValue())); } }); spinBox.valueChanged().trigger(spinBox.getValue()); spinBox = new WSpinBox(); spinBox.setValue(6); spinBox.setRange(0, 48); spinBox.setValidator(new WIntValidator(0, 48)); spinBox.setMaxLength(3); addField(column, "Font Size: ", spinBox, AlignmentFlag.AlignRight); spinBox.valueChanged().addListener(this, new Listener() { @Override public void trigger(Double value) { tipPainter.setFont(new Font("sansserif", Font.PLAIN, value.intValue())); } }); spinBox.valueChanged().trigger(spinBox.getValue()); column = new WVBoxLayout(); controlsLayout.addLayout(column, 0, AlignmentFlag.AlignJustify, AlignmentFlag.AlignMiddle); final WCheckBox midPointCheck = new WCheckBox("Midpoint root"); midPointCheck.setChecked(false); addField(column, null, midPointCheck, AlignmentFlag.AlignRight); midPointCheck.changed().addListener(this, new Signal.Listener() { @Override public void trigger() { if (midPointCheck.isChecked()) { treeWidget.getTreePane().setRootingOn(true); treeWidget.getTreePane().setRootingType(TreePane.RootingType.MID_POINT); } else { treeWidget.getTreePane().setRootingOn(false); treeWidget.getTreePane().setRootingType(TreePane.RootingType.USER_ROOTING); } } }); final WComboBox orderCombo = new WComboBox(); orderCombo.addItem("Off"); orderCombo.addItem("Increasing"); orderCombo.addItem("Decreasing"); orderCombo.resize(new WLength(120), WLength.Auto); addField(column, "Order: ", orderCombo, AlignmentFlag.AlignRight); orderCombo.changed().addListener(this, new Signal.Listener() { @Override public void trigger() { if (orderCombo.getCurrentIndex() == 0) { treeWidget.getTreePane().setOrderBranchesOn(false); } else { treeWidget.getTreePane().setOrderBranchesOn(true); treeWidget.getTreePane().setBranchOrdering(SortedRootedTree.BranchOrdering.values()[orderCombo.getCurrentIndex() - 1]); } } }); final WComboBox transformCombo = new WComboBox(); transformCombo.addItem("Off"); transformCombo.addItem(TransformedRootedTree.Transform.CLADOGRAM.toString()); transformCombo.addItem(TransformedRootedTree.Transform.PROPORTIONAL.toString()); transformCombo.addItem(TransformedRootedTree.Transform.EQUAL_LENGTHS.toString()); transformCombo.resize(new WLength(120), WLength.Auto); addField(column, "Transform: ", transformCombo, AlignmentFlag.AlignRight); transformCombo.changed().addListener(this, new Signal.Listener() { @Override public void trigger() { if (transformCombo.getCurrentIndex() == 0) { treeWidget.getTreePane().setTransformBranchesOn(false); } else { treeWidget.getTreePane().setTransformBranchesOn(true); treeWidget.getTreePane().setBranchTransform(TransformedRootedTree.Transform.values()[transformCombo.getCurrentIndex() - 1]); } } }); column = new WVBoxLayout(); controlsLayout.addLayout(column, 0, AlignmentFlag.AlignJustify, AlignmentFlag.AlignMiddle); WComboBox combo = addLabelCombo(column, tipPainter, "Tips: "); combo.setCurrentIndex(1); combo.changed().trigger(); addLabelCombo(column, nodePainter, "Nodes: "); addLabelCombo(column, branchPainter, "Branches: "); } private WComboBox addLabelCombo(WVBoxLayout column, final SimpleLabelPainter labelPainter, String title) { labelPainter.setNumberFormat(new DecimalFormat("#.####")); labelPainter.setFont(new Font("sansserif", Font.PLAIN, 8)); String[] attributes = labelPainter.getAttributes(); final WComboBox displayAttributeCombo = new WComboBox(); displayAttributeCombo.addItem("None"); for (String attr : attributes) { displayAttributeCombo.addItem(attr); } addField(column, title, displayAttributeCombo, AlignmentFlag.AlignRight); displayAttributeCombo.changed().addListener(this, new Signal.Listener() { @Override public void trigger() { String attribute = (String)displayAttributeCombo.getCurrentText().toString(); if (attribute.equals("none")) { labelPainter.setVisible(false); } else { labelPainter.setDisplayAttribute(attribute); labelPainter.setVisible(true); } } }); displayAttributeCombo.changed().trigger(); return displayAttributeCombo; } private void addField(WBoxLayout controlsLayout, String label, WFormWidget widget, AlignmentFlag alignment) { WContainerWidget w = new WContainerWidget(); if (label != null) { WLabel l; w.addWidget(l = new WLabel(label)); l.setBuddy(widget); } w.addWidget(widget); controlsLayout.addWidget(w, 0, alignment, AlignmentFlag.AlignTop); } protected boolean readData(Reader reader, boolean isNexus) throws IOException { List trees = new ArrayList(); try { if (isNexus) { FigTreeNexusImporter importer = new FigTreeNexusImporter(reader); while (importer.hasTree()) { Tree tree = importer.importNextTree(); trees.add(tree); } } else { NewickImporter importer = new NewickImporter(reader, true); while (importer.hasTree()) { Tree tree = importer.importNextTree(); trees.add(tree); } } if (trees.size() == 0) { throw new ImportException("This file contained no trees."); } treeWidget.getTreePane().setTree((RootedTree) trees.get(0)); } catch (ImportException ie) { // FIXME return false; } return true; } } figtree-1.4.3/src/figtree/webui/FileUploadWidget.java000066400000000000000000000027041277473563300225520ustar00rootroot00000000000000package figtree.webui; import eu.webtoolkit.jwt.Side; import eu.webtoolkit.jwt.Signal; import eu.webtoolkit.jwt.Signal1; import eu.webtoolkit.jwt.WApplication; import eu.webtoolkit.jwt.WContainerWidget; import eu.webtoolkit.jwt.WFileUpload; import eu.webtoolkit.jwt.WLabel; import eu.webtoolkit.jwt.WText; public class FileUploadWidget extends WContainerWidget { private WFileUpload fileUpload; private Signal1 fileUploaded = new Signal1(); private WLabel label; private WText currentTree; public FileUploadWidget() { currentTree = new WText(this); currentTree.setStyleClass("filename"); currentTree.setInline(false); currentTree.setFloatSide(Side.Right); label = new WLabel("Upload tree: ", this); createUpload(); } private void createUpload() { fileUpload = new WFileUpload(this); fileUpload.changed().addListener(this, new Signal.Listener() { @Override public void trigger() { fileUpload.upload(); } }); fileUpload.uploaded().addListener(this, new Signal.Listener() { @Override public void trigger() { handleUpload(); } }); } private void handleUpload() { WApplication.getInstance().setTitle("FigTree: " + fileUpload.getClientFileName()); currentTree.setText("Read file: " + fileUpload.getClientFileName() + ""); fileUploaded.trigger(fileUpload.getSpoolFileName()); fileUpload.remove(); createUpload(); } public Signal1 fileUploaded() { return fileUploaded; } } figtree-1.4.3/src/figtree/webui/Main.java000066400000000000000000000005731277473563300202500ustar00rootroot00000000000000package figtree.webui; import eu.webtoolkit.jwt.WApplication; import eu.webtoolkit.jwt.WEnvironment; import eu.webtoolkit.jwt.WtServlet; public class Main extends WtServlet { /** * */ private static final long serialVersionUID = -7955893733032239397L; @Override public WApplication createApplication(WEnvironment env) { return new FigTreeWebApplication(env); } } figtree-1.4.3/src/figtree/webui/TreeWidget.java000066400000000000000000000075041277473563300214300ustar00rootroot00000000000000package figtree.webui; import java.awt.Color; import java.awt.Graphics; import java.awt.event.MouseEvent; import eu.webtoolkit.jwt.KeyboardModifier; import eu.webtoolkit.jwt.Signal1; import eu.webtoolkit.jwt.WLength; import eu.webtoolkit.jwt.WMouseEvent; import eu.webtoolkit.jwt.WPaintDevice; import eu.webtoolkit.jwt.WPaintedWidget; import eu.webtoolkit.jwt.WPainter; import eu.webtoolkit.jwt.WMouseEvent.Button; import eu.webtoolkit.jwt.utils.WebGraphics2D; import figtree.treeviewer.TreePane; import figtree.treeviewer.TreePaneSelector; import figtree.treeviewer.treelayouts.RectilinearTreeLayout; public class TreeWidget extends WPaintedWidget { private TreePane treePane; private WebGraphics2D graphics = new WebGraphics2D(new WPainter()); public TreeWidget() { treePane = new TreePane() { private static final long serialVersionUID = 1L; @Override public void repaint() { TreeWidget.this.update(); } @Override public Graphics getGraphics() { return graphics; } }; treePane.setTreeLayout(new RectilinearTreeLayout()); treePane.setSelectionColor(new Color(90, 108, 128)); final TreePaneSelector selector = new TreePaneSelector(treePane); clicked().addListener(this, new Signal1.Listener() { @Override public void trigger(WMouseEvent event) { int dx = event.getDragDelta().x; int dy = event.getDragDelta().y; if (dx*dx + dy*dy < 4) selector.mouseClicked(convertMouseEvent(event, MouseEvent.MOUSE_CLICKED)); } }); mouseWentDown().addListener(this, new Signal1.Listener() { @Override public void trigger(WMouseEvent event) { selector.mousePressed(convertMouseEvent(event, MouseEvent.MOUSE_PRESSED)); } }); mouseWentUp().addListener(this, new Signal1.Listener() { @Override public void trigger(WMouseEvent event) { selector.mouseReleased(convertMouseEvent(event, MouseEvent.MOUSE_RELEASED)); } }); mouseDragged().addListener(this, new Signal1.Listener() { @Override public void trigger(WMouseEvent event) { selector.mouseDragged(convertMouseEvent(event, MouseEvent.MOUSE_DRAGGED)); } }); } MouseEvent convertMouseEvent(WMouseEvent event, int type) { int modifiers = 0; if (event.getModifiers().contains(KeyboardModifier.AltModifier)) modifiers |= MouseEvent.ALT_DOWN_MASK; if (event.getModifiers().contains(KeyboardModifier.ShiftModifier)) modifiers |= MouseEvent.SHIFT_DOWN_MASK; if (event.getModifiers().contains(KeyboardModifier.ControlModifier)) modifiers |= MouseEvent.CTRL_DOWN_MASK; if (event.getModifiers().contains(KeyboardModifier.MetaModifier)) modifiers |= MouseEvent.META_DOWN_MASK; int button = 0; if (event.getButton() == Button.LeftButton) { modifiers |= MouseEvent.BUTTON1_DOWN_MASK; button = MouseEvent.BUTTON1; } else if (event.getButton() == Button.MiddleButton) { modifiers |= MouseEvent.BUTTON2_DOWN_MASK; button = MouseEvent.BUTTON2; } else if (event.getButton() == Button.RightButton) { modifiers |= MouseEvent.BUTTON3_DOWN_MASK; button = MouseEvent.BUTTON3; } return new MouseEvent(treePane, type, System.currentTimeMillis(), modifiers, event.getWidget().x, event.getWidget().y, 1, event.getButton() == Button.RightButton, button); } @Override public void resize(WLength width, WLength height) { super.resize(width, height); treePane.setSize((int)width.toPixels(), (int)height.toPixels()); } @Override protected void layoutSizeChanged(int width, int height) { super.layoutSizeChanged(width, height); treePane.setSize(width, height); } @Override protected void paintEvent(WPaintDevice paintDevice) { WPainter painter = new WPainter(paintDevice); WebGraphics2D graphics = new WebGraphics2D(painter); treePane.paint(graphics); } public TreePane getTreePane() { return treePane; } }