populations-1.2.33+svn0120106.orig/0000755000175000017500000000000011701605073016646 5ustar georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/CPackSourceConfig.cmake0000644000175000017500000001224311701604740023142 0ustar georgeskgeorgesk# This file will be configured to contain variables for CPack. These variables # should be set in the CMake list file of the project before CPack module is # included. 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CPACK_PACKAGE_VERSION_PATCH - Package project version (patch) # There are certain generator specific ones # NSIS Generator: # CPACK_PACKAGE_INSTALL_REGISTRY_KEY - Name of the registry key for the installer # CPACK_NSIS_EXTRA_UNINSTALL_COMMANDS - Extra commands used during uninstall # CPACK_NSIS_EXTRA_INSTALL_COMMANDS - Extra commands used during install SET(CPACK_BINARY_BUNDLE "") SET(CPACK_BINARY_CYGWIN "") SET(CPACK_BINARY_DEB "") SET(CPACK_BINARY_DRAGNDROP "") SET(CPACK_BINARY_NSIS "") SET(CPACK_BINARY_OSXX11 "") SET(CPACK_BINARY_PACKAGEMAKER "") SET(CPACK_BINARY_RPM "") SET(CPACK_BINARY_STGZ "") SET(CPACK_BINARY_TBZ2 "") SET(CPACK_BINARY_TGZ "") SET(CPACK_BINARY_TZ "") SET(CPACK_BINARY_ZIP "") SET(CPACK_CMAKE_GENERATOR "Unix Makefiles") SET(CPACK_COMPONENTS_ALL "") SET(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE") SET(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE") SET(CPACK_DEBIAN_PACKAGE_MAINTAINER "Olivier Langella ") SET(CPACK_GENERATOR "TGZ;TZ") SET(CPACK_IGNORE_FILES 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SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Populations is population genetic software") SET(CPACK_PACKAGE_EXECUTABLES "populations;populations") SET(CPACK_PACKAGE_FILE_NAME "populations-1.2.33") SET(CPACK_PACKAGE_INSTALL_DIRECTORY "populations 1.2.33") SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "populations 1.2.33") SET(CPACK_PACKAGE_NAME "populations") SET(CPACK_PACKAGE_RELOCATABLE "true") SET(CPACK_PACKAGE_VENDOR "CNRS") SET(CPACK_PACKAGE_VERSION "1.2.33") SET(CPACK_PACKAGE_VERSION_MAJOR "1") SET(CPACK_PACKAGE_VERSION_MINOR "2") SET(CPACK_PACKAGE_VERSION_PATCH "33") SET(CPACK_RESOURCE_FILE_LICENSE "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106/ChangeLog") SET(CPACK_RESOURCE_FILE_README "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106/README") SET(CPACK_RESOURCE_FILE_WELCOME "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106/INSTALL") SET(CPACK_SET_DESTDIR "OFF") SET(CPACK_SOURCE_CYGWIN "") SET(CPACK_SOURCE_GENERATOR "TGZ;TZ") SET(CPACK_SOURCE_IGNORE_FILES "/devel_archives/;/figures/;/Soumis/;Makefile;install_manifest.txt;cmake_install.cmake;cmake_install.cmake;CMakeCache.txt;CPackConfig.cmake;CPackSourceConfig.cmake;install_manifest.txt;/CMakeFiles/;/_CPack_Packages/;/Debug/;/Release/;/\\.externalToolBuilders/;/\\.svn/;/\\.settings/;Makefile;\\.cdtbuild;\\.cdtproject;\\.project;/win32/") SET(CPACK_SOURCE_INSTALLED_DIRECTORIES "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106;/") SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "./CPackSourceConfig.cmake") SET(CPACK_SOURCE_PACKAGE_FILE_NAME "populations-1.2.33") SET(CPACK_SOURCE_STRIP_FILES "") SET(CPACK_SOURCE_TBZ2 "") SET(CPACK_SOURCE_TGZ "") SET(CPACK_SOURCE_TOPLEVEL_TAG "Linux-i686-Source") SET(CPACK_SOURCE_TZ "") SET(CPACK_SOURCE_ZIP "") SET(CPACK_STRIP_FILES "") SET(CPACK_SYSTEM_NAME "Linux-i686") SET(CPACK_TOPLEVEL_TAG "Linux-i686-Source") populations-1.2.33+svn0120106.orig/html/0000755000175000017500000000000011701602132017603 5ustar georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/html/old/0000755000175000017500000000000011701602132020361 5ustar georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/html/old/index_en.php_fichiers/0000755000175000017500000000000011701602132024614 5ustar georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/html/old/index_en.php_fichiers/valid-xhtml11.png0000644000175000017500000000357510563103263027735 0ustar georgeskgeorgeskPNG  IHDRXTgAMA a@PLTEsskkckccƽcccƽƭZcZcZcZ޵Z޵RR֭cޭR֭R֥RΥZΥRƥZZJƜJZZ{ތBJsƵZJsZ{ބB{BkBZc{s{9Bcs9Z{9Rk1{9{{{kcc1s1s9{skJ{s9sRsssB{{sRk)k1Z)Bsk1kkk9sc1scR9k{c1ccckcR1kR)J!J!sZ1sZ)ZZZ)cZZJkR)kR!ZRJcR)RRR!Z9RRJZZcJ)!RRJJZJ!BJJR9)ZB!RB!BBBJBBJJJJ!)99JJ9B999BB919JB191119111{)))1)){1!)!)!!LKtRNS@fbKGDH pHYs  ~tIME$[vBIDATxWE;!,A12]eK(XEGVT(1 EPRP4AkS!(֬[Fל}L$O{3S{$ ܣ[؅ݛw, y?|3eFGl^Ș3Y)jDHD"L ItaPe|m4ĵwS6T[ҀPV۷xGqNJe<9T<{)6=mP۬c 7A#6y˗"y+dYhL&1ƕCYK8兢V} {9nk 5ߣ%q\* cgb^< r~GO0D)"B! f>/Š>B㉣dSz/}sIoY¯r:XZ)nDvcMYo<_Q:"H>!VHKOi"aH7`sSr A]*H~TݼU|TEhA_A1_C:QН-nȽ1I@:,t]Ds Fx?Sj+ T%`z.g_F;|A \Ff`WdDϣ#3pV-%@MEC&'ӷ]IMZr7 #!Ӯ.FGA X=EY9*yyt)d!>qPiftTjۄ(DiQk@>X94}d2[ixlMZv{֦l]%ӴApb7 9\d;H^I0u; 8u|x3Ͽx "MظXڒ/F)%y}.ܜ {yPlF,'ųlG8kyH`-Q'#Wb0cDq5=2t*cJф6̣2!ͪ d?kٝyLq7!^|ۚSF:T*ؔ2lSOikn7xq~VG_aqF y~yeuvo ŕ\//E,d{֌˸E}IENDB`populations-1.2.33+svn0120106.orig/html/old/index_en.php_fichiers/bioinfo.css0000644000175000017500000000261510563103263026765 0ustar georgeskgeorgesk/********* * bioinfo * *********/ form { padding: 0.5em; margin: 0.5em; font-family:sans-serif; background-color: #E0F0F0; } div { font-family:sans-serif; } div.bas_de_page { font-style: italic; } div.plan{ font-weight:bold; padding: 0.2em; margin: 0.5em; text-align : left; // background-color: #E0F0F0; } div.enumeration{ // font-weight:bold; padding: 0.2em; margin: 0.5em; text-align : left; background-color: #E0F0F0; } div.script{ text-align : left; font-family: courrier; padding : 0.5em } div.paragraphe{ text-align : left; padding : 0.5em } div.article{ text-align : left; padding : 0.5em } div.titre { color:#0000ca; font-weight:bold; text-align:center; font-family:sans-serif; font-size:x-large; padding : 0.5em } div.titre2 { color:#0000ca; font-weight:bold; text-align:left; font-family:sans-serif; font-size:x-medium; padding : 0.5em }populations-1.2.33+svn0120106.orig/html/old/index_en.php_fichiers/valid-css.png0000644000175000017500000000215610563103263027221 0ustar georgeskgeorgeskPNG  IHDRXT)PLTE## GYUJvYތE dg}}}}Qmmm߷>!]]]$\UH\UHOOOݲjT|?<5ΧQK$s]K$^KNK@NK@̸OOQD<,$^n Ep__>lz^}e1޴X 6dmX+&YϒL>!U<1LLLWSP<<<9$ D//,,,ME͝>fE)s r8 LctRNS0 00zIDATx}S@j RDEAROĈQ'p.eL+rl/_{vf?pMrx://ǼbDQ`Rg FDۊEsT89@&W~ѧ4tR̨|D^NV3h|{/oc@TGliY Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96] next up previous
Next: Latter's (1972) Fst (=*) Up: IAM distances Previous: Nei's (1972) standard genetic

Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]


\begin{displaymath} Dm=\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old/formules/img47.png0000755000175000017500000000211411326636711023670 0ustar georgeskgeorgeskPNG  IHDR/[P0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxWOVe&d&J C)BS*E^v e=I=u`o+eOQ:dEAvB{~$d6ܥI~{} Kv}ZE+>*Vw RFt.Lks$_6{CZO:PI| $10ZdCƦpa0ԥg4ES`\`L\$tOqvi֘c9|F:Pbw4)Sc L!P 3b5ӈ8׌h9OHj՛Z4h298q~̝9ZۏuOmïyn#֗2j59Ki)-~vd>0p h7DV :MGvlTΌᕤCj]]Z$y!8dTVVN&8P` 3hXGt0@Yа+0HӃ.(?(Dn(rȜOA̚LQ<"+@5kc( FLbF]˶۷pʝKݻx _ Q{ h.L' 1ԏbI:h|OT РPPP(@,0SU6 :X==t ۂ4]^9QSx]=ku橥@Ua.2C!V.|HOW_UM2A=̐&U` I  `@TXp| X9lW HڃA L|UB(h?N@!`f1JVCy D]ihlp)ti8@&|]B) !L !qw^(V~AuĀ0iUQ7VlHd#.3hR8 F%߆Z$flJB&h!ܑPѼ#BM4HJXG VKpv2 x_ `Ub ؑ T3QGJl$̜6"[`{2-xm< H7$ObD*Rҕb 3ujAvq(%-I\ՋT 8ʏcU[RA+(z,҇S 4yb;˄a _OدGdzU$< ~.*j*@#*?1P[5 Pǀv,,@%~Ƴ<+҉г0A0 Vt$ `[H%hz Ӗdx GH(L W0";populations-1.2.33+svn0120106.orig/html/old/formules/img15.png0000755000175000017500000000162411326636711023670 0ustar georgeskgeorgeskPNG  IHDR( 0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxVMhA'&i^r 7="7=؊]) P(z*7 b|MDv7߼}31xu!!7FA7 @X`*ѐs"`A][vT;Yha^9#ʃV2:20B}ҜuKF`U+^M_Pך ,y`stwBd5MV-]dB1LlEJ{_r]@gmwX 6 {Qprx՘"2_2oJi+|̿a/MmB.L@SV]mh< m5#mK)SO&LG9@Yuz&ޞp@[:A5 G keԼDba KtFQ>Kv<7QL",J gi X̐p-(,y E[lpz綄K}R G}hKs|Vu]ތ0Iu﹮/"%ϴG*91p` vǾm_& bWpAn{3~?E4>:MŔ(O3uzt:xę^2&'tVEzMcS| :>rV AX8aSi&X36(j s*l̷ $ۅ3w}5ftҤaO)`)MsBcuB ȗƯRV[W`IENDB`populations-1.2.33+svn0120106.orig/html/old/formules/img1.gif0000755000175000017500000000121011326636711023553 0ustar georgeskgeorgeskGIF89a6xxxlll```TTTHHH<<<000$$$ !,6@I8ͻ`(Vh Wyf s$1,P`2I g)1I sH@$t0pL.acn|N }"a]f\tW+ ~Lby#  elJ ~@  {K  ɹ cj6   纣 Bi SSu^\("n>iȦN:A EЮƈz0,˗0呜Ir͛8sɳϟ@ JtC82&  G*m}d]{!=4w &tAN rX2E\=Ϧ3vGrHB6c5vtӐ8nVu2ߣjm2ck\[&[AV3Sp4|ڥڎN ?ڿM?Ϝz)ToꧡR Xx΂% ܶlc`8doE? TG«a2z0ѱ;e~+J_ѕiyۮ7OZmgB% ⊉U!ϊE*ʪ̫ǭMRْjxbc߾qa05RThjĐ@POV6>WHⰹ*9SV{3-d*1rzhEtFCB[R~ZW slr#AnSVCMT>z^c˽%*DUwQnn #_5-.$P/Yq1{{yj!.2Â#5e{/R,9֏2?.5?:&4Sq" ?3|i;h2d)t l(o=IENDB`populations-1.2.33+svn0120106.orig/html/old/formules/img57.png0000755000175000017500000000202711326636711023674 0ustar georgeskgeorgeskPNG  IHDR-k0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxVMhA$l؂"oU{h"4^OkDRQ{0*<X3,+VIk]h5(.1V񹪙JvT0CFuhl N_ߨqMɈ"cYT++ZRH̔ d@/ 9;CoJ؀H|b#:q]KZI5b$^)y5 a ׄ3;N8vj !4| K[*E6@Ci5ݏ*%a>TSi-To2DITxD絮C[otKiX d5ߡ:ecpp{w&EOI]+ElcZn[;<,Cҳ?_iܝ[HK[ZܵU9*(an}(3>#Y@3#=B$#PS<)'3D3}īlx4ʐˇs#D< ң D?-74iC׉(;|p[8avC3' y$`r>:V$cL6Ѭ2NlD.@V1 ߴQ)ψޞ2|CwB]Ʋ<͎ . 擣|҇0.9ݩ@^?cĨYBҪO?l^)&EҡD@x3}3$(% o>m5zjDu4Q7YEZU4bb37a!6u\;fSu)?9cQM` !b|$r ~0[Jt,<|['6򉦰1$ %CUI:K=εk0#U}9GQTorh1 FR+z-ow;n%&FO_RBM˿ $ LZѻ\Y)rfrrsnp_mC{%NAľt\wVzV!ˆzO-EgjNScrIA>">UmnIENDB`populations-1.2.33+svn0120106.orig/html/old/formules/img55.png0000755000175000017500000000045511326636711023675 0ustar georgeskgeorgeskPNG  IHDRI20PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxc```` t$&Lb )ta10X*qF4`c\Ya ' <`0H"p!_ [PE<=Es'q@< 7pD]F.À:j `IENDB`populations-1.2.33+svn0120106.orig/html/old/formules/img18.gif0000755000175000017500000000147111326636711023654 0ustar georgeskgeorgeskGIF89a6xxxlll```TTTHHH<<<000$$$ !,6@I8ͻ`(04f!! ֐`2I@wi>]*q$G(,^l­I2 r#oQ+Z j#"J;wuSlW 767 jJ4|sbi~{  qU g DYo߃~g$D*At@8!/X 0(Bd)L+Р.9@q ș'a U3ji&mW] Ҫ]WzJ8  R8·/  4CKL˘3k̹ϠAZA17r"MzBo )X| I!V*- pNHAM%t!} KLv| @Z\8t;/\2(Pq)uG !\sHU mq_L`Nsm0Que` Us b"2 vAzM"G@C5`$JnYba9<,_~y{Bpla" !j #+aj9#t`T=(tp$+ ulߓ;populations-1.2.33+svn0120106.orig/html/old/formules/node6.html0000755000175000017500000000473311326636711024145 0ustar georgeskgeorgesk Latter's (1972) Fst (=*) distance [Takezaki, N. 96] next up previous
Next: Rogers' (1972) distance [Takezaki, Up: IAM distances Previous: Nei's (1973) minimum genetic

Latter's (1972) Fst (=\( \phi \protect \)*) distance [Takezaki, N. 96]


\begin{displaymath} Fst=\frac{\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}}{1-J_{XY}}\end{displaymath}


Olivier Langella 2002-03-20
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Next: Shared allele distance (Chakraborty Up: Distances Previous: Distances

IAM distances

\( J_{X}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x^{2}_{ij}}{r} \) and \( J_{Y}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}y^{2}_{ij}}{r} \)are the average homozygoties over loci in populations X and Y, respectively, and \( J_{XY}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x_{ij}y_{ij}}{r} \).

\( x_{ij} \) and \( y_{ij} \) are the frequencies of the ith allele at the jth locus in populations X and Y, respectively, \( m_{j} \) is the number of alleles at the jth locus, and r is the number of loci examined.


Subsections
Olivier Langella 2002-03-20
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Next: Distances



Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old/formules/img7.gif0000755000175000017500000000076311326636711023575 0ustar georgeskgeorgeskGIF89axxxlll```TTTHHH<<<000$$$ !,@I8ͻ l! 0SBAH,r/8,% z``,D- 9 -+u6g /1]w|~'llf%0` z# "Dž>>|g ^ ;X< PK A BĺP|#/Pliױ8xpAA`"<NZP2$8@@؀i1d. :hRJ$^J`8@ H-6z!삱>@;A-X?P+ pYÃp 4e2oLӨS^ͺ_;populations-1.2.33+svn0120106.orig/html/old/formules/node7.html0000755000175000017500000000457511326636711024152 0ustar georgeskgeorgesk Rogers' (1972) distance [Takezaki, N. 96] next up previous
Next: Prevosti et al's (1975) Up: IAM distances Previous: Latter's (1972) Fst (=*)

Rogers' (1972) distance [Takezaki, N. 96]


\begin{displaymath} Dr=\frac{1}{r}\sum ^{r}_{j}\sqrt{\frac{\sum ^{m}_{i}\left( x_{ij}-y_{ij}\right) ^{2}}{2}}\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old/formules/img40.gif0000755000175000017500000000170111326636711023643 0ustar georgeskgeorgeskGIF89a,xxxlll```TTTHHH<<<000$$$ !,,@I8ͻ`(dib0"tl !8<ʲh:G0J3AHH[hD*;DN |" wVe<1݂&,  ]f . C>{U*AX\*Ӿ=Hŋ3jBƋ|@ ĴBɞ8,iJj@ Agjޤ3ezhaZ 0$`aAaZ zջWQM Lev A. Zhivotovsky (1999) [Takezaki, N. 96] next up previous
Next: Bibliography Up: SMM distances Previous: Shriver et al.'s (1995)

Lev A. Zhivotovsky (1999) [Takezaki, N. 96]

Consider two populations, X an Y and r autosomal microsatellite loci. \( \overline{\mu _{X}} \) and \( \overline{\mu _{Y}} \)are the mean of \( \mu _{X_{j}} \)and \( \mu _{Y_{j}} \)averall loci for population X and Y respectively.


\begin{displaymath} D_{R}=-\log \left( \frac{C_{XY}}{V_{XY}}\right) \end{displaymath}

with,

\( C_{XY}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}\mu _{Y_{j}}-r\overline{\mu _{X}}\overline{\mu _{Y}}\right) \) and \( V_{XY}=\frac{1}{2}\left( V_{X}+V_{Y}\right) \), where \( V_{X}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}^{2}-r\overline{\mu _{X}}^{2}\right) \), \( V_{Y}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{Y_{j}}^{2}-r\overline{\mu _{Y}}^{2}\right) \)

Attention, to avoid software crash, when \( C_{XY}<1 \), \( C_{XY} \) is set to 1.


Olivier Langella 2002-03-20
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Nei's (1972) standard genetic distance (Ds) [Takezaki, N. 96]

Ds = − ln J XY J X J Y Ds=-ln {left[ {J_{XY}}over{sqrt{J_{X}J_{Y}}} right]}
populations-1.2.33+svn0120106.orig/html/old/formules/node16.html0000755000175000017500000000622111326636711024220 0ustar georgeskgeorgesk SMM distances next up previous
Next: Goldstein et al. (1995a) Up: Distances Previous: least squares estimator :

SMM distances

\( \mu _{X_{j}}=\sum _{i}ix_{ij} \) and \( \mu _{Y_{j}}=\sum _{i}iy_{ij} \) are average allelic states at the jth locus, and \( x_{ij} \) and \( y_{ij} \) are the frequencies of the allele in state \( i \) at the jth locus in populations X an Y, respectively.


Subsections
Olivier Langella 2002-03-20
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Next: weighted average of single-locus Up: Reynold's genetic distance for Previous: Reynold's genetic distance for

unweighted average of single-locus ratio estimators, \( \tilde{\theta }_{U}\protect \):


\begin{displaymath} \tilde{\theta }_{U}=\frac{1}{m}\sum ^{m}_{l=1}\tilde{\theta }_{l}\end{displaymath}

, with \( \tilde{\theta }_{l}=\frac{a_{l}}{a_{l}+b_{l}} \). The estimates of the components of variance of interest for the lth locus are within populations, r is the number of populations examined:

\begin{displaymath} b_{l}=2\sum ^{r}_{i=1}\frac{n_{i}\tilde{\alpha }_{il}}{r(2\bar{n}-1)}\end{displaymath}

and between populations:


\begin{displaymath} a_{l}=\frac{\left[ 2\sum ^{r}_{i=1}n_{i}\sum ^{v_{l}}_{u=1}\... ...^{2}-\left( r-1\right) b_{l}\right] }{2\left( r-1\right) n_{c}}\end{displaymath}

When there are just two populations, r = 2, the usual genetic distance situation obtains, and the most convenient computing formulas for the variance components are (used in Populations)


\begin{displaymath} a_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tilde{p}_{... ...\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}


\begin{displaymath} a_{l}+b_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tild... ...\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old/formules/node21.html0000755000175000017500000000640111326636711024214 0ustar georgeskgeorgesk Bibliography next up previous
Next: About this document ... Up: formules Previous: Lev A. Zhivotovsky (1999)

Bibliography

Goldstein, D.B. 97
Goldstein, D.B. & Pollock, D.D.
Launching Microsatellites: A Review of Mutation Processes and Methods of Phylogenetic Inference.
Journal of Heredity, vol. 88, no. 335-342, pages 0022-1503, 31 1997.
1997.

Jin, L. 93
Jin, L. & Chakraborty, R.
Estimation of Genetic Distance and Coefficient of Gene Diversity from Single-Probe Multilocus DNA Fingerprinting Data.
Mol. Biol. Evol., vol. 11, no. 1, pages 120-127, 13 1993.
1994.

Reynolds, J. 83
Reynolds, J., Weir, B.S. & Cockerham, C.
Estimation of the coancestry coefficient: basis for a short-term genetic distance.
Genetics Society of America, vol. 105, pages 767-779, November 1983.
1983.

Shriver, M.D. 95
Shriver, M.D., Jin, L. & Boerwinkle, E.
A Novel Measure of Genetic Distance for Highly Polymorphic Tandem Repeat Loci.
Mol. Bio. Evol., vol. 12, no. 5, pages 914-920, 4 1995.

Takezaki, N. 96
Takezaki, N. & Nei, M.
Genetic Distances and Reconstruction of Phylogenetic Trees From Microsatellite DNA.
Genetics, no. 144, pages 189-399, 6 1996.
september, 1996.


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old/formules/img16.gif0000755000175000017500000000133211326636711023646 0ustar georgeskgeorgeskGIF89a7xxxlll```TTTHHH<<<000$$$ !,7@I8ͻ`(BTvItx|b1 8 D@bp,p,!I(lxL.zj@~ 2K# Qv,y 0 4rWWl o D  6m լ_w֊FHJKMO uj/_ l*(0 b (R ՂSB=E悒i4ߦsP`Z)]JO|ܺCI(UÞE}]˶۷pʝKݻxOm^,0xŁ_, &>hM*HɊ< d̡T<> ;ٶkm ;o0^E˿I ͡ JZ!umS>zTB9J@/8x]_$ hw>L- NVt2 @ N'8B(6لiT@$400HUY4eӥ❏5#^x+10yc1~ G`)dihl;populations-1.2.33+svn0120106.orig/html/old/formules/img37.gif0000755000175000017500000000142011326636711023647 0ustar georgeskgeorgeskGIF89a,xxxlll```TTTHHH<<<000$$$ !,,@I8ͻ`(d0RlL @!bH,H7 Aa(4H>E;kn?B P`'(rW,SCn [   {)J0 f.w /5w?˦ ^MoPɻiYmڧ!=]J`b;e."'0‘U! 0ʀcۄqJ'9ADG(@s(!O +@4A 7YRP8iDvP8 phA G9"_9p4YC:FڷpʝKݻx-uDdJ, p/ a"4IX hHq i<L ? jl]=%\Z0OCkz_ް ,H@v /~d)  66qm7=& bfYEdh^$S,pP I8 n# P SA I = ∑ j r S 2r P_{SA_{I}}={sum ^{r}_{j}S} over {2r} populations-1.2.33+svn0120106.orig/html/old/formules/previous_motif_gr.gif0000755000175000017500000000033411326636711026466 0ustar georgeskgeorgeskGIF89a?ooo!,?I޼j~㕶.Lq6z Hir"?$`)|J{Č\vSUM߬95[0Er5WxEWeCxhyfFfY)'#؈:+H4{[3 , Sanghvi's (1953) distance[Takezaki, N. 96] next up previous
Next: Reynold's genetic distance for Up: IAM distances Previous: Nei et al's (1983)

Sanghvi's (1953) \( X^{2}\protect \) distance[Takezaki, N. 96]


\begin{displaymath} X^{2}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}2\frac{\left( x_{ij}-y_{ij}\right) ^{2}}{\left( x_{ij}+y_{ij}\right) }}{r}\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old/formules/node17.html0000755000175000017500000000464011326636711024224 0ustar georgeskgeorgesk Goldstein et al. (1995a) [Goldstein, D.B. 97] next up previous
Next: average square distance (ASD) Up: SMM distances Previous: SMM distances

Goldstein et al. (1995a) [Goldstein, D.B. 97]


\begin{displaymath} \left( \delta \mu \right) ^{2}=\frac{\sum ^{r}_{j}\left( \mu _{X_{j}}-\mu _{Y_{j}}\right) ^{2}}{r}\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old/formules/img30.png0000755000175000017500000000045011326636711023661 0ustar georgeskgeorgeskPNG  IHDR%s40PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxc```8h@08p@i{ $:pf0uduvYϠ[ P1 `12A]@-(U} m4 `=< /X`0XetB{}qZIENDB`populations-1.2.33+svn0120106.orig/html/old/formules/img27.gif0000755000175000017500000000151011326636711023646 0ustar georgeskgeorgeskGIF89a8xxxlll```TTTHHH<<<000$$$ !,8@I8ͻ`($(8HP)E)2Ͳ0A#Y%0d|a"$ C `+!f#!DŽ1 IwJ$5 }WU mz-?f b,.WNU\t g!w)TF 0.5"v`Aw[4$Ö6| eB mhH/84d} P\AJP@S,q&͸U7O$,v A6&QK@4ş 4 =˷w 3$0J!yqxq#KL˘3k̹hl Y JdN59TXOLWdM] bwMX35=a;ND>BwӒ D*QӲT8 ;׎ڡ0VI\4TKm (`W<!,qS^v,$DM0Lf`;%%`J Tt88 !8DG@Gȁ! @H7ԁF N_aajZ%gDw8`D<Ȥ 0ix|'DCS1if K{,c4uhh% %@0r998si&38 x7X58/>y @~d0՝0_&.a}IENDB`populations-1.2.33+svn0120106.orig/html/old/formules/img20.gif0000755000175000017500000000032011326636711023635 0ustar georgeskgeorgeskGIF89axxx```TTTHHH<<<000$$$ !,@}IՀQ`"8l$ ( pTt,=adh! a8-Cqr-,1Ѡ$`EʼP 4E W*x' eqmj;populations-1.2.33+svn0120106.orig/html/old/formules/img36.png0000755000175000017500000000453611326636711023700 0ustar georgeskgeorgeskPNG  IHDR1b*0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxZo$Wy;=IY6=x ATY"r NP!GBﲛ~36/(_Hom.Ѷ{{{vs-]^WޫW{ TP H:U/0E4 3iP12̈́Q},.V}PH}>udh<2['!c[T 9ӻ+CQq`ɼuÉ +X:h6 l.Ig na DaLHP]8 &%Q)@1MӿKJ ;5_M| KuW|KU%l0/\YTo|nB#{(v4ԻEMњß [H`^wBZj7aoi>N d/7-Ť9e6N@N\RSji!.M ߣI2wlXum!cZQTѻnoNZP: D-ŵؓTȐZ|GGriFMcZYҎj-֗>~yeQ7U6rzWGntZ X tn dO9_]$J - _Y^'/% \ǛbPQ S#1-k ˤ ) u{ k'WS1T$u5{D N9ZK.B~Do)A+;p+&=B)/14Vu"8375Y{fCC{.>|J7Y=H3 7π8(_,^U[*[8[݄Fi>}ˡ750'1p3VtfX`MmN*ܒ5Abx.'u/NI>v(Yea2mC|GզGg85{;NϢ25n,R7Y0UJe I+v6!Bt's//⟅_>pROgSy}I)(qKQE)\o7~':RAAoe;b{I`[iNbGQ#=AZm-bW74BV Ln5X_^ű"%T8كîaB12a}p(F9?h1&m>iql*m7ҘYpWikn&nGwQqpnKtgtX9=uE 闳>l} /?˪dVͽq,ϓ8ѕ^T֞['5>xJN JG {3kXpkpZd<>ρ[I0rZq)I(pIIO꺻wKXD`,{ ҿ' y \O~WOs ~dZB YRb ɓ(Oc~"E 8yJs;wC|kω;9WH?,TjIQ]qzlcdˬ.>Wu4۰~!iTlo\đdIi$-FI"@5REhc(xQ삕"dGN5OT8Z9Fr#s B=Eܲ>}z$E)ߴ umgLoI+R7(:{a\fUu]wT$wa.KtBHv7/]D*RAƛطC}G+xG>z2ZmmhOĄ}:{;If9GoEK ڋTlȳM?G} KHHMo{L!W|[lxCnH[ғ Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83] next up previous
Next: unweighted average of single-locus Up: IAM distances Previous: Sanghvi's (1953) distance[Takezaki, N. 96]

Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83]


\begin{displaymath} DReynold=-\ln (1-\theta )\end{displaymath}

the following notation is used, for all \( \theta \) estimators:

\( \bar{n}=\sum ^{r}_{i=1}\frac{n_{i}}{r} \), \( n_{c}=\frac{\left( r\bar{n}-\sum ^{r}_{i=1}\frac{n^{2}_{i}}{r\bar{n}}\right) }{\left( r-1\right) } \), \( \tilde{p}_{lu}=\sum ^{r}_{i=1}\frac{n_{i}\tilde{p}_{ilu}}{r\bar{n}} \), \( \tilde{\alpha }_{il}=1-\sum ^{v_{l}}_{u=1}\tilde{p}_{ilu}^{2} \)


Subsections
Olivier Langella 2002-03-20
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Next: Cavali-Sforza and Edwards' (1967) Up: IAM distances Previous: Rogers' (1972) distance [Takezaki,

Prevosti et al's (1975) distance [Takezaki, N. 96] has a statistical property similar to that of Dr and is defined as


\begin{displaymath} Cp=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}\left\vert x_{ij}-y_{ij}\right\vert }{2r}\end{displaymath}


Olivier Langella 2002-03-20
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LN  sv{ u<2 3hM;populations-1.2.33+svn0120106.orig/html/old/formules/img23.png0000755000175000017500000000040211326636711023660 0ustar georgeskgeorgeskPNG  IHDRB 0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxc```g30410So2DЀCn86ۀaf f`WB XUčr-`8?c}р7,hw@w7 3}s21po#%A!IENDB`populations-1.2.33+svn0120106.orig/html/old/formules/img31.png0000755000175000017500000000152111326636711023662 0ustar georgeskgeorgeskPNG  IHDRa6RI0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxTkaYZR\Nq)V?CA}uIjd`@!C".[W%C!˽]|yC3SFK2t@R(WC#t\+ mvICq>:r2|?&(Es B}f{ &hsB`v:<fVQ,G3-jhyaݝYV ,VK%[ׅBiopjEftNG<[ڴx$MvM R)o4-ԴiIm#K搎jݚ2dT5!<ɰgխ q`Lh1١Tp0H-Rwl(@ V&{}= ),V㪁EB<;g[_ۈ&YJcR$w#eÒ:XgWH I4p56i5cI4<}J1k/ڦr}1ʢM>AQ}!*7Uf[?|fT >r="&yڞ`̎xiEu*9"PC_Ow.nZ n)onGm|P+~ URc?vyѕMV?oYoԡQ\q*‚s&lk>+PYWcsק;* c0kc{/6d:IENDB`populations-1.2.33+svn0120106.orig/html/old/formules/next_motif_gr.gif0000755000175000017500000000025411326636711025571 0ustar georgeskgeorgeskGIF89a%ooo!,%}ڋ2bUbK +7nj:f#a)gy5Nq+d]͈^fbjۜXL$XBXr8c)9IYi`Y;populations-1.2.33+svn0120106.orig/html/old/formules/img31.gif0000755000175000017500000000172311326636711023647 0ustar georgeskgeorgeskGIF89a6OOOGGGxxxllljjj```TTTHHHDDD>>><<<000,,,$$$""" !,6@%dihlp,t֤2be8]7+@Fh!IpZYI(:TO0Z d" ;D b"" W5l5$pv ˘oJ e]_]k&D'U D썋#~ 2UN_%HHA1Hŋ3jȱǏͩ"A A PRB$(m@;`PVfl >AYBm! -:F/< -13j CL(|#6Aمg<֭Ԫ&΍P([BL𹶭 )@JHY012"TKY5PjB240e3}b@r>Nȓ+_μУKj}Y׳Kb5IpmPɩ) lj*FC~bQ6 MWExgB' a!4Ypa8AD$PZ#(Qk'@L}]܉`kH#7 1H G% PbvB% F:]Vfy]Ś[qdHOk%Uc@v㈐]D؊8$>oHĥ+1/f+刧vH4ЀnY9f(Cqr]@lS) c.itXigГ\aϴSVkfn{eH%uZ^ElI#$ 8 NL_fl' 7G,+;populations-1.2.33+svn0120106.orig/html/old/formules/img42.png0000755000175000017500000000043511326636711023667 0ustar georgeskgeorgeskPNG  IHDR%(D0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxc```g@ H" f@Q큸Ę0C^"9Yh pku`3X 6A @8X <`E$7`lc2fc7xXf5 Ay  `ԙb8IENDB`populations-1.2.33+svn0120106.orig/html/old/formules/node9.html0000755000175000017500000000471611326636711024151 0ustar georgeskgeorgesk Cavali-Sforza and Edwards' (1967) chord distance [Takezaki, N. 96] next up previous
Next: Nei et al's (1983) Up: IAM distances Previous: Prevosti et al's (1975)

Cavali-Sforza and Edwards' (1967) chord distance [Takezaki, N. 96]


\begin{displaymath} Dc=\frac{2}{\Pi r}\sum ^{r}_{j}\sqrt{2\left( (1-\sum _{i}^{m_{j}}\sqrt{x_{ij}y_{ij}}\right) }\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old/formules/nei_dm.xhtml0000644000175000017500000000320510621075553024541 0ustar georgeskgeorgesk ]> Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]

Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]

D m = J X + J Y 2 - J XY Dm=(J_X + J_Y)over 2 - J_XY
populations-1.2.33+svn0120106.orig/html/old/formules/img10.gif0000755000175000017500000000044411326636711023643 0ustar georgeskgeorgeskGIF89a-#xxxlll```TTTHHH<<<000$$$ !,-#@I8[hSZ(J ,!< 2c|O0!d%ha0$uL.'E_CƁ{ ?   n  &{\ V ,m{}9 2rPbLVP r < /^kT;populations-1.2.33+svn0120106.orig/html/old/formules/img14.gif0000755000175000017500000000126711326636711023653 0ustar georgeskgeorgeskGIF89a(xxxlll```TTTHHH<<<000$$$ !,(@I8ͻ`(d|KrZaR0&d{@kuTS/V=իXjʵׯ`Ê+@ Jpv cM eʠR!;(TNy% &zK T*X1AABC v<(wM.D"@^ 4" ($!s˹`ݖr0if K 5/KP5 GX v"\{ ~7Pb~=fp ]@:$}Ā# 9dap4@rIk0ˁHNYf),Aĥ],#DiH&L6P;populations-1.2.33+svn0120106.orig/html/old/formules/node19.html0000755000175000017500000000630211326636711024223 0ustar georgeskgeorgesk Shriver et al.'s (1995) [Shriver, M.D. 95] next up previous
Next: Lev A. Zhivotovsky (1999) Up: SMM distances Previous: average square distance (ASD)

Shriver et al.'s (1995) [Shriver, M.D. 95]


\begin{displaymath} D_{SW}=W_{XY}-\frac{\left( W_{X}+W_{Y}\right) }{2}\end{displaymath}

where \( W_{X}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert x_{ik}x_{jk}\right) }{r} \), \( W_{Y}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert y_{ik}y_{jk}\right) }{r} \), \( W_{XY}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert x_{ik}y_{jk}\right) }{r} \)


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old/formules/formules.html0000755000175000017500000001045311326636711024762 0ustar georgeskgeorgesk formules next up previous
Next: Distances



Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old/formules/img13.gif0000755000175000017500000000124411326636711023645 0ustar georgeskgeorgeskGIF89a,xxxlll```TTTHHH<<<000$$$ !,,@I8ͻ`("xIV!M%OZ-|$bb Cj-.$(KXbpK~w&X} .  i~PMkdfhlnpYc0X-,#FL_:(sOCRTYWϾ Kmv3}״4bD bl)``}DHu$eB":Dx硍wrA= r>qSH>P͛8sɳgN!g}6P rQC IPNiA@<$XǬBH5'8JMI鬄Y`ujZ@POf}0O€@FaEeHE (ô,8 eVh`7`9Ae0/ N ,h07Ab)ޣSW~ 0ppB>}E^US @[pUP`:WUFC_Q gHP_a^a4ZF y jH;<,R2<@iT;populations-1.2.33+svn0120106.orig/html/old/formules/node10.html0000755000175000017500000000475011326636711024217 0ustar georgeskgeorgesk Nei et al's (1983) distance [Takezaki, N. 96] next up previous
Next: Sanghvi's (1953) distance[Takezaki, N. 96] Up: IAM distances Previous: Cavali-Sforza and Edwards' (1967)

Nei et al's (1983) \( D_{A}\protect \) distance [Takezaki, N. 96]


\begin{displaymath} D_{A}=1-\frac{1}{r}\sum ^{r}_{j}\sum ^{m_{j}}_{i}\sqrt{x_{ij}y_{ij}}\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old/formules/up_motif_gr.gif0000755000175000017500000000022111326636711025231 0ustar georgeskgeorgeskGIF89aooo!,b˭bZ `؅ҷ!9 zj*Kќ >X6 Lvbmbl2'^}WLv兽 QPY%krM/P;populations-1.2.33+svn0120106.orig/html/old/formules/node3.html0000755000175000017500000000674511326636711024147 0ustar georgeskgeorgesk Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93] next up previous
Next: Nei's (1972) standard genetic Up: IAM distances Previous: IAM distances

Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93]

between individuals:

\( D_{SA_{I}}=1-P_{SA_{I}} \), with \( P_{SA_{I}}=\frac{\sum ^{r}_{j}S}{2r} \)

where the number of shared alleles S is sumed over all loci r.

between populations:


\begin{displaymath} D_{SA_{B}}=1-\frac{2\overline{P}_{SA_{B}}}{\overline{P}_{SA_{X}}+\overline{P}_{SA_{Y}}}\end{displaymath}

where the average proportion of shared alleles between and within populations X and Y ( \( \overline{P}_{SA_{B}} \), \( \overline{P}_{SA_{X}} \), \( \overline{P}_{SA_{Y}} \) respectively) is computed overall possible combinations of individuals sampled.


Olivier Langella 2002-03-20
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Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93]

between individuals:
D SA I = 1 − P SA I D_{SA_{I}}=1-P_{SA_{I}} , with P SA I = ∑ j r S 2r P_{SA_{I}}={sum ^{r}_{j}S} over {2r}
where the number of shared alleles S is sumed over all loci r.
between populations:
D SA B = 1 − 2 P ˉ SA B P ˉ SA X + P ˉ SA Y D_{SA_{B}}=1-{2{bar{P}}_{SA_{B}}}over{{bar{P}}_{SA_{X}}+{bar{P}}_{SA_{Y}}}
where the average proportion of shared alleles between and within populations X and Y ( P ˉ SA B , P ˉ SA X , P ˉ SA Y respectively) is computed overall possible combinations of individuals sampled.
populations-1.2.33+svn0120106.orig/html/old/formules/img22.gif0000755000175000017500000000027411326636711023647 0ustar georgeskgeorgeskGIF89axxxlll```TTTHHH<<<000$$$ !,@iI5#X9!Ą؀< `t@)xi@:X.A*8#lKԣc)$D3`!ɀA),$OEC( Distances next up previous
Next: IAM distances Up: formules Previous: formules

Distances


Subsections
Olivier Langella 2002-03-20
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Next: SMM distances Up: Reynold's genetic distance for Previous: weighted average of single-locus

least squares \( \theta \) estimator :


\begin{displaymath} \tilde{\theta }_{L}=\frac{2x+y-z\pm \sqrt{\left( z-y\right) ^{2}+4x^{2}}}{2\left( y-z\right) }\end{displaymath}

where: \( z=\sum ^{m}_{l=1}a_{l}^{2} \), \( x=\sum ^{m}_{l=1}a_{l}b_{l} \) and \( y=\sum ^{m}_{l=1}b_{l}^{2} \) .

to check which of the two solutions for \( \tilde{\theta }_{L} \) provides the minimum, the residual sum of squares, R, should be calculated for each where:


\begin{displaymath} R=\frac{\left( 2x+y+z\right) \tilde{\theta }_{L}^{2}-2\left(... ...theta }_{L}+z}{1-2\tilde{\theta }_{L}+2\tilde{\theta }_{L}^{2}}\end{displaymath}


Olivier Langella 2002-03-20
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Up: formules Previous: Bibliography

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Olivier Langella 2002-03-20
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Next: Nei's (1973) minimum genetic Up: IAM distances Previous: Shared allele distance (Chakraborty

Nei's (1972) standard genetic distance (Ds) [Takezaki, N. 96]


\begin{displaymath} Ds=-\ln \left[ \frac{J_{XY}}{\sqrt{J_{X}J_{Y}}}\right] \end{displaymath}


Olivier Langella 2002-03-20
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Next: Shriver et al.'s (1995) Up: SMM distances Previous: Goldstein et al. (1995a)

average square distance (ASD) (Goldstein et al. 1995b; Slatkin 1995) [Goldstein, D.B. 97]


\begin{displaymath} ASD=\frac{\sum ^{r}_{k}\sum _{i,j}\left( \left( i-j\right) ^{2}x_{ik}y_{jk}\right) }{r}\end{displaymath}


Olivier Langella 2002-03-20
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Next: least squares estimator : Up: Reynold's genetic distance for Previous: unweighted average of single-locus

weighted average of single-locus ratio estimators :


\begin{displaymath} \tilde{\theta }_{W}=\frac{\left( \sum ^{m}_{l=1}a_{l}\right) }{\sum ^{m}_{l=1}\left( a_{l}+b_{l}\right) }\end{displaymath}


Olivier Langella 2002-03-20
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LEA
Populations
Treeplot
Nu�es
phpMesEchantillons
[ English | Fran�ais ]
Populations 1.2.28 (12/5/2002)
Logiciel de g�n�tique des populations (distances entre individus ou populations, arbres phylog�n�tiques)
Fonctionnalit�s
  • Prise en charge des g�notypes haplo�des, diplo�des ou n plo�des (voir formats d'entr�e)
  • Prise en charge de populations structur�es (voir formats d'entr�e, cas des populations structur�es
  • Pas de limite sur le nombre de populations, de locus, ou d'alleles par locus (voir formats d'entr�e)
  • Calcul de distances entre individus (15 m�thodes de distance disponibles)
  • Calcul de distances entre populations (15 m�thodes de distance disponibles)
  • Bootstrap sur les locus OU sur les individus
  • Reconstruction d'arbres phylog�n�tiques (individus ou populations), par Neighbor Joining ou UPGMA (au format PHYLIP)
  • Calcul de la diversit� all�lique sur des �chantillons r�duits
  • Conversion de formats de fichiers (Genepop, G�n�tix, Msat, Populations)
T�l�chargement
Populations, 1.2.28 (12/5/2002) Copyright (C) 1999, Olivier Langella, CNRS UPR9034
Ce programme est libre, vous pouvez le redistribuer et/ou le modifier selon les termes de la Licence Publique G�n�rale GNU publi�e par la Free Software Foundation (version 2 ou bien toute autre version ult�rieure choisie par vous).
Ce programme est distribu� car potentiellement utile, mais SANS AUCUNE GARANTIE, ni explicite ni implicite, y compris les garanties de commercialisation ou d'adaptation dans un but sp�cifique. Reportez-vous � la Licence Publique G�n�rale GNU pour plus de d�tails.
Vous devez avoir re�u une copie de la Licence Publique G�n�rale GNU en m�me temps que ce programme ; si ce n'est pas le cas, �crivez � la Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, Etats-Unis.
Auteurs
Olivier Langella, CNRS UPR9034
Paquet Debian GNU/Linux : populations_1.2.28-1_i386.deb
Paquet RPM GNU/Linux (RedHat ou Mandrake) : populations-1.2.28-2.i386.rpm
Sources : populations-1.2.28.tar.gz
Pour Windows : populations.exe
Note aux utilisateurs de Debian GNU/Linux
Pour compiler "populations", t�l�charger les sources .tar.gz, et utiliser ces commandes en root:
tar xvfz populations-1.2.28.tar.gz
cd populations-1.2.28
./configure
make
make install
Distances
DAS, shared allele distance (Chakraborty et Jin., 1993)
Nei, minimum genetic distance, Dm (Nei,1987)
Nei, standard genetic distance, Ds (Nei, 1987)
Cavalli-Sforza and Edwards, Dc (1967)
Nei et al's, Da (1983)
Latter, Fst (1972)
Prevosti et al.'s, Cp (1975)
Rogers', Dr (1972)
Reynolds J. unweighted, Dru (1983)
Reynolds J. weighted, Drw (1983)
Reynolds J. least squares, Drl (1983)
Distances microsatellites
Goldstein et al., dmu2 (1995a)
Average Square Distance ( ASD, Goldstein, Slatkin 1995)
Shriver et al's, Dsw (1995)
Lev A. Zhivotovsky, DR (1999)
Formats
- entr�e
- sortie
en entr�e
Populations peut lire les formats:
- Genepop
- G�n�tix
Et le format propre � Populations, qui permet de traiter un nombre illimit� d'all�les, et sur des populations haplo�des, diplo�des... ou N plo�des (en s�parant les all�les par ":").
exemple pour des populations diplo�des:
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , 02:01 03:03 01:02 03:02 10:11
Montpellier2 , 02:02 03:01 01:02 03:03 11:11
Montpellier3 , 01:02 04:01 02:02 01:02 10:10
Montpellier4 , 01:03 02:02 01:01 02:02 10:11
Montpellier5 , 02:03 02:04 01:01 01:02 10:10
POP Gigondas
Gigondas1 , 01:02 02:02 02:01 04:05 08:07
Gigondas2 , 01:02 02:01 02:01 04:05 03:07
Gigondas3 , 02:01 02:03 01:01 05:05 04:02
Gigondas4 , 02:01 03:03 03:01 03:03 06:03
Gigondas5 , 01:01 02:01 03:01 05:05 08:07
exemple pour des populations haplo�des:
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , 02 03 01 03 10
Montpellier2 , 02 03 01 03 11
Montpellier3 , 01 04 02 01 10
Montpellier4 , 01 02 01 02 10
Montpellier5 , 02 02 01 01 10
POP Gigondas
Gigondas1 , 01 02 02 04 08
Gigondas2 , 01 02 02 04 03
Gigondas3 , 02 02 01 05 04
Gigondas4 , 02 03 03 03 06
Gigondas5 , 01 02 03 05 08
exemple pour des populations haplo�des, en utilisant des noms d'all�les alphanum�riques (sans espaces):
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , all2 03 01 03 10
Montpellier2 , all2 03 01 03 11
Montpellier3 , all1 04 02 01 miss
Montpellier4 , all1 02 01 02 10
Montpellier5 , all2 02 01 01 10
POP Gigondas
Gigondas1 , all1 02 02 04 08
Gigondas2 , all1 02 02 04 miss
Gigondas3 , all2 02 01 05 04
Gigondas4 , all2 03 03 03 06
Gigondas5 , all1 02 03 05 08
cas des populations structur�es:
Les formats d�crits ci-dessus sont valables, il suffit d'indiquer derri�re le mot cl� "POP" un nom en forme de chemin de fichier.
exemple:
exemple de populations structur�es
locus1
locus2
locus3
POP Rennes/immeuble_sud/pop_3emeetage
ind1, (description des individus)
ind2, ...
ind3, ...
ind4, ...
POP Rennes/immeuble_sud/pop_2emeetage
ind1, (description des individus)
ind2, ...
ind3, ...
ind4, ...
Formats de sortie
Populations peut �crire des fichiers dans les formats suivants:
Genepop
G�n�tix
Populations
Lea
Immanc
microsat
Admix (G. Bertorelle)
Fstat (Jerome Goudet)
Les arbres g�n�r�s sont export�s au format "PHYLIP", lisible par : Treeview & par "Treeplot". Note: "treeplot" permet de convertir les fichiers Phylip en Adobe illustrator, PostScript, Gif... et de colorier automatiquement les individus en fonction de leur population.
Les matrices de distances peuvent �tre lues par Excell, Phylip, xgobi, NTsys.
Utilisation en ligne de commande
On peut maintenant utiliser "Populations" en ligne de commande pour produire des arbres phylog�n�tiques. il suffit de taper:
populations nom_du_fichier_de_donn�es -"arguments"
Les arguments disponibles sont les suivants:
-phylogeny ind ou pop (par d�faut) pour faire des arbres phylog�n�tiques sur les individus ou sur les populations
-dist m�thode (par d�faut, Nei standard, Ds) pour choisir la m�thode de distance utilis�e parmi ces possibilit�s: DAS, Dm, Ds, Dc, Da, dmu2, Fst, Cp, Dr, ASD, Dsw, Dr, Dru, Drw, Drl. voir distances calcul�es
construct m�thode (par d�faut, upgma) avec au choix: upgma ou nj (Neighbor Joining)
-bootstrap_ind nombre pour indiquer le nombre de bootstrap que vous voulez effectuer sur les individus (indisponible si l'on a choisi l'argument -ind)
-bootstrap_locus nombre pour indiquer le nombre de bootstrap que vous voulez effectuer sur les locus
-output nom_de_fichier_treeview pour indiquer le nom du fichier de sortie (au format treeview)
-level nombre , dans le cas de populations structur�es, permet d'indiquer le niveau sur lequel on d�sire faire l'arbre de m�tapopulations.
exemple de commande:
populations toutc2.txt -phylogeny pop -dist Dm -bootstrap_locus 10000 -output toutc2_10000_Dm.tre
On peut placer ces commandes dans un fichier .bat (pour DOS) ou un script (pour linux).
Bibliographie
Bruce Ranala and Joanna L. Mountain. Detecting immigration by using multilocus genotypes. Proc.Natl. Acad. Sci. USA, 94:9197-9201, 13/6/1997.
David B. Goldstein, Andres Ruiz Linares, Luigi Luca Cavalli-Sforza and Marcus W. Feldman. An Evaluation of Genetic Distances for Use With Microsatellite Loci. Genetics, 139:463-471, 5/10/1994.
D. B. Goldstein and D. D. Pollock. Launching Microsatellites: A Review of Mutation Processes and Methods of Phylogenetic Inference. Journal of Heredity, 88(335-342):0022-1503, 31/3/1997.
Li Jin and Ranajit Chakraborty. Estimation of Genetic Distance and Coefficient of Gene Diversity from Single-Probe Multilocus DNA Fingerprinting Data. Mol. Biol. Evol, 11(1):120-127, 13/9/1993.
Mark D. Shriver, Li Jin, Eric Boerwinkle, Ranjan Deka, Robert E. Ferrel and Ranajit Chakraborty. A Novel Measure of Genetic Distance for Highly Polymorphic Tandem Repeat Loci. Mol. Biol. Evol, 12(5):914-920, 13/4/1995.
Montgomery Slatkin. A Measure of Population Subdivision on Microsatellite Allele Frequencies. Genetics, (139):457-462, 19/6/1994.
Naruya Saitou and Masatoshi Nei. The Neigbhor-joining Method: A New Method for Reconstructing Phylogenetic Trees. Mol. Biol. Evol, 4(4):406-425, 18/2/1987.
Naoko Takezaki and Masatoshi Nei. Genetic Distances and Reconstruction of Phylogenetic Trees From Microsatellite DNA. Genetics, (144):189-399, 6/6/1996.
William J. Bruno, Nicholas D. Socci and Aaron L. Halpern. Weighted Neigbhor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction. Mol. Biol. Evol, 17(1):189-197, 11/10/1999.
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populations-1.2.33+svn0120106.orig/html/old/index_en.php.html0000644000175000017500000005774010566525154023663 0ustar georgeskgeorgesk Bioinfo PGE
Populations 1.2.28 (12/5/2002)
Population genetic software (individuals or populations distances, phylogenetic trees)
Contents
  • haploids, diploids or polyploids genotypes (see input formats)
  • structured populations (see input files structured populations
  • No limit of populations, loci, alleles per loci (see input formats)
  • Distances between individuals (15 different methods)
  • Distances between populations (15 methods)
  • Bootstraps on loci OR individuals
  • Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA (PHYLIP tree format)
  • Allelic diversity
  • Converts data files from Genepop to different formats (Genepop, Genetix, Msat, Populations...)
Download
Populations, 1.2.28 (12/5/2002) Copyright (C) 1999, Olivier Langella, CNRS UPR9034
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 licence
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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
Authors
Olivier Langella, CNRS UPR9034
Debian GNU/Linux package : populations_1.2.28-1_i386.deb
RPM GNU/Linux package (RedHat ou Mandrake) : populations-1.2.28-2.i386.rpm
Sources : populations-1.2.28.tar.gz
Windows : populations.exe
Note aux utilisateurs de Debian GNU/Linux
to compile "populations", download tar.gz sources an do the following with root privileges:
tar xvfz populations-1.2.28.tar.gz
cd populations-1.2.28
./configure
make
make install
Distances
DAS, shared allele distance (Chakraborty et Jin., 1993)
Nei, minimum genetic distance, Dm (Nei,1987)
Nei, standard genetic distance, Ds (Nei, 1987)
Cavalli-Sforza and Edwards, Dc (1967)
Nei et al's, Da (1983)
Latter, Fst (1972)
Prevosti et al.'s, Cp (1975)
Rogers', Dr (1972)
Reynolds J. unweighted, Dru (1983)
Reynolds J. weighted, Drw (1983)
Reynolds J. least squares, Drl (1983)
Microsatellites distances
Goldstein et al., dmu2 (1995a)
Average Square Distance ( ASD , Goldstein, Slatkin 1995)
Shriver et al's, Dsw (1995)
Lev A. Zhivotovsky, DR (1999)
Formats
- input
- output
input files
"Populations" accepts file from other population genetic softwares:
- Genepop
- Génétix
and it has its own format:
"Populations" format allows to use unlimited number of alleles, of haploids, diploids or nploids. The format is close to Genepop but alleles at a given locus are separated by ":". Thus, man can code alleles with all ASCII characters.
Diploid population example:
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , 02:01 03:03 01:02 03:02 10:11
Montpellier2 , 02:02 03:01 01:02 03:03 11:11
Montpellier3 , 01:02 04:01 02:02 01:02 10:10
Montpellier4 , 01:03 02:02 01:01 02:02 10:11
Montpellier5 , 02:03 02:04 01:01 01:02 10:10
POP Gigondas
Gigondas1 , 01:02 02:02 02:01 04:05 08:07
Gigondas2 , 01:02 02:01 02:01 04:05 03:07
Gigondas3 , 02:01 02:03 01:01 05:05 04:02
Gigondas4 , 02:01 03:03 03:01 03:03 06:03
Gigondas5 , 01:01 02:01 03:01 05:05 08:07
Haploid example :
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , 02 03 01 03 10
Montpellier2 , 02 03 01 03 11
Montpellier3 , 01 04 02 01 10
Montpellier4 , 01 02 01 02 10
Montpellier5 , 02 02 01 01 10
POP Gigondas
Gigondas1 , 01 02 02 04 08
Gigondas2 , 01 02 02 04 03
Gigondas3 , 02 02 01 05 04
Gigondas4 , 02 03 03 03 06
Gigondas5 , 01 02 03 05 08
example of haploid, using any ASCII character: no space in allele names:
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , all2 03 01 03 10
Montpellier2 , all2 03 01 03 11
Montpellier3 , all1 04 02 01 miss
Montpellier4 , all1 02 01 02 10
Montpellier5 , all2 02 01 01 10
POP Gigondas
Gigondas1 , all1 02 02 04 08
Gigondas2 , all1 02 02 04 miss
Gigondas3 , all2 02 01 05 04
Gigondas4 , all2 03 03 03 06
Gigondas5 , all1 02 03 05 08
Structured population
To code metapopulations, you can choose either "Genepop" or "Populations" format. You only need to give the name of population after the keyword "POP " (separator = "/")
example:
exemple de populations structurées
locus1
locus2
locus3
POP Rennes/immeuble_sud/pop_3emeetage
ind1, (description des individus)
ind2, ...
ind3, ...
ind4, ...
POP Rennes/immeuble_sud/pop_2emeetage
ind1, (description des individus)
ind2, ...
ind3, ...
ind4, ...
Output files
Populations is able to produce various population genetic software formats:
Genepop
Génétix
Populations
Lea
Immanc
microsat
Admix (G. Bertorelle)
Fstat (Jerome Goudet)
Phylogenetic trees are coded using the "Phylip" format. " Treeview" can be used for Windows or Linux, and you can use "Treeplot" to convert the phylip format into postscript, adobe illustrator, gif... with colors for each populations
Matrix distances files are "Excel (gnumeric compatible)", "Phylip", "xgobi", "NTsys" or any text editor compliant.
Command line
You can use "Populations" as a command line programm (very useful for batch treatment) to infer phylogenetic trees:
populations name_of_input_file -"arguments"
Available arguments:
-phylogeny ind ou pop (default) for phylogenetic trees based on individuals or populations
-dist method (default: Nei standard, Ds) you can choose among: DAS, Dm, Ds, Dc, Da, dmu2, Fst, Cp, Dr, ASD, Dsw, Dr, Dru, Drw, Drl. see distances for details.
-construct method (default: upgma) possibilities upgma or nj (Neighbor Joining)
-bootstrap_ind number to indicate the number of bootstraps to perform on individuals
-bootstrap_locus number to indicate the number of bootstraps to perform on loci
-output name_of_treeview_file to indicate the name of the tree file (phylip tree format)
-level number , structured populations allows to choose the structuration factor (in the example: town level is 1, building level is 2...).
example:
populations toutc2.txt -phylogeny pop -dist Dm -bootstrap_locus 10000 -output toutc2_10000_Dm.tre
Commands can be write in a .bat file (for DOS) or a script file (for UNIX).
Bibliography
Bruce Ranala and Joanna L. Mountain. Detecting immigration by using multilocus genotypes. Proc.Natl. Acad. Sci. USA, 94:9197-9201, 13/6/1997.
David B. Goldstein, Andres Ruiz Linares, Luigi Luca Cavalli-Sforza and Marcus W. Feldman. An Evaluation of Genetic Distances for Use With Microsatellite Loci. Genetics, 139:463-471, 5/10/1994.
D. B. Goldstein and D. D. Pollock. Launching Microsatellites: A Review of Mutation Processes and Methods of Phylogenetic Inference. Journal of Heredity, 88(335-342):0022-1503, 31/3/1997.
Li Jin and Ranajit Chakraborty. Estimation of Genetic Distance and Coefficient of Gene Diversity from Single-Probe Multilocus DNA Fingerprinting Data. Mol. Biol. Evol, 11(1):120-127, 13/9/1993.
Mark D. Shriver, Li Jin, Eric Boerwinkle, Ranjan Deka, Robert E. Ferrel and Ranajit Chakraborty. A Novel Measure of Genetic Distance for Highly Polymorphic Tandem Repeat Loci. Mol. Biol. Evol, 12(5):914-920, 13/4/1995.
Montgomery Slatkin. A Measure of Population Subdivision on Microsatellite Allele Frequencies. Genetics, (139):457-462, 19/6/1994.
Naruya Saitou and Masatoshi Nei. The Neigbhor-joining Method: A New Method for Reconstructing Phylogenetic Trees. Mol. Biol. Evol, 4(4):406-425, 18/2/1987.
Naoko Takezaki and Masatoshi Nei. Genetic Distances and Reconstruction of Phylogenetic Trees From Microsatellite DNA. Genetics, (144):189-399, 6/6/1996.
William J. Bruno, Nicholas D. Socci and Aaron L. Halpern. Weighted Neigbhor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction. Mol. Biol. Evol, 17(1):189-197, 11/10/1999.
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Populations 1.2.31

Population genetic software (individuals or populations distances, phylogenetic trees)

Contents

  • haploids, diploids or polyploids genotypes (see input formats)
  • structured populations (see input files structured populations
  • No limit of populations, loci, alleles per loci (see input formats)
  • Distances between individuals (15 different methods)
  • Distances between populations (15 methods)
  • Bootstraps on loci OR individuals
  • Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA (PHYLIP tree format)
  • Allelic diversity
  • Converts data files from Genepop to different formats (Genepop, Genetix, Msat, Populations...)

Download

Populations, 1.2.30 Copyright (C) 1999, Olivier Langella, CNRS UPR9034
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 licence
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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
Authors
Olivier Langella

all systems

download populations

Ubuntu packages

If you are using Ubuntu, you can find "populations" and "treeplot" packages here :
https://launchpad.net/~olivier-langella/+archive
Please modify your source list entries to add the repositorie that corresponds to your Ubuntu version ( Adding Repositories in Ubuntu how to )

Distances

Formats

- input
- output

input files

"Populations" accepts file from other population genetic softwares:
- Genepop
- Génétix
and it has its own format:
"Populations" format allows to use unlimited number of alleles, of haploids, diploids or nploids. The format is close to Genepop but alleles at a given locus are separated by ":". Thus, man can code alleles with all ASCII characters.
Diploid population example:
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , 02:01 03:03 01:02 03:02 10:11
Montpellier2 , 02:02 03:01 01:02 03:03 11:11
Montpellier3 , 01:02 04:01 02:02 01:02 10:10
Montpellier4 , 01:03 02:02 01:01 02:02 10:11
Montpellier5 , 02:03 02:04 01:01 01:02 10:10
POP Gigondas
Gigondas1 , 01:02 02:02 02:01 04:05 08:07
Gigondas2 , 01:02 02:01 02:01 04:05 03:07
Gigondas3 , 02:01 02:03 01:01 05:05 04:02
Gigondas4 , 02:01 03:03 03:01 03:03 06:03
Gigondas5 , 01:01 02:01 03:01 05:05 08:07
Haploid example :
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , 02 03 01 03 10
Montpellier2 , 02 03 01 03 11
Montpellier3 , 01 04 02 01 10
Montpellier4 , 01 02 01 02 10
Montpellier5 , 02 02 01 01 10
POP Gigondas
Gigondas1 , 01 02 02 04 08
Gigondas2 , 01 02 02 04 03
Gigondas3 , 02 02 01 05 04
Gigondas4 , 02 03 03 03 06
Gigondas5 , 01 02 03 05 08
example of haploid, using any ASCII character: no space in allele names:
"Grape populations in southern France"
ADHLocus1
ADH#2
ADHthree
ADH-4
ADH-5
Pop Montpellier
Montpellier1 , all2 03 01 03 10
Montpellier2 , all2 03 01 03 11
Montpellier3 , all1 04 02 01 miss
Montpellier4 , all1 02 01 02 10
Montpellier5 , all2 02 01 01 10
POP Gigondas
Gigondas1 , all1 02 02 04 08
Gigondas2 , all1 02 02 04 miss
Gigondas3 , all2 02 01 05 04
Gigondas4 , all2 03 03 03 06
Gigondas5 , all1 02 03 05 08

Structured population

To code metapopulations, you can choose either "Genepop" or "Populations" format. You only need to give the name of population after the keyword "POP " (separator = "/")
example:
exemple de populations structurées
locus1
locus2
locus3
POP Rennes/immeuble_sud/pop_3emeetage
ind1, (description des individus)
ind2, ...
ind3, ...
ind4, ...
POP Rennes/immeuble_sud/pop_2emeetage
ind1, (description des individus)
ind2, ...
ind3, ...
ind4, ...

Output files

Populations is able to produce various population genetic software formats:
Genepop
Génétix
Populations
Lea
Immanc
microsat
Admix (G. Bertorelle)
Fstat (Jerome Goudet)
Phylogenetic trees are coded using the "Phylip" format. " Treeview" can be used for Windows or Linux, and you can use ">Treeplot" to convert the phylip format into postscript, adobe illustrator, gif... with colors for each populations
Matrix distances files are "Excel (gnumeric compatible)", "Phylip", "xgobi", "NTsys" or any text editor compliant.

Command line

You can use "Populations" as a command line programm (very useful for batch treatment) to infer phylogenetic trees:
populations name_of_input_file -"arguments"
Available arguments:
-phylogeny ind ou pop (default) for phylogenetic trees based on individuals or populations
-dist method (default: Nei standard, Ds) you can choose among: DAS, Dm, Ds, Dc, Da, dmu2, Fst, Cp, Dr, ASD, Dsw, Dr, Dru, Drw, Drl. see distances for details.
-construct method (default: upgma) possibilities upgma or nj (Neighbor Joining)
-bootstrap_ind number to indicate the number of bootstraps to perform on individuals
-bootstrap_locus number to indicate the number of bootstraps to perform on loci
-output name_of_treeview_file to indicate the name of the tree file (phylip tree format)
-level number , structured populations allows to choose the structuration factor (in the example: town level is 1, building level is 2...).
example:
populations toutc2.txt -phylogeny pop -dist Dm -bootstrap_locus 10000 -output toutc2_10000_Dm.tre
Commands can be write in a .bat file (for DOS) or a script file (for UNIX).

Bibliography

Bruce Ranala and Joanna L. Mountain. Detecting immigration by using multilocus genotypes. Proc.Natl. Acad. Sci. USA, 94:9197-9201, 13/6/1997.
David B. Goldstein, Andres Ruiz Linares, Luigi Luca Cavalli-Sforza and Marcus W. Feldman. An Evaluation of Genetic Distances for Use With Microsatellite Loci. Genetics, 139:463-471, 5/10/1994.
D. B. Goldstein and D. D. Pollock. Launching Microsatellites: A Review of Mutation Processes and Methods of Phylogenetic Inference. Journal of Heredity, 88(335-342):0022-1503, 31/3/1997.
Li Jin and Ranajit Chakraborty. Estimation of Genetic Distance and Coefficient of Gene Diversity from Single-Probe Multilocus DNA Fingerprinting Data. Mol. Biol. Evol, 11(1):120-127, 13/9/1993.
Mark D. Shriver, Li Jin, Eric Boerwinkle, Ranjan Deka, Robert E. Ferrel and Ranajit Chakraborty. A Novel Measure of Genetic Distance for Highly Polymorphic Tandem Repeat Loci. Mol. Biol. Evol, 12(5):914-920, 13/4/1995.
Montgomery Slatkin. A Measure of Population Subdivision on Microsatellite Allele Frequencies. Genetics, (139):457-462, 19/6/1994.
Naruya Saitou and Masatoshi Nei. The Neigbhor-joining Method: A New Method for Reconstructing Phylogenetic Trees. Mol. Biol. Evol, 4(4):406-425, 18/2/1987.
Naoko Takezaki and Masatoshi Nei. Genetic Distances and Reconstruction of Phylogenetic Trees From Microsatellite DNA. Genetics, (144):189-399, 6/6/1996.
William J. Bruno, Nicholas D. Socci and Aaron L. Halpern. Weighted Neigbhor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction. Mol. Biol. Evol, 17(1):189-197, 11/10/1999.
populations-1.2.33+svn0120106.orig/html/libcss/0000755000175000017500000000000011701602131021061 5ustar georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/html/libcss/mathematica.css0000644000175000017500000000263410621075553024071 0ustar georgeskgeorgesk/* * The contents of this file are subject to the Mozilla Public * License Version 1.1 (the "License"); you may not use this file * except in compliance with the License. You may obtain a copy of * the License at http://www.mozilla.org/MPL/ * * Software distributed under the License is distributed on an "AS * IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or * implied. See the License for the specific language governing * rights and limitations under the License. * * The Original Code is Mozilla MathML Project. * * The Initial Developer of the Original Code is The University Of * Queensland. Portions created by The University Of Queensland are * Copyright (C) 1999 The University Of Queensland. All Rights Reserved. * * Contributor(s): * Roger B. Sidje */ /*******************************************************/ /* namespace for MathML elements */ /*******************************************************/ @namespace url(http://www.w3.org/1998/Math/MathML); /*******************************************************/ /* CSS rules to use Mathematica fonts */ /*******************************************************/ /* old: compatible with pre-1.4 builds */ :-moz-math-font-style-stretchy { font-family: Math1, Math2, Math4; } ::-moz-math-stretchy { font-family: Math1, Math2, Math4; } populations-1.2.33+svn0120106.orig/html/libcss/main.css0000644000175000017500000000124710570267045022541 0ustar georgeskgeorgesk* { margin: 0; padding: 0; border: 0; font-family: "Lucida Grande", Verdana, Lucida, Helvetica, Arial, sans-serif; font-size: 1em; font-weight: normal; font-style: normal; text-decoration: none; } h1 { font-size: 2em; font-weight: bold; margin: 1em; } h2 { font-size: 2em; font-weight: normal; margin-top: 1em; margin-left: 3em; } h3 { font-size: 1.2em; font-weight: bold; margin-top: 1em; margin-left: 4em; } body { margin-left: 3%; } ul.plan { list-style : disc; margin-top: 1em; margin-left: 3%; margin-bottom:1em; } ul.enumeration { list-style : square; margin-top: 1em; margin-left: 3%; margin-bottom:1em; }populations-1.2.33+svn0120106.orig/html/formules/0000755000175000017500000000000011701602132021437 5ustar georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/html/formules/reynold_least_square.xhtml0000644000175000017500000003310111071617032026744 0ustar georgeskgeorgesk ]> Reynold's genetic distance

Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83]

DReynold = − ln ( 1 − θ ) DReynold = -ln (1 - %theta)
the following notation is used, for all 𝚹 estimators:
n ˉ = ∑ i = 1 r n i r , n c = ( r n ˉ − ∑ i = 1 r n i 2 r n ˉ ) ( r − 1 ) , p lu ˜ = ∑ i = 1 r n i p ilu ˜ r n ˉ , α il ˜ = 1 − ∑ u = 1 v 1 p ilu 2 ˜ bar n = sum _{i=1} ^r {{n_i} over r } , n_c = (r bar n - sum _{i=1} ^r {n^2 _i over {r bar n}}) over (r-1), tilde p _lu = sum _{i=1} ^r {n_i tilde p _ilu} over {r bar n}, tilde %alpha _il = 1 - sum ^{v_1} _{u=1} tilde p _ilu ^2

least squares 𝛉 estimator :

θ L ˜ = 2x + y − z ± ( z − y ) 2 + 4x 2 2 ( y − z ) tilde{%theta }_{L} = {2x+y-z +- sqrt{( z-y) ^{2}+4x^{2}}} over {2( y-z) }
where: z = ∑ l = 1 m a l 2 z= sum ^{m}_{l=1}a_{l}^{2} , x = ∑ l = 1 m a l b l x= sum ^{m}_{l=1}a_{l}b_{l} and y = ∑ l = 1 m b l 2 y= sum ^{m}_{l=1}b_{l}^{2} . to check which of the two solutions for ̃𝛉 L provides the minimum, the residual sum of squares, R, should be calculated for each where:
R = ( 2x + y + z ) θ L 2 ˜ − 2 ( x + z ) θ L ˜ + z 1 − 2 θ L ˜ + 2 θ L 2 ˜ R={ ( 2x+y+z ) tilde{%theta }_{L}^{2}-2 ( x+z ) tilde{%theta }_{L}+z} over {1-2 tilde{%theta }_{L}+2 tilde{%theta }_{L}^{2}}
populations-1.2.33+svn0120106.orig/html/formules/latter_fst.xhtml0000644000175000017500000000431111071617032024670 0ustar georgeskgeorgesk ]> Latter's (1972) Fst (=ɸ*) distance

Latter's (1972) Fst (=ɸ*) distance

Fst = ( J X + J Y ) 2 − J XY 1 − J XY Fst = {{(J_X + J_Y)} over 2 - J_XY} over {1 - J_XY} populations-1.2.33+svn0120106.orig/html/formules/nei_da.xhtml0000644000175000017500000000441011071617032023740 0ustar georgeskgeorgesk ]> Nei et al's (1983)

Nei et al's (1983) DA distance

D A = 1 − 1 r ∑ j r ∑ i m j x ij y ij D_A = 1 - {1} over {r} sum from j to r sum from i to m_j sqrt{x_ij y_ij} populations-1.2.33+svn0120106.orig/html/formules/nei_ds.xhtml0000755000175000017500000000332010621076071023766 0ustar georgeskgeorgesk ]> Nei's (1972) standard genetic distance (Ds) [Takezaki, N. 96]

Nei's (1972) standard genetic distance (Ds) [Takezaki, N. 96]

Ds = − ln J XY J X J Y Ds=-ln {left[ {J_{XY}}over{sqrt{J_{X}J_{Y}}} right]}
populations-1.2.33+svn0120106.orig/html/formules/prevosti.xhtml0000644000175000017500000000436711071617032024407 0ustar georgeskgeorgesk ]> Prevosti et al's (1975) distance

Prevosti et al's (1975) distance [Takezaki, N. 96] has a statistical property similar to that of Dr and is defined as

Cp = ∑ j r ∑ i m j x ij − y ij 2r Cp = {sum _j ^r sum _i ^{m_j} abs{x_ij - y_ij}} over 2r populations-1.2.33+svn0120106.orig/html/formules/reynold_drw.xhtml0000644000175000017500000002122211071617032025051 0ustar georgeskgeorgesk ]> Reynold's genetic distance

Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83]

DReynold = − ln ( 1 − θ ) DReynold = -ln (1 - %theta)
the following notation is used, for all 𝚹 estimators:
n ˉ = ∑ i = 1 r n i r , n c = ( r n ˉ − ∑ i = 1 r n i 2 r n ˉ ) ( r − 1 ) , p lu ˜ = ∑ i = 1 r n i p ilu ˜ r n ˉ , α il ˜ = 1 − ∑ u = 1 v 1 p ilu 2 ˜ bar n = sum _{i=1} ^r {{n_i} over r } , n_c = (r bar n - sum _{i=1} ^r {n^2 _i over {r bar n}}) over (r-1), tilde p _lu = sum _{i=1} ^r {n_i tilde p _ilu} over {r bar n}, tilde %alpha _il = 1 - sum ^{v_1} _{u=1} tilde p _ilu ^2

weighted average of single-locus ratio estimators :

θ W ˜ = ( ∑ l = 1 m a l ) ∑ l = 1 m ( a l + b l ) tilde{%theta }_{W}= {( sum ^{m}_{l=1}a_{l}) } over {sum ^{m}_{l=1}( a_{l}+b_{l}) }
populations-1.2.33+svn0120106.orig/html/formules/nei_dm.xhtml0000755000175000017500000000320510621076071023762 0ustar georgeskgeorgesk ]> Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]

Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]

D m = J X + J Y 2 - J XY Dm=(J_X + J_Y)over 2 - J_XY
populations-1.2.33+svn0120106.orig/html/formules/das.xhtml0000755000175000017500000001147110621076701023302 0ustar georgeskgeorgesk ]> Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93]

Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93]

between individuals:
D SA I = 1 − P SA I , with P SA I = ∑ j r S 2r P_{SA_{I}}={sum ^{r}_{j}S} over {2r}
where the number of shared alleles S is sumed over all loci r.
between populations:
D SA B = 1 − 2 P ˉ SA B P ˉ SA X + P ˉ SA Y D_{SA_{B}}=1-{2{bar{P}}_{SA_{B}}}over{{bar{P}}_{SA_{X}}+{bar{P}}_{SA_{Y}}}
where the average proportion of shared alleles between and within populations X and Y ( P ˉ SA B , P ˉ SA X , P ˉ SA Y respectively) is computed overall possible combinations of individuals sampled.
populations-1.2.33+svn0120106.orig/html/formules/reynold_dru.xhtml0000644000175000017500000005423411071617032025060 0ustar georgeskgeorgesk ]> Reynold's genetic distance

Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83]

DReynold = − ln ( 1 − θ ) DReynold = -ln (1 - %theta)
the following notation is used, for all 𝚹 estimators:
n ˉ = ∑ i = 1 r n i r , n c = ( r n ˉ − ∑ i = 1 r n i 2 r n ˉ ) ( r − 1 ) , p lu ˜ = ∑ i = 1 r n i p ilu ˜ r n ˉ , α il ˜ = 1 − ∑ u = 1 v 1 p ilu 2 ˜ bar n = sum _{i=1} ^r {{n_i} over r } , n_c = (r bar n - sum _{i=1} ^r {n^2 _i over {r bar n}}) over (r-1), tilde p _lu = sum _{i=1} ^r {n_i tilde p _ilu} over {r bar n}, tilde %alpha _il = 1 - sum ^{v_1} _{u=1} tilde p _ilu ^2

unweighted average of single-locus ratio estimators, ̃𝛉 U:

θ U ˜ = 1 m ∑ l = 1 m θ l ˜ tilde %theta _U = 1 over m sum from l=1 to m tilde %theta _{l}
, with θ l = a l a l + b l %theta _{l} = {a_l} over {a_l + b_l} . The estimates of the components of variance of interest for the lth locus are within populations, r is the number of populations examined:
b l = 2 ∑ i = 1 r n i α il ˜ r ( 2 n ˉ − 1 ) b_l = 2 sum from {i=1} to r {{ n_i tilde %alpha _{il}} over {r(2 bar n - 1)}}
and between populations:
a l = [ 2 ∑ i = 1 r n i ∑ u = 1 v l ( p ilu ˜ − p lu ˜ ) 2 − ( r − 1 ) b l ] 2 ( r − 1 ) n c a_{l}= {[ 2 sum ^{r}_{i=1} n_{i} sum ^{v_{l}}_{u=1} ( tilde{p}_{ilu} - tilde{p}_{lu}) ^{2} - ( r - 1) b_{l}] } over {2 (r - 1) n_c}
When there are just two populations, r = 2, the usual genetic distance situation obtains, and the most convenient computing formulas for the variance components are (used in Populations)
a l = 1 2 ∑ u ( p 1lu ˜ − p 2lu ˜ ) 2 − ( n 1 + n 2 ) ( n 1 α 1l ˜ + n 2 α 2l ˜ ) 4n 1 n 2 ( n 1 + n 2 − 1 ) a_{l}={1} over {2} sum _{u} ( tilde{p}_{1lu}-tilde{p}_{2lu}) ^{2} - {( n_{1}+n_{2}) ( n_{1} tilde{%alpha }_{1l}+n_{2} tilde{%alpha }_{2l}) } over {4n_{1}n_{2} ( n_{1}+n_{2}-1 ) }
a l + b l = 1 2 ∑ u ( p 1lu ˜ − p 2lu ˜ ) 2 + ( 4n 1 n 2 − n 1 − n 2 ) ( n 1 α 1l ˜ + n 2 α 2l ˜ ) 4n 1 n 2 ( n 1 + n 2 − 1 ) a_{l}+b_{l} = {1} over {2} sum _{u} ( tilde{p}_{1lu}- tilde{p}_{2lu}) ^{2} + {( 4n_{1}n_{2}-n_{1}-n_{2}) ( n_{1} tilde{%alpha }_{1l}+n_{2} tilde{%alpha }_{2l}) } over {4n_{1}n_{2} ( n_{1}+n_{2}-1) }
populations-1.2.33+svn0120106.orig/html/formules/roger.xhtml0000644000175000017500000000465211071617032023647 0ustar georgeskgeorgesk ]> Rogers' (1972) distance

Rogers' (1972) distance [Takezaki, N. 96]

Dr = 1 r ∑ j r ∑ i m ( x ij − y ij ) 2 2 Dr = 1 over r sum from j to r sqrt{{sum _i ^m (x_ij - y_ij)^2} over 2} populations-1.2.33+svn0120106.orig/html/formules/reynold_general.mml0000644000175000017500000000530611071617032025330 0ustar georgeskgeorgesk R = ( 2x + y + z ) θ L 2 ˜ − 2 ( x + z ) θ L ˜ + z 1 − 2 θ L ˜ + 2 θ L 2 ˜ R={ ( 2x+y+z ) tilde{%theta }_{L}^{2}-2 ( x+z ) tilde{%theta }_{L}+z} over {1-2 tilde{%theta }_{L}+2 tilde{%theta }_{L}^{2}} populations-1.2.33+svn0120106.orig/html/formules/cavali_sforza.xhtml0000644000175000017500000000526211071617032025352 0ustar georgeskgeorgesk ]> Cavalli-Sforza and Edwards, Dc (1967)

Cavalli-Sforza and Edwards, Dc (1967)

Dc = 2 Π r ∑ j r 2 ( 1 − ∑ i m j x ij y ij ) Dc={2}over{{%PI}r} sum from{j} to{r} sqrt{2(1 - sum from i to m_j sqrt{x_ij y_ij} )} populations-1.2.33+svn0120106.orig/html/old_formula/0000755000175000017500000000000011701602132022106 5ustar georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/html/old_formula/node5.html0000755000175000017500000000454411545034324024030 0ustar georgeskgeorgesk Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96] next up previous
Next: Latter's (1972) Fst (=*) Up: IAM distances Previous: Nei's (1972) standard genetic

Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]


\begin{displaymath} Dm=\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}\end{displaymath}


Olivier Langella 2002-03-20
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Next: Rogers' (1972) distance [Takezaki, Up: IAM distances Previous: Nei's (1973) minimum genetic

Latter's (1972) Fst (=\( \phi \protect \)*) distance [Takezaki, N. 96]


\begin{displaymath} Fst=\frac{\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}}{1-J_{XY}}\end{displaymath}


Olivier Langella 2002-03-20
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Next: Shared allele distance (Chakraborty Up: Distances Previous: Distances

IAM distances

\( J_{X}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x^{2}_{ij}}{r} \) and \( J_{Y}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}y^{2}_{ij}}{r} \)are the average homozygoties over loci in populations X and Y, respectively, and \( J_{XY}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x_{ij}y_{ij}}{r} \).

\( x_{ij} \) and \( y_{ij} \) are the frequencies of the ith allele at the jth locus in populations X and Y, respectively, \( m_{j} \) is the number of alleles at the jth locus, and r is the number of loci examined.


Subsections
Olivier Langella 2002-03-20
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Next: Distances



Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/img7.gif0000755000175000017500000000076311545034324023461 0ustar georgeskgeorgeskGIF89axxxlll```TTTHHH<<<000$$$ !,@I8ͻ l! 0SBAH,r/8,% z``,D- 9 -+u6g /1]w|~'llf%0` z# "Dž>>|g ^ ;X< PK A BĺP|#/Pliױ8xpAA`"<NZP2$8@@؀i1d. :hRJ$^J`8@ H-6z!삱>@;A-X?P+ pYÃp 4e2oLӨS^ͺ_;populations-1.2.33+svn0120106.orig/html/old_formula/node7.html0000755000175000017500000000457511545034324024036 0ustar georgeskgeorgesk Rogers' (1972) distance [Takezaki, N. 96] next up previous
Next: Prevosti et al's (1975) Up: IAM distances Previous: Latter's (1972) Fst (=*)

Rogers' (1972) distance [Takezaki, N. 96]


\begin{displaymath} Dr=\frac{1}{r}\sum ^{r}_{j}\sqrt{\frac{\sum ^{m}_{i}\left( x_{ij}-y_{ij}\right) ^{2}}{2}}\end{displaymath}


Olivier Langella 2002-03-20
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Next: Bibliography Up: SMM distances Previous: Shriver et al.'s (1995)

Lev A. Zhivotovsky (1999) [Takezaki, N. 96]

Consider two populations, X an Y and r autosomal microsatellite loci. \( \overline{\mu _{X}} \) and \( \overline{\mu _{Y}} \)are the mean of \( \mu _{X_{j}} \)and \( \mu _{Y_{j}} \)averall loci for population X and Y respectively.


\begin{displaymath} D_{R}=-\log \left( \frac{C_{XY}}{V_{XY}}\right) \end{displaymath}

with,

\( C_{XY}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}\mu _{Y_{j}}-r\overline{\mu _{X}}\overline{\mu _{Y}}\right) \) and \( V_{XY}=\frac{1}{2}\left( V_{X}+V_{Y}\right) \), where \( V_{X}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}^{2}-r\overline{\mu _{X}}^{2}\right) \), \( V_{Y}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{Y_{j}}^{2}-r\overline{\mu _{Y}}^{2}\right) \)

Attention, to avoid software crash, when \( C_{XY}<1 \), \( C_{XY} \) is set to 1.


Olivier Langella 2002-03-20
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Next: Goldstein et al. (1995a) Up: Distances Previous: least squares estimator :

SMM distances

\( \mu _{X_{j}}=\sum _{i}ix_{ij} \) and \( \mu _{Y_{j}}=\sum _{i}iy_{ij} \) are average allelic states at the jth locus, and \( x_{ij} \) and \( y_{ij} \) are the frequencies of the allele in state \( i \) at the jth locus in populations X an Y, respectively.


Subsections
Olivier Langella 2002-03-20
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Next: weighted average of single-locus Up: Reynold's genetic distance for Previous: Reynold's genetic distance for

unweighted average of single-locus ratio estimators, \( \tilde{\theta }_{U}\protect \):


\begin{displaymath} \tilde{\theta }_{U}=\frac{1}{m}\sum ^{m}_{l=1}\tilde{\theta }_{l}\end{displaymath}

, with \( \tilde{\theta }_{l}=\frac{a_{l}}{a_{l}+b_{l}} \). The estimates of the components of variance of interest for the lth locus are within populations, r is the number of populations examined:

\begin{displaymath} b_{l}=2\sum ^{r}_{i=1}\frac{n_{i}\tilde{\alpha }_{il}}{r(2\bar{n}-1)}\end{displaymath}

and between populations:


\begin{displaymath} a_{l}=\frac{\left[ 2\sum ^{r}_{i=1}n_{i}\sum ^{v_{l}}_{u=1}\... ...^{2}-\left( r-1\right) b_{l}\right] }{2\left( r-1\right) n_{c}}\end{displaymath}

When there are just two populations, r = 2, the usual genetic distance situation obtains, and the most convenient computing formulas for the variance components are (used in Populations)


\begin{displaymath} a_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tilde{p}_{... ...\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}


\begin{displaymath} a_{l}+b_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tild... ...\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/node21.html0000755000175000017500000000640111545034324024100 0ustar georgeskgeorgesk Bibliography next up previous
Next: About this document ... Up: formules Previous: Lev A. Zhivotovsky (1999)

Bibliography

Goldstein, D.B. 97
Goldstein, D.B. & Pollock, D.D.
Launching Microsatellites: A Review of Mutation Processes and Methods of Phylogenetic Inference.
Journal of Heredity, vol. 88, no. 335-342, pages 0022-1503, 31 1997.
1997.

Jin, L. 93
Jin, L. & Chakraborty, R.
Estimation of Genetic Distance and Coefficient of Gene Diversity from Single-Probe Multilocus DNA Fingerprinting Data.
Mol. Biol. Evol., vol. 11, no. 1, pages 120-127, 13 1993.
1994.

Reynolds, J. 83
Reynolds, J., Weir, B.S. & Cockerham, C.
Estimation of the coancestry coefficient: basis for a short-term genetic distance.
Genetics Society of America, vol. 105, pages 767-779, November 1983.
1983.

Shriver, M.D. 95
Shriver, M.D., Jin, L. & Boerwinkle, E.
A Novel Measure of Genetic Distance for Highly Polymorphic Tandem Repeat Loci.
Mol. Bio. Evol., vol. 12, no. 5, pages 914-920, 4 1995.

Takezaki, N. 96
Takezaki, N. & Nei, M.
Genetic Distances and Reconstruction of Phylogenetic Trees From Microsatellite DNA.
Genetics, no. 144, pages 189-399, 6 1996.
september, 1996.


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/img16.gif0000755000175000017500000000133211545034324023532 0ustar georgeskgeorgeskGIF89a7xxxlll```TTTHHH<<<000$$$ !,7@I8ͻ`(BTvItx|b1 8 D@bp,p,!I(lxL.zj@~ 2K# Qv,y 0 4rWWl o D  6m լ_w֊FHJKMO uj/_ l*(0 b (R ՂSB=E悒i4ߦsP`Z)]JO|ܺCI(UÞE}]˶۷pʝKݻxOm^,0xŁ_, &>hM*HɊ< d̡T<> ;ٶkm ;o0^E˿I ͡ JZ!umS>zTB9J@/8x]_$ hw>L- NVt2 @ N'8B(6لiT@$400HUY4eӥ❏5#^x+10yc1~ G`)dihl;populations-1.2.33+svn0120106.orig/html/old_formula/images.pl0000755000175000017500000004125211545034324023727 0ustar georgeskgeorgesk# LaTeX2HTML 2K.1beta (1.48) # Associate images original text with physical files. $key = q/(y_{ij});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( y_{ij} \)|; $key = q/{displaymath}a_{l}=frac{1}{2}sum_{u}left(tilde{p}_{1lu}-tilde{p}_{2lu}right)^{2}alpha}_{2l}right)}{4n_{1}n_{2}left(n_{1}+n_{2}-1right)}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} a_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tilde{p}_{... ...\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}|; $key = q/{displaymath}Ds=-lnleft[frac{J_{XY}}{sqrt{J_{X}J_{Y}}}right]{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} Ds=-\ln \left[ \frac{J_{XY}}{\sqrt{J_{X}J_{Y}}}\right] \end{displaymath}|; $key = q/(n_{c}=frac{left(rbar{n}-sum^{r}_{i=1}frac{n^{2}_{i}}{rbar{n}}right)}{left(r-1right)});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( n_{c}=\frac{\left( r\bar{n}-\sum ^{r}_{i=1}\frac{n^{2}_{i}}{r\bar{n}}\right) }{\left( r-1\right) } \)|; $key = q/{displaymath}R=frac{left(2x+y+zright)tilde{theta}_{L}^{2}-2left(x+zright)tilde{theta}_{L}+z}{1-2tilde{theta}_{L}+2tilde{theta}_{L}^{2}}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} R=\frac{\left( 2x+y+z\right) \tilde{\theta }_{L}^{2}-2\left(... ...theta }_{L}+z}{1-2\tilde{\theta }_{L}+2\tilde{\theta }_{L}^{2}}\end{displaymath}|; $key = q/(X^{2});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( X^{2}\protect \)|; $key = q/{displaymath}X^{2}=frac{sum^{r}_{j}sum^{m_{j}}_{i}2frac{left(x_{ij}-y_{ij}right)^{2}}{left(x_{ij}+y_{ij}right)}}{r}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} X^{2}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}2\frac{\left( x_{ij}-y_{ij}\right) ^{2}}{\left( x_{ij}+y_{ij}\right) }}{r}\end{displaymath}|; $key = q/(tilde{theta}_{l}=frac{a_{l}}{a_{l}+b_{l}});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \tilde{\theta }_{l}=\frac{a_{l}}{a_{l}+b_{l}} \)|; $key = q/{displaymath}DReynold=-ln(1-theta){displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} DReynold=-\ln (1-\theta )\end{displaymath}|; $key = q/{displaymath}Dc=frac{2}{Pir}sum^{r}_{j}sqrt{2left((1-sum_{i}^{m_{j}}sqrt{x_{ij}y_{ij}}right)}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} Dc=\frac{2}{\Pi r}\sum ^{r}_{j}\sqrt{2\left( (1-\sum _{i}^{m_{j}}\sqrt{x_{ij}y_{ij}}\right) }\end{displaymath}|; $key = q/(tilde{p}_{lu}=sum^{r}_{i=1}frac{n_{i}tilde{p}_{ilu}}{rbar{n}});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \tilde{p}_{lu}=\sum ^{r}_{i=1}\frac{n_{i}\tilde{p}_{ilu}}{r\bar{n}} \)|; $key = q/(x_{ij});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( x_{ij} \)|; $key = q/{displaymath}Dr=frac{1}{r}sum^{r}_{j}sqrt{frac{sum^{m}_{i}left(x_{ij}-y_{ij}right)^{2}}{2}}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} Dr=\frac{1}{r}\sum ^{r}_{j}\sqrt{\frac{\sum ^{m}_{i}\left( x_{ij}-y_{ij}\right) ^{2}}{2}}\end{displaymath}|; $key = q/{displaymath}a_{l}=frac{left[2sum^{r}_{i=1}n_{i}sum^{v_{l}}_{u=1}left(tilde{p}_{t)^{2}-left(r-1right)b_{l}right]}{2left(r-1right)n_{c}}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} a_{l}=\frac{\left[ 2\sum ^{r}_{i=1}n_{i}\sum ^{v_{l}}_{u=1}\... ...^{2}-\left( r-1\right) b_{l}\right] }{2\left( r-1\right) n_{c}}\end{displaymath}|; $key = q/(z=sum^{m}_{l=1}a_{l}^{2});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( z=\sum ^{m}_{l=1}a_{l}^{2} \)|; $key = q/(tilde{theta}_{L});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \tilde{\theta }_{L} \)|; $key = q/(C_{XY});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( C_{XY} \)|; $key = q/{displaymath}Dm=frac{left(J_{X}+J_{Y}right)}{2}-J_{XY}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} Dm=\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}\end{displaymath}|; $key = q/{displaymath}D_{R}=-logleft(frac{C_{XY}}{V_{XY}}right){displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} D_{R}=-\log \left( \frac{C_{XY}}{V_{XY}}\right) \end{displaymath}|; $key = q/{displaymath}tilde{theta}_{L}=frac{2x+y-zpmsqrt{left(z-yright)^{2}+4x^{2}}}{2left(y-zright)}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} \tilde{\theta }_{L}=\frac{2x+y-z\pm \sqrt{\left( z-y\right) ^{2}+4x^{2}}}{2\left( y-z\right) }\end{displaymath}|; $key = q/(W_{Y}=frac{sum^{r}_{k}sum_{ineqj}left(left|i-jright|y_{ik}y_{jk}right)}{r});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( W_{Y}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert y_{ik}y_{jk}\right) }{r} \)|; $key = q/(J_{Y}=frac{sum^{r}_{j}sum^{m_{j}}_{i}y^{2}_{ij}}{r});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( J_{Y}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}y^{2}_{ij}}{r} \)|; $key = q/{displaymath}D_{A}=1-frac{1}{r}sum^{r}_{j}sum^{m_{j}}_{i}sqrt{x_{ij}y_{ij}}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} D_{A}=1-\frac{1}{r}\sum ^{r}_{j}\sum ^{m_{j}}_{i}\sqrt{x_{ij}y_{ij}}\end{displaymath}|; $key = q/(overline{P}_{SA_{X}});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \overline{P}_{SA_{X}} \)|; $key = q/(mu_{Y_{j}}=sum_{i}iy_{ij});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \mu _{Y_{j}}=\sum _{i}iy_{ij} \)|; $key = q/{displaymath}b_{l}=2sum^{r}_{i=1}frac{n_{i}tilde{alpha}_{il}}{r(2bar{n}-1)}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} b_{l}=2\sum ^{r}_{i=1}\frac{n_{i}\tilde{\alpha }_{il}}{r(2\bar{n}-1)}\end{displaymath}|; $key = q/(overline{mu_{X}});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \overline{\mu _{X}} \)|; $key = q/(J_{X}=frac{sum^{r}_{j}sum^{m_{j}}_{i}x^{2}_{ij}}{r});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( J_{X}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x^{2}_{ij}}{r} \)|; $key = q/(W_{X}=frac{sum^{r}_{k}sum_{ineqj}left(left|i-jright|x_{ik}x_{jk}right)}{r});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( W_{X}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert x_{ik}x_{jk}\right) }{r} \)|; $key = q/(mu_{Y_{j}});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \mu _{Y_{j}} \)|; $key = q/{displaymath}ASD=frac{sum^{r}_{k}sum_{i,j}left(left(i-jright)^{2}x_{ik}y_{jk}right)}{r}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} ASD=\frac{\sum ^{r}_{k}\sum _{i,j}\left( \left( i-j\right) ^{2}x_{ik}y_{jk}\right) }{r}\end{displaymath}|; $key = q/{displaymath}Fst=frac{frac{left(J_{X}+J_{Y}right)}{2}-J_{XY}}{1-J_{XY}}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} Fst=\frac{\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}}{1-J_{XY}}\end{displaymath}|; $key = q/(theta);MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \theta \)|; $key = q/(y=sum^{m}_{l=1}b_{l}^{2});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( y=\sum ^{m}_{l=1}b_{l}^{2} \)|; $key = q/{displaymath}Cp=frac{sum^{r}_{j}sum^{m_{j}}_{i}left|x_{ij}-y_{ij}right|}{2r}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} Cp=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}\left\vert x_{ij}-y_{ij}\right\vert }{2r}\end{displaymath}|; $key = q/(W_{XY}=frac{sum^{r}_{k}sum_{ineqj}left(left|i-jright|x_{ik}y_{jk}right)}{r});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( W_{XY}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert x_{ik}y_{jk}\right) }{r} \)|; $key = q/(mu_{X_{j}}=sum_{i}ix_{ij});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \mu _{X_{j}}=\sum _{i}ix_{ij} \)|; $key = q/(phi);MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \phi \protect \)|; $key = q/{displaymath}D_{SW}=W_{XY}-frac{left(W_{X}+W_{Y}right)}{2}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} D_{SW}=W_{XY}-\frac{\left( W_{X}+W_{Y}\right) }{2}\end{displaymath}|; $key = q/(C_{XY}=frac{1}{r-1}left(sum^{r}_{j}mu_{X_{j}}mu_{Y_{j}}-roverline{mu_{X}}overline{mu_{Y}}right));MSF=1.6;AAT/; $cached_env_img{$key} = q|\( C_{XY}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}\mu _{Y_{j}}-r\overline{\mu _{X}}\overline{\mu _{Y}}\right) \)|; $key = q/(overline{P}_{SA_{Y}});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \overline{P}_{SA_{Y}} \)|; $key = q/(mu_{X_{j}});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \mu _{X_{j}} \)|; $key = q/(C_{XY}<1);MSF=1.6;AAT/; $cached_env_img{$key} = q|\( C_{XY}<1 \)|; $key = q/(overline{mu_{Y}});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \overline{\mu _{Y}} \)|; $key = q/(P_{SA_{I}}=frac{sum^{r}_{j}S}{2r});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( P_{SA_{I}}=\frac{\sum ^{r}_{j}S}{2r} \)|; $key = q/{displaymath}left(deltamuright)^{2}=frac{sum^{r}_{j}left(mu_{X_{j}}-mu_{Y_{j}}right)^{2}}{r}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} \left( \delta \mu \right) ^{2}=\frac{\sum ^{r}_{j}\left( \mu _{X_{j}}-\mu _{Y_{j}}\right) ^{2}}{r}\end{displaymath}|; $key = q/(D_{SA_{I}}=1-P_{SA_{I}});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( D_{SA_{I}}=1-P_{SA_{I}} \)|; $key = q/{displaymath}tilde{theta}_{U}=frac{1}{m}sum^{m}_{l=1}tilde{theta}_{l}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} \tilde{\theta }_{U}=\frac{1}{m}\sum ^{m}_{l=1}\tilde{\theta }_{l}\end{displaymath}|; $key = q/(tilde{alpha}_{il}=1-sum^{v_{l}}_{u=1}tilde{p}_{ilu}^{2});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \tilde{\alpha }_{il}=1-\sum ^{v_{l}}_{u=1}\tilde{p}_{ilu}^{2} \)|; $key = q/(x=sum^{m}_{l=1}a_{l}b_{l});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( x=\sum ^{m}_{l=1}a_{l}b_{l} \)|; $key = q/(D_{A});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( D_{A}\protect \)|; $key = q/(V_{X}=frac{1}{r-1}left(sum^{r}_{j}mu_{X_{j}}^{2}-roverline{mu_{X}}^{2}right));MSF=1.6;AAT/; $cached_env_img{$key} = q|\( V_{X}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}^{2}-r\overline{\mu _{X}}^{2}\right) \)|; $key = q/(V_{Y}=frac{1}{r-1}left(sum^{r}_{j}mu_{Y_{j}}^{2}-roverline{mu_{Y}}^{2}right));MSF=1.6;AAT/; $cached_env_img{$key} = q|\( V_{Y}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{Y_{j}}^{2}-r\overline{\mu _{Y}}^{2}\right) \)|; $key = q/(i);MSF=1.6;AAT/; $cached_env_img{$key} = q|\( i \)|; $key = q/(V_{XY}=frac{1}{2}left(V_{X}+V_{Y}right));MSF=1.6;AAT/; $cached_env_img{$key} = q|\( V_{XY}=\frac{1}{2}\left( V_{X}+V_{Y}\right) \)|; $key = q/(tilde{theta}_{U});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \tilde{\theta }_{U}\protect \)|; $key = q/(J_{XY}=frac{sum^{r}_{j}sum^{m_{j}}_{i}x_{ij}y_{ij}}{r});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( J_{XY}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x_{ij}y_{ij}}{r} \)|; $key = q/(overline{P}_{SA_{B}});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \overline{P}_{SA_{B}} \)|; $key = q/{displaymath}D_{SA_{B}}=1-frac{2overline{P}_{SA_{B}}}{overline{P}_{SA_{X}}+overline{P}_{SA_{Y}}}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} D_{SA_{B}}=1-\frac{2\overline{P}_{SA_{B}}}{\overline{P}_{SA_{X}}+\overline{P}_{SA_{Y}}}\end{displaymath}|; $key = q/(m_{j});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( m_{j} \)|; $key = q/{displaymath}a_{l}+b_{l}=frac{1}{2}sum_{u}left(tilde{p}_{1lu}-tilde{p}_{2lu}righalpha}_{2l}right)}{4n_{1}n_{2}left(n_{1}+n_{2}-1right)}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} a_{l}+b_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tild... ...\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}|; $key = q/(bar{n}=sum^{r}_{i=1}frac{n_{i}}{r});MSF=1.6;AAT/; $cached_env_img{$key} = q|\( \bar{n}=\sum ^{r}_{i=1}\frac{n_{i}}{r} \)|; $key = q/{displaymath}tilde{theta}_{W}=frac{left(sum^{m}_{l=1}a_{l}right)}{sum^{m}_{l=1}left(a_{l}+b_{l}right)}{displaymath};MSF=1.6;AAT/; $cached_env_img{$key} = q|\begin{displaymath} \tilde{\theta }_{W}=\frac{\left( \sum ^{m}_{l=1}a_{l}\right) }{\sum ^{m}_{l=1}\left( a_{l}+b_{l}\right) }\end{displaymath}|; 1; populations-1.2.33+svn0120106.orig/html/old_formula/img37.gif0000755000175000017500000000142011545034324023533 0ustar georgeskgeorgeskGIF89a,xxxlll```TTTHHH<<<000$$$ !,,@I8ͻ`(d0RlL @!bH,H7 Aa(4H>E;kn?B P`'(rW,SCn [   {)J0 f.w /5w?˦ ^MoPɻiYmڧ!=]J`b;e."'0‘U! 0ʀcۄqJ'9ADG(@s(!O +@4A 7YRP8iDvP8 phA G9"_9p4YC:FڷpʝKݻx-uDdJ, p/ a"4IX hHq i<L ? jl]=%\Z0OCkz_ް ,H@v /~d)  66qm7=& bfYEdh^$S,pP I8 n# Sanghvi's (1953) distance[Takezaki, N. 96] next up previous
Next: Reynold's genetic distance for Up: IAM distances Previous: Nei et al's (1983)

Sanghvi's (1953) \( X^{2}\protect \) distance[Takezaki, N. 96]


\begin{displaymath} X^{2}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}2\frac{\left( x_{ij}-y_{ij}\right) ^{2}}{\left( x_{ij}+y_{ij}\right) }}{r}\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/node17.html0000755000175000017500000000464011545034324024110 0ustar georgeskgeorgesk Goldstein et al. (1995a) [Goldstein, D.B. 97] next up previous
Next: average square distance (ASD) Up: SMM distances Previous: SMM distances

Goldstein et al. (1995a) [Goldstein, D.B. 97]


\begin{displaymath} \left( \delta \mu \right) ^{2}=\frac{\sum ^{r}_{j}\left( \mu _{X_{j}}-\mu _{Y_{j}}\right) ^{2}}{r}\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/img30.png0000755000175000017500000000045011545034324023545 0ustar georgeskgeorgeskPNG  IHDR%s40PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxc```8h@08p@i{ $:pf0uduvYϠ[ P1 `12A]@-(U} m4 `=< /X`0XetB{}qZIENDB`populations-1.2.33+svn0120106.orig/html/old_formula/img27.gif0000755000175000017500000000151011545034324023532 0ustar georgeskgeorgeskGIF89a8xxxlll```TTTHHH<<<000$$$ !,8@I8ͻ`($(8HP)E)2Ͳ0A#Y%0d|a"$ C `+!f#!DŽ1 IwJ$5 }WU mz-?f b,.WNU\t g!w)TF 0.5"v`Aw[4$Ö6| eB mhH/84d} P\AJP@S,q&͸U7O$,v A6&QK@4ş 4 =˷w 3$0J!yqxq#KL˘3k̹hl Y JdN59TXOLWdM] bwMX35=a;ND>BwӒ D*QӲT8 ;׎ڡ0VI\4TKm (`W<!,qS^v,$DM0Lf`;%%`J Tt88 !8DG@Gȁ! @H7ԁF N_aajZ%gDw8`D<Ȥ 0ix|'DCS1if K{,c4uhh% %@0r998si&38 x7X58/>y @~d0՝0_&.a}IENDB`populations-1.2.33+svn0120106.orig/html/old_formula/img20.gif0000755000175000017500000000032011545034324023521 0ustar georgeskgeorgeskGIF89axxx```TTTHHH<<<000$$$ !,@}IՀQ`"8l$ ( pTt,=adh! a8-Cqr-,1Ѡ$`EʼP 4E W*x' eqmj;populations-1.2.33+svn0120106.orig/html/old_formula/img36.png0000755000175000017500000000453611545034324023564 0ustar georgeskgeorgeskPNG  IHDR1b*0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxZo$Wy;=IY6=x ATY"r NP!GBﲛ~36/(_Hom.Ѷ{{{vs-]^WޫW{ TP H:U/0E4 3iP12̈́Q},.V}PH}>udh<2['!c[T 9ӻ+CQq`ɼuÉ +X:h6 l.Ig na DaLHP]8 &%Q)@1MӿKJ ;5_M| KuW|KU%l0/\YTo|nB#{(v4ԻEMњß [H`^wBZj7aoi>N d/7-Ť9e6N@N\RSji!.M ߣI2wlXum!cZQTѻnoNZP: D-ŵؓTȐZ|GGriFMcZYҎj-֗>~yeQ7U6rzWGntZ X tn dO9_]$J - _Y^'/% \ǛbPQ S#1-k ˤ ) u{ k'WS1T$u5{D N9ZK.B~Do)A+;p+&=B)/14Vu"8375Y{fCC{.>|J7Y=H3 7π8(_,^U[*[8[݄Fi>}ˡ750'1p3VtfX`MmN*ܒ5Abx.'u/NI>v(Yea2mC|GզGg85{;NϢ25n,R7Y0UJe I+v6!Bt's//⟅_>pROgSy}I)(qKQE)\o7~':RAAoe;b{I`[iNbGQ#=AZm-bW74BV Ln5X_^ű"%T8كîaB12a}p(F9?h1&m>iql*m7ҘYpWikn&nGwQqpnKtgtX9=uE 闳>l} /?˪dVͽq,ϓ8ѕ^T֞['5>xJN JG {3kXpkpZd<>ρ[I0rZq)I(pIIO꺻wKXD`,{ ҿ' y \O~WOs ~dZB YRb ɓ(Oc~"E 8yJs;wC|kω;9WH?,TjIQ]qzlcdˬ.>Wu4۰~!iTlo\đdIi$-FI"@5REhc(xQ삕"dGN5OT8Z9Fr#s B=Eܲ>}z$E)ߴ umgLoI+R7(:{a\fUu]wT$wa.KtBHv7/]D*RAƛطC}G+xG>z2ZmmhOĄ}:{;If9GoEK ڋTlȳM?G} KHHMo{L!W|[lxCnH[ғ Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83] next up previous
Next: unweighted average of single-locus Up: IAM distances Previous: Sanghvi's (1953) distance[Takezaki, N. 96]

Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83]


\begin{displaymath} DReynold=-\ln (1-\theta )\end{displaymath}

the following notation is used, for all \( \theta \) estimators:

\( \bar{n}=\sum ^{r}_{i=1}\frac{n_{i}}{r} \), \( n_{c}=\frac{\left( r\bar{n}-\sum ^{r}_{i=1}\frac{n^{2}_{i}}{r\bar{n}}\right) }{\left( r-1\right) } \), \( \tilde{p}_{lu}=\sum ^{r}_{i=1}\frac{n_{i}\tilde{p}_{ilu}}{r\bar{n}} \), \( \tilde{\alpha }_{il}=1-\sum ^{v_{l}}_{u=1}\tilde{p}_{ilu}^{2} \)


Subsections
Olivier Langella 2002-03-20
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Next: Cavali-Sforza and Edwards' (1967) Up: IAM distances Previous: Rogers' (1972) distance [Takezaki,

Prevosti et al's (1975) distance [Takezaki, N. 96] has a statistical property similar to that of Dr and is defined as


\begin{displaymath} Cp=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}\left\vert x_{ij}-y_{ij}\right\vert }{2r}\end{displaymath}


Olivier Langella 2002-03-20
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LN  sv{ u<2 3hM;populations-1.2.33+svn0120106.orig/html/old_formula/images.tex0000755000175000017500000004253311545034324024117 0ustar georgeskgeorgesk\batchmode \documentclass[english]{report} \RequirePackage{ifthen} \usepackage[T1]{fontenc} \usepackage[latin1]{inputenc} \usepackage{babel} \setlength\parskip{\medskipamount} \setlength\parindent{0pt} \makeatletter % \providecommand{\LyX}{L\kern-.1667em\lower.25em\hbox{Y}\kern-.125emX\@} \makeatother \usepackage[dvips]{color} \pagecolor[gray]{.7} \usepackage[]{inputenc} \makeatletter \makeatletter \count@=\the\catcode`\_ \catcode`\_=8 \newenvironment{tex2html_wrap}{}{}% \catcode`\<=12\catcode`\_=\count@ \newcommand{\providedcommand}[1]{\expandafter\providecommand\csname #1\endcsname}% \newcommand{\renewedcommand}[1]{\expandafter\providecommand\csname #1\endcsname{}% \expandafter\renewcommand\csname #1\endcsname}% \newcommand{\newedenvironment}[1]{\newenvironment{#1}{}{}\renewenvironment{#1}}% \let\newedcommand\renewedcommand \let\renewedenvironment\newedenvironment \makeatother \let\mathon=$ \let\mathoff=$ \ifx\AtBeginDocument\undefined \newcommand{\AtBeginDocument}[1]{}\fi \newbox\sizebox \setlength{\hoffset}{0pt}\setlength{\voffset}{0pt} \addtolength{\textheight}{\footskip}\setlength{\footskip}{0pt} \addtolength{\textheight}{\topmargin}\setlength{\topmargin}{0pt} \addtolength{\textheight}{\headheight}\setlength{\headheight}{0pt} \addtolength{\textheight}{\headsep}\setlength{\headsep}{0pt} \setlength{\textwidth}{349pt} \newwrite\lthtmlwrite \makeatletter \let\realnormalsize=\normalsize \global\topskip=2sp \def\preveqno{}\let\real@float=\@float \let\realend@float=\end@float \def\@float{\let\@savefreelist\@freelist\real@float} \def\liih@math{\ifmmode$\else\bad@math\fi} \def\end@float{\realend@float\global\let\@freelist\@savefreelist} \let\real@dbflt=\@dbflt \let\end@dblfloat=\end@float \let\@largefloatcheck=\relax \let\if@boxedmulticols=\iftrue \def\@dbflt{\let\@savefreelist\@freelist\real@dbflt} 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evensidemargin=\the\evensidemargin}% \else\lthtmltypeout{latex2htmlLength evensidemargin=\the\oddsidemargin}\fi% \lthtmltypeout{}% \makeatother \setcounter{page}{1} \onecolumn % !!! IMAGES START HERE !!! {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline797}% \( \theta \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline481}% \( J_{X}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x^{2}_{ij}}{r} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline482}% \( J_{Y}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}y^{2}_{ij}}{r} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline483}% \( J_{XY}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x_{ij}y_{ij}}{r} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline484}% \( x_{ij} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline485}% \( y_{ij} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline486}% \( m_{j} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline487}% \( D_{SA_{I}}=1-P_{SA_{I}} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline488}% \( P_{SA_{I}}=\frac{\sum ^{r}_{j}S}{2r} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath569}% \begin{displaymath} D_{SA_{B}}=1-\frac{2\overline{P}_{SA_{B}}}{\overline{P}_{SA_{X}}+\overline{P}_{SA_{Y}}}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline489}% \( \overline{P}_{SA_{B}} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline490}% \( \overline{P}_{SA_{X}} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline491}% \( \overline{P}_{SA_{Y}} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath570}% \begin{displaymath} Ds=-\ln \left[ \frac{J_{XY}}{\sqrt{J_{X}J_{Y}}}\right] \end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath571}% \begin{displaymath} Dm=\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline492}% \( \phi \protect \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath572}% \begin{displaymath} Fst=\frac{\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}}{1-J_{XY}}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath573}% \begin{displaymath} Dr=\frac{1}{r}\sum ^{r}_{j}\sqrt{\frac{\sum ^{m}_{i}\left( x_{ij}-y_{ij}\right) ^{2}}{2}}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath574}% \begin{displaymath} Cp=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}\left| x_{ij}-y_{ij}\right| }{2r}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath575}% \begin{displaymath} Dc=\frac{2}{\Pi r}\sum ^{r}_{j}\sqrt{2\left( (1-\sum _{i}^{m_{j}}\sqrt{x_{ij}y_{ij}}\right) }\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline493}% \( D_{A}\protect \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath576}% \begin{displaymath} D_{A}=1-\frac{1}{r}\sum ^{r}_{j}\sum ^{m_{j}}_{i}\sqrt{x_{ij}y_{ij}}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline494}% \( X^{2}\protect \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath577}% \begin{displaymath} X^{2}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}2\frac{\left( x_{ij}-y_{ij}\right) ^{2}}{\left( x_{ij}+y_{ij}\right) }}{r}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath578}% \begin{displaymath} DReynold=-\ln (1-\theta )\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline496}% \( \bar{n}=\sum ^{r}_{i=1}\frac{n_{i}}{r} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline497}% \( n_{c}=\frac{\left( r\bar{n}-\sum ^{r}_{i=1}\frac{n^{2}_{i}}{r\bar{n}}\right) }{\left( r-1\right) } \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline498}% \( \tilde{p}_{lu}=\sum ^{r}_{i=1}\frac{n_{i}\tilde{p}_{ilu}}{r\bar{n}} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline499}% \( \tilde{\alpha }_{il}=1-\sum ^{v_{l}}_{u=1}\tilde{p}_{ilu}^{2} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline500}% \( \tilde{\theta }_{U}\protect \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath579}% \begin{displaymath} \tilde{\theta }_{U}=\frac{1}{m}\sum ^{m}_{l=1}\tilde{\theta }_{l}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline501}% \( \tilde{\theta }_{l}=\frac{a_{l}}{a_{l}+b_{l}} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath580}% \begin{displaymath} b_{l}=2\sum ^{r}_{i=1}\frac{n_{i}\tilde{\alpha }_{il}}{r(2\bar{n}-1)}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath581}% \begin{displaymath} a_{l}=\frac{\left[ 2\sum ^{r}_{i=1}n_{i}\sum ^{v_{l}}_{u=1}\left( \tilde{p}_{ilu}-\tilde{p}_{lu}\right) ^{2}-\left( r-1\right) b_{l}\right] }{2\left( r-1\right) n_{c}}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath582}% \begin{displaymath} a_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tilde{p}_{2lu}\right) ^{2}-\frac{\left( n_{1}+n_{2}\right) \left( n_{1}\tilde{\alpha }_{1l}+n_{2}\tilde{\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath583}% \begin{displaymath} a_{l}+b_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tilde{p}_{2lu}\right) ^{2}+\frac{\left( 4n_{1}n_{2}-n_{1}-n_{2}\right) \left( n_{1}\tilde{\alpha }_{1l}+n_{2}\tilde{\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath584}% \begin{displaymath} \tilde{\theta }_{W}=\frac{\left( \sum ^{m}_{l=1}a_{l}\right) }{\sum ^{m}_{l=1}\left( a_{l}+b_{l}\right) }\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} \stepcounter{subsubsection} {\newpage\clearpage \lthtmldisplayA{displaymath585}% \begin{displaymath} \tilde{\theta }_{L}=\frac{2x+y-z\pm \sqrt{\left( z-y\right) ^{2}+4x^{2}}}{2\left( y-z\right) }\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline503}% \( z=\sum ^{m}_{l=1}a_{l}^{2} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline504}% \( x=\sum ^{m}_{l=1}a_{l}b_{l} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline505}% \( y=\sum ^{m}_{l=1}b_{l}^{2} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline506}% \( \tilde{\theta }_{L} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath586}% \begin{displaymath} R=\frac{\left( 2x+y+z\right) \tilde{\theta }_{L}^{2}-2\left( x+z\right) \tilde{\theta }_{L}+z}{1-2\tilde{\theta }_{L}+2\tilde{\theta }_{L}^{2}}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline507}% \( \mu _{X_{j}}=\sum _{i}ix_{ij} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline508}% \( \mu _{Y_{j}}=\sum _{i}iy_{ij} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline511}% \( i \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath587}% \begin{displaymath} \left( \delta \mu \right) ^{2}=\frac{\sum ^{r}_{j}\left( \mu _{X_{j}}-\mu _{Y_{j}}\right) ^{2}}{r}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath588}% \begin{displaymath} ASD=\frac{\sum ^{r}_{k}\sum _{i,j}\left( \left( i-j\right) ^{2}x_{ik}y_{jk}\right) }{r}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath589}% \begin{displaymath} D_{SW}=W_{XY}-\frac{\left( W_{X}+W_{Y}\right) }{2}\end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline512}% \( W_{X}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left| i-j\right| x_{ik}x_{jk}\right) }{r} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline513}% \( W_{Y}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left| i-j\right| y_{ik}y_{jk}\right) }{r} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline514}% \( W_{XY}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left| i-j\right| x_{ik}y_{jk}\right) }{r} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline515}% \( \overline{\mu _{X}} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline516}% \( \overline{\mu _{Y}} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline517}% \( \mu _{X_{j}} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline518}% \( \mu _{Y_{j}} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmldisplayA{displaymath590}% \begin{displaymath} D_{R}=-\log \left( \frac{C_{XY}}{V_{XY}}\right) \end{displaymath}% \lthtmldisplayZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline519}% \( C_{XY}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}\mu _{Y_{j}}-r\overline{\mu _{X}}\overline{\mu _{Y}}\right) \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline520}% \( V_{XY}=\frac{1}{2}\left( V_{X}+V_{Y}\right) \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline521}% \( V_{X}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}^{2}-r\overline{\mu _{X}}^{2}\right) \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline522}% \( V_{Y}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{Y_{j}}^{2}-r\overline{\mu _{Y}}^{2}\right) \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline523}% \( C_{XY}<1 \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} {\newpage\clearpage \lthtmlinlinemathA{tex2html_wrap_inline524}% \( C_{XY} \)% \lthtmlinlinemathZ \lthtmlcheckvsize\clearpage} \end{document} populations-1.2.33+svn0120106.orig/html/old_formula/img23.png0000755000175000017500000000040211545034324023544 0ustar georgeskgeorgeskPNG  IHDRB 0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxc```g30410So2DЀCn86ۀaf f`WB XUčr-`8?c}р7,hw@w7 3}s21po#%A!IENDB`populations-1.2.33+svn0120106.orig/html/old_formula/img31.png0000755000175000017500000000152111545034324023546 0ustar georgeskgeorgeskPNG  IHDRa6RI0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxTkaYZR\Nq)V?CA}uIjd`@!C".[W%C!˽]|yC3SFK2t@R(WC#t\+ mvICq>:r2|?&(Es B}f{ &hsB`v:<fVQ,G3-jhyaݝYV ,VK%[ׅBiopjEftNG<[ڴx$MvM R)o4-ԴiIm#K搎jݚ2dT5!<ɰgխ q`Lh1١Tp0H-Rwl(@ V&{}= ),V㪁EB<;g[_ۈ&YJcR$w#eÒ:XgWH I4p56i5cI4<}J1k/ڦr}1ʢM>AQ}!*7Uf[?|fT >r="&yڞ`̎xiEu*9"PC_Ow.nZ n)onGm|P+~ URc?vyѕMV?oYoԡQ\q*‚s&lk>+PYWcsק;* c0kc{/6d:IENDB`populations-1.2.33+svn0120106.orig/html/old_formula/next_motif_gr.gif0000755000175000017500000000025411545034324025455 0ustar georgeskgeorgeskGIF89a%ooo!,%}ڋ2bUbK +7nj:f#a)gy5Nq+d]͈^fbjۜXL$XBXr8c)9IYi`Y;populations-1.2.33+svn0120106.orig/html/old_formula/img31.gif0000755000175000017500000000172311545034324023533 0ustar georgeskgeorgeskGIF89a6OOOGGGxxxllljjj```TTTHHHDDD>>><<<000,,,$$$""" !,6@%dihlp,t֤2be8]7+@Fh!IpZYI(:TO0Z d" ;D b"" W5l5$pv ˘oJ e]_]k&D'U D썋#~ 2UN_%HHA1Hŋ3jȱǏͩ"A A PRB$(m@;`PVfl >AYBm! -:F/< -13j CL(|#6Aمg<֭Ԫ&΍P([BL𹶭 )@JHY012"TKY5PjB240e3}b@r>Nȓ+_μУKj}Y׳Kb5IpmPɩ) lj*FC~bQ6 MWExgB' a!4Ypa8AD$PZ#(Qk'@L}]܉`kH#7 1H G% PbvB% F:]Vfy]Ś[qdHOk%Uc@v㈐]D؊8$>oHĥ+1/f+刧vH4ЀnY9f(Cqr]@lS) c.itXigГ\aϴSVkfn{eH%uZ^ElI#$ 8 NL_fl' 7G,+;populations-1.2.33+svn0120106.orig/html/old_formula/img42.png0000755000175000017500000000043511545034324023553 0ustar georgeskgeorgeskPNG  IHDR%(D0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxc```g@ H" f@Q큸Ę0C^"9Yh pku`3X 6A @8X <`E$7`lc2fc7xXf5 Ay  `ԙb8IENDB`populations-1.2.33+svn0120106.orig/html/old_formula/node9.html0000755000175000017500000000471611545034324024035 0ustar georgeskgeorgesk Cavali-Sforza and Edwards' (1967) chord distance [Takezaki, N. 96] next up previous
Next: Nei et al's (1983) Up: IAM distances Previous: Prevosti et al's (1975)

Cavali-Sforza and Edwards' (1967) chord distance [Takezaki, N. 96]


\begin{displaymath} Dc=\frac{2}{\Pi r}\sum ^{r}_{j}\sqrt{2\left( (1-\sum _{i}^{m_{j}}\sqrt{x_{ij}y_{ij}}\right) }\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/img10.gif0000755000175000017500000000044411545034324023527 0ustar georgeskgeorgeskGIF89a-#xxxlll```TTTHHH<<<000$$$ !,-#@I8[hSZ(J ,!< 2c|O0!d%ha0$uL.'E_CƁ{ ?   n  &{\ V ,m{}9 2rPbLVP r < /^kT;populations-1.2.33+svn0120106.orig/html/old_formula/img14.gif0000755000175000017500000000126711545034324023537 0ustar georgeskgeorgeskGIF89a(xxxlll```TTTHHH<<<000$$$ !,(@I8ͻ`(d|KrZaR0&d{@kuTS/V=իXjʵׯ`Ê+@ Jpv cM eʠR!;(TNy% &zK T*X1AABC v<(wM.D"@^ 4" ($!s˹`ݖr0if K 5/KP5 GX v"\{ ~7Pb~=fp ]@:$}Ā# 9dap4@rIk0ˁHNYf),Aĥ],#DiH&L6P;populations-1.2.33+svn0120106.orig/html/old_formula/node19.html0000755000175000017500000000630211545034324024107 0ustar georgeskgeorgesk Shriver et al.'s (1995) [Shriver, M.D. 95] next up previous
Next: Lev A. Zhivotovsky (1999) Up: SMM distances Previous: average square distance (ASD)

Shriver et al.'s (1995) [Shriver, M.D. 95]


\begin{displaymath} D_{SW}=W_{XY}-\frac{\left( W_{X}+W_{Y}\right) }{2}\end{displaymath}

where \( W_{X}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert x_{ik}x_{jk}\right) }{r} \), \( W_{Y}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert y_{ik}y_{jk}\right) }{r} \), \( W_{XY}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert x_{ik}y_{jk}\right) }{r} \)


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/formules.html0000755000175000017500000001045311545034324024646 0ustar georgeskgeorgesk formules next up previous
Next: Distances



Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/img13.gif0000755000175000017500000000124411545034324023531 0ustar georgeskgeorgeskGIF89a,xxxlll```TTTHHH<<<000$$$ !,,@I8ͻ`("xIV!M%OZ-|$bb Cj-.$(KXbpK~w&X} .  i~PMkdfhlnpYc0X-,#FL_:(sOCRTYWϾ Kmv3}״4bD bl)``}DHu$eB":Dx硍wrA= r>qSH>P͛8sɳgN!g}6P rQC IPNiA@<$XǬBH5'8JMI鬄Y`ujZ@POf}0O€@FaEeHE (ô,8 eVh`7`9Ae0/ N ,h07Ab)ޣSW~ 0ppB>}E^US @[pUP`:WUFC_Q gHP_a^a4ZF y jH;<,R2<@iT;populations-1.2.33+svn0120106.orig/html/old_formula/node10.html0000755000175000017500000000475011545034324024103 0ustar georgeskgeorgesk Nei et al's (1983) distance [Takezaki, N. 96] next up previous
Next: Sanghvi's (1953) distance[Takezaki, N. 96] Up: IAM distances Previous: Cavali-Sforza and Edwards' (1967)

Nei et al's (1983) \( D_{A}\protect \) distance [Takezaki, N. 96]


\begin{displaymath} D_{A}=1-\frac{1}{r}\sum ^{r}_{j}\sum ^{m_{j}}_{i}\sqrt{x_{ij}y_{ij}}\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/up_motif_gr.gif0000755000175000017500000000022111545034324025115 0ustar georgeskgeorgeskGIF89aooo!,b˭bZ `؅ҷ!9 zj*Kќ >X6 Lvbmbl2'^}WLv兽 QPY%krM/P;populations-1.2.33+svn0120106.orig/html/old_formula/node3.html0000755000175000017500000000674511545034324024033 0ustar georgeskgeorgesk Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93] next up previous
Next: Nei's (1972) standard genetic Up: IAM distances Previous: IAM distances

Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93]

between individuals:

\( D_{SA_{I}}=1-P_{SA_{I}} \), with \( P_{SA_{I}}=\frac{\sum ^{r}_{j}S}{2r} \)

where the number of shared alleles S is sumed over all loci r.

between populations:


\begin{displaymath} D_{SA_{B}}=1-\frac{2\overline{P}_{SA_{B}}}{\overline{P}_{SA_{X}}+\overline{P}_{SA_{Y}}}\end{displaymath}

where the average proportion of shared alleles between and within populations X and Y ( \( \overline{P}_{SA_{B}} \), \( \overline{P}_{SA_{X}} \), \( \overline{P}_{SA_{Y}} \) respectively) is computed overall possible combinations of individuals sampled.


Olivier Langella 2002-03-20
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Next: IAM distances Up: formules Previous: formules

Distances


Subsections
Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/images.bbl0000755000175000017500000000265211545034324024054 0ustar georgeskgeorgesk\begin{thebibliography}{{Goldstein, D.B.}~97} \bibitem[{Goldstein, D.B.}~97]{GP97} {Goldstein, D.B.} \& {Pollock, D.D.} \newblock {\em Launching Microsatellites: A Review of Mutation Processes and Methods of Phylogenetic Inference}. \newblock Journal of Heredity, vol.~88, no.~335-342, pages 0022--1503, 31 1997. \newblock 1997. \bibitem[{Jin, L.}~93]{JC93} {Jin, L.} \& {Chakraborty, R.} \newblock {\em Estimation of {G}enetic {D}istance and {C}oefficient of {G}ene {D}iversity from {S}ingle-{P}robe {M}ultilocus {DNA} {F}ingerprinting {D}ata}. \newblock Mol. Biol. Evol., vol.~11, no.~1, pages 120--127, 13 1993. \newblock 1994. \bibitem[{Reynolds, J.}~83]{RWC83} {Reynolds, J.}, {Weir, B.S.} \& {Cockerham, C.} \newblock {\em Estimation of the coancestry coefficient: basis for a short-term genetic distance}. \newblock Genetics Society of America, vol.~105, pages 767--779, November 1983. \newblock 1983. \bibitem[{Shriver, M.D.}~95]{SJB95} {Shriver, M.D.}, {Jin, L.} \& {Boerwinkle, E.} \newblock {\em A Novel Measure of Genetic Distance for Highly Polymorphic Tandem Repeat Loci}. \newblock Mol. Bio. Evol., vol.~12, no.~5, pages 914--920, 4 1995. \bibitem[{Takezaki, N.}~96]{TN96} {Takezaki, N.} \& {Nei, M.} \newblock {\em Genetic {D}istances and {R}econstruction of {P}hylogenetic {T}rees {F}rom {M}icrosatellite {DNA}}. \newblock Genetics, no.~144, pages 189--399, 6 1996. \newblock september, 1996. \end{thebibliography} populations-1.2.33+svn0120106.orig/html/old_formula/img41.gif0000755000175000017500000000166511545034324023541 0ustar georgeskgeorgeskGIF89a,xxxlll```TTTHHH<<<000$$$ !,,@I8ͻ`(di>0")tl J el: LOa8Tċ#!AhIݨ&vb(rX sW -65pa m!   u"D > y" tU 18',{  Z4 ⫟pb =<Ç#JH pB0 sdf *& Qÿ lW"@ F7 t  p.Ƈ\4(XC> &ù;vrfh~xB&46gw.(8,!Ra8@Sj&86AtreT0a` xM 񨃲EH Nȓ+_n5h?Ps%"[oܠ.N6bp;D"w!9>A 8(TUjmB4 D JࠀX!@c\]!^aD% Qe)6y=<( :Jp̉&v$vỉHa$X5~̖\Ӥ]@w$f;I|] 8`I$8B ؀A 3`t^yg:0m9)Υgm(U0@_}40|i> BJ* k]p&Oe$8肳G/=$l0_uiPJ:Xv-`C튀<"dQߡZGnqG,WlgqB;populations-1.2.33+svn0120106.orig/html/old_formula/img38.png0000755000175000017500000000273411545034324023564 0ustar georgeskgeorgeskPNG  IHDR9L˿0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fZIDATxXOUOL63=SEًJJes\K//}APuA hb+^RCCfE+͛dftwEGxy}|ߛ=6֨@B8CB&8P &G{L;V1S3;B֬~\`WVA4$5;^:VIy{:btڂȿ3I}0e?* z8=Nn|,z0 772F8A[ere.ُ1Jz'o#RijAx΂ w 4 kB*aC޲ iHYD.4TÎeU`.ͳy/t$= ,CNt\x@:jrkV3& bL5WuGah&ݵE8ȯtF0/z4 ~7fTvމ@ÉQ%H3/FEUl#Q/\vNsBġYS ѝ[,TSΔ,Q݂_)^HZtPQI1Y[\DXՋ s8)%%~pc (n u[AwnŎ1&цw^);((Q%+QFvjѴrFcŷrи%Նcµ^r4(@2S R-`ma-o$2&PgJHw"8.;QͿ4V7kV]! 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Next: SMM distances Up: Reynold's genetic distance for Previous: weighted average of single-locus

least squares \( \theta \) estimator :


\begin{displaymath} \tilde{\theta }_{L}=\frac{2x+y-z\pm \sqrt{\left( z-y\right) ^{2}+4x^{2}}}{2\left( y-z\right) }\end{displaymath}

where: \( z=\sum ^{m}_{l=1}a_{l}^{2} \), \( x=\sum ^{m}_{l=1}a_{l}b_{l} \) and \( y=\sum ^{m}_{l=1}b_{l}^{2} \) .

to check which of the two solutions for \( \tilde{\theta }_{L} \) provides the minimum, the residual sum of squares, R, should be calculated for each where:


\begin{displaymath} R=\frac{\left( 2x+y+z\right) \tilde{\theta }_{L}^{2}-2\left(... ...theta }_{L}+z}{1-2\tilde{\theta }_{L}+2\tilde{\theta }_{L}^{2}}\end{displaymath}


Olivier Langella 2002-03-20
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Up: formules Previous: Bibliography

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The translation was initiated by Olivier Langella on 2002-03-20

Olivier Langella 2002-03-20
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Next: Nei's (1973) minimum genetic Up: IAM distances Previous: Shared allele distance (Chakraborty

Nei's (1972) standard genetic distance (Ds) [Takezaki, N. 96]


\begin{displaymath} Ds=-\ln \left[ \frac{J_{XY}}{\sqrt{J_{X}J_{Y}}}\right] \end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/img46.png0000755000175000017500000000027111545034324023555 0ustar georgeskgeorgeskPNG  IHDR Xs$PLTExxxlll```TTTHHH000 DttRNS@fCIDATxc`&6!"h4 ,```RX;‡ Zt q *%YIENDB`populations-1.2.33+svn0120106.orig/html/old_formula/labels.pl0000755000175000017500000000125511545034324023723 0ustar georgeskgeorgesk# LaTeX2HTML 2K.1beta (1.48) # Associate labels original text with physical files. $key = q/cite_RWC83/; $external_labels{$key} = "$URL/" . q|node21.html|; $noresave{$key} = "$nosave"; $key = q/cite_SJB95/; $external_labels{$key} = "$URL/" . q|node21.html|; $noresave{$key} = "$nosave"; $key = q/cite_TN96/; $external_labels{$key} = "$URL/" . q|node21.html|; $noresave{$key} = "$nosave"; $key = q/cite_GP97/; $external_labels{$key} = "$URL/" . q|node21.html|; $noresave{$key} = "$nosave"; $key = q/cite_JC93/; $external_labels{$key} = "$URL/" . q|node21.html|; $noresave{$key} = "$nosave"; 1; # LaTeX2HTML 2K.1beta (1.48) # labels from external_latex_labels array. 1; populations-1.2.33+svn0120106.orig/html/old_formula/img30.gif0000755000175000017500000000172611545034324023535 0ustar georgeskgeorgeskGIF89a6OOOGGGxxxllljjj```TTTHHHDDD>>><<<000,,,$$$""" !,6@%dihlp,t ֤2be8]7+@Fh!IpZ[I(:TO0Z d|~e;D b$ DWRl6$pH boJ"%l^&%k]_#&U Dآh$y u%wA\ȰÇ#JHŋMdD@h@F0C(v !5oVb؜*AYls\0;y͜!R1p:BK&Pƀ z]+ '"Φ%Ѡ m#m!`&ܔY MSWȼUPP"\YDӨ#gidu8@I7%6RhbXW'tMeBmnb~ECK*Ս0M782\q}Kh27h VUkBV(T1Ք6ϊ~݊iTځK.B]2$Q 5 =ߍz/ }+W ^ծ,Zi[%HTgv?/al7KNKnNc%t4fjĐ rrU\VI_O9jQĶqH [%tgϠY4S:xOw'Gx3cJlMTn=%(VbRQ ԅ`Ǎ;;? IENDB`populations-1.2.33+svn0120106.orig/html/old_formula/img21.gif0000755000175000017500000000163511545034324023534 0ustar georgeskgeorgeskGIF89a"xxxlll```TTTHHH<<<000$$$ !,"@I8ͻ`(,@dhX}g$ DAXF!CP-2Ó`{D0ĢAI BL$tH  pcnw, T *x \% \I.U<, $ɠ b+k<<njk׵:a$ `  *\pȶ4Hg}#d`@XXgG L2#Ea^%ϟ@Ux8)@i ?@,3 AĐ kX86 [ҪmW@B{xwC5H uF,`]!{ H ڣ@T ejr̀8!s*g (Tۼcs3 Nk4Ue;h`nVbuTui7DX yWf xL31Ddς 6 ; D+d]dHB%H $%N֩Pnq~H @]K$BHRt䈇5~3L=|BD9F BMM0KPQ=姙T=!Zf f"n 䒄\,8yDLZDLY2't|_[JP*3tjLSi8*Ŵ(V8D ;D* &0#MRc˪8#JBf䅭 „Bz}"PI*ϵ ,lG;populations-1.2.33+svn0120106.orig/html/old_formula/img11.png0000755000175000017500000000054511545034324023551 0ustar georgeskgeorgeskPNG  IHDR-#9O0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxc` 6 !t#TQp P$ k > 8  J H7*ǰ`gwt0TL`xfu:806py\L  8&8 If`؏E3!,`1Dzx\8 ::$ ә.#ے)2[AG${i3~ˇIENDB`populations-1.2.33+svn0120106.orig/html/old_formula/img2.png0000755000175000017500000000137611545034324023474 0ustar georgeskgeorgeskPNG  IHDR60PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@f|IDATx핽k`WwK )R7[ nFD29깔 `8ch}3^b(V DP`&Uh PiJe6R'*8R4¸C\ "41Vhpmˍ2T߳iÕPPI jpY=0ͷ/!HZ \`3O^qslDŽ!@3_d9"ǧ_CHS',x*і,=K!*Xg%u$FT8M&̚%B :WLSm/O?!Xk.6r,Wwl[TV2 u—]| =nqIgFE&WmޕoiًhD&rDēq}=*/,m. jnz?_'G %CZԠ=_٢$ԝ ' H!"k/V ЮdAu"LﰝsSͱYWPs(L㩸^IENDB`populations-1.2.33+svn0120106.orig/html/old_formula/node18.html0000755000175000017500000000502311545034324024105 0ustar georgeskgeorgesk average square distance (ASD) (Goldstein et al. 1995b; Slatkin 1995) [Goldstein, D.B. 97] next up previous
Next: Shriver et al.'s (1995) Up: SMM distances Previous: Goldstein et al. (1995a)

average square distance (ASD) (Goldstein et al. 1995b; Slatkin 1995) [Goldstein, D.B. 97]


\begin{displaymath} ASD=\frac{\sum ^{r}_{k}\sum _{i,j}\left( \left( i-j\right) ^{2}x_{ik}y_{jk}\right) }{r}\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/img3.gif0000755000175000017500000000134211545034324023447 0ustar georgeskgeorgeskGIF89a6xxxlll```TTTHHH<<<000$$$ !,6@I8ͻ`($8H̀i!!Z&0dB4$˟#$FazL+N oh¸|N}} p#!jfzJn67Ize b^TKkr  # U\  ԃ @$  H\{ǡ@F# "q@C: i 8)`G "3)q./;XC &J^A -0wիX&¦`ÊKٳhӪ]˶e @)ĕ)@ /ow!+&[qp98(-Z#8z~hƄ% rwU@+E.bÄC~F\Pep7 1F 8FU,k˘J/ǐ#=B~@D "IfopB̛"ɳϟ@ JԃE8Cx ;$%-h>` &V[<#g%*%:Rfb΢UW9 0A L*@PŜĬsm.Itp*-@4I/C5Npf 4g@'_ݛ5|4/E,#p8 Z#I"0r}]ۦpYdטXq &L* `@ ti<3hW2M2S#XzcAKxAK0M&J#i\@/?MRTq"#H9(eT^D/NfT(zpi @?5/Xpva 5@9qrj˨aZ$͌=*=k?n<' Ԗs'my*>e—,3sI'"21`m=hz\NFI&9ZyEhG=L@ dވ7ږw"ۄZէl5T@n?9;{D0*{jb=~XpjixTCշawm=r xЏ{?aCf8sħVy1oޚcʲilNՋ_{Cāx˩{o#65x-U/&N O.VEC=4* |`Gy /-ӆHN,zMQM;0锶[$ETTT8|Ι G8ouqesiӠ:GJ`.R0N!:MzP 8)(ێ,-5`ZXpˁl8U0T۪?~0 h펚8q2D7܈uR3Qz]e6ϻm%qW30hߟP5騰Pݩ pto!f"7FyŽy?;wvcw hc֓dW b$5%T]ҍ7!d0itmmW! 9eAID;&Y/B y;6T=Ҭ{-sEGFkjp ;vhWY3%utQ- |8~>qq|=s.2 ?&{9nf4jDhi̭j1cN7V ʡؾUV3}Y}wj`Ҫ< qWj鱗.fGF${PQ+.{ؘjm]|3"MU}QT}=)^-5I+qzZ .VX/F% 2L*%_d^,o% Sha` ?uƱ]C)_"1=@%F^ca3N0UK:AFQz\WJ7o ,=ѪQoګŢl szec㨰 WJr pV;nFI-0$c|Ov!2H';!F]ߎ1SL &-_eC)WSԇfHPnB^0l7ͷW9 BLϙi>IZ=*Quϛb@ @UZ4#jZIǯ S+eB 0M6ZtdffM1?\ꀹ|58fJu]J5d6QRIr঱Ԁ]vwgsQAm1k9lS2$v}0*Gn;E).ypHC"q"p5)/ٖg Fרub$@U#woDg؎pyP262'ˆ7k #s nfӿ IC_Pu';V>S#,[~6 ܤXɨ"謥pΣYfEƾ.Op=Ei% ̍bbx02; o-||UvrJ*W7_]IK< @}bUyS"vR}],@%8i7WFjle~Bt=X2cr(V[p=d$j~Ͳ=L߾7dIENDB`populations-1.2.33+svn0120106.orig/html/old_formula/img35.gif0000755000175000017500000000034211545034324023533 0ustar georgeskgeorgeskGIF89axxxlll```TTTHHH<<<000$$$ !,@I5ID$&%>HtmW ^R%]< Ca(pJ En3ax t>U4gwd3 X c{ga~) V1[H oUr*;populations-1.2.33+svn0120106.orig/html/old_formula/node14.html0000755000175000017500000000466411545034324024113 0ustar georgeskgeorgesk weighted average of single-locus ratio estimators : next up previous
Next: least squares estimator : Up: Reynold's genetic distance for Previous: unweighted average of single-locus

weighted average of single-locus ratio estimators :


\begin{displaymath} \tilde{\theta }_{W}=\frac{\left( \sum ^{m}_{l=1}a_{l}\right) }{\sum ^{m}_{l=1}\left( a_{l}+b_{l}\right) }\end{displaymath}


Olivier Langella 2002-03-20
populations-1.2.33+svn0120106.orig/html/old_formula/img60.png0000755000175000017500000000211711545034324023552 0ustar georgeskgeorgeskPNG  IHDR,Oz0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fIDATxW͋[U%yoR*-}K3 F\`6B D[Dw"tS\A(5~.pЍE~̠Ϲ}޼, H;s~{Ͻ/`G*$vbt%!N&D_Oz$quE5JFs& c4%+5B]@O*OU p*^E}臅8&*tdyyt8t.#E:WFD1( olHv[ͨ #:9Eڹz07C*{X}Zn@Z_UUnAڥZ.EyAu,mtKtf?Xo,Xh.ZfQG:00I𤇓gYQk|ic Ju)ema=FP3(eebhDW)Jla?M0ҘL0n㷀MTTnSaϱ) GIU% *7zaK `|sMgTr(ѾraF~{}C?,*E+7$ACi3d^5K׬}-Nar/#<ӄOGCSۼ:>3Z+WCϠA5g$Ou={Qg.涇=,T.IENDB`populations-1.2.33+svn0120106.orig/html/old_formula/img32.gif0000755000175000017500000000177611545034324023544 0ustar georgeskgeorgeskGIF89a6OOOGGGxxxllljjj```TTTHHHDDD>>><<<000,,,$$$""" !,6@%dihlp,tm5X.՛ #aH= f@N5'-T-Lp5җ1/SX4D}@>@|~f<E c$ E#" XSm,5$q ˒eq%m_% "l^`#&V E#y Cרj $͜ՠ&jȱǏ CIɓ5Υ"A A vAe0m9pOVl@ F=AJr! ,A:=L4DŽ8%H`EpTc B.M`("% tkc`H F5؄EP`28;Zz:#6u<́o <@ ӸsGHJQ88 &TbKسkνËO6= P};Kj0e@^#UCCfo*Wt%$7^a S6@hJM "XIȇ' !EgAB +7EPF' Fz\Mw` L# C*ǀoIp1J ߒ/fE%KE!D% *Ti_IP}9"+^[>yA(\e? t@&t*40@2 ]@9҂ YTkbf PgI0]j.MMG~src ^Q.!4F+ko/Vė'PH4e^nkd( ΈDP+kW%#F ,#l(,0,4lG!;populations-1.2.33+svn0120106.orig/html/old_formula/img17.png0000755000175000017500000000171411545034324023556 0ustar georgeskgeorgeskPNG  IHDR0aO>}0PLTExxxlll```TTTHHH<<<000$$$ Y˞tRNS@fJIDATxVMhA6li""h.`AK/Ye{s/JUЀ^)](֨K#(xQ(QۓQC,9J vzd̛o{of>DtN_1faK;p(`.=Ay/foOvʇ&r]CA@o$Ȟ jektݰ]ӣch"@10̡Yy<0,[E<$e H;\S 6*>&U;* rIuZeoZqlblru͞6\ɳV R;~')Bw' ШLdE b/ׂKtQ0 =RZ' 7]x)7:P~T}v/M A|?8[8 @r{u"j^چu*CѩUPafm-hPaxTe>ϝ=c!0F$n;ףWYъ9hO8IkFO-mN&5H2C( g3=(VòaKYjmmy9)ݓYtk'Ldj3װs˴W@OVxk>P{Bn6 uH @4PIENDB`populations-1.2.33+svn0120106.orig/html/libjs/0000755000175000017500000000000011701602131020705 5ustar georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/html/libjs/entity.js0000644000175000017500000015045110621075553022601 0ustar georgeskgeorgesk/* * The contents of this file are subject to the Mozilla Public * License Version 1.1 (the "License"); you may not use this file * except in compliance with the License. You may obtain a copy of * the License at http://www.mozilla.org/MPL/ * * Software distributed under the License is distributed on an "AS * IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or * implied. See the License for the specific language governing * rights and limitations under the License. * * The Original Code is Mozilla MathML Project. * * The Initial Developer of the Original Code is The University of * Queensland. Portions created by The University of Queensland are * Copyright (C) 2002 The University of Queensland. All * Rights Reserved. * * Contributor(s): * Roger B. Sidje */ var gEntityTable = new Array(1480); gEntityTable["0009"] = "Tab"; gEntityTable["000A"] = "NewLine"; gEntityTable["0021"] = "excl"; gEntityTable["0022"] = "quot"; gEntityTable["0023"] = "num"; gEntityTable["0024"] = "dollar"; gEntityTable["0025"] = "percnt"; gEntityTable["0027"] = "apos"; gEntityTable["0028"] = "lpar"; gEntityTable["0029"] = "rpar"; gEntityTable["002A"] = "midast"; gEntityTable["002B"] = "plus"; gEntityTable["002C"] = "comma"; gEntityTable["002E"] = "period"; gEntityTable["002F"] = "sol"; gEntityTable["003A"] = "colon"; gEntityTable["003B"] = "semi"; gEntityTable["003D"] = "equals"; gEntityTable["003F"] = "quest"; gEntityTable["0040"] = "commat"; gEntityTable["005B"] = "lbrack"; gEntityTable["005C"] = "bsol"; gEntityTable["005D"] = "rbrack"; gEntityTable["005E"] = "circ"; gEntityTable["005F"] = "lowbar"; gEntityTable["0060"] = "DiacriticalGrave"; gEntityTable["007B"] = "lbrace"; gEntityTable["007C"] = "VerticalLine"; gEntityTable["007D"] = "rbrace"; gEntityTable["00A0"] = "NonBreakingSpace"; gEntityTable["00A1"] = "iexcl"; gEntityTable["00A2"] = "cent"; gEntityTable["00A3"] = "pound"; gEntityTable["00A4"] = "curren"; gEntityTable["00A5"] = "yen"; gEntityTable["00A6"] = "brvbar"; gEntityTable["00A7"] = "sect"; gEntityTable["00A8"] = "DoubleDot"; gEntityTable["00A9"] = "copy"; gEntityTable["00AA"] = "ordf"; gEntityTable["00AB"] = "laquo"; gEntityTable["00AC"] = "not"; gEntityTable["00AD"] = "shy"; gEntityTable["00AE"] = "circledR"; gEntityTable["00AF"] = "OverBar"; gEntityTable["00B0"] = "deg"; gEntityTable["00B1"] = "PlusMinus"; gEntityTable["00B2"] = "sup2"; gEntityTable["00B3"] = "sup3"; gEntityTable["00B4"] = "DiacriticalAcute"; gEntityTable["00B5"] = "micro"; gEntityTable["00B6"] = "para"; gEntityTable["00B7"] = "CenterDot"; gEntityTable["00B8"] = "Cedilla"; gEntityTable["00B9"] = "sup1"; gEntityTable["00BA"] = "ordm"; gEntityTable["00BB"] = "raquo"; gEntityTable["00BC"] = "frac14"; gEntityTable["00BD"] = "frac12"; gEntityTable["00BE"] = "frac34"; gEntityTable["00BF"] = "iquest"; gEntityTable["00C0"] = "Agrave"; gEntityTable["00C1"] = "Aacute"; gEntityTable["00C2"] = "Acirc"; gEntityTable["00C3"] = "Atilde"; gEntityTable["00C4"] = "Auml"; gEntityTable["00C5"] = "Aring"; gEntityTable["00C6"] = "AElig"; gEntityTable["00C7"] = "Ccedil"; gEntityTable["00C8"] = "Egrave"; gEntityTable["00C9"] = "Eacute"; gEntityTable["00CA"] = "Ecirc"; gEntityTable["00CB"] = "Euml"; gEntityTable["00CC"] = "Igrave"; gEntityTable["00CD"] = "Iacute"; gEntityTable["00CE"] = "Icirc"; gEntityTable["00CF"] = "Iuml"; gEntityTable["00D0"] = "ETH"; gEntityTable["00D1"] = "Ntilde"; gEntityTable["00D2"] = "Ograve"; gEntityTable["00D3"] = "Oacute"; gEntityTable["00D4"] = "Ocirc"; gEntityTable["00D5"] = "Otilde"; gEntityTable["00D6"] = "Ouml"; gEntityTable["00D7"] = "times"; gEntityTable["00D8"] = "Oslash"; gEntityTable["00D9"] = "Ugrave"; gEntityTable["00DA"] = "Uacute"; gEntityTable["00DB"] = "Ucirc"; gEntityTable["00DC"] = "Uuml"; gEntityTable["00DD"] = "Yacute"; gEntityTable["00DE"] = "THORN"; gEntityTable["00DF"] = "szlig"; gEntityTable["00E0"] = "agrave"; gEntityTable["00E1"] = "aacute"; gEntityTable["00E2"] = "acirc"; gEntityTable["00E3"] = "atilde"; gEntityTable["00E4"] = "auml"; gEntityTable["00E5"] = "aring"; gEntityTable["00E6"] = "aelig"; gEntityTable["00E7"] = "ccedil"; gEntityTable["00E8"] = "egrave"; gEntityTable["00E9"] = "eacute"; gEntityTable["00EA"] = "ecirc"; gEntityTable["00EB"] = "euml"; gEntityTable["00EC"] = "igrave"; gEntityTable["00ED"] = "iacute"; gEntityTable["00EE"] = "icirc"; gEntityTable["00EF"] = "iuml"; gEntityTable["00F0"] = "eth"; gEntityTable["00F1"] = "ntilde"; gEntityTable["00F2"] = "ograve"; gEntityTable["00F3"] = "oacute"; gEntityTable["00F4"] = "ocirc"; gEntityTable["00F5"] = "otilde"; gEntityTable["00F6"] = "ouml"; gEntityTable["00F7"] = "divide"; gEntityTable["00F8"] = "oslash"; gEntityTable["00F9"] = "ugrave"; gEntityTable["00FA"] = "uacute"; gEntityTable["00FB"] = "ucirc"; gEntityTable["00FC"] = "uuml"; gEntityTable["00FD"] = "yacute"; gEntityTable["00FE"] = "thorn"; gEntityTable["00FF"] = "yuml"; gEntityTable["0100"] = "Amacr"; gEntityTable["0101"] = "amacr"; gEntityTable["0102"] = "Abreve"; gEntityTable["0103"] = "abreve"; gEntityTable["0104"] = "Aogon"; gEntityTable["0105"] = "aogon"; gEntityTable["0106"] = "Cacute"; gEntityTable["0107"] = "cacute"; gEntityTable["0108"] = "Ccirc"; gEntityTable["0109"] = "ccirc"; gEntityTable["010A"] = "Cdot"; gEntityTable["010B"] = "cdot"; gEntityTable["010C"] = "Ccaron"; gEntityTable["010D"] = "ccaron"; gEntityTable["010E"] = "Dcaron"; gEntityTable["010F"] = "dcaron"; gEntityTable["0110"] = "Dstrok"; gEntityTable["0111"] = "dstrok"; gEntityTable["0112"] = "Emacr"; gEntityTable["0113"] = "emacr"; gEntityTable["0116"] = "Edot"; gEntityTable["0117"] = "edot"; gEntityTable["0118"] = "Eogon"; gEntityTable["0119"] = "eogon"; gEntityTable["011A"] = "Ecaron"; gEntityTable["011B"] = "ecaron"; gEntityTable["011C"] = "Gcirc"; gEntityTable["011D"] = "gcirc"; gEntityTable["011E"] = "Gbreve"; gEntityTable["011F"] = "gbreve"; gEntityTable["0120"] = "Gdot"; gEntityTable["0121"] = "gdot"; gEntityTable["0122"] = "Gcedil"; gEntityTable["0124"] = "Hcirc"; gEntityTable["0125"] = "hcirc"; gEntityTable["0126"] = "Hstrok"; gEntityTable["0127"] = "hstrok"; gEntityTable["0128"] = "Itilde"; gEntityTable["0129"] = "itilde"; gEntityTable["012A"] = "Imacr"; gEntityTable["012B"] = "imacr"; gEntityTable["012E"] = "Iogon"; gEntityTable["012F"] = "iogon"; gEntityTable["0130"] = "Idot"; gEntityTable["0131"] = "inodot"; gEntityTable["0132"] = "IJlig"; gEntityTable["0133"] = "ijlig"; gEntityTable["0134"] = "Jcirc"; gEntityTable["0135"] = "jcirc"; gEntityTable["0136"] = "Kcedil"; gEntityTable["0137"] = "kcedil"; gEntityTable["0138"] = "kgreen"; gEntityTable["0139"] = "Lacute"; gEntityTable["013A"] = "lacute"; gEntityTable["013B"] = "Lcedil"; gEntityTable["013C"] = "lcedil"; gEntityTable["013D"] = "Lcaron"; gEntityTable["013E"] = "lcaron"; gEntityTable["013F"] = "Lmidot"; gEntityTable["0140"] = "lmidot"; gEntityTable["0141"] = "Lstrok"; gEntityTable["0142"] = "lstrok"; gEntityTable["0143"] = "Nacute"; gEntityTable["0144"] = "nacute"; gEntityTable["0145"] = "Ncedil"; gEntityTable["0146"] = "ncedil"; gEntityTable["0147"] = "Ncaron"; gEntityTable["0148"] = "ncaron"; gEntityTable["0149"] = "napos"; gEntityTable["014A"] = "ENG"; gEntityTable["014B"] = "eng"; gEntityTable["014C"] = "Omacr"; gEntityTable["014D"] = "omacr"; gEntityTable["0150"] = "Odblac"; gEntityTable["0151"] = "odblac"; gEntityTable["0152"] = "OElig"; gEntityTable["0153"] = "oelig"; gEntityTable["0154"] = "Racute"; gEntityTable["0155"] = "racute"; gEntityTable["0156"] = "Rcedil"; gEntityTable["0157"] = "rcedil"; gEntityTable["0158"] = "Rcaron"; gEntityTable["0159"] = "rcaron"; gEntityTable["015A"] = "Sacute"; gEntityTable["015B"] = "sacute"; gEntityTable["015C"] = "Scirc"; gEntityTable["015D"] = "scirc"; gEntityTable["015E"] = "Scedil"; gEntityTable["015F"] = "scedil"; gEntityTable["0160"] = "Scaron"; gEntityTable["0161"] = "scaron"; gEntityTable["0162"] = "Tcedil"; gEntityTable["0163"] = "tcedil"; gEntityTable["0164"] = "Tcaron"; gEntityTable["0165"] = "tcaron"; gEntityTable["0166"] = "Tstrok"; gEntityTable["0167"] = "tstrok"; gEntityTable["0168"] = "Utilde"; gEntityTable["0169"] = "utilde"; gEntityTable["016A"] = "Umacr"; gEntityTable["016B"] = "umacr"; gEntityTable["016C"] = "Ubreve"; gEntityTable["016D"] = "ubreve"; gEntityTable["016E"] = "Uring"; gEntityTable["016F"] = "uring"; gEntityTable["0170"] = "Udblac"; gEntityTable["0171"] = "udblac"; gEntityTable["0172"] = "Uogon"; gEntityTable["0173"] = "uogon"; gEntityTable["0174"] = "Wcirc"; gEntityTable["0175"] = "wcirc"; gEntityTable["0176"] = "Ycirc"; gEntityTable["0177"] = "ycirc"; gEntityTable["0178"] = "Yuml"; gEntityTable["0179"] = "Zacute"; gEntityTable["017A"] = "zacute"; gEntityTable["017B"] = "Zdot"; gEntityTable["017C"] = "zdot"; gEntityTable["017D"] = "Zcaron"; gEntityTable["017E"] = "zcaron"; gEntityTable["0192"] = "fnof"; gEntityTable["01F5"] = "gacute"; gEntityTable["025B"] = "varepsilon"; gEntityTable["02C6"] = "circ"; gEntityTable["02C7"] = "Hacek"; gEntityTable["02D8"] = "Breve"; gEntityTable["02D9"] = "DiacriticalDot"; gEntityTable["02DA"] = "ring"; gEntityTable["02DB"] = "ogon"; gEntityTable["02DC"] = "DiacriticalTilde"; gEntityTable["02DD"] = "DiacriticalDoubleAcute"; gEntityTable["0302"] = "Hat"; gEntityTable["0311"] = "DownBreve"; gEntityTable["0332"] = "UnderBar"; gEntityTable["0391"] = "Alpha"; gEntityTable["0392"] = "Beta"; gEntityTable["0393"] = "Gamma"; gEntityTable["0394"] = "Delta"; gEntityTable["0395"] = "Epsilon"; gEntityTable["0396"] = "Zeta"; gEntityTable["0397"] = "Eta"; gEntityTable["0398"] = "Theta"; gEntityTable["0399"] = "Iota"; gEntityTable["039A"] = "Kappa"; gEntityTable["039B"] = "Lambda"; gEntityTable["039C"] = "Mu"; gEntityTable["039D"] = "Nu"; gEntityTable["039E"] = "Xi"; gEntityTable["039F"] = "Omicron"; gEntityTable["03A0"] = "Pi"; gEntityTable["03A1"] = "Rho"; gEntityTable["03A3"] = "Sigma"; gEntityTable["03A4"] = "Tau"; gEntityTable["03A5"] = "Upsilon"; gEntityTable["03A6"] = "Phi"; gEntityTable["03A7"] = "Chi"; gEntityTable["03A8"] = "Psi"; gEntityTable["03A9"] = "Omega"; gEntityTable["03B1"] = "alpha"; gEntityTable["03B2"] = "beta"; gEntityTable["03B3"] = "gamma"; gEntityTable["03B4"] = "delta"; gEntityTable["03B5"] = "straightepsilon"; gEntityTable["03B6"] = "zeta"; gEntityTable["03B7"] = "eta"; gEntityTable["03B8"] = "theta"; gEntityTable["03B9"] = "iota"; gEntityTable["03BA"] = "kappa"; gEntityTable["03BB"] = "lambda"; gEntityTable["03BC"] = "mu"; gEntityTable["03BD"] = "nu"; gEntityTable["03BE"] = "xi"; gEntityTable["03BF"] = "omicron"; gEntityTable["03C0"] = "pi"; gEntityTable["03C1"] = "rho"; gEntityTable["03C2"] = "varsigma"; gEntityTable["03C3"] = "sigma"; gEntityTable["03C4"] = "tau"; gEntityTable["03C5"] = "upsilon"; gEntityTable["03C6"] = "straightphi"; gEntityTable["03C7"] = "chi"; gEntityTable["03C8"] = "psi"; gEntityTable["03C9"] = "omega"; gEntityTable["03D1"] = "thetasym"; gEntityTable["03D2"] = "Upsilon"; gEntityTable["03D5"] = "varphi"; gEntityTable["03D6"] = "varpi"; gEntityTable["03DC"] = "digamma"; gEntityTable["03F0"] = "varkappa"; gEntityTable["03F1"] = "varrho"; gEntityTable["03F6"] = "backepsilon"; gEntityTable["0401"] = "IOcy"; gEntityTable["0402"] = "DJcy"; gEntityTable["0403"] = "GJcy"; gEntityTable["0404"] = "Jukcy"; gEntityTable["0405"] = "DScy"; gEntityTable["0406"] = "Iukcy"; gEntityTable["0407"] = "YIcy"; gEntityTable["0408"] = "Jsercy"; gEntityTable["0409"] = "LJcy"; gEntityTable["040A"] = "NJcy"; gEntityTable["040B"] = "TSHcy"; gEntityTable["040C"] = "KJcy"; gEntityTable["040E"] = "Ubrcy"; gEntityTable["040F"] = "DZcy"; gEntityTable["0410"] = "Acy"; gEntityTable["0411"] = "Bcy"; gEntityTable["0412"] = "Vcy"; gEntityTable["0413"] = "Gcy"; gEntityTable["0414"] = "Dcy"; gEntityTable["0415"] = "IEcy"; gEntityTable["0416"] = "ZHcy"; gEntityTable["0417"] = "Zcy"; gEntityTable["0418"] = "Icy"; gEntityTable["0419"] = "Jcy"; gEntityTable["041A"] = "Kcy"; gEntityTable["041B"] = "Lcy"; gEntityTable["041C"] = "Mcy"; gEntityTable["041D"] = "Ncy"; gEntityTable["041E"] = "Ocy"; gEntityTable["041F"] = "Pcy"; gEntityTable["0420"] = "Rcy"; gEntityTable["0421"] = "Scy"; gEntityTable["0422"] = "Tcy"; gEntityTable["0423"] = "Ucy"; gEntityTable["0424"] = "Fcy"; gEntityTable["0425"] = "KHcy"; gEntityTable["0426"] = "TScy"; gEntityTable["0427"] = "CHcy"; gEntityTable["0428"] = "SHcy"; gEntityTable["0429"] = "SHCHcy"; gEntityTable["042A"] = "HARDcy"; gEntityTable["042B"] = "Ycy"; gEntityTable["042C"] = "SOFTcy"; gEntityTable["042D"] = "Ecy"; gEntityTable["042E"] = "YUcy"; gEntityTable["042F"] = "YAcy"; gEntityTable["0430"] = "acy"; gEntityTable["0431"] = "bcy"; gEntityTable["0432"] = "vcy"; gEntityTable["0433"] = "gcy"; gEntityTable["0434"] = "dcy"; gEntityTable["0435"] = "iecy"; gEntityTable["0436"] = "zhcy"; gEntityTable["0437"] = "zcy"; gEntityTable["0438"] = "icy"; gEntityTable["0439"] = "jcy"; gEntityTable["043A"] = "kcy"; gEntityTable["043B"] = "lcy"; gEntityTable["043C"] = "mcy"; gEntityTable["043D"] = "ncy"; gEntityTable["043E"] = "ocy"; gEntityTable["043F"] = "pcy"; gEntityTable["0440"] = "rcy"; gEntityTable["0441"] = "scy"; gEntityTable["0442"] = "tcy"; gEntityTable["0443"] = "ucy"; gEntityTable["0444"] = "fcy"; gEntityTable["0445"] = "khcy"; gEntityTable["0446"] = "tscy"; gEntityTable["0447"] = "chcy"; gEntityTable["0448"] = "shcy"; gEntityTable["0449"] = "shchcy"; gEntityTable["044A"] = "hardcy"; gEntityTable["044B"] = "ycy"; gEntityTable["044C"] = "softcy"; gEntityTable["044D"] = "ecy"; gEntityTable["044E"] = "yucy"; gEntityTable["044F"] = "yacy"; gEntityTable["0451"] = "iocy"; gEntityTable["0452"] = "djcy"; gEntityTable["0453"] = "gjcy"; gEntityTable["0454"] = "jukcy"; gEntityTable["0455"] = "dscy"; gEntityTable["0456"] = "iukcy"; gEntityTable["0457"] = "yicy"; gEntityTable["0458"] = "jsercy"; gEntityTable["0459"] = "ljcy"; gEntityTable["045A"] = "njcy"; gEntityTable["045B"] = "tshcy"; gEntityTable["045C"] = "kjcy"; gEntityTable["045E"] = "ubrcy"; gEntityTable["045F"] = "dzcy"; gEntityTable["2002"] = "ensp"; gEntityTable["2003"] = "emsp"; gEntityTable["2004"] = "emsp13"; gEntityTable["2005"] = "emsp14"; gEntityTable["2007"] = "numsp"; gEntityTable["2008"] = "puncsp"; gEntityTable["2009"] = "ThinSpace"; gEntityTable["200A"] = "VeryThinSpace"; gEntityTable["200B"] = "InvisibleComma"; gEntityTable["200C"] = "zwnj"; gEntityTable["200D"] = "zwj"; gEntityTable["200E"] = "lrm"; gEntityTable["200F"] = "rlm"; gEntityTable["2010"] = "hyphen"; gEntityTable["2013"] = "ndash"; gEntityTable["2014"] = "mdash"; gEntityTable["2015"] = "horbar"; gEntityTable["2016"] = "Verbar"; gEntityTable["2018"] = "OpenCurlyQuote"; gEntityTable["2019"] = "CloseCurlyQuote"; gEntityTable["201A"] = "lsquor"; gEntityTable["201C"] = "OpenCurlyDoubleQuote"; gEntityTable["201D"] = "CloseCurlyDoubleQuote"; gEntityTable["201E"] = "ldquor"; gEntityTable["2020"] = "dagger"; gEntityTable["2021"] = "ddagger"; gEntityTable["2022"] = "bullet"; gEntityTable["2025"] = "nldr"; gEntityTable["2026"] = "hellip"; gEntityTable["2030"] = "permil"; gEntityTable["2031"] = "pertenk"; gEntityTable["2032"] = "prime"; gEntityTable["2033"] = "Prime"; gEntityTable["2034"] = "tprime"; gEntityTable["2035"] = "backprime"; gEntityTable["2039"] = "lsaquo"; gEntityTable["203A"] = "rsaquo"; gEntityTable["203E"] = "oline"; gEntityTable["2041"] = "caret"; gEntityTable["2043"] = "hybull"; gEntityTable["2044"] = "frasl"; gEntityTable["204F"] = "bsemi"; gEntityTable["2057"] = "qprime"; gEntityTable["205F"] = "MediumSpace"; gEntityTable["2061"] = "ApplyFunction"; gEntityTable["2062"] = "InvisibleTimes"; gEntityTable["20AC"] = "euro"; gEntityTable["20DB"] = "TripleDot"; gEntityTable["20DC"] = "DotDot"; gEntityTable["2102"] = "complexes"; gEntityTable["2105"] = "incare"; gEntityTable["210A"] = "gscr"; gEntityTable["210B"] = "HilbertSpace"; gEntityTable["210C"] = "Poincareplane"; gEntityTable["210D"] = "quaternions"; gEntityTable["210E"] = "planckh"; gEntityTable["210F"] = "hslash"; gEntityTable["2110"] = "imagline"; gEntityTable["2111"] = "imagpart"; gEntityTable["2112"] = "Laplacetrf"; gEntityTable["2113"] = "lscr"; gEntityTable["2115"] = "naturals"; gEntityTable["2116"] = "numero"; gEntityTable["2117"] = "copysr"; gEntityTable["2118"] = "weierp"; gEntityTable["2119"] = "primes"; gEntityTable["211A"] = "rationals"; gEntityTable["211B"] = "realine"; gEntityTable["211C"] = "realpart"; gEntityTable["211D"] = "reals"; gEntityTable["211E"] = "rx"; gEntityTable["2122"] = "trade"; gEntityTable["2124"] = "integers"; gEntityTable["2126"] = "ohm"; gEntityTable["2127"] = "mho"; gEntityTable["2128"] = "zeetrf"; gEntityTable["2129"] = "iiota"; gEntityTable["212B"] = "angst"; gEntityTable["212C"] = "Bernoullis"; gEntityTable["212D"] = "Cayleys"; gEntityTable["212F"] = "escr"; gEntityTable["2130"] = "expectation"; gEntityTable["2131"] = "Fouriertrf"; gEntityTable["2133"] = "Mellintrf"; gEntityTable["2134"] = "orderof"; gEntityTable["2135"] = "alefsym"; gEntityTable["2136"] = "beth"; gEntityTable["2137"] = "gimel"; gEntityTable["2138"] = "daleth"; gEntityTable["2145"] = "CapitalDifferentialD"; gEntityTable["2146"] = "DifferentialD"; gEntityTable["2147"] = "ExponentialE"; gEntityTable["2148"] = "ImaginaryI"; gEntityTable["2153"] = "frac13"; gEntityTable["2154"] = "frac23"; gEntityTable["2155"] = "frac15"; gEntityTable["2156"] = "frac25"; gEntityTable["2157"] = "frac35"; gEntityTable["2158"] = "frac45"; gEntityTable["2159"] = "frac16"; gEntityTable["215A"] = "frac56"; gEntityTable["215B"] = "frac18"; gEntityTable["215C"] = "frac38"; gEntityTable["215D"] = "frac58"; gEntityTable["215E"] = "frac78"; gEntityTable["2190"] = "LeftArrow"; gEntityTable["2191"] = "UpArrow"; gEntityTable["2192"] = "RightArrow"; gEntityTable["2193"] = "DownArrow"; gEntityTable["2194"] = "LeftRightArrow"; gEntityTable["2195"] = "UpDownArrow"; gEntityTable["2196"] = "UpperLeftArrow"; gEntityTable["2197"] = "UpperRightArrow"; gEntityTable["2198"] = "LowerRightArrow"; gEntityTable["2199"] = "LowerLeftArrow"; gEntityTable["219A"] = "nleftarrow"; gEntityTable["219B"] = "nrightarrow"; gEntityTable["219D"] = "rightsquigarrow"; gEntityTable["219E"] = "twoheadleftarrow"; gEntityTable["219F"] = "Uarr"; gEntityTable["21A0"] = "twoheadrightarrow"; gEntityTable["21A1"] = "Darr"; gEntityTable["21A2"] = "leftarrowtail"; gEntityTable["21A3"] = "rightarrowtail"; gEntityTable["21A4"] = "LeftTeeArrow"; gEntityTable["21A5"] = "UpTeeArrow"; gEntityTable["21A6"] = "RightTeeArrow"; gEntityTable["21A7"] = "DownTeeArrow"; gEntityTable["21A9"] = "hookleftarrow"; gEntityTable["21AA"] = "hookrightarrow"; gEntityTable["21AB"] = "looparrowleft"; gEntityTable["21AC"] = "looparrowright"; gEntityTable["21AD"] = "leftrightsquigarrow"; gEntityTable["21AE"] = "nleftrightarrow"; gEntityTable["21B0"] = "Lsh"; gEntityTable["21B1"] = "Rsh"; gEntityTable["21B2"] = "ldsh"; gEntityTable["21B3"] = "rdsh"; gEntityTable["21B5"] = "crarr"; gEntityTable["21B6"] = "curvearrowleft"; gEntityTable["21B7"] = "curvearrowright"; gEntityTable["21BA"] = "circlearrowleft"; gEntityTable["21BB"] = "circlearrowright"; gEntityTable["21BC"] = "leftharpoonup"; gEntityTable["21BD"] = "leftharpoondown"; gEntityTable["21BE"] = "upharpoonright"; gEntityTable["21BF"] = "upharpoonleft"; gEntityTable["21C0"] = "rightharpoonup"; gEntityTable["21C1"] = "rightharpoondown"; gEntityTable["21C2"] = "downharpoonright"; gEntityTable["21C3"] = "downharpoonleft"; gEntityTable["21C4"] = "RightArrowLeftArrow"; gEntityTable["21C5"] = "UpArrowDownArrow"; gEntityTable["21C6"] = "LeftArrowRightArrow"; gEntityTable["21C7"] = "leftleftarrows"; gEntityTable["21C8"] = "upuparrows"; gEntityTable["21C9"] = "rightrightarrows"; gEntityTable["21CA"] = "downdownarrows"; gEntityTable["21CB"] = "ReverseEquilibrium"; gEntityTable["21CC"] = "rightleftharpoons"; gEntityTable["21CD"] = "nLeftarrow"; gEntityTable["21CE"] = "nLeftrightarrow"; gEntityTable["21CF"] = "nRightarrow"; gEntityTable["21D0"] = "DoubleLeftArrow"; gEntityTable["21D1"] = "DoubleUpArrow"; gEntityTable["21D2"] = "DoubleRightArrow"; gEntityTable["21D3"] = "DoubleDownArrow"; gEntityTable["21D4"] = "DoubleLeftRightArrow"; gEntityTable["21D5"] = "DoubleUpDownArrow"; gEntityTable["21D6"] = "nwArr"; gEntityTable["21D7"] = "neArr"; gEntityTable["21D8"] = "seArr"; gEntityTable["21D9"] = "swArr"; gEntityTable["21DA"] = "Lleftarrow"; gEntityTable["21DB"] = "Rrightarrow"; gEntityTable["21DD"] = "zigrarr"; gEntityTable["21E4"] = "LeftArrowBar"; gEntityTable["21E5"] = "RightArrowBar"; gEntityTable["21F5"] = "DownArrowUpArrow"; gEntityTable["21FD"] = "loarr"; gEntityTable["21FE"] = "roarr"; gEntityTable["21FF"] = "hoarr"; gEntityTable["2200"] = "ForAll"; gEntityTable["2201"] = "complement"; gEntityTable["2202"] = "PartialD"; gEntityTable["2203"] = "Exists"; gEntityTable["2204"] = "NotExists"; gEntityTable["2205"] = "varnothing"; gEntityTable["2207"] = "nabla"; gEntityTable["2208"] = "Element"; gEntityTable["2209"] = "NotElement"; gEntityTable["220B"] = "ReverseElement"; gEntityTable["220C"] = "NotReverseElement"; gEntityTable["220F"] = "Product"; gEntityTable["2210"] = "Coproduct"; gEntityTable["2211"] = "Sum"; gEntityTable["2212"] = "minus"; gEntityTable["2213"] = "MinusPlus"; gEntityTable["2214"] = "dotplus"; gEntityTable["2216"] = "Backslash"; gEntityTable["2217"] = "lowast"; gEntityTable["2218"] = "SmallCircle"; gEntityTable["221A"] = "radic"; gEntityTable["221D"] = "Proportional"; gEntityTable["221E"] = "infin"; gEntityTable["221F"] = "angrt"; gEntityTable["2220"] = "angle"; gEntityTable["2221"] = "measuredangle"; gEntityTable["2222"] = "angsph"; gEntityTable["2223"] = "VerticalBar"; gEntityTable["2224"] = "NotVerticalBar"; gEntityTable["2225"] = "DoubleVerticalBar"; gEntityTable["2226"] = "NotDoubleVerticalBar"; gEntityTable["2227"] = "wedge"; gEntityTable["2228"] = "vee"; gEntityTable["2229"] = "cap"; gEntityTable["222A"] = "cup"; gEntityTable["222B"] = "Integral"; gEntityTable["222C"] = "Int"; gEntityTable["222D"] = "iiint"; gEntityTable["222E"] = "ContourIntegral"; gEntityTable["222F"] = "DoubleContourIntegral"; gEntityTable["2230"] = "Cconint"; gEntityTable["2231"] = "cwint"; gEntityTable["2232"] = "ClockwiseContourIntegral"; gEntityTable["2233"] = "CounterClockwiseContourIntegral"; gEntityTable["2234"] = "Therefore"; gEntityTable["2235"] = "Because"; gEntityTable["2236"] = "ratio"; gEntityTable["2237"] = "Proportion"; gEntityTable["2238"] = "dotminus"; gEntityTable["223A"] = "mDDot"; gEntityTable["223B"] = "homtht"; gEntityTable["223C"] = "Tilde"; gEntityTable["223D"] = "backsim"; gEntityTable["223E"] = "mstpos"; gEntityTable["223F"] = "acd"; gEntityTable["2240"] = "VerticalTilde"; gEntityTable["2241"] = "NotTilde"; gEntityTable["2242"] = "EqualTilde"; gEntityTable["2243"] = "TildeEqual"; gEntityTable["2244"] = "NotTildeEqual"; gEntityTable["2245"] = "TildeFullEqual"; gEntityTable["2246"] = "simne"; gEntityTable["2247"] = "NotTildeFullEqual"; gEntityTable["2248"] = "TildeTilde"; gEntityTable["2249"] = "NotTildeTilde"; gEntityTable["224A"] = "approxeq"; gEntityTable["224B"] = "apid"; gEntityTable["224C"] = "backcong"; gEntityTable["224D"] = "CupCap"; gEntityTable["224E"] = "HumpDownHump"; gEntityTable["224F"] = "HumpEqual"; gEntityTable["2250"] = "DotEqual"; gEntityTable["2251"] = "doteqdot"; gEntityTable["2252"] = "fallingdotseq"; gEntityTable["2253"] = "risingdotseq"; gEntityTable["2254"] = "coloneq"; gEntityTable["2255"] = "eqcolon"; gEntityTable["2256"] = "eqcirc"; gEntityTable["2257"] = "circeq"; gEntityTable["2259"] = "wedgeq"; gEntityTable["225A"] = "veeeq"; gEntityTable["225B"] = "easter"; gEntityTable["225C"] = "triangleq"; gEntityTable["225F"] = "questeq"; gEntityTable["2260"] = "NotEqual"; gEntityTable["2261"] = "Congruent"; gEntityTable["2262"] = "NotCongruent"; gEntityTable["2264"] = "leq"; gEntityTable["2265"] = "GreaterEqual"; gEntityTable["2266"] = "LessFullEqual"; gEntityTable["2267"] = "GreaterFullEqual"; gEntityTable["2268"] = "lneqq"; gEntityTable["2269"] = "gneqq"; gEntityTable["226A"] = "NestedLessLess"; gEntityTable["226B"] = "NestedGreaterGreater"; gEntityTable["226C"] = "between"; gEntityTable["226D"] = "NotCupCap"; gEntityTable["226E"] = "NotLess"; gEntityTable["226F"] = "NotGreater"; gEntityTable["2270"] = "NotGreaterFullEqual"; gEntityTable["2271"] = "NotGreaterSlantEqual"; gEntityTable["2272"] = "lessapprox"; gEntityTable["2273"] = "GreaterTilde"; gEntityTable["2274"] = "NotLessTilde"; gEntityTable["2275"] = "NotGreaterTilde"; gEntityTable["2276"] = "LessGreater"; gEntityTable["2277"] = "GreaterLess"; gEntityTable["2278"] = "NotLessGreater"; gEntityTable["2279"] = "NotGreaterLess"; gEntityTable["227A"] = "Precedes"; gEntityTable["227B"] = "Succeeds"; gEntityTable["227C"] = "PrecedesSlantEqual"; gEntityTable["227D"] = "SucceedsSlantEqual"; gEntityTable["227E"] = "PrecedesTilde"; gEntityTable["227F"] = "SucceedsTilde"; gEntityTable["2280"] = "NotPrecedes"; gEntityTable["2281"] = "NotSucceeds"; gEntityTable["2282"] = "subset"; gEntityTable["2283"] = "Superset"; gEntityTable["2284"] = "NotSubset"; gEntityTable["2285"] = "NotSuperset"; gEntityTable["2286"] = "SubsetEqual"; gEntityTable["2287"] = "SupersetEqual"; gEntityTable["2288"] = "NotSubsetEqual"; gEntityTable["2289"] = "NotSupersetEqual"; gEntityTable["228A"] = "subsetneqq"; gEntityTable["228B"] = "supsetneqq"; gEntityTable["228D"] = "cupdot"; gEntityTable["228E"] = "UnionPlus"; gEntityTable["228F"] = "SquareSubset"; gEntityTable["2290"] = "SquareSuperset"; gEntityTable["2291"] = "SquareSubsetEqual"; gEntityTable["2292"] = "SquareSupersetEqual"; gEntityTable["2293"] = "SquareIntersection"; gEntityTable["2294"] = "SquareUnion"; gEntityTable["2295"] = "CirclePlus"; gEntityTable["2296"] = "CircleMinus"; gEntityTable["2297"] = "CircleTimes"; gEntityTable["2298"] = "osol"; gEntityTable["2299"] = "CircleDot"; gEntityTable["229A"] = "circledcirc"; gEntityTable["229B"] = "circledast"; gEntityTable["229D"] = "circleddash"; gEntityTable["229E"] = "boxplus"; gEntityTable["229F"] = "boxminus"; gEntityTable["22A0"] = "boxtimes"; gEntityTable["22A1"] = "dotsquare"; gEntityTable["22A2"] = "RightTee"; gEntityTable["22A3"] = "LeftTee"; gEntityTable["22A4"] = "DownTee"; gEntityTable["22A5"] = "bottom"; gEntityTable["22A7"] = "models"; gEntityTable["22A8"] = "DoubleRightTee"; gEntityTable["22A9"] = "Vdash"; gEntityTable["22AA"] = "Vvdash"; gEntityTable["22AB"] = "VDash"; gEntityTable["22AC"] = "nvdash"; gEntityTable["22AD"] = "nvDash"; gEntityTable["22AE"] = "nVdash"; gEntityTable["22AF"] = "nVDash"; gEntityTable["22B0"] = "prurel"; gEntityTable["22B2"] = "vartriangleleft"; gEntityTable["22B3"] = "vartriangleright"; gEntityTable["22B4"] = "LeftTriangleEqual"; gEntityTable["22B5"] = "RightTriangleEqual"; gEntityTable["22B6"] = "origof"; gEntityTable["22B7"] = "imof"; gEntityTable["22B8"] = "multimap"; gEntityTable["22B9"] = "hercon"; gEntityTable["22BA"] = "intercal"; gEntityTable["22BB"] = "veebar"; gEntityTable["22BC"] = "barwedge"; gEntityTable["22BD"] = "barvee"; gEntityTable["22BE"] = "vangrt"; gEntityTable["22BF"] = "lrtri"; gEntityTable["22C0"] = "bigwedge"; gEntityTable["22C1"] = "bigvee"; gEntityTable["22C2"] = "Intersection"; gEntityTable["22C3"] = "bigcup"; gEntityTable["22C4"] = "Diamond"; gEntityTable["22C5"] = "sdot"; gEntityTable["22C6"] = "sstarf"; gEntityTable["22C7"] = "divideontimes"; gEntityTable["22C8"] = "bowtie"; gEntityTable["22C9"] = "ltimes"; gEntityTable["22CA"] = "rtimes"; gEntityTable["22CB"] = "leftthreetimes"; gEntityTable["22CC"] = "rightthreetimes"; gEntityTable["22CD"] = "backsimeq"; gEntityTable["22CE"] = "curlyvee"; gEntityTable["22CF"] = "curlywedge"; gEntityTable["22D0"] = "Subset"; gEntityTable["22D1"] = "Supset"; gEntityTable["22D2"] = "Cap"; gEntityTable["22D3"] = "Cup"; gEntityTable["22D4"] = "pitchfork"; gEntityTable["22D5"] = "epar"; gEntityTable["22D6"] = "lessdot"; gEntityTable["22D7"] = "gtrdot"; gEntityTable["22D8"] = "Ll"; gEntityTable["22D9"] = "ggg"; gEntityTable["22DA"] = "LessEqualGreater"; gEntityTable["22DB"] = "GreaterEqualLess"; gEntityTable["22DC"] = "eqslantless"; gEntityTable["22DD"] = "eqslantgtr"; gEntityTable["22DE"] = "curlyeqprec"; gEntityTable["22DF"] = "curlyeqsucc"; gEntityTable["22E0"] = "NotPrecedesSlantEqual"; gEntityTable["22E1"] = "NotSucceedsSlantEqual"; gEntityTable["22E2"] = "NotSquareSubsetEqual"; gEntityTable["22E3"] = "NotSquareSupersetEqual"; gEntityTable["22E6"] = "lnsim"; gEntityTable["22E7"] = "gnsim"; gEntityTable["22E8"] = "precnapprox"; gEntityTable["22E9"] = "succnapprox"; gEntityTable["22EA"] = "NotLeftTriangle"; gEntityTable["22EB"] = "NotRightTriangle"; gEntityTable["22EC"] = "NotLeftTriangleEqual"; gEntityTable["22ED"] = "NotRightTriangleEqual"; gEntityTable["22EE"] = "vellip"; gEntityTable["22EF"] = "ctdot"; gEntityTable["22F0"] = "utdot"; gEntityTable["22F1"] = "dtdot"; gEntityTable["22F2"] = "disin"; gEntityTable["22F3"] = "isinsv"; gEntityTable["22F4"] = "isins"; gEntityTable["22F5"] = "isindot"; gEntityTable["22F6"] = "notinvc"; gEntityTable["22F7"] = "notinvb"; gEntityTable["22F9"] = "isinE"; gEntityTable["22FA"] = "nisd"; gEntityTable["22FB"] = "xnis"; gEntityTable["22FC"] = "nis"; gEntityTable["22FD"] = "notnivc"; gEntityTable["22FE"] = "notnivb"; gEntityTable["2306"] = "doublebarwedge"; gEntityTable["2308"] = "LeftCeiling"; gEntityTable["2309"] = "RightCeiling"; gEntityTable["230A"] = "LeftFloor"; gEntityTable["230B"] = "RightFloor"; gEntityTable["230C"] = "drcrop"; gEntityTable["230D"] = "dlcrop"; gEntityTable["230E"] = "urcrop"; gEntityTable["230F"] = "ulcrop"; gEntityTable["2310"] = "bnot"; gEntityTable["2312"] = "profline"; gEntityTable["2313"] = "profsurf"; gEntityTable["2315"] = "telrec"; gEntityTable["2316"] = "target"; gEntityTable["231C"] = "ulcorner"; gEntityTable["231D"] = "urcorner"; gEntityTable["231E"] = "llcorner"; gEntityTable["231F"] = "lrcorner"; gEntityTable["2322"] = "frown"; gEntityTable["2323"] = "smile"; gEntityTable["2329"] = "LeftAngleBracket"; gEntityTable["232A"] = "RightAngleBracket"; gEntityTable["232D"] = "cylcty"; gEntityTable["232E"] = "profalar"; gEntityTable["2336"] = "topbot"; gEntityTable["233D"] = "ovbar"; gEntityTable["233F"] = "solbar"; gEntityTable["237C"] = "angzarr"; gEntityTable["23B0"] = "lmoustache"; gEntityTable["23B1"] = "rmoustache"; gEntityTable["23B4"] = "OverBracket"; gEntityTable["23B5"] = "UnderBracket"; gEntityTable["2423"] = "blank"; gEntityTable["24C8"] = "circledS"; gEntityTable["2500"] = "HorizontalLine"; gEntityTable["2502"] = "boxv"; gEntityTable["250C"] = "boxdr"; gEntityTable["2510"] = "boxdl"; gEntityTable["2514"] = "boxur"; gEntityTable["2518"] = "boxul"; gEntityTable["251C"] = "boxvr"; gEntityTable["2524"] = "boxvl"; gEntityTable["252C"] = "boxhd"; gEntityTable["2534"] = "boxhu"; gEntityTable["253C"] = "boxvh"; gEntityTable["2550"] = "boxH"; gEntityTable["2551"] = "boxV"; gEntityTable["2552"] = "boxdR"; gEntityTable["2553"] = "boxDr"; gEntityTable["2554"] = "boxDR"; gEntityTable["2555"] = "boxdL"; gEntityTable["2556"] = "boxDl"; gEntityTable["2557"] = "boxDL"; gEntityTable["2558"] = "boxuR"; gEntityTable["2559"] = "boxUr"; gEntityTable["255A"] = "boxUR"; gEntityTable["255B"] = "boxuL"; gEntityTable["255C"] = "boxUl"; gEntityTable["255D"] = "boxUL"; gEntityTable["255E"] = "boxvR"; gEntityTable["255F"] = "boxVr"; gEntityTable["2560"] = "boxVR"; gEntityTable["2561"] = "boxvL"; gEntityTable["2562"] = "boxVl"; gEntityTable["2563"] = "boxVL"; gEntityTable["2564"] = "boxHd"; gEntityTable["2565"] = "boxhD"; gEntityTable["2566"] = "boxHD"; gEntityTable["2567"] = "boxHu"; gEntityTable["2568"] = "boxhU"; gEntityTable["2569"] = "boxHU"; gEntityTable["256A"] = "boxvH"; gEntityTable["256B"] = "boxVh"; gEntityTable["256C"] = "boxVH"; gEntityTable["2580"] = "uhblk"; gEntityTable["2584"] = "lhblk"; gEntityTable["2588"] = "block"; gEntityTable["2591"] = "blk14"; gEntityTable["2592"] = "blk12"; gEntityTable["2593"] = "blk34"; gEntityTable["25A1"] = "Square"; gEntityTable["25AA"] = "blacksquare"; gEntityTable["25AD"] = "rect"; gEntityTable["25AE"] = "marker"; gEntityTable["25B3"] = "bigtriangleup"; gEntityTable["25B4"] = "blacktriangle"; gEntityTable["25B5"] = "triangle"; gEntityTable["25B8"] = "blacktriangleright"; gEntityTable["25B9"] = "triangleright"; gEntityTable["25BD"] = "bigtriangledown"; gEntityTable["25BE"] = "blacktriangledown"; gEntityTable["25BF"] = "triangledown"; gEntityTable["25C2"] = "blacktriangleleft"; gEntityTable["25C3"] = "triangleleft"; gEntityTable["25CA"] = "lozenge"; gEntityTable["25CB"] = "cir"; gEntityTable["25EC"] = "tridot"; gEntityTable["25EF"] = "bigcirc"; gEntityTable["25F8"] = "ultri"; gEntityTable["25F9"] = "urtri"; gEntityTable["25FA"] = "lltri"; gEntityTable["25FD"] = "EmptySmallSquare"; gEntityTable["25FE"] = "FilledSmallSquare"; gEntityTable["2605"] = "bigstar"; gEntityTable["260E"] = "phone"; gEntityTable["2640"] = "female"; gEntityTable["2642"] = "male"; gEntityTable["2660"] = "spadesuit"; gEntityTable["2661"] = "heartsuit"; gEntityTable["2663"] = "clubsuit"; gEntityTable["2665"] = "hearts"; gEntityTable["2666"] = "diamondsuit"; gEntityTable["266A"] = "sung"; gEntityTable["266D"] = "flat"; gEntityTable["266E"] = "natural"; gEntityTable["266F"] = "sharp"; gEntityTable["2713"] = "checkmark"; gEntityTable["2717"] = "cross"; gEntityTable["2720"] = "maltese"; gEntityTable["2736"] = "sext"; gEntityTable["2758"] = "VerticalSeparator"; gEntityTable["2905"] = "Map"; gEntityTable["290C"] = "lbarr"; gEntityTable["290D"] = "bkarow"; gEntityTable["290E"] = "lBarr"; gEntityTable["290F"] = "dbkarow"; gEntityTable["2910"] = "drbkarow"; gEntityTable["2911"] = "DDotrahd"; gEntityTable["2912"] = "UpArrowBar"; gEntityTable["2913"] = "DownArrowBar"; gEntityTable["2916"] = "Rarrtl"; gEntityTable["2919"] = "latail"; gEntityTable["291B"] = "lAtail"; gEntityTable["291C"] = "rAtail"; gEntityTable["291D"] = "larrfs"; gEntityTable["291E"] = "rarrfs"; gEntityTable["291F"] = "larrbfs"; gEntityTable["2920"] = "rarrbfs"; gEntityTable["2923"] = "nwarhk"; gEntityTable["2924"] = "nearhk"; gEntityTable["2925"] = "hksearow"; gEntityTable["2926"] = "hkswarow"; gEntityTable["2927"] = "nwnear"; gEntityTable["2928"] = "nesear"; gEntityTable["2929"] = "seswar"; gEntityTable["292A"] = "swnwar"; gEntityTable["2933"] = "rarrc"; gEntityTable["2935"] = "cudarrr"; gEntityTable["2936"] = "ldca"; gEntityTable["2937"] = "rdca"; gEntityTable["2938"] = "cudarrl"; gEntityTable["2939"] = "larrpl"; gEntityTable["293C"] = "curarrm"; gEntityTable["293D"] = "cularrp"; gEntityTable["2945"] = "rarrpl"; gEntityTable["2948"] = "harrcir"; gEntityTable["2949"] = "Uarrocir"; gEntityTable["294A"] = "lurdshar"; gEntityTable["294B"] = "ldrushar"; gEntityTable["294E"] = "LeftRightVector"; gEntityTable["294F"] = "RightUpDownVector"; gEntityTable["2950"] = "DownLeftRightVector"; gEntityTable["2951"] = "LeftUpDownVector"; gEntityTable["2952"] = "LeftVectorBar"; gEntityTable["2953"] = "RightVectorBar"; gEntityTable["2954"] = "RightUpVectorBar"; gEntityTable["2955"] = "RightDownVectorBar"; gEntityTable["2956"] = "DownLeftVectorBar"; gEntityTable["2957"] = "DownRightVectorBar"; gEntityTable["2958"] = "LeftUpVectorBar"; gEntityTable["2959"] = "LeftDownVectorBar"; gEntityTable["295A"] = "LeftTeeVector"; gEntityTable["295B"] = "RightTeeVector"; gEntityTable["295C"] = "RightUpTeeVector"; gEntityTable["295D"] = "RightDownTeeVector"; gEntityTable["295E"] = "DownLeftTeeVector"; gEntityTable["295F"] = "DownRightTeeVector"; gEntityTable["2960"] = "LeftUpTeeVector"; gEntityTable["2961"] = "LeftDownTeeVector"; gEntityTable["2962"] = "lHar"; gEntityTable["2963"] = "uHar"; gEntityTable["2964"] = "rHar"; gEntityTable["2965"] = "dHar"; gEntityTable["2966"] = "luruhar"; gEntityTable["2967"] = "ldrdhar"; gEntityTable["2968"] = "ruluhar"; gEntityTable["2969"] = "rdldhar"; gEntityTable["296A"] = "lharul"; gEntityTable["296B"] = "llhard"; gEntityTable["296C"] = "rharul"; gEntityTable["296D"] = "lrhard"; gEntityTable["296E"] = "UpEquilibrium"; gEntityTable["296F"] = "ReverseUpEquilibrium"; gEntityTable["2970"] = "RoundImplies"; gEntityTable["2971"] = "erarr"; gEntityTable["2972"] = "simrarr"; gEntityTable["2973"] = "larrsim"; gEntityTable["2974"] = "rarrsim"; gEntityTable["2975"] = "rarrap"; gEntityTable["2976"] = "ltlarr"; gEntityTable["2978"] = "gtrarr"; gEntityTable["2979"] = "subrarr"; gEntityTable["297B"] = "suplarr"; gEntityTable["297C"] = "lfisht"; gEntityTable["297D"] = "rfisht"; gEntityTable["297E"] = "ufisht"; gEntityTable["297F"] = "dfisht"; gEntityTable["298B"] = "lbrke"; gEntityTable["298C"] = "rbrke"; gEntityTable["298D"] = "lbrkslu"; gEntityTable["298E"] = "rbrksld"; gEntityTable["298F"] = "lbrksld"; gEntityTable["2990"] = "rbrkslu"; gEntityTable["2991"] = "langd"; gEntityTable["2992"] = "rangd"; gEntityTable["2993"] = "lparlt"; gEntityTable["2994"] = "rpargt"; gEntityTable["2995"] = "gtlPar"; gEntityTable["2996"] = "ltrPar"; gEntityTable["299A"] = "vzigzag"; gEntityTable["299D"] = "angrtvbd"; gEntityTable["29A4"] = "ange"; gEntityTable["29A5"] = "range"; gEntityTable["29A6"] = "dwangle"; gEntityTable["29A7"] = "uwangle"; gEntityTable["29A8"] = "angmsdaa"; gEntityTable["29A9"] = "angmsdab"; gEntityTable["29AA"] = "angmsdac"; gEntityTable["29AB"] = "angmsdad"; gEntityTable["29AC"] = "angmsdae"; gEntityTable["29AD"] = "angmsdaf"; gEntityTable["29AE"] = "angmsdag"; gEntityTable["29AF"] = "angmsdah"; gEntityTable["29B0"] = "bemptyv"; gEntityTable["29B1"] = "demptyv"; gEntityTable["29B2"] = "cemptyv"; gEntityTable["29B3"] = "raemptyv"; gEntityTable["29B4"] = "laemptyv"; gEntityTable["29B5"] = "ohbar"; gEntityTable["29B6"] = "omid"; gEntityTable["29B7"] = "opar"; gEntityTable["29B9"] = "operp"; gEntityTable["29BB"] = "olcross"; gEntityTable["29BC"] = "odsold"; gEntityTable["29BE"] = "olcir"; gEntityTable["29BF"] = "ofcir"; gEntityTable["29C0"] = "olt"; gEntityTable["29C1"] = "ogt"; gEntityTable["29C2"] = "cirscir"; gEntityTable["29C3"] = "cirE"; gEntityTable["29C4"] = "solb"; gEntityTable["29C5"] = "bsolb"; gEntityTable["29C9"] = "boxbox"; gEntityTable["29CD"] = "trisb"; gEntityTable["29CE"] = "rtriltri"; gEntityTable["29CF"] = "LeftTriangleBar"; gEntityTable["29D0"] = "RightTriangleBar"; gEntityTable["29DA"] = "race"; gEntityTable["29DB"] = "acE"; gEntityTable["29DC"] = "iinfin"; gEntityTable["29DE"] = "nvinfin"; gEntityTable["29E3"] = "eparsl"; gEntityTable["29E4"] = "smeparsl"; gEntityTable["29E5"] = "eqvparsl"; gEntityTable["29EB"] = "blacklozenge"; gEntityTable["29F4"] = "RuleDelayed"; gEntityTable["29F6"] = "dsol"; gEntityTable["2A0C"] = "iiiint"; gEntityTable["2A0D"] = "fpartint"; gEntityTable["2A10"] = "cirfnint"; gEntityTable["2A11"] = "awint"; gEntityTable["2A12"] = "rppolint"; gEntityTable["2A13"] = "scpolint"; gEntityTable["2A14"] = "npolint"; gEntityTable["2A15"] = "pointint"; gEntityTable["2A16"] = "quatint"; gEntityTable["2A17"] = "intlarhk"; gEntityTable["2A22"] = "pluscir"; gEntityTable["2A23"] = "plusacir"; gEntityTable["2A24"] = "simplus"; gEntityTable["2A25"] = "plusdu"; gEntityTable["2A26"] = "plussim"; gEntityTable["2A27"] = "plustwo"; gEntityTable["2A29"] = "mcomma"; gEntityTable["2A2A"] = "minusdu"; gEntityTable["2A2D"] = "loplus"; gEntityTable["2A2E"] = "roplus"; gEntityTable["2A2F"] = "Cross"; gEntityTable["2A30"] = "timesd"; gEntityTable["2A31"] = "timesbar"; gEntityTable["2A33"] = "smashp"; gEntityTable["2A34"] = "lotimes"; gEntityTable["2A35"] = "rotimes"; gEntityTable["2A36"] = "otimesas"; gEntityTable["2A37"] = "Otimes"; gEntityTable["2A38"] = "odiv"; gEntityTable["2A39"] = "triplus"; gEntityTable["2A3A"] = "triminus"; gEntityTable["2A3B"] = "tritime"; gEntityTable["2A3C"] = "intprod"; gEntityTable["2A3F"] = "amalg"; gEntityTable["2A40"] = "capdot"; gEntityTable["2A42"] = "ncup"; gEntityTable["2A43"] = "ncap"; gEntityTable["2A44"] = "capand"; gEntityTable["2A45"] = "cupor"; gEntityTable["2A46"] = "cupcap"; gEntityTable["2A47"] = "capcup"; gEntityTable["2A48"] = "cupbrcap"; gEntityTable["2A49"] = "capbrcup"; gEntityTable["2A4A"] = "cupcup"; gEntityTable["2A4B"] = "capcap"; gEntityTable["2A4C"] = "ccups"; gEntityTable["2A4D"] = "ccaps"; gEntityTable["2A50"] = "ccupssm"; gEntityTable["2A53"] = "And"; gEntityTable["2A54"] = "Or"; gEntityTable["2A55"] = "andand"; gEntityTable["2A56"] = "oror"; gEntityTable["2A57"] = "orslope"; gEntityTable["2A58"] = "andslope"; gEntityTable["2A5A"] = "andv"; gEntityTable["2A5B"] = "orv"; gEntityTable["2A5C"] = "andd"; gEntityTable["2A5D"] = "ord"; gEntityTable["2A5F"] = "wedbar"; gEntityTable["2A66"] = "sdote"; gEntityTable["2A6A"] = "simdot"; gEntityTable["2A6D"] = "congdot"; gEntityTable["2A6F"] = "apacir"; gEntityTable["2A71"] = "eplus"; gEntityTable["2A72"] = "pluse"; gEntityTable["2A73"] = "Esim"; gEntityTable["2A74"] = "Colone"; gEntityTable["2A75"] = "Equal"; gEntityTable["2A77"] = "ddotseq"; gEntityTable["2A78"] = "equivDD"; gEntityTable["2A79"] = "ltcir"; gEntityTable["2A7A"] = "gtcir"; gEntityTable["2A7B"] = "ltquest"; gEntityTable["2A7C"] = "gtquest"; gEntityTable["2A7D"] = "LessSlantEqual"; gEntityTable["2A7E"] = "GreaterSlantEqual"; gEntityTable["2A7F"] = "lesdot"; gEntityTable["2A80"] = "gesdot"; gEntityTable["2A81"] = "lesdoto"; gEntityTable["2A82"] = "gesdoto"; gEntityTable["2A83"] = "lesdotor"; gEntityTable["2A84"] = "gesdotol"; gEntityTable["2A89"] = "lnapprox"; gEntityTable["2A8A"] = "gnapprox"; gEntityTable["2A8D"] = "lsime"; gEntityTable["2A8E"] = "gsime"; gEntityTable["2A8F"] = "lsimg"; gEntityTable["2A90"] = "gsiml"; gEntityTable["2A91"] = "lgE"; gEntityTable["2A92"] = "glE"; gEntityTable["2A93"] = "lesges"; gEntityTable["2A94"] = "gesles"; gEntityTable["2A97"] = "elsdot"; gEntityTable["2A98"] = "egsdot"; gEntityTable["2A99"] = "el"; gEntityTable["2A9A"] = "eg"; gEntityTable["2A9D"] = "siml"; gEntityTable["2A9E"] = "simg"; gEntityTable["2A9F"] = "simlE"; gEntityTable["2AA0"] = "simgE"; gEntityTable["2AA1"] = "LessLess"; gEntityTable["2AA2"] = "GreaterGreater"; gEntityTable["2AA4"] = "glj"; gEntityTable["2AA5"] = "gla"; gEntityTable["2AA6"] = "ltcc"; gEntityTable["2AA7"] = "gtcc"; gEntityTable["2AA8"] = "lescc"; gEntityTable["2AA9"] = "gescc"; gEntityTable["2AAA"] = "smt"; gEntityTable["2AAB"] = "lat"; gEntityTable["2AAC"] = "smte"; gEntityTable["2AAD"] = "late"; gEntityTable["2AAE"] = "bumpE"; gEntityTable["2AAF"] = "PrecedesEqual"; gEntityTable["2AB5"] = "precneqq"; gEntityTable["2AB6"] = "succneqq"; gEntityTable["2ABB"] = "Pr"; gEntityTable["2ABC"] = "Sc"; gEntityTable["2ABD"] = "subdot"; gEntityTable["2ABE"] = "supdot"; gEntityTable["2ABF"] = "subplus"; gEntityTable["2AC0"] = "supplus"; gEntityTable["2AC1"] = "submult"; gEntityTable["2AC2"] = "supmult"; gEntityTable["2AC3"] = "subedot"; gEntityTable["2AC4"] = "supedot"; gEntityTable["2AC7"] = "subsim"; gEntityTable["2AC8"] = "supsim"; gEntityTable["2ACF"] = "csub"; gEntityTable["2AD0"] = "csup"; gEntityTable["2AD1"] = "csube"; gEntityTable["2AD2"] = "csupe"; gEntityTable["2AD3"] = "subsup"; gEntityTable["2AD4"] = "supsub"; gEntityTable["2AD5"] = "subsub"; gEntityTable["2AD6"] = "supsup"; gEntityTable["2AD7"] = "suphsub"; gEntityTable["2AD8"] = "supdsub"; gEntityTable["2AD9"] = "forkv"; gEntityTable["2ADA"] = "topfork"; gEntityTable["2ADB"] = "mlcp"; gEntityTable["2AE4"] = "DoubleLeftTee"; gEntityTable["2AE6"] = "Vdashl"; gEntityTable["2AE7"] = "Barv"; gEntityTable["2AE8"] = "vBar"; gEntityTable["2AE9"] = "vBarv"; gEntityTable["2AEB"] = "Vbar"; gEntityTable["2AEC"] = "Not"; gEntityTable["2AED"] = "bNot"; gEntityTable["2AEE"] = "rnmid"; gEntityTable["2AEF"] = "cirmid"; gEntityTable["2AF0"] = "midcir"; gEntityTable["2AF1"] = "topcir"; gEntityTable["2AF2"] = "nhpar"; gEntityTable["2AF3"] = "parsim"; gEntityTable["300A"] = "Lang"; gEntityTable["300B"] = "Rang"; gEntityTable["3014"] = "lbbrk"; gEntityTable["3015"] = "rbbrk"; gEntityTable["3018"] = "lopar"; gEntityTable["3019"] = "ropar"; gEntityTable["301A"] = "LeftDoubleBracket"; gEntityTable["301B"] = "RightDoubleBracket"; gEntityTable["EEEE"] = "bne"; gEntityTable["EEEF"] = "bsolhsub"; gEntityTable["EEF0"] = "jmath"; gEntityTable["EEF1"] = "NegativeThickSpace"; gEntityTable["EEF2"] = "ThickSpace"; gEntityTable["EEF3"] = "NegativeThinSpace"; gEntityTable["EEF4"] = "NegativeVeryThinSpace"; gEntityTable["EEF5"] = "NegativeMediumSpace"; gEntityTable["EEF6"] = "planck"; gEntityTable["EEF7"] = "ShortLeftArrow"; gEntityTable["EEF8"] = "ShortRightArrow"; gEntityTable["EEF9"] = "nrarrw"; gEntityTable["EEFA"] = "npart"; gEntityTable["EEFB"] = "emptyset"; gEntityTable["EEFC"] = "notinva"; gEntityTable["EEFD"] = "smallsetminus"; gEntityTable["EEFE"] = "nang"; gEntityTable["EEFF"] = "shortmid"; gEntityTable["EF00"] = "nshortmid"; gEntityTable["EF01"] = "shortparallel"; gEntityTable["EF02"] = "nparsl"; gEntityTable["EF03"] = "nshortparallel"; gEntityTable["EF04"] = "caps"; gEntityTable["EF05"] = "cups"; gEntityTable["EF06"] = "thicksim"; gEntityTable["EF07"] = "nvsim"; gEntityTable["EF08"] = "NotEqualTilde"; gEntityTable["EF09"] = "thickapprox"; gEntityTable["EF0A"] = "nvap"; gEntityTable["EF0B"] = "napid"; gEntityTable["EF0C"] = "NotHumpDownHump"; gEntityTable["EF0D"] = "NotHumpEqual"; gEntityTable["EF0E"] = "nedot"; gEntityTable["EF0F"] = "bnequiv"; gEntityTable["EF10"] = "lvertneqq"; gEntityTable["EF11"] = "gvertneqq"; gEntityTable["EF12"] = "nLt"; gEntityTable["EF13"] = "NotLessLess"; gEntityTable["EF14"] = "nGt"; gEntityTable["EF15"] = "NotGreaterGreater"; gEntityTable["EF16"] = "NotLessEqual"; gEntityTable["EF17"] = "NotGreaterEqual"; gEntityTable["EF18"] = "NotSucceedsTilde"; gEntityTable["EF19"] = "suphsol"; gEntityTable["EF1A"] = "varsubsetneqq"; gEntityTable["EF1B"] = "varsupsetneqq"; gEntityTable["EF1C"] = "NotSquareSubset"; gEntityTable["EF1D"] = "NotSquareSuperset"; gEntityTable["EF1E"] = "sqcaps"; gEntityTable["EF1F"] = "sqcups"; gEntityTable["EF20"] = "nLl"; gEntityTable["EF21"] = "nGg"; gEntityTable["EF22"] = "lesg"; gEntityTable["EF23"] = "gesl"; gEntityTable["EF24"] = "nvltrie"; gEntityTable["EF25"] = "nvrtrie"; gEntityTable["EF26"] = "notindot"; gEntityTable["EF27"] = "ShortUpArrow"; gEntityTable["EF28"] = "ShortDownArrow"; gEntityTable["EF29"] = "NotNestedLessLess"; gEntityTable["EF2A"] = "NotNestedGreaterGreater"; gEntityTable["EF2B"] = "nrarrc"; gEntityTable["EF2C"] = "angrtvb"; gEntityTable["EF2D"] = "NotLeftTriangleBar"; gEntityTable["EF2E"] = "NotRightTriangleBar"; gEntityTable["EF2F"] = "ncongdot"; gEntityTable["EF30"] = "napE"; gEntityTable["EF31"] = "smtes"; gEntityTable["EF32"] = "lates"; gEntityTable["EF33"] = "NotPrecedesEqual"; gEntityTable["EF34"] = "NotSucceedsEqual"; gEntityTable["EF35"] = "Ascr"; gEntityTable["EF36"] = "Cscr"; gEntityTable["EF37"] = "Dscr"; gEntityTable["EF38"] = "Gscr"; gEntityTable["EF39"] = "Jscr"; gEntityTable["EF3A"] = "Kscr"; gEntityTable["EF3B"] = "Nscr"; gEntityTable["EF3C"] = "Oscr"; gEntityTable["EF3D"] = "Pscr"; gEntityTable["EF3E"] = "Qscr"; gEntityTable["EF3F"] = "Sscr"; gEntityTable["EF40"] = "Tscr"; gEntityTable["EF41"] = "Uscr"; gEntityTable["EF42"] = "Vscr"; gEntityTable["EF43"] = "Wscr"; gEntityTable["EF44"] = "Xscr"; gEntityTable["EF45"] = "Yscr"; gEntityTable["EF46"] = "Zscr"; gEntityTable["EF47"] = "ascr"; gEntityTable["EF48"] = "bscr"; gEntityTable["EF49"] = "cscr"; gEntityTable["EF4A"] = "dscr"; gEntityTable["EF4B"] = "fscr"; gEntityTable["EF4C"] = "hscr"; gEntityTable["EF4D"] = "iscr"; gEntityTable["EF4E"] = "jscr"; gEntityTable["EF4F"] = "kscr"; gEntityTable["EF50"] = "mscr"; gEntityTable["EF51"] = "nscr"; gEntityTable["EF52"] = "pscr"; gEntityTable["EF53"] = "qscr"; gEntityTable["EF54"] = "rscr"; gEntityTable["EF55"] = "sscr"; gEntityTable["EF56"] = "tscr"; gEntityTable["EF57"] = "uscr"; gEntityTable["EF58"] = "vscr"; gEntityTable["EF59"] = "wscr"; gEntityTable["EF5A"] = "xscr"; gEntityTable["EF5B"] = "yscr"; gEntityTable["EF5C"] = "zscr"; gEntityTable["EF5D"] = "Afr"; gEntityTable["EF5E"] = "Bfr"; gEntityTable["EF5F"] = "Dfr"; gEntityTable["EF60"] = "Efr"; gEntityTable["EF61"] = "Ffr"; gEntityTable["EF62"] = "Gfr"; gEntityTable["EF63"] = "Jfr"; gEntityTable["EF64"] = "Kfr"; gEntityTable["EF65"] = "Lfr"; gEntityTable["EF66"] = "Mfr"; gEntityTable["EF67"] = "Nfr"; gEntityTable["EF68"] = "Ofr"; gEntityTable["EF69"] = "Pfr"; gEntityTable["EF6A"] = "Qfr"; gEntityTable["EF6B"] = "Sfr"; gEntityTable["EF6C"] = "Tfr"; gEntityTable["EF6D"] = "Ufr"; gEntityTable["EF6E"] = "Vfr"; gEntityTable["EF6F"] = "Wfr"; gEntityTable["EF70"] = "Xfr"; gEntityTable["EF71"] = "Yfr"; gEntityTable["EF72"] = "afr"; gEntityTable["EF73"] = "bfr"; gEntityTable["EF74"] = "cfr"; gEntityTable["EF75"] = "dfr"; gEntityTable["EF76"] = "efr"; gEntityTable["EF77"] = "ffr"; gEntityTable["EF78"] = "gfr"; gEntityTable["EF79"] = "hfr"; gEntityTable["EF7A"] = "ifr"; gEntityTable["EF7B"] = "jfr"; gEntityTable["EF7C"] = "kfr"; gEntityTable["EF7D"] = "lfr"; gEntityTable["EF7E"] = "mfr"; gEntityTable["EF7F"] = "nfr"; gEntityTable["EF80"] = "ofr"; gEntityTable["EF81"] = "pfr"; gEntityTable["EF82"] = "qfr"; gEntityTable["EF83"] = "rfr"; gEntityTable["EF84"] = "sfr"; gEntityTable["EF85"] = "tfr"; gEntityTable["EF86"] = "ufr"; gEntityTable["EF87"] = "vfr"; gEntityTable["EF88"] = "wfr"; gEntityTable["EF89"] = "xfr"; gEntityTable["EF8A"] = "yfr"; gEntityTable["EF8B"] = "zfr"; gEntityTable["EF8C"] = "Aopf"; gEntityTable["EF8D"] = "Bopf"; gEntityTable["EF8E"] = "Dopf"; gEntityTable["EF8F"] = "Eopf"; gEntityTable["EF90"] = "Fopf"; gEntityTable["EF91"] = "Gopf"; gEntityTable["EF92"] = "Iopf"; gEntityTable["EF93"] = "Jopf"; gEntityTable["EF94"] = "Kopf"; gEntityTable["EF95"] = "imped"; gEntityTable["EF96"] = "Mopf"; gEntityTable["EF97"] = "Oopf"; gEntityTable["EF98"] = "Sopf"; gEntityTable["EF99"] = "Topf"; gEntityTable["EF9A"] = "Uopf"; gEntityTable["EF9B"] = "Vopf"; gEntityTable["EF9C"] = "Wopf"; gEntityTable["EF9D"] = "Xopf"; gEntityTable["EF9E"] = "Yopf"; gEntityTable["EF9F"] = "aopf"; gEntityTable["EFA0"] = "bopf"; gEntityTable["EFA1"] = "copf"; gEntityTable["EFA2"] = "dopf"; gEntityTable["EFA3"] = "eopf"; gEntityTable["EFA4"] = "fopf"; gEntityTable["EFA5"] = "gopf"; gEntityTable["EFA6"] = "hopf"; gEntityTable["EFA7"] = "iopf"; gEntityTable["EFA8"] = "jopf"; gEntityTable["EFA9"] = "kopf"; gEntityTable["EFAA"] = "lopf"; gEntityTable["EFAB"] = "mopf"; gEntityTable["EFAC"] = "nopf"; gEntityTable["EFAD"] = "oopf"; gEntityTable["EFAE"] = "popf"; gEntityTable["EFAF"] = "qopf"; gEntityTable["EFB0"] = "ropf"; gEntityTable["EFB1"] = "sopf"; gEntityTable["EFB2"] = "topf"; gEntityTable["EFB3"] = "uopf"; gEntityTable["EFB4"] = "vopf"; gEntityTable["EFB5"] = "wopf"; gEntityTable["EFB6"] = "xopf"; gEntityTable["EFB7"] = "yopf"; gEntityTable["EFB8"] = "zopf"; gEntityTable["F558"] = "loang"; gEntityTable["F559"] = "roang"; gEntityTable["F576"] = "LongLeftArrow"; gEntityTable["F577"] = "LongRightArrow"; gEntityTable["F578"] = "LongLeftRightArrow"; gEntityTable["F579"] = "DoubleLongLeftArrow"; gEntityTable["F57A"] = "DoubleLongRightArrow"; gEntityTable["F57B"] = "DoubleLongLeftRightArrow"; gEntityTable["F57D"] = "longmapsto"; gEntityTable["F59B"] = "FilledVerySmallSquare"; gEntityTable["F59C"] = "EmptyVerySmallSquare"; gEntityTable["F5A2"] = "dzigrarr"; gEntityTable["FB00"] = "fflig"; gEntityTable["FB01"] = "filig"; gEntityTable["FB02"] = "fllig"; gEntityTable["FB03"] = "ffilig"; gEntityTable["FB04"] = "ffllig"; gEntityTable["FE35"] = "OverParenthesis"; gEntityTable["FE36"] = "UnderParenthesis"; gEntityTable["FE37"] = "OverBrace"; gEntityTable["FE38"] = "UnderBrace"; gEntityTable["FEFF"] = "NoBreak"; function unicode2entity(text) { var str = ''; for (var i = 0; i < text.length; i++) { var c = text.charCodeAt(i); if (c < 0x7F) { if (text[i] == '<') str += '&lt;'; else if (text[i] == '>') str += '&gt;'; else str += text[i]; } else { var unichar = c.toString(16).toUpperCase(); while (unichar.length < 4) unichar = '0' + unichar; if (unichar in gEntityTable) str += '&' + gEntityTable[unichar] + ';'; else str += '&#x' + unichar + ';'; } } return str; } populations-1.2.33+svn0120106.orig/html/libjs/viewmath.js0000644000175000017500000001223410621075553023105 0ustar georgeskgeorgesk/* * The contents of this file are subject to the Mozilla Public * License Version 1.1 (the"License"); you may not use this file * except in compliance with the License. You may obtain a copy of * the License at http://www.mozilla.org/MPL/ * * Software distributed under the License is distributed on an"AS * IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or * implied. See the License for the specific language governing * rights and limitations under the License. * * The Original Code is Mozilla MathML Project. * * The Initial Developer of the Original Code is The University Of * Queensland. Portions created by The University Of Queensland are * Copyright (C) 2002 The University Of Queensland. All Rights Reserved. * * Contributor(s): * Roger B. Sidje * Steve Swanson * */ var gDebug = 0; var gLineCount = 0; var gStartTargetLine = 0; var gEndTargetLine = 0; var gTargetNode = null; var gWYSIWYGWindow = null; // had to use an absolute path here, otherwise Mozilla is confused when the // script is loaded from a directory different from where the CSS resides var gViewSourceCSS = 'http://www.mozilla.org/projects/mathml/demo/viewsource.css'; function viewmath(evt) { evt.preventBubble(); gLineCount = 0; gStartTargetLine = 0; gEndTargetLine = 0; gTargetNode = evt.target; if (gTargetNode.nodeType == Node.TEXT_NODE) { // leaf text gTargetNode = gTargetNode.parentNode; } var m = findmathparent(evt.target); if (m) { gWYSIWYGWindow = open("", "wysiwyg", "scrollbars=1,resizable=1,width=500,height=200"); gWYSIWYGWindow.document.open(); with (gWYSIWYGWindow.document) { writeln(''); writeln('MathML WYSIWYG Source'); writeln(''); writeln(''); writeln(''); writeln(''); write(''); //if wrapping... write(''); write('
');
      writeln(getOuterMarkup(m,0));
      writeln('
'); } gWYSIWYGWindow.document.close(); } } function findmathparent(node) { while (node && node.nodeName.indexOf("math") == -1) node = node.parentNode; return node; } function getInnerMarkup(n, indent) { var str = ''; for (var i = 0; i... newline = ''; if (gLineCount > 0) { newline = '\n'; } if (gLineCount == gStartTargetLine || gLineCount == gEndTargetLine) { newline = ''; } gLineCount++; if (gDebug) { newline += gLineCount; } for (var k=0; k' + n.nodeName + ''; for (var i=0; i' + n.nodeName + '>'; break; case Node.TEXT_NODE: // Text var tmp = n.nodeValue; tmp = tmp.toString(); tmp = tmp.replace(/(\n|\r|\t)+/g, " "); tmp = tmp.replace(/\s+/," "); tmp = tmp.replace(/^\s+/, ""); tmp = tmp.replace(/\s+$/,""); if (tmp.length != 0) { str += '' + unicode2entity(tmp) + ''; } break; default: break; } if (n == gTargetNode) { gEndTargetLine = gLineCount; str += '
';
  }
  return str;
}
populations-1.2.33+svn0120106.orig/.cdtproject0000644000175000017500000000420311071406470021007 0ustar  georgeskgeorgesk























































populations-1.2.33+svn0120106.orig/INSTALL0000644000175000017500000001547211071406470017710 0ustar  georgeskgeorgeskBasic Installation
==================

   These are generic installation instructions.

   The `configure' shell script attempts to guess correct values for
various system-dependent variables used during compilation.  It uses
those values to create a `Makefile' in each directory of the package.
It may also create one or more `.h' files containing system-dependent
definitions.  Finally, it creates a shell script `config.status' that
you can run in the future to recreate the current configuration, a file
`config.cache' that saves the results of its tests to speed up
reconfiguring, and a file `config.log' containing compiler output
(useful mainly for debugging `configure').

   If you need to do unusual things to compile the package, please try
to figure out how `configure' could check whether to do them, and mail
diffs or instructions to the address given in the `README' so they can
be considered for the next release.  If at some point `config.cache'
contains results you don't want to keep, you may remove or edit it.

   The file `configure.in' is used to create `configure' by a program
called `autoconf'.  You only need `configure.in' if you want to change
it or regenerate `configure' using a newer version of `autoconf'.

The simplest way to compile this package is:

  1. `cd' to the directory containing the package's source code and type
     `./configure' to configure the package for your system.  If you're
     using `csh' on an old version of System V, you might need to type
     `sh ./configure' instead to prevent `csh' from trying to execute
     `configure' itself.

     Running `configure' takes a while.  While running, it prints some
     messages telling which features it is checking for.

  2. Type `make' to compile the package.

  3. Type `make install' to install the programs and any data files and
     documentation.

  4. You can remove the program binaries and object files from the
     source code directory by typing `make clean'.  

Compilers and Options
=====================

   Some systems require unusual options for compilation or linking that
the `configure' script does not know about.  You can give `configure'
initial values for variables by setting them in the environment.  Using
a Bourne-compatible shell, you can do that on the command line like
this:
     CC=c89 CFLAGS=-O2 LIBS=-lposix ./configure

Or on systems that have the `env' program, you can do it like this:
     env CPPFLAGS=-I/usr/local/include LDFLAGS=-s ./configure

Compiling For Multiple Architectures
====================================

   You can compile the package for more than one kind of computer at the
same time, by placing the object files for each architecture in their
own directory.  To do this, you must use a version of `make' that
supports the `VPATH' variable, such as GNU `make'.  `cd' to the
directory where you want the object files and executables to go and run
the `configure' script.  `configure' automatically checks for the
source code in the directory that `configure' is in and in `..'.

   If you have to use a `make' that does not supports the `VPATH'
variable, you have to compile the package for one architecture at a time
in the source code directory.  After you have installed the package for
one architecture, use `make distclean' before reconfiguring for another
architecture.

Installation Names
==================

   By default, `make install' will install the package's files in
`/usr/local/bin', `/usr/local/man', etc.  You can specify an
installation prefix other than `/usr/local' by giving `configure' the
option `--prefix=PATH'.

   You can specify separate installation prefixes for
architecture-specific files and architecture-independent files.  If you
give `configure' the option `--exec-prefix=PATH', the package will use
PATH as the prefix for installing programs and libraries.
Documentation and other data files will still use the regular prefix.

   If the package supports it, you can cause programs to be installed
with an extra prefix or suffix on their names by giving `configure' the
option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.

Optional Features
=================

   Some packages pay attention to `--enable-FEATURE' options to
`configure', where FEATURE indicates an optional part of the package.
They may also pay attention to `--with-PACKAGE' options, where PACKAGE
is something like `gnu-as' or `x' (for the X Window System).  The
`README' should mention any `--enable-' and `--with-' options that the
package recognizes.

   For packages that use the X Window System, `configure' can usually
find the X include and library files automatically, but if it doesn't,
you can use the `configure' options `--x-includes=DIR' and
`--x-libraries=DIR' to specify their locations.

Specifying the System Type
==========================

   There may be some features `configure' can not figure out
automatically, but needs to determine by the type of host the package
will run on.  Usually `configure' can figure that out, but if it prints
a message saying it can not guess the host type, give it the
`--host=TYPE' option.  TYPE can either be a short name for the system
type, such as `sun4', or a canonical name with three fields:
     CPU-COMPANY-SYSTEM

See the file `config.sub' for the possible values of each field.  If
`config.sub' isn't included in this package, then this package doesn't
need to know the host type.

   If you are building compiler tools for cross-compiling, you can also
use the `--target=TYPE' option to select the type of system they will
produce code for and the `--build=TYPE' option to select the type of
system on which you are compiling the package.

Sharing Defaults
================

   If you want to set default values for `configure' scripts to share,
you can create a site shell script called `config.site' that gives
default values for variables like `CC', `cache_file', and `prefix'.
`configure' looks for `PREFIX/share/config.site' if it exists, then
`PREFIX/etc/config.site' if it exists.  Or, you can set the
`CONFIG_SITE' environment variable to the location of the site script.
A warning: not all `configure' scripts look for a site script.

Operation Controls
==================

   `configure' recognizes the following options to control how it
operates.

`--cache-file=FILE'
     Use and save the results of the tests in FILE instead of
     `./config.cache'.  Set FILE to `/dev/null' to disable caching, for
     debugging `configure'.

`--help'
     Print a summary of the options to `configure', and exit.

`--quiet'
`--silent'
`-q'
     Do not print messages saying which checks are being made.

`--srcdir=DIR'
     Look for the package's source code in directory DIR.  Usually
     `configure' can determine that directory automatically.

`--version'
     Print the version of Autoconf used to generate the `configure'
     script, and exit.

`configure' also accepts some other, not widely useful, options.

populations-1.2.33+svn0120106.orig/COPYING0000644000175000017500000010451311601277303017705 0ustar  georgeskgeorgesk                    GNU GENERAL PUBLIC LICENSE
                       Version 3, 29 June 2007

 Copyright (C) 2007 Free Software Foundation, Inc. 
 Everyone is permitted to copy and distribute verbatim copies
 of this license document, but changing it is not allowed.

                            Preamble

  The GNU General Public License is a free, copyleft license for
software and other kinds of works.

  The licenses for most software and other practical works are designed
to take away your freedom to share and change the works.  By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users.  We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors.  You can apply it to
your programs, too.

  When we speak of free software, we are referring to freedom, not
price.  Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
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  For example, if you distribute copies of such a program, whether
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  Developers that use the GNU GPL protect your rights with two steps:
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.
populations-1.2.33+svn0120106.orig/README0000644000175000017500000000061611601277303017531 0ustar  georgeskgeorgesk#  Description : "populations" is a population genetics software
#
#
#  Copyright   : Olivier Langella
#
#  License     : GPLv3
#
#   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 3 of the License, or     *
#   (at your option) any later version.
populations-1.2.33+svn0120106.orig/.cproject0000644000175000017500000000500211254645447020471 0ustar  georgeskgeorgesk






























































populations-1.2.33+svn0120106.orig/.settings/0000755000175000017500000000000011701602133020556 5ustar  georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/.settings/org.eclipse.cdt.core.prefs0000644000175000017500000000015011254645447025547 0ustar  georgeskgeorgesk#Thu Apr 30 23:49:32 CEST 2009
eclipse.preferences.version=1
indexerId=org.eclipse.cdt.core.fastIndexer
populations-1.2.33+svn0120106.orig/src/0000755000175000017500000000000011701605003017426 5ustar  georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/src/couleur.h0000644000175000017500000000533510531115342021265 0ustar  georgeskgeorgesk/***************************************************************************
                          couleur.h  -  description
                             -------------------
    begin                : Mon Jun 4 2001
    copyright            : (C) 2001 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#ifndef COULEUR_H
#define COULEUR_H


/**stockage de couleur (RGB ou nom en Anglais)
  *@author Olivier Langella
  */
#include "vecteurs.h"

//typedef biolib::vecteurs::ChaineCar ChaineCar;

class Couleur {
public:

	static const string & get_couleur_diff();

	Couleur(const biolib::vecteurs::ChaineCar & couleur);
	Couleur(unsigned long rouge, unsigned long vert, unsigned long bleu);
	~Couleur();

//	void set_rgb(unsigned long rouge, unsigned long vert, unsigned long bleu);

	bool EstNom() const {return(_boolnom);};
	bool EstRGB() const {return(_boolrgb);};

	void set_nom(const char * nom) {_boolrgb = false; _boolnom = true; _nom.assign(nom);};
	const string & get_nom() const {return(_nom);};
	unsigned long get_rouge() const {return(_rouge);};
	unsigned long get_vert() const {return(_vert);};
	unsigned long get_bleu() const {return(_bleu);};


	bool operator== (const Couleur &rval) const;

protected:

	static void f_rempli_tab_couleurs();

	static vector _tab_couleurs;
	static unsigned int _pos_tab_couleurs;

	bool _boolrgb;
	bool _boolnom;

	string _nom;

	unsigned long _rouge;
	unsigned long _vert;
	unsigned long _bleu;

	
};

//unsigned int Couleur::_pos_tab_couleurs = 0;
/*
inline const string & Couleur::get_couleur_diff() {
	unsigned int i;

	if ( Couleur::_tab_couleurs.size() == 0 ) Couleur::f_rempli_tab_couleurs();
	i = Couleur::_pos_tab_couleurs;
	Couleur::_pos_tab_couleurs++;
	if (Couleur::_pos_tab_couleurs == Couleur::_tab_couleurs.size()) Couleur::_pos_tab_couleurs = 0;

	return (Couleur::_tab_couleurs[i]);
}
*/
/*
inline void Couleur::f_rempli_tab_couleurs() {
	_pos_tab_couleurs = 0;

	_tab_couleurs.push_back("red");
	_tab_couleurs.push_back("green");
	_tab_couleurs.push_back("blue");

}
*/
#endif


populations-1.2.33+svn0120106.orig/src/distgnt.cpp0000644000175000017500000020170511327002100021604 0ustar  georgeskgeorgesk
/***************************************************************************
                          distgnt.cpp -  Librairie d'objets permettant de manipuler
                          des distances entre populations
                             -------------------
    begin                : ven sep 01 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/
#include "distgnt.h"
#include "arbreplus.h"


vector DistancesGnt::_tab_noms_methodes;

DistancesGnt::DistancesGnt(int methode, bool square_distance, Jeupop * Pjeupop, unsigned int niveau) {
//cerr << "DistancesGnt::DistancesGnt debut" << endl;
	unsigned long j;

	_methode = methode;
	_Pjeupop = Pjeupop;

	if ((niveau == 100) & (Pjeupop->_VcalcStrucPop.size() >0)) {
		//stuct pop level is already defined
	}
	else {Pjeupop->f_rempliVcalcStrucPop(niveau);
	}

	_tabPstrucpop = Pjeupop->_VcalcStrucPop;

	_tabPloc = Pjeupop->_tabPloc;
	_nbpop = Pjeupop->get_nbstrucpopVcalc();
	_PtabFreq = 0;
	_PtabMu = 0;
	_tabEviteLocus = 0;
 	_squareDistance = square_distance;
	_pi = ((long double) acos((double)-1));
//	_tabNbAll = 0;

	_nbloc = Pjeupop->get_nbloc();
	_tabNbAll = new unsigned long [_nbloc];

	_bootind = false;

	for (j=0; j < _nbloc; j++) {
		_tabNbAll[j] = _tabPloc[j]->get_nball();
	}
//cerr << "DistancesGnt::DistancesGnt fin" << endl;
}

DistancesGnt::~DistancesGnt() {
	if (_tabNbAll != 0)	delete[] _tabNbAll;
	if (_PtabFreq != 0) {
		delete[] _PtabFreq[0];
		delete[] _PtabFreq;
	}
	if (_PtabMu != 0) {
		delete[] _PtabMu;
	}
	if (_tabEviteLocus != 0) delete[] _tabEviteLocus;

//	_nbloc = Pjeupop->get_nbloc();
}

long double DistancesGnt::r_allsimilnul(Individu * pind1, Individu * pind2) const{
	//Calcul de la similarit� entre deux individus
	//valable pour nploides
	Vecteur tabPall1;//, tabPallNuls;
	long pos;//, nballnuls(0);
	unsigned long allele, taille, nb_all_communs(0);
	unsigned long j, i;
	unsigned long nploidie(_Pjeupop->get_nploidie());
	unsigned long nb_all_comparables(0);
	unsigned long nblocus(_VcalcLocus.size());

	taille = nblocus * nploidie;

	for (j = 0 ; j < nblocus; j++) {
		i = pind1->get_nballnuls(_VcalcLocus[j]);
		if (pind2->get_nballnuls(_VcalcLocus[j]) > i) i = pind2->get_nballnuls(_VcalcLocus[j]);
		nb_all_comparables += nploidie - i;
	}
	if (nb_all_comparables == 0) {	
		throw Jeupop::Anomalie(6);
		return (0);
	}

//cerr << nb_all_comparables << " ";

	for (j = 0 ; j < nblocus; j++) {
		for (i = 0; i < nploidie; i++) {
			allele = (_VcalcLocus[j] * nploidie) + i;
			if (pind1->_tabPall[allele]->_miss) {}
			else tabPall1.push_back(pind1->_tabPall[allele]);
		}
	}

//cerr << pind1->get_nom() << " " << pind2->get_nom() << endl;
	for (j = 0 ; j < nblocus; j++) {
		for (i = 0; i < nploidie; i++) {
			allele = (_VcalcLocus[j] * nploidie) + i;
			if (pind2->_tabPall[allele]->_miss) {}
			else {
				pos = tabPall1.Position(pind2->_tabPall[allele]);
				if (pos != -1) {
//					cerr << pind2->_tabPall[allele]->get_Nom() << " " << tabPall1[pos]->get_Nom() << endl;

					nb_all_communs++;
					tabPall1.Suppr(pos);	
				}
			}
		}
	}
//cerr << nb_all_communs << " " << nb_all_comparables << endl;
	return ((long double) nb_all_communs / (long double) nb_all_comparables);
}

long double DistancesGnt::r_dist2ind(unsigned long nbind1, unsigned long nbind2) const {
	//renvoi de la distance
	long double resultat(0);
//	int Smoy(get_nbloc()), nball;
//	int nbloc(get_nbloc());
//	long i;

	switch (_methode) {
	case 5:
		//methode simple correct: moyenne de ressemblance
		//sur population nploide
		// 0 allele en commun => 1
		// 1 allele en commun => 0.5
		// 2 alleles en commun => 0
		// ne fait pas de calcul sur les all�les 00 && 00
		// applique 0.5 pour 0001 avec 0101 ou 0103
		//     et  0 pour 0001 avec 0302
// ATTENTION pour les donn�es manquantes: la similitude est maximisee
		resultat = (double) 1 - (double) r_allsimilnul(_tabPind[nbind1], _tabPind[nbind2]);
//cerr << r_allsimilnul(pind1, pind2) << endl;
		break;
	default:
		resultat = r_dist2pop(nbind1, nbind2);
		break;
	}

	return resultat;
}

long double DistancesGnt::r_distDasPsAi(unsigned long nbind1, unsigned long nbind2) const {
	return (r_distDasPsAi(_tabPind[nbind1], _tabPind[nbind2]));
}

long double DistancesGnt::r_distDasPsAi(const Individu * Pind1, const Individu * Pind2) const {
	//Calcul de la similarit� entre deux individus (Das)
	//valable pour nploides
	Vecteur tabPall1;//, tabPallNuls;
	long pos;//, nballnuls(0);
	unsigned long allele, taille, nb_all_communs(0);
	unsigned long j, i;
	unsigned long nploidie(_Pjeupop->get_nploidie());
	unsigned long nb_all_comparables(0);
	unsigned long nblocus(_VcalcLocus.size());

	taille = nblocus * nploidie;

	for (j = 0 ; j < nblocus; j++) {
		i = Pind1->get_nballnuls(_VcalcLocus[j]);
		if (Pind2->get_nballnuls(_VcalcLocus[j]) > i) i = Pind2->get_nballnuls(_VcalcLocus[j]);
		nb_all_comparables += nploidie - i;
	}
	if (nb_all_comparables == 0) {	
		throw Jeupop::Anomalie(6);
		return (0);
	}

//cerr << nb_all_comparables << " ";

	for (j = 0 ; j < nblocus; j++) {
		for (i = 0; i < nploidie; i++) {
			allele = (_VcalcLocus[j] * nploidie) + i;
			if (Pind1->_tabPall[allele]->_miss) {}
			else tabPall1.push_back(Pind1->_tabPall[allele]);
		}
	}

//cerr << pind1->get_nom() << " " << pind2->get_nom() << endl;
	for (j = 0 ; j < nblocus; j++) {
		for (i = 0; i < nploidie; i++) {
			allele = (_VcalcLocus[j] * nploidie) + i;
			if (Pind2->_tabPall[allele]->_miss) {}
			else {
				pos = tabPall1.Position(Pind2->_tabPall[allele]);
				if (pos != -1) {
//					cerr << pind2->_tabPall[allele]->get_Nom() << " " << tabPall1[pos]->get_Nom() << endl;

					nb_all_communs++;
					tabPall1.Suppr(pos);	
				}
			}
		}
	}
//cerr << nb_all_communs << " " << nb_all_comparables << endl;
	return ((long double) nb_all_communs / (long double) nb_all_comparables);
}


long double DistancesGnt::r_dist2ind(Individu* Pind1, Individu* Pind2) const {
	//renvoi de la distance
	long double resultat(0);

	switch (_methode) {
	case 5:
		//methode simple correct: moyenne de ressemblance
		//sur population nploide
		// 0 allele en commun => 1
		// 1 allele en commun => 0.5
		// 2 alleles en commun => 0
		// ne fait pas de calcul sur les all�les 00 && 00
		// applique 0.5 pour 0001 avec 0101 ou 0103
		//     et  0 pour 0001 avec 0302
// ATTENTION pour les donn�es manquantes: la similitude est maximisee
		resultat = (double) 1 - (double) r_allsimilnul(Pind1,Pind2);
//cerr << r_allsimilnul(pind1, pind2) << endl;
		break;
	}

	return resultat;
}

void DistancesGnt::newTabFreq() {
	//calcul et stockage des frequences alleliques
	// tabPfreq contient les adresses de tableaux de frequences
	// tabNbAll contient le nombre d'alleles a chaque locus
	// _tabEviteLocus contient les locus � �viter (qui ne contiennent que des all�les nuls)

	unsigned long i, j;
	unsigned long indice(0);

//cerr << "coucou newTabFreq" < * PVcalcLocusRef, bool sur_ind) {
	// Boostrap sur les locus
	// ********creer des exceptions pour v�rifier l'arbreRef *********
	unsigned long i, j;
	unsigned int tirage;
	MatriceLD distancesRef;
	unsigned long nbLocus(PVcalcLocusRef->size());
	Arbre bootArbre;
	MatriceLD distancesBoot;
	unsigned long taillemat;

// calcul de l'arbre de r�f�rence arbreRef
//	arbreRef => arbre vide !!!
//ofstream sortie_test;
//sortie_test.open("test_boot", ios::out);


cerr << "distances ref:";
	if (sur_ind) f_distgntInd(distancesRef, PVcalcLocusRef);
	else f_distgntpop(distancesRef, PVcalcLocusRef);
cerr << "+"<< endl;

cerr << "arbre ref:";
	arbreRef.f_forceiDistances(distancesRef,methodeArbre);
//	arbreRef.iDistances(distancesRef,methodeArbre);
cerr << "+"<< endl;
	//_tabPOtu de arbre est cree avec les titres des lignes 
	//    de la matrice, dans le meme ordre
//cerr << "sortie du fichier" << endl;
//sortie_test << arbreRef << endl;


	srand ((unsigned) time( NULL ) );

	taillemat = distancesRef.GetNC();
	distancesBoot.resize(taillemat, taillemat);
	distancesBoot.SetType(2);
	distancesBoot.SetFlag(1);
	for (j = 0; j < taillemat; j++) {
		distancesBoot._tcol[j] = distancesBoot._tlig[j] = distancesRef._tcol[j];
	}
//cerr << distancesBoot._tcol[1] << endl;
//cerr << distancesRef._tcol[1] << endl;

//	arbreRef.fRempliTabNumOtusNoeuds();
//	arbreRef.f_load_vectind();
	arbreRef.f_load_vect_id_ind();

	for (i = 0; i < nbrepet; i ++ ) { //boucle du bootstrap

cerr <operator[](tirage);
		}

cerr < * PVcalcLocusRef) {
	// Boostrap sur les individus
	// ********creer des exceptions pour v�rifier l'arbreRef *********
	unsigned long i, j;
	MatriceLD distancesRef;
	Arbre bootArbre;
	MatriceLD distancesBoot;

// calcul de l'arbre de r�f�rence arbreRef
//	arbreRef => arbre vide !!!
	_bootind = false;

cerr << "distances ref:";
	f_distgntpop(distancesRef, PVcalcLocusRef);
cerr << "+"<< endl;

cerr << "arbre ref:";
	arbreRef.f_forceiDistances(distancesRef,methodeArbre);
//	bootArbre.iDistances(distancesRef,methodeArbre);
cerr << "+"<< endl;
	//_tabPOtu de arbre est cree avec les titres des lignes
	//    de la matrice, dans le meme ordre


	srand ((unsigned) time( NULL ) );
	_bootind = true;

	distancesBoot.resize(_nbpop, _nbpop);
	distancesBoot.SetType(2);
	distancesBoot.SetFlag(1);
	for (j = 0; j < _nbpop; j++) {
		distancesBoot._tcol[j] = distancesBoot._tlig[j] = _tabPstrucpop[j]->get_nom();
	}
//cerr << distancesBoot._tcol[1] << endl;
//cerr << distancesRef._tcol[1] << endl;

//	arbreRef.fRempliTabNumOtusNoeuds();
//cerr << "DistancesGnt::f_bootstrapIndividus top1" < *PVcalcLocus) {
	//distances G�n�tiques entre Populations
	unsigned long i;
// pr�paration de _VcalcLoc:
	_VcalcLocus = *PVcalcLocus;

	biolib::vecteurs::ChaineCar mot;

	resultat.resize(_nbpop, _nbpop);
	resultat._titre.push_back(_("Genetic distances on "));
	mot.AjEntier(_nbpop);
	
	resultat._titre[resultat._titre.size() - 1] += mot;
	resultat._titre[resultat._titre.size() - 1] += " populations";

	resultat._titre.push_back(get_nom_methode(_methode));
	if (_squareDistance) resultat._titre[resultat._titre.size() - 1] += _(" (squared distances)");

	switch (_methode) {
	case 5:
		break;
	case 101:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	case 102:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	case 103:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	case 104:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	case 106:
		// stockage des Mu
		newTabMu();
		f_calcTabMu();
		break;
	case 107:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	case 108:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	case 109:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	case 110:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	case 111:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	case 112:
		// stockage des Mu
		newTabMu();
		f_calcTabMu();
		break;
	case 113:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	case 114:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	case 115:
		// stockage des fr�quences
		newTabFreq();
		f_calcTabFreq();
		break;
	default:
		break;
	}
	resultat.SetType(2);
	resultat.SetFlag(1); //titres sur les lignes

	for (i = 0; i < _nbpop; i++) {
		resultat._tcol[i] = resultat._tlig[i] = _tabPstrucpop[i]->get_nom();
	}

	f_distgntpopVcalc (resultat._tab);
//	try {
//		f_distgntpopVcalc (resultat._tab);
//	}
//	catch (Anomalie lepb) {
//		cerr << endl << lepb.fmessage(lepb.le_pb) << endl;
//	}
}

void DistancesGnt::f_distgntInd (MatriceLD &resultat, Vecteur *PVcalcLocus) {
//	_VcalcLocus.resize(PVcalcLocus->size());
	_VcalcLocus = *PVcalcLocus;

//cerr << "f_distgntIndVcalc deb" << endl;

	unsigned long i, k, nbind; //(_Pjeupop->get_nbind());
	unsigned long j;
	biolib::vecteurs::ChaineCar mot;
	//vector tabPind;
	nbind = get_nbind();

	_tabPind.resize(nbind);
	
	resultat.resize(nbind, nbind);
	resultat._titre.push_back(_("Genetic distances on "));
	resultat._titre[resultat._titre.size() - 1].AjEntier(nbind); // += mot;
	resultat._titre[resultat._titre.size() - 1] += _(" individuals");

	resultat._titre.push_back(get_nom_methode(_methode));
	if (_squareDistance) resultat._titre[resultat._titre.size() - 1] += _(" (squared distances)");
	
 	resultat.SetType(2);
	resultat.SetFlag(1); //titres sur les lignes

	k=0;
	for (i = 0; i < _nbpop; i++) {
		for (j = 0; j < _tabPstrucpop[i]->get_nbind(); j++) {
			mot.assign(_tabPstrucpop[i]->_tabPind[j]->_nom);
//			mot.AjEntier(i+1);
//			mot += '_';
//			mot += _tabPstrucpop[i]->_tabPind[j]->_nom;
			resultat._tlig[k] = mot;
			resultat._tcol[k] = mot;
			_tabPind[k] = _tabPstrucpop[i]->_tabPind[j];
			k++;
		}
	}

	resultat._titre.push_back(get_nom_methode(_methode));
	switch (_methode) {
	case 5:
		break;
	case 101:
		// stockage des fr�quences
		newTabFreqInd();
		f_calcTabFreqInd();
		break;
	case 102:
		// stockage des fr�quences
		newTabFreqInd();
		f_calcTabFreqInd();
		break;
	case 103:
		// stockage des fr�quences
		newTabFreqInd();
		f_calcTabFreqInd();
		break;
	case 104:
		// stockage des fr�quences
		newTabFreqInd();
		f_calcTabFreqInd();
		break;
	case 106:
		// stockage des Mu
		newTabMuInd();
		f_calcTabMuInd();
		break;
	case 107:
		// stockage des fr�quences
		newTabFreqInd();
		f_calcTabFreqInd();
		break;
	case 108:
		// stockage des fr�quences
		newTabFreqInd();
		f_calcTabFreqInd();
		break;
	case 109:
		// stockage des fr�quences
		newTabFreqInd();
		f_calcTabFreqInd();
		break;
	case 110:
		// stockage des fr�quences
		newTabFreqInd();
		f_calcTabFreqInd();
		break;
	case 111:
		// stockage des fr�quences
		newTabFreqInd();
		f_calcTabFreqInd();
		break;
	case 112:
		// stockage des Mu
		newTabMuInd();
		f_calcTabMuInd();
		break;
	case 113:
		throw Anomalie(4, get_nom_methode(13));
		break;
	case 114:
		throw Anomalie(4, get_nom_methode(14));
		break;
	case 115:
		throw Anomalie(4, get_nom_methode(15));
		break;
	default:
		break;
	}
	resultat.SetType(2);
	resultat.SetFlag(1); //titres sur les lignes

	f_distgntIndVcalc (resultat._tab);
}

void DistancesGnt::f_distgntpopDas(long double * Ptab) const {
	// calcul de distance g�n�tique avec la Das entre Populations
	// combinaison des individus entre les 2 pops (moyPsAB),
	//   combinaison des individus dans la pop1 (moyPsA1),
	//   combinaison des individus dans la pop2 (moyPsA2)

	long double moyPsAB(0);
	long double moyPsA1(0);
	long double moyPsA2(0);
	unsigned long i,j;
	
	if (_bootind) {
		for (j = 0; j < _nbpop; j++) {
			_tabPstrucpop[j]->f_bootstrap();
		}
	}

	for (j = 0; j < _nbpop; j++) {
		for (i = 0; i < j; i++) {
			moyPsAB = r_distDasMoyPsAB(_tabPstrucpop[i], _tabPstrucpop[j]);
			moyPsA1 = r_distDasMoyPsA(_tabPstrucpop[i]);
			moyPsA2 = r_distDasMoyPsA(_tabPstrucpop[j]);

			Ptab[(i * _nbpop) + j] = Ptab[(j * _nbpop) + i] = (long double)1 - (((long double) 2 * moyPsAB)/(moyPsA1 + moyPsA2));
		}
	}	
}

long double DistancesGnt::r_distDasMoyPsA(const StrucPop * Ppop) const {
	//n�cessaire au calcul de distance � l'int�rieur d'une population pour la Das

	long double somme(0);
	unsigned long calcsomme(0);
	unsigned long k,l, nbind;

								
	if (_bootind) {
		nbind = (Ppop->_VcalcInd.size());

		if (nbind < 2) throw Anomalie(2, Ppop->get_nom() );

		for (k=0; k < nbind; k++) {	//scan des individus de la pop	
			for (l=(k+1); l < nbind; l++) {	//scan des individus de la pop
				calcsomme++;
				try {
					somme += r_distDasPsAi(Ppop->_VcalcInd[k], Ppop->_VcalcInd[l]);
				}
				catch (Jeupop::Anomalie erreur) {
					if (erreur.le_pb == 6) calcsomme--;
				}
			}
		}
	}
	else {
		nbind = (Ppop->get_nbind());

		if (nbind < 2) throw Anomalie(2, Ppop->get_nom());

		for (k=0; k < nbind; k++) {	//scan des individus de la pop	
			for (l=(k+1); l < nbind; l++) {	//scan des individus de la pop
				calcsomme++;
				try {
					somme += r_distDasPsAi(Ppop->get_Pind(k), Ppop->get_Pind(l));
				}
				catch (Jeupop::Anomalie erreur) {
					if (erreur.le_pb == 6) calcsomme--;
				}
			}
		}
	}

	return (somme / ((long double) calcsomme));
}

long double DistancesGnt::r_distDasMoyPsAB(const StrucPop * Ppop1, const StrucPop * Ppop2) const {
	//n�cessaire au calcul de distance entre 2 pops pour la Das

	long double somme(0);
	unsigned long calcsomme;
	unsigned long k,l, nbind1(0), nbind2(0);

								
	if (_bootind) {
		nbind1 = (Ppop1->_VcalcInd.size());
		nbind2 = (Ppop2->_VcalcInd.size());
		calcsomme = nbind1 * nbind2;

		for (k=0; k < nbind1; k++) {	//scan des individus de la pop1	
			for (l=0; l < nbind2; l++) {	//scan des individus de la pop2
				try {
					somme += r_distDasPsAi(Ppop1->_VcalcInd[k], Ppop2->_VcalcInd[l]);
				}
				catch (Jeupop::Anomalie erreur) {
					if (erreur.le_pb == 6) calcsomme--;
				}
			}
		}
	}
	else {
		nbind1 = (Ppop1->get_nbind());
		nbind2 = (Ppop2->get_nbind());
		calcsomme = nbind1 * nbind2;

		for (k=0; k < nbind1; k++) {	//scan des individus de la pop1	
			for (l=0; l < nbind2; l++) {	//scan des individus de la pop2
				try {
					somme += r_distDasPsAi(Ppop1->get_Pind(k), Ppop2->get_Pind(l));
				}
				catch (Jeupop::Anomalie erreur) {
					if (erreur.le_pb == 6) calcsomme--;
				}
			}
		}
	}

	return (somme / ((long double) calcsomme));
}

void DistancesGnt::f_distgntpopVcalc(long double * Ptab) const {
	unsigned long i,j;


	if (_methode == 5) f_distgntpopDas(Ptab);
	else {
		if (_bootind) f_calcTabBootInd();

		for (j = 0; j < _nbpop; j++) {
			for (i = 0; i < j; i++) {
				Ptab[(i * _nbpop) + j] = Ptab[(j * _nbpop) + i] = r_dist2pop(i, j);
			}
		}
	}
}

long double DistancesGnt::r_dist2pop(unsigned long pop1, unsigned long pop2) const{
  	long double result(0);
	//renvoi de la distance entre 2 Populations
		switch (_methode) {
		case 101:
			// Nei's minimum genetic distance (1972)	
     	result = r_dpopNei(pop1, pop2, false);
//			return(r_dpopNei(pop1, pop2, false));
			break;
		case 102:
				// Nei's standard genetic distance (1972)			
     	result = r_dpopNei(pop1, pop2, true);
//			return(r_dpopNei(pop1, pop2, true));
			break;
		case 103:
			// Cavalli-Sforza and Edwards' (1967)		
     	result = r_dpopCavalli(pop1, pop2);
			break;
		case 104:
			// Nei et al's, Da (1983)
     	result = r_dpopNeiDa(pop1, pop2);
//			return(r_dpopNeiDa(pop1,pop2));
			break;
		case 106:
			// Goldstein et al. (1995a)
     	result = r_dpopGoldsteinMu(pop1, pop2);
//			return(r_dpopGoldsteinMu(pop1,pop2));
			break;
		case 107:
			// Latter's Fst (1972)
     	result = r_dpopFst(pop1, pop2);
//			return(r_dpopFst(pop1, pop2));
			break;
		case 108:
			// Prevosti et al.'s, Cp (1975)
     	result = r_dpopPrevosti(pop1, pop2);
//			return(r_dpopPrevosti(pop1, pop2));
			break;
		case 109:
			// Rogers', Dr (1972)
     	result = r_dpopRoger(pop1, pop2);
//			return(r_dpopRoger(pop1, pop2));
			break;
		case 110:
			// Goldstein et al. (1995b) Slatkin 1995
     	result = r_dpopGoldsteinASD(pop1, pop2);
//			return(r_dpopGoldsteinASD(pop1, pop2));
			break;
		case 111:
			// Shriver et al's, Dsw (1995)
     	result = r_dpopShriver(pop1, pop2);
//			return(r_dpopShriver(pop1, pop2));
			break;
		case 112:
			// Zhivotovsky , DR (1999)
     	result = r_dpopZhivotovsky(pop1, pop2);
		//	return(r_dpopZhivotovsky(pop1, pop2));
			break;
		case 113:
			// Reynolds unweighted (1983)
     	result = r_dpopReynoldsUnweighted(pop1, pop2);
//			return(r_dpopReynoldsUnweighted(pop1, pop2));
			break;
		case 114:
			// Reynolds weighted (1983)
     	result = r_dpopReynoldsWeighted(pop1, pop2);
//			return(r_dpopReynoldsWeighted(pop1, pop2));
			break;
		case 115:
			// Reynolds least squares (1983)
     	result = r_dpopReynoldsLeast(pop1, pop2);
//			return(r_dpopReynoldsLeast(pop1, pop2));
			break;
			
		}
  if (_squareDistance) return (result * result);
	else return (result);

	throw Anomalie(1);
	return(0);
}


long double DistancesGnt::r_dpopCavalli(unsigned long pop1,unsigned long pop2) const {

	//distances de Cavalli-Sforza and Edwards' (1967) entre 2 populations
	// tir� de Naoko Takezaki and Masatoshi Nei
	// "Genetic Distances and Reconstruction of Phylogenetic
	//        Trees From Microsatellite DNA"
	// Genetics society of America 144: 389-399.1996.

	long double Sracinelocus(0);
	long double Sracinealleles;
	unsigned long i, l, locus;
	unsigned long nblocus(_VcalcLocus.size()); // soit r
	unsigned long nblocusdivise;
	long double ** tabfreq1;
	long double ** tabfreq2;
	tabfreq1 = ( _PtabFreq + (pop1 * _nbloc));
	tabfreq2 = ( _PtabFreq + (pop2 * _nbloc));

	nblocusdivise = nblocus;


	for (l = 0; l < nblocus; l++) {
		// l numero du locus 
//cerr << "DistancesGnt::r_dpopCavalli entre " << l << endl;
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}
//cerr << "DistancesGnt::r_dpopCavalli sort " << l << endl;

		Sracinealleles = 0;
		for (i = 0; i < _tabNbAll[locus]; i++) {
			//i numero de l'allele
			//Pall = _tabPloc[locus]->getPall(i);
			//if (_Pjeupop->_tabPloc[locus]->getPall(i)->_nul) continue;
			
			Sracinealleles += (long double) sqrt(*(tabfreq1[locus] + i) * *(tabfreq2[locus] + i));
		}

		//necessaire: racine carree de zero ne fonctionne pas.
		if (Sracinealleles < 1) Sracinelocus += (long double)sqrt ((long double)2 * ((long double)1 - Sracinealleles));
	}

	if (nblocusdivise < 1) throw Anomalie(3);
	return (((long double)2 * Sracinelocus) / (_pi * (long double)nblocusdivise));
}

long double DistancesGnt::r_dpopFst(unsigned long pop1,unsigned long pop2) const {

	//Latter's Fst (1972) entre 2 populations
	// tir� de Naoko Takezaki and Masatoshi Nei
	// "Genetic Distances and Reconstruction of Phylogenetic
	//        Trees From Microsatellite DNA"
	// Genetics society of America 144: 389-399.1996.

	long double resultat(0), inter;
	long double Jx(0), Jy(0), Jxy(0);
	unsigned long i, l, locus;
	unsigned long nblocus(_VcalcLocus.size());
	unsigned long nblocusdivise;
	long double ** tabfreq1;
	long double ** tabfreq2;
	tabfreq1 = (_PtabFreq + (pop1 * _nbloc));
	tabfreq2 = (_PtabFreq + (pop2 * _nbloc));

	nblocusdivise = nblocus;

	for (l = 0; l < nblocus; l++) {
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}

		for (i = 0; i < _tabNbAll[locus]; i++) {
			//Pall = _tabPloc[locus]->getPall(i);
			if (_Pjeupop->_tabPloc[locus]->getPall(i)->_miss) continue;

			//frequence de l'allele  i dans la population 1
			inter = *(tabfreq1[locus] + i);
			//inter = ((long double) ppop1->r_nbcopall(Pall) / (long double) nballpop1);
			resultat = inter * inter;
	//		resultat /= nblocus;
			Jx += resultat;

			//frequence de l'allele  i dans la population 2
			resultat = *(tabfreq2[locus] + i);
			//resultat = ((long double) ppop2->r_nbcopall(Pall) / (long double) nballpop2);
			inter = inter * resultat;
			resultat = resultat * resultat;
	//		resultat /= nblocus;
			Jy += resultat;

	//		inter /= nblocus;
			Jxy += inter;
		}
	}

	if (nblocusdivise < 1) throw Anomalie(3);
	Jx /= (long double)nblocusdivise;
	Jy /= (long double)nblocusdivise;
	Jxy /= (long double)nblocusdivise;

	//distance de Nei classique:
	resultat = ((Jx + Jy) / (long double)2 ) - Jxy;

	// Fst :
	resultat /= ((long double)1 - Jxy);


	return (resultat);
}

/*
long double DistancesGnt::r_dpopFstClassique(long double ** tabfreq1,long double ** tabfreq2) const {

	//Fst entre 2 populations

	long double somme;
	long double HT, moyHS;
	unsigned long i, l, locus;
	long double nblocus((long double) _VcalcLocus.size());


	for (l = 0; l < nblocus; l++) {
		locus = _VcalcLocus[l];

		for (i = 0; i < _tabNbAll[locus]; i++) {
			if (_Pjeupop->_tabPloc[locus]->getPall(i)->_nul) continue;

			//pour chaque locus, chaque allele
			//calcul de HT
			somme = (*(tabfreq1[locus] + i) * nbind1)
		}
	}

	// Fst :
	resultat /= ((long double)1 - Jxy);


	return (resultat);
}
*/

long double DistancesGnt::r_dpopGoldsteinASD(unsigned long pop1,unsigned long pop2) const {

	//distances de Goldstein et al., ASD (1995b; Slatkin 1995) entre 2 populations
	// Average Square Distance
	// tir� de Naoko Takezaki and Masatoshi Nei
	// "Genetic Distances and Reconstruction of Phylogenetic
	//        Trees From Microsatellite DNA"
	// Genetics society of America 144: 389-399.1996.

	long double freqxil;
	long double freqyjl;
	long double Slocus(0);
	long double DblSommeij(0);
	unsigned long i,j, l, locus;
	unsigned long nblocus(_VcalcLocus.size()); // soit r
	unsigned long nballdiff;
	unsigned long nblocusdivise;
	long double ** tabfreq1;
	long double ** tabfreq2;
	tabfreq1 = (_PtabFreq + (pop1 * _nbloc));
	tabfreq2 = (_PtabFreq + (pop2 * _nbloc));

	nblocusdivise = nblocus;

	for (l = 0; l < nblocus; l++) {
		// l numero du locus 
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
//cerr << "DistancesGnt::r_dpopGoldsteinASD" << nblocusdivise << endl;
			continue;
		}

		nballdiff = _tabNbAll[locus];
		DblSommeij = 0;
		for (i = 0; i < nballdiff; i++) {
			//Palli = _tabPloc[locus]->getPall(i);
			if (_Pjeupop->_tabPloc[locus]->getPall(i)->_miss) continue;

			//frequence de l'allele  i dans la population 1
			freqxil = *(tabfreq1[locus] + i);
			//freqxil = ((long double) ppop1->r_nbcopall(Palli) / (long double) nballpop1);
//cerr << "DistancesGnt::r_dpopGoldsteinASD freqxil" << freqxil << endl;
			if (freqxil == 0) continue;
			
			for (j = 0; j < nballdiff; j++) {
				//double somme
				if (i == j) continue;
				//Pallj = _tabPloc[locus]->getPall(j);
				if (_Pjeupop->_tabPloc[locus]->getPall(j)->_miss) continue;
				
				
//cerr << "DistancesGnt::r_dpopGoldsteinASD nbrepet1" << _tabPloc[locus]->getPall(i)->_nbrepet << endl;
//cerr << "DistancesGnt::r_dpopGoldsteinASD nbrepet2" << _tabPloc[locus]->getPall(j)->_nbrepet << endl;
				freqyjl =  ((long double)_tabPloc[locus]->getPall(i)->_nbrepet - (long double)_tabPloc[locus]->getPall(j)->_nbrepet);
//cerr << "DistancesGnt::r_dpopGoldsteinASD freqyjl" << freqyjl << endl;
				freqyjl = freqyjl * freqyjl;
//cerr << "DistancesGnt::r_dpopGoldsteinASD freqyjl" << freqyjl << endl;
				//frequence de l'allele  j dans la population 2
				freqyjl = freqyjl * (*(tabfreq2[locus] + j));
//cerr << "DistancesGnt::r_dpopGoldsteinASD freqyjl" << freqyjl << endl;
				//freqyjl *= ((long double) ppop2->r_nbcopall(Pallj) / (long double) nballpop2);

				DblSommeij += (freqxil * freqyjl);
//cerr << "DistancesGnt::r_dpopGoldsteinASD DblSommeij" << DblSommeij << endl;
			}
		}

		//Slocus += (DblSommeij / nblocus);
		Slocus += DblSommeij;
//cerr << "DistancesGnt::r_dpopGoldsteinASD Slocus" << Slocus << endl;
	}

//	resultat = (long double)1 - (Sracinelocus * ((long double)1 / nblocus));
	if (nblocusdivise == 0) throw Anomalie(3);
	Slocus /= (long double) nblocusdivise;

	return (Slocus);
}


long double DistancesGnt::r_dpopGoldsteinMu(unsigned long pop1,unsigned long pop2) const {

	//distances de Goldstein et al. (1995a) entre 2 populations
	// deltaMu carre
	// tir� de Naoko Takezaki and Masatoshi Nei
	// "Genetic Distances and Reconstruction of Phylogenetic
	//        Trees From Microsatellite DNA"
	// Genetics society of America 144: 389-399.1996.

	long double Slocus(0);
	long double Mu2;
	unsigned long l, locus;
	unsigned long nblocus(_VcalcLocus.size()); // soit r
	unsigned long nblocusdivise;
	long double * tabmu1(_PtabMu + (pop1 * _nbloc));
	long double * tabmu2(_PtabMu + (pop2 * _nbloc));

	nblocusdivise = nblocus;

	for (l = 0; l < nblocus; l++) {
		// l numero du locus 
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}

		//Muxj = Muxj - Muyj;
		Mu2 = tabmu1[locus] - tabmu2[locus];
		Mu2 *= Mu2;

		//Slocus += (Muxj / nblocus);
		Slocus += Mu2;
	}

	if (nblocusdivise < 1) throw Anomalie(3);
	Slocus /= (long double) nblocusdivise;

//	resultat = (long double)1 - (Sracinelocus * ((long double)1 / nblocus));

	return (Slocus);
}


long double DistancesGnt::r_dpopZhivotovsky(unsigned long pop1,unsigned long pop2) const {

	//distances de Lev A. Zhivotovsky (1999) entre 2 populations
	// tir� de Lev A. Zhivotovsky
	// "A new Genetic Distance with Application to constrained 
	//       Variation at Microsatellite Loci"
	// Mol. Biol. Evol. 16(4) 144: 389-399.1996.

	long double Cab(0);
	long double MoyRa(0), MoyRb(0);
	long double SRa2(0), SRb2(0);
	unsigned long l, locus;
	unsigned long nblocus(_VcalcLocus.size());
	unsigned long nblocusdivise;
	long double * tabmu1(_PtabMu + (pop1 * _nbloc));
	long double * tabmu2(_PtabMu + (pop2 * _nbloc));

	nblocusdivise = nblocus;

//cerr << "zhivotovski deb" << endl;
	//ce calcul peut �tre externalis�
	for (l = 0; l < nblocus; l++) {
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}

		MoyRa += tabmu1[locus];
		MoyRb += tabmu2[locus];
		SRa2 += (tabmu1[locus] * tabmu1[locus]);
		SRb2 += (tabmu2[locus] * tabmu2[locus]);
		Cab += (tabmu1[locus] * tabmu2[locus]);
	}

	if (nblocusdivise < 1) throw Anomalie(3);

	MoyRa /= (long double) nblocusdivise;
	MoyRb /= (long double) nblocusdivise;
	//--------------

//cerr << Cab << " - " << (((long double) nblocus) * MoyRa * MoyRb) << endl;
	Cab -= (((long double) nblocusdivise) * MoyRa * MoyRb);
	Cab /= (long double)(nblocusdivise - 1);
	// c'est bon pour Cab
	// pour Va et Vb, utilisons respectivement SRa2 et SRb2
	SRa2 -= (((long double) nblocusdivise) * MoyRa * MoyRa);
	SRb2 -= (((long double) nblocusdivise) * MoyRb * MoyRb);
	SRa2 /= (long double)(nblocusdivise - 1);
	SRb2 /= (long double)(nblocusdivise - 1);

	SRa2 += SRb2;
	SRa2 /= (long double) 2;

//cerr << Cab << " " <<  SRa2 << endl;
	//Attention a l'approximation:
	if (Cab < 1) Cab = 1; //sans ca, ca risque de planter...
	Cab = ((long double) log(Cab / SRa2) * (long double)-1);

//cerr << "zhivotovski fin " << Cab << endl;
	return (Cab);

}

long double DistancesGnt::r_dpopNei(unsigned long pop1,unsigned long pop2, bool standard) const {
	//distances de Nei (1972) entre 2 populations (standard et minimum)
	// Ds et Dm
	// tir� de Jin et Chakraborty
	// mol.Biol. Evol. 11(1): 120-127.1994.
	long double ** tabfreq1;
	long double ** tabfreq2;
	tabfreq1 = (_PtabFreq + (pop1 * _nbloc));
	tabfreq2 = (_PtabFreq + (pop2 * _nbloc));

//	long double * tabfreq1( _PtabFreq[(pop1 * _nbloc)]);
//	long double * tabfreq2( _PtabFreq[(pop2 * _nbloc)]);
//	tabfreq1 = *tabfreq1 + (pop1 * _nbloc);

	long double resultat(0), inter;
	long double Jx(0), Jy(0), Jxy(0);
	unsigned long i, l, locus;
	unsigned long nblocus(_VcalcLocus.size());
	unsigned long nblocusdivise;

	nblocusdivise = nblocus;
//	long nballdiff, nballpop1, nballpop2;
//	Allele * Pall;

	for (l = 0; l < nblocus; l++) {
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}
//		nballdiff = tabNbAll[locus];
		for (i = 0; i < _tabNbAll[locus]; i++) {
			if (_Pjeupop->_tabPloc[locus]->getPall(i)->_miss) continue;

			//frequence de l'allele  i dans la population 1
			inter = *(tabfreq1[locus] + i);
			resultat = inter * inter;
			Jx += resultat;

			//frequence de l'allele  i dans la population 2
			resultat = *(tabfreq2[locus] + i);
			inter = inter * resultat;
			resultat = resultat * resultat;
			Jy += resultat;

			Jxy += inter;
		}
	}
	if (nblocusdivise == 0) throw Anomalie(3);

	Jx /= (long double)nblocusdivise;
	Jy /= (long double)nblocusdivise;
	Jxy /= (long double)nblocusdivise;

	if (standard) {
		//resultat = ((log(Jx) + log(Jy)) / 2 ) - log(Jxy);
		//cerr << "Ds Nei " << endl;
		resultat = ( - log (Jxy/(sqrt(Jx * Jy))));
	}
	else {
		resultat = ((Jx + Jy) / 2 ) - Jxy;
	}

	return (resultat);
}


long double DistancesGnt::r_dpopNeiDa(unsigned long pop1,unsigned long pop2) const {

	//distances de Nei et al's, Da (1983) entre 2 populations
	// tir� de Naoko Takezaki and Masatoshi Nei
	// "Genetic Distances and Reconstruction of Phylogenetic
	//        Trees From Microsatellite DNA"
	// Genetics society of America 144: 389-399.1996.

	long double resultat(0);
	long double freqil;
	long double Sracinelocus(0);
	long double Sracinealleles(0);
//	long double pi(acos(-1));
	unsigned long i, l, locus;
	unsigned long nblocus(_VcalcLocus.size()); // soit r
	unsigned long nblocusdivise;
	long double ** tabfreq1;
	long double ** tabfreq2;
	tabfreq1 = (_PtabFreq + (pop1 * _nbloc));
	tabfreq2 = (_PtabFreq + (pop2 * _nbloc));


	nblocusdivise = nblocus;

	for (l = 0; l < nblocus; l++) {
		// l numero du locus 
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}

		Sracinealleles = 0;
		for (i = 0; i < _tabNbAll[locus]; i++) {
			//i numero de l'allele
			//Pall = _tabPloc[locus]->getPall(i);
			if (_Pjeupop->_tabPloc[locus]->getPall(i)->_miss) continue;

			//frequence de l'allele  i dans la population 1
			freqil = *(tabfreq1[locus] + i);
			//freqil = ((long double) ppop1->r_nbcopall(Pall) / (long double) nballpop1);

			//frequence de l'allele  i dans la population 2
			freqil *= *(tabfreq2[locus] + i);
			//freqil *= ((long double) ppop2->r_nbcopall(Pall) / (long double) nballpop2);

			Sracinealleles += (long double) sqrt(freqil);
		}

		Sracinelocus += Sracinealleles;
	}

	if (nblocusdivise < 1) throw Anomalie(3);
	resultat = (long double)1 - (Sracinelocus / (long double)nblocusdivise);

	return (resultat);
}

long double DistancesGnt::r_dpopPrevosti(unsigned long pop1,unsigned long pop2) const {

	//distances de Prevosti et al.'s, Cp (1975) entre 2 populations
	// tir� de Naoko Takezaki and Masatoshi Nei
	// "Genetic Distances and Reconstruction of Phylogenetic
	//        Trees From Microsatellite DNA"
	// Genetics society of America 144: 389-399.1996.

	long double freqil;
	long double Sracinelocus(0);
	long double Salleles(0);
	unsigned long i, l, locus;
	unsigned long nblocus(_VcalcLocus.size()); // soit r
	unsigned long nblocusdivise;
	long double ** tabfreq1;
	long double ** tabfreq2;
	tabfreq1 = (_PtabFreq + (pop1 * _nbloc));
	tabfreq2 = (_PtabFreq + (pop2 * _nbloc));

	nblocusdivise = nblocus;
	
	for (l = 0; l < nblocus; l++) {
		// l numero du locus 
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}

		Salleles = 0;
		for (i = 0; i < _tabNbAll[locus]; i++) {
			//i numero de l'allele
			if (_Pjeupop->_tabPloc[locus]->getPall(i)->_miss) continue;
			//frequence de l'allele  i dans la population 1
			freqil = *(tabfreq1[locus] + i);

			//frequence de l'allele  i dans la population 2
			freqil -= *(tabfreq2[locus] + i);

			Salleles += (freqil < 0)?((long double)-1 * freqil):(freqil);
		}

		//Sracinelocus += (Salleles / ((long double)2 * nblocus));
		Sracinelocus += Salleles;
	}

	if (nblocusdivise < 1) throw Anomalie(3);
	Sracinelocus /= (((long double)2 * (long double)nblocusdivise));

	return (Sracinelocus);
}


long double DistancesGnt::r_dpopRoger(unsigned long pop1,unsigned long pop2) const {

	//distances de Rogers', Dr (1972) entre 2 populations
	// tir� de Naoko Takezaki and Masatoshi Nei
	// "Genetic Distances and Reconstruction of Phylogenetic
	//        Trees From Microsatellite DNA"
	// Genetics society of America 144: 389-399.1996.

	long double freqil;
	long double Sracinelocus(0);
	long double Salleles(0);
	unsigned long i, l, locus;
	unsigned long nblocus(_VcalcLocus.size()); // soit r
	unsigned long nblocusdivise;
	long double ** tabfreq1;
	long double ** tabfreq2;
	tabfreq1 = (_PtabFreq + (pop1 * _nbloc));
	tabfreq2 = (_PtabFreq + (pop2 * _nbloc));


	nblocusdivise = nblocus;


	for (l = 0; l < nblocus; l++) {
		// l numero du locus 
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}

		Salleles = 0;
		for (i = 0; i < _tabNbAll[locus]; i++) {
			//i numero de l'allele
			//Pall = _tabPloc[locus]->getPall(i);
			if (_Pjeupop->_tabPloc[locus]->getPall(i)->_miss) continue;
			//frequence de l'allele  i dans la population 1
			freqil = *(tabfreq1[locus] + i);
			//freqil = ((long double) ppop1->r_nbcopall(Pall) / (long double) nballpop1);

			//frequence de l'allele  i dans la population 2
			freqil -= *(tabfreq2[locus] + i);
			//freqil -= ((long double) ppop2->r_nbcopall(Pall) / (long double) nballpop2);

			Salleles += freqil * freqil;
		}

		Sracinelocus += (long double)sqrt (Salleles / (long double)2);
	}

//	resultat = Sracinelocus * ((long double)2 / (pi * nblocus));

	if (nblocusdivise < 1) throw Anomalie(3);
	return (Sracinelocus / (long double) nblocusdivise);
}

long double DistancesGnt::r_dpopShriver(unsigned long pop1,unsigned long pop2) const {

	// Dsw Shriver et al's(1995)
	//distances de Shriver (1995) entre 2 populations
	// "A novel Measure of Genetic Distance for Highly Polymorphic Tandem Repeat Loci"
	// Mark D. Shriver, Li Jin, Eric Boerwinkle, Ranjan Deka, Robert E. Ferrell and Ranajit Chakraborty
	// Mol. Bio. Evol. 12(5):914-920. 1995.

	long double freqxil;
	long double freqxjl;
	long double freqyil;
	long double freqyjl;
	long double Resultat(0);
	int Absdiffij(0);
//	long double Wxy(0);
//	long double Wx(0);
//	long double Wy(0);
	long double SWxy(0);
	long double SWx(0);
	long double SWy(0);
//	long double pi(acos(-1));
	unsigned long i,j, l, locus;
	unsigned long nblocus(_VcalcLocus.size()); // soit r
//	long nploidie(get_nploidie());
//	long nballdiff, nballpop1, nballpop2;
	unsigned long nballdiff;
	unsigned long nbrepet;
	unsigned long nblocusdivise;
	long double ** tabfreq1;
	long double ** tabfreq2;
	tabfreq1 = (_PtabFreq + (pop1 * _nbloc));
	tabfreq2 = (_PtabFreq + (pop2 * _nbloc));

	nblocusdivise = nblocus;

	for (l = 0; l < nblocus; l++) {
		// l numero du locus 
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}

		nballdiff = _tabNbAll[locus];
		//SWxy = 0;
		//SWy = 0;
		//SWx = 0;
		for (i = 0; i < nballdiff; i++) {
			//Palli = _tabPloc[locus]->getPall(i);
			if (_Pjeupop->_tabPloc[locus]->getPall(i)->_miss) continue;

			//frequence de l'allele  i dans la population 1
			freqxil = *(tabfreq1[locus] + i);
			//freqxil = ((long double) ppop1->r_nbcopall(Palli) / (long double) nballpop1);
			//frequence de l'allele  i dans la population 2
			freqyil = *(tabfreq2[locus] + i);
			//freqyil = ((long double) ppop2->r_nbcopall(Palli) / (long double) nballpop2);

			nbrepet = _tabPloc[locus]->getPall(i)->_nbrepet;
			for (j = 0; j < nballdiff; j++) {
				//double somme
				if (i == j) continue;
				//Pallj = _tabPloc[locus]->getPall(j);
				if (_tabPloc[locus]->getPall(j)->_miss) continue;
				
//cerr << Palli->_nom << " " << Pallj->_nom << endl;
				Absdiffij = (int)nbrepet - (int)_tabPloc[locus]->getPall(j)->_nbrepet;
				Absdiffij = (Absdiffij < 0)?(-1 * Absdiffij):(Absdiffij);

				//frequence de l'allele  j dans la population 2
				freqyjl = *(tabfreq2[locus] + j);
				//freqyjl = ((long double) ppop2->r_nbcopall(Pallj) / (long double) nballpop2);
				//frequence de l'allele  j dans la population 1
				freqxjl = *(tabfreq1[locus] + j);
				//freqxjl = ((long double) ppop1->r_nbcopall(Pallj) / (long double) nballpop1);


				SWxy += freqxil * freqyjl * (long double)Absdiffij;
				SWx += freqxil * freqxjl * (long double)Absdiffij;
				SWy += freqyil * freqyjl * (long double)Absdiffij;
//cerr << SWxy << " " << SWx  << " " << SWy << endl;
			}
		}

		//Wxy += (SWxy / nblocus);
		//Wx += (SWx / nblocus);
		//Wy += (SWy / nblocus);
	}
//cin >> Resultat;

	if (nblocusdivise < 1) throw Anomalie(3);
	SWxy /= (long double) nblocusdivise;
	SWx /= (long double) nblocusdivise;
	SWy /= (long double) nblocusdivise;

	Resultat = SWxy - ((SWx + SWy)/(long double)2);

//	cerr << SWxy << " " << SWx  << " " << SWy  << " " << Resultat << endl;
//cin >> SWxy;

	return (Resultat);
}


inline void DistancesGnt::f_calcTabFreq() const{
	//calcul des frequences alleliques
	// tabPfreq contient les adresses de tableaux de frequences
	// tabNbAll contient le nombre d'alleles a chaque locus

	unsigned long nball, nballnonnuls;
	unsigned long i, j, k;

	long double* adresse(_PtabFreq[0]);

	for (i=0; i < _nbpop; i++) {
		for (j=0; j < _nbloc; j++) {
			nball = _tabNbAll[j];
			nballnonnuls = _tabPstrucpop[i]->r_nballnonnuls(j);
			if (nballnonnuls == 0) {
				_tabEviteLocus[(i*_nbloc)+j] = true; // calculs de fr�quences impossible sur ce locus

				for (k=0; k < nball; k++, adresse++) *adresse = 0;
				continue;
//				throw Anomalie(3, _tabPstrucpop[i]->get_nom());
			}

			for (k=0; k < nball; k++) {
				if (_tabPloc[j]->getPall(k)->_miss) *adresse = 0;
				else *adresse = (long double) _tabPstrucpop[i]->r_nbcopall(_tabPloc[j]->getPall(k)) / (long double) nballnonnuls;
				adresse++;
			}
		}
	}
}

void DistancesGnt::f_calcTabFreqTot() const{
	//calcul des frequences alleliques moyennes � chaque locus pour toutes les pops
	//�a ne sert pas pour l'instant (26/02/2002)
	unsigned long j,k,nball, nballnonnuls;
	MetaPop * Pracinepop(_Pjeupop->get_Pracinepop());
	long double* adresse(_PtabFreqTot);
	
	f_calcTabFreq();
	
	for (j=0; j < _nbloc; j++) {
		nball = _tabNbAll[j];
		nballnonnuls = Pracinepop->r_nballnonnuls(j);
		if (nballnonnuls == 0) {
			// calculs impossibles non trait�
			
			//_tabEviteLocus[(i*_nbloc)+j] = true; // calculs de fr�quences impossible sur ce locus
			
			//for (k=0; k < nball; k++, adresse++) *adresse = 0;
			//continue;
//				throw Anomalie(3, _tabPstrucpop[i]->get_nom());
		}

		for (k=0; k < nball; k++) {
			if (_tabPloc[j]->getPall(k)->_miss) *adresse = 0;
			else *adresse = (long double) Pracinepop->r_nbcopall(_tabPloc[j]->getPall(k)) / (long double) nballnonnuls;
			adresse++;
		}
	}
	
	
}

void DistancesGnt::f_calcTabFreqInd() const{
	//calcul des frequences alleliques
	// pour chaque individu
	// tabPfreq contient les adresses de tableaux de frequences
	// tabNbAll contient le nombre d'alleles a chaque locus
	// _tabEviteLocus contient les locus � �viter (qui ne contiennent que des all�les nuls)

	unsigned long nball, nballnonnuls;
	unsigned long nbind(_tabPind.size());
	unsigned int nploidie(_Pjeupop->get_nploidie());
	unsigned long i, j, k;

	long double* adresse(_PtabFreq[0]);

	for (i=0; i < nbind; i++) {
		for (j=0; j < _nbloc; j++) {
			nball = _tabNbAll[j];
			nballnonnuls = _tabPind[i]->r_nballnonnuls(j, nploidie);

			if (nballnonnuls == 0) {
				_tabEviteLocus[(i*_nbloc)+j] = true; // calculs de fr�quences impossible sur ce locus

				for (k=0; k < nball; k++, adresse++) *adresse = 0;
				continue;
			}

			for (k=0; k < nball; k++) {
				if (_tabPloc[j]->getPall(k)->_miss) *adresse = 0;
				else *adresse = (long double) _tabPind[i]->r_nbcopall(_tabPloc[j]->getPall(k)) / (long double) nballnonnuls;
				adresse++;
			}
		}
	}
}

void DistancesGnt::f_calcTabFreqBootInd() const{
	//calcul des frequences alleliques
	// tabPfreq contient les adresses de tableaux de frequences
	// tabNbAll contient le nombre d'alleles a chaque locus
	// sp�cifique aux calculs avec des bootstrap sur les individus

	unsigned long nball, nballnonnuls;
	unsigned long i, j, k;

	long double* adresse(_PtabFreq[0]);

//cerr << "f_calcTabFreqBootInd deb" << endl;
	for (i=0; i < _nbpop; i++) {
		_tabPstrucpop[i]->f_bootstrap();
		for (j=0; j < _nbloc; j++) {
			nball = _tabNbAll[j];
			nballnonnuls = _tabPstrucpop[i]->r_nballnonnulsBootInd(j);

			if (nballnonnuls == 0) {
				_tabEviteLocus[(i*_nbloc)+j] = true; // calculs de fr�quences impossible sur ce locus
				for (k=0; k < nball; k++, adresse++) *adresse = 0;
//cerr << "f_calcTabFreqBootInd" << endl;
				continue;
			}

			for (k=0; k < nball; k++) {
				if (_tabPloc[j]->getPall(k)->_miss) *adresse = 0;
				else *adresse = (long double) _tabPstrucpop[i]->r_nbcopallBootInd(_tabPloc[j]->getPall(k)) / (long double) nballnonnuls;
				adresse++;
			}
		}
	}
//cerr << "f_calcTabFreqBootInd fin" << endl;

}

inline void DistancesGnt::f_calcTabBootInd() const{
	//recalcul des tableaux
	switch (_methode) {
	case 106:
		// calculs des Mu
		f_calcTabMuBootInd();
		break;
	case 112:
		// calculs des Mu
		f_calcTabMuBootInd();
		break;

	default:
		// calculs des fr�quences
		f_calcTabFreqBootInd();
		break;
	}
}

void DistancesGnt::f_calcTabMu() const{
	//calcul des Mu (moyenne du nombre de repetitions (au sens
	//    microsat) pond�r�e par la frequence allelique pour chaque locus)
	// tabNbAll contient le nombre d'alleles a chaque locus

	unsigned long nball;
	long double nballnonnuls;
	unsigned long i, j, k;

	long double* adresse(_PtabMu);

	for (i=0; i < _nbpop; i++) {
		for (j=0; j < _nbloc; j++) {
			nball = _tabNbAll[j];
			nballnonnuls = (long double)  _tabPstrucpop[i]->r_nballnonnuls(j);
			if (nballnonnuls == 0) {
				_tabEviteLocus[(i*_nbloc)+j] = true; // calculs de fr�quences impossible sur ce locus

				for (k=0; k < nball; k++, adresse++) *adresse = 0;
				continue;
//				throw Anomalie(3, _tabPstrucpop[i]->get_nom());
			}
			*adresse = 0;

			for (k=0; k < nball; k++) {
				if (_tabPloc[j]->getPall(k)->_miss) continue;
				*adresse += (long double) _tabPloc[j]->getPall(k)->_nbrepet * ((long double) _tabPstrucpop[i]->r_nbcopall(_tabPloc[j]->getPall(k)) / nballnonnuls);
			}
			adresse++;
		}
	}
}

void DistancesGnt::f_calcTabMuInd() const{
	//calcul des Mu (moyenne du nombre de repetitions (au sens
	//    microsat) pond�r�e par la frequence allelique pour chaque locus)
	// tabNbAll contient le nombre d'alleles a chaque locus

	//pour chaque individu

	unsigned long nball;
	long double nballnonnuls;
	unsigned long nbind(_tabPind.size());
	unsigned int nploidie(_Pjeupop->get_nploidie());
	unsigned long i, j, k;

	long double* adresse(_PtabMu);

	for (i=0; i < nbind; i++) {
		for (j=0; j < _nbloc; j++) {
			nball = _tabNbAll[j];
			nballnonnuls = (long double) _tabPind[i]->r_nballnonnuls(j, nploidie);
			if (nballnonnuls == 0) {
				_tabEviteLocus[(i*_nbloc)+j] = true; // calculs de fr�quences impossible sur ce locus
				for (k=0; k < nball; k++, adresse++) *adresse = 0;
				continue;
			}

			*adresse = 0;

			for (k=0; k < nball; k++) {
				if (_tabPloc[j]->getPall(k)->_miss) continue;
				*adresse += (long double) _tabPloc[j]->getPall(k)->_nbrepet * ((long double) _tabPind[i]->r_nbcopall(_tabPloc[j]->getPall(k)) / nballnonnuls);
			}
			adresse++;
		}
	}
}

void DistancesGnt::f_calcTabMuBootInd() const{
	//calcul des Mu (moyenne du nombre de repetitions (au sens
	//    microsat) pond�r�e par la frequence allelique pour chaque locus)
	// tabNbAll contient le nombre d'alleles a chaque locus
	// sp�cifique aux calculs avec des bootstrap sur les individus


	unsigned long nball;
	long double nballnonnuls;
	unsigned long i, j, k;

	long double* adresse(_PtabMu);

	for (i=0; i < _nbpop; i++) {
		_tabPstrucpop[i]->f_bootstrap();
		for (j=0; j < _nbloc; j++) {
			nball = _tabNbAll[j];
			nballnonnuls = (long double) _tabPstrucpop[i]->r_nballnonnulsBootInd(j);
			if (nballnonnuls == 0) {
				_tabEviteLocus[(i*_nbloc)+j] = true; // calculs de fr�quences impossible sur ce locus
				for (k=0; k < nball; k++, adresse++) *adresse = 0;
				continue;
			}

			*adresse = 0;

			for (k=0; k < nball; k++) {
				if (_tabPloc[j]->getPall(k)->_miss) continue;
				*adresse += (long double) _tabPloc[j]->getPall(k)->_nbrepet * ((long double) _tabPstrucpop[i]->r_nbcopallBootInd(_tabPloc[j]->getPall(k)) / nballnonnuls);
			}
			adresse++;
		}
	}
}

void DistancesGnt::f_distgntIndVcalc (long double * Ptab) const{
	//distances G�n�tiques entre individus
	long nbind (_tabPind.size());
	long j,i;

	for (j = 0; j < nbind; j++) {
		for (i = 0; i < j; i++) {
			try {
				Ptab[(j * nbind) + i] = r_dist2ind(i, j);
				Ptab[(i * nbind) + j] = Ptab[(j * nbind) + i];
			}
			catch (Jeupop::Anomalie erreur) {
				if (erreur.le_pb == 6) {
					Ptab[(j * nbind) + i] = -1;
					Ptab[(i * nbind) + j] = Ptab[(j * nbind) + i];
				}
			}
		}
	}
//cerr << "f_distgntIndVcalc fin" << endl;

}

unsigned long DistancesGnt::get_nbind() const {
	unsigned long i, res(0);

	for (i = 0; i < _nbpop; i++) {
		res += _tabPstrucpop[i]->get_nbind();
	}
	return (res);
}


unsigned int DistancesGnt::get_nb_methodes() {
	if (_tab_noms_methodes.size() == 0) f_rempli_tab_noms_methodes();
	return(_tab_noms_methodes.size());
}

const string & DistancesGnt::get_nom_methode(unsigned int methode) {
	if (_tab_noms_methodes.size() == 0) f_rempli_tab_noms_methodes();
	if (methode > 100) methode -= 100;
	if (methode < _tab_noms_methodes.size()) return (_tab_noms_methodes[methode]);
	else throw Anomalie(6);
}

void DistancesGnt::f_rempli_tab_noms_methodes() {
//	_map_noms_methodes.resize(0);
	
/*	_map_noms_methodes[1] = string("Nei's minimum genetic distance, Dm (1972)");
	_map_noms_methodes[2] = string("Nei's standard genetic distance, Ds (1972)");
	_map_noms_methodes[3] = string("Cavalli-Sforza and Edwards, Dc (1967)"); //3
	//_map_noms_methodes[16] = string("Cavalli-Sforza and Edwards, Dc (1967)"); //3
	_map_noms_methodes[4] = string("Nei et al's, Da (1983)"); //4
	_map_noms_methodes[5] = string("DAS"); //5
	_map_noms_methodes[6] = string("Goldstein et al. , dmu2 (1995a)"); //6
	_map_noms_methodes[7] = string("Latter, Fst (1972)"); //7
	_map_noms_methodes[8] = string("Prevosti et al.'s, Cp (1975)"); //8
	_map_noms_methodes[9] = string("Rogers', Dr (1972)"); //9
	_map_noms_methodes[10] = string("Goldstein et al. (1995b) Slatkin, ASD (1995)"); //10
	_map_noms_methodes[11] = string("Shriver et al's, Dsw (1995)"); //11
	_map_noms_methodes[12] = string("Lev A. Zhivotovsky, DR (1999)"); //12
	_map_noms_methodes[13] = string("Reynolds J., unweighted (1983)"); //13
	_map_noms_methodes[14] = string("Reynolds J., weighted (1983)"); //14
	_map_noms_methodes[15] = string("Reynolds J., least squares (1983)"); //15

*/ 	_tab_noms_methodes.resize(0);
//	_tab_numeros_methodes.resize(0);
	_tab_noms_methodes.push_back(""); //0
	_tab_noms_methodes.push_back("Nei's minimum genetic distance, Dm (1972)"); //1
	_tab_noms_methodes.push_back("Nei's standard genetic distance, Ds (1972)"); //2
	_tab_noms_methodes.push_back("Cavalli-Sforza and Edwards, Dc (1967)"); //3
	_tab_noms_methodes.push_back("Nei et al's, Da (1983)"); //4
	_tab_noms_methodes.push_back("DAS"); //5
	_tab_noms_methodes.push_back("Goldstein et al. , dmu2 (1995a)"); //6
	_tab_noms_methodes.push_back("Latter, Fst (1972)"); //7
	_tab_noms_methodes.push_back("Prevosti et al.'s, Cp (1975)"); //8
	_tab_noms_methodes.push_back("Rogers', Dr (1972)"); //9
	_tab_noms_methodes.push_back("Goldstein et al. (1995b) Slatkin, ASD (1995)"); //10
	_tab_noms_methodes.push_back("Shriver et al's, Dsw (1995)"); //11
	_tab_noms_methodes.push_back("Lev A. Zhivotovsky, DR (1999)"); //12
	_tab_noms_methodes.push_back("Reynolds J., unweighted (1983)"); //13
	_tab_noms_methodes.push_back("Reynolds J., weighted (1983)"); //14
	_tab_noms_methodes.push_back("Reynolds J., least squares (1983)"); //15

}

long double DistancesGnt::r_dpopReynoldsUnweighted(unsigned long pop1,unsigned long pop2) const {

	//distance de Reynolds (1983) entre 2 populations
	// tir� de {Reynolds, J.} and {Weir, B.S.} and {Cockerham, C.}
	// "Estimation of the coancestry coefficient: basis for a short-term genetic distance"
	// Genetics society of America
	// 105: 767-779.1983.

	long double al, alpbl;
	long double sommeu(0);
	long double sommetheta(0);
	long double alpha1(0), alpha2(0);
	long double intermediaire;
	long double effpop1(_tabPstrucpop[pop1]->get_nbind()), effpop2(_tabPstrucpop[pop2]->get_nbind());
	// _nbpop => nombre de populations
	
	unsigned long i, l, locus;
	unsigned long nblocus(_VcalcLocus.size());
	unsigned long nblocusdivise;
	long double ** tabfreq1;
	long double ** tabfreq2;
	tabfreq1 = (_PtabFreq + (pop1 * _nbloc));
	tabfreq2 = (_PtabFreq + (pop2 * _nbloc));

	nblocusdivise = nblocus;
	
	for (l = 0; l < nblocus; l++) {
		// l numero du locus
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}

		sommeu = 0;
		alpha1 = 0;
		alpha2 = 0;
		
		for (i = 0; i < _tabNbAll[locus]; i++) {
			//i numero de l'allele
			if (_Pjeupop->_tabPloc[locus]->getPall(i)->_miss) continue;
			//frequence de l'allele  i dans la population 1
			alpha1 += ( (*(tabfreq1[locus] + i)) * (*(tabfreq1[locus] + i)) );

			//frequence de l'allele  i dans la population 2
			alpha2 += ( (*(tabfreq2[locus] + i)) * (*(tabfreq2[locus] + i)) );

			intermediaire = ((*(tabfreq1[locus] + i)) - (*(tabfreq2[locus] + i)));
			intermediaire *= intermediaire;
			sommeu += intermediaire;
		}
		sommeu /= ((long double) 2);
		
		alpha1 = (long double)1 - alpha1;
		alpha2 = (long double)1 - alpha2;
		
		al = (effpop1 * alpha1);
		al += (effpop2 * alpha2);
		al /= (((long double)4 * effpop1 * effpop2) * (effpop1 + effpop2 - (long double)1));
		
		alpbl = (((long double)4 * effpop1 * effpop2) - effpop1 - effpop2);
		alpbl *= al;
		
		al *= (effpop1 + effpop2);
		al *= (- (long double)1);
		
		al += sommeu;
		alpbl += sommeu;
		
		
		//Sracinelocus += (Salleles / ((long double)2 * nblocus));
		sommetheta += (al / alpbl);
	}

	if (nblocusdivise < 1) throw Anomalie(3);
	sommetheta /= ((long double)nblocusdivise);

	return ( - log ((long double)1 - sommetheta));
}

long double DistancesGnt::r_dpopReynoldsWeighted(unsigned long pop1,unsigned long pop2) const {

	//distance de Reynolds (1983) entre 2 populations
	// tir� de {Reynolds, J.} and {Weir, B.S.} and {Cockerham, C.}
	// "Estimation of the coancestry coefficient: basis for a short-term genetic distance"
	// Genetics society of America
	// 105: 767-779.1983.

	long double al, alpbl;
	long double sommeal(0);
	long double sommealpbl(0);
	long double sommeu(0);
	long double thetaw(0);
	long double alpha1(0), alpha2(0);
	long double intermediaire;
	long double effpop1(_tabPstrucpop[pop1]->get_nbind()), effpop2(_tabPstrucpop[pop2]->get_nbind());
	// _nbpop => nombre de populations
	
	unsigned long i, l, locus;
	unsigned long nblocus(_VcalcLocus.size());
	unsigned long nblocusdivise;
	long double ** tabfreq1;
	long double ** tabfreq2;
	tabfreq1 = (_PtabFreq + (pop1 * _nbloc));
	tabfreq2 = (_PtabFreq + (pop2 * _nbloc));

	nblocusdivise = nblocus;
	
	for (l = 0; l < nblocus; l++) {
		// l numero du locus
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}

		//sommeal = 0;
		//sommealpbl = 0;
		sommeu = 0;
		alpha1 = 0;
		alpha2 = 0;
		
		for (i = 0; i < _tabNbAll[locus]; i++) {
			//i numero de l'allele
			if (_Pjeupop->_tabPloc[locus]->getPall(i)->_miss) continue;
			//frequence de l'allele  i dans la population 1
			alpha1 += ( (*(tabfreq1[locus] + i)) * (*(tabfreq1[locus] + i)) );

			//frequence de l'allele  i dans la population 2
			alpha2 += ( (*(tabfreq2[locus] + i)) * (*(tabfreq2[locus] + i)) );

			intermediaire = ((*(tabfreq1[locus] + i)) - (*(tabfreq2[locus] + i)));
			intermediaire *= intermediaire;
			sommeu += intermediaire;
		}
		sommeu /= ((long double) 2);
		
		alpha1 = (long double)1 - alpha1;
		alpha2 = (long double)1 - alpha2;
		
		al = (effpop1 * alpha1);
		al += (effpop2 * alpha2);
		al /= (((long double)4 * effpop1 * effpop2) * (effpop1 + effpop2 - (long double)1));
		
		alpbl = (((long double)4 * effpop1 * effpop2) - effpop1 - effpop2);
		alpbl *= al;
		
		al *= (effpop1 + effpop2);
		al *= (- (long double)1);
		
		al += sommeu; // al
		alpbl += sommeu; // al + bl
		
		
		//Sracinelocus += (Salleles / ((long double)2 * nblocus));
		sommeal += al;
		sommealpbl += alpbl;
	}

	if (nblocusdivise < 1) throw Anomalie(3);
	thetaw = sommeal / sommealpbl;

	return ( - log ((long double)1 - thetaw));
}


long double DistancesGnt::r_dpopReynoldsLeast(unsigned long pop1,unsigned long pop2) const {

	//distance de Reynolds (1983) entre 2 populations
	// tir� de {Reynolds, J.} and {Weir, B.S.} and {Cockerham, C.}
	// "Estimation of the coancestry coefficient: basis for a short-term genetic distance"
	// Genetics society of America
	// 105: 767-779.1983.

	long double al, alpbl, bl;
	long double sommealcarre(0);
	long double sommeblcarre(0);
	long double sommealbl(0);
	long double sommeu(0);
	long double thetal1(0);
	long double thetal2(0);
	long double alpha1(0), alpha2(0);
	long double intermediaire;
	long double effpop1(_tabPstrucpop[pop1]->get_nbind()), effpop2(_tabPstrucpop[pop2]->get_nbind());
	// _nbpop => nombre de populations
	
	unsigned long i, l, locus;
	unsigned long nblocus(_VcalcLocus.size());
	unsigned long nblocusdivise;
	long double ** tabfreq1;
	long double ** tabfreq2;
	tabfreq1 = (_PtabFreq + (pop1 * _nbloc));
	tabfreq2 = (_PtabFreq + (pop2 * _nbloc));

	nblocusdivise = nblocus;
	
	for (l = 0; l < nblocus; l++) {
		// l numero du locus
		locus = _VcalcLocus[l];
		if ((_tabEviteLocus[(pop1 * _nbloc) + locus]) || (_tabEviteLocus[(pop2 * _nbloc) + locus])) {
			nblocusdivise--;
			continue;
		}

		//sommealcarre = 0;
		//sommeblcarre = 0;
		//sommealpbl = 0;
		sommeu = 0;
		alpha1 = 0;
		alpha2 = 0;
		
		for (i = 0; i < _tabNbAll[locus]; i++) {
			//i numero de l'allele
			if (_Pjeupop->_tabPloc[locus]->getPall(i)->_miss) continue;
			//frequence de l'allele  i dans la population 1
			alpha1 += ( (*(tabfreq1[locus] + i)) * (*(tabfreq1[locus] + i)) );

			//frequence de l'allele  i dans la population 2
			alpha2 += ( (*(tabfreq2[locus] + i)) * (*(tabfreq2[locus] + i)) );

			intermediaire = ((*(tabfreq1[locus] + i)) - (*(tabfreq2[locus] + i)));
			intermediaire *= intermediaire;
			sommeu += intermediaire;
		}
		sommeu /= ((long double) 2);
		
		alpha1 = (long double)1 - alpha1;
		alpha2 = (long double)1 - alpha2;
		
		al = (effpop1 * alpha1);
		al += (effpop2 * alpha2);
		al /= (((long double)4 * effpop1 * effpop2) * (effpop1 + effpop2 - (long double)1));
		
		alpbl = (((long double)4 * effpop1 * effpop2) - effpop1 - effpop2);
		alpbl *= al;
		
		al *= (effpop1 + effpop2);
		al *= (- (long double)1);
		
		al += sommeu; // al
		alpbl += sommeu; // al + bl
		bl = alpbl - al; // bl
		
		
		//Sracinelocus += (Salleles / ((long double)2 * nblocus));
		sommealcarre += (al * al);
		sommealbl += (al * bl);
		sommeblcarre += (bl * bl);
	}

	if (nblocusdivise < 1) throw Anomalie(3);
	
//cerr << "DistancesGnt::r_dpopReynoldsLeast" << endl;	
	//caclcul des 2 solutions possibles
	intermediaire = (long double)2 * (sommeblcarre - sommealcarre);
	al = (((long double)2 * sommealbl) + sommeblcarre + sommealcarre);
	bl = sqrt(((sommealcarre - sommeblcarre)*(sommealcarre - sommeblcarre)) + ( (long double)4 * sommealbl * sommealbl) );
	thetal1 = (al + bl) / intermediaire;
	thetal2 = (al - bl) / intermediaire;
	
//cerr << "numerateur de theta: " << intermediaire << endl;	
	
	// calcul des "Residual sum of squares" pour pouvoir choisir thetal1 ou thetal2
	alpbl = ((long double)2 * sommealbl) + sommealcarre + sommeblcarre;
	
	//al devient la Residual sum of squares 1
	intermediaire = ((long double)1 - ((long double)2 * thetal1) + ((long double)2 * thetal1 * thetal1));

//cerr << "numerateur de R1: " << intermediaire << endl;	
	al = ((alpbl * thetal1 * thetal1) - ((long double)2 * (sommealbl + sommealcarre) * thetal1) + sommealcarre) / intermediaire;
	
	//bl devient la Residual sum of squares 2
	intermediaire = ((long double)1 - ((long double)2 * thetal2) + ((long double)2 * thetal2 * thetal2));
//cerr << "numerateur de R2: " << intermediaire << endl;	
	bl = ((alpbl * thetal2 * thetal2) - ((long double)2 * (sommealbl + sommealcarre) * thetal2) + sommealcarre) / intermediaire;
	
	//calculs des distances:
//cerr << "thetal1: " << thetal1 << " thetal2: " << thetal2 << endl;	

//cerr << "D1: " << thetal1 << " D2: " << thetal2 << endl;	
//cerr << "R1: " << al << " R2: " << bl << endl;	
	if ((al < bl) && (thetal1 < 1)) return (- log ((long double)1 - thetal1));
	else if (thetal2 < 1) return (- log ((long double)1 - thetal2));
	else throw Anomalie(5);
}
populations-1.2.33+svn0120106.orig/src/jeupopexp.cpp0000644000175000017500000002676010531115342022166 0ustar  georgeskgeorgesk/***************************************************************************
                          jeupopexp.cpp  -  description
                             -------------------
    begin                : Tue Oct 24 2000
    copyright            : (C) 2000 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

//#include "strucpop.h"
#include "jeupopexp.h"

JeuPopExp::JeuPopExp(Jeupop * Pjeu):_Pjeu(Pjeu) {

	_Pcopie = 0;
}

JeuPopExp::~JeuPopExp(){
	if (_Pcopie != 0) delete _Pcopie;

}


void JeuPopExp::oLea(unsigned long P1,unsigned long P2,unsigned long H, ostream & sortie, ostream & infos) {
	f_prepP1P2H(P1,P2,H,infos);

	unsigned long nbpop;
	unsigned long nbloc(_Pcopie->get_nbloc());
	unsigned long nball;    //nb d'alleles pour chaque locus
	unsigned long i,l,p;
	Locus * Plocus;
	bool proms;

	nbpop = _Pcopie->get_nbpop();

	sortie << "0" << endl;
	sortie << nbpop << endl;
	sortie << nbloc << endl;

	for (l=0; l < nbloc; l++) {
		Plocus = _Pcopie->get_Plocus(l);
		nball = Plocus->get_nball();
		sortie << Plocus->get_nballnonnuls() <getPall(i)->r_nonnul()) {
//					sortie << _Pcopie->get_Ppop(p)->f_calcfreq(Plocus->getPall(i));
					sortie << _Pcopie->get_Ppop(p)->f_calcfreqabsolue(Plocus->getPall(i));
					if (proms) proms = false;
				}		
			}
			sortie << endl;		
		}
	}
	
}
/** Exportation au format "admix" de G. Bertorelle
voir le site:
http://www.unife.it/genetica/Giorgio/giorgio.html
 */
void JeuPopExp::oAdmix_dat(unsigned long P1,unsigned long P2,unsigned long H, ostream & sortie, ostream & infos){

	f_prepP1P2H(H,P1,P2,infos); //inversion de l'ordre pour corriger le bug trouvé par Andrea Taylor (15/5/2002)


	unsigned long nbpop;
	unsigned long nbloc(_Pcopie->get_nbloc());
	unsigned long nball;    //nb d'alleles pour chaque locus
	unsigned long i,l,p;
	Locus * Plocus;
	bool proms;

	nbpop = _Pcopie->get_nbpop();

	for (l=0; l < nbloc; l++) {
		Plocus = _Pcopie->get_Plocus(l);
		sortie << Plocus->get_nom() << endl;
		proms = true;		
		for (p=0; p < nbpop; p++) {
			// affichage du total (nb d'alles non nuls de chaque pop pour ce locus)
			if (!proms) sortie << " ";
			sortie << _Pcopie->get_Ppop(p)->r_nballnonnuls(l);
			if (proms) proms = false;		
		}
		sortie << endl;
		
		nball = Plocus->get_nball();
		for (i=0; i < nball; i++) {
			if (Plocus->getPall(i)->r_nonnul()) {
				proms = true;		
				for (p=0; p < nbpop; p++) {
					if (!proms) sortie << " ";
					sortie << _Pcopie->get_Ppop(p)->f_calcfreqabsolue(Plocus->getPall(i));
					if (proms) proms = false;
				}
				sortie << endl;		
			}	
		}
	}
}

void JeuPopExp::oAdmix_mtx(ostream & sortie, ostream & infos){
//	f_prepP1P2H(P1,P2,H,infos);

	unsigned long nbpop;
	unsigned long nbloc(_Pcopie->get_nbloc());
	unsigned long nball;    //nb d'alleles pour chaque locus
	unsigned long i,l,p;
	unsigned long diffcarre;
	Locus * Plocus;
//	bool proms;

	if (_Pcopie == 0) throw Anomalie(1, "Admix_mtx");
	nbpop = _Pcopie->get_nbpop();
	if (nbpop != 3) throw Anomalie(1, "Admix_mtx");

	sortie << nbloc << endl;
	for (l=0; l < nbloc; l++) {
		Plocus = _Pcopie->get_Plocus(l);
		sortie << Plocus->get_nom() << endl;
		nball = Plocus->get_nballnonnuls();
		// nb d'alleles différents non nuls pour ce locus
		sortie << nball << endl;
		// matrice de distance "squared difference in allele size"
		for (i=0; i < Plocus->get_nball(); i++) {
			if (Plocus->getPall(i)->r_estnul()) continue;
			for (p=0; p < i; p++) {
				if (Plocus->getPall(p)->r_estnul()) continue;
				diffcarre =(Plocus->getPall(p)->get_nbrepet() - Plocus->getPall(i)->get_nbrepet());
				diffcarre *= diffcarre;
				sortie << diffcarre << " ";				
//cerr << ",nrepet:" << Plocus->getPall(p)->get_nbrepet();
			}
			sortie << "0" << endl;
		}
	}
}

/** Prépare une copie de jeupop avec 3
populations P1, P2, H (special admixture) */
void JeuPopExp::f_prepP1P2H(unsigned long P1,unsigned long P2,unsigned long H, ostream & infos){
	unsigned long nbpop(_Pjeu->get_nbpop());
	unsigned long p;
	Population * PP1;
	Population * PP2;
	Population * PH;
	Population * Ppop;
	//-------préparation des données:
	if (_Pcopie != 0) delete (_Pcopie);
	_Pcopie = new Jeupop(*_Pjeu);

	PP1 = _Pcopie->get_Ppop(P1);
	PP2 = _Pcopie->get_Ppop(P2);
	PH = _Pcopie->get_Ppop(H);

	_Pcopie->f_deplacePop(PP1,0);
	_Pcopie->f_deplacePop(PP2,1);
	_Pcopie->f_deplacePop(PH,2);


//cerr << "JeuPopExp::oAile" << endl;
//cerr << _Pcopie->get_nbpop() << " " <<_Pcopie->get_nbind() << endl;

  p=nbpop;
	while (nbpop > 3) {
		p--;
	  Ppop = _Pcopie->get_Ppop(p);
		if (Ppop == PP1) continue;
		if (Ppop == PP2) continue;
		if (Ppop == PH) continue;
		_Pcopie->SupprPop(Ppop);
		nbpop--;
//cerr << _Pcopie->get_nbpop() << " " <<_Pcopie->get_nbind() << endl;
	}

//	_Pcopie->oGenepop(cout);	
	// elimination des alleles inutiles (non présents dans l'échantillon)
	_Pcopie->f_nettoieAlleles();

}

void JeuPopExp::oGenetix(ostream & sortie, ostream & infos){
// sortie au format Genetix
// http://www.univ-montp2.fr/~genetix/genetix.htm
// 1ere ligne : nb de locus
// 2eme ligne : nb de populations
//description des locus:
// nom de locus sur une ligne (5 caracteres max)
// nombre d'alleles, et numéros d'allèles sur 3 chiffres
// description des populations:
// nom de population sur une ligne
// taille de l'échantillon sur une ligne
// Identifiant de l'individu sur 10 caractères, suivi du génotype
// retour chariot : CRLF

//cerr << "JeuPopExp::oGenetix(ostream & sortie, ostream & infos)" << endl;
	unsigned long nbpop;
	unsigned long nbind;
	unsigned long nbloc(_Pjeu->get_nbloc());
	unsigned long nball;    //nb d'alleles pour chaque locus
	unsigned long i,l,p;
	Locus * Plocus;
	Population * Ppop;
	Individu * Pind;
	
	char crlf[3];
	
	crlf[0] = 13;
	crlf[1] = 10;
	crlf[2] = '\0';
//	bool proms;

	if (_Pjeu == 0) throw Anomalie(1, "Genetix");
	
	if (_Pjeu->get_nploidie() != 2) {
		//le format Genetix ne permet que le stockage de pop diploïdes
		throw Anomalie(100, "Genetix");
	}

	if (!(_Pjeu->f_verifnum(3))) {
		//il faut renuméroter les allèles pour le format génétix
		throw Anomalie(2, "Genetix");
	}


	nbpop = _Pjeu->get_nbpop();
//	if (nbpop != 3) throw Anomalie(1);

	sortie << nbloc << crlf;
	sortie << nbpop << crlf;
	
	for (l=0; l < nbloc; l++) {
		Plocus = _Pjeu->get_Plocus(l);
		sortie << Plocus->get_nom() << crlf; //attention ! pas plus de 5 caractères
		if (Plocus->get_nom().size() > 5) throw Anomalie(1000, "Genetix");
		nball = Plocus->get_nball();
		// nb d'alleles pour ce locus
		sortie << Plocus->get_nballnonnuls();
		// matrice de distance "squared difference in allele size"
		for (i=0; i < nball; i++) {
			if (Plocus->getPall(i)->r_estnul() != true) {
				sortie << " ";
				if (Plocus->getPall(i)->get_nom().size() == 2) sortie << "0";
				else if (Plocus->getPall(i)->get_nom().size() == 1) sortie << "00";
				sortie << Plocus->getPall(i)->get_nom();
			}
		}
		sortie << crlf;
	}
	
	for (p=0; p < nbpop; p++) {
		// _Pcopie->get_Ppop(p);
		Ppop = _Pjeu->get_Ppop(p);
		sortie << Ppop->get_nom() << crlf;
		nbind = Ppop->get_nbind();
		sortie << nbind << crlf;
		
		for (i=0; i < nbind; i++) {
			Pind = Ppop->get_Pind(i);
			if (Pind->get_nom().size() > 10) throw Anomalie(1001, "Genetix");		
			Pind->affiche (sortie, 4); //affichage de l'individu au format genetix
			sortie << crlf;		
		}
	}
}

void JeuPopExp::oFstat(ostream & sortie, ostream & infos){
// sortie au format FSTAT 2.91
// http://www.unil.ch/izea/softwares/fstat.html
// 1ere ligne : nb de pop, nb de locus, plus grand numero d'allele, nb de digits
// nom des locus sur n lignes

	unsigned long nbpop;
	unsigned long nbind;
	unsigned long nbloc(_Pjeu->get_nbloc());
	unsigned long i,l,p;
	Locus * Plocus;
	Population * Ppop;
	Individu * Pind;
	char crlf[3];
	
	crlf[0] = 13;
	crlf[1] = 10;
	crlf[2] = '\0';
//	bool proms;

	if (_Pjeu == 0) throw Anomalie(1, "Fstat");
	
	if (_Pjeu->get_nploidie() != 2) {
		//le format Fstat ne permet que le stockage de pop diploïdes
		throw Anomalie(100, "Fstat");
	}

	if (!(_Pjeu->f_verifnum(2))) {
		//il faut renuméroter les allèles pour le format Fstat
		throw Anomalie(2, "Fstat");
	}


	nbpop = _Pjeu->get_nbpop();
//	if (nbpop != 3) throw Anomalie(1);

	p = 0;
	for (l=0; l < nbloc; l++) {
		if (_Pjeu->get_Plocus(l)->get_nballnonnuls() > p) p = _Pjeu->get_Plocus(l)->get_nballnonnuls();
	}
	
	//sortie << nbpop << "\t" << nbloc << "\t" << p << "\t2"<< crlf;
	sortie << nbpop << "\t" << nbloc << "\t" << "99" << "\t2"<< crlf;
	
	for (l=0; l < nbloc; l++) {
		Plocus = _Pjeu->get_Plocus(l);
		sortie << Plocus->get_nom() << crlf;
	}
	
	for (p=0; p < nbpop; p++) {
		// _Pcopie->get_Ppop(p);
		Ppop = _Pjeu->get_Ppop(p);
		nbind = Ppop->get_nbind();
		
		for (i=0; i < nbind; i++) {
			if (p < 9) sortie << "   ";
			else if (p < 99) sortie << "  ";
			else if (p < 999) sortie << " ";
			
			sortie << (p+1);
			Pind = Ppop->get_Pind(i);
			//if (Pind->get_nom().size() > 10) throw Anomalie(1001, "Fstat");		
			Pind->affiche (sortie, 5); //affichage de l'individu au format Fstat
			sortie << crlf;		
		}
	}
}

void JeuPopExp::oPopulationsXML(ostream & sortie, ostream & infos) const{
  unsigned int l, i, nball(0), nbloc(_Pjeu->get_nbloc());
	Locus * Plocus;
  biolib::vecteurs::ChaineCar idXML;
  
  //export into "populations" XML format
  // pas fini
  sortie << "" << endl;
  sortie << "" << endl;
  
  sortie << "" << endl;
  sortie << "" << endl;
	for (l=0; l < _Pjeu->get_commentaires().size(); l++) {
    sortie << _Pjeu->get_commentaires().operator[](l) << endl;
  }
  sortie << "" << endl;
  
  sortie << "" << endl;
	for (l=0; l < nbloc; l++) {
		Plocus = _Pjeu->get_Plocus(l);
    sortie << "get_nom() << "\"";
    sortie << ">" << endl;
		//if (Plocus->get_nom().size() > 5) throw Anomalie(1000, "Genetix");
		nball = Plocus->get_nball();
		// nb d'alleles pour ce locus
		for (i=0; i < nball; i++) {
      sortie << "getPall(i)->set_idXML((string) idXML);
      sortie << " id=\"" << Plocus->getPall(i)->get_idXML() << "\"";
      if (Plocus->getPall(i)->r_estnul()) sortie << " name=\"missing\"";
	  	else {
        sortie << " name=\"" << Plocus->getPall(i)->get_nom() << "\"";
	  	  sortie << " nbrepeat=\"" << Plocus->getPall(i)->get_nbrepet() << "\"";
      }
      sortie << ">" << endl;
      
      sortie << "" << endl;
		}
    sortie << "" << endl;
	}
  sortie << "" << endl;
  
  _Pjeu->get_Pracinepop()->oPopulationsXML(0, sortie, infos);

  sortie << "" << endl;
  
}

populations-1.2.33+svn0120106.orig/src/vecteurs.h0000644000175000017500000001233511326563351021457 0ustar  georgeskgeorgesk/***************************************************************************
 vecteurs.h  -  Librairie d'objets permettant
 de manipuler des vecteurs
 -------------------
 begin                : ven aug 14 10:25:55 CEST 2000
 copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
 email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

// Objets permettant de manipuler des vecteurs
// Olivier Langella le 12/5/99
// langella@pge.cnrs-gif.fr

#ifndef VECTEUR_H
#define VECTEUR_H

//#define __ENABLE_WSTRING

#include 
#include 
#include 
#include 
#include 
#include 

using namespace std;

namespace biolib {
namespace vecteurs {

class VecteurLD: public vector {
};

template class Vecteur: public vector {
public:

	unsigned long getNbOccurence(const T& element) const {
		unsigned long i;
		unsigned long res(0);

		for (i = 0; i < vector::size(); i++) {
			if (vector::operator[](i) == element)
				res++;
			//				if (this->operator[](i) == element) res++;
		}

		return (res);
	}

	bool Existe(const T& element) const {
		unsigned long i;
		bool res(false);

		for (i = 0; i < vector::size(); i++) {
			if (vector::operator[](i) == element) {
				res = true;
				break;
			}
		}

		return (res);
	}

	signed long Position(const T& element) const {
		unsigned long i;
		signed long res(-1);

		//	long taille(vector::size());

		for (i = 0; i < vector::size(); i++) {
			if (vector::operator[](i) == element) {
				res = i;
				break;
			}
		}
		return (res);
	}

	void Suppr(unsigned long pos) {
		erase(vector::begin() + pos);
	}

};

class ChaineCar: public string {
public:
	ChaineCar() {
		assign("");
	}

	ChaineCar(long i) {
		AjEntier(i);
	}

	ChaineCar(const char * tag) {
		assign(tag);
	}

	ChaineCar(const string& chaine) {
		assign(chaine);
	}

	~ChaineCar() {
	}

	void assigner(const string& chaine, signed long deb, signed long fin);

	operator double() const {
		return (atof(c_str()));
	}

	operator int() const {
		return (atoi(c_str()));
	}

	operator unsigned int() const {
		return (atoi(c_str()));
	}

	void GetLigneFlot(istream& entree);

	long GetNbMots() const; //retourne le nombre de mots contenus 
	void GetMot(unsigned int numero, string &mot) const;
	// dans la chaine (s�parateur= ' ' ou '/t')
	unsigned long GetNbMots(const string & separateur) const; //retourne le nombre de mots contenus
	void
	GetMot(unsigned int numero, string &mot, const string & separateur) const;

	const char * GetStr() {
		return (c_str());
	}
	;

	ChaineCar& AjEntier(long i); //conversion automatique en base 10 et concat�nation
	//	ChaineCar& operator+= (char car) {return (string::operator+=(car));};
	bool EstUnChiffre() const;

	void fmajus();
	void fsupprchiffres();
	void fsupprgauche();
	void fsupprdroite();
	void fnettoie(const string &);
	/** remplacer les occurences de "couper" par "coller" */
	void Remplacer(const string & couper, const string & coller);
	int Position(const string & motif) const;

	//	const ChaineCar& operator= (const string &rval) {*this = (ChaineCar) rval; return (*this);};

	//	const ChaineCar& operator= (const char * chaine) ;
};

class Titre: public vector {

public:
	~Titre();
	Titre() {
	}

	//	Titre(const Titre& rval);
	Titre(char ** commandes, int nbcommandes);

	//d�pr�ci�:
	const ChaineCar& get_titre(long i) const {
		return (*(vector::operator[](i)));
	}

	ChaineCar& GetTitre(long i) const;
	void GetArguments(const string &);
	ChaineCar& operator[](unsigned long i) const {
		if (i >= size())
			throw Anomalie(1);
		return (GetTitre(i));
	}

	ChaineCar& back() {
		return (*(vector::back()));
	}

	long Position(const ChaineCar& chaine) const;

	void push_back(const char * pcar) {
		vector::push_back(new ChaineCar(pcar));
	}
	;
	void push_back(const string & chaine) {
		vector::push_back(new ChaineCar(chaine.c_str()));
	}

	void pop_back() {
		delete vector::back();
		vector::pop_back();
	}

	void resize(long nouvtaille);

	//	void Suppr (unsigned long pos) {if (pos >= size()) throw Anomalie(1); delete (operator[](pos)); erase(begin()+pos);};
	void Suppr(unsigned long pos);

	const Titre& operator=(const Titre &rval);
	bool operator==(const Titre &rval);
	Titre operator+(const Titre &rval) const;

	//string & affiche() const;

public:

	struct Anomalie {
		Anomalie(int i) :
			le_pb(i) {
		}

		// 1-> titre inexistant
		int le_pb;
	};
};

void GetLigneFlot(istream& entree, string & ligne);

} //namespace biolib {
} //namespace vecteurs {

#endif

populations-1.2.33+svn0120106.orig/src/individu.cpp0000644000175000017500000002625610531115342021762 0ustar  georgeskgeorgesk/***************************************************************************
                          individu.cpp  -  description
                             -------------------
    begin                : Thu Sep 14 2000
    copyright            : (C) 2000 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/


#include "individu.h"
#include "population.h"
#include "jeupop.h"


void Individu::creation (Population * Ppop) {
	_Ppop = Ppop;
	_nploidie = Ppop->get_nploidie();
	if (Ppop->get_nploidie() == 0) _nploidie = 0;
	else _nploidie = Ppop->get_nploidie();
	_tabPall.resize(Ppop->get_nbloc() * _nploidie);
}

//constructeur
Individu::Individu (Population * Ppop) {

	creation(Ppop);
	_nom.assign("");
}

Individu::Individu (Population * Ppop, const string& nom) {

	creation(Ppop);
	_nom.assign(nom);
}

//destructeur
Individu::~Individu () {
//cerr << "Individu::~Individu ()" << endl;
//	delete [] _tabPall;
}

void Individu::resize_alleles() {
	
	_nploidie = _Ppop->get_nploidie();
	_tabPall.resize(_Ppop->get_nbloc() * _nploidie);	
}

const Individu& Individu::operator= (const Individu & rval) {
	unsigned long i; //index
	unsigned long j; //locus
	string nomlocus;
	unsigned long nball(rval._tabPall.size());
	unsigned long nploidie(_Ppop->get_nploidie());
	unsigned long nbloc(_Ppop->get_nbloc());

	if (_tabPall.size() != nball) throw Anomalie (1);


	_nom = rval._nom;

//cerr << "operator= individu debut " << _nom << endl;
	for (j=0; j < nbloc; j ++) {
		nomlocus = rval._Ppop->_Pjeu->get_nomlocus(j);
		for (i=0; i < nploidie; i ++) {
//cerr << "operator= individu numall " << (j*nploidie) + i << endl;
			if (rval._tabPall[(j * nploidie) + i] == 0) {
				_tabPall[(j * nploidie) + i] = (_Ppop->_Pjeu->get_Plocus(nomlocus))->getPallNul();
			}
			else {
//cerr << "operator= individu nom de l'allele " << rval._tabPall[(j * nploidie) + i]->_nom << endl;
				_tabPall[(j * nploidie) + i] = _Ppop->get_Pall(nomlocus, rval._tabPall[(j * nploidie) + i]->_nom);
			}
		}
	}
//cerr << "operator= individu fin" << endl;

	return(*this);
}

bool Individu::r_estnul() const {
	long i; //index
	long nball(_tabPall.size());

	for (i=0; i < nball; i ++) if (_tabPall[i]->_miss == false ) return (false);
	return (true);
}

bool Individu::r_esthetero (unsigned long locus) const {
	//lancer une exception si l'individu n'est pas diploide !!!!

	unsigned long nploidie(_Ppop->get_nploidie());
	unsigned long nbloc(_Ppop->get_nbloc());

	if (locus >= nbloc) throw Anomalie(11);
	if (nploidie != 2) throw Anomalie(12);

	if ((_tabPall[(locus * 2)]->_miss)||(_tabPall[(locus * 2)+1]->_miss)) {
		throw Anomalie(13);
		return(false);
	}
	if (_tabPall[(locus * 2)] == _tabPall[(locus * 2) + 1]) return(false);
	else return (true);

}

bool Individu::operator== (const Individu & rval) const {

	//pas operationnel !!!!

	unsigned long i; //index
	unsigned long j; //locus
	string nomlocus;
	unsigned long nball(rval._tabPall.size());
	unsigned long nploidie(_Ppop->get_nploidie());
	unsigned long nbloc(_Ppop->get_nbloc());

//	cerr << "truc";
	if (rval == 0) {
//		cerr << "truc";
		nball = _tabPall.size();
		for (i=0; i < nball; i ++) if (_tabPall[i]->_miss == false ) return (false);
		return (true);
	}

	if (_tabPall.size() != nball) return (false);


//	_nom = rval._nom;

	for (j=0; j < nbloc; j ++) {
//		nomlocus = rval._Ppop->_Pjeu->get_nomlocus(j);
		for (i=0; i < nploidie; i ++) {
			if (_tabPall[(j*nploidie) + i] != rval._tabPall[(j*nploidie) + i]) return (false);
//			_tabPall[(j*nploidie) + i] = _Ppop->get_Pall(nomlocus, rval._tabPall[(j*nploidie) + i]->_nom);
		}
	}

	return(true);
}


Individu::Individu (const Individu & rval, Population * Ppop){
	unsigned long i; //index
	unsigned long j; //locus
	string nomlocus;
	unsigned long nball(rval._tabPall.size());
//cerr << "Individu::Individu construct copie début "<< nball << endl;
	unsigned long nploidie(Ppop->get_nploidie());
//cerr << "Individu::Individu construct copie début "<< nball << endl;
	unsigned long nbloc(Ppop->get_nbloc());

//cerr << "Individu::Individu construct copie début " << endl;
	_Ppop = Ppop;
	resize_alleles();
	if (_tabPall.size() != nball) throw Anomalie (1);

	_nom = rval._nom;

//cerr << "operator= individu debut " << _nom << endl;
	for (j=0; j < nbloc; j ++) {
		nomlocus = rval._Ppop->_Pjeu->get_nomlocus(j);
		for (i=0; i < nploidie; i ++) {
//cerr << "operator= individu numall " << (j*nploidie) + i << endl;
			if (rval._tabPall[(j * nploidie) + i] == 0) {
				_tabPall[(j * nploidie) + i] = (_Ppop->_Pjeu->get_Plocus(nomlocus))->getPallNul();
			}
			else {
//cerr << "operator= individu nom de l'allele " << rval._tabPall[(j * nploidie) + i]->_nom << endl;
				_tabPall[(j * nploidie) + i] = _Ppop->get_Pall(nomlocus, rval._tabPall[(j * nploidie) + i]->_nom);
			}
		}
	}
//cerr << "operator= individu fin" << endl;
//cerr << "Individu::Individu construct copie fin " << endl;

}


void Individu::ifPlacerAllele(Locus* Ploc, long position, const Allele * Pall) {
	// numall < nploidie
//	long position((Ploc->get_numloc()
//cerr << "coucou 3" << endl;
	if ((_tabPall[position] == 0) || (_tabPall[position]->_miss)) {
		//on remplace, normal
//cerr << "coucou 3 if" << endl;
		_tabPall[position] = Ploc->getPall(Pall->get_nom());
	}
	else {
		if (*_tabPall[position] == *Pall) {
			//c'est bon
			return;
		}
		else {
			// ca veut dire qu'il y a un allele, et qu'il est different
			//   => pb, mais on ignore pour l'instant
			return;
		}
	}
}

void Individu::ifFusionnerIndividu(const Individu& individu) {
	unsigned long nbloc(_Ppop->get_nbloc());
	unsigned long nploidie(_Ppop->get_nploidie());
	unsigned long taille,i,j;
	Locus * Ploc;
//	string nomloc;

	taille = nbloc * nploidie;

	while (_tabPall.size() < taille) {
		_tabPall.push_back(0);
	}
//cerr << "coucou 1" << endl;

	taille = individu._tabPall.size();
	for (i = 0; i < taille; i += nploidie) {
		Ploc = _Ppop->_Pjeu->get_Plocus(individu._tabPall[i]->get_NomLocus());
//cerr << "coucou 2" << Ploc->get_nom() << endl;
		for (j=0; j < nploidie; j++) {
			ifPlacerAllele(Ploc,((Ploc->get_numloc() * nploidie) + j),individu._tabPall[i+j]);
		}
	}
}


unsigned long Individu::r_nballnonnuls(unsigned long locus, unsigned int nploidie) const {
	// retourne le nb de copies d'allèles non nuls pour un locus
	unsigned long resultat(0);
	unsigned int j;
	
	for (j=0;j < nploidie;j++) {
		if (_tabPall[(locus * nploidie) + j]->_miss) continue;
		resultat++;
	}

	return(resultat);
}


const string& Individu::get_nom_all(unsigned long numlocus, unsigned long numall) const {
//	unsigned long nploidie(_Ppop->get_nploidie());
	unsigned long nbloc(_Ppop->get_nbloc());

	if (numlocus >= nbloc) throw Anomalie(11);
	if (numall >= _nploidie) throw Anomalie(12);

	return(_tabPall[(numlocus * _nploidie) + numall]->get_Nom());
}



void Individu::affiche (ostream& sortie, int choix) const {
	unsigned long i,j;
	unsigned int nploidie(_Ppop->get_nploidie());

	switch (choix) {
	case 1:
		//affichage d'un individu au format genepop
		sortie << _nom << " ,";

		for (i=0;i< _tabPall.size(); i+=2) {
			sortie << " " << _tabPall[i]->_nom << _tabPall[i+1]->_nom;
		}
		break;		

	case 2:
		//affichage d'un individu au format genepop en tenant compte des introgressions
		sortie << _nom << " ,";

		for (i=0;i< _tabPall.size(); i+=2) {
			sortie << " ";
			if (_Ppop->_tabAllIntrogressant.Existe(_tabPall[i])) {
				sortie << "00";
			}
			else {
				sortie << _tabPall[i]->_nom;
			}
			if (_Ppop->_tabAllIntrogressant.Existe(_tabPall[i+1])) {
				sortie << "00";
			}
			else {
				sortie << _tabPall[i+1]->_nom;
			}
		}
		break;

	case 3:
		//affichage d'un individu au format populations en tenant compte des introgressions
		sortie << _nom << " ,";

		for (i=0;i< _tabPall.size(); i+=nploidie) {
			for (j=0; j < nploidie; j++) {
				if (j==0) sortie << " ";
				else sortie << ":";
				if (_Ppop->_tabAllIntrogressant.Existe(_tabPall[i+j])) {
					sortie << "*";
				}
				if (_tabPall[i+j]->r_estnul()) {
					sortie << "00";
				}
				else {
					sortie << _tabPall[i+j]->_nom;
				}
	//			sortie << _tabPall[i+j]->_nom;
			}
		}
		break;
	case 4:
		//affichage d'un individu au format genetix
		sortie << _nom;
		for (i=0; i < (10 - _nom.size());i ++) sortie << " ";

		for (i=0;i< _tabPall.size(); i+=2) {
			if ((_tabPall[i]->r_estnul()) || (_tabPall[i+1]->r_estnul())) sortie << " 000000";
			else {
				sortie << " ";
				if (_tabPall[i]->_nom.size() == 2) sortie << "0";
				else if (_tabPall[i]->_nom.size() == 1) sortie << "00";
				sortie << _tabPall[i]->_nom;
				if (_tabPall[i+1]->_nom.size() == 2) sortie << "0";
				else if (_tabPall[i+1]->_nom.size() == 1) sortie << "00";
				sortie << _tabPall[i+1]->_nom;
				
			}
		}
		break;		
	case 5:
		//affichage d'un individu au format Fstat

		for (i=0;i< _tabPall.size(); i+=2) {
			if ((_tabPall[i]->r_estnul()) || (_tabPall[i+1]->r_estnul())) sortie << "\t0";
			else sortie << "\t" << _tabPall[i]->_nom << _tabPall[i+1]->_nom;
		}
		break;		
	default:
		break;
	}

}


unsigned long Individu::get_nballnuls (unsigned long locus) const {
	//retourne le nombre d'alleles nuls de l'individu pour le locus
//	long taille (_tabPall.size());
	unsigned long i;
//	unsigned long nploidie(_Ppop->get_nploidie());
	unsigned long resultat(0);

	for (i = 0; i < _nploidie; i++) {
		if (_tabPall[(locus * _nploidie) + i]->_miss) resultat++;
	}
	return(resultat);
}
/** Suppresssion d'un locus */
void Individu::supprLocus(unsigned int numlocus){
	unsigned int nbloc(_Ppop->get_nbloc());
	unsigned int i;

	if (numlocus >= nbloc) throw Anomalie(11);

	for (i = 0; i < _nploidie; i ++) {
		_tabPall.Suppr(numlocus * _nploidie);
	}		
}

void Individu::oPopulationsXML(unsigned int id, ostream & sortie, ostream & infos) const {
  unsigned int i, j, nploidie(_Ppop->get_nploidie()), nbloc(_Ppop->get_nbloc());
  biolib::vecteurs::ChaineCar idXML;

  sortie << "get_idXML();
  idXML += "i";
  idXML.AjEntier(id);
  //set_idXML(idXML);
  sortie << " id=\"" << idXML << "\"";
  sortie << " nploidy=\"" << nploidie << "\"";
  sortie << " name=\"" << get_nom() << "\"";
  sortie << ">" << endl;

  for (i=0; i < nbloc; i++) {
    sortie << "get_idXML();
      if (j < (nploidie-1)) sortie << " ";
    }
    sortie << "\">";
    sortie << "" << endl;
  }

  sortie << "" << endl;
  


}

void Individu::set_Pallele (Allele * Pall, unsigned int pos) {
  unsigned int nploidie(get_nploidie());
  
  if (pos >= nploidie) throw Anomalie(12);

  pos = (Pall->get_Ploc()->get_numloc() * nploidie) + pos;

  _tabPall[pos] = Pall;
  
}
populations-1.2.33+svn0120106.orig/src/jeupop.cpp0000644000175000017500000012625110531115342021445 0ustar  georgeskgeorgesk/***************************************************************************
                          jeupop.cpp  -  Librairie d'objets permettant de manipuler des donn�es
                          						sp�cifiques aux populations
                             -------------------
    begin                : ven sep 06 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/



#include "jeupop.h"
#include "distgnt.h"

//constructeur
Jeupop::Jeupop () {

//cerr << "Jeupop::Jeupop ()  debut" << endl;


	_nbpop = 0;
	_nbloc = 0;
	_nploidie = 0;

	_tabPpop.resize(0);
	_tabPloc.resize(0);

	_Pracinepops = new MetaPop(this);
//cerr << "Jeupop::Jeupop ()  fin" << endl;
}

/*Jeupop::Jeupop (long nbpop, long nbloc) {
	long i;


	_nbpop = nbpop;
	_nbloc = nbloc;
	_nploidie = 0;

	_tabPpop.resize(0);
	_tabPloc.resize(0);
//	_tabPpop = new (Population*[nbpop]);
//	_tabPloc = new (Locus*[nbloc]);

	for (i=0;i < nbpop;i++) _tabPpop.push_back(new Population (this));
	for (i=0;i < nbloc;i++) _tabPloc.push_back(new Locus (this,0));

	_Pracinepops = new MetaPop(this);

}
*/
Jeupop::Jeupop(const Jeupop& original) {
	//constructeur de copies
	unsigned long i;

//cerr << "Jeupop::Jeupop construct copie debut " << endl;
	_nploidie = original.get_nploidie();
	_commentaires = original._commentaires;

//cerr << "Jeupop::Jeupop construct delete _Pracine " << endl;
//	delete _Pracinepops;
//cerr << "Jeupop::Jeupop construct delete _Pracine " << endl;
	_tabPpop.resize(0);
//cerr << "Jeupop::Jeupop construct delete _Pracine " << endl;
//	for (i=0;i < _tabPloc.size();i++) delete (_tabPloc[i]);
	_tabPloc.resize(0);


 	_nbloc = original.get_nbloc();
	for (i=0;i < _nbloc;i++) {
//cerr << "Jeupop::Jeupop construct copie locus " << endl;
		_tabPloc.push_back(new Locus (*original._tabPloc[i], this));
	}

//cerr << "Jeupop::Jeupop construct copie metapop " << endl;
	_Pracinepops = new MetaPop(*original._Pracinepops,0, this);
//cerr << "Jeupop::Jeupop construct copie fin " << endl;
}

//destructeur
Jeupop::~Jeupop () {
	unsigned long i;

	//for (i=0;i < _tabPpop.size();i++) delete (_tabPpop[i]);
	for (i=0;i < _tabPloc.size();i++) delete (_tabPloc[i]);

	delete _Pracinepops;
}


void Jeupop::reset() {

	unsigned long i;

//cerr << "Jeupop::reset(long nbpop, long nbloc) debut"<< endl;
	_nbloc = _tabPloc.size();
	delete _Pracinepops;
	_tabPpop.resize(0);
	_nbpop = 0;

	for (i=0;i < _nbloc;i++) delete (_tabPloc[i]);
	_nbloc = 0;
	_tabPloc.resize(0);
	_VcalcStrucPop.resize(0);
	_VcalcLocus.resize(0);

	
	_Pracinepops = new MetaPop(this);	

//cerr << "Jeupop::reset(long nbpop, long nbloc) fin" << endl;

}


void Jeupop::oGenepopCano(ostream& sortie) const{
	//�criture de fichiers au format genepop
	//    type canonique (avec Pop nomdepop)
// pas adapt�e � un traitement sur fichiers haploides
	unsigned long i,j;
	char car(0);
	unsigned long nbpop(get_nbpop());
	unsigned long nbloc(get_nbloc());
	unsigned long nbind;
	int format(1);

	if (_nploidie != 2) {
		//le format Genepop ne permet que le stockage de pop diplo�des
		throw Anomalie(1);
	}

	if (!(f_verifnum(1))) {
		//il faut renum�roter les all�les pour le format genepop
		throw Anomalie(2);
	}


	//commentaires
	car = '"';
	if (_commentaires.size() == 0) sortie << car << endl;
	else {
		sortie << _commentaires.get_titre(0) << endl;
		for (i=1; i < _commentaires.size(); i++) {
			sortie << car << _commentaires.get_titre(i) << endl;
		}
	}

	//nom des locus
	for (i=0; i < nbloc;i++) {
		sortie << _tabPloc[i]->get_nom() << endl ;
	}

	// populations
	for (i=0; i < nbpop;i++) {
		sortie << "POP " << _tabPpop[i]->get_nom_chemin() << endl ;
		// individus
		if (_tabPpop[i]->_tabAllIntrogressant.size() > 0) format = 2;
		else format = 1;


		nbind = _tabPpop[i]->get_nbind();
		for (j=0; j < nbind;j++) {
			_tabPpop[i]->_tabPind[j]->affiche(sortie,format);
			sortie << endl;
		}
	}
	
}

void Jeupop::oGenepop(ostream& sortie) const{
	//�criture de fichiers au format genepop
// pas adapt�e � un traitement sur fichiers haploides
	long i,j;
	char car;
	long nbpop(get_nbpop());
	long nbloc(get_nbloc());
	long nbind;
	int format(1);

	if (_nploidie != 2) {
		//le format Genepop ne permet que le stockage de pop diplo�des
		throw Anomalie(1);
	}

	if (!(f_verifnum(1))) {
		//il faut renum�roter les all�les pour le format genepop
		throw Anomalie(2);
	}


	//nom des populations
	car = '"';
	sortie << car;

	i = 0;
	for (i=0; i < (nbpop-1);i++) {
		sortie << _tabPpop[i]->get_nom() << ";" ;
	}
	sortie << _tabPpop[i]->get_nom() << car << endl;


	//nom des locus
	for (i=0; i < nbloc;i++) {
		sortie << _tabPloc[i]->get_nom() << endl ;
	}

	// populations
	for (i=0; i < nbpop;i++) {
		sortie << "POP" << endl ;
		// individus
		if (_tabPpop[i]->_tabAllIntrogressant.size() > 0) format = 2;
		else format = 1;

		nbind = _tabPpop[i]->get_nbind();
		for (j=0; j < nbind;j++) {
			_tabPpop[i]->_tabPind[j]->affiche(sortie,format);
			sortie << endl;
		}
	}
	
}

void Jeupop::oPopulations(ostream& sortie) const{
	//�criture de fichiers au format populations
// adapt� � toutes les ploidies
	unsigned long i,j;
	char car;
	unsigned long nbpop(get_nbpop());
	unsigned long nbloc(get_nbloc());
	unsigned long nbind;
	int format(3);

	//commentaires
//cerr << "Jeupop::oPopulations(ostream& sortie)" << _commentaires.size()  << "comm size" << endl;
	car = '"';
	if (_commentaires.size() == 0) sortie << car << endl;
	else {
		for (i=0; i < _commentaires.size(); i++) {
			sortie << car << _commentaires.get_titre(i) << endl;
		}
	}

//	sortie << _tabPpop[i]->get_nom() << car << endl;


	//nom des locus
	for (i=0; i < nbloc;i++) {
		sortie << _tabPloc[i]->get_nom() << endl ;
	}
//cerr << "Jeupop::oPopulations(ostream& sortie) 2" << endl;

	// populations
	for (i=0; i < nbpop;i++) {
		sortie << "POP " << _tabPpop[i]->get_nom_chemin() << endl ;
//cerr << "Jeupop::oPopulations(ostream& sortie) pop " << _tabPpop[i]->get_nom_chemin() << endl;
		// individus
		nbind = _tabPpop[i]->get_nbind();
//cerr << "Jeupop::oPopulations(ostream& sortie) nbind " << nbind << endl;
		for (j=0; j < nbind;j++) {
			_tabPpop[i]->_tabPind[j]->affiche(sortie,format);
			sortie << endl;
		}
	}
//cerr << "Jeupop::oPopulations(ostream& sortie) 3" << endl;
	
}

void Jeupop::oImmanc(ostream& sortie) const{
	//format d'entr�e pour :
	//Immanc - detects individual that are immigrants or have recent immigrant ancestry
    //by using multilocus genotypes. 
    //Version 5.0, released October 8, 1998    
    //Reference: Rannala, B., and J.L., Mountain. 1997. Detecting immigration by using
    //multilocus genotypes. Proceedings of the National Academy of Sciences USA 94:
    //9197-9201. 

// pas adapt�e � un traitement sur fichiers haploides
	if (_nploidie != 2) {
		//le format Immanc ne permet que le stockage de pop diplo�des
		throw Anomalie(1);
	}

	if (!(f_verifnum(1))) {
		//il faut renum�roter les all�les pour le format Immanc
		throw Anomalie(2);
	}

	long i,j,k, nbind, nbloc(get_nbloc()), nbpop(get_nbpop());
	string nomloc; 
	string nompop; 
	for (i=0; i< nbloc-1;i++) {//scan de chaque locus
		nomloc = _tabPloc[i]->_nom;
		for (j=0; j< nbpop;j++) {//scan des pops
			nompop = _tabPpop[j]->get_nom();
			nbind = _tabPpop[j]->get_nbind();
			for (k=0; k < nbind;k++) {// scan des individus
				//nom de l'ind, nom de la pop, nom du locus, les 2 all�les
				sortie << " " << _tabPpop[j]->_tabPind[k]->_nom;
				sortie << " " << nompop;
				sortie << " " << nomloc;
				sortie << " " << _tabPpop[j]->_tabPind[k]->_tabPall[i * 2]->_nom;
				sortie << " " << _tabPpop[j]->_tabPind[k]->_tabPall[(i * 2) + 1]->_nom;
				sortie << " " << endl;
			}
		}
	}	
}

void Jeupop::oMsat(ostream& sortie) const{
	//format d'entr�e pour :
	//distances microsat de D. Goldstein

	if (!(f_verifnum(2))) {
		//les noms d'alleles ne correspondent pas a des tailles de microsat
		throw Anomalie(2);
	}

	// 1 ligne = 1 allele, d'un locus d'un individu

	long i,j,k,l , nbind, nbloc(get_nbloc()), nbpop(get_nbpop());
	long nploidie(get_nploidie());
	string nomind;
	string nomloc; 
	string nomall;

	Individu * Pind;

	for (i=0; i< nbpop;i++) {//scan des pops
		nbind = _tabPpop[i]->get_nbind();
		for (j=0; j< nbind;j++) {// scan des individus
		//	nomind = _tabPpop[i]->_tabPind[j]->get_nom();
			Pind = _tabPpop[i]->_tabPind[j];
			nomind = Pind->get_nom();

			for (k=0; k < nbloc;k++) {// scan des locus
				nomloc = _tabPloc[k]->_nom;

				for (l=0; l < nploidie;l++) {// scan des alleles
					nomall = Pind->get_nom_all(k,l);
					//nom de l'ind, nom de la pop, nom du locus, les 2 all�les
					sortie << nomind << " " << nomloc << " " << nomall << endl;
				}
			}
		}
	}	
}

void Jeupop::oMsatFreq(ostream& sortie) const{
	//format d'entr�e pour :
	//distances microsat de D. Goldstein

	if (!(f_verifnum(2))) {
		//les noms d'alleles ne correspondent pas a des tailles de microsat
		throw Anomalie(2);
	}

	// 1 ligne = 1 allele, d'un locus d'un individu

	long i,k,l , nball, nbloc(get_nbloc()), nbpop(get_nbpop());
//	long nploidie(get_nploidie());
	string nompop;
	string nomloc; 
	string nomall;

//	Individu * Pind;

	for (i=0; i< nbpop;i++) {//scan des pops
		nompop = _tabPpop[i]->get_nom();


		for (k=0; k < nbloc;k++) {// scan des locus
			nomloc = _tabPloc[k]->_nom;
			nball = _tabPloc[k]->get_nball();

			for (l=0; l < nball;l++) {// scan des alleles
				nomall = _tabPloc[k]->_tabPall[l]->get_Nom();
				//nom de l'ind, nom de la pop, nom du locus, les 2 all�les
				sortie << nompop << " " << nomloc << " " << nomall << endl;
				sortie << " " << _tabPpop[i]->r_nbcopall(_tabPloc[k]->_tabPall[l]) << endl;
			}
		}
	}	
}

/*int Jeupop::r_allcommun(Individu * pind1, Individu * pind2, unsigned int numlocus) const{
	//renvoi du nombre d'all�les en commun
	// fonctionne pour N ploides
	Vecteur tabPall1;
	unsigned int i,j;
	long pos;

	j = numlocus * _nploidie;

	for (i = 0; i < _nploidie; i++) {
		tabPall1.push_back(pind1->_tabPall[i+j]);
	}

	for (i = 0; i < _nploidie; i++) {
		pos = tabPall1.Position(pind2->_tabPall[i+j]);
		if (pos != -1) tabPall1.Suppr(pos);
	}

	return (_nploidie - tabPall1.size());
}
*/
/*
int Jeupop::r_allcommunnul(Individu * pind1, Individu * pind2, int numlocus) const{
	//renvoi du nombre d'all�les en commun
	// saute les all�les nuls
	// fonctionne pour N ploides
	Vecteur tabPall1;
	unsigned int i,j;
	int pos;

	j = numlocus * _nploidie;

	for (i = 0; i < _nploidie; i++) {
		tabPall1.push_back(pind1->_tabPall[i+j]);
	}

	for (i = 0; i < _nploidie; i++) {
		if (pind2->_tabPall[i+j]->_nul) {}
		else {
			pos = tabPall1.Position(pind2->_tabPall[i+j]);
			if (pos != -1) tabPall1.Suppr(pos);
		}
	}

	return (_nploidie - tabPall1.size());
}
*/
/*
long Jeupop::r_allcommunnul(Individu * pind1, Individu * pind2) const{
	//renvoi du nombre d'all�les en commun
	// saute les all�les nuls
	// fonctionne pour N ploides
	Vecteur tabPall1;
	int i,pos;
	long taille;

	taille = pind2->_tabPall.size();

	tabPall1 = pind1->_tabPall;

	for (i = 0; i < taille; i++) {
		if (pind2->_tabPall[i]->_nul) {}
		else {
			pos = tabPall1.Position(pind2->_tabPall[i]);
			if (pos != -1) tabPall1.Suppr(pos);
		}
	}

	return (taille - tabPall1.size());
}
*/

void Jeupop::f_rarefaction(MatriceLD& resultat, int effectif) const {

	//calcul de la nouvelle diversit� all�lique, pour un �chantillon
	// r�duit: r�sultats stock�s dans Matrice, int => effectif r�duit
	long i,j;
//	char temp[10];
	int nbloc(get_nbloc());
	int nbpop(get_nbpop());

	resultat.resize(nbpop,nbloc);

	resultat._titre.push_back("Nouvelle diversit� all�lique pour un effectif r�duit de : ");
	
//	resultat._titre[resultat._titre.size()-1] += itoa(effectif,temp,10);
	resultat._titre[resultat._titre.size()-1].AjEntier(effectif);
	resultat.SetType(1);
	resultat.SetFlag(3);

	for (i=0;i_nom;
	}

	for (j=0;j_nom;

		for (i=0;ir_rare(effectif,i);
//	cerr << "coucou";
		}
	}
}



const string & Jeupop::get_nomlocus(long nblocus) const {
	// donne le nom du locus nblocus
	return (_tabPloc[nblocus]->get_nom());
}

const string & Jeupop::get_nompop(long nbpop) const{
	// donne le nom de la populations nbpop
	return (_tabPpop[nbpop]->get_nom());

}

Locus* Jeupop::get_Plocus(const string & nom) const{
	// donne un pointeur sur le locus du nom 'nom'
	Locus* res;
	unsigned long i;

	res = 0;
	for (i=0; i < _tabPloc.size(); i++) {
		if(_tabPloc[i]->_nom == nom) {
			res = _tabPloc[i];
			break;
		}
	}
	if (res == 0) throw Anomalie(8);

	return (res);
}

Locus* Jeupop::get_Plocus(unsigned long i) const {
	// donne le pointeur sur le locus i
	if (i >= _tabPloc.size()) throw Anomalie(8);

	return (_tabPloc[i]);
}

Population* Jeupop::get_Ppop(string & nom) const{
	// donne un pointeur sur le locus du nom 'nom'
	Population* res;
	unsigned long i;

	res = 0;
	for (i=0; i < _tabPpop.size(); i++) {
		if(_tabPpop[i]->_nom == nom) {
			res = _tabPpop[i];
			break;
		}
	}
	if (res == 0) throw Anomalie(9);

	return (res);
}

Population* Jeupop::get_Ppop(unsigned long p) const{
	// donne un pointeur sur la population p
	if (p >= _tabPpop.size()) throw Anomalie(9);

	return (_tabPpop[p]);
}

/*
long double Jeupop::r_dist2pop(long double ** tabFreq1, long double ** tabFreq2, long * tabNbAll, Population * ppop1, Population * ppop2, int methode) const {
	//renvoi de la distance entre 2 Populations
	long double resultat(0);
	long double somme;
	long nbpop1(ppop1->get_nbind()), nbpop2(ppop2->get_nbind());
	long calcsomme(ppop1->get_nbind() * ppop2->get_nbind());
	long i,j;

	if (methode < 100) {
		//distance entre populations bas�e sur distances entre individus
		somme = 0;
		for (i=0; i < nbpop1; i++) {	//scan des individus de la pop1	
			for (j=0; j < nbpop2; j++) {	//scan des individus de la pop2
				try {
					somme += r_dist2ind(ppop1->get_Pind(i), ppop2->get_Pind(j), methode);
				}
				catch (Anomalie erreur) {
					if (erreur.le_pb == 6) calcsomme--;
				}
			}
		}
	
		if (calcsomme < 1) return (0);
		resultat = somme / calcsomme;
	}
	else {
		switch (methode) {
		case 101:
			// Nei's minimum genetic distance (1972)	
			resultat = r_dpopNei(tabFreq1, tabFreq2, tabNbAll, false);
			break;
		case 102:
			// Nei's standard genetic distance (1972)			
			resultat = r_dpopNei(tabFreq1, tabFreq2, tabNbAll, true);
			break;
		case 103:
			// Cavalli-Sforza and Edwards' (1967)			
			resultat = r_dpopCavalli(tabFreq1, tabFreq2, tabNbAll);
			break;

		case 104:
			// Nei et al's, Da (1983)
			resultat = r_dpopNeiDa(tabFreq1, tabFreq2, tabNbAll);
			break;
		case 106:
			// Goldstein et al. (1995a)
			resultat = r_dpopGoldsteinMu(tabFreq1, tabFreq2, tabNbAll);
			break;
		case 107:
			// Latter's Fst (1972)
			resultat = r_dpopFst(tabFreq1, tabFreq2, tabNbAll);
			break;
		case 108:
			// Prevosti et al.'s, Cp (1975)
			resultat = r_dpopPrevosti(tabFreq1, tabFreq2, tabNbAll);
			break;
		case 109:
			// Rogers', Dr (1972)
			resultat = r_dpopRoger(tabFreq1, tabFreq2, tabNbAll);
			break;
		case 110:
			// Goldstein et al. (1995b) Slatkin 1995
			resultat = r_dpopGoldsteinASD(tabFreq1, tabFreq2, tabNbAll);
			break;
		case 111:
			// Shriver et al's, Dsw (1995)
			resultat = r_dpopShriver(tabFreq1, tabFreq2, tabNbAll);
			break;

		}
	}

	return resultat;
}
*/


istream& operator>>(istream& ientree,Jeupop& LesPops) {
	int nbformat(5),i(1);
	char car;
	bool autre(true);

	ientree.get(car);
	if (ientree.fail()) {
		cerr << _("The file is not readable... ") << endl;
		throw Jeupop::Anomalie(5);
	}
	while ((autre) && (i < nbformat)) {
		try {
			ientree.clear();
			ientree.seekg(0);
			LesPops.iFichier(ientree,i);

			autre = false;
		}
		catch (Jeupop::Anomalie erreur) {
			if (erreur.le_pb > 0) {
				autre = true;
				if (i == (nbformat-1)) {
					cerr << _("unknown file format") << endl;
					autre = false;
					throw Jeupop::Anomalie(5);
				}
				erreur.le_pb = 0;
			}
		}
		i++;
	}

	return (ientree);
}

void Jeupop::iFichier(istream & entree, int i) {
//cerr << "Jeupop::iFichier debut " << i << endl;
	switch (i) {
		case 1:
			iPopulationsXML(entree);
//			set_nploidie(_nploidie);
			return;
		case 2:
			iGenepop(entree);
//			set_nploidie(_nploidie);
			return;
		case 3:
			iPopulations(entree);
//			set_nploidie(_nploidie);
			return;
		case 4:
			iGenetix(entree);
//			set_nploidie(_nploidie);
			return;
		default:
			return;
	}
}


void Jeupop::iGenepop(istream &fichier){
	//lecture de fichiers au format genepop
// pas adapt�e � un traitement sur fichiers haploides

//cerr << "Jeupop::iGenepop debut" << endl;
	ChaineFicPop lecturePop(fichier);
	biolib::vecteurs::ChaineCar mot;
	biolib::vecteurs::ChaineCar nomall1;
	biolib::vecteurs::ChaineCar nomall2;

	Titre titres;
	
	Population * Ppop;	
	Individu * Pind;

	unsigned int nbloc,i,j;
	unsigned int nbdigits(0);

//cerr << "Jeupop::iGenepop debut2" << endl;
	// lecture des commentaires
	try {
		lecturePop.get_titre(_commentaires);
	}
	catch (ChaineFicPop::Anomalie pb) {
		throw Anomalie(4);
	}
//cerr << "Jeupop::iGenepop get_titre " << _commentaires[0] << endl;

	reset();

	// lecture des locus
	try {
		lecturePop.get_locus(titres);
	}
	catch (ChaineFicPop::Anomalie pb) {
		throw Anomalie(4);
	}
	nbloc = titres.size();

	for (i=0; i < nbloc; i++) {
		_tabPloc.push_back(new Locus(this, 0));
		_tabPloc.back()->set_nom(titres[i]);
	}
//cerr << "Jeupop::iGenepop locus " << titres[0] << " " << nbloc << " " << _tabPloc.size() << endl;


	//lecture des populations
//	_nploidie = 2;
	set_nploidie(2);

	while (lecturePop.estunepop()) {
		//creation d'une nouvelle population
//cerr << "Jeupop::iGenepop get_nompop(mot) " << mot << endl;
		lecturePop.get_nompop(mot);
//cerr << "Jeupop::iGenepop get_nompop(mot) " << mot << endl;

		Ppop = NewPop(mot);
//cerr << "Jeupop::iGenepop get_nompop(mot) " << mot << endl;
		
		try {
			if (lecturePop.get_lignepop()==1) break;
		}
		catch (ChaineFicPop::Anomalie pb) {
			throw Anomalie(4);
		}
		while (lecturePop.estunindividu()) {
			//creation d'un nouvel individu
			lecturePop.get_nomind(mot);
			Pind = new Individu(_tabPpop.back(), mot);
			Ppop->AjouterIndividu(Pind);

			lecturePop.get_alleles(titres);

			if (titres.size() != nbloc) {//erreur
				cout << endl;
				cout << _("error in data file.") << endl;
				cout << _("wrong number of locus at line : ") << lecturePop.get_numeroligne() << endl;

				throw Anomalie(4);
			}
				
			//enregistrement de chaque locus
			for (i=0; i < nbloc; i++) {
				mot = titres[i];
				if (nbdigits == 0) nbdigits = (mot.size() / 2);
				if (nbdigits == 1) {
					throw Anomalie(4);
				}
				if (mot.size() != (nbdigits * 2)) {
					throw Anomalie(4);
				}
				if (mot.EstUnChiffre() == false) {
					throw Anomalie(4);
				}

				nomall1.assigner(mot, 0, nbdigits - 1);
				nomall2.assigner(mot, nbdigits, (nbdigits * 2) - 1);

				Pind->_tabPall[i*2] = _tabPloc[i]->getPall(nomall1);
				if (Pind->_tabPall[i*2] == 0) {
					Pind->_tabPall[i*2] = new Allele(_tabPloc[i], nomall1);
					_tabPloc[i]->_tabPall.push_back(Pind->_tabPall[i*2]);
				}

				Pind->_tabPall[i*2 + 1] = _tabPloc[i]->getPall(nomall2);
				if (Pind->_tabPall[i*2 + 1] == 0) {
					Pind->_tabPall[i*2 + 1] = new Allele(_tabPloc[i], nomall2);
					_tabPloc[i]->_tabPall.push_back(Pind->_tabPall[i*2 + 1]);
				}
			}

			try {
				if (lecturePop.get_lignepop()==1) break;
//				lecturePop.get_lignepop();
			}
			catch (ChaineFicPop::Anomalie pb) {
				throw Anomalie(4);
			}
		}//lecture est un individu
	}

	// traitement sp�cifique au cas des fichiers JM Cornuet
	if (lecturePop.get_boolnompop() == false) { //il n'y avait pas de noms de pop
		// derriere le mot cle pop => tentative d'extraction style JMC
//cerr << "coucou";

		// lecture des noms de populations dans les commentaires
		for (i=0,j=0; i < _commentaires.size(); i++) {
//cerr << "coucou " << _commentaires[i].GetNbMots(",") << " " << _tabPpop.size();
			if (_commentaires[i].GetNbMots(",") == _tabPpop.size()) {
				//extraction des noms;
				for (j=0; j < _tabPpop.size(); j++) {
					_commentaires[i].GetMot(j+1,_tabPpop[j]->_nom,",");
				}
				break;
			}
		}

		if (j ==  0) {
			//il n'y a vraiment pas de noms... on num�rote
			for (i=0; i < _tabPpop.size(); i++) {
				if (_tabPpop[i]->_nom == "") {
          ostringstream tampon;
					tampon << "POP_";
					tampon << (i+1);
          _tabPpop[i]->_nom = tampon.str();
				}
			}
		}
	}
}


void Jeupop::iPopulations(istream &fichier){
	//lecture de fichiers au format Populations
// adapt�s � un traitement sur fichiers haploides
// 
// modification du 31/07/2000:
// rajout du mot cl� "DIFF" (nom d'all�le) qui permet de compter comme diff�rents 2 all�les
// utile pour le traitement de donn�es RFLP
// 
// refait le 07/9/2000

	ChaineFicPop lecturePop(fichier);
	biolib::vecteurs::ChaineCar mot;
	biolib::vecteurs::ChaineCar nomall;

	Titre titres;
	
	Population * Ppop;	
	Individu * Pind;
	Allele * Palldiff;
	Allele * Pall;

	bool allestintrogressant(false);

	unsigned int nbloc,i, j;

	// lecture des commentaires
	try {
		lecturePop.get_titre(_commentaires);
	}
	catch (ChaineFicPop::Anomalie pb) {
		throw Anomalie(4);
	}
//cerr << "Jeupop::iGenepop get_titre " << _commentaires[0] << endl;

	reset();

	// lecture des locus
	try {
		lecturePop.get_locus(titres);
	}
	catch (ChaineFicPop::Anomalie pb) {
		throw Anomalie(4);
	}
	_nbloc = nbloc = titres.size();

	for (i=0; i < nbloc; i++) {
		_tabPloc.push_back(new Locus(this, 0));
		_tabPloc.back()->set_nom(titres[i]);
	}
//cerr << "Jeupop::iGenepop locus " << titres[0] << " " << nbloc << " " << _tabPloc.size() << endl;


	//lecture des populations
	_nploidie = 0; //pas encore d�termin�

	while (lecturePop.estunepop()) {
		//creation d'une nouvelle population
		lecturePop.get_nompop(mot);
		Ppop = NewPop(mot);
		
		try {
			if (lecturePop.get_lignepop()==1) break;
//			lecturePop.get_lignepop();
		}
		catch (ChaineFicPop::Anomalie pb) {
			throw Anomalie(4);
		}
		while (lecturePop.estunindividu()) {
			//creation d'un nouvel individu
			//
			lecturePop.get_nomind(mot);
			
			Pind = new Individu(Ppop, mot);
			Ppop->AjouterIndividu(Pind);
		
//cerr << "Jeupop::iGenepop lecture: " <_nom);
//cerr << "Jeupop::iGenepop individu: " << Pind->_nom << endl;


			lecturePop.get_alleles(titres);
//cerr << "Jeupop::iGenepop alleles : " << titres.size() << endl;
//for (j =0 ; j < titres.size(); j++) cerr << titres[j] << " ";
			if (titres.size() != nbloc) {//erreur
				cout << endl;
				cout << _("error in data file.") << endl;
				cout << _("wrong number of locus at line : ") << lecturePop.get_numeroligne() << endl;

				throw Anomalie(4);
			}
//cerr << "Jeupop::iPopulations nbloc " <set_nploidie();
				}
				
//cerr << "Jeupop::iPopulations set_nploidie : " << mot.GetNbMots(":") << " "<< _nploidie << endl;
				if (mot.GetNbMots(":") != _nploidie) {//erreur
					cout << endl;
					cout << _("error in data file.") << endl;
					cout << _("wrong number of alleles at line : ") << lecturePop.get_numeroligne() << endl;

					throw Anomalie(4);
				}

				Palldiff = 0;
				for (j = 0; j < _nploidie; j++) { //boucle pour chaque allele d'un locus
					Pall = 0;
					allestintrogressant = false;
					
					mot.GetMot(j+1 ,nomall, ":");
					//cas des alleles introgressants:
					// marqu�s par une *
					if (nomall[0] == '*') {
//cerr << "Jeupop::iPopulations all introgressant" << endl;
						allestintrogressant = true;
						nomall.erase(0,1);
					}
//cerr << "Jeupop::iPopulations nomall" <<  nomall << endl;
				
					if ((Palldiff == 0) && (nomall == "DIFF")) {
						// creation d'un allele diff�rent pour ce locus pour cet individu
						Pall = Palldiff = new Allele(_tabPloc[i], "DIFF");
						Pind->_tabPall[i*_nploidie + j] = Palldiff;
						_tabPloc[i]->_tabPall.push_back(Palldiff);
					}
					else {
						if (nomall == "DIFF") {
							// assignation de l'all�le diff�rent
							Pind->_tabPall[i*_nploidie + j] = Pall = Palldiff;
						}
						else {
							// recherche de l'allele
							Pall = Pind->_tabPall[i*_nploidie + j] = _tabPloc[i]->getPall(nomall);
							
							if (Pall == 0) {
								// si la recherche n'a rien donner: creation de l'all�le
								Pall = Pind->_tabPall[i*_nploidie + j] = new Allele(_tabPloc[i], nomall);
								_tabPloc[i]->_tabPall.push_back(Pall);

							}
						}
					}

					if (allestintrogressant) {
						// si il n'est pas deja not� dans le tableau de la pop, l'indiquer
//cerr << "Jeupop::iPopulations all introgressant" << endl;
						Ppop->AjouterAllIntrogressant(Pall);
					//	allestintrogressant = false;
					}					
				}

			}

//Pind->affiche(cout,1);
			
			try {
				if (lecturePop.get_lignepop()==1) break;
//				lecturePop.get_lignepop();
			}
			catch (ChaineFicPop::Anomalie pb) {
				throw Anomalie(4);
			}
		} // boucle while (lecturePop.estunepop())
	} // boucle while (lecturePop.estunepop())
	
	// lecture des noms de populations dans les commentaires

/*	for (i=0; i < _tabPpop.size(); i++) {
		if (_tabPpop[i]->_nom == "_") {
			_tabPpop[i]->_nom = "POP_";
			_tabPpop[i]->_nom.AjEntier(i+1);
		}
	}*/
}

bool Jeupop::f_verifnum(int typedenum) const {
	// V�rification du type de num�rotation des all�les
//	1 => type Genepop stricte (2digits)
//	2 => nom d'alleles = num�ros
//	3 => nom d'alleles = num�ros < 999
		//Anomalie 2-> les num�ros d'all�les format genepop ne sont pas pr�sents

	long nbloc(get_nbloc());
	long i;

	for (i=0; i < nbloc; i++) {
		if (!(_tabPloc[i]->f_verifnum(typedenum))) return(false);
	}

	return(true);
}

void Jeupop::f_rempliVcalcStrucPop(unsigned int niveau) {
	// remplir le tableau _VcalcStrucPop,
	// en vue de calcul sur des m�tapopulations (ex: DistGnt)
	unsigned long i;

	f_resetVcalcStrucPop();
//cerr << "Jeupop::f_rempliVcalcStrucPop(unsigned int niveau) debut" << endl;
//	if (_VcalcStrucPop.size() != 0) return;

	if (niveau == 100) {
		//Populations normales
		_VcalcStrucPop.resize(_tabPpop.size());

		for (i = 0; i < _VcalcStrucPop.size(); i++) _VcalcStrucPop[i] = _tabPpop[i];
		return;
		
	}
	//cerr << "Jeupop::f_rempliVcalcStrucPop(unsigned int niveau) " << niveau << endl;
	_Pracinepops->f_rempliTabStrucPop(_VcalcStrucPop, niveau);

//cerr << "Jeupop::f_rempliVcalcStrucPop(unsigned int niveau)" << endl;
//for (i = 0; i < _VcalcStrucPop.size(); i++) cerr << _VcalcStrucPop[i]->get_nom();

}

void Jeupop::f_trad2Gpop(ostream& tableCorrespondances) {

	long nbloc(get_nbloc());
	long i;

// 1-> op�ration possible seulement sur les diploides
	if (get_nploidie() != 2) throw Anomalie(1);

	//verification sur le nombre d'alleles maximum (99)
	//pas fait
	tableCorrespondances << "correspondances Anciens_Noms <---> Noms_Genepop" << endl;
	for (i=0; i < nbloc; i++) {
		_tabPloc[i]->f_trad2Gpop(tableCorrespondances);
	}
}

void Jeupop::ifAjouterLocus(const Locus * Ploc) {
	//ajout d'un locus dans une pop, avec les alleles correspondants
	// => recherche un locus preexistant
	long i, taille(_tabPloc.size()), nbloc(-1);
	string nomloc;
	nomloc = Ploc->get_nom();

	for (i = 0 ; i < taille; i++) {
		if (nomloc == get_nomlocus(i)) {
			nbloc = i;
			break;
		}
	}
	if (nbloc >= 0) { //le locus existe deja
		//il faut ajouter les alleles que l'original n'a pas
		taille = Ploc->get_nball();
		for (i = 0; i < taille; i++ ){
			get_Plocus(nbloc)->ifAjouterAllele(Ploc->getPall(i));
		}
	}
	else { //il faut le creer, avec les alleles du nouveau locus
		_tabPloc.push_back(new Locus(*Ploc, this));
	}

	_nbloc = _tabPloc.size(); //precaution
}

/*void Jeupop::ifAjouterPop(const Population * Ppop) {
	//ajout d'un population dans un jeupop, avec les individus correspondants
	// => recherche d'une population preexistante
	long i, taille(get_nbpop()), nbpop(-1);
	const string nompop(Ppop->get_nom());

	for (i = 0 ; i < taille; i++) {
		if (nompop == get_nompop(i)) {
			nbpop = i;
			break;
		}
	}
	if (nbpop >= 0) { //la population existe deja
		//il faut ajouter les individus que l'original n'a pas
		// et completer les alleles des individus preexistants
		// pb � r�soudre: incoh�rence entre alleles d'un meme locus,
		//   d'un meme individu...
		get_pop(nbpop)->_nploidie = get_nploidie();
		get_pop(nbpop)->_nbloc = 0;// _Pjeu->get_nbloc();

		get_pop(nbpop)->resize_loc();

		taille = Ppop->get_nbind();
		for (i = 0; i < taille; i++ ){

//cerr << "if	ajouterpop" << endl;
			get_pop(nbpop)->ifAjouterIndividu(Ppop->get_Pind(i));
		}
	}
	else { //il faut creer une nouvelle population
		_tabPpop.push_back(new Population(this, *Ppop));
	}
}

*/
/*
Jeupop Jeupop::operator+ (const Jeupop &rval) const {
	long i , taille;

	if (get_nploidie() != rval.get_nploidie()) throw Anomalie(7);
	//	if (_nc != rval._nc) throw Anomalie(4);
//	for (i=0; i < rval._commentaires.size(); i++) {
//cerr << rval.GetTitre(i);
//		_commentaires.push_back(rval._commentaires.GetTitre(i));
//	}

//cerr << _commentaires[0] << " " << _commentaires[1];

	Jeupop Resultat;
	//on peut fixer la ploidie, et commencer � remplir Resultat
	// avec le 1er jeu de populations:
//cerr << "operator + debut " << endl;
	Resultat = *this;

	Resultat._commentaires = _commentaires + rval._commentaires;
	// Il faut savoir combien de locus differents comportera le r�sultat
	// => parcours du tableau de locus du 2eme JeuPop
	taille = rval.get_nbloc();
	for (i = 0; i < taille; i++) {
//cerr << "ajout locus " << i << endl;
		Resultat.ifAjouterLocus(rval.get_Plocus(i));
	}

	// A ce stade, Resultat contient tout le 1er jeupop 
	//    et tous les locus et alleles du 2eme
	//   Il faut maintenant remplir les populations de resultat
	taille = rval.get_nbpop();
	for (i = 0; i < taille; i++) {
//cerr << "ajout pop " << i << endl;
		Resultat.ifAjouterPop(rval.get_pop(i));
	}

	taille = Resultat.get_nbpop();
	for (i = 0; i < taille; i++) {
//cerr << "resize " << i << endl;
		Resultat.get_pop(i)->resize_loc();
	}

//cerr << "operator + fin " << endl;
	return Resultat;

}*/


void Jeupop::f_BootstrapLocus(Arbre &arbreRef, int methodeArbre, int methodeDist, bool square_distance, int nbrepet,bool sur_ind, Vecteur * PVcalcLocus) {
	// Boostrap sur les locus => arbre d'individus si sur_ind est vrai
	// Boostrap sur les locus => arbre de populations si sur_ind est faux
	// ********creer des exceptions pour v�rifier l'arbreRef *********

	DistancesGnt distgnt(methodeDist, square_distance, this);
	unsigned long i;

// pr�paration de _VcalcLoc:
	if (PVcalcLocus == NULL) {
		PVcalcLocus = new Vecteur;
		_VcalcLocus.resize(get_nbloc());
		PVcalcLocus->resize(get_nbloc());
		for (i = 0; i < _VcalcLocus.size(); i ++) {
			_VcalcLocus[i] = i;
			PVcalcLocus->operator[](i) = i;
		}
	}

	try {
		distgnt.f_bootstrapLocus(arbreRef, methodeArbre, nbrepet, PVcalcLocus, sur_ind);
	}
	catch (DistancesGnt::Anomalie lepb) {
		cerr << endl << lepb.fmessage() << endl;
		throw Anomalie(101);
	}
}

void Jeupop::f_BootstrapIndividus(Arbre &arbreRef, int methodeArbre, int methodeDist, bool square_distance, int nbrepet, Vecteur * PVcalcLocus) {
	// Boostrap sur les locus => arbre d'individus si sur_ind est vrai
	// Boostrap sur les locus => arbre de populations si sur_ind est faux
	// ********creer des exceptions pour v�rifier l'arbreRef *********

	DistancesGnt distgnt(methodeDist, square_distance, this);
	unsigned long i;

// pr�paration de _VcalcLoc:
	if (PVcalcLocus == NULL) {
		PVcalcLocus = new Vecteur;
		_VcalcLocus.resize(get_nbloc());
		PVcalcLocus->resize(get_nbloc());
		for (i = 0; i < _VcalcLocus.size(); i ++) {
			_VcalcLocus[i] = i;
			PVcalcLocus->operator[](i) = i;
		}
	}

	try {
		distgnt.f_bootstrapIndividus(arbreRef, methodeArbre, nbrepet, PVcalcLocus);
	}
	catch (DistancesGnt::Anomalie lepb) {
		cerr << endl << lepb.fmessage() << endl;
		throw Anomalie(101);
	}
}

void Jeupop::f_distgntpop (MatriceLD &resultat,int methode, bool square_distance, unsigned int niveau, Vecteur *PVcalcLocus) {
//cerr << "Jeupop::f_distgntpop debut" << endl;
	//distances G�n�tiques entre Populations 
	DistancesGnt distgntpop(methode, square_distance, this, niveau);
	unsigned long i;

// pr�paration de _VcalcLoc:
	if (PVcalcLocus == NULL) {
		_VcalcLocus.resize(get_nbloc());
		for (i = 0; i < _VcalcLocus.size(); i ++) {
			_VcalcLocus[i] = i;
		}
	}
	else {
		_VcalcLocus = *PVcalcLocus;
	}
//cerr << "Jeupop::f_distgntpop 1" << endl;

	try {
		distgntpop.f_distgntpop(resultat, &_VcalcLocus);
	}
	catch (DistancesGnt::Anomalie lepb) {
		cerr << endl << lepb.fmessage() << endl;
		throw Anomalie(101);
	}

//cerr << "Jeupop::f_distgntpop fin" << endl;

}

void Jeupop::f_distgnt (MatriceLD &resultat,int methode, bool square_distance,  Vecteur *PVcalcLocus) {
	//distances G�n�tiques entre individus 
	DistancesGnt distgntind(methode, square_distance, this);
	unsigned long i;
// pr�paration de _VcalcLoc:
//cerr << "f_distgnt (jeupop) deb" << endl;
	if (PVcalcLocus == NULL) {
		_VcalcLocus.resize(get_nbloc());
		for (i = 0; i < _VcalcLocus.size(); i ++) {
			_VcalcLocus[i] = i;
		}
	}
	else {
		_VcalcLocus = *PVcalcLocus;
	}

//	f_distgntVcalc (resultat, methode);
	
	try {
		distgntind.f_distgntInd(resultat, &_VcalcLocus);
	}
	catch (DistancesGnt::Anomalie lepb) {
		cerr << endl << lepb.fmessage() << endl;
		throw Anomalie(101);
	}
//cerr << "f_distgnt (jeupop) fin" << endl;

}


/*long Jeupop::get_numloc(Locus * Ploc) const {
	long i;
	
	for (i= 0; i < _nbloc; i++) {
//		cerr << "getnumloc" << endl;
		if (_tabPloc[i] == Ploc) return (i);
	}
	return (-1);
}*/



Population* Jeupop::get_pop(unsigned long numpop) const{
	if (numpop < get_nbpop()) { //ok
		return(_tabPpop[numpop]);
	}
	else {
		return (0);
	}
}

unsigned int Jeupop::get_nploidie() const {
	return(_nploidie);
}

unsigned long Jeupop::get_nbloc() const {
	return(_tabPloc.size());
}

unsigned long Jeupop::get_nbpop() const {
	return(_tabPpop.size());
}

unsigned long Jeupop::get_nbind() const {
	return(_Pracinepops->get_nbind());
}

/*Allele* Jeupop::get_Pall(int loc, int all) const {
	return(_tabPloc[loc]->_tabPall[all]);
}
*/

Allele* Jeupop::get_Pall(unsigned long loc, unsigned long all) const {
	return(_tabPloc[loc]->_tabPall[all]);
}

void Jeupop::get_nomniveauxstruc(Titre & nom_niveaux) const {

	_Pracinepops->get_nomniveauxstruc(nom_niveaux);
	
}


void Jeupop::set_nploidie(unsigned int nploidie) {
	_nploidie = nploidie;
	_nbloc = get_nbloc();

//cerr << "Jeupop::set_nploidie " << _nploidie << " " << _nbloc << endl;
	_Pracinepops->set_nploidie();
//cerr << "Jeupop::set_nploidie fin" << _nploidie << " " << _nbloc << endl;
}


void Jeupop::AjouterPopulation(Population * Ppop) {
//	_tabPpop.push_back(Ppop);
  //AjouterTabPop(Ppop);
	_Pracinepops->AjouterPopulation(Ppop);
}

void Jeupop::AjouterTabPop(Population * Ppop) {
	_tabPpop.push_back(Ppop);
	_nbpop++;
//	_Pracinepops->AjouterPopulation(Ppop);
}

Locus * Jeupop::new_locus(const string & name) {
  Locus * Plocus (new Locus(this, 0));
  Plocus->set_nom(name);
  _tabPloc.push_back(Plocus);
  return (Plocus);
}

Population * Jeupop::NewPop(const biolib::vecteurs::ChaineCar & chemin) {
// cr�ation de Population et de MetaPop en fonction du chemin
	Titre tabchemin;
	biolib::vecteurs::ChaineCar mot;
	unsigned long i;
	MetaPop * Pmetapop(_Pracinepops);
	Population * Ppop;

//cerr << "Jeupop::NewPop(ChaineCar & chemin) d�but " << endl;

	mot.assign("");

	for (i = 0; i < chemin.GetNbMots("/"); i ++) {
		chemin.GetMot(i+1,mot, "/");
		if (mot == "") continue;
		tabchemin.push_back(mot);
	}

	if (tabchemin.size() > 0) {
		for (i = 0; i < tabchemin.size()-1; i ++) {
			//cr�er une m�tapopulation
			Pmetapop = Pmetapop->NewMetaPop(tabchemin[i]);
			mot = tabchemin[tabchemin.size()-1];
		}
	}

	Ppop = new Population(Pmetapop);
//cerr << "Jeupop::NewPop(ChaineCar & chemin) set_nom " << endl;
	Ppop->set_nom(mot);
	
	Pmetapop->AjouterPopulation(Ppop);

//cerr << "Jeupop::NewPop(ChaineCar & chemin) fin " << endl;

	return (Ppop);
}


void Jeupop::affind (int numpop, int numind) const {
	_tabPpop[numpop]->_tabPind[numind]->affiche(cout,1);
}

/** Suppression de la population p du Jeupop */
void Jeupop::SupprPop(StrucPop * Ppop){
//cerr << "Jeupop::SupprPop debut" << endl;
	unsigned long i;
	
	_Pracinepops->SupprPop(Ppop);
	for (i = 0; i < _tabPpop.size(); i++) {
		if (_tabPpop[i] == Ppop) _tabPpop.Suppr(i);
	}
	_nbpop--;
//cerr << "Jeupop::SupprPop fin" << endl;
}
/** D�place la pop Ppop a � la position b */
void Jeupop::f_deplacePop(Population * Ppop, unsigned long b){
	signed long a;
	a = _tabPpop.Position(Ppop);
	if (a < 0) return;
	if (b > _tabPpop.size()) return;
	if ((unsigned long)a == b) return;
	
	_tabPpop[a] = _tabPpop[b];
	_tabPpop[b] = Ppop;
}
/** enl�ve les all�les qui ne sont pas repr�sent�s dans les populations
 */
void Jeupop::f_nettoieAlleles(){
	unsigned long l;

	for (l = 0; l < _tabPloc.size(); l++) _tabPloc[l]->f_nettoieAlleles();
}

/** Retourne vrai, si l'allele n'est pas pr�sent dans jeupop */
bool Jeupop::r_allelenonpresent(Allele * Pall) const{

	return(_Pracinepops->r_allelenonpresent(Pall));
}
/** construit le vecteur Vlocus avec les numeros de tous les locus */
void Jeupop::f_selectlocustous(vector & Vlocus) const{
	unsigned int nblocus(get_nbloc());
	unsigned int i;

	Vlocus.resize(0);
		
	for (i = 0; i < nblocus; i ++) Vlocus.push_back(i);	
}
/** Suppression des locus qui ne sont pas pr�sents dans Vnumloc */
void Jeupop::GarderVlocus(Vecteur & Vnumloc){

	unsigned int i;
	_nbloc = _tabPloc.size();

//cerr << "Jeupop::GarderVlocus " << _nbloc << endl ;
	for (i = _nbloc; i > 0 ; i--) {
//cerr << "Jeupop::GarderVlocus " << i-1 << endl ;
		// si i-1 n'est pas pr�sent dans  Vnumloc: on supprime le locus
		if (!Vnumloc.Existe(i-1)) supprLocus(i-1);
	}
}
/** Suppression d'un locus */
void Jeupop::supprLocus(unsigned int numlocus){
	unsigned long i;

	if (numlocus >= _tabPloc.size()) throw Anomalie(8);
	//suppression du locus chez tous les individus
	for (i = 0; i < _Pracinepops->_tabPind.size(); i++) _Pracinepops->_tabPind[i]->supprLocus(numlocus);
	
	delete _tabPloc[numlocus];
	_tabPloc.Suppr(numlocus);

	set_nbloc();
}
/** R�affectation du nombre de locus */
void Jeupop::set_nbloc(){

	_nbloc = _tabPloc.size();
	_Pracinepops->set_nbloc();

}
/** obtenir le num�ro d'un locus avec son nom */
signed int Jeupop::get_numloc(const string & nomlocus) const{
	signed int numloc(-1);
	unsigned int nbloc(get_nbloc()), i;

	for (i=0; i < nbloc; i++) {
//cerr << "Jeupop::get_numloc " << nomlocus << " " << _tabPloc[i]->get_nom()<get_nom()) {
			numloc = i;
			break;
		}
	}	

	return (numloc);	
}


void Jeupop::iGenetix(istream &fichier){
	//lecture de fichiers au format Genetix
// pas adapt�e � un traitement sur fichiers haploides ou nploides

//cerr << "Jeupop::iGenetix debut" << endl;
	ChaineFicPop objetGenetix(fichier);
	Titre titres;
	biolib::vecteurs::ChaineCar mot, nomall1, nomall2;
	
	Population * Ppop;	
	Individu * Pind;

	unsigned int nbpop, nbloc, nball(0), nbind, i,j, k;
	unsigned int nbdigits(3);

	reset();

	set_nploidie(2);

	objetGenetix.get_lignepop();
	objetGenetix.GetMot(1, mot);
	nbloc = (int) mot;
	if ((nbloc < 1) || (nbloc > 100)) throw Anomalie(5);
	_commentaires.push_back(objetGenetix);


//cerr << "Jeupop::iGenetix nbloc " << nbloc << endl;
	objetGenetix.get_lignepop();
	objetGenetix.GetMot(1, mot);
	nbpop = (int) mot;
//	fichier >> nbpop;
	if ((nbpop < 1) || (nbpop > 1000)) throw Anomalie(5);
	_commentaires.push_back(objetGenetix);

//cerr << "Jeupop::iGenetix nbpop " << nbpop << endl;

	//lecture et cr�ation des locus et des all�les
	for (i=0; i < nbloc; i++) {
		_tabPloc.push_back(new Locus(this, 0));
		objetGenetix.get_lignepop();
		_tabPloc.back()->set_nom(objetGenetix);	
//cerr << "Jeupop::iGenetix locus " << objetGenetix << endl;
		fichier >> nball;
		objetGenetix.get_lignepop();
		if (objetGenetix.GetNbMots() != (int) nball) throw Anomalie(5);
		for (j=0; j < nball; j++) {
			objetGenetix.GetMot(j+1, nomall1);
			_tabPloc[i]->_tabPall.push_back(new Allele(_tabPloc[i], nomall1));
		}
	}
	set_nbloc();

	for (i=0; i < nbpop; i++) {
		objetGenetix.get_lignepop();
		
		Ppop = NewPop(objetGenetix);

//cerr << "Jeupop::iGenetix pop " << objetGenetix << endl;
		objetGenetix.get_lignepop();
		if (objetGenetix.EstUnChiffre() == false) {
				cout << endl;
				cout << _("error in Genetix data file.") << endl;
				cout << _("wrong number of individuals at line : ") << objetGenetix.get_numeroligne() << endl;

				throw Anomalie(201);
		}
		else nbind = (unsigned int) objetGenetix;

//cerr << "Jeupop::iGenetix nbind " << nbind << endl;
		for (j=0; j < nbind; j++) {
			//creation d'un nouvel individu
			fichier >> mot;
			Pind = new Individu(_tabPpop.back(), mot);
			Ppop->AjouterIndividu(Pind);

//cerr << "Jeupop::iGenetix ind " << mot << endl;

			objetGenetix.get_lignepop();
			if (objetGenetix.GetNbMots() != (int) nbloc){
				cout << endl;
				cout << _("error in Genetix data file.") << endl;
				cout << _("wrong number of locus at line : ") << objetGenetix.get_numeroligne() << endl;

				throw Anomalie(201);
			}

			for (k=0; k < nbloc; k++) {
//cerr << "Jeupop::iGenetix nbloc nbmots " << nbloc << " " << objetGenetix.GetNbMots() << endl;
				objetGenetix.GetMot(k+1, mot);
				if (mot.EstUnChiffre() == false) {
					throw Anomalie(5);
				}
//cerr << "Jeupop::iGenetix mot " << mot << endl;
				nomall1.assigner(mot, 0, nbdigits - 1);
				nomall2.assigner(mot, nbdigits, (nbdigits * 2) - 1);

//cerr << "Jeupop::iGenetix all  " << nomall1 << " " << nomall2 << endl;
				if (nomall1 == "000") Pind->_tabPall[k*2] = _tabPloc[k]->getPallNul();
				else Pind->_tabPall[k*2] = _tabPloc[k]->getPall(nomall1);

				if (nomall2 == "000") Pind->_tabPall[k*2 + 1] = _tabPloc[k]->getPallNul();
				else Pind->_tabPall[k*2 + 1] = _tabPloc[k]->getPall(nomall2);
//cerr << "Jeupop::iGenetix Pall  " << Pind->_tabPall[k*2] << " " << Pind->_tabPall[k*2 + 1] << endl;
			}	
		}
	}
//cerr << "Jeupop::iGenetix fin "<< endl;
}

void Jeupop::iPopulationsXML(istream &fichier){
  #ifdef XMLREADPOPULATIONS_H
//cerr << "Jeupop::iPopulationsXML debut "<< endl;
  //  string mot;

  //  fichier >> mot;
//cerr << "Jeupop::iPopulationsXML mot " << mot << endl;
 //   if (mot != "iParseFlux(fichier);
cerr << "Jeupop::iPopulationsXML(istream &fichier)"        << endl;
    }
    catch (XMLreadPopulations::Anomalie pb) {
      cout << endl << pb.message << endl << endl;
      throw Jeupop::Anomalie(5);
    }
    
  #else
    throw Anomalie(5);
  #endif
}

void Jeupop::set_commentaires(const string & commentaires){
  _commentaires.push_back(commentaires);
}

populations-1.2.33+svn0120106.orig/src/individu.h0000644000175000017500000000653210531115342021422 0ustar  georgeskgeorgesk/***************************************************************************
                          individu.h  -  description
                             -------------------
    begin                : Thu Sep 14 2000
    copyright            : (C) 2000 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

// individu
#ifndef INDIVIDU_H
#define INDIVIDU_H

#include "allele.h"

using namespace biolib::vecteurs;

class Individu {
public :
//	
	Individu (Population *);
	Individu (Population * Ppop, const string& nom);
	Individu (Population *, const ConstGnt &, int);

	Individu (const Individu &, Population *);

//	Individu (int nball=0);
	~Individu();

	const Individu& operator= (const Individu &);
	bool operator== (const Individu &) const;
	bool r_estnul () const;
	bool r_esthetero (unsigned long locus) const;
	inline unsigned long r_nbcopall(Allele * Pall) const {return(_tabPall.getNbOccurence(Pall));};
	unsigned long r_nballnonnuls(unsigned long locus, unsigned int nploidie) const;

	inline unsigned long get_nballnuls () const;
	unsigned long get_nballnuls (unsigned long) const;
  void set_Pallele (Allele * Pall, unsigned int pos);

	inline const string& get_nom() const {return(_nom);};
  unsigned int get_nploidie() const {return(_nploidie);};
	const Vecteur& get_tabPall() const {return(_tabPall);};
	const string& get_nom_all(unsigned long numlocus, unsigned long numall) const;

	void resize_alleles();

	void affiche (ostream&, int) const;

	friend class Population;
	friend class StrucPop;
	friend class DistancesGnt;
	friend class Allele;
	friend class Jeupop;

	void ifFusionnerIndividu(const Individu& individu);
	void ifPlacerAllele(Locus* Ploc, long position, const Allele * Pall);

  void oPopulationsXML(unsigned int id, ostream & sortie, ostream & infos) const;

private :
	void creation (Population * Ppop);
  /** Suppresssion d'un locus */
  void supprLocus(unsigned int);

	string _nom;
//	char _nom[20];
	Population * _Ppop;
//	unsigned long _nball; //nb allèles= nb de loci* n ploidie
	unsigned int _nploidie;
	Vecteur _tabPall;

public:
	struct Anomalie{
		// 1-> copie impossible: pas le meme nombre d'alleles
		// 11-> numero de locus inexistant
		// 12-> numéro d'allele inexistant
		// 13-> un allele nul fausse la determination de l'heterozygotie de l'individu pour un locus
		int le_pb;
		Anomalie (int i):le_pb(i){};
	};

};


inline unsigned long Individu::get_nballnuls () const {
	//retourne le nombre d'alleles nuls de l'individu
	unsigned long taille (_tabPall.size());
	unsigned long i;
	unsigned long resultat(0);

	for (i = 0; i < taille; i++) {
		if (_tabPall[i]->_miss) resultat++;
	}
	return(resultat);
}

#endif

populations-1.2.33+svn0120106.orig/src/strucpop.h0000644000175000017500000001620010531115342021457 0ustar  georgeskgeorgesk
/***************************************************************************
                          strucpop.h  -  Librairie d'objets permettant de manipuler des données
                          						spécifiques aux StrucPops
                             -------------------
    begin                : ven sep 01 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/


#ifndef STRUCPOP_H
#define STRUCPOP_H


//#include"arbres.h"
#include "vecteurs.h"
#include "individu.h"

//typedef biolib::vecteurs::ChaineCar ChaineCar;

class Jeupop;
class MetaPop;


class StrucPop { //StrucPops structurée
public :
	StrucPop(Jeupop * pdonnees);
//constructeur de copies
	StrucPop(const StrucPop & popori, MetaPop * Pmetapop, Jeupop * Pjeu);
	//allocation et désallocation
//	StrucPop(int nbind = 0);
//	StrucPop(Jeupop * pdonnees, long nbind);
//	StrucPop(Jeupop * pdonnees, const StrucPop & popori);
//	StrucPop(const StrucPop &);
	virtual ~StrucPop();

	virtual bool DuType(const string &) const {return(false);};

	virtual void AjouterIndividu(Individu * Pind) {};
//	virtual void AjouterPopulation(StrucPop * Pstrucpop) {};
	virtual void AjouterPopulation(MetaPop * ) {};
	virtual void AjouterPopulation(Population * ) {};

	void AjouterAllIntrogressant(Allele * Pall);
	//génétique

	//**** fonctions de base
	Allele* get_Pall(unsigned long ind,unsigned long all) const;
	Allele* get_Pall(unsigned long ind, unsigned long locus, unsigned int numall) const;
	Allele * get_Pall(const string & nomlocus, const string & nomall) const;
	//nombre d'individus
	unsigned long get_nbind() const {return(_tabPind.size());};
//	long get_nbloc() const {return(_nbloc = _Pjeu->get_nbloc());}; 
	unsigned long get_nbloc() const {return(_nbloc);};
//	unsigned long get_nballloc(unsigned long i) const {return(_Pjeu->get_Plocus(i)->get_nball());};
	unsigned int get_nploidie() const {return(_nploidie);};
	virtual Individu* get_Pind(unsigned long i) const {return(_tabPind[i]);};
	inline Jeupop* get_Pjeu() const;
	//nom de la StrucPop
	//const char * get_nom() {return(_nom.c_str());};
	const string & get_nom() const {return(_nom);};
	const string & get_couleur() const {return(_couleur);};
	const string & get_nomind(long nbind) const;
	virtual void get_nomniveauxstruc(Titre & nom_niveaux) const {};
	virtual unsigned int get_niveau() const {return(0);};
	virtual unsigned long get_nbpop() const {return(0);};
	virtual MetaPop* get_Pmetapop() const {return(_Pmetapop);};
	virtual const string & get_idXML() const {return(_idXML);};

	virtual void set_nploidie() {};
	virtual void set_nom(const string & nom);

	//nombres d'allèles pour un locus
	void r_alldiff(int, Vecteur&) const; //num locus, tableau sur les Alleles differents de ce locus
	//nombres de copies d'un allèle d'un locus
	//pointeur sur allèle
//	Allele* r_Pall(int, int) const; //num locus, num allèle
	inline unsigned long r_nbcopall(Allele *) const; //num locus, num allèle
	inline unsigned long r_nbcopallBootInd(Allele *) const; //num locus, num allèle
	inline unsigned long r_nballnonnuls(unsigned long locus) const; //nombre d'alleles non nuls pour un locus
	unsigned long r_nballnonnulsBootInd(unsigned long locus) const;

	long double f_heterozygotieatt(unsigned long locus, unsigned long * Pnbpopcalc) const; //Hs
	long double f_heterozygotieobs(unsigned long locus, unsigned long * Pnbpopcalc) const;
	long double f_calcfreq(Allele * Pall) const;
	long f_calcfreqabsolue(Allele * Pall) const;

	//**** fonctions évoluées
	//raréfaction de l'effectif d'une StrucPop
	double r_rare(unsigned long, unsigned int) const; //nouvel effectif, num locus


	virtual void f_rempliTabStrucPop(Vecteur &, unsigned int) {};
	//const StrucPop& operator= (const StrucPop &);
  /** Suppression de la population */
  virtual void SupprPop(StrucPop * Ppop) {};

  /** réaffectation du nombre de locus */
  virtual void set_nbloc();

  virtual void oPopulationsXML(unsigned int id, ostream & sortie, ostream & infos) {};

  
	friend class DistancesGnt;
	friend class Jeupop;
	friend class Individu;

protected :
	virtual void set_idXML(const string & id) {_idXML=id;};
//	void sort_all();//tri de _tabPall par loci
	void resize_loc();
	virtual void reset();

	void f_bootstrap(); //bootstrap sur les individus

	virtual void ifAjouterIndividu(const Individu * Pind);

  /** Supprime l'individu Pind du tableau */
  void SupprtabIndividu(Individu * Pind);

	unsigned int _nploidie;
//	string _nom;
	string _nom;
	Jeupop * _Pjeu;
	MetaPop * _Pmetapop;
	
	unsigned long _nbind; //nb d'individus dans cette pop
	
	vector _tabPind;
	unsigned long _nbloc; //nb de loci
//	vector _tabPall;

	Vecteur _tabAllIntrogressant;

	vector _VcalcInd;

	string _couleur;

  string _idXML;


public:

	struct Anomalie{
		// 1-> acces hors borne dans alleles
		// 2-> copie impossible: nploidie differents
		// 3-> copie impossible: nbloc differents
		// 5-> copie impossible: nom d'allele non present dans le jeu de donnees
		// 6-> copie impossible: nom de locus non present dans le jeu de donnees
		// 7-> acces hors borne dans les locus
		int le_pb;
		Anomalie (int i):le_pb(i){};
	};

};



unsigned long StrucPop::r_nbcopallBootInd(Allele * Pall) const {
	// retourne le nb de copies d'un allèle pour un locus
	// specifique aux calculs avec bootstrap sur individus
	unsigned long resultat(0);
	unsigned long nbind(_VcalcInd.size());
	unsigned long i;
	
	for (i=0;i < nbind;i++) {
//		resultat += _VcalcInd[i]->_tabPall.getNbOccurence(Pall);
		resultat += _VcalcInd[i]->r_nbcopall(Pall);
	}

	return(resultat);
}

inline unsigned long StrucPop::r_nbcopall(Allele * Pall) const {
	// retourne le nb de copies d'un allèle pour un locus
	unsigned long resultat(0);
	unsigned long nbind(_tabPind.size());
	unsigned long i;
	
	for (i=0;i < nbind;i++) {
		resultat += _tabPind[i]->_tabPall.getNbOccurence(Pall);
//		resultat += _tabPind[i]->r_nbcopall(Pall);
	}

	return(resultat);
}


inline unsigned long StrucPop::r_nballnonnuls(unsigned long locus) const {
	// retourne le nb de copies d'allèles non nuls pour un locus
	unsigned long resultat(0);
	unsigned long nbind(_tabPind.size());
	unsigned long nploidie(get_nploidie());
	unsigned long i, j;
	
	for (i=0;i < nbind;i++) {
		for (j=0;j < nploidie;j++) {
			if (_tabPind[i]->_tabPall[(locus * nploidie) + j]->_miss) continue;
			resultat++;
		}
	}

	return(resultat);
}


inline Jeupop* StrucPop::get_Pjeu() const {
	return(_Pjeu);
}

#endif

populations-1.2.33+svn0120106.orig/src/distgnt.h0000644000175000017500000001455610531115342021270 0ustar  georgeskgeorgesk
/***************************************************************************
                          distgnt.h  -  Librairie d'objets permettant de manipuler
                          des distances entre populations
                             -------------------
    begin                : ven sep 01 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#ifndef DISTGNT_H
#define DISTGNT_H

#include 
//#include
#include 

#include "matrices.h"
#include "jeupop.h"
//class Arbre;

// calculs de distances génétiques
class DistancesGnt {
public :
	static const string & get_nom_methode(unsigned int methode);
	static unsigned int get_nb_methodes();

	DistancesGnt(int methode, bool square_distance, Jeupop * Pjeupop, unsigned int niveau=100);
	~DistancesGnt();

	unsigned long get_nbind() const;


private :
	static void f_rempli_tab_noms_methodes();

	void f_distgntpop (MatriceLD &resultat, Vecteur *PVcalcLocus);
	void f_distgntInd (MatriceLD &resultat, Vecteur *PVcalcLocus);
	void f_distgntpopDas(long double * Ptab) const;
	void f_distgntpopVcalc(long double * Ptab) const;
	void f_distgntIndVcalc (long double * Ptab) const;
	void f_bootstrapIndividus(Arbre &arbreRef, int methodeArbre, unsigned int nbrepet, Vecteur * PVcalcLocusRef);
	void f_bootstrapLocus(Arbre &arbreRef, int methodeArbre, unsigned int nbrepet, Vecteur * PVcalcLocus, bool sur_ind);
	long double r_dist2pop(unsigned long pop1, unsigned long pop2) const;
	long double r_dist2ind(unsigned long nbind1, unsigned long nbind2) const;
	long double r_dist2ind(Individu* Pind1, Individu* Pind2) const;
	long double r_allsimilnul(Individu * pind1, Individu * pind2) const;
	long double r_distDasPsAi(unsigned long nbind1, unsigned long nbind2) const;
	long double r_distDasPsAi(const Individu * Pind1, const Individu * Pind2) const;
	long double r_distDasMoyPsAB(const StrucPop * Ppop1, const StrucPop * Ppop2) const;
	long double r_distDasMoyPsA(const StrucPop * Ppop) const;

	long double r_dpopCavalli(unsigned long pop1, unsigned long pop2) const;
	long double r_dpopFst(unsigned long pop1,unsigned long pop2) const;
//	long double r_dpopFstClassique(long double ** tabfreq1,long double ** tabfreq2) const;
	long double r_dpopGoldsteinASD(unsigned long pop1,unsigned long pop2) const;
	long double r_dpopGoldsteinMu(unsigned long pop1,unsigned long pop2) const;
	long double r_dpopNei(unsigned long pop1,unsigned long pop2, bool standard) const;
	long double r_dpopNeiDa(unsigned long pop1,unsigned long pop2) const;
	long double r_dpopPrevosti(unsigned long pop1,unsigned long pop2) const;
	long double r_dpopRoger(unsigned long pop1,unsigned long pop2) const;
	long double r_dpopShriver(unsigned long pop1,unsigned long pop2) const;
	long double r_dpopZhivotovsky(unsigned long pop1,unsigned long pop2) const;
	long double r_dpopReynoldsUnweighted(unsigned long pop1,unsigned long pop2) const;
	long double r_dpopReynoldsWeighted(unsigned long pop1,unsigned long pop2) const;
	long double r_dpopReynoldsLeast(unsigned long pop1,unsigned long pop2) const;

	void f_calcTabFreq() const;
	void f_calcTabFreqInd() const;
	void f_calcTabFreqTot() const;
	void f_calcTabFreqBootInd() const;
	void f_calcTabMu() const;
	void f_calcTabMuInd() const;
	void f_calcTabMuBootInd() const;
	void f_calcTabBootInd() const;
	void newTabMu();
	void newTabMuInd();
	void newTabFreq();
	void newTabFreqInd();
	void newTabFreqTot();

//	static map _map_noms_methodes;
	static vector _tab_noms_methodes;
//	static vector _tab_numeros_methodes;

	Vecteur _VcalcLocus;
	Vecteur _tabPloc;
	vector _tabPind;
	vector _tabPstrucpop;

	Jeupop * _Pjeupop;
	int _methode;
	unsigned long _nbpop;
	unsigned long _nbloc;
	long double _pi;

	long double ** _PtabFreq;
	long double * _PtabFreqTot; // moyennes des fréquences allèliques sur toutes les pops
	long double * _PtabMu;
	unsigned long * _tabNbAll;
	bool * _tabEviteLocus;// pour ne pas tenir compte des locus qui ne contiennent que des allèles nuls

	bool _bootind;
	bool _squareDistance;

public:
	friend class Jeupop;

	struct Anomalie{
		// 1-> _methode non précisée, calcul impossible
		// 2-> Pas assez d'individus dans la pop pour calculer la distance

		int le_pb;
		Anomalie (int i, const string & nompop=""):le_pb(i){
			switch (i) {
			case 1:
				_message = _("ERROR 1 in \"DistancesGnt\": The distance method was not precised");
				break;
			case 2:
				_message = _("ERROR 2 in \"DistancesGnt\": Too few individuals in the population \"");
				_message += nompop;
				_message += _("\" to compute distances");
				break;
			case 3:
				_message = _("ERROR 3 in \"DistancesGnt\": division by zero computing allelic frequencies for population \"");
				_message += nompop;
				_message += "\"";
				break;
				
			case 4:
				//_message += "\"";
				_message = _("ERROR 4 in \"DistancesGnt\": this distance method \"");
				_message += nompop;
				_message += "\" could not be applied to individuals";
				break;
			
			case 5:
				//_message += "\"";
				_message = _("ERROR 5 in \"DistancesGnt\": log of a negative number is  not defined ");
				//_message += nompop;
				//_message += "\" could not be applied to individuals";
				break;
			
			case 6:
				//_message += "\"";
				_message = _("ERROR 6 in \"DistancesGnt\": this distance method does not exist ");
				//_message += nompop;
				//_message += "\" could not be applied to individuals";
				break;

			default:
				_message = _("ERROR in \"DistancesGnt\"");
				break;
			}
		};

		string _message;

		string& fmessage(){
			return(_message);
		}
	};


};

#endif

populations-1.2.33+svn0120106.orig/src/arbre.cpp0000644000175000017500000013533511606241313021243 0ustar  georgeskgeorgesk/***************************************************************************
                          arbre.cpp  -  description
                             -------------------
    begin                : Mon Dec 18 2000
    copyright            : (C) 2000 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/


#include "arbre.h"

namespace biolib {
namespace arbres {

Arbre::~Arbre() {
	//destruction des noeuds et individus
	unsigned int i;

	for (i=0; i < _tabPind.size(); i++) delete _tabPind[i];
	for (i=0; i < _tabPnoeuds.size(); i++) delete _tabPnoeuds[i];

}

Arbre::Arbre() {
	reset();
//	_oui_taille_branches = false;
//	_oui_bootstrap = false;
//	_Pracine = 0;
}

ArbreNdBase::ArbreNdBase(Arbre * Parbre) {
	
	_Parbre = Parbre;
}

ArbreNdBase::~ArbreNdBase() {
}

void ArbreNdBase::set_Pnoeud(unsigned int pos, ArbreNdBase * Pnoeud) {
	_tabPNoeuds[pos] = Pnoeud;
}

unsigned int ArbreNdBase::get_nbbranches() const {
	return(_tabPNoeuds.size());
}
bool ArbreNdBase::est_racine() const {
	return(false);
}

void ArbreNdBase::set_nom(const string & nom) {
}

ArbreNdOTU * Arbre::new_ArbreNdOTU(const string & nom) {
	unsigned int i, taille, j;
	ArbreNdOTU * Pindswap;

	_tabPind.push_back(new ArbreNdOTU(this, nom));


	Pindswap = _tabPind.back();

	taille = _tabPind.size();
	if ((taille == 1) || (nom == "")) {Pindswap->set_id(taille-1);return(Pindswap);}
//	_tabPind.back()->set_id(taille-1);
//classement de l'individu
	// on avance jusqu'à son emplacement:
	i = 0;
	while ((i < (taille-1)) && (strcmp(_tabPind[i]->get_reference(), Pindswap->get_reference()) < 0)) i++;

	_tabPind.back()->set_id(i);
	
	if ((taille-1) == i) return (Pindswap);

	
	for ( j = (taille-1); j > i; j--) {
		_tabPind[j] = _tabPind[j-1];
		_tabPind[j]->set_id(j);
	}
	_tabPind[i] = Pindswap;

	return(Pindswap);
}

ArbreNdOTU * Arbre::new_ArbreNdOTU(ArbreNdNoeud * PArbreNdNoeudPere) {
	_tabPind.push_back(new ArbreNdOTU(this, PArbreNdNoeudPere));
	_tabPind.back()->set_id(_tabPind.size()-1);
	return(_tabPind.back());
}

ArbreNdNoeud * Arbre::new_ArbreNdNoeud(unsigned int nbbranches){
//cerr << "Arbre::new_ArbreNdNoeud(unsigned int nbbranches)" << endl;
	_tabPnoeuds.push_back(new ArbreNdNoeud(this, nbbranches));
//cerr << "Arbre::new_ArbreNdNoeud(unsigned int nbbranches) fin" << endl;
	return(_tabPnoeuds.back());
}

ArbreNdNoeud * Arbre::new_ArbreNdNoeud(ArbreNdNoeud * PArbreNdNoeudere) {
	_tabPnoeuds.push_back(new ArbreNdNoeud(this, PArbreNdNoeudere));
	return(_tabPnoeuds.back());
}

void ArbreNdBase::f_chgt_sens(ArbreNdNoeud * Pracine, ArbreNdNoeud * Psens) {
//cerr << "ArbreNdBase::f_chgt_sens" << endl;

}

void ArbreNdNoeud::f_chgt_sens(ArbreNdNoeud * Pracine, ArbreNdNoeud * Psens) {
	//Psens devient le pointeur vers la racine de l'arbre
	// => a la place de tabPNoeuds[0]
	unsigned int i;
	unsigned int pos(0);
	unsigned int taille (_tabPNoeuds.size());
	ArbreNdBase * Pswap;
	float lgbranche;

//cerr << "ArbreNdNoeud::f_chgt_sens debut" << endl;

	Pswap = _tabPNoeuds[0];
	
	for (i=0; i < taille; i++) if (_tabPNoeuds[i] == Psens) pos = i;

	if (pos != 0) {

		_tabPNoeuds[0] = _tabPNoeuds[pos];
		_tabPNoeuds[pos] = Pswap;

		lgbranche = _tabLgBranches[0];
		set_longueur(0, _tabLgBranches[pos]);
	
//	_tabLgBranches[0] = _tabLgBranches[pos];
		set_longueur(pos, lgbranche);
//	_tabLgBranches[pos] = lgbranche;
	}

	if ( Pracine == this) {
		return;
//		_tabLgBranches[pos] = _tabPNoeuds[pos]->get_tabLgBranches(0);
	}
	else {
		Pswap->f_chgt_sens(Pracine, this);
	}
//cerr << "ArbreNdNoeud::f_chgt_sens fin" << endl;
	
}

void ArbreNdNoeud::f_chgt_racine(ArbreNdNoeud * Pancracine) {
//cerr << "ArbreNdNoeud::f_chgt_racine debut" << endl;
	if (_racine) {
		set_longueur(0, _tabLgBranches[0]);
		_tabPNoeuds[0]->f_chgt_sens(Pancracine, this);
//		if (_tabLgBranches[0] != -999) _tabLgBranches[0] = -999;

//cerr << "ArbreNdNoeud::f_chgt_racine " << Pancracine->get_nbbranches() << endl;
		if (Pancracine->get_nbbranches() == 1) { //le noeud est inutile
			// il faut le squizer
			_Parbre->SquizNoeud(Pancracine);
	  }
	}
	else {
		if (Pancracine == this) {
		}
	}
//cerr << "ArbreNdNoeud::f_chgt_racine fin" << endl;
}

void ArbreNdBase::oPhylipRec(ostream & fichier) const {}//écriture d'arbres au format Phylip

ArbreNdBase * ArbreNdBase::get_Pracine() const {
	return (_tabPNoeuds[0]);
}

double ArbreNdBase::get_tabLgBranches(unsigned int i) const{
	return (_tabLgBranches[i]);
}

double ArbreNdBase::get_longueur_branche() const{
	//longueur de la branche racine
	if (est_racine()) return(0);
	else return (_tabLgBranches[0]);
}

double ArbreNdNoeud::get_longueur_max() const {
	//donne la longueur de la plus grande branche
	double taille(-1), temp;
	unsigned int i;

//	if (_oui_taille_branche) {
		if (est_racine()) {
			temp = _tabPNoeuds[0]->get_longueur_max();
			if (taille < temp) taille = temp;
		}
		for (i=1; i < _tabPNoeuds.size();i++) {
			temp = _tabPNoeuds[i]->get_longueur_max();
			if (taille < temp) taille = temp;
		}
		temp = get_longueur_branche();
		if (temp < 0) return (taille);
		else return (temp + taille);
//	}
	return(0);
}

unsigned int ArbreNdNoeud::get_nbnoeuds_max() const {
	//donne le nombre de noeuds de la plus grande branche
	unsigned int i, temp, nbnoeuds(0);

//	if (_oui_taille_branche) {
		if (est_racine()) {
			temp = _tabPNoeuds[0]->get_nbnoeuds_max();
			if (nbnoeuds < temp) nbnoeuds = temp;
		}
		for (i=1; i < _tabPNoeuds.size();i++) {
			temp = _tabPNoeuds[i]->get_nbnoeuds_max();
			if (nbnoeuds < temp) nbnoeuds = temp;
		}
		return (1 + nbnoeuds);
//	}
}

double ArbreNdNoeud::get_val_bootstrap() const{
	return (_force);
}

ArbreNdBase * ArbreNdNoeud::get_Pracine() const {
	if (_racine) return(0);
	else return (_tabPNoeuds[0]);
}

void ArbreNdNoeud::AjBootstrap() {
	_accuvalboot++;
}

ArbreVectUINT* ArbreNdOTU::f_load_id_ind() {
	ArbreVectUINT * Ptab_id_ind;

//cerr << "ArbreNdOTU::f_load_id_ind debut" <push_back(_id);


//cerr << "ArbreNdOTU::f_load_id_ind fin" <f_load_id_ind());
	}
	else _tabP_tab_id_ind.push_back(new ArbreVectUINT);
  	
	for (i = 1; i < _tabPNoeuds.size(); i++) {
		_tabP_tab_id_ind.push_back(_tabPNoeuds[i]->f_load_id_ind());
	}
  if (_racine) return (0);

  Ptab_id_ind = new ArbreVectUINT;
//cerr << "ArbreNdNoeud::f_load_id_ind tri " << _tabP_tab_id_ind[0] << " " << _tabP_tab_id_ind[0]->size() << endl;	
	for (i = 1; i < _tabPNoeuds.size(); i++) {
//cerr << "ArbreNdNoeud::f_load_id_ind tri " << _tabP_tab_id_ind[i] << " " << _tabP_tab_id_ind[i]->size() << endl;	
		for (j = 0; j < _tabP_tab_id_ind[i]->size(); j++) {
			Ptab_id_ind->push_back(_tabP_tab_id_ind[i]->operator[](j));
		}
	}
	// => tri de  Ptab_id_ind

//cerr << "ArbreNdNoeud::f_load_id_ind tri" <f_tri();
//cerr << "ArbreNdNoeud::f_load_id_ind tri fin tri" <get_nbind());
//cerr << "ArbreNdNoeud::f_load_id_ind fin Ptab_id_ind " <affiche();
	for (i=0; i < nbind; i++) if (!Ptab_id_ind->Existe(i)) _tabP_tab_id_ind[0]->push_back(i);
//cerr << "ArbreNdNoeud::f_load_id_ind fin" <affiche();
//cerr <set_Pracine(this);
	}
	else {
		_racine = false;
		_tabPNoeuds.resize(1);
		_tabLgBranches.resize(1);
		_tabPNoeuds[0] = Pnoeud;
		_tabLgBranches[0] = 0;
		Pnoeud->AjouterFils(this);
	}
}

ArbreNdNoeud::ArbreNdNoeud(Arbre * Parbre, unsigned int nbbranches):ArbreNdBase(Parbre) {
// création d'un noeud neutre (dont on ne connait pas encore le noeud père)
// avec 'nbbranches' branches
	unsigned int i;

	_force = 0;
	_accuvalboot = 0;
	_racine = false;
	_tabPNoeuds.resize(nbbranches);
	_tabLgBranches.resize(nbbranches);
	for (i=0; i < _tabP_tab_id_ind.size(); i++) delete _tabP_tab_id_ind[i];
//	_tabPNoeuds[0] = 0;
//	_tabLgBranches[0] = 0;
//	Pnoeud->AjouterFils(this);
}

ArbreNdNoeud::~ArbreNdNoeud() {};

unsigned int ArbreNdNoeud::get_nbbranches() const {
	if (_racine) return(_tabPNoeuds.size());
	else  return(_tabPNoeuds.size()-1);
}


ArbreNdOTU::ArbreNdOTU(Arbre * Parbre, ArbreNdNoeud * Pnoeud):ArbreNdBase(Parbre) {
	_tabPNoeuds.resize(1);
	_tabLgBranches.resize(1);
	_tabPNoeuds[0] = Pnoeud;
	_tabLgBranches[0] = 0;
	Pnoeud->AjouterFils(this);

//	_Parbre->AjouterIndividu(this);
}

ArbreNdOTU::ArbreNdOTU(Arbre * Parbre, const string & nom):ArbreNdBase(Parbre) {
	//création d'un individu orphelin de noeud
	_tabPNoeuds.resize(1);
	_tabLgBranches.resize(1);
	_tabPNoeuds[0] = 0;
	_tabLgBranches[0] = 0;
	set_nom(nom);
	set_reference(nom);
//	Pnoeud->AjouterFils(this);
//	_Parbre->AjouterIndividu(this);
}

ArbreNdOTU::~ArbreNdOTU() {
}

/*
bool ArbreNdOTU::operator== (const ArbreNdOTU &rval){
//cerr << "ArbreNdOTU::operator==" << endl;		
	return (_nom == rval._nom);
}
*/
void ArbreNdNoeud::AjouterFils(ArbreNdBase * Pnoeud) {
	_tabLgBranches.push_back(Pnoeud->get_tabLgBranches(0));
	_tabPNoeuds.push_back(Pnoeud);
}

void ArbreNdBase::set_longueur(unsigned int pos, float taille) {
	_tabLgBranches[pos] = taille;

//cerr << "ArbreNdBase::set_longueur" << endl;	
	if (_tabPNoeuds[pos] != 0) _tabPNoeuds[pos]->set_longueur(this,taille);
//cerr << "ArbreNdBase::set_longueur fin" << endl;	
	
}

void ArbreNdNoeud::set_longueur(unsigned int pos, float taille) {
	_tabLgBranches[pos] = taille;
	
//cerr << "ArbreNdNoeud::set_longueur debut" << endl1
	if (_tabPNoeuds[pos] != 0) {
		if ((_racine == true) && (pos == 0)) _tabPNoeuds[0]->set_longueur(this,taille);
		else if (pos > 0) _tabPNoeuds[pos]->set_longueur(this,taille);
	}
//cerr << "ArbreNdNoeud::set_longueur fin" << endl;	
	
}

void ArbreNdNoeud::oPhylipRec(ostream & fichier) const {
	//écriture d'arbres au format Phylip
	unsigned int i;
//	char car;
//cerr << "ArbreNdNoeud::oPhylipRec debut" << endl;

	fichier << "(";
	if (_racine) {
		_tabPNoeuds[0]->oPhylipRec(fichier);
		fichier << ",";
	}
	for (i=1; i < _tabPNoeuds.size(); i++) {
		if (i>1) fichier << ",";
		_tabPNoeuds[i]->oPhylipRec(fichier);
	}
	fichier << ")";
	if (_Parbre->get_oui_bootstrap() && _force != -999) fichier << _force;
	if ((_racine == false) && (_Parbre->get_oui_taille_branches())) {
		fichier << ":";
		fichier << _tabLgBranches[0];
//		if ((_tabLgBranches[0] < 1e-6) || (_tabLgBranches[0] < 0)) fichier << 0;
//		else fichier << _tabLgBranches[0];
	}
}

void ArbreNdOTU::oPhylipRec(ostream & fichier) const {
	//écriture d'arbres au format Phylip
	fichier << _nom;
	if ( _tabLgBranches[0]!=-999) fichier << ":" << _tabLgBranches[0];
}

void ArbreNdBase::set_longueur(ArbreNdBase * Pnoeudbase, float taille) {
	unsigned int i;

	for (i=0; i < _tabPNoeuds.size();i++) {
		if (Pnoeudbase == _tabPNoeuds[i]) _tabLgBranches[i] = taille;
	}
}

int ArbreNdBase::get_posnoeuds(ArbreNdNoeud * Pnoeud) const {
	unsigned int i;

	for (i=0; i < _tabPNoeuds.size();i++) {
		if (Pnoeud == _tabPNoeuds[i]) return ((int) i);
	}
	return (-1);
}


int Arbre::PositionInd(const char * nom_ind) const {
	unsigned int taille(_tabPind.size()),i;

	for (i = 0; i < taille; i++) {
//cerr << "Arbre::PositionInd " << endl;
//cerr << _tabPind[i]->get_nom_c_str() << "[" << endl;
//cerr << nom_ind << "[" << endl ;
		if ( strcmp(_tabPind[i]->get_reference(),nom_ind) == 0) return ((int)i);
	}

	string nom(nom_ind);
	for (i = 0; i < taille; i++) {
//cerr << "Arbre::PositionInd " << endl;
//cerr << _tabPind[i]->get_nom_c_str() << "[" << endl;
//cerr << nom_ind << "[" << endl ;
		if (_tabPind[i]->get_nom() == nom) return ((int)i);
	}

	return (-1);
}

void Arbre::AjBootstrap(Arbre & rval) {

//	if (!_ind_charge) f_load_vectind();
	if (!_ind_charge) f_load_vect_id_ind();
	if (!rval._ind_charge) rval.f_load_vect_id_ind();
//cerr << "Arbre::AjBootstrap" << endl;		
	unsigned int i,j, taille(_tabPnoeuds.size());

	bool * tab_dejatrouve;
	tab_dejatrouve = new bool[taille];
  for (i = 0; i < taille; i++) tab_dejatrouve[i] = false;

//cerr << "Arbre::AjBootstrap for debut" << endl;
	for (i = 0; i < taille; i++) {
//cerr << "Arbre::AjBootstrap for " << i << endl;
		for (j = 0; j < taille; j++) {
			if (!tab_dejatrouve[j]){
				if (*(_tabPnoeuds[i]) == *(rval._tabPnoeuds[j])) {
					_tabPnoeuds[i]->AjBootstrap();
					tab_dejatrouve[j] = true;
					break;
				}
			}
		}	
	}
//cerr << "Arbre::AjBootstrap fin" << endl;
	_cumulbootstrap++;
}

void Arbre::set_Pracine(ArbreNdNoeud * Pracine) {
	if (Pracine == 0) return;

	if (_Pracine == 0) {
		_Pracine = Pracine;
		return;
	}
	if (Pracine == _Pracine) return;
	// si il ya déjà un pointeur Pracine =>
	//   changement de racine de l'arbre
	ArbreNdNoeud * Pancien(_Pracine);
	_Pracine = Pracine;

	Pancien->set_racine(false);
	_Pracine->set_racine(true);
//cerr << "Arbre::set_Pracine" << endl;
	// réarrangement de l'arbre par propagation dans les noeuds
		
	_Pracine->f_chgt_racine(Pancien);
}

void Arbre::iFichier(istream & fichier) {
	_oui_taille_branches =  false;
	iPhylip(fichier);
	f_tri_ind_alpha();
}

void Arbre::iPhylip(istream & fichier) {
//lecture d'arbres au format Phylip

//cerr << "Arbre::iPhylip debut" << endl;
	char car;
	unsigned int i;

	car = fichier.peek();
	if (car == '[') {
		ChaineCar ligne;
		fichier.get(car);
		fichier.get(car);

		while (fichier.good() && (car != ']')) {
			ligne += car;
			fichier.get(car);		
		}
		if (fichier.fail()) throw Anomalie(100);
		else {
			unsigned int nblignes(ligne.GetNbMots("\\"));
			for (i=0; i < nblignes; i++) {
				_titre.push_back("");
				ligne.GetMot(i+1,_titre.back(),"\\");
			}
		}
		GetLigneFlot(fichier, ligne);
	}

	fichier.get(car);
	if (car != '(') throw Anomalie(100);
	iPhylipRec(fichier,0);

	f_tri_ind_alpha();
	for (i=0; i < _titre.size(); i++) {
		if (_titre[i].Position("#G") == 0) {
			//définition d'un groupe
			iPhylipDefGroupe(_titre[i]);
			_titre.Suppr(i);
			i--;
		}
	}

//cerr << "Arbre::iPhylip fin " << _oui_taille_branches << endl;

//	if (_tabPnoeuds.size() > 0) set_Pracine(_tabPnoeuds[0]);
}

void Arbre::oFichier(ostream & fichier, unsigned int format) const {
	if ((format == 0) || (format > 2)) format = _oFormat;

	switch (format) {
		case 1:
			oPhylip(fichier);
			break;
		case 2:
			oXML(fichier);
			break;

		default:
			oPhylip(fichier);
			break;
	}

}

void Arbre::oPhylip(ostream & fichier) const {
//lecture d'arbres au format Phylip
	unsigned int i;

	if (_titre.size() > 0) {
		fichier << "[";
		for (i=0; i < _titre.size() ; i++) {
			fichier << _titre[i];
			if (i != (_titre.size()-1)) fichier << "\\";
		}
		oPhylipEcritGroupes(fichier);
		fichier << "]" << endl;
	}
	else {
		oPhylipEcritGroupes(fichier);
	}
	_Pracine->oPhylipRec(fichier);

	fichier << ";" << endl;
}

void Arbre::iPhylipRec(istream & fichier, ArbreNdNoeud * Pnoeudracine) {
	char nomcar[50];
//	string individu;
	float force, taille;
	char car;
	ArbreNdNoeud * Pnoeud(new_ArbreNdNoeud(Pnoeudracine));


//	fichier.clear();

//	_tabPnoeuds.push_back(new ArbreNdNoeud(this, Pnoeudracine));
//	ArbreNdNoeud * Pnoeud(_tabPnoeuds.back());

	fichier.get(car);
	while (fichier.good()) {
//cerr << "Arbre::iPhylipRec deb " << car << endl;
		switch (car) {
		case ';': //fin de l'arbre
			return;
			break;

		case ')': //fin du noeud
		// force du noeud
		// taille de la branche mere
//			iPhylipRecPasser(fichier);
			force = iPhylipRecGetForce(fichier);
			taille = iPhylipRecGetTaille(fichier);
			Pnoeud->set_force(force);
			if (Pnoeud->est_racine() == false) Pnoeud->set_longueur(0, taille);
//			if ((taille == -999) && (Pnoeud.est_racine())) _taille_branches = false;
			if (force > 0) _oui_bootstrap = true;
			return;
			break;

		case '(': //nouveau noeud
			iPhylipRec(fichier, Pnoeud);
			break;
		case ',': //nouvelle branche
			break;
		case ' ': //rien
			break;
		case 13: //retour chariot CR
			break;
		case 9: //tabulation
			break;
		case 10: //LF Line Feed
			break;
		default: //branche terminale
//			_tabPind.push_back(new ArbreNdOTU(this, Pnoeud));
			//new ArbreNdOTU(this, Pnoeud);
			new_ArbreNdOTU(Pnoeud);
			nomcar[0] = car;
//cerr << "//branche terminale deb" << endl;
			i_PhylipRecGetNom(fichier, nomcar);
			_tabPind.back()->set_nom(nomcar);
			_tabPind.back()->set_reference(nomcar);
//			iPhylipRecPasser(fichier);
			taille = iPhylipRecGetTaille(fichier);
			_tabPind.back()->set_longueur((unsigned int) 0,taille);
			break;
		}
		fichier.get(car);
	}
	// traitement du noeud terminé
}

/*void Arbre::iPhylipRecPasser(istream & fichier) {
	char car;

	car = fichier.peek();
//	car = fichier[pos]; pos++;
	while ((((car > 47 ) && (car < 58)) || (car == '.') || (car == ':')) && fichier.good()) {
		fichier.get(car);
		car = fichier.peek();
	}
}
*/

float Arbre::iPhylipRecGetForce(istream & fichier) {
	char car;
	char temp[10]; //ATTENTION à la taille de temp !!!!!
	int i(0);

	car = fichier.peek();
//	car = fichier[pos]; pos++;

	while ((car == 13) || (car == 10) || (car == '\'')) {//passage du retour chariot
		fichier.get(car);
		car = fichier.peek();		
	}

	while (((car > 47 ) && (car < 58)) || (car == '.') && fichier.good() && (car != '\'')) {
		_oui_bootstrap = true;
		temp[i] = car;
		i++;
		fichier.get(car);
		car = fichier.peek();
	}
	temp[i] = '\0';
	if (car == '\'') {
		fichier.get(car);
		car = fichier.peek();
	}
	if (i == 0) return(-999);

	if (fichier.fail()) cerr << "Arbre::iPhylipRecGetForce fichier.fail()" << endl;
	
	return(atof(temp));
}

float Arbre::iPhylipRecGetTaille(istream & fichier) {
	char car;
	char temp[15]; //ATTENTION à la taille de temp !!!!!
	int i(0);
//	bool neg(false);
//cerr << "Arbre::iPhylipRecGetTaille" << endl;

	car = fichier.peek();
	while ((car == 13) || (car == 10)) {//passage du retour chariot
		fichier.get(car);
		car = fichier.peek();		
	}

	if (car == ':') {
		_oui_taille_branches = true;
		fichier.get(car);
		car = fichier.peek();
		if (car == '-') {
			fichier.get(car);
			temp[i] = car;
			i++;
			car = fichier.peek();
		}
		while ((((car > 47 ) && (car < 58)) || (car == '.') || (car == 'e'))) {
			if (car == 'e') {
				temp[i] = car;
				i++;
				fichier.get(car);
				car = fichier.peek();
				if (car == '-') {
					temp[i] = car;
					i++;
					fichier.get(car);
					car = fichier.peek();
				}
			}
			temp[i] = car;
			i++;
			fichier.get(car);
			car = fichier.peek();
		}
	}
//cerr << "Arbre::iPhylipRecGetTaille " << car << endl;
	temp[i] = '\0';
//	if (i == 0) _oui_taille_branches =  false;

	if (fichier.fail()) cerr << "Arbre::iPhylipRecGetTaille fichier.fail()" << endl;

//	return(0);
	return(atof(temp));
}

void Arbre::i_PhylipRecGetNom(istream & fichier, char * nom) {
//	string nom;
	char car;
	unsigned int i(1);

	car = fichier.peek();
	
	if (nom[0] == '\'') {
		i = 0;
//		nom[0] = car;
//		fichier.get(car);
//		car = fichier.peek();
	}
	while ((car != ':' ) && (car != ',' ) && (car != ')' ) && (car != '\'' )) {
		nom[i] = car;
		i++;
		fichier.get(car);
		car = fichier.peek();
	}
	if (car == '\'') {
		fichier.get(car);
		car = fichier.peek();
	}
	nom[i] = '\0';

//	if (fichier.fail()) cerr << "Arbre::i_PhylipRecGetNom fichier.fail()" << endl;

//	return(nom);
}

void Arbre::f_test() {

	set_Pracine(_tabPnoeuds[4]);
}

void Arbre::SquizNoeud(ArbreNdNoeud * Pndaeffacer) {
	//élimination d'un noeud à 1 branche

//	cerr << "Arbre::SquizNoeud" << endl;

	if (Pndaeffacer->get_nbbranches()!=1) {
		cerr << "erreur Arbre::SquizNoeud" << endl;
		return;
	}

	ArbreNdBase * Phaut;
	ArbreNdBase * Pbas;
	float longueur(0);
	int pos;
	unsigned int i;

	Phaut = Pndaeffacer->get_Pnoeud(0);
	Pbas = Pndaeffacer->get_Pnoeud(1);
	pos = Phaut->get_posnoeuds(Pndaeffacer);
	if (pos == -1) {
		cerr << "Erreur Arbre::SquizNoeud" << endl;
		return;
	}
//	cerr << "Arbre::SquizNoeud "<< longueur << endl;
	if (Phaut->get_tabLgBranches(pos) != -999) longueur = Phaut->get_tabLgBranches(pos);
//	cerr << "Arbre::SquizNoeud "<< longueur << endl;
	if (Pbas->get_tabLgBranches(0) != -999) longueur += Pbas->get_tabLgBranches(0);
	if ((Pbas->get_tabLgBranches(0) == -999) && (Phaut->get_tabLgBranches(pos) == -999))
		longueur = -999;
	Phaut->set_longueur(pos, longueur);
	Pbas->set_longueur((unsigned int)0, longueur);
	Phaut->set_Pnoeud(pos, Pbas);
	Pbas->set_Pnoeud(0, Phaut);
	
	for (i = 0; i < _tabPnoeuds.size(); i++) {
		if (_tabPnoeuds[i] == Pndaeffacer) _tabPnoeuds.erase(_tabPnoeuds.begin()+i);
	}

	delete Pndaeffacer;
}

bool ArbreNdNoeud::ExisteBranche(const ArbreVectUINT & tabInd) const {
  unsigned int i;

	for (i=0; i < _tabP_tab_id_ind.size(); i++) {
			if (tabInd == *(_tabP_tab_id_ind[i])) {
				return (true);
			}
	}
	
	return (false);	
}


ArbreNdNoeud * Arbre::RechercheNoeud(const ArbreVectUINT & tabInd) const {
  ArbreNdNoeud * Presultat(0);
  unsigned int i;

	for (i=0; i < _tabPnoeuds.size(); i++) {
			if (_tabPnoeuds[i]->ExisteBranche(tabInd)) {
				Presultat = _tabPnoeuds[i];
				break;
			}
	}
	
	return (Presultat);	
}

void Arbre::f_load_vect_id_ind() {
	//chargement du vecteur d'id d'individus
	//à partir de la racine, déclenche une fonction récursive de remplissage
//cerr << "Arbre::f_load_vect_id_ind debut" <f_load_id_ind();

	_ind_charge = true;
//cerr << "Arbre::f_load_vect_id_ind fin" <f_load_vectind();
	// chargement ascendant
	for (i = 0; i < taille; i++) {
		_tabPind[i]->f_load_vectind_parent();
	}
	_ind_charge = true;
cerr << "Arbre::f_load_vectind fin" <fCalcValBootstrap(_cumulbootstrap);

	_oui_bootstrap = true;
}

void ArbreNdNoeud::fCalcValBootstrap(unsigned int total_bootstrap) {
	
	double resultat;

	if (modf ((((double) _accuvalboot / (double) total_bootstrap) * (double) 100),&resultat) > 0.5) {
		_force = (int)resultat + 1;
	}
	else _force = (int)resultat;

	unsigned int i;

	if (_racine) _tabPNoeuds[0]->fCalcValBootstrap(total_bootstrap);
	for (i=1; i < _tabPNoeuds.size();i++) {
		_tabPNoeuds[i]->fCalcValBootstrap(total_bootstrap);
	}
}

void Arbre::reset() {
//remise à zéro de l'arbre
	//destruction des noeuds et individus
	unsigned int i;

	for (i=0; i < _tabPind.size(); i++) delete _tabPind[i];
	for (i=0; i < _tabPnoeuds.size(); i++) delete _tabPnoeuds[i];
  _tabPind.resize(0);
  _tabPnoeuds.resize(0);

	_ind_charge = false;
	_oui_taille_branches = false;
	_oui_bootstrap = false;
	_cumulbootstrap = 0;
	_Pracine = 0;
}

void Arbre::iNeighborJoining(Matrice & distances) {
//cerr << "nj" << endl;
	//pour accelerer le traitement des bootstrap:
//	if (_PtabPnoeud == 0) _PtabPnoeud = new vector;
//	else _PtabPnoeud->resize(0);
	reset();
//cerr << "Arbre::iNeighborJoining debut "  << distances.GetType() << endl;

	bool *etatMat;
//	Vecteur tabPbranches;
	vector tabPNoeuds;
	long nblignemat;
	long taille(distances.GetNL());
	long i, j, pos1(0), pos2(0), pos3, id, jd, refi, refj;
	long double sumbr1, sumbr2;
	long double comparer;
	long double critere;
	long double * Ptab(distances._tab);
	vector accDistances;
	long double distance;


	ArbreNdNoeud * Pnoeud;

	if (distances.GetType() != 2) throw Anomalie(4);

//cerr << "Arbre::iNeighborJoining debut 2" << endl;
	if (taille < 3) throw Anomalie(5);

	for (i = 0; i < taille; i++) {
		for (j = 0; j < i; j++) {
			if (distances.GetCase(i,j) < 0) throw Anomalie(6);
		}
	}
//cerr << "Arbre::iNeighborJoining debut3" << endl;

	etatMat = new bool[taille];
//	tabPbranches.resize(taille);
	tabPNoeuds.resize(taille);
//	_tabPotu.resize(taille);
	accDistances.resize(taille);

	for (i=0; i < taille ; i++) {
		etatMat[i] = true;
//		cerr << distances._tlig[i] << endl;
//		_tabPotu[i] = new Otu(distances._tlig[i]);
//		_tabPind[i] = new ArbreNdOTU(this, distances._tlig[i]);
//		tabPNoeuds[i] = _tabPind[i];
		tabPNoeuds[i] = new_ArbreNdOTU(distances._tlig[i]);
//		tabPNoeuds[i] = new ArbreNdOTU(this, distances._tlig[i]);
//		tabPbranches[i] = new Branche(this, _tabPotu[i]);
	}

	nblignemat = taille;

	while (nblignemat > 3) {
//cerr << "Arbre::iNeighborJoining Critere Q debut" << endl;
		comparer = 9999999;
		for (i = 1; i < taille; i++) {
			if (etatMat[i]) {
				for (j = 0;  j < i; j++) {
					if (etatMat[j]) {
						for (critere = 0, refj = (j * taille), refi = (i * taille),id = 0; id < taille; id++, refi++, refj++) {
							if (etatMat[id]) {
								if (id != i) critere += *(Ptab + refi);
											
								if (id != j) critere += *(Ptab + refj);
							}
						}
						critere = ((nblignemat - 2) * *(Ptab + ((i * taille) + j))) - critere;

						//recherche du couple ou la distance est minimum
						if (comparer > critere) {
							comparer = critere;
							pos1 = j;
							pos2 = i;
						}
					}
				}
			}
		}
	// ----- Critere Q Fin ----

//cerr << "Arbre::iNeighborJoining Critere Q fin" << endl;

		//--------------calcul des longueurs de branches
		distance = Ptab[(pos1 * taille) + pos2];
		sumbr1 = 0;
		sumbr2 = 0;
		for (i = 0; i < taille; i ++) {
			if ((etatMat[i]) && (i != pos1) && (i != pos2)) {
				sumbr1 += Ptab[(pos1 * taille) + i];
				sumbr2 += Ptab[(pos2 * taille) + i];
			}
		}
		sumbr1 /= (nblignemat - 2);
		sumbr2 /= (nblignemat - 2);

		tabPNoeuds[pos1]->set_longueur((unsigned int)0,((distance + sumbr1 - sumbr2) /2) - accDistances[pos1]);
//cerr << "Arbre::iNeighborJoining set_longueur" << endl;
		//tabPbranches[pos1]->_taille = (distance + sumbr1 - sumbr2) /2;
		tabPNoeuds[pos2]->set_longueur((unsigned int)0,((distance + sumbr2 - sumbr1) /2) - accDistances[pos2]);
		//tabPbranches[pos2]->_taille = (distance + sumbr2 - sumbr1) /2;

		accDistances[pos1] = (distance / 2);
		//------------fin du calcul des longueurs de branches

		//grouper les branches dans un Noeud
		//creer une nouvelle Branche

//		Pnoeud = new Noeud(new Branche(this));
		Pnoeud =  new_ArbreNdNoeud((unsigned int) 1);
		//pour accelerer le traitement des bootstrap:
//		_PtabPnoeud->push_back(Pnoeud);
//		_tabPnoeuds.push_back(Pnoeud);

//		Pnoeud->_tabPbranche.resize(2);
//		Pnoeud->_tabPbranche[0] = tabPbranches[pos1];
//		Pnoeud->_tabPbranche[1] = tabPbranches[pos2];
//cerr << "Arbre::iNeighborJoining AjouterFils" << endl;
		Pnoeud->AjouterFils(tabPNoeuds[pos1]);
		tabPNoeuds[pos1]->set_Pnoeud(0,Pnoeud);
		Pnoeud->AjouterFils(tabPNoeuds[pos2]);
		tabPNoeuds[pos2]->set_Pnoeud(0,Pnoeud);
		
		
//		tabPbranches[pos1] = Pnoeud->_PbrMere;
//		tabPbranches[pos1]->_type = 1;
		tabPNoeuds[pos1] = Pnoeud;
		etatMat[pos2] = false;
		nblignemat--;

		//recalculer les distances
		jd = pos1; //colonne pos1
		id = (pos1 * taille); //ligne pos1
		for (i = 0; i < taille; i ++,id ++,jd += taille) {
			if ((etatMat[i]) && (i != pos1)) {
//				distances.GetCase(pos1,i) = (distances.GetCase(pos1,i) + distances.GetCase(pos2,i)) / 2;
				Ptab[id] += Ptab[(pos2 * taille) + i];
				Ptab[id] /= (long double) 2;
				Ptab[jd] = Ptab[id];
			}
		}
//cerr << "+" << endl;

	}

	pos2 = pos3 = -1;
	for (i = 0; i < taille; i++) {
		if ((etatMat[i]) && (i != pos1)) {
			if (pos2 < 0) pos2 = i;
			else if (pos3 < 0) pos3 = i;
	//		else pos3 = i;
		}
	}

//	_PndRoot = 	new Noeud(new Branche(this));
//cerr << "Arbre::iNeighborJoining racine" << endl;
	_Pracine = new_ArbreNdNoeud();
	//pour accelerer le traitement des bootstrap:
//	_PtabPnoeud->push_back(_PndRoot);
//	_tabPnoeuds.push_back(_Pracine);

	_Pracine->AjouterFils(tabPNoeuds[pos1]);
	_Pracine->AjouterFils(tabPNoeuds[pos2]);
	_Pracine->AjouterFils(tabPNoeuds[pos3]);
	tabPNoeuds[pos1]->set_Pnoeud(0,_Pracine);
	tabPNoeuds[pos2]->set_Pnoeud(0,_Pracine);
	tabPNoeuds[pos3]->set_Pnoeud(0,_Pracine);

	_Pracine->set_longueur(0,((Ptab[(pos2 * taille) + pos1] + Ptab[(pos3 * taille) + pos1] - Ptab[(pos3 * taille) + pos2]) /2) - accDistances[pos1]);
	_Pracine->set_longueur(1,((Ptab[(pos1 * taille) + pos2] + Ptab[(pos3 * taille) + pos2] - Ptab[(pos3 * taille) + pos1]) /2) - accDistances[pos2]);
	_Pracine->set_longueur(2,((Ptab[(pos1 * taille) + pos3] + Ptab[(pos2 * taille) + pos3] - Ptab[(pos1 * taille) + pos2]) /2) - accDistances[pos3]);

	delete[] etatMat;

	_oui_bootstrap = false;
	_oui_taille_branches = true;
	//_construction = 2;
}

void Arbre::iUPGMA(Matrice & distances) {
	reset();

	Vecteur etatMat;
	vector accDistances;
	Vecteur tabPNoeuds;
	long taille(distances.GetNL());
	long i, j, pos1(0), pos2(0);
	long double comparer;
	ArbreNdNoeud * Pnoeud(0);

	if (distances.GetType() != 2) throw Anomalie(4);

	if (taille < 2) throw Anomalie(5);

	for (i = 0; i < taille; i++) {
		for (j = 0; j < i; j++) {
			if (distances.GetCase(i,j) < 0) throw Anomalie(6);
		}
	}

	etatMat.resize(taille);
	accDistances.resize(taille);

	tabPNoeuds.resize(taille);

	for (i=0; i < taille ; i++) {
		accDistances[i] = 0;
		etatMat[i] = 1;

		tabPNoeuds[i] = new_ArbreNdOTU(distances._tlig[i]);
	}

	while (etatMat.getNbOccurence(1) > 1) {
		//trouver la + courte distance
		comparer = -1;
		for (i = 1; i < taille; i++) {
			for (j = 0;  j < i; j++) {
				if ((etatMat[i] == 1)&&(etatMat[j] == 1)) {
					if (comparer == -1) {
						comparer = distances.GetCase(i,j);
						pos1 = j;
						pos2 = i;
					}
					else {
						if (comparer > distances.GetCase(i,j)) {
							comparer = distances.GetCase(i,j);
							pos1 = j;
							pos2 = i;
						}
					}
				}
			}
		}
		//grouper les branches dans un Noeud
		Pnoeud =  new_ArbreNdNoeud((unsigned int) 1);
		Pnoeud->AjouterFils(tabPNoeuds[pos1]);
		tabPNoeuds[pos1]->set_Pnoeud(0,Pnoeud);
		Pnoeud->AjouterFils(tabPNoeuds[pos2]);
		tabPNoeuds[pos2]->set_Pnoeud(0,Pnoeud);



		tabPNoeuds[pos1]->set_longueur((unsigned int)0,(comparer/2) - accDistances[pos1]);
		tabPNoeuds[pos2]->set_longueur((unsigned int)0,(comparer/2) - accDistances[pos2]);
		accDistances[pos1] = (comparer/2);

		tabPNoeuds[pos1] = Pnoeud;
		etatMat[pos2] = 0;

		//recalculer les distances
		for (i = 0; i < taille; i ++) {
			if ((etatMat[i] == 1 ) && (i != pos1)) {
				distances.GetCase(pos1,i) = (distances.GetCase(pos1,i) + distances.GetCase(pos2,i))/2;
			}
		}

	}

	_Pracine = Pnoeud;
	_oui_bootstrap = false;
	_oui_taille_branches = true;
}

void Arbre::iNeighborJoiningTopo(Matrice & distances) {
	reset();
//cerr << "Arbre::iNeighborJoiningTopo debut" << endl;

	bool *etatMat;
	vector tabPNoeuds;
	long nblignemat;
	long taille(distances.GetNL());
	long i, j, pos1(0), pos2(0), pos3, id, jd, refi, refj;
	long double comparer;
	long double critere;
	long double * Ptab(distances._tab);
	vector accDistances;


	ArbreNdNoeud * Pnoeud;

	if (distances.GetType() != 2) throw Anomalie(4);

	if (taille < 3) throw Anomalie(5);

	for (i = 0; i < (taille * taille); i++) {
		if (Ptab[i] < 0) throw Anomalie(6);
	}
/*	for (i = 0; i < taille; i++) {
		for (j = 0; j < i; j++) {
			if (distances.GetCase(i,j) < 0) throw Anomalie(6);
		}
	}
*/
	etatMat = new bool[taille];
	tabPNoeuds.resize(taille);
	accDistances.resize(taille);

	for (i=0; i < taille ; i++) {
		etatMat[i] = true;
		tabPNoeuds[i] = new_ArbreNdOTU(distances._tlig[i]);
	}

	nblignemat = taille;

	while (nblignemat > 3) {
//cerr << "Arbre::iNeighborJoiningTopo Critere Q debut" << endl;
		comparer = 9999999;
		for (i = 1; i < taille; i++) {
			if (etatMat[i]) {
				for (j = 0;  j < i; j++) {
					if (etatMat[j]) {
						for (critere = 0, refj = (j * taille), refi = (i * taille),id = 0; id < taille; id++, refi++, refj++) {
							if (etatMat[id]) {
								if (id != i) critere += *(Ptab + refi);
											
								if (id != j) critere += *(Ptab + refj);
							}
						}
						critere = ((nblignemat - 2) * *(Ptab + ((i * taille) + j))) - critere;

						//recherche du couple ou la distance est minimum
						if (comparer > critere) {
							comparer = critere;
							pos1 = j;
							pos2 = i;
						}
					}
				}
			}
		}
	// ----- Critere Q Fin ----

//cerr << "Arbre::iNeighborJoining Critere Q fin" << endl;

		//grouper les branches dans un Noeud
		//creer une nouvelle Branche

//		Pnoeud = new Noeud(new Branche(this));
		Pnoeud =  new_ArbreNdNoeud((unsigned int) 1);
		Pnoeud->AjouterFils(tabPNoeuds[pos1]);
		tabPNoeuds[pos1]->set_Pnoeud(0,Pnoeud);
		Pnoeud->AjouterFils(tabPNoeuds[pos2]);
		tabPNoeuds[pos2]->set_Pnoeud(0,Pnoeud);
		
		
		tabPNoeuds[pos1] = Pnoeud;
		etatMat[pos2] = false;
		nblignemat--;

		//recalculer les distances
		jd = pos1; //colonne pos1
		id = (pos1 * taille); //ligne pos1
		for (i = 0; i < taille; i ++,id ++,jd += taille) {
			if ((etatMat[i]) && (i != pos1)) {
				Ptab[id] += Ptab[(pos2 * taille) + i];
				Ptab[id] /= (long double) 2;
				Ptab[jd] = Ptab[id];
			}
		}
//cerr << "+" << endl;

	}

	pos2 = pos3 = -1;
	for (i = 0; i < taille; i++) {
		if ((etatMat[i]) && (i != pos1)) {
			if (pos2 < 0) pos2 = i;
			else if (pos3 < 0) pos3 = i;
	//		else pos3 = i;
		}
	}

//	_PndRoot = 	new Noeud(new Branche(this));
//cerr << "Arbre::iNeighborJoining racine" << endl;
	_Pracine = new_ArbreNdNoeud();

	_Pracine->AjouterFils(tabPNoeuds[pos1]);
	_Pracine->AjouterFils(tabPNoeuds[pos2]);
	_Pracine->AjouterFils(tabPNoeuds[pos3]);
	tabPNoeuds[pos1]->set_Pnoeud(0,_Pracine);
	tabPNoeuds[pos2]->set_Pnoeud(0,_Pracine);
	tabPNoeuds[pos3]->set_Pnoeud(0,_Pracine);


	delete[] etatMat;

	_oui_bootstrap = false;
	_oui_taille_branches = false;
	//_construction = 2;
}

double ArbreNdOTU::get_longueur_max()const {
	if (get_longueur_branche() < 0) return (0);
	else return (get_longueur_branche());
}

unsigned int ArbreNdOTU::get_nbnoeuds_max()const {
	return (1);
}


void Arbre::f_tri_ind_alpha() {

	unsigned int i;
	
//cerr << "Arbre::f_tri_ind_alpha debut " << _tabPind.size() << endl;
	if (_tabPind.size() < 2) return;

	//f_tribulle_ind_alpha();
	sort (_tabPind.begin(),_tabPind.end(),moins ());
/*	if (_tabPind.size() < 4) f_tribulle_ind_alpha();
//	if (size() < 4) return;	
	else f_trishell_ind_alpha(0, _tabPind.size()-1);
//cerr << "Arbre::f_tri_ind_alpha num"<< endl;
*/
	for (i=0; i < _tabPind.size(); i++) {
		_tabPind[i]->set_id(i);

//cerr << _tabPind[i]->get_nom_c_str() << endl;
	}
//cerr << "Arbre::f_tri_ind_alpha fin"<< endl;
}


void Arbre::f_tribulle_ind_alpha() {
	unsigned int ok,i;
	ArbreNdOTU * swap;
	unsigned int n(_tabPind.size());

	do{
		ok=1;
		for(i=1;iget_reference(), _tabPind[i]->get_reference()) > 0) {
			ok=0;
			swap = _tabPind[i];
			_tabPind[i] = _tabPind[i-1];
			_tabPind[i-1] = swap;
		}
	}while(!ok);
}

void Arbre::f_trishell_ind_alpha(unsigned int lb, unsigned int ub) {
	//tri de _tabPind en fonction du nom des individus
	//T *a,
	unsigned int n, h, i, j;
//	unsigned int t;
	ArbreNdOTU * Pswap;

   /**************************
    *  sort array a[lb..ub]  *
    **************************/
//cerr << "Arbre::f_trishell_ind_alpha debut "<< lb << " " << ub << endl;

    /* compute largest increment */
	n = ub - lb + 1;
	h = 1;
	if (n < 14) h = 1;
//    else if (sizeof(unsigned int) == 2 && n > 29524)
 //       h = 3280;
	else {
		while (h < n) h = 3*h + 1;
		h /= 3;
		h /= 3;
	}

	while (h > 0) {

        /* sort-by-insertion in increments of h */
		for (i = lb + h; i <= ub; i++) {
//cerr << "Arbre::f_trishell_ind_alpha i "<< i << endl;
			Pswap = _tabPind[i];
//cerr << "Arbre::f_trishell_ind_alpha ok " << endl;
//cerr << "i-h " << (i-h) << endl;
			for (j = i-h; ((j >= lb) && (strcmp(_tabPind[j]->get_reference(), Pswap->get_reference()) > 0)); j -= h)
				_tabPind[j+h] = _tabPind[j];
			_tabPind[j+h] = Pswap;
		}

        /* compute next increment */
		h /= 3;
	}
//cerr << "Arbre::f_trishell_ind_alpha fin "<< lb << " " << ub << endl;
}

void ArbreVectUINT::f_tri() {
	//tri du vecteur
	sort(begin(), end(), less());
	//return;
	//vector::sort();
	//return;
//cerr << "ArbreVectUINT::f_tri debut " << endl;
	//if (size() < 2) return;
	//if (size() == 2) {
	//	unsigned int swap;
	//	if (operator[](0) > operator[](1)) {
	//		swap = operator[](0);
	//		operator[](0) = operator[](1);
	//		operator[](1) = swap;
	//	}
	//	return;
	//}
	//if (size() == 3) f_tribulle();
//	if (size() < 4) return;	
	//else f_tribulle();
//	else f_trishell(0,size()-1);
//cerr << "ArbreVectUINT::f_tri fin " << endl;
}


void ArbreVectUINT::f_tribulle() {
	unsigned int ok,i, swap;
	unsigned int n(size());

	do{
		ok=1;
		for(i=1;ioperator[](i)) {
			ok=0;
			swap = operator[](i-1);
			operator[](i-1) = operator[](i);
			operator[](i) = swap;
		}
	} while(!ok);
}

void ArbreVectUINT::f_trishell(unsigned int lb, unsigned int ub) {
	//T *a,
	unsigned int n, h, i, j;
	unsigned int t;

   /**************************
    *  sort array a[lb..ub]  *
    **************************/

    /* compute largest increment */
    n = ub - lb + 1;
    h = 1;
    if (n < 14)
        h = 1;
//    else if (sizeof(unsigned int) == 2 && n > 29524)
 //       h = 3280;
    else {
        while (h < n) h = 3*h + 1;
        h /= 3;
        h /= 3;
    }

    while (h > 0) {

        /* sort-by-insertion in increments of h */
        for (i = lb + h; i <= ub; i++) {
            t = operator[](i);
//            for (j = i-h; j >= lb && compGT(operator[](j), t); j -= h)
            for (j = i-h; ((j >= lb) && (operator[](j)> t)); j -= h)
                operator[](j+h) = operator[](j);
            operator[](j+h) = t;
        }

        /* compute next increment */
        h /= 3;
    }
}

bool ArbreVectUINT::operator== (const ArbreVectUINT &rval) {
	//=>remplir les vecteurs avant
//cerr << "ArbreNdNoeud::operator==" << endl;		
	unsigned int i, taille (size());
	
	if (taille != rval.size()) return (false);

	for (i = 0; i < taille; i ++) {
  	if (operator[](i) != rval[i]) return (false); 	
	}	
  return (true);
}

void ArbreVectUINT::affiche() const {

	string affichage;
	unsigned int i, taille (size());

	for (i = 0; i < taille; i ++) {
		cout << " " << operator[](i);
	}	
	
}

void Arbre::iDistances(MatriceLD & matrice) {
	iNeighborJoining(matrice);
//	f_tri_ind_alpha();
}

void Arbre::iDistances(MatriceLD & distances, int methode) {
//reconstruction d'arbres a partir d'une matrice de distances:
	// int -> methode de reconstruction
		// 1 -> UPGMA	
		// 2 -> Neighbor Joining	
	//on efface l'arbre si il yen a deja un
//cerr << "Arbre::iDistances(MatriceLD & distances, int methode) debut" << endl;
	reset();

	switch (methode) {
	case 1: // UPGMA
			 iUPGMA(distances);
			 break;
	case 101: // UPGMA, topologie seulement
			 iUPGMA(distances);
			 break;
	case 2: // Neighbor Joining
			 iNeighborJoining(distances);
			 break;
	case 102: // Neighbor Joining, topologie seulement
			 iNeighborJoiningTopo(distances);
			 break;
	}
//cerr << "Arbre::iDistances(MatriceLD & distances, int methode) tri" << endl;
//	f_tri_ind_alpha();
}

void Arbre::f_forceiDistances(MatriceLD & distancesRef,int methodeArbre) {
	bool continuer(true);

	while (continuer) {
		try {
			continuer = false;
			iDistances(distancesRef,methodeArbre);
		}
		catch (Anomalie pb) {
			cout << _("Error while building tree...") << endl;
			switch (pb.le_pb) {
				case 4:
					cout << _("Inconsistant matrix file format") << endl;
					throw Anomalie(4);					
					break;
				case 5:
					cout << _("the matrix is too small") << endl;
					throw Anomalie(5);					
					break;
				case 6:
					cout << _("Negative distances in the matrix...") << endl;
					cout << _("the smallest value is: ") << distancesRef.get_ppvaleur() << endl;
					cout << _("all negative values are replaced by zero to proceed") << endl;
					distancesRef.f_neg2zero();
					continuer = true;
					break;
				default:
					throw Anomalie(pb.le_pb);
					break;
			}
		}
	}
}

void Arbre::iNimbus(unsigned int nbessais , unsigned int nbind, unsigned int * Ptemp, char * * PPotu) {
	unsigned int i, j;
	ChaineCar nom;
	MatriceLD tab_nimbus(nbind, nbessais) ;
	unsigned int * Puint(Ptemp);
//cerr << "Arbre::iNimbus debut"  << endl;
//	Visu.reset((long unsigned int) nbind, (long unsigned int) nbessais);
	for (i=0; i < nbind ; i++) {
		tab_nimbus._tlig[i].assign(PPotu[i]);
		for (j=0; j < nbessais ; j++) {
			tab_nimbus.GetCase(i, j) = *Puint;
			Puint++;
		}
	}
	tab_nimbus.SetFlag(1);
//	tab_nimbus.oExcel(cerr);

	reset();

	for (i=0; i < nbind ; i++) {
		new_ArbreNdOTU("");
		_tabPind[i]->set_nom(tab_nimbus._tlig[i]);
	}

	_Pracine = new_ArbreNdNoeud();

	iNimbusRec(_Pracine, tab_nimbus, 0, 0, nbind);

	_Pracine->AjouterFils(new_ArbreNdOTU(""));
	_tabPind.back()->set_nom("____");
	_tabPind.back()->set_longueur((unsigned int) 0, (float) nbessais);

	_oui_bootstrap = false;
	_oui_taille_branches = true;

//cerr << "Arbre::iNimbus fin " << _tabPind.size() << endl;

}

void Arbre::iNimbusRec(ArbreNdNoeud * Pnoeud, MatriceLD & tab_nimbus, unsigned int numessai, unsigned int deb, unsigned int fin, unsigned int longueur) {
// pos: position en nb d'essais
	// branche regroupant les otus de 'deb' a 'fin'
	unsigned int i, nbessais(tab_nimbus.GetNC());
	unsigned int pos;
//  ArbreNdNoeud * Pnoeud (_tabPnoeud.back());

//cerr << "Arbre::iNimbusRec debut"  << endl;
	if ((numessai >= nbessais)&&(numessai != 0)) { //dernière colonne
//cerr << "Arbre::iNimbusRec derniere col numessai " << numessai  << endl;
		Pnoeud->AjouterFils(new_ArbreNdNoeud((unsigned int) 1));
//cerr << "coucou1 " << Pnoeud->get_nbbranches() << endl;
//		PPnoeudnov = _tabPnoeuds.back();
//cerr << "coucou2 nbb " << _tabPnoeuds.back()->get_nbbranches() << endl;
		_tabPnoeuds.back()->set_longueur(0, longueur);
//cerr << "coucou3" << endl;
//cerr << "Arbre::iNimbusRec dernier deb " << _tabPind[deb]->get_nom() << endl;
			_tabPnoeuds.back()->AjouterFils(_tabPind[deb]);
			_tabPind[deb]->set_longueur((unsigned int) 0, 0.25);
		for (i = deb+1; i < fin; i++) {
//cerr << "coucou4" << endl;
//cerr << "Arbre::iNimbusRec dernier " << _tabPind[i]->get_nom() << endl;
			_tabPnoeuds.back()->AjouterFils(_tabPind[i]);
			_tabPind[i]->set_longueur((unsigned int) 0, 0.25);
		}
		return;
	}

	if ((fin - deb) == 1) {
//cerr << "Arbre::iNimbusRec one " << _tabPind[deb]->get_nom() << endl;
		// branche terminale
		Pnoeud->AjouterFils(_tabPind[deb]);
		_tabPind[deb]->set_longueur((unsigned int) 0, nbessais - numessai);
		return;
	}

	for (pos = numessai; pos < nbessais; pos ++) {

//cerr << "Arbre::iNimbusRec pos "<< pos << " numessai " << numessai  << endl;
		for (i = deb+1; i < fin; i ++) {
			if (tab_nimbus.GetCase(i-1, pos) != tab_nimbus.GetCase(i, pos)) {
				//nouveau noeud
				Pnoeud->AjouterFils(new_ArbreNdNoeud((unsigned int) 1));
				Pnoeud = _tabPnoeuds.back();
				Pnoeud->set_longueur(0, pos-numessai);
				iNimbusRec(Pnoeud, tab_nimbus, pos, deb,i,pos-numessai);
				//les autres
				deb = i;
				i++;
				while (i < fin) {
          if (tab_nimbus.GetCase(i-1, pos) != tab_nimbus.GetCase(i, pos)){
						iNimbusRec(Pnoeud, tab_nimbus, pos, deb,i,pos-numessai);
						deb = i;
					}
					i ++;
				}
				iNimbusRec(Pnoeud, tab_nimbus, pos, deb,fin,pos-numessai);
				return;
			}

		}

	}

	iNimbusRec(Pnoeud, tab_nimbus, pos, deb,fin,pos-numessai);
}

void Arbre::operator>>(ostream& sortie) {
	switch (_oFormat) {
		case 1:
			oPhylip(sortie);
			break;
		default:
			oPhylip(sortie);
			break;
	}
}

const ArbreNdOTU * Arbre::RecherchePOTU(unsigned int id) const {

	unsigned int i;

	for (i=0 ; i < _tabPind.size(); i++) {
		if (_tabPind[i]->get_id() == id) return(_tabPind[i]);
	}
	return (0);
}

void ArbreNdOTU::set_nom(const string & nom) {
	//a faire : vérifier l'unicité du nom
	_nom.assign(nom);
}

void Arbre::oXML(ostream & fichier) const {
//écriture d'arbres au format XML
/*







*/
  fichier << "" << endl;
  fichier << "" << endl;
  fichier << "" << endl;

  fichier << "" << endl;
  fichier << "" << endl;
	unsigned int i;

	if (_titre.size() > 0) {
		fichier << "" << endl;
		for (i=0; i < _titre.size() ; i++) {
			fichier << _titre[i];
		}
		//oPhylipEcritGroupes(fichier);
		fichier << "" << endl;
	}

	_Pracine->oXML(fichier);

  fichier << "" << endl;
  fichier << "" << endl;
}


void ArbreNdNoeud::oXML(ostream & fichier) const {
	//écriture d'arbres au format Phylip
	unsigned int i;
//	char car;
//cerr << "ArbreNdNoeud::oPhylipRec debut" << endl;

	if (_racine) {
  	fichier << "" << endl;
		_tabPNoeuds[0]->oXML(fichier);
  	fichier << "" << endl;
	}
  else fichier << "" << endl;

	for (i=1; i < _tabPNoeuds.size(); i++) {
  	fichier << "" << endl;
		_tabPNoeuds[i]->oXML(fichier);
	  fichier << "" << endl;
	}
  if (!(_racine)) fichier << "" << endl;
	if (_Parbre->get_oui_bootstrap() && _force != -999) {
	  fichier << "" << endl;
    fichier << _force;
	  fichier << "" << endl;
  }
	if ((_racine == false) && (_Parbre->get_oui_taille_branches())) {
	  fichier << "" << endl;
		fichier << _tabLgBranches[0] << endl;
	  fichier << "" << endl;
//		if ((_tabLgBranches[0] < 1e-6) || (_tabLgBranches[0] < 0)) fichier << 0;
//		else fichier << _tabLgBranches[0];
	}

}

void ArbreNdOTU::oXML(ostream & fichier) const {
	//écriture d'arbres au format Phylip
//	char car;
//cerr << "ArbreNdNoeud::oPhylipRec debut" << endl;

  fichier << "" << endl;
  fichier << "" << endl;
  fichier << get_nom() << endl;
  fichier << "" << endl;
	if (_Parbre->get_oui_taille_branches()) {
	  fichier << "" << endl;
		fichier << _tabLgBranches[0] << endl;
	  fichier << "" << endl;
	}
  fichier << "" << endl;
}

} //namespace biolib {
} //namespace arbres {

populations-1.2.33+svn0120106.orig/src/strucpop.cpp0000644000175000017500000003057410531115342022024 0ustar  georgeskgeorgesk
/***************************************************************************
                          strucpop.cpp  -  Librairie d'objets permettant de manipuler des données
                          						spécifiques aux StrucPops
                             -------------------
    begin                : ven sep 01 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/
//constructeur


#include"locus.h"
#include"jeupop.h"
#include "strucpop.h"

StrucPop::StrucPop (Jeupop * pdonnees) {
//cerr << "StrucPop::StrucPop (Jeupop * pdonnees) constructeur debut" << endl;

	_nom.assign("_");
	_Pjeu = pdonnees;
	_nbind = 0;

	_nploidie = _Pjeu->get_nploidie();
	_nbloc = _Pjeu->get_nbloc();
//cerr << "StrucPop::StrucPop (Jeupop * pdonnees) constructeur fin" << endl;

}


StrucPop::StrucPop(const StrucPop & rval,MetaPop * Pmetapop, Jeupop * Pjeu) {
	// constructeur de copies
	// vérifié le 11/09/2000
	unsigned long i;

//cerr << "StrucPop(const StrucPop & rval,MetaPop * Pmetapop, Jeupop * Pjeu) début" << endl;
	//if (popori.get_nploidie() != _nploidie) throw Anomalie(2);
	// => effacer l'ancien contenu
	reset();

	_nom = rval._nom;
	_Pjeu = Pjeu;
	_Pmetapop = Pmetapop;
	_nbloc = rval.get_nbloc();
	_nploidie = rval.get_nploidie();

	_tabAllIntrogressant.resize(rval._tabAllIntrogressant.size());

	for (i=0; i < _tabAllIntrogressant.size(); i++) {
		_tabAllIntrogressant[i] = get_Pall(rval._tabAllIntrogressant[i]->get_NomLocus(),rval._tabAllIntrogressant[i]->get_Nom());
	}
//cerr << "StrucPop(const StrucPop & rval,MetaPop * Pmetapop, Jeupop * Pjeu) fin" << endl;

}

StrucPop::~StrucPop () {
}

void StrucPop::reset() {
	// remise à zéro
	unsigned long i;

	_tabAllIntrogressant.resize(0);
	_VcalcInd.resize(0);

	for (i=0; i < _tabPind.size();i++) delete _tabPind[i];

	_tabPind.resize(0);
	_nbind = 0;
	_nbloc = 0;
	
}


void StrucPop::r_alldiff(int numlocus, Vecteur &tabPall) const {
//num locus, tableau sur les Alleles differents de ce locus
	unsigned int i, j;
	unsigned int nbind(get_nbind());
	
	tabPall.resize(0);
	tabPall.push_back(_tabPind[0]->_tabPall[numlocus * _nploidie]);
	for (i=0;i < nbind;i++) {
		for (j=0;j < _nploidie;j++) {
			if (tabPall.Existe(_tabPind[i]->_tabPall[(numlocus * _nploidie) + j])) {}
			else {
				tabPall.push_back(_tabPind[i]->_tabPall[(numlocus * _nploidie) + j]);
			}	
		}
	}

//	return(tabPall.size());
}

unsigned long StrucPop::r_nballnonnulsBootInd(unsigned long locus) const {
	// retourne le nb de copies d'allèles non nuls pour un locus
	//spécifique aux calculs avec bootstrap sur les individus
	unsigned long resultat(0);
	unsigned long nbind(_VcalcInd.size());
	unsigned long nploidie(get_nploidie());
	unsigned long i, j;
	
	for (i=0;i < nbind;i++) {
		for (j=0;j < nploidie;j++) {
			if (_VcalcInd[i]->_tabPall[(locus * nploidie) + j]->_miss) continue;
			resultat++;
		}
	}

	return(resultat);
}

void StrucPop::f_bootstrap() {
	//bootstrap sur les individus
	unsigned long nbind(_tabPind.size());
	unsigned long j, tirage;

	if (_VcalcInd.size() != nbind) _VcalcInd.resize(nbind);

	// tirage des individus
	for (j = 0; j < nbind; j ++ ) {
		tirage = (unsigned long) (nbind * ((long double)rand() / ((long double) RAND_MAX)));
		_VcalcInd[j] = _tabPind[tirage];
	}
}

double StrucPop::r_rare(unsigned long nreduit, unsigned int numlocus) const{
	//nouvelle diversité allèlique pour un échantillon
	// réduit: nreduit, pour un locus
//	cerr << "coucou";
//	cerr << nreduit << " " << numlocus << " " << get_nbind() << endl;
	int i;
	long double resultat(0);
	long double inter;
//	long double inter2;
	int nploidie(get_nploidie());
	Vecteur tabPallDiff;

	//taille de l'échantillon allèlique
	unsigned long nechall(get_nbind() * nploidie);
	nreduit *= nploidie;
	if (nreduit > nechall) return(resultat);

	//nombre d'allèles différents
	r_alldiff(numlocus, tabPallDiff);
//	cerr << "coucou";
	int nball(tabPallDiff.size());

//cerr << nball  << endl;
	// ne compte pas les allèles nuls (manquants)
	for (i=0;i_miss) {
			nechall -= (unsigned long) r_nbcopall(tabPallDiff[i]);
			tabPallDiff.Suppr(i);
			nball--;
			if (nreduit > nechall) return(resultat);
			break;
		}
	}
//cerr << nball  << endl;
//cerr << endl;

//	if (nreduit == nechall) return(nball);

	//nombre de copies d'un allèle
	unsigned long ncopies;

	for (i=0;i> ncopies;  
	}

	return((double) resultat);
}


void StrucPop::ifAjouterIndividu(const Individu * Pind) {

}


Allele* StrucPop::get_Pall(unsigned long ind, unsigned long locus, unsigned int numall) const {
	unsigned long index;
	unsigned int nploidie(get_nploidie());

	if (locus >= get_nbloc()) throw Anomalie(1);
	if (numall >= nploidie) throw Anomalie(1);

	index = (locus * nploidie) + numall;
	return(_tabPind[ind]->_tabPall[index]);
}


Allele * StrucPop::get_Pall(const string & nomlocus, const string & nomall) const {
	//recherche l'allele correspondant dans son propre jeu de pop:
	/// n'utiliser que lors d'une copie
	Allele * res;
	Locus * lelocus;

	lelocus = _Pjeu->get_Plocus(nomlocus);
	if (lelocus==0) throw Anomalie (5);

	res = 0;
//cerr << "get_Pall debut " << lelocus << " " << lelocus->get_nom() << " " << nomall << endl;
	res = lelocus->getPall(nomall);
//cerr << "get_Pall allele fin" << res << " " << nomlocus << " " << nomall << endl;

	if (res==0) throw Anomalie (6);

	return(res);
}


void StrucPop::resize_loc() {
	// allocation de mémoire pour un changement de nb de locus
	/// ATTENTION, ne marche que pour agrandir _tabPall !!!
	unsigned long i, j, k;
	vector tabPallnuls;

	if (_nbloc == _Pjeu->get_nbloc()) return;

	if (_Pjeu->get_nploidie() != _nploidie) throw Anomalie(2);

	_nbind = _tabPind.size();
//	_nploidie = _Pjeu->get_nploidie();

	_nbloc = _Pjeu->get_nbloc();


	tabPallnuls.resize(_nbloc);
	for (j = 0; j < _nbloc; j++) {
		tabPallnuls[j] = _Pjeu->get_Plocus(j)->getPallNul();
	}

	for (i=0;i < _nbind;i++) {
		//on remplit les nouveaux alleles des individus
		// par des alleles nuls

		for (j = 0; j < _nbloc; j++) {
			for (k = 0; k < _nploidie; k++) {
				if (((j * _nploidie) + k) >= _tabPind[i]->_tabPall.size()) {

					_tabPind[i]->_tabPall.push_back(tabPallnuls[j]);
				}
			}			
		}
	}

}

inline Allele* StrucPop::get_Pall(unsigned long ind,unsigned long all) const {
	return(_tabPind[ind]->_tabPall[all]);
}

const string & StrucPop::get_nomind(long nbind) const {
	// donne le nom de l'individu nbind
//cerr << "StrucPop::get_nomind(long nbind) " << nbind << endl;
	return (_tabPind[nbind]->get_nom());
}

void StrucPop::AjouterAllIntrogressant(Allele * Pall) {
	if (_tabAllIntrogressant.Existe(Pall) == false) {
//cerr << "StrucPop::AjouterAllIntrogressant" << endl;
		_tabAllIntrogressant.push_back(Pall);
	}
}

long double StrucPop::f_heterozygotieatt(unsigned long locus, unsigned long * Pnbpopcalc) const {
//Calcul de l'heterozygotie attendue pour un locus
// Hs expected heterozygosity
// 1- somme des frequences au carre de chaque allele
// ok verifie le 11/10/2000

	long unsigned i,nballloc,allnonnuls;
	long double sfreqcarre, freq;//, Hs;
	Allele * Pall;

	nballloc = _Pjeu->get_Plocus(locus)->get_nball();
	allnonnuls = r_nballnonnuls(locus);
	if (allnonnuls == 0) {
		*Pnbpopcalc -= 1;
		return (0); // a verifier
	}

	for (sfreqcarre=0,i=0; i < nballloc; i++) {
		Pall = _Pjeu->get_Pall(locus,i);
		if (Pall->_miss) continue;
		freq = ((long double) r_nbcopall(Pall)) / ((long double) allnonnuls);
		sfreqcarre += (freq * freq);			
//cerr <<"StrucPop::f_heterozygotieatt freq" <<  freq << endl;
	}		
	//Hs += (long double) 1 - sfreqcarre;
//cerr <<"StrucPop::f_heterozygotieatt Hs" << ((long double) 1) - sfreqcarre << endl;
	return (((long double) 1) - sfreqcarre);	
}

long double StrucPop::f_heterozygotieobs(unsigned long locus, unsigned long * Pnbpopcalc) const {
//Calcul de l'heterozygotie observée pour un locus
//frequence des hétérozygotes dans cette population à ce locus
// verifie le 11/10/2000 "génétique et Evolution" Solignac

	long unsigned i, nbindcalc, nbind(get_nbind()),nbhetero;

	for (nbindcalc=1, i=0, nbhetero = 0; i < nbind; i++,nbindcalc++) {
		try {
			if (_tabPind[i]->r_esthetero(locus)) nbhetero++;
		}
		catch (Individu::Anomalie pb) {
 			switch (pb.le_pb) {
			case 13:
				//cerr << _("tt ERROR in Individu object: ") << pb.le_pb << endl;
				nbindcalc--;				
				break;
			default:
				cerr << _("ERROR in Individu object: ") << pb.le_pb << endl;
				break;
			}
		}
		
	}
	nbindcalc--;
//	cerr << "StrucPop::f_heterozygotieobs" << endl;
//	cerr << locus << " nbindcalc : " << nbindcalc << " nbhetero : " << nbhetero << endl;
	
  if (nbindcalc == 0) {
		*Pnbpopcalc -= 1;
		return(0);
	}
//cerr <<"StrucPop::f_heterozygotieobs Hi" << ((long double) nbhetero) / ((long double) nbind) << endl;
//cerr <<"StrucPop::f_heterozygotieobs nbhetero" <<  nbhetero << " nbind" << nbind << endl;
	return (((long double) nbhetero) / ((long double) nbindcalc));	
}

long double StrucPop::f_calcfreq(Allele * Pall) const {
	//calcul de la fréquence de l'allèle Pall dans cette population
	long double nballnonnuls(r_nballnonnuls(_Pjeu->get_numloc(Pall->get_Ploc())));

//	r_nballnonnuls(_Pjeu->get_numloc(Pall->get_Ploc());

	return(((long double) r_nbcopall(Pall)) / nballnonnuls);
}


void StrucPop::set_nom(const string & nom) {
//	int pos;

	_nom.assign(nom);

/*	pos = _nom.find(" ", 0);
	while (pos != -1) {
		_nom.replace(pos, _nom.size(), "_");
		pos = _nom.find(" ", 0);
	}
  */
}

/*
const StrucPop& StrucPop::operator= (const StrucPop & rval) {
	long i;
	long nbind(rval.get_nbind());

//cerr << "operator = pop, debut " << nbind << " " << rval._nom << endl;
	if (get_nploidie() != rval.get_nploidie()) throw Anomalie(2);
	if (get_nbloc() != rval.get_nbloc()) throw Anomalie(3);

	reset(_Pjeu, nbind);

	_nom = rval._nom;

	try {
		for (i=0; i < nbind; i++) {
//cerr << "operator = pop, individu " << endl;
			*(_tabPind[i]) = *(rval._tabPind[i]);
		}
	}
	catch (Individu::Anomalie pb) {
		cerr << "erreur de type: " << pb.le_pb << " dans l'operateur = de Population" << endl;
	}
//cerr << "operator = pop, coucou2 " << endl;

	_tabAllIntrogressant.resize(rval._tabAllIntrogressant.size());

	for (i=0; i < rval._tabAllIntrogressant.size(); i++) {
		_tabAllIntrogressant[i] = get_Pall(rval._tabAllIntrogressant[i]->get_NomLocus(),rval._tabAllIntrogressant[i]->get_Nom());
	}
//cerr << "operator = pop, fin " << endl;

	return(*this);
}

*/
 

/** Supprime l'individu Pind du tableau */
void StrucPop::SupprtabIndividu(Individu * Pind){
//cerr << "StrucPop::SupprtabIndividu debut" << endl;
	unsigned long i;
	for (i = 0 ; i < _tabPind.size(); i++) {
		if (_tabPind[i] == Pind) {
//cerr << "StrucPop::SupprtabIndividu" << Pind->get_nom() << endl;
			_tabPind.erase(_tabPind.begin() + i);
			_nbind--;
		}
	}
	if (get_niveau() !=0) _Pmetapop->SupprtabIndividu(Pind);
//cerr << "StrucPop::SupprtabIndividu fin" << endl;
}

long StrucPop::f_calcfreqabsolue(Allele * Pall) const {
	//calcul de la fréquence absolue de l'allèle Pall dans cette population

	return(r_nbcopall(Pall));
}
/** réaffectation du nombre de locus */
void StrucPop::set_nbloc(){
	_nbloc = _Pjeu->get_nbloc();
}


populations-1.2.33+svn0120106.orig/src/locus.h0000644000175000017500000000571010531115342020731 0ustar  georgeskgeorgesk/***************************************************************************
                          locus.h  -  Librairie d'objets permettant de manipuler des données
                          						spécifiques aux locus
                             -------------------
    begin                : ven sep 01 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

// bibliothèque d'objets permettant de manipuler des
// donnees sur des populations
// ecrit par Olivier Langella le 21/4/98
// modifie le 01/09/2000 par Olivier Langella pour apporter les capacités de structurations
// de populations


#ifndef LOCUS_H
#define LOCUS_H

class Jeupop;
#include"allele.h"
#include "vecteurs.h"
//typedef biolib::vecteurs::ChaineCar ChaineCar;


long double fact (int n);
long double fact (int n, int m);
long double comb (int n, int m);

// locus
class Locus {
public :
//	Locus(const Locus&); //constructeur de copies
	Locus(const Locus& original, Jeupop * Pjeu);//constructeur de copies
	Locus(long nball);
	Locus(Jeupop *, long nball);
	~Locus();
	void reset(Jeupop *,long);//pointeur sur Jeupop,nball
  Allele * new_allele(const string & name, unsigned int nbrepeat);


//	int getnballdif() const;
	unsigned long get_nball() const {return(_tabPall.size());};
	unsigned long get_numloc() ;
	Allele * getPall(const string & nom) const ;
	Allele * getPallNul();
	Allele * getPall(long i) const {return(_tabPall[i]);};
	const char * get_nomall(int i) const {return(_tabPall[i]->_nom.c_str());};
//	const char * get_nom() {return(_nom.c_str());};
	const string& get_nom() const {return(_nom);};
	bool f_verifnum(int) const;

	inline void set_PJeupop(Jeupop * Pjeu);
	void set_nom(const string& mot) {_nom.assign(mot);};
	void set_microsat_correction(long double valmin, long double valmax, unsigned int value);

	void ifAjouterAllele(const Allele * Pall);


	friend class Jeupop;

	const Locus & operator= (const Locus &);
  /** Enlève les allèles non représentés dans Jeupop
 */
  void f_nettoieAlleles();
  /** Retourne le nombre d'allèles non nuls pour ce locus */
  unsigned long get_nballnonnuls() const;

private :
	void f_trad2Gpop(ostream&);

	string _nom;
	Jeupop * _Pjeu;
	vector _tabPall;
};

#endif

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L6HHHHH;tX1HtHD$@HHHIL;l$HHh[]A\A]A^A_HHT$0HHT$@HHT$PlhAHJHt$^$i$hAHJbHt$_$+$LH|$HHHHHHLH=H|$ H뷋Jqr@LHJqr_fDH\$Hl$HHHvHSHk HhFHǃHǃHǃHǃHǃHǃHl$H\$HATIUHSLLM)IMtHHHHLHPhHEHHP H[]A\HHHl@SHH#H{HhFHǃHǃHǃ	HǃHǃkhFHǃHC ǃHHH)HHtHH[HHD$}HQHYHD$Hfff.UHSHHHHH)HHtLH1	fDHH릺hAHPHt$?H|$ HH|$HHhAHt.P(Ht$=H|$H~븋PJH딋PJHKHHHHfHH;HSHgPJH-@AUIATUHSH(H_0Lg8H8H}7CI)HEHIM~o1HL9t_HHH4$H8HNH;OuH9uHEHHP0LH蜤H$HxHHgH([]A\A]@0HHHH}Hu8H;u@H\$t$1HtHHE8HHE8HxL,H}0HT$|HE8HHHHH`HhAHt!PPHt$APJHސfff.SHHHt$Hw8H;w@t91HtHD$HHG8HHC8H{ HC(Ht$HPH[@H0HT$AWAVAUATIUSHHHJ3HiFID$8I+D$0HHE1L{0G@1HtH.HC8H,$HHC8H{ HC(HHPID$8I+D$0IHI9sMI$LLP00ISHLHHJHs8H;s@H,$uHLH,$H[]A\A]A^A_HH.HnIHLfDHHHvH;pH<$t1HtH>HPHHPHHH5fffff.Hl$Ld$H-!L%P!Ll$Lt$L|$H\$H8L)AIHI{Ht1@LLDAHH9rH\$Hl$Ld$Ll$ Lt$(L|$0H8ÐUHSHHh!Ht8BgDHHHuH[]ÐHHAAAA0AAxgobi" to compute distancesERROR in "DistancesGnt"Nei et al's, Da (1983)DASLatter, Fst (1972)Prevosti et al.'s, Cp (1975)Rogers', Dr (1972)Shriver et al's, Dsw (1995)Lev A. Zhivotovsky, DR (1999)Reynolds J., weighted (1983)Genetic distances on  (squared distances)distances ref:+arbre ref:tirage:  sur: distances:arbre:ajboot: vector::_M_fill_insertajboot:ERROR 1 in "DistancesGnt": The distance method was not precisedERROR 2 in "DistancesGnt": Too few individuals in the population "ERROR 3 in "DistancesGnt": division by zero computing allelic frequencies for population "ERROR 4 in "DistancesGnt": this distance method "" could not be applied to individualsERROR 5 in "DistancesGnt": log of a negative number is  not defined ERROR 6 in "DistancesGnt": this distance method does not exist Nei's minimum genetic distance, Dm (1972)Nei's standard genetic distance, Ds (1972)Cavalli-Sforza and Edwards, Dc (1967)Goldstein et al. , dmu2 (1995a)Goldstein et al. (1995b) Slatkin, ASD (1995)Reynolds J., unweighted (1983)Reynolds J., least squares (1983)8AAAAPAAAAAAAA A0A@APA`ApAAAAAצAAA7ADA0AwAAAAA0AAWAAAA7AWAdAPAAA׹AAAPAAwAAAAAAAAAAAAAAAAOAgAgAgAgAA|AgAgAgAgAgA|AAA"A0Jgp-F-FPAAA@AA0CC=DCC:DpCCAAA0)D2DCPC0C0Jg-F0Jg-F0Jg .FN6Jeupop8AnomalieELgP.FXFN6biolib8vecteurs7Matrice8AnomalieEN12DistancesGnt8AnomalieEN6biolib8vecteurs5Titre8AnomalieEN6biolib8vecteurs9MatriceLDE_??@?AAdmix_mtxGenetixFstat	99	2   http://www.pge.cnrs-gif.fr/bioinfo/populations0Jg/FN9JeuPopExp8AnomalieEFis:  Fst:  Fit: exception dans strucpop: root) and  subpopulationslocus by columnsrows:FisFstFitHoHsHtFis, Fst, Fit for one population (Ho --> observed heterozygosity (mean overall subpopulations)Hs --> expected heterozygosity (mean overall subpopulations)Ht --> total expected heterozygosity0Jg`1FN8StrucPop8AnomalieEbasic_string::_S_construct null not validcorrespondances Anciens_Noms <---> Noms_GenepopNouvelle diversit� all�lique pour un effectif r�duit de : wrong number of individuals at line : wrong number of locus at line : wrong number of alleles at line : POP ;POPerror in Genetix data file.error in data file.DIFFPOP_The file is not readable... unknown file format0Jg 3FN12ChaineFicPop8AnomalieEName of input file (Populations or Genepop format) ?The file format seems incorrect...***************************************                                    **      langella@moulon.inra.fr       ** http://www.cnrs-gif.fr/pge/bioinfo *Please, choose a population among these ones:ApplPop::set_groupes_individus() anomalie Jeupop  has not been found.the population 7ApplPopLg4F`\F4F`B@BPDD@D0DBD@DPDD DDpDD@DPB0BName or number of the locus:  was not foundThe locus Output tree file:*     Populations 1.2.33Error n°100 in JeuPopExp:  require diploid populationsError in JeuPopExpWhich level ?level has been set to: Sample size ?Computing...Results matrix output :correspondances.txtStructured PopulationLevel Structured PopulationsbackShow structure levelSet level3)  in the object: Error number: UPGMANeighbor JoiningYour choice: Distance methodsBackSquared distance: yesSquared distance: no inidividuals,  bootstraps on individuals bootstraps on locusOnline help missingPlease visit our website :test du jourCopie d'objet Jeupoptoutc2.txtErreur de lecture...Fst, Fis and Fit computationOutput file name ?computing...Allelic frequencies, FstatsFst, Fis, Fit per populationsCompute allelic diversity for reduced sampleTry the linux version.Neighbor-Joiningthe matrix is too smallthe smallest value is: Phylogenetic tree saved in : Reading distance matrix: Locus selection:Select all loci (default)Remove all lociAdd a particular locusRemove a particular locus4) Display selected loci5) Output format:Populations formatPopulations XML formatGenepop formatGenepop modified formatImmanc format6) microsat individuals format7) 8) 9) Admix (G. Bertorelle)10) 11) Fstat (Jerome Goudet)12) -output-phylogeny-distDmDsneiDccavDadmu2goldsteinlatterCpprevostiDrrogerASDDswshriverDRzhivDrureynoldsuDrwreynoldswDrlreynoldsl-constructupgmanj-bootstrap_ind-level-bootstrap_locus--testMain menuExitStructured populationsName of output file (Phylip tree file) ?**********************************************************                                 **      langella@moulon.inra.fr                           **     http://bioinformatics.org/project/?group_id=84     *Error n°1 in JeuPopExp while exporting to Error n°2 in JeuPopExp: incompatible alleles names to export in Error n°1000 in JeuPopExp: locus names do not exceed 5 caracters in Error n°1001 in JeuPopExp: individual names do not exceed 10 caracters in ApplPopulations::fsetniveau() 1any compute using metapopulation will use this(ex: computing distances or making treesOutput file name (Genepop modified format) ?Genepop format allows only diploid genetic datasetsOutput file name (canonical Genepop format) ?Output file name (Populations format) ?Error writing Populations file...Display Wright indices per lociOutput file format (Immanc format) ?Immanc format allows only diploid genetic datasetsWhat is the name of the population P1 (parental population) ?What is the name of the population P2 (parental population) ?What is the name of the population H (hybrid population)?Output file name (LEA format, M.A. Beaumont, L. Chikhi) ?Output file name (Admix .dat format, G. Bertorelle) ?Output file name (Admix .mtx format, G. Bertorelle) ?Output file (Microsat format) ?Populations is not able to export dataset:Alleles names should be numeric, corresponding to allele size (or number of repetition).Computing distances between populations...Computing distances between individuals...How many times do you want to perform bootstraps ?Populations tree filename (Phylip format):Phylogenetic tree reconstruction aborted, tree file was not writtenCombien de tirages voulez-vous effectuer ?Output file name (Phylip tree format) ?Individuals distance matrix filename :Populations distance matrix filename :http://www.bioinformatics.org/~tryphon/populations/Output file name (Genetix format) ?Output file name (Fstat format) ?Allelic diversity for reduced sampleSorry this version of Populations is unable to read XML files.Output file name (XML Populations format) ?Building phylogenetic tree with UPGMA...Building phylogenetic tree with Neighbor-Joining...Error missing construction method to build phylogenetic treeInconsistant matrix file formatNegative distances in the matrix...to build a tree, you must set negative values to zero.Do you want to set negative values to zero (Y/N) ?The tree file was not written.Individuals tree filename (Phylip format):Error while reading the matrix fileFailure reading matrix file : the matrix is not symetric
Populations only works with euclidian distance matrix
Please check your file and retry

Out of range access in the matrixChoose locus to export (default: all)microsat populations + frequencies formatLEA Likelihood Estimation of AdmixtureDEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) debug output : DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) debug phylogeny : indDEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) debug phylogeny : popDEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) metdist : DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) metconstructarbre : ERROR: Populations is unable to bootstrap on individuals to make a phylogenetic tree of individualsDEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) bootstrap_locus : DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) nb_iterations : DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) phylogeny on individuals DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) Pjeupop->f_distgnt(distances, metdist, _square_distance); DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) larbre.iDistances DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) end larbre.iDistances DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) set_groupes_arbre(larbre); Input file format seems incorrect...ApplPopulations::fLiPhylogeny(Titre & tab_commandes) ERROR: Negative distances in the matrixReconstructing phylogenetic trees with populationsGet distance matrix between populationsPhylogenetic tree of populationsPhylogenetic tree of populations with bootstraps on locusPhylogenetic tree of populations with bootstraps on individualsChoose locus to compute distances (default: all)Reconstructing phylogenetic trees with individualsGet distance matrix between individualsPhylogenetic tree of individualsPhylogenetic tree of individuals with bootstraps on locusCompute individuals distances + treeCompute populations distances + treeBuild phylogenetic tree with a distance matrixFormated output for other softwaresChoose the output format of matrixmicrosatellites number of repeats corrections}CCCCCBCCCCCCCCCCiCpC(^C[C_C^CH^C8_CfCpfC`fCPfC@fC0fC fCfCeCeCeCeC0gCCpC`C@C8CCCCCCCCXCCCC0C`CC0C15ApplPopulationsLgQF4FRFpBBPDDC0D@BD`CPDD DDpDD@DPB0B0JgRFN6biolib6arbres5Arbre8AnomalieE#0.000000SheetfalseDisplayFormulasHideZeroHideGridHideColHeaderHideRowHeadertrueDisplayOutlinesOutlineSymbolsBelowOutlineSymbolsRightMaxColMaxRow1.000000ZoomNamesCellsCell60ValueType40ValueFormatgmrxsiWorkbookschemaLocationAttributesAttributename4typeTRUEvalueSummaryItembiology softwaresval-stringauthorSheetNameIndexMatrix 1SheetNameSheets.dat.doc.row.col   @//vector::reserveproduit scalaireespace �  dimensionsaxe_Valeur_PropreInertieCumulxml version="1.0"Calcul impossibleMatrice AMatrice Chttp://www.gnumeric.org/v10.dtdhttp://www.w3.org/2001/XMLSchema-instancehttp://www.gnumeric.org/v8.xsdWorkbookView::show_horizontal_scrollbarWorkbookView::show_vertical_scrollbarWorkbookView::show_notebook_tabsWorkbookView::do_auto_completionhttp://www.pge.cnrs-gif.fr/bioinfoOlivier Langella coordonn�es spatiales sur les colonnesstatistiques des coordonn�es spatiales sur les colonnesdiagonalisation par la methode Q-LErreur pendant la lecture du fichier...Cette matrice ne peut être diagonaliséeOpération impossible sur ce type de matriceEchec de la conversion de la matrice en matrice symétriqueErreur pendant l'ecriture du fichierAcces hors bornes dans la matricejDjDjDjDvjD;jDjDN6biolib8vecteurs7MatriceE0JgXFXF AAA@AA0CC=DCC:DpCCAAA0)D2DCPC0CB|=ư> already exist.The file Matrix outputfile format:NtSysPhylipGnumeric spreadsheet0) Quitter*  *NDemandeEntier defaut ERRORMatrix filename ?Reading file...Error writing matrix MatriceLD::Anomalie Writing error...Choose Y if you to overwrite it: ASCII, (excell or gnumeric compliant)*      langella@moulon.inra.fr      *Programmation: Olivier Langellae-mail: langella@moulon.inra.frThis Matrix file format is not recognized...Matrix filename to write into ?Filename of the set of matrix ?This file format is not recognized...Name of the file to write the set of matrix ?D0DDDDИD11Application0JgH\F`\F@BBPDD@D0DDD@DPDD DDpDD@D<(ArbreNdNoeud::operator== vide[\]erreur Arbre::SquizNoeudErreur Arbre::SquizNoeudcreated by biolib library____Error while building tree...#GArbre::iPhylipRecGetForce fichier.fail()Arbre::iPhylipRecGetTaille fichier.fail()Olivier Langella all negative values are replaced by zero to proceedBDBDrDrDBDrDrDrDrDrDrDrDrDrDrDrDrDrDrDrDrDrDrDBDrDrDrDrDrDrDrDD(DrDrDBDrDrDrDrDrDrDrDrDrDrDrDrDrDrDzDN6biolib6arbres11ArbreNdBaseE0Jg`FN6biolib6arbres10ArbreNdOTUELg`F`FN6biolib6arbres12ArbreNdNoeudELg aF`FN6biolib6arbres5ArbreE0Jg`aFaF@DPDEE@EPE0!ED(E(E`F DpD D`DPD'E`D'E@DDpDPD`DpDD'E'E'E'E@aFDDмD`DDDD'EDDpDD`DDD0DDpD"EDaFpDD D`DpDPD`D'E@DDpDPD DpDD'EpDD@DY@?8y>K@#G '' 'Erreur was  not foundArbrePlus::iPhylipDefGroupe(const string & ligne)Erreur TreePlotter::define_outgroupN6biolib6arbres9ArbrePlusELgdFaFeFCEPDEEE@EPE0!ED@SEP?Eredturquoisepinkyellowbrownpurplesea greensalmonsky blueyellow greenbrown1aquamarineorangebrown2navy bluegoldenrodtomatovioletgoldbasic_string::substrbasic_string::eraseLocus:  <--> erreur...nullNULLmiss , 000000	0EEFEnE}EE0JggFN8Individu8AnomalieEERROR in Individu object: 8StrucPop0Jg@gFPgFEEPE`EpEEEEEEEEEEEEE E0E`EE_basic_string::assignTitle line: MetaPopTOP_LEVEL7MetaPopLguhFPgFhF EEE`	FF
FEpFpFPFEEPEE	FEE E0EFE10PopulationLgriFPgFiFFPFFp"FpEEEpFFEEE@FE#F0FEF0E`E!F;H'ؼ)X:`H8xHd_q8Ľp8h$Ⱦ')(6X@:0GHW\qHtx8v|h8Ђh(xp(08(08Xx8XX(pxHh0(8((xx`xP  X!h !H!!( H"!"I(#(p#w@$~$(80X`Xh(P8Ȓ@8hh! ""H"#%HX%Xp%%%80&&&8('ȹ'0%( (8(x(()x)))) *p**+h++,0,H,h,,H,,-X-p---(-8-X-h..0.H.xx..(.8.X/@/X/8p/h/H/8000	P1	2
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0ustar  georgeskgeorgesk/***************************************************************************
 applpopulations.cpp  -  description
 -------------------
 begin                : Mon Oct 30 2000
 copyright            : (C) 2000 by Olivier Langella
 email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#include "applpopulations.h"

ApplPopulations::ApplPopulations() :
	ApplPop() {
	_square_distance = false;
}

ApplPopulations::~ApplPopulations() {
}

int ApplPopulations::menu_principal() {
	// calcul de distance entre tous les individus de n pop
	int choix;
	_choix = 0;

	cout << endl << endl;
	cout << _("Main menu") << endl << endl;
	cout << "0) " << _("Exit") << endl;
	cout << "1) " << _("Compute individuals distances + tree") << endl;
	cout << "2) " << _("Compute populations distances + tree") << endl;
	cout << "3) " << _("Allelic frequencies, Fstats") << endl;
	cout << "4) " << _("Build phylogenetic tree with a distance matrix")
			<< endl;
	cout << "5) " << _("Formated output for other softwares") << endl;
	cout << "6) " << _("Choose the output format of matrix") << endl;
	cout << "7) " << _("Structured populations") << endl;
	cout << "8) " << _("microsatellites number of repeats corrections") << endl;
	//	cout << "8) Concatenation de populations" << endl;

	choix = DemandeChoix(0, 8);

	switch (choix) {
	case 0:
		return (0);
		break;
	case 1:
		if (!iPopulations())
			return (1);
		menu_arbreind();
		return (1);
		break;

	case 2:
		if (!iPopulations())
			return (1);
		menu_arbrepop();
		return (2);
		break;

	case 3:
		if (!iPopulations())
			return (1);
		menu_calculs();
		return (3);
		break;

	case 4:
		cout << endl << endl;
		cout << _("Build phylogenetic tree with a distance matrix") << endl;
		//		cout << " a partir d'une matrice de distance" << endl;
		fmat2arbre();
		return (4);
		break;

	case 5:
		if (!iPopulations())
			return (1);
		menu_formats();
		return (5);
		break;

	case 6:
		menu_formatMatrice();
		return (6);
		break;

	case 7:
		if (!iPopulations())
			return (7);
		menu_popstructurees();
		return (7);
		break;

	case 8:
		if (!iPopulations())
			return (8);
		fmicrosatcorrections();
		return (7);
		break;

		/*	case 8:
		 if (!iPopulations()) return(8);
		 cout << endl << endl;
		 //		cout << "Format de sortie des matrices:" << endl;
		 fconcatenationpop();
		 return(8);
		 break;
		 */
	default:
		return (0);
		break;
	}
}

void ApplPopulations::fdistind() {
	MatriceLD distances;
	string nomFichier;

	nomFichier = DemandeFichier("Individuals distance matrix filename :");

	if (fcompdistind(distances) == false)
		return;

	ecritMatriceLD(distances, nomFichier);
}

void ApplPopulations::ftreeind() {
	MatriceLD distances;
	string nomFichier;
	int metdist;
	int metconstruct;
	//	unsigned int i;

	metdist = menu_metdistpop();
	if (_choix == -1)
		return;

	metconstruct = menu_metconstructarbre();
	if (_choix == -1)
		return;

	nomFichier = DemandeFichier("Individuals tree filename (Phylip format):");

	if (fcompdistind(distances, metdist) == false)
		return;

	fconstructarbre(distances, nomFichier, metconstruct);

	cout << _("Phylogenetic tree saved in : ") << nomFichier << endl;
}

void ApplPopulations::ftreeindBootLocus() {
	MatriceLD distances;
	int metdist;
	int metconstructarbre;
	ArbrePlus larbre;

	larbre._titre.resize(2);
	larbre._titre[0].assign(""); // individus, populations
	larbre._titre[1].assign(""); // m�thode de distance, nb bootstrap

	metdist = menu_metdistpop();
	if (_choix == -1)
		return;

	cout << _("Computing distances between individuals...") << endl;
	larbre._titre[0].AjEntier(_Pjeupop->get_nbind());
	larbre._titre[0] += " inidividuals, ";
	larbre._titre[0].AjEntier(_Pjeupop->get_nbpop());
	larbre._titre[0] += " populations";

	larbre._titre[1] += DistancesGnt::get_nom_methode(metdist);

	int nbtirages;

	metconstructarbre = menu_metconstructarbre();
	nbtirages = DemandeEntier(
			_("How many times do you want to perform bootstraps ?"), 1,
			30000);

	larbre._titre[1] += ", ";
	larbre._titre[1].AjEntier(nbtirages);
	larbre._titre[1] += " bootstraps on locus";

	//	cout << _("Output file name (Phylip tree format) ?") << endl;
	//	cin >> _nomFichier;
	_nomFichier = DemandeFichier("Output file name (Phylip tree format) ?");

	if (_VcalcLocus.size() == 0)
		_Pjeupop->f_BootstrapLocus(larbre, metconstructarbre, metdist,
				_square_distance, nbtirages, true);
	else
		_Pjeupop->f_BootstrapLocus(larbre, metconstructarbre, metdist,
				_square_distance, nbtirages, true, &_VcalcLocus);
	//	_Pjeupop->f_BootstrapLocus(larbre, metconstructarbre, metdist, nbtirages, true);

	//	larbre.fElimineTrifurcation();
	ecritArbre(larbre, _nomFichier);
}

void ApplPopulations::fsetniveau() {
	// r�glage du niveau de structure pour calculs sur des m�tapops

	_niveau = DemandeEntier(_("Which level ?"), 1, 100);

	_Pjeupop->f_rempliVcalcStrucPop(_niveau);

	cerr << "ApplPopulations::fsetniveau() 1" << _VcalcLocus.size() << endl;
	cout << _("level has been set to: ") << _niveau << endl;
	cout << _("any compute using metapopulation will use this") << endl;
	cout << _("(ex: computing distances or making trees") << endl;

}

void ApplPopulations::fmat2arbre() {
	// calcul de distance entre tous les individus de n pop
	MatriceLD distances;
	string nomficarbre("");

	cout << _("Reading distance matrix: ") << endl;
	while (litMatriceLD(distances) == false) {
		//		cout << "Lecture en cours..."<< endl;
	}

	//cerr << "ApplPopulations::fmat2arbre " << distances.GetNC() << " " << distances.GetNL() << endl;

	try {

		/*
		 if (distances.GetType() != 2) {
		 long i, j;
		 for (i = 0; i < distances.GetNC(); i++) {
		 for (j = 0; j < i; j++) {
		 distances.GetCase(j, i) = distances.GetCase(i, j);
		 }
		 }
		 distances.SetType(2);
		 }
		 */
		if (distances.SetType(2) == false) {
			throw biolib::vecteurs::MatriceLD::Anomalie(5);
		}

		//cerr << "ApplPopulations::fmat2arbre" << endl;
		//distances.oExcel(cout);
		fconstructarbre(distances, nomficarbre, menu_metconstructarbre());
	} catch (MatriceLD::Anomalie pb) {
		_fichier.close();
		switch (pb.le_pb) {
		case 1:
			_fichier.close();
			cout << _("Error while reading the matrix file");
			break;

		case 5:
			cerr
					<< _("Failure reading matrix file : the matrix is not symetric\n");
			cerr
					<< _("Populations only works with euclidian distance matrix\n");
			cerr << _("Please check your file and retry\n\n");
			break;
		case 7:
			cout << _("Out of range access in the matrix");
			break;
		}
	}

}

void ApplPopulations::frarefaction() {
	MatriceLD distances;
	int taille;

	//cerr << _Pjeupop->get_nbpop();
	taille = DemandeEntier(_("Sample size ?"), 2, 1000);

	cout << _("Computing...") << endl;
	_Pjeupop->f_rarefaction(distances, taille);

	cout << _("Results matrix output :") << endl;

	//	cerr << distances.GetCase (1,1);
	ecritMatriceLD(distances);
}

bool ApplPopulations::fcompdistind(MatriceLD & distances, int metdist) {
	_temp.resize(2);
	_temp[0].assign(""); // individus, populations
	_temp[1].assign(""); // m�thode de distance, nb bootstrap

	if (metdist == 0) {
		metdist = menu_metdistpop();
		if (_choix == -1)
			return (false);
	}

	cout << _("Computing distances between individuals...") << endl;
	_temp[0].AjEntier(_Pjeupop->get_nbind());
	_temp[0] += " inidividuals, ";
	_temp[0].AjEntier(_Pjeupop->get_nbpop());
	_temp[0] += " populations";

	_temp[1] += DistancesGnt::get_nom_methode(metdist);

	if (_VcalcLocus.size() == 0)
		_Pjeupop->f_distgnt(distances, metdist, _square_distance);
	else
		_Pjeupop->f_distgnt(distances, metdist, _square_distance, &_VcalcLocus);

	return (true);
}

bool ApplPopulations::fcompdistpop(MatriceLD & distances, int metdist) {
	// calcul de distance entre toutes les populations
	_temp.resize(2);
	_temp[0].assign(""); // individus, populations
	_temp[1].assign(""); // m�thode de distance, nb bootstrap

	if (metdist == 0) {
		metdist = menu_metdistpop();
		if (_choix == -1)
			return (false);
	}

	cout << _("Computing distances between populations...") << endl;
	_temp[0].AjEntier(_Pjeupop->get_nbpop());
	_temp[0] += " populations";

	_temp[1] += DistancesGnt::get_nom_methode(metdist);

	try {
		//cerr << "ApplPopulations::fcompdistpop(MatriceLD & distances, int metdist) 1" <<  _VcalcLocus.size() << endl;
		if (_VcalcLocus.size() == 0) {
			//cerr << "ApplPopulations::fcompdistpop(MatriceLD & distances, int metdist) niveau " <<  _niveau << endl;
			_Pjeupop->f_distgntpop(distances, metdist, _square_distance,
					_niveau);
		} else {
			_Pjeupop->f_distgntpop(distances, metdist, _square_distance,
					_niveau, &_VcalcLocus);
		}
	} catch (Jeupop::Anomalie lepb) {
		//		cerr << endl << lepb.fmessage() << endl;
		return (false);
	}

	return (true);
}

void ApplPopulations::fdistpop() {
	// sortie des distance entre toutes les populations
	MatriceLD distances;
	string nomFichier;

	nomFichier = DemandeFichier(_("Populations distance matrix filename :"));

	if (fcompdistpop(distances) == false)
		return;

	ecritMatriceLD(distances, nomFichier);
}

void ApplPopulations::ftreepop() {
	// sortie de l'arbre phylogenetic des pops
	MatriceLD distances;
	string nomFichier;
	int metdist;
	int metconstruct;

	metdist = menu_metdistpop();
	if (_choix == -1)
		return;

	metconstruct = menu_metconstructarbre();
	if (_choix == -1)
		return;

	nomFichier
			= DemandeFichier(_("Populations tree filename (Phylip format):"));

	if (fcompdistpop(distances, metdist)) {
		fconstructarbre(distances, nomFichier, metconstruct);

		cout << _("Phylogenetic tree saved in : ") << nomFichier << endl;
	} else {
		cout
				<< _("Phylogenetic tree reconstruction aborted, tree file was not written")
				<< endl;
	}
}

void ApplPopulations::ftreepopBootLocus() {
	// calcul de distance entre toutes les populations
	// avec bootstrap sur les locus
	MatriceLD distances;
	int metdist;
	int metconstructarbre;

	ArbrePlus larbre;
	int nbtirages;

	metdist = menu_metdistpop();
	if (_choix == -1) {
		_choix = 1;
		return;
	}

	metconstructarbre = menu_metconstructarbre();
	nbtirages = DemandeEntier("Combien de tirages voulez-vous effectuer ?", 1,
			10000);

	larbre._titre.resize(2);
	larbre._titre[0].assign(""); // individus, populations
	larbre._titre[1].assign(""); // m�thode de distance, nb bootstrap

	larbre._titre[0].AjEntier(_Pjeupop->get_nbpop());
	larbre._titre[0] += " populations";

	larbre._titre[1] += DistancesGnt::get_nom_methode(metdist);
	larbre._titre[1] += ", ";
	larbre._titre[1].AjEntier(nbtirages);
	larbre._titre[1] += " bootstraps on locus";

	_nomFichier = DemandeFichier(
			_("Populations tree filename (Phylip format):"));

	try {
		if (_VcalcLocus.size() == 0)
			_Pjeupop->f_BootstrapLocus(larbre, metconstructarbre, metdist,
					_square_distance, nbtirages, false);
		else
			_Pjeupop->f_BootstrapLocus(larbre, metconstructarbre, metdist,
					_square_distance, nbtirages, false, &_VcalcLocus);
	} catch (Jeupop::Anomalie lepb) {
		cout
				<< _("Phylogenetic tree reconstruction aborted, tree file was not written")
				<< endl;
		return;
	}

	//	larbre.fElimineTrifurcation();
	ecritArbre(larbre, _nomFichier);
}

void ApplPopulations::ftreepopBootInd() {
	// calcul de distance entre toutes les populations
	// avec bootstrap sur les individus
	MatriceLD distances;
	int metdist;
	int metconstructarbre;

	ArbrePlus larbre;
	int nbtirages;

	metdist = menu_metdistpop();
	if (_choix == -1) {
		_choix = 1;
		return;
	}

	metconstructarbre = menu_metconstructarbre();
	nbtirages = DemandeEntier(
			_("How many times do you want to perform bootstraps ?"), 1,
			30000);

	larbre._titre.resize(2);
	larbre._titre[0].assign(""); // individus, populations
	larbre._titre[1].assign(""); // m�thode de distance, nb bootstrap

	larbre._titre[0].AjEntier(_Pjeupop->get_nbpop());
	larbre._titre[0] += " populations";

	larbre._titre[1] += DistancesGnt::get_nom_methode(metdist);
	larbre._titre[1] += ", ";
	larbre._titre[1].AjEntier(nbtirages);
	larbre._titre[1] += " bootstraps on individuals";

	_nomFichier = DemandeFichier(
			_("Populations tree filename (Phylip format):"));

	try {
		if (_VcalcLocus.size() == 0)
			_Pjeupop->f_BootstrapIndividus(larbre, metconstructarbre, metdist,
					_square_distance, nbtirages);
		else
			_Pjeupop->f_BootstrapIndividus(larbre, metconstructarbre, metdist,
					_square_distance, nbtirages, &_VcalcLocus);
	} catch (Jeupop::Anomalie lepb) {
		cout
				<< _("Phylogenetic tree reconstruction aborted, tree file was not written")
				<< endl;
		return;
	}

	//	larbre.fElimineTrifurcation();
	ecritArbre(larbre, _nomFichier);
}

void ApplPopulations::ecritGenepop() {
	//	cout << _("Output file name (Genepop modified format) ?") << endl;
	//	cin >> _nomFichier;
	_nomFichier = DemandeFichier(
			_("Output file name (Genepop modified format) ?"));

	try {
		_sortie.open(_nomFichier.c_str(), ios::out);
		_Pjeupop->oGenepop(_sortie);
		_sortie.close();
	} catch (Jeupop::Anomalie pb) {
		_sortie.close();
		switch (pb.le_pb) {
		case 1:
			cerr << endl
					<< _("Genepop format allows only diploid genetic datasets")
					<< endl;
			break;
		case 2:
			//la numerotation est a refaire, avec une table de conversion
			//cerr << "ApplPop::ecritGenepop() impossible" << endl;
			Jeupop traduction(*_Pjeupop);

			_sortie.open("correspondances.txt", ios::out);
			traduction.f_trad2Gpop(_sortie);
			//			_sortie << ends;
			_sortie.close();

			_sortie.open(_nomFichier.c_str(), ios::out);
			traduction.oGenepopCano(_sortie);
			_sortie.close();

			break;
		}
	}
}

void ApplPopulations::ecritGenepopCano() {
	//	cout << _("Output file name (canonical Genepop format) ?") << endl;
	//	cin >> _nomFichier;
	_nomFichier = DemandeFichier(
			_("Output file name (canonical Genepop format) ?"));

	try {
		_sortie.open(_nomFichier.c_str(), ios::out);
		_Pjeupop->oGenepopCano(_sortie);
		_sortie.close();
	} catch (Jeupop::Anomalie pb) {
		_sortie.close();
		switch (pb.le_pb) {
		case 1:
			cerr << endl
					<<_("Genepop format allows only diploid genetic datasets")
					<< endl;
			break;
		case 2:
			//la numerotation est a refaire, avec une table de conversion
			Jeupop traduction(*_Pjeupop);

			_sortie.open("correspondances.txt", ios::out);
			traduction.f_trad2Gpop(_sortie);
			//			_sortie << ends;
			_sortie.close();

			_sortie.open(_nomFichier.c_str(), ios::out);
			traduction.oGenepop(_sortie);
			_sortie.close();

			break;
		}
	}
}

void ApplPopulations::ecritPopulations() {
	//	cout << _("Output file name (Populations format) ?") << endl;
	//	cin >> _nomFichier;
	_nomFichier = DemandeFichier(_("Output file name (Populations format) ?"));

	try {
		_sortie.open(_nomFichier.c_str(), ios::out);
		_Pjeupop->oPopulations(_sortie);
		_sortie.close();
	} catch (Jeupop::Anomalie pb) {
		_sortie.close();
		switch (pb.le_pb) {
		default:
			cerr << _("Error writing Populations file...") << endl;
		}
	}
}

void ApplPopulations::menu_formats() {

	Vecteur Vlocus;
	Jeupop * Pjeupopsvg(0);

	int choix(1);
	while (choix != 0) {
		cout << endl << endl;
		cout << _("Output format:") << endl;
		cout << "0) " << _("Back") << endl;
		cout << "1) " << _("Choose locus to export (default: all)") << endl;
		cout << "2) " << _("Populations format") << endl;
		cout << "3) " << _("Populations XML format") << endl;
		cout << "4) " << _("Genepop format") << endl;
		cout << "5) " << _("Genepop modified format") << endl;
		cout << "6) " << _("Immanc format") << endl;
		cout << "7) " << _("microsat individuals format") << endl;
		cout << "8) " << _("microsat populations + frequencies format") << endl;
		cout << "9) " << _("LEA Likelihood Estimation of Admixture") << endl;
		cout << "10) " << _("Admix (G. Bertorelle)") << endl;
		cout << "11) " << _("Genetix") << endl;
		cout << "12) " << _("Fstat (Jerome Goudet)") << endl;

		choix = DemandeChoix(0, 12);

		switch (choix) {
		case 0:
			if (Pjeupopsvg != 0) {
				delete _Pjeupop;
				_Pjeupop = Pjeupopsvg;
			}
			break;
		case 1:
			//choix des locus
			Vlocus = menu_choixlocus();
			if (Vlocus.size() != 0) {
				Pjeupopsvg = _Pjeupop;
				_Pjeupop = new Jeupop(*Pjeupopsvg);
				_Pjeupop->GarderVlocus(Vlocus);
			}
			break;
		case 2:
			ecritPopulations();
			break;
		case 3:
			ecritPopulationsXML();
			break;
		case 4:
			ecritGenepopCano();
			break;
		case 5:
			ecritGenepop();
			break;
		case 6:
			ecritImmanc();
			break;
		case 7:
			ecritMsat(1);
			break;
		case 8:
			ecritMsat(2);
			break;
		case 9:
			ecritLea();
			break;
		case 10:
			ecritAdmix();
			break;
		case 11:
			ecritGenetix();
			break;
		case 12:
			ecritFstat();
			break;
		}
	}

}

void ApplPopulations::menu_popstructurees() {

	int choix(0);
	_choix = 1;
	while (_choix > 0) {
		cout << endl << endl;
		cout << _("Structured Populations") << endl;
		cout << endl << endl;
		cout << "0) " << _("back") << endl;
		cout << "1) " << _("Show structure level") << endl;
		cout << "2) " << _("Set level") << endl;
		cout << "3) " << _("Display Wright indices per loci") << endl;

		choix = DemandeChoix(0, 3);

		switch (choix) {
		case 0:
			_choix = -1;
			return;
			break;
		case 1:
			AffNiveauxPopStruc(cout);
			break;
		case 2:
			fsetniveau();
		case 3:
			Fstat lesfstats(_Pjeupop->get_Pracinepop());
			lesfstats.f_affparlocus(cout);
			break;
		}
	}
}

void ApplPopulations::menu_calculs() {

	int choix(0);
	_choix = 1;
	while (_choix > 0) {
		cout << endl << endl;
		cout << _("Allelic frequencies, Fstats") << endl;
		cout << endl << endl;
		cout << "0) " << _("back") << endl;
		cout << "1) " << _("Allelic diversity for reduced sample") << endl;
		cout << "2) " << _("Fst, Fis, Fit per populations") << endl;

		choix = DemandeChoix(0, 3);

		switch (choix) {
		case 0:
			_choix = -1;
			return;
			break;
		case 1:
			cout << endl << endl;
			cout << _("Compute allelic diversity") << endl;
			cout << _(" for reduced sample") << endl;
			frarefaction();
			break;
		case 2:
			ecritRapportFst();
			break;
		}
	}
}

void ApplPopulations::menu_arbrepop() {

	int choix(0);

	set_groupes_populations();

	_choix = 1;
	while (_choix > 0) {
		cout << endl << endl;
		cout << _("Reconstructing phylogenetic trees with populations") << endl;
		cout << endl << endl;
		cout << "0) " << _("back") << endl;
		cout << "1) " << _("Get distance matrix between populations") << endl;
		cout << "2) " << _("Phylogenetic tree of populations") << endl;
		cout << "3) "
				<< _("Phylogenetic tree of populations with bootstraps on locus")
				<< endl;
		cout << "4) "
				<< _("Phylogenetic tree of populations with bootstraps on individuals")
				<< endl;
		cout << "5) " << _("Choose locus to compute distances (default: all)")
				<< endl;

		choix = DemandeChoix(0, 5);

		switch (choix) {
		case 0:
			_choix = -1;
			return;
			break;
		case 1:
			fdistpop();
			break;
		case 2:
			ftreepop();
			break;
		case 3:
			ftreepopBootLocus();
			break;
		case 4:
			ftreepopBootInd();
			break;
		case 5:
			_VcalcLocus = menu_choixlocus();
			affVlocus(_VcalcLocus);
			break;
		}
	}
	reset_groupes();
}

void ApplPopulations::menu_arbreind() {

	int choix(0);

	set_groupes_individus();

	_choix = 1;
	while (_choix > 0) {
		cout << endl << endl;
		cout << _("Reconstructing phylogenetic trees with individuals") << endl;
		cout << endl << endl;
		cout << "0) " << _("back") << endl;
		cout << "1) " << _("Get distance matrix between individuals") << endl;
		cout << "2) " << _("Phylogenetic tree of individuals") << endl;
		cout << "3) "
				<< _("Phylogenetic tree of individuals with bootstraps on locus")
				<< endl;
		cout << "4) " << _("Choose locus to compute distances (default: all)")
				<< endl;

		choix = DemandeChoix(0, 4);

		switch (choix) {
		case 0:
			_choix = -1;
			return;
			break;
		case 1:
			fdistind();
			break;
		case 2:
			ftreeind();
			break;
		case 3:
			ftreeindBootLocus();
			break;
		case 4:
			_VcalcLocus = menu_choixlocus();
			affVlocus(_VcalcLocus);
			break;
		}
	}

	reset_groupes();
}

void ApplPopulations::AffNiveauxPopStruc(ostream &) {

	//Affichage des niveaux de structuration des populations
	Titre nom_niveaux;
	unsigned long i;

	_Pjeupop->get_nomniveauxstruc(nom_niveaux);

	cout << endl << endl;
	cout << _("Structured Population") << endl;
	cout << endl;

	for (i = 0; i < nom_niveaux.size(); i++) {
		cout << _("Level ") << i << ":" << endl;
		cout << nom_niveaux[i] << endl;
	}

}

void ApplPopulations::ecritImmanc() {
	//	cout << _("Output file format (Immanc format) ?") << endl;
	//	cin >> _nomFichier;
	_nomFichier = DemandeFichier(_("Output file format (Immanc format) ?"));

	try {
		_sortie.open(_nomFichier.c_str(), ios::out);
		_Pjeupop->oImmanc(_sortie);
		_sortie.close();
	} catch (Jeupop::Anomalie pb) {
		_sortie.close();
		switch (pb.le_pb) {
		case 1:
			cerr << endl
					<< _("Immanc format allows only diploid genetic datasets")
					<< endl;
			break;
		case 2:
			//la numerotation est a refaire, avec une table de conversion
			Jeupop traduction(*_Pjeupop);

			_sortie.open("correspondances.txt", ios::out);
			traduction.f_trad2Gpop(_sortie);
			_sortie << ends;
			_sortie.close();

			_sortie.open(_nomFichier.c_str(), ios::out);
			traduction.oImmanc(_sortie);
			_sortie.close();

			break;
		}
	}
}

void ApplPopulations::ecritLea() {
	//		format LEA Likelihood Estimation of Admixture
	unsigned long P1, P2, H;

	P1
			= DemandePopulation(
					_("What is the name of the population P1 (parental population) ?"));
	P2
			= DemandePopulation(
					_("What is the name of the population P2 (parental population) ?"));
	H
			= DemandePopulation(
					_("What is the name of the population H (hybrid population)?"));

	//	cout << _("Output file name (LEA format, M.A. Beaumont, L. Chikhi) ?") << endl;
	//	cin >> _nomFichier;
	_nomFichier
			= DemandeFichier(
					_("Output file name (LEA format, M.A. Beaumont, L. Chikhi) ?"));

	try {
		_sortie.open(_nomFichier.c_str(), ios::out);

		JeuPopExp exportation(_Pjeupop);

		exportation.oLea(P1, P2, H, _sortie, cout);

		_sortie.close();
	} catch (JeuPopExp::Anomalie pb) {
		_sortie.close();
		switch (pb.le_pb) {
		case 1:
			break;
		case 2:
			break;
		default:
			cerr << _("Error number: ") << pb.le_pb << _(" in the object: ")
					<< "JeuPopExp" << endl;
			break;
		}
	}
}

void ApplPopulations::ecritAdmix() {
	//		format Admix http://www.unife.it/genetica/Giorgio/giorgio.html
	unsigned long P1, P2, H;
	string fichier_mtx;

	P1
			= DemandePopulation(
					_("What is the name of the population P1 (parental population) ?"));
	P2
			= DemandePopulation(
					_("What is the name of the population P2 (parental population) ?"));
	H
			= DemandePopulation(
					_("What is the name of the population H (hybrid population)?"));

	cout << _("Output file name (Admix .dat format, G. Bertorelle) ?") << endl;
	cin >> _nomFichier;

	cout << _("Output file name (Admix .mtx format, G. Bertorelle) ?") << endl;
	cin >> fichier_mtx;

	try {
		_sortie.open(_nomFichier.c_str(), ios::out);
		JeuPopExp exportation(_Pjeupop);
		exportation.oAdmix_dat(P1, P2, H, _sortie, cout);
		_sortie.close();

		_sortie.open(fichier_mtx.c_str(), ios::out);
		exportation.oAdmix_mtx(_sortie, cout);
		_sortie.close();
	} catch (JeuPopExp::Anomalie pb) {
		_sortie.close();
		switch (pb.le_pb) {
		case 1:
			break;
		case 2:
			break;
		default:
			cerr << _("Error number: ") << pb.le_pb << _(" in the object: ")
					<< "JeuPopExp" << endl;
			break;
		}
	}
}

void ApplPopulations::ecritMsat(int choix) {
	//	cout << _("Output file (Microsat format) ?") << endl;
	//	cin >> _nomFichier;
	_nomFichier = DemandeFichier(_("Output file (Microsat format) ?"));

	try {
		_sortie.open(_nomFichier.c_str(), ios::out);
		switch (choix) {
		case 1:
			_Pjeupop->oMsat(_sortie);
			break;
		default:
			_Pjeupop->oMsatFreq(_sortie);
			break;
		}
		_sortie.close();
	} catch (Jeupop::Anomalie pb) {
		_sortie.close();
		switch (pb.le_pb) {
		//		case 1:
		//			cerr << endl << "le format Immanc ne permet que le stockage de pop diploides" << endl;
		//			break;
		case 2:
			//les noms d'alleles ne sont pas des tailles de msat
			cout << _("Populations is not able to export dataset:") << endl;
			//			cout << _("Les noms d'alleles doivent correspondre a des tailles de microsatellites (ou au nombre de repetitions).") << endl;
			cout
					<< _("Alleles names should be numeric, corresponding to allele size (or number of repetition).")
					<< endl;

			break;
		}
	}
}

int ApplPopulations::menu_metconstructarbre() {

	int choix;
	_choix = 0;

	//	while (_choix != 0) {
	cout << endl << endl;
	//		cout << "0) Menu principal" << endl;
	cout << "1) " << _("UPGMA") << endl;
	cout << "2) " << _("Neighbor Joining") << endl;
	cout << endl << _("Your choice: ");
	cin >> choix;

	switch (choix) {
	//		case 0:
	//			_choix = -1;
	//			return;
	//			break;
	case 1:
		return (1);
		break;
	case 2:
		return (2);
		break;
	default:
		return (2);
		break;
	}
	//	}

}

int ApplPopulations::menu_metdistpop() {

	int choix;
	unsigned int i, nb_methods(DistancesGnt::get_nb_methodes());
	_choix = 0;

	//	while (_choix != 0) {
	cout << endl << _("Distance methods") << endl;
	cout << "0) " << _("Back") << endl;
	for (i = 1; i < nb_methods; i++) {
		cout << (i) << ") " << DistancesGnt::get_nom_methode(i) << endl;
	}
	if (_square_distance)
		cout << nb_methods << ") " << _("Squared distance: yes") << endl;
	else
		cout << nb_methods << ") " << _("Squared distance: no") << endl;
	/*
	 cout << "1) " << _("DAS, Allelic Shared Distance (Chakraborty et Jin., 1993)") << endl;
	 cout << "2) " << _("Nei, minimum genetic distance, Dm (Nei,1987)") << endl;
	 cout << "3) " << _("Nei, standard genetic distance, Ds (Nei, 1987)") << endl;
	 cout << "4) " << _("Cavalli-Sforza and Edwards, Dc (1967)") << endl;
	 cout << "5) " << _("Nei et al's, Da (1983)") << endl;
	 cout << "6) " << _("Goldstein et al., dmu2 (1995a)") << endl;
	 cout << "7) " << _("Latter, Fst (1972)") << endl;
	 cout << "8) " << _("Prevosti et al.'s, Cp (1975)") << endl;
	 cout << "9) " << _("Rogers', Dr (1972)") << endl;
	 cout << "10) " << _("Average Square Distance (ASD, Goldstein, Slatkin 1995)") << endl;
	 cout << "11) " << _("Shriver et al's, Dsw (1995)") << endl;
	 cout << "12) " << _("Lev A. Zhivotovsky, DR (1999)") << endl;
	 */

	choix = DemandeChoix(0, nb_methods + 1);

	switch (choix) {
	case 0:
		_choix = -1;
		return (-1);
		break;
	case 1:
		return (101); //Das sur les individus
		break;
	case 2:
		return (102); //Nei sur les populations
		break;
	case 3:
		return (103); //Nei sur les populations
		break;
	case 4:
		return (104); //Cavalli-Sforza and Edwards' (1967)sur les populations
		break;
	case 5:
		return (5); // Nei et al's, Da (1983) sur les populations
		break;
	case 6:
		return (106); // Goldstein et al., Mu (1995a) sur les populations
		break;
	case 7:
		return (107); // Latter's Fst (1972) sur les populations
		break;
	case 8:
		return (108); // Prevosti et al.'s, Cp (1975) sur les populations
		break;
	case 9:
		return (109); // Rogers', Dr (1972) sur les populations
		break;
	case 10:
		return (110); // Goldstein et al. (1995b) Slatkin 1995
		break;
	case 11:
		return (111); // Shriver et al's, Dsw (1995)
		break;
	case 12:
		return (112); // Lev A. Zhivotovsky, DR (1999)
		break;
	case 13:
		return (113); // Reynolds unweighted (1983)
		break;
	case 14:
		return (114); // Reynolds weighted (1983)
		break;
	case 15:
		return (115); // Reynolds least squares (1983)
		break;

	case 16:
		_square_distance = !_square_distance;
		return (menu_metdistpop());
		break;

	default:
		return (5);
		break;
	}
}

void ApplPopulations::fconstructarbre(MatriceLD &distances,
		string & nomficarbre, int methodearbre) {
	ArbrePlus larbre;
	bool continuer(true);

	if (_temp.size() != 0)
		larbre._titre = _temp;
	switch (methodearbre) {
	case 1:
		cerr << _("Building phylogenetic tree with UPGMA...") << endl;
		larbre._titre.push_back("UPGMA");
		break;
	case 2:
		cerr << _("Building phylogenetic tree with Neighbor-Joining...")
				<< endl;
		larbre._titre.push_back("Neighbor-Joining");
		break;
	case 101:
		cerr << _("Building phylogenetic tree with UPGMA...") << endl;
		larbre._titre.push_back("UPGMA");
		break;
	case 102:
		cerr << _("Building phylogenetic tree with Neighbor-Joining...")
				<< endl;
		larbre._titre.push_back("Neighbor-Joining");
		break;
	default:
		cerr
				<< _("Error missing construction method to build phylogenetic tree")
				<< endl;
		//		larbre._titre.push_back("UPGMA");
		return;
	}

	while (continuer) {
		continuer = false;
		try {
			//		_sortie.open("debug.txt", ios::out);
			//		distances.oExcel(_sortie);
			//		_sortie.close();
			//cerr << "ApplPopulations::fconstructarbre debut iDistances" << endl;
			larbre.iDistances(distances, methodearbre);
			//			larbre.fElimineTrifurcation();
			//cerr << "ApplPopulations::fconstructarbre fin iDistances" << endl;

			ecritArbre(larbre, nomficarbre);
		} catch (Arbre::Anomalie pb) {
			switch (pb.le_pb) {
			case 4:
				cout << _("Inconsistant matrix file format") << endl;
				break;
			case 5:
				cout << _("the matrix is too small") << endl;
				break;
			case 6:
				cout << _("Negative distances in the matrix...") << endl;
				cout << _("the smallest value is: ")
						<< distances.get_ppvaleur() << endl;
				cout
						<< _("to build a tree, you must set negative values to zero.")
						<< endl;
				if (DemandeOuiNon(
						_("Do you want to set negative values to zero (Y/N) ?"))) {
					distances.f_neg2zero();
					continuer = true;
				}
				break;
			}
			if (continuer == false)
				cout << _("The tree file was not written.") << endl;

		}
	}// continuer
	_temp.resize(0);
}

void ApplPopulations::ecritArbre(ArbrePlus & larbre, string nomFichier) {
	//cerr << "ApplPopulations::ecritArbre(ArbrePlus & larbre, string nomFichier) debut" << endl;
	set_groupes_arbre(larbre);

	if (nomFichier == "") {
		cout << _("Output tree file:") << endl;
		nomFichier = DemandeFichier(
				_("Name of output file (Phylip tree file) ?"));
	}

	_sortie.open(nomFichier.c_str(), ios::out);
	larbre.oFichier(_sortie, 1);
	//	_sortie << larbre;
	//	_sortie << endl << ends;
	_sortie.close();
	//cerr << "ApplPopulations::ecritArbre(ArbrePlus & larbre, string nomFichier) fin" << endl;
}

void ApplPopulations::fLigneCommande(char ** commandes, int nbcommandes) {
	Titre tab_commandes(commandes, nbcommandes);

	if (tab_commandes.Position("-phylogeny") > 0)
		fLiPhylogeny(tab_commandes);
	else if (tab_commandes.Position("--test") >= 0)
		fLiTest(tab_commandes);
	else
		fLiHelp();
}

void ApplPopulations::fLiPhylogeny(Titre & tab_commandes) {
	// demande d'arbre phylog�n�tique
	int pos;
	//	unsigned int niveau(100); //niveau pour populations structur�es
	ArbrePlus larbre;

	istream * Pentree(&cin);
	ostream * Psortie(&cout);

	tab_commandes.Suppr(0);

	//fichiers d'entree ou entree standard (par d�faut)
	_fichier.open(tab_commandes[0].c_str(), ios::in);

	if (_fichier.is_open())
		Pentree = &_fichier;
	try {
		_Pjeupop = new Jeupop();
		*Pentree >> *(_Pjeupop);
		_fichier.close();
		_fichier.clear();
	} catch (Jeupop::Anomalie pb) {
		_fichier.close();
		_fichier.clear();
		delete _Pjeupop;

		switch (pb.le_pb) {
		case 4:
			cerr << _("Input file format seems incorrect...") << endl;
			return;
			break;
		}
	}

	//fichiers de sortie ou sortie standard (sortie standard par d�faut)
	pos = tab_commandes.Position("-output");
	if ((pos > 0) && (pos + 1 != (long) tab_commandes.size())) {
		_sortie.open(tab_commandes[pos + 1].c_str(), ios::out);
		cerr
				<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) debug output : "
				<< tab_commandes[pos + 1].c_str() << endl;
		if (_sortie.is_open() != 0)
			Psortie = &_sortie;
		tab_commandes.Suppr(pos + 1);
		tab_commandes.Suppr(pos);
	}

	// Individus ou Populations ? (populations par d�faut)
	bool sur_pop(true);

	//tab_commandes.Suppr(tab_commandes.Position("-phylogeny"));
	pos = tab_commandes.Position("-phylogeny");

	if ((pos + 1 != (long) tab_commandes.size()) && (tab_commandes[pos + 1]
			== "ind")) {
		sur_pop = false;
		tab_commandes.Suppr(pos + 1);
		cerr
				<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) debug phylogeny : ind"
				<< endl;
	} else if ((pos + 1 != (long) tab_commandes.size()) && (tab_commandes[pos
			+ 1] == "pop")) {
		tab_commandes.Suppr(pos + 1);
		cerr
				<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) debug phylogeny : pop"
				<< endl;
	}
	tab_commandes.Suppr(pos);

	// Methode de distance ? (Nei standard par d�faut)
	int metdist(102);
	pos = tab_commandes.Position("-dist");
	if ((pos > 0) && (pos + 1 != (long) tab_commandes.size())) {
		if (tab_commandes[pos + 1] == "DAS") {
			metdist = 5;
			tab_commandes.Suppr(pos + 1);
		} else if (tab_commandes[pos + 1] == "Dm") {
			metdist = 101;
			tab_commandes.Suppr(pos + 1);
		} else if ((tab_commandes[pos + 1] == "Ds") || (tab_commandes[pos + 1]
				== "nei")) {
			metdist = 102;
			tab_commandes.Suppr(pos + 1);
		} else if ((tab_commandes[pos + 1] == "Dc") || (tab_commandes[pos + 1]
				== "cav")) {
			metdist = 103;
			tab_commandes.Suppr(pos + 1);
		} else if (tab_commandes[pos + 1] == "Da") {
			metdist = 104;
			tab_commandes.Suppr(pos + 1);
		} else if ((tab_commandes[pos + 1] == "dmu2")
				|| (tab_commandes[pos + 1] == "goldstein")) {
			metdist = 106;
			tab_commandes.Suppr(pos + 1);
		} else if ((tab_commandes[pos + 1] == "Fst") || (tab_commandes[pos + 1]
				== "latter")) {
			metdist = 107;
			tab_commandes.Suppr(pos + 1);
		} else if ((tab_commandes[pos + 1] == "Cp") || (tab_commandes[pos + 1]
				== "prevosti")) {
			metdist = 108;
			tab_commandes.Suppr(pos + 1);
		} else if ((tab_commandes[pos + 1] == "Dr") || (tab_commandes[pos + 1]
				== "roger")) {
			metdist = 109;
			tab_commandes.Suppr(pos + 1);
		} else if (tab_commandes[pos + 1] == "ASD") {
			metdist = 110;
			tab_commandes.Suppr(pos + 1);
		} else if ((tab_commandes[pos + 1] == "Dsw") || (tab_commandes[pos + 1]
				== "shriver")) {
			metdist = 111;
			tab_commandes.Suppr(pos + 1);
		} else if ((tab_commandes[pos + 1] == "DR") || (tab_commandes[pos + 1]
				== "zhiv")) {
			metdist = 112;
			tab_commandes.Suppr(pos + 1);
		} else if ((tab_commandes[pos + 1] == "Dru") || (tab_commandes[pos + 1]
				== "reynoldsu")) {
			metdist = 113;
			tab_commandes.Suppr(pos + 1);
		} else if ((tab_commandes[pos + 1] == "Drw") || (tab_commandes[pos + 1]
				== "reynoldsw")) {
			metdist = 114;
			tab_commandes.Suppr(pos + 1);
		} else if ((tab_commandes[pos + 1] == "Drl") || (tab_commandes[pos + 1]
				== "reynoldsl")) {
			metdist = 115;
			tab_commandes.Suppr(pos + 1);
		}
		/*			return(5); //Das sur les individus
		 return(101); //Nei sur les populations, Dm
		 return(102); //Nei sur les populations, Ds
		 return(103); //Cavalli-Sforza and Edwards' (1967), Dc
		 return(104); // Nei et al's, Da (1983)
		 return(106); // Goldstein et al., Mu (1995a), dmu2
		 return(107); // Latter's Fst (1972)
		 return(108); // Prevosti et al.'s, Cp (1975)
		 return(109); // Rogers', Dr (1972)
		 return(110); // Goldstein et al. (1995b) Slatkin 1995, ASD
		 return(111); // Shriver et al's, Dsw (1995)
		 return(112); // Lev A. Zhivotovsky, DR (1999)
		 */
		tab_commandes.Suppr(pos);
	}
	cerr
			<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) metdist : "
			<< metdist << endl;

	// Methode de construction d'arbre ? (Neigbhor Joining par d�faut)
	int metconstructarbre(2);
	pos = tab_commandes.Position("-construct");
	if ((pos > 0) && (pos + 1 != (long) tab_commandes.size())) {
		if (tab_commandes[pos + 1] == "upgma") {
			metconstructarbre = 1;
			tab_commandes.Suppr(pos + 1);
			tab_commandes.Suppr(pos);
		} else if (tab_commandes[pos + 1] == "nj") {
			metconstructarbre = 2;
			tab_commandes.Suppr(pos + 1);
			tab_commandes.Suppr(pos);
		}
	}
	cerr
			<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) metconstructarbre : "
			<< metconstructarbre << endl;

	//nombre d'it�rations pour le bootstrap
	int nb_iterations(0);

	// bootstrap locus ou bootstrap individus ? (bootstrap locus par d�faut)
	bool bootstrap_locus(true);

	if (sur_pop) {

		pos = tab_commandes.Position("-bootstrap_ind");
		if (pos > 0) {
			nb_iterations = 100;
			bootstrap_locus = false;
			if ((pos + 1 != (long) tab_commandes.size()) && (tab_commandes[pos
					+ 1].EstUnChiffre())) {
				nb_iterations = tab_commandes[pos + 1];
				tab_commandes.Suppr(pos + 1);
			}
			tab_commandes.Suppr(pos);
		}

		pos = tab_commandes.Position("-level");
		if (pos > 0) {
			_niveau = 100;
			if ((pos + 1 != (long) tab_commandes.size()) && (tab_commandes[pos
					+ 1].EstUnChiffre())) {
				_niveau = tab_commandes[pos + 1];
				tab_commandes.Suppr(pos + 1);
			}
			tab_commandes.Suppr(pos);
		}
	} else {
		pos = tab_commandes.Position("-bootstrap_ind");
		if (pos > 0) {
			cerr
					<< "ERROR: Populations is unable to bootstrap on individuals to make a phylogenetic tree of individuals"
					<< endl;
			return;
		}
	}

	pos = tab_commandes.Position("-bootstrap_locus");
	if (pos > 0) {
		nb_iterations = 100;
		if ((pos + 1 != (long) tab_commandes.size())
				&& (tab_commandes[pos + 1].EstUnChiffre())) {
			nb_iterations = tab_commandes[pos + 1];
			tab_commandes.Suppr(pos + 1);
		}
		tab_commandes.Suppr(pos);
	}
	cerr
			<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) bootstrap_locus : "
			<< bootstrap_locus << endl;
	cerr
			<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) nb_iterations : "
			<< nb_iterations << endl;

	//---------------------------------------------
	// Décryptage de la ligne de commande terminé
	// ----------------------------------------------

	if (sur_pop) {
		//phylogenie sur les populations
		set_groupes_populations();
		larbre._titre.resize(2);
		larbre._titre[0].assign(""); // individus, populations
		larbre._titre[1].assign(""); // méthode de distance, nb bootstrap

		larbre._titre[0].AjEntier(_Pjeupop->get_nbpop());
		larbre._titre[0] += " populations";

		larbre._titre[1] += DistancesGnt::get_nom_methode(metdist);

		if (nb_iterations == 0) {
			//pas de bootstrap
			// calcul de distance entre toutes les populations
			MatriceLD distances;

			try {
				_Pjeupop->f_distgntpop(distances, metdist, _niveau);
			} catch (Jeupop::Anomalie pb) {
				cerr
						<< "ApplPopulations::fLiPhylogeny(Titre & tab_commandes) ERROR: "
						<< pb.le_pb << endl;
				return;
			}
			try {
				larbre.iDistances(distances, metconstructarbre);
				//				larbre.fElimineTrifurcation();
			} catch (Arbre::Anomalie pb) {
				switch (pb.le_pb) {
				case 4:
					cout << _("Inconsistant matrix file format");
					break;
				case 5:
					cout << _("the matrix is too small");
					break;
				case 6:
					cout << _("Negative distances in the matrix");
					break;
				}
				return;
			}
		} else {
			larbre._titre[1] += ", ";
			larbre._titre[1].AjEntier(nb_iterations);

			if (bootstrap_locus) {
				larbre._titre[1] += " bootstraps on locus";
				_Pjeupop->f_BootstrapLocus(larbre, metconstructarbre, metdist,
						_square_distance, nb_iterations, false);
			} else {
				larbre._titre[1] += " bootstraps on individuals";
				_Pjeupop->f_BootstrapIndividus(larbre, metconstructarbre,
						metdist, _square_distance, nb_iterations);
			}

			//			larbre.fElimineTrifurcation();
		}
	} else {
		//phylogenie sur les individus
		set_groupes_individus();
		larbre._titre.resize(2);
		larbre._titre[0].assign(""); // individus, populations
		larbre._titre[1].assign(""); // m�thode de distance, nb bootstrap

		larbre._titre[0].AjEntier(_Pjeupop->get_nbind());
		larbre._titre[0] += " individuals";

		cerr
				<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) phylogeny on individuals "
				<< endl;

		larbre._titre[1] += DistancesGnt::get_nom_methode(metdist);

		if (nb_iterations == 0) {
			//pas de bootstrap
			// calcul de distance entre tous les individus
			MatriceLD distances;

			try {

				cerr
						<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) Pjeupop->f_distgnt(distances, metdist, _square_distance); "
						<< endl;
				_Pjeupop->f_distgnt(distances, metdist, _square_distance);
			} catch (Jeupop::Anomalie pb) {
				cerr
						<< "ApplPopulations::fLiPhylogeny(Titre & tab_commandes) ERROR: "
						<< pb.le_pb << endl;
				return;
			}

			try {
				cerr
						<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) larbre.iDistances "
						<< endl;
				larbre.iDistances(distances, metconstructarbre);
				//				larbre.fElimineTrifurcation();
				cerr
						<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) end larbre.iDistances "
						<< endl;
			} catch (Arbre::Anomalie pb) {
				switch (pb.le_pb) {
				case 4:
					cout << _("Inconsistant matrix file format");
					break;
				case 5:
					cout << _("the matrix is too small");
					break;
				case 6:
					cout << _("Negative distances in the matrix");
				}
			}
			//return;
		} else {
			//bootstrap sur les locus
			larbre._titre[1] += ", ";
			larbre._titre[1].AjEntier(nb_iterations);
			larbre._titre[1] += " bootstraps on locus";
			_Pjeupop->f_BootstrapLocus(larbre, metconstructarbre, metdist,
					nb_iterations, true);

			//			larbre.fElimineTrifurcation();
		}
	}

	cerr
			<< "DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) set_groupes_arbre(larbre); "
			<< endl;
	set_groupes_arbre(larbre);
	larbre.oFichier(*Psortie);
	reset_groupes();

	//	*Psortie << larbre;
	//	larbre.oFichier(*Psortie);

	if (_sortie.is_open() != 0)
		_sortie.close();

}

void ApplPopulations::fLiHelp() const {
	cout << _("Online help missing") << endl;
	cout << _("Please visit our website :") << endl;
	cout << "http://www.bioinformatics.org/~tryphon/populations/" << endl;
}

void ApplPopulations::fLiTest(Titre & tab_commandes) {
	cout << "test du jour" << endl;
	cout << "Copie d'objet Jeupop" << endl;

	istream * Pentree(&cin);
	//	ostream * Psortie(&cout);

	//	tab_commandes.Suppr(0);

	//fichiers d'entree ou entree standard (par d�faut)
	_fichier.open("toutc2.txt", ios::in);

	if (_fichier.is_open())
		Pentree = &_fichier;
	try {
		_Pjeupop = new Jeupop();
		*Pentree >> *(_Pjeupop);
		_fichier.close();
		_fichier.clear();
	} catch (Jeupop::Anomalie pb) {
		_fichier.close();
		_fichier.clear();
		delete _Pjeupop;

		switch (pb.le_pb) {
		case 4:
			cerr << "Erreur de lecture..." << endl;
			return;
			break;
		}
	}

	//	_Pjeupop->oGenepop(cout);
	Jeupop copie(*_Pjeupop);

	//	copie.oGenepopCano(cout);

}

void ApplPopulations::affPubEntree() const {

	cout << endl << endl;
	cout << "**********************************************************"
			<< endl;
	cout << "*     Populations " << version_populations
			<< "                                 *" << endl;
	cout << "*      langella@moulon.inra.fr                           *"
			<< endl;
	cout << "*     http://bioinformatics.org/project/?group_id=84     *"
			<< endl;
	cout << "**********************************************************"
			<< endl;
	cout << endl << endl;

	// cout << log (10) << endl; //log n�perien
}

/** Choix de locus */
Vecteur ApplPopulations::menu_choixlocus() const {

	Vecteur Vlocus;
	_Pjeupop->f_selectlocustous(Vlocus);
	signed int pos;

	int choix(1);
	while (choix > 0) {
		cout << endl << endl;
		cout << _("Locus selection:") << endl;
		cout << "0) " << _("back") << endl;
		cout << "1) " << _("Select all loci (default)") << endl;
		cout << "2) " << _("Remove all loci") << endl;
		cout << "3) " << _("Add a particular locus") << endl;
		cout << "4) " << _("Remove a particular locus") << endl;
		cout << "5) " << _("Display selected loci") << endl;

		choix = DemandeChoix(0, 5);

		switch (choix) {
		case 0:
			return (Vlocus);
			break;
		case 1: // ajouter tous les locus
			_Pjeupop->f_selectlocustous(Vlocus);
			break;
		case 2: //enlever tous les locus
			Vlocus.resize(0);
			break;
		case 3: //ajouter un locus
			pos = DemandeLocus();
			if (pos != -1)
				Vlocus.push_back((unsigned int) pos);
			break;
		case 4: //enlever un locus
			pos = DemandeLocus();
			if (pos != -1) {
				pos = Vlocus.Position((unsigned int) pos);
				if (pos >= 0)
					Vlocus.Suppr(pos);
			}
			break;
		case 5: //affichage des locus selectionnes
			affVlocus(Vlocus);
			break;
		}
	}
	return (Vlocus);
}
/**  */
void ApplPopulations::affVlocus(const Vecteur & Vlocus) const {
	unsigned int i;

	cout << endl;
	for (i = 0; i < Vlocus.size(); i++)
		cout << _Pjeupop->get_nomlocus(Vlocus[i]) << " ";
	cout << endl;
}
/** Demande le nom ou le numero d'un locus */
int ApplPopulations::DemandeLocus(const char laquestion[]) const {
	// float Application::DemandeReel(char laquestion[], float inf, float sup) const{
	biolib::vecteurs::ChaineCar rep;
	int nblocus(_Pjeupop->get_nbloc());
	int numlocus(-1);

	if (laquestion == 0)
		cout << _("Name or number of the locus: ") << endl;
	else
		cout << laquestion << endl;
	cin >> rep;

	numlocus = _Pjeupop->get_numloc(rep);
	if (numlocus == -1) {
		numlocus = rep;
		numlocus--;
	}

	if ((numlocus < 0) || (numlocus >= nblocus)) {
		cerr << _("The locus ") << rep << _(" was not found") << endl;
		numlocus = -1;
	}
	return (numlocus);
}

void ApplPopulations::ecritGenetix() {
	_nomFichier = DemandeFichier(_("Output file name (Genetix format) ?"));

	try {
		_sortie.open(_nomFichier.c_str(), ios::out);
		JeuPopExp jeuaexporter(_Pjeupop);

		jeuaexporter.oGenetix(_sortie, cerr);

		_sortie.close();
	} catch (JeuPopExp::Anomalie pb) {
		_sortie.close();
		cerr << pb.fmessage(pb.le_pb) << endl;
	}
}

void ApplPopulations::ecritFstat() {
	_nomFichier = DemandeFichier(_("Output file name (Fstat format) ?"));

	try {
		_sortie.open(_nomFichier.c_str(), ios::out);
		JeuPopExp jeuaexporter(_Pjeupop);

		jeuaexporter.oFstat(_sortie, cerr);

		_sortie.close();
	} catch (JeuPopExp::Anomalie pb) {
		_sortie.close();
		cerr << pb.fmessage(pb.le_pb) << endl;
	}
}

void ApplPopulations::ecritRapportFst() {
	cout << endl;
	cout << _("Fst, Fis and Fit computation") << endl;
	cout << "" << endl;
	JeuMatriceLD mat_resultat;
	_nomFichier = DemandeFichier(_("Output file name ?"));

	cout << endl;
	cout << _("computing...") << endl;
	cout << "" << endl;
	Fstat lesfstats(_Pjeupop->get_Pracinepop());
	//	lesfstats.f_affparlocus(cout);
	lesfstats.f_calcFstFisFit(mat_resultat);

	ecritJeuMatriceLD(mat_resultat, _nomFichier);

}

void ApplPopulations::fmicrosatcorrections() {
#ifdef XMLREADMICROSATCORRECTION_H
	while (_fichier.is_open() == 0) {
		cout << _("Name of the XML file containing corrections ?") << endl;
		cin >> _nomFichier;

		_fichier.open(_nomFichier.c_str(), ios::in);
		_fichier.clear();
	}

	try {
		XMLreadMicrosatCorrection parser(*_Pjeupop);
		parser.iParseFlux(_fichier);
		_fichier.close();
	}
	catch (XMLreadMicrosatCorrection::Anomalie pb) {
		_fichier.close();
		//throw Anomalie(1);
	}

#else
	cout << endl;
	cout << _("Sorry this version of Populations is unable to read XML files.")
			<< endl;
	cout << _("Try the linux version.") << endl;
	cout << "" << endl;
#endif  
}

void ApplPopulations::ecritPopulationsXML() {
	//	cout << _("Output file name (Populations format) ?") << endl;
	//	cin >> _nomFichier;
	_nomFichier = DemandeFichier(
			_("Output file name (XML Populations format) ?"));

	try {
		_sortie.open(_nomFichier.c_str(), ios::out);
		JeuPopExp jeuaexporter(_Pjeupop);

		jeuaexporter.oPopulationsXML(_sortie, cerr);

		_sortie.close();
	} catch (JeuPopExp::Anomalie pb) {
		_sortie.close();
		cerr << pb.fmessage(pb.le_pb) << endl;
	}
}
populations-1.2.33+svn0120106.orig/src/fstat.cpp0000644000175000017500000001075110531115342021261 0ustar  georgeskgeorgesk/***************************************************************************
                          fstat.cpp  -  bibliotheque permettant de calculer et de
																		présenter les indices de Wright
                             -------------------
    begin                : Wed Oct 11 2000
    copyright            : (C) 2000 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/


#include "fstat.h"

Fstat::Fstat(MetaPop * Pmetapop):_Pmetapop(Pmetapop) {
	_Pjeupop = _Pmetapop->get_Pjeu();
}

Fstat::~Fstat() {

}

void Fstat::f_affparlocus (ostream & sortie) const {

//affichage simple
	unsigned long nbloc (_Pjeupop->get_nbloc()),l;

	try {
		for (l=0;l < nbloc;l++) {
			sortie << "locus: " << _Pjeupop->get_nomlocus(l) << endl;
			sortie << "Fis: " << _Pmetapop->f_M_Fis(l);
			sortie << " Fst: " << _Pmetapop->f_M_Fst(l);

			sortie << " Fit: " << _Pmetapop->f_M_Fit(l) << endl << endl;
		}
	}
	catch (StrucPop::Anomalie lepb) {
		cerr << "exception dans strucpop: " << lepb.le_pb;
	}
}

void Fstat::f_calcFstFisFit (MatriceLD & matrice, const MetaPop * Pmetapop) const {
	
	unsigned long nbloc (_Pjeupop->get_nbloc()),l;

	matrice.resize(6,nbloc);
	
	//get_nbpop()
	
//	matrice._titre.push_back(_("generated by Populations "));
//	matrice._titre.back() += version_populations;
	matrice._titre.push_back(_("Fis, Fst, Fit for one population ("));
	if (Pmetapop == _Pmetapop) matrice._titre.back() += _("root");
	else matrice._titre.back() += Pmetapop->get_nom();
	matrice._titre.back() += _(") and ");
	matrice._titre.back().AjEntier(Pmetapop->get_nbpop());
	matrice._titre.back() += _(" subpopulations");
	matrice._titre.push_back(_("locus by columns"));
	matrice._titre.push_back(_("rows:"));
	matrice._titre.push_back(_("Fis"));
	matrice._titre.push_back(_("Fst"));
	matrice._titre.push_back(_("Fit"));
	matrice._titre.push_back(_("Ho --> observed heterozygosity (mean overall subpopulations)"));
	matrice._titre.push_back(_("Hs --> expected heterozygosity (mean overall subpopulations)"));
	matrice._titre.push_back(_("Ht --> total expected heterozygosity"));
	
	matrice.SetFlag(3);
	matrice.SetType(1);
	
	matrice._tlig[0] = "Fis";
	matrice._tlig[1] = "Fst";
	matrice._tlig[2] = "Fit";
	matrice._tlig[3] = "Ho";
	matrice._tlig[4] = "Hs";
	matrice._tlig[5] = "Ht";
//affichage simple

	try {
		for (l=0;l < nbloc;l++) {
			matrice._tcol[l] = _Pjeupop->get_nomlocus(l);
			matrice.GetCase(0,l) = Pmetapop->f_M_Fis(l);
			matrice.GetCase(1,l) = Pmetapop->f_M_Fst(l);
			matrice.GetCase(2,l) = Pmetapop->f_M_Fit(l);
			matrice.GetCase(3,l) = Pmetapop->f_Mheterozygotieobs(l);
			matrice.GetCase(4,l) = Pmetapop->f_Mheterozygotieatt(l);
			matrice.GetCase(5,l) = Pmetapop->f_Mheterozygotietotale(l);
			//sortie << "locus: " << _Pjeupop->get_nomlocus(l) << endl;
			//sortie << "Fis: " << _Pjeupop->_Pracinepops->f_M_Fis(l);
			//sortie << " Fst: " << _Pjeupop->_Pracinepops->f_M_Fst(l);

			//sortie << " Fit: " << _Pjeupop->_Pracinepops->f_M_Fit(l) << endl << endl;
		}
	}
	catch (StrucPop::Anomalie lepb) {
		cerr << "exception dans strucpop: " << lepb.le_pb;
	}
}

void Fstat::f_calcFstFisFit (JeuMatriceLD & matrices) const {
//calcul récursif de toutes les Fst, Fis, Fit possibles (pour les populations hiérarchisées
	f_calcFstFisFit(matrices, _Pmetapop);

}

void Fstat::f_calcFstFisFit (JeuMatriceLD & matrices, const MetaPop * Pmetapop) const {
//calcul récursif de toutes les Fst, Fis, Fit possibles (pour les populations hiérarchisées
	unsigned int i;


	// ajouter une matrice
	if (Pmetapop == _Pmetapop) matrices.push_back(new(MatriceLD), _("root"));
	else matrices.push_back(new(MatriceLD), Pmetapop->get_nom());
	
	
	//remplir la matrice
	f_calcFstFisFit (matrices.back(), Pmetapop);
	
	//on fait le reste:
	for (i=0; i < Pmetapop->get_nbmetapop(); i++) {
		f_calcFstFisFit (matrices, Pmetapop->get_tabPmetapop(i));
	}

}

populations-1.2.33+svn0120106.orig/src/Makefile.in0000644000175000017500000002674310531115342021511 0ustar  georgeskgeorgesk# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am

# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.


SHELL = @SHELL@

srcdir = @srcdir@
top_srcdir = @top_srcdir@
VPATH = @srcdir@
prefix = @prefix@
exec_prefix = @exec_prefix@

bindir = @bindir@
sbindir = @sbindir@
libexecdir = @libexecdir@
datadir = @datadir@
sysconfdir = @sysconfdir@
sharedstatedir = @sharedstatedir@
localstatedir = @localstatedir@
libdir = @libdir@
infodir = @infodir@
mandir = @mandir@
includedir = @includedir@
oldincludedir = /usr/include

DESTDIR =

pkgdatadir = $(datadir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@

top_builddir = ..

ACLOCAL = @ACLOCAL@
AUTOCONF = @AUTOCONF@
AUTOMAKE = @AUTOMAKE@
AUTOHEADER = @AUTOHEADER@

INSTALL = @INSTALL@
INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
INSTALL_DATA = @INSTALL_DATA@
INSTALL_SCRIPT = @INSTALL_SCRIPT@
transform = @program_transform_name@

NORMAL_INSTALL = :
PRE_INSTALL = :
POST_INSTALL = :
NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
host_alias = @host_alias@
host_triplet = @host@
AR = @AR@
AS = @AS@
CC = @CC@
CXX = @CXX@
CXXCPP = @CXXCPP@
DLLTOOL = @DLLTOOL@
ECHO = @ECHO@
EGREP = @EGREP@
EXEEXT = @EXEEXT@
F77 = @F77@
GCJ = @GCJ@
GCJFLAGS = @GCJFLAGS@
HAVE_LIB = @HAVE_LIB@
LIB = @LIB@
LIBTOOL = @LIBTOOL@
LN_S = @LN_S@
LTLIB = @LTLIB@
MAKEINFO = @MAKEINFO@
OBJDUMP = @OBJDUMP@
OBJEXT = @OBJEXT@
PACKAGE = @PACKAGE@
RANLIB = @RANLIB@
RC = @RC@
STRIP = @STRIP@
VERSION = @VERSION@

bin_PROGRAMS = populations
populations_SOURCES = populations.cpp applications.cpp applpopulations.cpp 	arbreplus.cpp arbre.cpp couleur.cpp fstat.cpp jeupop.cpp allele.cpp individu.cpp 	strucpop.cpp metapop.cpp locus.cpp population.cpp chaineficpop.cpp applpop.cpp 	jeupopexp.cpp distgnt.cpp matrices.cpp vecteurs.cpp


# set the include path found by configure
INCLUDES = $(all_includes)

# the library search path.
populations_LDFLAGS = $(all_libraries) 
noinst_HEADERS = applpopulations.h internat.h matrices.h vecteurs.h arbreplus.h 	arbre.h couleur.h fstat.h jeupop.h allele.h individu.h strucpop.h metapop.h 	metapop.h locus.h population.h chaineficpop.h applpop.h jeupopexp.h distgnt.h 	applications.h

mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
CONFIG_HEADER = ../config.h
CONFIG_CLEAN_FILES = 
bin_PROGRAMS =  populations$(EXEEXT)
PROGRAMS =  $(bin_PROGRAMS)


DEFS = @DEFS@ -I. -I$(srcdir) -I..
CPPFLAGS = @CPPFLAGS@
LDFLAGS = @LDFLAGS@
LIBS = @LIBS@
populations_OBJECTS =  populations.$(OBJEXT) applications.$(OBJEXT) \
applpopulations.$(OBJEXT) arbreplus.$(OBJEXT) arbre.$(OBJEXT) \
couleur.$(OBJEXT) fstat.$(OBJEXT) jeupop.$(OBJEXT) allele.$(OBJEXT) \
individu.$(OBJEXT) strucpop.$(OBJEXT) metapop.$(OBJEXT) locus.$(OBJEXT) \
population.$(OBJEXT) chaineficpop.$(OBJEXT) applpop.$(OBJEXT) \
jeupopexp.$(OBJEXT) distgnt.$(OBJEXT) matrices.$(OBJEXT) \
vecteurs.$(OBJEXT)
populations_LDADD = $(LDADD)
populations_DEPENDENCIES = 
CXXFLAGS = @CXXFLAGS@
CXXCOMPILE = $(CXX) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
LTCXXCOMPILE = $(LIBTOOL) --mode=compile $(CXX) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
CXXLD = $(CXX)
CXXLINK = $(LIBTOOL) --mode=link $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@
HEADERS =  $(noinst_HEADERS)

DIST_COMMON =  Makefile.am Makefile.in


DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)

TAR = tar
GZIP_ENV = --best
DEP_FILES =  .deps/allele.P .deps/applications.P .deps/applpop.P \
.deps/applpopulations.P .deps/arbre.P .deps/arbreplus.P \
.deps/chaineficpop.P .deps/couleur.P .deps/distgnt.P .deps/fstat.P \
.deps/individu.P .deps/jeupop.P .deps/jeupopexp.P .deps/locus.P \
.deps/matrices.P .deps/metapop.P .deps/population.P .deps/populations.P \
.deps/strucpop.P .deps/vecteurs.P
SOURCES = $(populations_SOURCES)
OBJECTS = $(populations_OBJECTS)

all: all-redirect
.SUFFIXES:
.SUFFIXES: .S .c .cpp .lo .o .obj .s
$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4) 
	cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile

Makefile: $(srcdir)/Makefile.in  $(top_builddir)/config.status $(BUILT_SOURCES)
	cd $(top_builddir) \
	  && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status


mostlyclean-binPROGRAMS:

clean-binPROGRAMS:
	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)

distclean-binPROGRAMS:

maintainer-clean-binPROGRAMS:

install-binPROGRAMS: $(bin_PROGRAMS)
	@$(NORMAL_INSTALL)
	$(mkinstalldirs) $(DESTDIR)$(bindir)
	@list='$(bin_PROGRAMS)'; for p in $$list; do \
	  if test -f $$p; then \
	    echo " $(LIBTOOL)  --mode=install $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
	    $(LIBTOOL)  --mode=install $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
	  else :; fi; \
	done

uninstall-binPROGRAMS:
	@$(NORMAL_UNINSTALL)
	list='$(bin_PROGRAMS)'; for p in $$list; do \
	  rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
	done

# FIXME: We should only use cygpath when building on Windows,
# and only if it is available.
.c.obj:
	$(COMPILE) -c `cygpath -w $<`

.s.o:
	$(COMPILE) -c $<

.S.o:
	$(COMPILE) -c $<

mostlyclean-compile:
	-rm -f *.o core *.core
	-rm -f *.$(OBJEXT)

clean-compile:

distclean-compile:
	-rm -f *.tab.c

maintainer-clean-compile:

.s.lo:
	$(LIBTOOL) --mode=compile $(COMPILE) -c $<

.S.lo:
	$(LIBTOOL) --mode=compile $(COMPILE) -c $<

mostlyclean-libtool:
	-rm -f *.lo

clean-libtool:
	-rm -rf .libs _libs

distclean-libtool:

maintainer-clean-libtool:

populations$(EXEEXT): $(populations_OBJECTS) $(populations_DEPENDENCIES)
	@rm -f populations$(EXEEXT)
	$(CXXLINK) $(populations_LDFLAGS) $(populations_OBJECTS) $(populations_LDADD) $(LIBS)
.cpp.o:
	$(CXXCOMPILE) -c $<
.cpp.obj:
	$(CXXCOMPILE) -c `cygpath -w $<`
.cpp.lo:
	$(LTCXXCOMPILE) -c $<

tags: TAGS

ID: $(HEADERS) $(SOURCES) $(LISP)
	list='$(SOURCES) $(HEADERS)'; \
	unique=`for i in $$list; do echo $$i; done | \
	  awk '    { files[$$0] = 1; } \
	       END { for (i in files) print i; }'`; \
	here=`pwd` && cd $(srcdir) \
	  && mkid -f$$here/ID $$unique $(LISP)

TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) $(LISP)
	tags=; \
	here=`pwd`; \
	list='$(SOURCES) $(HEADERS)'; \
	unique=`for i in $$list; do echo $$i; done | \
	  awk '    { files[$$0] = 1; } \
	       END { for (i in files) print i; }'`; \
	test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
	  || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags  $$unique $(LISP))

mostlyclean-tags:

clean-tags:

distclean-tags:
	-rm -f TAGS ID

maintainer-clean-tags:

distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)

subdir = src

distdir: $(DISTFILES)
	here=`cd $(top_builddir) && pwd`; \
	top_distdir=`cd $(top_distdir) && pwd`; \
	distdir=`cd $(distdir) && pwd`; \
	cd $(top_srcdir) \
	  && $(AUTOMAKE) --include-deps --build-dir=$$here --srcdir-name=$(top_srcdir) --output-dir=$$top_distdir --gnu src/Makefile
	@for file in $(DISTFILES); do \
	  d=$(srcdir); \
	  if test -d $$d/$$file; then \
	    cp -pr $$d/$$file $(distdir)/$$file; \
	  else \
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populations-1.2.33+svn0120106.orig/src/config.h0000644000175000017500000000016511701604740021055 0ustar  georgeskgeorgesk#ifndef _CONFIG_H
#define _CONFIG_H

#define POPULATIONS_VERSION "1.2.33"

#include 

#endif /* _CONFIG_H */
populations-1.2.33+svn0120106.orig/src/jeupop.h0000644000175000017500000002112410531115342021103 0ustar  georgeskgeorgesk/***************************************************************************
                          jeupop.h  -  Librairie d'objets permettant de manipuler des donn�es
                          						sp�cifiques aux populations
                             -------------------
    begin                : ven sep 06 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#ifndef JEUPOP_H
#define JEUPOP_H

//#include"internat.h"

#include "matrices.h"
#include "allele.h"
#include "individu.h"
#include "strucpop.h"
#include "metapop.h"
#include "population.h"
#include "locus.h"

#include "chaineficpop.h"

#include "arbre.h"

//# ifdef XmlParse_INCLUDED
//# include "xmlreadpopulations.h"
//# endif
//#include "vecteurs.h"

//typedef biolib::arbres::ArbrePlus ArbrePlus;
typedef biolib::arbres::Arbre Arbre;
//typedef biolib::vecteurs::ChaineCar ChaineCar;
//class Arbre;

// jeu de populations
class Jeupop {
public :
	Jeupop();//npop, nloc
	//Jeupop(long nbpop, long nbloc);//npop, nloc

	Jeupop(const Jeupop&); //constructeur de copies

	~Jeupop();

	Population * NewPop(const biolib::vecteurs::ChaineCar &);
	Locus * new_locus(const string &);

	void reset();//npop, nloc
	Population* get_pop(unsigned long) const;
	//mieux en inline
	unsigned int get_nploidie() const;
	unsigned long get_nbloc() const;
	unsigned long get_nbpop() const;
	//unsigned long Jeupop::get_nbpop() const {
	
	unsigned long get_nbstrucpopVcalc() const {return (_VcalcStrucPop.size());};
	MetaPop * get_Pracinepop() const {return (_Pracinepops);};
	const StrucPop * get_PstrucpopVcalc(unsigned int numpop) const {return (_VcalcStrucPop[numpop]);};
	unsigned long get_nbind() const;
	//inline Allele* get_Pall(int loc, int all) const;
	Allele* get_Pall(unsigned long loc, unsigned long all) const;

	void AjouterPopulation(Population * Ppop);
	void AjouterTabPop(Population * Ppop);

	Locus* get_Plocus(const string &) const;
	Locus* get_Plocus(unsigned long i) const;
	Population* get_Ppop(string &) const;
	Population* get_Ppop(unsigned long p) const;
	const string & get_nomlocus(long nblocus) const;
	const string & get_nompop(long nbpop) const;
	signed long get_numloc(Locus * Ploc) const {return((signed long)_tabPloc.Position(Ploc));};
	signed long get_numpop(Population * Ppop) const {return((signed long)_tabPpop.Position(Ppop));};
//	long get_numloc(Locus * Ploc) const;
	void get_nomniveauxstruc(Titre & nom_niveaux) const;
	const Titre & get_commentaires() const {return(_commentaires);};

	void set_nploidie(unsigned int nploidie);
  void set_commentaires(const string & commentaires);

	void iFichier(istream & entree, int i);

	void iIntrogression(istream&);
	void oPopulations(ostream& sortie) const;
	void oGenepop(ostream&) const;
	void oGenepopCano(ostream&) const;

	void oImmanc(ostream&) const;
	//Immanc - detects individual that are immigrants or have recent immigrant ancestry
    //by using multilocus genotypes. 
    //Version 5.0, released October 8, 1998    
    //Reference: Rannala, B., and J.L., Mountain. 1997. Detecting immigration by using
    //multilocus genotypes. Proceedings of the National Academy of Sciences USA 94:
    //9197-9201. 

	void oMsat(ostream&) const;
	void oMsatFreq(ostream&) const;
	 //       microsat.c version 1.5e
      //  Eric Minch
     //   Dept. of Genetics
     //   Stanford University Medical Center
     //   Stanford, CA 94305
      //  minch@lotka.stanford.edu
	//http://lotka.stanford.edu/microsat/microsat.html

	void affind(int, int) const; //num�ro de la pop, num�ro de l'ind

// g�n�tique

	void f_trad2Gpop(ostream&);

	//calcul de la nouvelle diversit� all�lique, pour un �chantillon
	// r�duit: r�sultats stock�s dans Matrice, int => effectif r�duit
	void f_rarefaction(MatriceLD &, int) const;

	// calcul de distance g�n�tique entre Populations sur tous les individus, 2 a 2 
	void f_distgntpop (MatriceLD &resultat, int methode, bool square_distance, unsigned int niveau=100, Vecteur * PVcalcLocus = NULL);
	// calcul de distance g�n�tique sur tous les individus, 2 a 2
	void f_distgnt (MatriceLD &resultat, int methode, bool square_distance, Vecteur * PVcalcLocus = NULL);

	// V�rification du type de num�rotation des all�les
	bool f_verifnum (int) const;

	// Boostrap sur les locus => arbre d'individus ou populations
	void f_BootstrapLocus(Arbre & arbreRef, int methodeArbre, int methodeDist, bool square_distance, int nbrepet, bool sur_ind=true , Vecteur * PVcalcLocus = NULL);
	void f_BootstrapIndividus(Arbre & arbreRef, int methodeArbre, int methodeDist, bool square_distance, int nbrepet , Vecteur * PVcalcLocus = NULL);
//	void f_BootstrapLocus(Arbre & arbreRef, int methodeArbre, int methodeDist, int nbrepet , Vecteur * PVcalcLocus = NULL);
//	void f_BootstrapLocuspop(Arbre & arbreRef, int methodeArbre, int methodeDist, int nbrepet , Vecteur * PVcalcLocus = NULL);

	void f_rempliVcalcStrucPop(unsigned int niveau=100);
	void f_resetVcalcStrucPop() {_VcalcStrucPop.resize(0);};

	friend class Population;
	friend class DistancesGnt;
	friend class Fstat;
///	friend class Locus;

//	static int _tmot;

//	const Jeupop& operator= (const Jeupop &);
	Jeupop operator+ (const Jeupop &rval) const;
  /** Suppression de la population p du Jeupop */
  void SupprPop(StrucPop * Ppop);
  /** D�place la pop a � la position b */
  void f_deplacePop(Population * Ppop, unsigned long b);
  /** enl�ve les all�les qui ne sont pas repr�sent�s dans les populations
 */
  void f_nettoieAlleles();
  /** Retourne vrai, si l'allele n'est pas pr�sent dans jeupop */
  bool r_allelenonpresent(Allele * Pall) const;
  /** construit le vecteur Vlocus avec les numeros de tous les locus */
  void f_selectlocustous(vector & Vlocus) const;
  /** Suppression des locus qui ne sont pas pr�sents dans Vnumloc */
  void GarderVlocus(Vecteur & Vnumloc);
  /** obtenir le num�ro d'un locus avec son nom */
  signed int get_numloc(const string &) const;

private :
	MetaPop * _Pracinepops;

	Titre _commentaires;
	void iGenetix(istream&);
	void iGenepop(istream&);
	void iPopulations(istream&);
	void ifAjouterLocus(const Locus * Ploc);
  void iPopulationsXML(istream &fichier);
//	void ifAjouterPop(const Population * Ppop);
	//nombre d'alleles en commun sur un locus
//	int r_allcommun(Individu *, Individu *, unsigned int) const; //renvoi du nombre d'all�les en commun
//	int r_allcommunnul(Individu *, Individu *, int) const; //renvoi du nombre d'all�les en commun
//	long r_allcommunnul(Individu *, Individu *) const; //renvoi du nombre d'all�les en commun
//	long double r_allsimilnul(Individu *, Individu *) const;
	//distance entre 2 individus
//	double r_dist2ind(Individu *, Individu *, int) const; //renvoi de la distance
	
	unsigned int _nploidie; // haploide=1 diploide=2...
	unsigned int _nbpop; //nb de populations dans ce jeu
	Vecteur _tabPpop;
	unsigned int _nbloc; //nb de loci dans ce jeu
	Vecteur _tabPloc;

	Vecteur _VcalcLocus;
	Vecteur _VcalcStrucPop;

protected: // Protected methods
  /** Suppression d'un locus */
  void supprLocus(unsigned int);
  /** R�affectation du nombre de locus */
  void set_nbloc();

public :
	struct Anomalie{
		// 1-> op�ration possible seulement sur les diploides
		// 2-> les num�ros d'all�les format genepop ne sont pas pr�sents
		// 3-> donnee erronee dans le fichier d'entree
		// 4-> format Genepop incorrect en entree
		// 5-> format de fichier non reconnu
		// 6-> calcul de similitude impossible
		// 7-> op�ration impossible sur des populations de ploidie differentes
		// 8-> Locus introuvable
		// 9-> Population introuvable
		// 101-> erreur dans un calcul de distances
		// 201-> erreur de lecture dans un fichier G�n�tix

		unsigned int le_pb;
		Anomalie (unsigned int i):le_pb(i){};
	};

};



istream& operator>>(istream& ientree,Jeupop& LesPops);



#endif

populations-1.2.33+svn0120106.orig/src/matrices.cpp0000644000175000017500000020255511606241313021756 0ustar  georgeskgeorgesk/***************************************************************************
 matrices.cpp  -  Librairie d'objets pour manipuler des matrices
 -------------------
 begin                : ven aug 14 10:25:55 CEST 2000
 copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
 email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#include "matrices.h"

namespace biolib {
namespace vecteurs {


Matrice::Matrice(const Matrice& original) {
	//constructeur de copie
	unsigned long i;

	//	if (_tab != 0) delete [] _tab;
	_oformat = 1;
	_nc = original._nc;
	_nl = original._nl;
	_t = _nc * _nl;

	_tab = new long double[_t];

	_titre = original._titre;
	_flag = original._flag;
	_tcol = original._tcol;
	_tlig = original._tlig;
	_miss = original._miss;
	_type = original._type;

	for (i = 0; i < _t; i++) {
		//nouvelle s�quence
		_tab[i] = original._tab[i];
	}

}

Matrice::Matrice() {

	//		_Pointeur = *( new (Pointeur));
	_oformat = 1;
	_nc = 0;
	_nl = 0;
	_t = 0;
	_tab = 0;
	_type = 0;
	_miss = 0;
	_flag = 0;
}

Matrice::Matrice(unsigned long nl, unsigned long nc) {
	unsigned long i;

	_oformat = 1;
	_nc = nc;
	_nl = nl;
	_t = nc * nl;
	_tab = new long double[_t];
	_type = 1;

	_miss = 0;
	_flag = 0;
	_titre.resize(0);

	_tcol.reserve(_nc);
	_tlig.reserve(_nl);
	for (i = 0; i < _nc; i++)
		_tcol.push_back("");
	for (i = 0; i < _nl; i++)
		_tlig.push_back("");

	for (i = 0; i < _t; i++)
		_tab[i] = 0;

}

bool Matrice::SetType(int type) {

	switch (type) {
	case 1: //rectangulaire normale
		_type = type;
		break;
	case 2: //matrice triangulaire (distances)
		if (_nc == _nl) {
			unsigned long i, j;
			for (i = 0; i < _nc; i++) {
				for (j = 0; j < i; j++) {
					if (GetCase(i, j) != GetCase(j, i)) {
						qDebug() << "Matrices::Anomalie  "
								<< "failed to convert into symetric matrix (i,j)!=(j,i) "
								<< (float) GetCase(i, j) << " "
								<< (float) GetCase(j, i) << " i " << i << " j "
								<< j;
						return (false);
						//throw typename biolib::vecteurs::Matrice::Anomalie(5);
					}
				}
			}
			_type = type;
		} else {
			qDebug() << "Matrices::Anomalie  "
					<< "failed to convert into symetric matrix nc!=nl " << _nc
					<< " " << _nl;
			return (false);
			//throw typename biolib::vecteurs::Matrice::Anomalie(5); //Echec de conversion
		}
		break;
	default:
		break;
	}
	return (true);
}

const Matrice& Matrice::operator=(
		const Matrice &rval) {

	unsigned long i;

	if (_tab != 0)
		delete[] _tab;

	_type = rval._type;
	_flag = rval._flag;
	_nc = rval._nc;
	_nl = rval._nl;
	_t = rval._t;
	_tab = new long double[rval._t];

	_titre = rval._titre;

	_tlig = rval._tlig;
	_tcol = rval._tcol;

	for (i = 0; i < _t; i++)
		_tab[i] = rval._tab[i];

	return (*this);
}

const Matrice& Matrice::operator=(vector &rval) {

	int i;

	if (_tab != 0)
		delete[] _tab;

	_type = 1;
	_flag = 0;
	_nc = rval.size();
	_nl = 1;
	_t = _nc;
	_tab = new long double[_nc];

	//	_titre = rval._titre;

	//	_tlig = rval._tlig;
	//	_tcol = rval._tcol;

	for (i = 0; i < _t; i++)
		_tab[i] = rval[i];

	return (*this);
}

void Matrice::oExcel(ostream& fichier) {
	unsigned long i, j;

	//	fichier.setf(ios::scientific);
	//fichier << "coucou";
	// �criture du titre
	for (i = 0; i < _titre.size(); i++) {
		fichier << _titre[i];
		fichier << endl;
	}

	fichier << "#";
	if ((_flag == 2) || (_flag == 3)) {
		//�tiquettes des colonnes
		fichier << '\t' << _tcol[0];
		for (i = 1; i < _nc; i++)
			fichier << '\t' << _tcol[i];
	}
	fichier << endl;

	//�criture de la matrice
	for (i = 0; i < _nl; i++) {
		if ((_flag == 1) || (_flag == 3)) {
			//�tiquettes des lignes
			fichier << _tlig[i];
		}

		for (j = 0; j < _nc; j++) {
			//			fichier << '\t' << _tab [i * _nc + j];
			fichier << '\t' << GetCase(i, j);
		}
		fichier << endl;
	}

}

void Matrice::oGnumeric(ostream& fichier) {
	QString * p_output_xml = new QString("");
	QXmlStreamWriter xml_stream(p_output_xml);
	xml_stream.setAutoFormatting(true);
	xml_stream.writeStartDocument();

	xml_stream.writeNamespace("http://www.gnumeric.org/v10.dtd", "gmr");
	xml_stream.writeNamespace("http://www.w3.org/2001/XMLSchema-instance",
			"xsi");
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Workbook");
	xml_stream.writeAttribute("http://www.w3.org/2001/XMLSchema-instance",
			"schemaLocation", "http://www.gnumeric.org/v8.xsd");

	//fichier
	//		<< ""
	//		<< endl;

	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd",
			"Attributes");
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Attribute");
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"WorkbookView::show_horizontal_scrollbar");
	//fichier << "" << endl;
	//fichier << "   " << endl;
	//fichier << "WorkbookView::show_horizontal_scrollbar"
	//		<< endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "type", "4");
	//fichier << " 4" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "value",
			"TRUE");
	//fichier << "  TRUE" << endl;
	xml_stream.writeEndElement();
	//	fichier << " " << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Attribute");
	//fichier << " " << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"WorkbookView::show_vertical_scrollbar");
	//fichier << "  WorkbookView::show_vertical_scrollbar"
	//	<< endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "type", "4");
	//fichier << "  4" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "value",
			"TRUE");
	//fichier << "  TRUE" << endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Attribute");
	//fichier << " " << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"WorkbookView::show_notebook_tabs");
	//fichier << "   WorkbookView::show_notebook_tabs"
	//		<< endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "type", "4");
	//fichier << "   4" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "value",
			"TRUE");
	//fichier << "   TRUE" << endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;

	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Attribute");
	//fichier << " " << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"WorkbookView::do_auto_completion");
	//fichier << "   WorkbookView::do_auto_completion"
	//		<< endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "type", "4");
	//fichier << "   4" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "value",
			"TRUE");
	//fichier << "   TRUE" << endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Summary");
	//fichier << " " << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Item");
	//fichier << "  " << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"biology softwares");
	//fichier << "  biology softwares" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd",
			"val-string", "http://www.pge.cnrs-gif.fr/bioinfo");
	//fichier
	//		<< "  http://www.pge.cnrs-gif.fr/bioinfo"
	//		<< endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Item");
	//fichier << " " << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"author");
	//fichier << "   author" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd",
			"val-string", "Olivier Langella ");
	//fichier
	//		<< "   Olivier Langella, Olivier.Langella@pge.cnrs-gif.fr"
	//		<< endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;
	xml_stream.writeEndElement();
	//fichier << "" << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd",
			"SheetNameIndex");
	//fichier << "" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "SheetName",
			"Matrix 1");
	//fichier << "  Matrix 1" << endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Sheets");
	//fichier << "	 " << endl;
	//	fichier.setf(ios::scientific);

	QString sheetname("Matrix 1");
	oGnumericSheet(xml_stream, sheetname);

	//fichier << "  " << endl;
	//fichier << " " << endl;

	xml_stream.writeEndDocument();

	fichier << p_output_xml->toStdString();
	delete (p_output_xml);

}

void Matrice::oGnumericSheet(QXmlStreamWriter& xml_stream,
		const QString & sheetname) const {

	qDebug()
			<< "Matrice::oGnumericSheet(QXmlStreamWriter& xml_stream, const QString & sheetname) begin";
	unsigned long i, j, irow(0), jcol(0);
	const QString value_format("0.000000");

	/*fichier << ""
	 << endl;*/
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Sheet");
	xml_stream.writeAttribute("DisplayFormulas", "false");
	xml_stream.writeAttribute("HideZero", "false");
	xml_stream.writeAttribute("HideGrid", "false");
	xml_stream.writeAttribute("HideColHeader", "false");
	xml_stream.writeAttribute("HideRowHeader", "false");
	xml_stream.writeAttribute("DisplayOutlines", "true");
	xml_stream.writeAttribute("OutlineSymbolsBelow", "true");
	xml_stream.writeAttribute("OutlineSymbolsRight", "true");

	/*_p_xml_stream->writeAttribute("xml", "lang", "en");
	 _p_xml_stream->writeStartElement("body");
	 _p_xml_stream->writeStartElement("table");
	 _p_xml_stream->writeStartElement("tbody");*/

	// 	fichier.imbue();
	//	fichier << "" << sheetname << "" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "Name",
			sheetname);

	//fichier << "" << (GetNC() + 2) << "" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "MaxCol",
			QString::number(GetNC() + 2));
	//fichier << "" << (GetNL() + 5 + _titre.size())
	//		<< "" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "MaxRow",
			QString::number((GetNL() + 5 + _titre.size())));
	//fichier << "1.000000" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "Zoom",
			"1.000000");

	//fichier << "" << endl;
	xml_stream.writeEmptyElement("http://www.gnumeric.org/v10.dtd", "Names");

	//fichier << "" << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Cells");
	// �criture du titre
	for (i = 0; i < _titre.size(); i++, irow++) {
		xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Cell");
		//fichier << "";
		xml_stream.writeAttribute("Row", QString::number(irow));
		xml_stream.writeAttribute("Col", "0");
		xml_stream.writeAttribute("ValueType", "60");
		//fichier << _titre[i];
		xml_stream.writeCharacters(_titre[i].c_str());
		//fichier << "" << endl;
		xml_stream.writeEndElement();
	}
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Cell");
	xml_stream.writeAttribute("Col", "0");
	xml_stream.writeAttribute("Row", QString::number(irow));
	xml_stream.writeAttribute("ValueType", "60");
	xml_stream.writeCharacters("#");
	xml_stream.writeEndElement();

	//fichier << "#";
	if ((_flag == 2) || (_flag == 3)) {
		//�tiquettes des colonnes
		jcol = 1;
		xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Cell");
		xml_stream.writeAttribute("Col", QString::number(jcol));
		xml_stream.writeAttribute("Row", QString::number(irow));
		xml_stream.writeAttribute("ValueType", "60");
		xml_stream.writeCharacters(_tcol[0].c_str());
		xml_stream.writeEndElement();

		//fichier << "";
		//fichier << _tcol[0];
		//fichier << "" << endl;
		jcol++;
		for (i = 1; i < _nc; i++, jcol++) {
			xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd",
					"Cell");
			xml_stream.writeAttribute("Col", QString::number(jcol));
			xml_stream.writeAttribute("Row", QString::number(irow));
			xml_stream.writeAttribute("ValueType", "60");
			xml_stream.writeCharacters(_tcol[i].c_str());
			xml_stream.writeEndElement();
			//fichier << "";
			//fichier << _tcol[i];
			//fichier << "" << endl;
		}
	}
	irow++;

	//fichier.setf(ios::scientific);
	//�criture de la matrice
	for (i = 0; i < _nl; i++, irow++) {
		if ((_flag == 1) || (_flag == 3)) {
			//�tiquettes des lignes
			xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd",
					"Cell");
			xml_stream.writeAttribute("Col", "0");
			xml_stream.writeAttribute("Row", QString::number(irow));
			xml_stream.writeAttribute("ValueType", "60");
			xml_stream.writeCharacters(_tlig[i].c_str());
			xml_stream.writeEndElement();
			//fichier << "";
			//fichier << _tlig[i];
			//fichier << "" << endl;
		}
		jcol = 1;
		for (j = 0; j < _nc; j++, jcol++) {
			//			fichier << '\t' << _tab [i * _nc + j];
			xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd",
					"Cell");
			xml_stream.writeAttribute("Col", QString::number(jcol));
			xml_stream.writeAttribute("Row", QString::number(irow));
			xml_stream.writeAttribute("ValueType", "40");
			xml_stream.writeAttribute("ValueFormat", value_format);
			xml_stream.writeCharacters(QString::number((double) GetCase(i, j)));
			xml_stream.writeEndElement();
			//fichier << "";
			//fichier << GetCase(i, j);
			//fichier << "" << endl;
		}
		//fichier << endl;
	}
	//fichier << "" << endl;
	//fichier << "  " << endl;
	qDebug()
			<< "Matrice::oGnumericSheet(QXmlStreamWriter& xml_stream, const QString & sheetname) end";

}

void Matrice::oNtsys(ostream& sortie) {
	unsigned long i, j, k, tmaxligne(100);
	long pos;

	//	sortie << setf(ios::fixed);

	// �criture du titre
	for (i = 0; i < _titre.size(); i++) {
		sortie << "\"";
		sortie << _titre[i];
		sortie << endl;
	}

	sortie << _type << " " << _nl;
	if ((_flag == 1) || (_flag == 3))
		sortie << "L";

	sortie << " " << _nc;
	if ((_flag == 2) || (_flag == 3))
		sortie << "L";

	sortie << " " << _miss << endl;

	//�criture des �tiquettes, lignes puis colonnes
	if ((_flag == 1) || (_flag == 3)) {
		//�tiquettes des lignes
		pos = sortie.tellp();
		sortie << _tlig[0];
		for (i = 1; i < _nl; i++) {
			sortie << " " << _tlig[i];
			j = sortie.tellp();
			if ((j - pos) > tmaxligne) {
				sortie << endl;
				pos = j;
			}
		}
		sortie << endl;
	}

	if ((_flag == 2) || (_flag == 3)) {
		//�tiquettes des colonnes
		pos = sortie.tellp();
		sortie << _tcol[0];
		for (i = 1; i < _nc; i++) {
			sortie << " " << _tcol[i];
			j = sortie.tellp();
			if ((j - pos) > tmaxligne) {
				sortie << endl;
				pos = j;
			}
		}
		sortie << endl;
	}

	//�criture de la matrice
	switch (_type) {
	case 2:
		// matrice triangulaire
		// attention, ne sort que la partie triangle du bas
		for (i = 0; i < _nc; i++) {
			pos = sortie.tellp();
			sortie << _tab[i * _nc];
			for (j = 1; j <= i; j++) { //scan d'une moiti� (triangle)
				//[ligne i] [colonne j] triangle du bas
				sortie << " " << _tab[(i * _nc) + j];
				k = sortie.tellp();
				if ((k - pos) > tmaxligne) {
					sortie << endl;
					pos = k;
				}

			}
			sortie << endl;
		}
		break;

	case 1:
		for (i = 0; i < _nl; i++) {

			pos = sortie.tellp();
			sortie << _tab[i * _nc];
			for (j = 1; j < _nc; j++) {
				sortie << " " << _tab[i * _nc + j];
				k = sortie.tellp();
				if ((k - pos) > tmaxligne) {
					sortie << endl;
					pos = k;
				}
			}
			sortie << endl;
		}
		break;

	default:
		break;
	}
}

long double Matrice::get_ppvaleur() const {
	//retourne la plus petite valeur de la matrice
	unsigned long taille(_nc * _nl);
	unsigned long j;
	long double ppvaleur(_tab[0]);

	for (j = 1; j < taille; j++)
		if (_tab[j] < ppvaleur)
			ppvaleur = _tab[j];
	return (ppvaleur);
}

void Matrice::f_neg2zero() {
	//remet � z�ro les chiffres n�gatifs
	unsigned long taille(_nc * _nl);
	unsigned long j(_nc * _nl);

	for (j = 0; j < taille; j++)
		if (_tab[j] < 0)
			_tab[j] = 0;
}

void Matrice::iGnumeric(istream& entree) {
	//lecture de matrices contenues dans les fichiers Gnumeric XML
#ifdef XmlParse_INCLUDED
	//entree.seekg(0);

	//cerr << "void Matrice::iGnumeric(istream& entree) 1" << endl;

	try {
		olivxml::ImportGnumeric parser;
		parser.iParseFlux(entree);
		*this = parser.get_set_of_matrix().GetConstMatrice(0);
	}
	catch (olivxml::ImportGnumeric::Anomalie pb) {
		throw Anomalie(1);
	}
	//cerr << "void Matrice::iGnumeric(istream& entree)" << endl;
	//cerr << "void Matrice::iGnumeric(istream& entree) apres" << endl;
#else
	throw Anomalie(1);
#endif
}

void Matrice::iNtsys(istream& entree) {
	//lecture de matrices contenues dans les fichiers NTSYS
	char car;
	ChaineCar mot;
	ChaineCar sousmot;
	int titres; //1=> titres des lignes 2=> titres des colonnes
	//3=> les 2 //0=> rien
	unsigned long i, j, nc, nl;
	int miss, type;

	//cerr << "Matrice::iNtsys(istream& entree)" << endl;
	entree.seekg(0);

	car = entree.peek();
	//	entree.get(car);
	//	while ((car != '"') && (entree.eof()==0))	entree.get(car);
	while ((car == '"') && (entree.eof() == 0)) {
		entree.get(car);
		GetLigneFlot(entree, mot);
		//		entree.getline(mot,200,'\n');
		_titre.push_back(mot);
		//		entree.get(car);
		car = entree.peek();
	}
	//cerr << "Matrice::iNtsys(istream& entree) 2" << endl;
	if ((entree.eof() != 0) || (entree.fail()))
		throw Anomalie(1);//erreur de lecture
	//cerr << "Matrice::iNtsys(istream& entree) 3" << endl;

	//	mot[0] = car;
	//	mot[1] = '\0';
	//	type = atoi(mot);

	GetLigneFlot(entree, mot); //ligne 0 L23 L34 missing_value
	if ((mot.GetNbMots() != 4) || (entree.fail()) || (entree.eof() != 0))
		throw Anomalie(1);

	mot.GetMot(1, sousmot);
	type = atoi(sousmot.c_str());
	if ((_type > 2) || (_type < 0))
		throw Anomalie(1);

	titres = 0;
	//nombre de lignes
	mot.GetMot(2, sousmot);
	//	entree >> mot;
	if (sousmot[sousmot.size() - 1] == 'L') {
		sousmot.Remplacer("L", "");
		titres = 1;
		//		strcpy(mot + strlen(mot) - 1,"");
	}
	nl = atoi(sousmot.c_str());
	if ((nl > 9999) || (nl < 1))
		throw Anomalie(1);

	//nombre de colonnes
	mot.GetMot(3, sousmot);
	if (sousmot[sousmot.size() - 1] == 'L') {
		sousmot.Remplacer("L", "");
		titres = titres + 2;
		//		strcpy(mot + strlen(mot) - 1,"");
	}
	nc = atoi(sousmot.c_str());
	if ((nc > 9999) || (nc < 1))
		throw Anomalie(1);

	//	entree >> mot; //missing value
	mot.GetMot(4, sousmot);
	miss = atoi(mot.c_str());

	resize(nl, nc);
	//cerr << "Matrice::iNtsys(istream& entree) nc nl " << _nc << _nl << endl;

	_miss = miss;
	_type = type;

	_flag = titres;
	//cerr << "Matrice::iNtsys(istream& entree) 2" << endl;
	//lecture des �tiquettes, lignes puis colonnes
	if ((titres == 1) || (titres == 3)) {
		//�tiquettes des lignes
		for (i = 0; i < _nl; i++) {
			entree >> _tlig[i];
			//cerr << "Matrice::iNtsys(istream& entree) _tlig " << _tlig[i] << endl;
			if (entree.fail())
				throw Anomalie(1);//erreur de lecture
			//			_tlig[i].assign(mot);
		}
	}
	//cerr << "Matrice::iNtsys(istream& entree) 3" << endl;

	if ((titres == 2) || (titres == 3)) {
		//�tiquettes des colonnes
		for (i = 0; i < _nc; i++) {
			entree >> _tcol[i];
			//cerr << "Matrice::iNtsys(istream& entree) tcol " << _tcol[i] << endl;
			if (entree.fail())
				throw Anomalie(1);//erreur de lecture
		}
	}

	//lecture de la matrice proprement dite
	switch (_type) {
	case 1:
		// cas des matrices rectangulaires ou carr�es
		_t = _nc * _nl;
		//		long double chiffre;

		for (i = 0; i < _t; i++) {
			entree >> _tab[i];
			if (entree.fail())
				throw Anomalie(1);//erreur de lecture
			//	_tab[i] = (T) chiffre;
			//	_tab[i] =  atof (mot);
		}
		break;

	case 2:
		// cas des matrices triangulaires
		if (_flag == 2)
			_tlig = _tcol;
		if (_flag == 1)
			_tcol = _tlig;

		entree.clear();

		for (i = 0; i < _nc; i++) {
			for (j = 0; j <= i; j++) {
				//				entree >> (long double) _tab[(i*_nc) + j];
				entree >> _tab[(i * _nc) + j];
				//cerr << "Matrice::iNtsys(istream& entree) 4 " << _tab[(i*_nc) + j] << " " << i << " " << j << endl;
				if (entree.fail())
					throw Anomalie(1);//erreur de lecture
				_tab[(j * _nc) + i] = _tab[(i * _nc) + j];
			}
		}
		break;

	default:
		throw Anomalie(1);
		break;
	}

}

void Matrice::iPhylip(istream& entree) {
	//lecture de matrices contenues dans des fichiers Phylip
	ChaineCar mot;
	ChaineCar sousmot;
	unsigned long nbmot;
	unsigned long i, j;
	long nl(0), nc(0), top(0);

	//	entree.seekg(0);
	entree.clear();

	//cerr << "Matrice::iPhylip(istream& entree)" << endl;
	mot.GetLigneFlot(entree);

	//cerr << "Matrice::iPhylip(istream& entree) 2" << endl;
	nbmot = mot.GetNbMots();
	if ((nbmot < 1) || (nbmot > 2))
		throw Anomalie(1);

	mot.GetMot(1, sousmot);
	if (sousmot.EstUnChiffre() == false)
		throw Anomalie(1);
	nl = atol(sousmot.c_str());

	//cerr << "Matrice::iPhylip(istream& entree) 3" << endl;
	_flag = 0;
	if (nbmot == 1) {
		resize(nl, nl);
		//		_type = 3;
	} else {
		mot.GetMot(2, sousmot);
		if (sousmot.EstUnChiffre() == false)
			throw Anomalie(1);
		nc = atol(sousmot.c_str());
		resize(nl, nc);
	}
	//cerr << nl << " " << nc << endl;
	top = entree.tellg();
	//	GetLigneFlot(entree, mot);
	GetLigneFlot(entree, mot);
	mot.GetMot(1, sousmot);
	//cerr << "Matrice::iPhylip(istream& entree) coucou 1 " << sousmot << endl;
	if (sousmot.EstUnChiffre())
		_flag = 0;
	else { // titre de ligne
		_flag = 1;
		_tlig.resize(nl);
	}
	/*	nbmot = mot.GetNbMots();
	 if (nbmot == (_nc + 1)) {
	 _flag = 1;
	 }
	 else if (nbmot == _nc) {
	 _flag = 0;
	 }
	 else throw Anomalie(1);
	 */
	entree.seekg(top);

	for (i = 0; i < _nl; i++) {
		if ((_flag == 1) || (_flag == 3))
			entree >> _tlig[i];
		//cerr << "Matrice::iPhylip(istream& entree) coucou 2 " << _tlig[i] << endl;
		if (entree.fail())
			throw Anomalie(1);//erreur de lecture
		for (j = 0; j < _nc; j++) {
			entree >> GetCase(i, j);
			if (entree.fail())
				throw Anomalie(1);//erreur de lecture
		}
	}
	SetType(1);
	SetType(2);

	//cerr << "Matrice::iPhylip(istream& entree) fin" << endl;

}

void Matrice::iExcel(istream& entree) {
	//lecture de matrices contenues dans des fichiers Excel
	// la matrice doit �tre indiqu�e par "/" ou "#" et commencer
	// 1 case en dessous et � gauche.
	char car;
	qDebug() << "Matrice::iExcel(istream& entree) begin";
	ChaineCar mot;
	//	char mot[200];
	//	string ligne;
	//1=> titres des lignes 2=> titres des colonnes
	//3=> les 2 //0=> rien
	unsigned long i, j;
	long nc(0), nl(0);
	long debut, top;

	entree.seekg(0);
	qDebug() << "Matrice::iExcel(istream& entree) 1";

	entree.get(car);
	//	while ((car != '"') && (entree.eof()==0))	entree.get(car);
	while (((car != '/') && (car != '#')) && (entree.good())) {
		//		mot = car;
		GetLigneFlot(entree, mot);
		mot = car + mot;
		_titre.push_back(mot);
		entree.get(car);
	}

	qDebug() << "Matrice::iExcel(istream& entree) 2";
	//cerr << "coucou excel 2";
	if (entree.fail())
		throw Anomalie(1);//erreur de lecture
	nc = 0;
	nl = 0;
	_flag = 0;
	debut = entree.tellg();
	GetLigneFlot(entree, mot);
	if ((mot[0] > 4) && (mot[1] != '\t')) {
		_flag = 2; //il ya des titres de colonnes
	}
	if (entree.eof() != 0)
		throw Anomalie(1);//erreur de lecture
	//cerr << "coucou " << mot << endl ;
	qDebug() << "Matrice::iExcel(istream& entree) 3 " << mot.c_str();

	top = entree.tellg();
	//cerr << top << endl;

	GetLigneFlot(entree, mot);
	for (i = 0; i < mot.size(); i++) {
		if (mot[i] > 64) {
			_flag++; //il ya les titres des lignes
			//cerr << mot << endl;
			break;
		}
	}
	qDebug() << "Matrice::iExcel(istream& entree) 4 ";

	//determination du nombre de colonnes:
	nc = 0;
	entree.seekg(top);
	entree.clear();
	if ((_flag == 1) || (_flag == 3)) {
		entree >> mot;
	}
	car = '3';
	GetLigneFlot(entree, mot);
	nc = mot.GetNbMots();
	//cerr << " nc " << nc << endl;
	qDebug() << "Matrice::iExcel(istream& entree) 5 nc " << nc;

	//cerr << "coucou " << mot << endl ;
	//	if (entree.eof() != 0) throw Anomalie(1);//erreur de lecture
	//cerr << "coucou2 " << mot << endl ;
	//determination du nombre de lignes:
	nl = 1;
	entree.seekg(top);
	GetLigneFlot(entree, mot);
	entree >> mot;
	while ((mot.GetNbMots() > 0) && (entree.eof() == 0)) {
		GetLigneFlot(entree, mot);
		nl++;
		entree >> mot;
		//cerr << mot << endl;
		//cin >> i;
	}
	entree.clear();

	qDebug() << "Matrice::iExcel(istream& entree) 6 nl " << nl << " nc "
			<< nc;
	//cerr << nl << endl;
	//cerr << nc << endl;

	//  on a le nb de colonnes, le nb de lignes, les �tiquettes,
	// remplissons !!!
	resize(nl, nc);
	entree.clear();

	if ((_flag == 2) || (_flag == 3)) { //saisie des titres des colonnes
		entree.seekg(debut);
		//		entree >> _tcol[i];
		for (i = 0; i < _nc; i++) {
			entree >> _tcol[i];
			//cerr << _tcol[i] << endl;
			if (entree.fail())
				throw Anomalie(1);//erreur de lecture
		}
	}
	entree.clear();

	qDebug() << "Matrice::iExcel(istream& entree) 7 ";

	//	entree.seekg(top);
	entree.seekg(debut);
	GetLigneFlot(entree, mot);
	//cerr << "coucou" << top << endl;
	for (i = 0; i < _nl; i++) {
		if ((_flag == 1) || (_flag == 3))
			entree >> _tlig[i];
		//cerr << _tlig[i] << endl;
		for (j = 0; j < _nc; j++) {
			entree >> _tab[(i * _nc) + j];
			//cerr << _tab[(i * _nc) + j] << endl;
			if (entree.fail())
				throw Anomalie(1);//erreur de lecture
		}
	}
	qDebug() << "Matrice::iExcel(istream& entree) 8 ";

	//try {
	SetType(1);
	SetType(2);
	//} catch (biolib::vecteurs::Matrice::Anomalie erreur) {
	//	cerr << erreur.fmessage(erreur.le_pb);
	//SetType(1);
	//}
}

void Matrice::resize(unsigned long nblig,
		unsigned long nbcol) {
	unsigned long i;

	if (_tab != 0)
		delete[] _tab;

	if (_nl > nblig)
		_tlig.erase(_tlig.begin() + _nl, _tlig.end());
	if (_nc > nbcol)
		_tcol.erase(_tcol.begin() + _nc, _tcol.end());

	_tcol.reserve(nbcol);
	_tlig.reserve(nblig);

	for (i = _nc; i < nbcol; i++)
		_tcol.push_back("");
	for (i = _nl; i < nblig; i++)
		_tlig.push_back("");

	_nc = nbcol;
	_nl = nblig;
	_t = _nc * _nl;
	_tab = new long double[_t];
	//	_miss = 0;
	//	_flag = 0;

	for (i = 0; i < _t; i++)
		_tab[i] = 0;

}

bool Matrice::redim(unsigned long nblig,
		unsigned long nbcol) {
	unsigned long i, j, t;
	long double* Ptab;

	if (_tab == 0)
		return (false);
	if ((_type == 3) && (nblig != nbcol))
		return (false);

	if (_nl > nblig)
		_tlig.erase(_tlig.begin() + _nl, _tlig.end());
	if (_nc > nbcol)
		_tcol.erase(_tcol.begin() + _nc, _tcol.end());

	_tcol.reserve(nbcol);
	_tlig.reserve(nblig);
	for (i = _nc; i < nbcol; i++)
		_tcol.push_back("");
	for (i = _nl; i < nblig; i++)
		_tlig.push_back("");

	Ptab = _tab;
	t = nblig * nbcol;
	_tab = new long double[t];

	for (i = 0; i < nblig; i++) {
		for (j = 0; j < nbcol; j++) {
			if ((j < _nc) && (i < _nl))
				*(_tab + (i * nbcol) + j) = *(Ptab + (i * _nc) + j);
			else
				*(_tab + (i * nbcol) + j) = 0;
		}
	}

	delete[] Ptab;
	_nc = nbcol;
	_nl = nblig;
	_t = t;
	return (true);
}

void Matrice::fslig(vector& somme) const {

	int i, j;

	if (_type == 3)
		throw Anomalie(3); //op�ration impossible sur ce type de matrice

	if (somme.size() < _nl)
		somme.resize(_nl);

	for (i = 0; i < _nl; i++) {
		somme[i] = _tab[i * _nc];
	}
	for (j = 1; j < _nc; j++) {
		for (i = 0; i < _nl; i++) {
			somme[i] += _tab[j + (i * _nc)];
		}
	}
}

void Matrice::fscol(vector& somme) const {

	int pos, i, j;

	if (_type == 3)
		throw Anomalie(3); //op�ration impossible sur ce type de matrice

	if (somme.size() < _nc)
		somme.resize(_nc);

	for (i = 0; i < _nc; i++) {
		somme[i] = _tab[i];
	}
	pos = _nc;
	for (j = 1; j < _nl; j++) {
		for (i = 0; i < _nc; i++) {
			somme[i] += _tab[pos];
			pos++;
		}
	}
}

void Matrice::ftranspose() {
	//transposition de matrices:

	Titre swap;
	unsigned long i, j;

	swap = _tcol;
	_tcol = _tlig;
	_tlig = swap;

	if (_type == 3)
		return;

	//_flag = 2;
	if (_flag == 1)
		_flag = 2;
	else if (_flag == 2)
		_flag = 1;

	long double* Ptab;
	Ptab = new long double[_t];

	for (i = 0; i < _nl; i++) {
		for (j = 0; j < _nc; j++) {
			*(Ptab + (j * _nl) + i) = *(_tab + rindice(i, j));
		}
	}

	i = _nc;
	_nc = _nl;
	_nl = i;

	delete[] _tab;
	_tab = Ptab;
}

Matrice Matrice::operator*(Matrice &rval) const {

	//produit matriciel
	Matrice Resultat(_nl, rval._nc);
	//	long double limite(1e-030);

	if (_nc != rval._nl)
		throw Anomalie(4); // 4-> calcul impossible
	//	if (_nl != rval._nc) throw Anomalie(4); // 4-> calcul impossible

	int i, j, k; //ligne, colonne


	Resultat.SetFlag(0);
	if ((rval.GetFlag() == 2) || (rval.GetFlag() == 3)) {
		Resultat._tcol = rval._tcol;
		Resultat.SetFlag(2);
	}
	if ((_flag == 1) || (_flag == 3)) {
		Resultat._tlig = _tlig;
		Resultat._flag++;
	}

	for (i = 0; i < _nl; i++) {
		for (j = 0; j < rval._nc; j++) {
			Resultat.GetCase(i, j) = 0;
			for (k = 0; k < _nc; k++) {
				Resultat.GetCase(i, j) = Resultat.GetCase(i, j)
						+ ((long double) GetCase(i, k) * rval.GetCase(k, j));
			}
		}
	}

	//v�rification limite
	/*	for (i=0; i < _t; i++) {
	 if (Resultat._tab[i] < limite) Resultat._tab[i] = 0;
	 }*/

	return Resultat;
}

vector Matrice::operator*(const vector &rval) {
	//produit d'une matrice par un vecteur

	vector Resultat;
	Matrice& lamatrice = *this;
	long i, k; //ligne, colonne

	Resultat.resize(lamatrice._nl);

	if (lamatrice._nl != rval.size())
		throw Anomalie(4); // 4-> calcul impossible


	for (i = 0; i < Resultat.size(); i++) {
		Resultat[i] = 0;
		for (k = 0; k < lamatrice._nc; k++) {
			Resultat[i] = Resultat[i] + (lamatrice.GetCase(i, k) * rval[i]);
		}
	}

	return Resultat;
}

Matrice Matrice::operator*(long double scalaire) {

	Matrice Resultat(_nl, _nc);
	long i;

	//	Resultat.resize(_nl,_nc);
	//	cout << "coucou";
	Resultat.SetType(1);
	Resultat._titre = _titre;
	//	Resultat._titre.push_back("Produit par un scalaire");
	Resultat._flag = 0;

	if ((_flag == 2) || (_flag == 3)) {
		//copie des �tiquettes des colonnes
		Resultat._flag = 2;
		Resultat._tcol = _tcol;
		Resultat._tlig = _tcol;
	}

	for (i = 0; i < _t; i++) {
		Resultat._tab[i] = _tab[i] * scalaire;
	}

	return Resultat;
}

Matrice Matrice::operator-(Matrice& rval) {

	Matrice Resultat(_nl, _nc);
	long i;

	if (_nl != rval._nl)
		throw Anomalie(4);
	if (_nc != rval._nc)
		throw Anomalie(4);

	//	cout << "coucou";
	Resultat.SetType(_type);
	Resultat._titre = _titre;
	//	Resultat._titre.push_back("Produit par un scalaire");
	Resultat._flag = _flag;

	if ((_flag == 2) || (_flag == 3)) {
		//copie des �tiquettes des colonnes
		Resultat._tcol = _tcol;
	}
	if ((_flag == 1) || (_flag == 3)) {
		//copie des �tiquettes des lignes
		Resultat._tlig = _tlig;
	}

	for (i = 0; i < _t; i++) {
		Resultat._tab[i] = _tab[i] - rval._tab[i];
	}

	return Resultat;

}

Matrice Matrice::operator+(Matrice &rval) {
	long i;

	Matrice Resultat;

	if (_nl != rval._nl)
		throw Anomalie(4);
	if (_nc != rval._nc)
		throw Anomalie(4);

	Resultat.resize(_nl, _nc);
	//	cout << "coucou";
	Resultat.SetType(_type);
	Resultat._titre = _titre;
	//	Resultat._titre.push_back("Produit par un scalaire");
	Resultat._flag = _flag;

	if ((_flag == 2) || (_flag == 3)) {
		//copie des �tiquettes des colonnes
		Resultat._tcol = _tcol;
	}
	if ((_flag == 1) || (_flag == 3)) {
		//copie des �tiquettes des lignes
		Resultat._tlig = _tlig;
	}

	for (i = 0; i < _t; i++) {
		Resultat._tab[i] = _tab[i] + rval._tab[i];
	}

	return Resultat;

}

long double Matrice::fdet() const {
	//calcul du d�terminant d'une matrice par r�cursivit
	// Olivier Langella 29 oct 98
	// D'apr�s J. Lefebvre "introduction aux analyses statistiques
	// multidimensionnelle" p 36
	long double det;
	if (_nc != _nl)
		throw Anomalie(4); //calcul impossible

	MatriceLD calculs;

	calculs = *this;

	det = calculs.fdetrec();

	return (det);
}

long double Matrice::fdetrec() const {
	//calcul du d�terminant d'une matrice par r�cursivit
	// utilis� par fdet;
	long double det(0);
	unsigned long i;
	long cofacteur(1);
	Matrice calculs;

	if (_nc == 2) {
		//solution
		det = ((long double) GetCase(0, 0) * GetCase(1, 1))
				- ((long double) GetCase(1, 0) * GetCase(0, 1));
		return (det);
	} else {

		for (i = 0; i < _nl; i++) {
			calculs = *this;
			calculs.SupprCol(0);
			calculs.SupprLig(i);

			det = det + ((long double) calculs.fdetrec()
					* ((long double) GetCase(i, 0) * cofacteur));
			cofacteur = cofacteur * -1;
		}
		return (det);
	}
}

void Matrice::SupprCol(unsigned long nbcol) {
	unsigned long i, j, k, n;
	long double * Ptab;

	//	if (_nl > nblig) _tlig.erase(_tlig.begin() + _nl,_tlig.end());
	if (nbcol < _tcol.size())
		_tcol.erase(_tcol.begin() + nbcol);

	n = _nc - 1;

	Ptab = new long double[n * _nl];
	k = 0;

	for (i = 0; i < _nl; i++) {
		for (j = 0; j < _nc; j++) {
			if (j != nbcol) {
				Ptab[k] = GetCase(i, j);
				k++;
			}
		}
	}

	_nc = _nc - 1;
	_t = _nc * _nl;

	if (_tab != 0)
		delete[] _tab;
	_tab = Ptab;
	_type = 1;

}

void Matrice::SupprLig(unsigned long nblig) {
	unsigned long i, j, k, n;
	long double* Ptab;

	//	if (_nl > nblig) _tlig.erase(_tlig.begin() + _nl,_tlig.end());
	if (nblig < _tlig.size())
		_tlig.erase(_tlig.begin() + nblig);

	n = _nl - 1;

	Ptab = new long double[n * _nc];
	k = 0;

	for (i = 0; i < _nl; i++) {
		for (j = 0; j < _nc; j++) {
			if (i != nblig) {
				Ptab[k] = GetCase(i, j);
				k++;
			}
		}
	}

	_nl = _nl - 1;
	_t = _nc * _nl;

	if (_tab != 0)
		delete[] _tab;
	_tab = Ptab;
	_type = 1;

}

void MatriceLD::finv(MatriceLD& inverse) const {
	//calcul de l'inverse d'une matrice
	// Olivier Langella 29 oct 98
	// D'apr�s J. Lefebvre "introduction aux analyses statistiques
	// multidimensionnelle" p 42
	if (_nc != _nl)
		throw Anomalie(4); //calcul impossible

	long double detA;
	MatriceLD calculs;
	int cofacteur, cofl(-1);
	unsigned long i, j;

	inverse = *this;

	detA = fdet();

	for (i = 0; i < _nl; i++) {
		cofacteur = cofl;
		for (j = 0; j < _nc; j++) {
			cofacteur *= -1;
			calculs = *this;
			calculs.SupprCol(i);
			calculs.SupprLig(j);

			inverse.GetCase(i, j) = (calculs.fdet() * cofacteur) / detA;
		}

		cofl *= -1;
	}

}

void MatriceLD::fvalpropres(MatriceLD& vectpropres,
		vector& valpropres, float precision) {

	//Calcul des valeurs propres pour une matrice sym�trique
	// M�thode de Jacobi
	// Olivier Langella 29 oct 98
	// D'apr�s J. Lefebvre "introduction aux analyses statistiques
	// multidimensionnelle" p 67
	// (m�thode it�rative)

	if (GetType() != 3)
		throw Anomalie(3); //calcul impossible
	//ATTENTION, ne v�rifie pas si la matrice est bien symetrique !!

	valpropres.resize(_nc);
	vectpropres.resize(_nc, _nc);
	vectpropres.SetType(1);
	MatriceLD matC;
	MatriceLD matA;
	matA = *this;

	matA._titre.push_back("Matrice A");
	matC._titre.push_back("Matrice C");
	vectpropres = vectpropres + 1;

	//it�rations de C'AC
	unsigned long poss, posr;
	long double temp, teta;
	unsigned long i, j, nc(_nc);
	long ind1, ind2;

	long double scarre(0), tracecar;

	for (i = 0; i < _t; i++) {
		scarre = scarre + (_tab[i] * _tab[i]);
	}

	matC.resize(nc, nc);
	MatriceLD matInter(nc, nc); //matrice pour les calculs
	//intermediaires
	do {
		// choix du point � annuler
		// : le plus grand non situ� sur la diagonale
		posr = 0;
		poss = 0;
		temp = -1;
		for (i = 1; i < nc; i++) {
			for (j = 0; j < i; j++) {
				teta = fabs(matA._tab[(i * nc) + j]);
				if (temp < teta) {
					temp = teta;
					poss = i;
					posr = j;
				}
			}
		}

		// calcul de teta
		teta = (matA._tab[(posr * nc) + poss] * 2) / (matA._tab[(posr * nc)
				+ posr] - matA._tab[(poss * nc) + poss]);
		teta = atan(teta) / 2;

		// fabriquer la matrice C'
		for (i = 0; i < nc; i++) {
			matC._tab[(i * nc) + i] = 1;
			if ((i == poss) || (i == posr)) {
				matC._tab[(i * nc) + i] = cos(teta);
			}
			for (j = 0; j < i; j++) {
				ind1 = (j * nc) + i;
				ind2 = (i * nc) + j;
				if ((i == poss) && (j == posr)) {
					matC._tab[ind1] = sin(teta);
					matC._tab[ind2] = matC._tab[ind1] * -1;
				} else {
					matC._tab[ind1] = 0;
					matC._tab[ind2] = 0;
				}
			}
		}

		//	matA = matC * matA;
		matInter.fmultiplier(matC, matA); // ajoute pour optimiser
		matC.ftranspose();
		//	matA = matA * matC;
		matA.fmultiplier(matInter, matC); // ajoute pour optimiser

		//	vectpropres = vectpropres * matC;
		for (i = 0; i < _t; i++) {
			matInter._tab[i] = vectpropres._tab[i];
		}
		vectpropres.fmultiplier(matInter, matC);

		tracecar = 0;
		for (i = 0; i < nc; i++) {
			teta = matA._tab[(i * nc) + i];
			tracecar = tracecar + (teta * teta);
		}
	} while (((scarre - tracecar) / tracecar) > precision);

	for (i = 0; i < _nc; i++) {
		valpropres[i] = matA.GetCase(i, i);
	}

}

long double Matrice::ftrace() const {
	//calcul de la trace d'une matrice (somme des E diagonaux)
	// Olivier Langella 29 oct 98
	if (_nc != _nl)
		throw Anomalie(4); //calcul impossible

	int i, j(0);

	long double res(0);

	for (i = 0; i < _nc; i++) {
		res += _tab[i + j];
		j += _nc;
	}

	return res;
}

Matrice Matrice::operator+(long double rval) {

	Matrice Resultat;

	Resultat = *this;
	unsigned long i;

	for (i = 0; i < _nc; i++) {
		Resultat.GetCase(i, i) = Resultat.GetCase(i, i) + rval;
	}

	return Resultat;

}

void Matrice::fswapcol(long i, long j) {
	long double swap;
	long k;

	for (k = 0; k < _nc; k++) {
		swap = GetCase(k, i);
		GetCase(k, i) = GetCase(k, j);
		GetCase(k, j) = swap;
	}
}

void Matrice::fmultiplier(const Matrice& matA,
		const Matrice& matB) {
	//pour multiplier 2 matrices plus rapidement
	// A et B sont carrees !!!!
	long i, j, k, nc(_nc);
	long double res;

	for (i = 0; i < nc; i++) {
		for (j = 0; j < nc; j++) {
			res = 0;
			for (k = 0; k < nc; k++) {
				res += matA._tab[(i * nc) + k] * matB._tab[(k * nc) + j];
			}
			_tab[(i * nc) + j] = res;
		}
	}
}

void Matrice::oXgobi(const string &fnom) {
	unsigned long i, j;
	ofstream fichier;
	//	string fnom(nomfichier);
	string fnomplus(fnom);

	if (_type != 1)
		throw Anomalie(3);

	fnomplus = fnom + ".dat";
	fichier.open(fnomplus.c_str(), ios::out);
	if (fichier.is_open() == false)
		throw Anomalie(6);

	for (i = 0; i < _nl; i++) {
		fichier << _tab[i * _nc];
		for (j = 1; j < _nc; j++) {
			fichier << " " << _tab[(i * _nc) + j];
		}
		fichier << endl;
	}

	fichier.close();

	if (_titre.size() > 0) {
		fnomplus = fnom + ".doc";
		fichier.open(fnomplus.c_str(), ios::out);
		if (fichier.is_open() == false)
			throw Anomalie(6);

		for (i = 0; i < _titre.size(); i++) {
			fichier << _titre[i];
			fichier << endl;
		}
		fichier.close();
	}

	if ((_flag == 1) || (_flag == 3)) {
		fnomplus = fnom + ".row";
		fichier.open(fnomplus.c_str(), ios::out);
		if (fichier.is_open() == false)
			throw Anomalie(6);

		for (i = 0; i < _tlig.size(); i++) {
			fichier << _tlig[i];
			fichier << endl;
		}

		fichier.close();
	}

	if ((_flag == 2) || (_flag == 3)) {
		fnomplus = fnom + ".col";
		fichier.open(fnomplus.c_str(), ios::out);
		if (fichier.is_open() == false)
			throw Anomalie(6);

		for (i = 0; i < _tcol.size(); i++) {
			fichier << _tcol[i];
			fichier << endl;
		}

		fichier.close();
	}

}

////////////////////////////////////////////////
// GLOBAL
///////////////////////////////////////////////
ostream& operator<<(ostream& sortie, Matrice& lamatrice) {
	//1= Excel
	//2= Ntsys
	//3= xgobi ==!!!! seulement en ofstream !!!!!

	lamatrice.oFormat(sortie, lamatrice._oformat);
	return (sortie);

}

ofstream& operator<<(ofstream& sortie, Matrice& lamatrice) {
	//1= Excel
	//2= Ntsys
	//3= xgobi  ==!!!! seulement en ofstream !!!!!

	if (lamatrice._oformat == 3) {
		lamatrice.oXgobi("xgobi");
	} else {
		lamatrice.oFormat(sortie, lamatrice._oformat);
	}
	return (sortie);

}

/*ofstream& operator<<(ofstream& sortie,MatriceLD& lamatrice) {
 //1= Excel
 //2= Ntsys
 //3= xgobi  ==!!!! seulement en ofstream !!!!!

 if (lamatrice._oformat == 3) {
 lamatrice.oXgobi("xgobi");
 }
 else {
 lamatrice.oFormat(sortie, lamatrice._oformat);
 }
 return(sortie);

 }*/

istream& operator>>(istream& ientree, Matrice& lamatrice) {

	//cerr << "coucou";
	lamatrice.iFichier(ientree);
	//cerr << "coucou";
	return (ientree);
}

void Matrice::oPhylip(ostream& fichier) {
	unsigned long i, j;

	fichier.setf(ios::scientific);

	/*	// �criture du titre
	 for (i=0; i < _titre.size();i++) {
	 fichier << _titre[i];
	 fichier << endl;
	 }*/
	if (_type == 3) { //matrice triangulaire
		fichier << '\t' << GetNL() << endl;
		_tlig = _tcol;
	} else {
		fichier << '\t' << GetNL() << '\t' << GetNC() << endl;
	}

	//	fichier << "#";
	/*	if ((_flag == 2)||(_flag == 3)){
	 //�tiquettes des colonnes
	 fichier << '\t' << _tcol[0];
	 for (i=1; i<_nc; i++) fichier << '\t' << _tcol[i];
	 }
	 fichier << endl;
	 */
	//�criture de la matrice
	for (i = 0; i < _nl; i++) {
		if ((_flag == 1) || (_flag == 3)) {
			//�tiquettes des lignes
			fichier << _tlig[i];
		}

		for (j = 0; j < _nc; j++) {
			fichier << '\t' << GetCase(i, j);
		}
		fichier << endl;
	}

}

void Matrice::iFichier(istream& ientree) {
	int nbformat(6), i(1);
	char car;
	bool autre(true);

	//	entree = ientree;
	qDebug() << "Matrice::iFichier(istream& ientree) begin nbformat "
			<< nbformat;
	ientree.get(car);
	if (ientree.fail()) {
		//		cerr << "Le fichier n'a pas pu �tre ouvert... "<< endl;
		throw Anomalie(1);
	}
	while ((autre) & (i < nbformat)) {
		qDebug() << "Matrice::iFichier(istream& ientree) ifichier " << i
				<< " autre " << autre;
		//cerr << "coucou ifichier"  << i << endl;
		if (i == 3) {
			i = 4;
			continue;
		} //xgobi
		try {
			ientree.clear();
			ientree.seekg(0);
			//ientree.seekg (0, ios::beg);
			//		ientree.rewind();
			_titre.resize(0);
			//cerr << "coucou ifichier" << i << endl;
			iFichier(ientree, i);
			//cerr << "coucou ifichier" << endl;

			autre = false;
			qDebug() << "Matrice::iFichier(istream& ientree) 1 autre "
					<< autre;
		} catch (Anomalie erreur) {
			if (erreur.le_pb > 0) {
				autre = true;
				if (i == (nbformat - 1)) {
					//					cerr << erreur.fmessage(erreur.le_pb)<< endl;
					throw Anomalie(erreur.le_pb);
					autre = false;
				}
				erreur.le_pb = 0;
			}
		}
		qDebug() << "Matrice::iFichier(istream& ientree) 2 autre " << autre;
		i++;
	}
	qDebug() << "Matrice::iFichier(istream& ientree) end";
}

MatriceLD::MatriceLD() :
	Matrice () {
}
;

void MatriceLD::fdiagonalisation(MatriceLD & matdiag, vector& pvlp) {
	/******************************************************************************/
	/*                  DIAGONALISATION DE LA MATRICE  (Householder)        */
	/*                        1) tridiagonalisation (tridiag)                              */
	/*                	  2) diagonalisation par la methode Q-L (diaggl)          */
	/******************************************************************************/
	int m;
	unsigned long i;
	long double *ps;

	if (_type != 2)
		throw Anomalie(3);
	// 3-> op�ration impossible sur ce type de matrice
	pvlp.resize(_nc);

	matdiag.resize(_nc, _nc);
	matdiag.SetType(2);

	ps = new long double[_nc];

	matdiag._titre = _titre;
	matdiag._titre.push_back("diagonalisation par la methode Q-L");
	matdiag._flag = _flag;

	if ((_flag == 2) || (_flag == 3)) {
		matdiag._tcol = _tcol;
		matdiag._tlig = _tcol;
	}

	//copie du tableau
	for (i = 0; i < _t; i++) {
		matdiag._tab[i] = _tab[i];
	}

	m = matdiag.ftridiag(ps, pvlp);

	matdiag.fmdiagql(m, ps, pvlp);

	delete[] ps;

}

/*======================   methode  Q-L  =====================================*/

void MatriceLD::fmdiagql(int m, long double *ps, vector & pvlp) {
	long double *pcov;
	unsigned long i, ij, j, k, l;
	long ijk, is;
	long double q, h, t, xp, u, b, a, v;
	long double p1;

	if (_type != 2)
		throw Anomalie(3);
	// 3-> op�ration impossible sur ce type de matrice
	pcov = _tab;
	a = (long double) 1e-10;

	for (i = 1; i < _nc; i++) {
		*(ps + i - 1) = *(ps + i);
	}
	*(ps + _nc - 1) = 0;

	for (k = 0; k < _nc; k++) {
		j = k;
		while ((long double) (((long double) j < (long double) _nc - 1)
				&& fabs((long double) *(ps + j))) >= (long double) (a * (fabs(
				(long double) pvlp[j]) + fabs((long double) pvlp[j + 1]))))
			j++;
		while (j != k) {
			h = pvlp[k];
			m = m + 1;
			q = (pvlp[k + 1] - h) * 0.5 / (*(ps + k));
			t = sqrt((long double) q * q + 1);
			if (q < 0)
				is = -1;
			else
				is = 1;
			q = pvlp[j] - h + (*(ps + k)) / (q + t * is);
			u = 1;
			v = 1;
			h = 0;
			for (ijk = 1; ijk <= (long) (j - k); ijk++) {
				i = j - ijk;
				xp = u * (*(ps + i));
				b = v * (*(ps + i));
				if (q == 0 || xp == 0) {
					//	printf("cette matrice ne peut etre diagonalisee\n");
					// erreur
					//	return();
					delete[] ps;
					throw Anomalie(2);
				}
				if (fabs((long double) xp) >= fabs((long double) q)) {
					u = xp / q;
					t = sqrt((long double) u * u + 1);
					*(ps + i + 1) = q * t;
					v = 1 / t;
					u = u * v;
				} else {
					v = q / xp;
					t = sqrt((long double) 1 + v * v);
					*(ps + i + 1) = t * xp;
					u = 1 / t;
					v = v * u;
				}
				q = pvlp[i + 1] - h;
				t = ((pvlp[i]) - q) * u + 2 * v * b;
				h = u * t;
				pvlp[i + 1] = q + h;
				q = v * t - b;
				l = 0;
				while (l < _nc) {
					xp = *(pcov + rindice(l, i + 1));
					*(pcov + rindice(l, i + 1)) = u * (*(pcov + rindice(l, i)))
							+ v * xp;
					*(pcov + rindice(l, i)) = v * (*(pcov + rindice(l, i))) - u
							* xp;
					l = l + 1;
				}
			}
			pvlp[k] = pvlp[k] - h;
			*(ps + k) = q;
			*(ps + j) = 0;
			j = k;
			while (j < _nc - 1 && fabs((long double) *(ps + j)) >= a * (fabs(
					(long double) pvlp[j]) + fabs((long double) pvlp[j + 1])))
				j++;

		}
	}
	for (ij = 1; ij < _nc; ij++) {
		i = ij - 1;
		l = i;
		h = pvlp[i];
		for (m = ij; m < (int) _nc; m++) {
			if (pvlp[m] >= h) {
				l = m;
				h = pvlp[m];
			}
		}
		if (l != i) {
			pvlp[l] = pvlp[i];
			pvlp[i] = h;
			for (m = 0; m < (int) _nc; m++) {
				p1 = *(pcov + rindice(m, i));
				*(pcov + rindice(m, i)) = *(pcov + rindice(m, l));
				*(pcov + rindice(m, l)) = p1;
			}
		}
	}
}

int MatriceLD::ftridiag(long double *ps, vector & pvlp) {
	long double *pcov;
	unsigned long i, j;
	int k, l, m(0);
	long double b, c, q, x, xp, bp;

	pcov = _tab;

	for (j = 1; j < _nc; j++) {
		b = 0;
		c = 0;
		i = (_nc - 1) - j + 1;
		k = i - 1;

		if (k < 1) {
			*(ps + i) = *(pcov + rindice(i, k));
			pvlp[i] = b;
			continue;
		}
		for (l = 0; l <= k; l++) {
			c = c + fabs((long double) *(pcov + rindice(i, l)));
		}
		if (c == 0) {
			*(ps + i) = *(pcov + rindice(i, k));
			pvlp[i] = b;
			continue;
		}
		for (l = 0; l <= k; l++) {
			x = (*(pcov + rindice(i, l))) / c;
			*(pcov + rindice(i, l)) = x;
			b = b + (x * x);
		}
		xp = *(pcov + rindice(i, k));
		if (xp < 0) {
			q = sqrt((long double) b);
		} else {
			q = (sqrt((long double) b)) * (-1);
		}
		*(ps + i) = c * q;
		b = b - xp * q;
		*(pcov + rindice(i, k)) = xp - q;
		xp = 0;
		for (m = 0; m <= k; m++) {
			*(pcov + rindice(m, i)) = (*(pcov + rindice(i, m))) / (b * c);
			q = 0;
			for (l = 0; l <= m; l++) {
				q = q + (*(pcov + rindice(m, l))) * (*(pcov + rindice(i, l)));
			}
			for (l = m + 1; l <= k; l++) {
				q = q + ((*(pcov + rindice(l, m))) * (*(pcov + rindice(i, l))));

			}
			*(ps + m) = q / b;
			xp = xp + (*(ps + m)) * (*(pcov + rindice(i, m)));
		}
		bp = xp * 0.5 / b;
		for (m = 0; m <= k; m++) {
			xp = *(pcov + rindice(i, m));
			q = (*(ps + m)) - bp * xp;
			*(ps + m) = q;
			for (l = 0; l <= m; l++) {
				*(pcov + rindice(m, l)) = (*(pcov + rindice(m, l))) - xp
						* (*(ps + l)) - q * (*(pcov + rindice(i, l)));
			}
		}
		for (l = 0; l <= k; l++) {
			*(pcov + rindice(i, l)) = c * (*(pcov + rindice(i, l)));
		}
		pvlp[i] = b;
	}
	*ps = 0;
	pvlp[0] = 0;
	for (i = 0; i < _nc; i++) {
		k = i - 1;
		if (pvlp[i] != 0) {
			for (m = 0; m <= k; m++) {
				q = 0;
				for (l = 0; l <= k; l++) {
					q = q + (*(pcov + rindice(i, l)))
							* (*(pcov + rindice(l, m)));
				}
				for (l = 0; l <= k; l++) {
					*(pcov + rindice(l, m)) = (*(pcov + rindice(l, m))) - q
							* (*(pcov + rindice(l, i)));
				}
			}
		}
		pvlp[i] = *(pcov + rindice(i, i));
		*(pcov + rindice(i, i)) = 1;
		for (m = 0; m <= k; m++) {
			*(pcov + rindice(i, m)) = 0;
			*(pcov + rindice(m, i)) = 0;
		}
	}
	return (m);
}

void MatriceLD::fcoordcol(MatriceLD& stat, MatriceLD& res, MatriceLD& norm,
		vector & pvlp) {
	/******************************************************************************/
	/*                         calcul des coordonnees                             */
	/******************************************************************************/
	/*===================  coordonnees des colonnes  =============================*/
	unsigned long p0; //nb d'axes
	unsigned long i, j;
	int PC, k;
	long double tr; //somme des valeurs propres
	long double limite; //limite des possibilit�s de calculs
	float t; //cumul des pourcentages
	float v; //inertie (pourcentage sur un axe)
	long double *pcov, a1;
	char * temp;
	//	string temps;

	limite = 0.000001; //1e-010;//1e-030;

	if (norm._type != 2)
		throw Anomalie(3);
	// 3-> op�ration impossible sur ce type de matrice

	temp = new (char[50]);
	p0 = _nc - 1;

	// redimensionnement
	res.resize(_nc, p0);
	//
	res.SetType(1);
	res._titre = _titre;
	res._titre.push_back("coordonn�es spatiales sur les colonnes");
	res._titre.push_back("espace � ");
	//	itoa (p0,temp,10);
	res._titre[res._titre.size() - 1].AjEntier(p0); //temp ;
	res._titre[res._titre.size() - 1] += " dimensions";
	res._flag = 0;

	// redimensionnement
	stat.resize(p0, 3);
	//
	stat.SetType(1);
	stat._titre = _titre;
	stat._titre.push_back(
			"statistiques des coordonn�es spatiales sur les colonnes");
	stat._titre.push_back("espace � ");
	//	temps = p0;
	//	itoa (p0,temp,10);
	stat._titre[stat._titre.size() - 1].AjEntier(p0); //temps.c_str() ;
	stat._titre[stat._titre.size() - 1] += " dimensions";
	stat._flag = 3;

	if ((_flag == 2) || (_flag == 3)) {
		res._flag = 1;
		//copie des �tiquettes des lignes
		//		res._tlig = _tcol;
		res._tlig = _tlig;
	}

	res._flag = res._flag + 2; //num�rotation des axes
	for (i = 0; i < res._nc; i++) {
		//		strcpy(temp,"axe_");
		//		itoa(i + 1,temp + 4,10);
		//		strcat(temp,"");
		res._tcol[i].assign("axe_");
		res._tcol[i].AjEntier(i + 1);

		//		res._tcol[i].assign(temp);
		stat._tlig[i].assign(res._tcol[i]);
	}
	stat._tcol[0].assign("Valeur_Propre");
	stat._tcol[1].assign("Inertie");
	stat._tcol[2].assign("Cumul");

	pcov = norm._tab;
	PC = 100;

	//test sur les valeurs propres pour �liminer l'effet Ariane V
	j = 0;
	while ((fabs(pvlp[j]) > limite) && (j < _nc)) {
		j++;
	}
	if (j < _nc)
		for (i = j; i < _nc; i++)
			pvlp[i] = 0;

	//somme des valeurs propres
	tr = 0;
	for (j = 0; j < _nc; j++)
		tr = tr + pvlp[j];

	v = 0;
	t = 0;
	for (i = 0; i < p0; i++) {
		a1 = pvlp[i] / tr;
		v = PC * (float) a1;
		t = t + v;
		stat._tab[i * 3] = pvlp[i];
		stat._tab[(i * 3) + 1] = v;
		stat._tab[(i * 3) + 2] = t;
	}

	k = 0;
	for (i = 0; i < norm._nc; i++) { //scan sur les colonnes
		for (j = 0; j < p0; j++) { //coord col i, axe j
			a1 = (*(pcov + rindice(i, j))) * (sqrt((long double) pvlp[j]));
			res._tab[k] = a1 * PC;
			k++;
		}
	}
}

void MatriceLD::fscalaire(MatriceLD& pscalaire) {
	/******************************************************************************/
	/*                     calcul du produit scalaire                             */
	/******************************************************************************/
	unsigned long i, a, j;

	long double dt, x, x2, z;
	long double *pcov, *pvp, *ps;
	unsigned long nbcolonnes(GetNC());
	//cerr << "MatriceLD::fscalaire(MatriceLD& pscalaire) debut " << nbcolonnes << endl;
	pvp = new long double[nbcolonnes];
	ps = new long double[nbcolonnes];
	//cerr << "MatriceLD::fscalaire(MatriceLD& pscalaire) coucou 1" << endl;
	for (i = 0; i < nbcolonnes; i++) {
		pvp[i] = 0;
		ps[i] = 0;
	}

	pscalaire.resize(nbcolonnes, nbcolonnes);
	pscalaire.SetType(2);
	//cerr << "MatriceLD::fscalaire(MatriceLD& pscalaire) coucou 2" << endl;
	pscalaire._titre = _titre;
	pscalaire._titre.push_back("produit scalaire");
	pscalaire._flag = _flag;

	if ((_flag == 2) || (_flag == 3)) {
		//copie des �tiquettes des colonnes
		pscalaire._tcol = _tcol;
		pscalaire._tlig = _tcol;
	}

	//cerr << "MatriceLD::fscalaire(MatriceLD& pscalaire) coucou 3" << endl;
	//copie du tableau
	a = nbcolonnes * nbcolonnes;
	for (i = 0; i < a; i++) {
		if (i < _t)
			pscalaire._tab[i] = _tab[i];
		else
			pscalaire._tab[i] = 0;
	}

	pcov = pscalaire._tab;

	dt = 0.;
	z = (long double) 1 / nbcolonnes;

	//cerr << "MatriceLD::fscalaire(MatriceLD& pscalaire) coucou 4" << endl;
	for (i = 0; i < nbcolonnes; i++) {
		for (j = 0; j < nbcolonnes; j++) {
			x = *(pcov + rindice(i, j));
			x2 = x * x;
			*(ps + i) = (*(ps + i)) + x2;
			dt = dt + x2;
		}
		*(ps + i) = (*(ps + i)) * z;
	}
	//cerr << "MatriceLD::fscalaire(MatriceLD& pscalaire) coucou 5 " << nbcolonnes << " " << z << endl;
	dt = dt * z * z;
	for (i = 0; i < nbcolonnes; i++) {
		//cerr << "MatriceLD::fscalaire(MatriceLD& pscalaire) coucou i " << i << endl;
		for (j = 0; ((i > 0) && (j <= (i - 1))); j++) {
			//cerr << "MatriceLD::fscalaire(MatriceLD& pscalaire) coucou j " << j << endl;
			a = rindice(i, j);
			*(pcov + a) = 0.5 * ((*(ps + i)) + (*(ps + j)) - dt - (*(pcov + a))
					* (*(pcov + a)));
			*(pcov + rindice(j, i)) = *(pcov + a);
		}
		//cerr << "MatriceLD::fscalaire(MatriceLD& pscalaire) coucou 1i " << i << endl;
		*(pcov + rindice(i, j)) = 0.5 * (2 * (*(ps + i)) - dt);
		*(pvp + i) = (*(pcov + rindice(i, i))) / z;
	}

	//cerr << "MatriceLD::fscalaire(MatriceLD& pscalaire) delete" << endl;
	delete[] pvp;
	delete[] ps;
	//cerr << "MatriceLD::fscalaire(MatriceLD& pscalaire) fin" << endl;

}

void MatriceLD::fatd(MatriceLD& pcoord, MatriceLD& pstat) {
	//pmat1, matrice de d�part: tableau de distances (matrice
	//triangulaire inf�rieure, de type 2 pour NTSYS
	//pstat: matrice contenant les statistiques sur l'importance de
	//chaque axe dans un espace � n dimensions
	//pcoord: matrice contenant les coordonn�es des OTUs (r�sultat) dans cet
	// espace � n dimensions

	MatriceLD& pmat1 = *this;
	pmat1.SetType(1);

	//cerr << "MatriceLD::fatd (MatriceLD& pcoord, MatriceLD& pstat) debut" << endl;
	if (pmat1.GetFlag() == 2)
		pmat1.ftranspose();

	// au fomat NTSys: mettre les labels sur les colonnes (2� chiffre)

	MatriceLD mscalaire; //produit scalaire
	MatriceLD mdiag;//matrice diagonalis�e

	MatriceLD mnormalisee; //matrice normalisee
	vector pvlp; //vecteurs propres

	try {
		//travail sur une matrice de distances
		if (_type != 2)
			pmat1.SetType(2);

		//cerr << "MatriceLD::fatd (MatriceLD& pcoord, MatriceLD& pstat) coucou 1" << endl;
		pmat1.fscalaire(mscalaire);

		//cerr << "MatriceLD::fatd (MatriceLD& pcoord, MatriceLD& pstat) coucou 2" << endl;

		mscalaire.fdiagonalisation(mdiag, pvlp);

		//cerr << "MatriceLD::fatd (MatriceLD& pcoord, MatriceLD& pstat) coucou 3" << endl;
	} catch (MatriceLD::Anomalie erreur) {
		cout << erreur.fmessage(erreur.le_pb);
	}

	//	mdiag.normalise(&mnormalisee, pmat1, pvlp) ;

	//coordcol redimensionne pstat et pcoord
	pmat1.fcoordcol(pstat, pcoord, mdiag, pvlp);
	//cerr << "MatriceLD::fatd (MatriceLD& pcoord, MatriceLD& pstat) fin" << endl;

}

JeuMatriceLD::JeuMatriceLD(istream& entree) {
	// Lecture de fichiers contenant plusieurs matrices
	iFlux(entree);
}

// Lecture de fichiers contenant plusieurs matrices
void JeuMatriceLD::iFluxXML(istream& entree) {

}

void JeuMatriceLD::iFlux(istream& entree) {
	// Lecture de fichiers contenant plusieurs matrices

	stringstream* tampon;
	bool is_xml(false);
	//	iostream ensortie(tampon.rdbuf());
	char car;
	ChaineCar ligne;
	vector positions;
	MatriceLD* pmat;
	unsigned long i, j;

	//balayage de l'entree pour trouver les positions
	// (delimitee par //)
	entree.clear();
	entree.seekg(0);
	positions.push_back(0);
	positions.push_back(0);

	entree.get(car);
	while (entree.good()) {
		if ((car == '/') && (entree.peek() == '/')) {
			positions.back() = entree.tellg();
			positions.back() -= 2;

			//cerr <<"coucou";
			GetLigneFlot(entree, ligne);
			positions.push_back(entree.tellg());

			positions.push_back(entree.tellg());
		} else {
			GetLigneFlot(entree, ligne);
			if (ligne.find("xml version=\"1.0\"", 0) > 0) {
				// c'est du ricqlèèèès !!!!!
				is_xml = true;
				break;
			}
		}
		positions.back() = entree.tellg();
		entree.get(car);
	}

	if (is_xml) {
		iFluxXML(entree);
		return;
	}
	// remplissage du buffer de matrices

	for (i = 0; i < (positions.size() - 1); i += 2) {
		if ((positions[i + 1] - positions[i]) < 6)
			continue;

		entree.clear();
		entree.seekg(positions[i]);

		_titres.push_back("");
		if (entree.peek() == '@') {
			entree.get(car);
			GetLigneFlot(entree, ligne);//_titres.back());

			//cerr << ligne;
			ligne.GetMot(1, _titres.back());
			//cerr << _titres.back();
		}

		tampon = new stringstream();
		for (j = positions[i]; j < positions[i + 1]; j++) {
			entree.get(car);
			*tampon << car;
			j = entree.tellg();

		}
		*tampon << ends;

		//cin >> car;
		//		cout << tampon->str() <> *pmat;
			_tableau.push_back(pmat);
		} catch (MatriceLD::Anomalie pb) {
			delete pmat;
			_titres.pop_back();
		}

		delete tampon;
		//		delete pmat;
		//		delete pensortie;
	}
}

void JeuMatriceLD::oFlux(ostream& sortie, int format) const {
	// Ecriture de fichiers contenant plusieurs matrices
	if (format == 5) {
		oGnumeric(sortie);
		return;
	}
	long i, taille(_tableau.size());

	for (i = 0; i < taille; i++) {
		sortie << "@" << _titres[i] << endl;
		_tableau[i]->oFormat(sortie, format);
		sortie << endl << "//" << endl;
	}

}

void JeuMatriceLD::oGnumeric(ostream& fichier) const {
	QString * p_output_xml = new QString("");
	QXmlStreamWriter xml_stream(p_output_xml);
	xml_stream.setAutoFormatting(true);
	xml_stream.writeStartDocument();
	// Ecriture de fichiers contenant plusieurs matrices
	long i, taille(_tableau.size());

	xml_stream.writeNamespace("http://www.gnumeric.org/v10.dtd", "gmr");
	xml_stream.writeNamespace("http://www.w3.org/2001/XMLSchema-instance",
			"xsi");
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Workbook");
	xml_stream.writeAttribute("http://www.w3.org/2001/XMLSchema-instance",
			"schemaLocation", "http://www.gnumeric.org/v8.xsd");

	//fichier
	//		<< ""
	//		<< endl;

	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd",
			"Attributes");
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Attribute");
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"WorkbookView::show_horizontal_scrollbar");
	//fichier << "" << endl;
	//fichier << "   " << endl;
	//fichier << "WorkbookView::show_horizontal_scrollbar"
	//		<< endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "type", "4");
	//fichier << " 4" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "value",
			"TRUE");
	//fichier << "  TRUE" << endl;
	xml_stream.writeEndElement();
	//	fichier << " " << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Attribute");
	//fichier << " " << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"WorkbookView::show_vertical_scrollbar");
	//fichier << "  WorkbookView::show_vertical_scrollbar"
	//	<< endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "type", "4");
	//fichier << "  4" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "value",
			"TRUE");
	//fichier << "  TRUE" << endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Attribute");
	//fichier << " " << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"WorkbookView::show_notebook_tabs");
	//fichier << "   WorkbookView::show_notebook_tabs"
	//		<< endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "type", "4");
	//fichier << "   4" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "value",
			"TRUE");
	//fichier << "   TRUE" << endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;

	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Attribute");
	//fichier << " " << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"WorkbookView::do_auto_completion");
	//fichier << "   WorkbookView::do_auto_completion"
	//		<< endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "type", "4");
	//fichier << "   4" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "value",
			"TRUE");
	//fichier << "   TRUE" << endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Summary");
	//fichier << " " << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Item");
	//fichier << "  " << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"biology softwares");
	//fichier << "  biology softwares" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd",
			"val-string", "http://www.pge.cnrs-gif.fr/bioinfo");
	//fichier
	//		<< "  http://www.pge.cnrs-gif.fr/bioinfo"
	//		<< endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Item");
	//fichier << " " << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "name",
			"author");
	//fichier << "   author" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd",
			"val-string", "Olivier Langella ");
	//fichier
	//		<< "   Olivier Langella, Olivier.Langella@pge.cnrs-gif.fr"
	//		<< endl;
	xml_stream.writeEndElement();
	//fichier << " " << endl;
	xml_stream.writeEndElement();
	//fichier << "" << endl;
	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd",
			"SheetNameIndex");

	//fichier << "  Matrix 1" << endl;


	//fichier << "" << endl;
	xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd", "SheetName",
			"Matrix 1");
	for (i = 0; i < taille; i++) {
		xml_stream.writeTextElement("http://www.gnumeric.org/v10.dtd",
				"SheetName", _titres[i].c_str());
		//fichier << "" << _titres[i] << ""
		//		<< endl;
	}
	xml_stream.writeEndElement();
	//fichier << " " << endl;

	xml_stream.writeStartElement("http://www.gnumeric.org/v10.dtd", "Sheets");
	//	fichier.setf(ios::scientific);

	for (i = 0; i < taille; i++) {
		QString sheetname(_titres[i].c_str());
		_tableau[i]->oGnumericSheet(xml_stream, sheetname);
	}

	fichier << "  " << endl;
	fichier << " " << endl;

	xml_stream.writeEndDocument();

	fichier << p_output_xml->toStdString();
	delete (p_output_xml);

}

void JeuMatriceLD::SetTitre(long i, const char * chaine) {

	//	if ((i < 0) || (i >= _titres.size())) throw Anomalie(1);
	//	cerr << chaine << endl;
	_titres[i].assign(chaine);
	//	cerr << "fini" << endl;
}

void JeuMatriceLD::resize(long nouvtaille) {
	//on efface:
	long i, taille(_tableau.size());

	_titres.resize(nouvtaille);

	for (i = 0; i < taille; i++)
		delete _tableau[i];

	//on r�alloue
	_tableau.resize(nouvtaille);
	for (i = 0; i < nouvtaille; i++)
		_tableau[i] = new MatriceLD;

}

} //namespace biolib {
} //namespace vecteurs {
populations-1.2.33+svn0120106.orig/src/chaineficpop.h0000644000175000017500000000463311326407630022246 0ustar  georgeskgeorgesk// 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 Library 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

//created:
//mer sep 06 14:23:39 CEST 2000 Langella 


/***************************************************************************
 chaineficpop.h  -  Objet pour faciliter la lecture de fichiers genepop/populations
 -------------------
 begin                : ven sep 06 10:25:55 CEST 2000
 copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
 email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

#ifndef CHAINEFICPOP_H
#define CHAINEFICPOP_H

#include"vecteurs.h"

//typedef biolib::vecteurs::ChaineCar ChaineCar;

class ChaineFicPop: public biolib::vecteurs::ChaineCar {
public:
	ChaineFicPop(istream & fichier);
	~ChaineFicPop();

	int get_titre(biolib::vecteurs::Titre & titres);
	int get_locus(biolib::vecteurs::Titre & locus);

	int get_lignepop();
	int get_nompop(biolib::vecteurs::ChaineCar & nompop) const;
	int get_nomind(biolib::vecteurs::ChaineCar & nomind) const;
	int get_alleles(biolib::vecteurs::Titre & alleles) const;

	long get_numeroligne() const;

	bool estunepop();
	bool estunindividu() const;
	bool findefichier() const;
	bool get_boolnompop() const;

protected:
	void ajout_locus(biolib::vecteurs::Titre & locus) const;

	bool get_ligne();
	bool estuntitre();

	int _type_fichier; //1-> genepop 2-> populations 0-> indéterminé -1 -> non reconnu
	long _numeroligne;
	bool _danspop;
	bool _findefichier;
	bool _boolnompop;

	istream & _fichier;

	string _chainetemp;
	string _nompop;
public:
	struct Anomalie {
		// 1-> fin de fichier précoce
		// 2-> Le début de pop n'est pas indiqu
		// 3-> fichier XML

		int le_pb;
		Anomalie(int i) :
			le_pb(i) {
		}
		;
	};

};

#endif

populations-1.2.33+svn0120106.orig/src/matrices.h0000644000175000017500000002475411606241313021426 0ustar  georgeskgeorgesk/***************************************************************************
 matrices.h  -  Librairie d'objets pour manipuler des matrices
 -------------------
 begin                : ven aug 14 10:25:55 CEST 2000
 copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
 email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

// Objets permettant de manipuler des matrices
// Olivier Langella le 11/3/98
// langella@pge.cnrs-gif.fr

//#include "vecteurs.h"

// les matrices
#ifndef MATRICES_H
#define MATRICES_H

//#define WITHOUT_EXPAT
//#ifndef WITHOUT_EXPAT
//#include "expat.h"
//#endif

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
//#include 
#include "vecteurs.h"

namespace biolib {
namespace vecteurs {

class MatriceLD;
// les matrices
class Matrice {
public:
	Matrice();
	Matrice(unsigned long nl, unsigned long nc = 0);
	Matrice(const Matrice&); //constructeur de copie
	//Matrice(const MatriceLD& lamatrice):Matrice(lamatrice) {}; //constructeur de copie
	//Matrice(const MatriceF& lamatrice):Matrice(lamatrice) {}; //constructeur de copie
	virtual ~Matrice() {
		if (_tab != 0)
			delete[] _tab;
	}

	virtual long double& GetCase(const ChaineCar& nomLig, const ChaineCar& nomCol) const {
		long ni(_tlig.Position(nomLig));
		long nj(_tcol.Position(nomCol));
		//cerr << nomLig << "GetCase ni " << ni;
		//cerr << nomCol << "GetCase nj " << nj;
		if ((ni < 0) || (nj < 0))
			throw Anomalie(7);
		return (GetCase(ni, nj));
	}

	virtual long double& GetCase(unsigned long i, unsigned long j) const {
		if ((i >= _nl) || (j >= _nc))
			throw Anomalie(7);
		//renvoie la valeur de la case i (ligne), j (colonne)
		long swap;
		if ((_type == 3) && (j > i)) {
			swap = i;
			i = j;
			j = swap;
		}
		return (_tab[(i * _nc) + j]);
	}

	virtual void SetFlag(int i) {
		_flag = i;
	}
	//etiquettes sur lignes ou colonnes


	long GetNC() const {
		return (_nc);
	}

	long GetNL() const {
		return (_nl);
	}

	int GetType() const {
		return (_type);
	}

	int GetFlag() const {
		return (_flag);
	}

	virtual long double get_ppvaleur() const; //recherche la plus petite valeur

	virtual bool SetType(int type); //type de matrice:
	//1 -> rectangulaire
	//3 -> triangulaire
	virtual void resize(unsigned long nblig, unsigned long nbcol); //efface et réalloue de la mémoire
	virtual void SupprCol(unsigned long); //efface et réalloue de la mémoire
	virtual void SupprLig(unsigned long); //efface et réalloue de la mémoire
	virtual bool redim(unsigned long, unsigned long); //redimensionne la matrice

	void ftranspose();
	virtual void f_neg2zero();
	void fscol(vector & somme) const; //somme des colonnes
	void fslig(vector & somme) const; //somme des colonnes
	void fswapcol(long i, long j);
	long double fdet() const;
	long double ftrace() const;

	inline void fmultiplier(const Matrice& matA, const Matrice& matB);

	Titre _titre;

	Titre _tcol;
	Titre _tlig;

	virtual void iFichier(istream& ientree);
	void iFichier(istream & entree, int i) {
		//cerr << "coucou " << i << endl;

		switch (i) {
		case 1:
			iExcel(entree);
			return;
			break;
		case 2:
			iNtsys(entree);
			return;
			break;
		case 4:
			iPhylip(entree);
			return;
			break;
		case 5:
			iGnumeric(entree);
			return;
			break;
		default:
			return;
		}
	}

	virtual void oFormat(ostream & sortie, int i) {
		switch (i) {
		case 1:
			oExcel(sortie);
			break;
		case 2:
			oNtsys(sortie);
			break;
		case 3:
			//	oXgobi(sortie);
			throw Anomalie(6);
			break;
		case 4:
			oPhylip(sortie);
			//	throw Anomalie(6);
			break;
		case 5:
			oGnumeric(sortie);
			//	throw Anomalie(6);
			break;
		default:
			break;
		}

	}

	//1= Excel
	//2= Ntsys
	//3= xgobi  ==!!!! seulement en ofstream !!!!!

	virtual void ofFormat(ofstream & sortie, int i = 1) {
		if (i == 3) {
			string fichier("xgobi");
			oXgobi(fichier);
		} else {
			oFormat(sortie, i);
		}
	}

	virtual void ofFormat(ofstream & sortie, int i, const string &fichier) {
		if (i == 3) {
			oXgobi(fichier);
		} else {
			oFormat(sortie, i);
		}
	}

	virtual void iNtsys(istream & entree);
	virtual void iExcel(istream & entree);
	virtual void iGnumeric(istream & entree);
	virtual void iPhylip(istream & entree);
	void oNtsys(ostream & sortie);
	void oExcel(ostream & sortie);
	void oGnumeric(ostream & sortie);
	void
			oGnumericSheet(QXmlStreamWriter& xml_stream,
					const QString & sheetname) const;
	void oPhylip(ostream& sortie);
	void oXgobi(const string&);

	virtual const Matrice& operator=(const Matrice &rval);
	const Matrice& operator=(vector &rval);
	Matrice operator*(Matrice &rval) const;
	vector operator*(const vector &rval);
	Matrice operator*(long double scalaire);
	Matrice operator-(Matrice &rval);
	Matrice operator+(Matrice &rval);
	Matrice operator+(long double rval);

protected:

	long double fdetrec() const;

	long rindice(long ligne, long colonne) {
		//if (_type == 3) if (colonne > ligne) return((colonne * _nc) + ligne);
		return ((ligne * GetNC()) + colonne);
	}

	unsigned long _t; //taille (_nc * _nl)
	unsigned long _nc; //nb de colonnes (i)
	unsigned long _nl; //nb de lignes (j)
	unsigned int _type; //type de matrice
	int _miss; //missing value
	unsigned int _flag; //étiquettes
	//1=> titres des lignes 2=> titres des colonnes
	//3=> les 2 //0=> rien

public:

	long double* _tab; // matrice
	//formats de fichiers
	unsigned int _oformat; //1-> Excel 2->NTsys 3->xgobi (UNIX) 4->phylip

	struct Anomalie {
		Anomalie(int i) :
			le_pb(i) {
		}

		// 1-> erreur pendant lecture de fichier
		// 2-> erreur dans mdiaggl
		// 3-> opération impossible sur ce type de matrice
		// 4-> calcul impossible
		// 5-> Echec de la conversion de la matrice en matrice symétrique

		// 6-> erreur pendant l'écriture du fichier
		// 7-> acces hors bornes dans la matrice
		int le_pb;
		string _message;

		string& fmessage(int num) {
			switch (num) {
			case 1:
				_message = "Erreur pendant la lecture du fichier...";
				break;
			case 2:
				_message = "Cette matrice ne peut être diagonalisée";
				break;
			case 3:
				_message = "Opération impossible sur ce type de matrice";
				break;
			case 4:
				_message = "Calcul impossible";
				break;
			case 5:
				_message
						= "Echec de la conversion de la matrice en matrice symétrique";
				break;
			case 6:
				_message = "Erreur pendant l'ecriture du fichier";
				break;
			case 7:
				_message = "Acces hors bornes dans la matrice";
				break;

			default:
				_message = "";
				break;
			}
			return (_message);
		}
	};

};

// les matrices
class MatriceLD: public Matrice {
public:
	MatriceLD();
	MatriceLD(long nl, long nc = 0) :
		Matrice (nl, nc) {
	}

	MatriceLD(const MatriceLD& lamatrice) :
		Matrice (lamatrice) {
	}
	//constructeur de copie
	MatriceLD(const Matrice& lamatrice) :
		Matrice (lamatrice) {
	}
	//constructeur de copie
	virtual ~MatriceLD() {
	}

	void fatd(MatriceLD&, MatriceLD&);
	void fscalaire(MatriceLD& pscalaire);
	void fdiagonalisation(MatriceLD &, vector &);
	void fmdiagql(int m, long double *ps, vector & pvlp);
	int ftridiag(long double *ps, vector & pvlp);
	void fcoordcol(MatriceLD& stat, MatriceLD& res, MatriceLD& norm, vector<
			long double> & pvlp);
	/*

	 void folicovariance(MatriceLD& pcov, bool facteur=false); //ya un truc
	 void fcovariance(MatriceLD& pcov); //ya un truc
	 // pourquoi on n eprend qu'une partie de l'originale ?
	 void fnormalise(MatriceLD & ,MatriceLD & , vector &) const;
	 void ftrivectshell(int, int, vector & pvlp);
	 void fprojection(MatriceLD& mccord,MatriceLD& mstat,MatriceLD& vectpropres,  vector & pvlp) const;

	 void fafc (MatriceLD&, MatriceLD&);
	 void foliafc (MatriceLD&, MatriceLD&, long double precision=0.000001);
	 void foliatd (MatriceLD&, MatriceLD&, long double precision=0.000001);
	 void facp (MatriceLD&, MatriceLD&, long double precision=0.000001);
	 void fvalpropres (MatriceLD&, vector &, long double precision=0.000001);

	 */

	void finv(MatriceLD& resultat) const;

	void fvalpropres(MatriceLD&, vector &, float precision =
			0.000001);

};

// les tableaux de matrices
class JeuMatriceLD {
public:

	JeuMatriceLD(istream& entree);
	JeuMatriceLD() {
	}

	//	JeuMatriceLD(deque, Titre &, ) {};
	~JeuMatriceLD() {
		long i, t(_tableau.size());
		for (i = 0; i < t; i++)
			delete _tableau[i];
	}

	MatriceLD& GetMatrice(long i) {
		return *(_tableau[i]);
	}
	const MatriceLD& GetConstMatrice(long i) const {
		return *(_tableau[i]);
	}
	MatriceLD& GetMatrice(ChaineCar chaine) {
		long i(_titres.Position(chaine));
		if (i < 0)
			throw Anomalie(1);
		return GetMatrice(i);
	}
	MatriceLD& back() {
		return *(_tableau.back());
	}

	void iFlux(istream& entree);

	void oFlux(ostream& sortie, int format = 1) const;

	void push_back(MatriceLD* Pmatrice, const string titre) {
		_titres.push_back(titre);
		_tableau.push_back(Pmatrice);
	}

	void SetTitre(long i, const char * chaine);
	void resize(long i);
	long size() const {
		return (_tableau.size());
	}

private:
	void iFluxXML(istream& entree);
	void oGnumeric(ostream& sortie) const;

	vector _tableau;
	Titre _titres;

public:
	struct Anomalie {
		Anomalie(int i) :
			le_pb(i) {
		}

		// 1-> Matrice introuvable
		int le_pb;
		string _message;

		string& fmessage(int num) {
			switch (num) {
			case 1:
				_message = "Matrice introuvable...";
				break;

			default:
				_message = "";
				break;
			}
			return (_message);
		}
	};

};

ostream& operator<<(ostream& sortie, Matrice& lamatrice);

//ofstream& operator<<(ofstream& sortie,MatriceLD& lamatrice);
ofstream& operator<<(ofstream& sortie, Matrice& lamatrice);

istringstream& operator>>(istringstream& ientree,
		Matrice& lamatrice);

} //namespace biolib {
} //namespace vecteurs {

#endif

populations-1.2.33+svn0120106.orig/src/arbre.h0000644000175000017500000002444711606241313020711 0ustar  georgeskgeorgesk/***************************************************************************
                          arbre.h  -  description
                             -------------------
    begin                : Mon Dec 18 2000
    copyright            : (C) 2000 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/


//modifications le 2/1/2001
//modifications le 4/6/2001

#ifndef ARBRE_H
#define ARBRE_H

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 

#include "internat.h"
#include "matrices.h"
//#define _(String) gettext (String)
#   ifndef _
#    define _(String) gettext (String)
#   endif

namespace biolib {
namespace arbres {


using namespace std;
using namespace biolib::vecteurs;

template 
struct moins
{
  bool operator()(const _Tp& x, const _Tp& y) const { return *x < *y; }
};

class ArbreVectUINT:public vector  {
public:
	void f_tri();

	bool Existe (unsigned int element) const {
//cerr << "ArbreVectUINT::Existe "  << endl;
//affiche();
			unsigned int i;
			for (i= 0 ; i < size(); i++) {
//cerr << "ArbreVectUINT::Existe i " << i << endl;
				if (operator[](i) == element) return(true);
			}

			return (false);
		};

	void affiche() const;

	bool operator== (const ArbreVectUINT &rval);

private:
	void f_trishell(unsigned int n,unsigned int j);
	void f_tribulle();
};

class Arbre;
class ArbreNdNoeud;
class ArbreNdOTU;

class ArbreNdBase {
public:
	ArbreNdBase(Arbre * Parbre);
	ArbreNdBase(const ArbreNdBase &) {};
	virtual ~ArbreNdBase();

	virtual void set_longueur(unsigned int pos, float taille);
//	virtual void set_longueur(float longueur) {};

	virtual void set_longueur(ArbreNdBase * Pnoeudbase, float taille);
	virtual void oPhylipRec(ostream & fichier) const;//écriture d'arbres au format Phylip
	virtual void oXML(ostream & fichier) const {};//écriture d'arbres au format XML
	virtual ArbreNdBase * get_Pracine() const;
	virtual ArbreNdBase * get_Pnoeud(unsigned int i) const {return(_tabPNoeuds[i]);};
	virtual unsigned int get_nbbranches() const;
	virtual double get_longueur_branche() const;
	virtual double get_tabLgBranches(unsigned int i) const;
	virtual bool est_racine() const ;
	virtual void set_nom(const string & nom);
	virtual void f_chgt_sens(ArbreNdNoeud * Pancracine, ArbreNdNoeud * Pnvsens);
	virtual int get_posnoeuds(ArbreNdNoeud * Pnoeud) const;

	void set_Pnoeud(unsigned int pos, ArbreNdBase * Pnoeud);

	virtual void fCalcValBootstrap(unsigned int total_bootstrap) {return;};
	virtual double get_longueur_max()const {return(0);} ;
	virtual unsigned int get_nbnoeuds_max()const {return(0);} ;

	virtual ArbreVectUINT* f_load_id_ind() {return (0);};

//interface pour PointPlotArbreBase
protected:

	Arbre * _Parbre;
	vector _tabPNoeuds;
	vector _tabLgBranches;
};


class ArbreNdOTU: public ArbreNdBase {
public:
	ArbreNdOTU(Arbre * Parbre, ArbreNdNoeud * Pnoeud);
	ArbreNdOTU(Arbre * Parbre, const string & nom);
	ArbreNdOTU(const ArbreNdOTU & original):ArbreNdBase(original) {};
	virtual ~ArbreNdOTU();

	void set_nom(const string & nom);
//	void set_nom(const char * nom){_nom.assign(nom);};

//	void set_longueur(float longueur){ArbreNdBase::set_longueur((unsigned int) 0,longueur);};

	void set_reference(const string & ref) {strcpy(_reference, ref.c_str());};
	void set_reference(const char * ref){strcpy(_reference, ref);};
	const char * get_reference() const {return (_reference);};

	void set_id(unsigned int id) { _id = id;};
	const string & get_nom() const {return(_nom);};

	inline bool operator== (const ArbreNdOTU &rval){return (_nom == rval._nom);};
	virtual void oPhylipRec(ostream & fichier) const;//écriture d'arbres au format Phylip
	virtual void oXML(ostream & fichier) const;//écriture d'arbres au format XML
	virtual double get_longueur_max()const;
	virtual unsigned int get_nbnoeuds_max()const;
	unsigned int get_id() const {return(_id);};

	virtual ArbreVectUINT* f_load_id_ind();

	inline bool operator< (const ArbreNdOTU &rval){return (strcmp(_reference, rval._reference) < 0);};

private:

//	char _nomchar[50];
	char _reference[50];
	string _nom;

	unsigned int _id;
};


class ArbreNdNoeud: public ArbreNdBase {
public:
	ArbreNdNoeud(Arbre * Parbre, ArbreNdNoeud * Pnoeud=0);
	ArbreNdNoeud(const ArbreNdNoeud & original):ArbreNdBase(original) {};
	ArbreNdNoeud(Arbre * Parbre, unsigned int nbbranches);
	virtual ~ArbreNdNoeud();
	inline bool operator== (const ArbreNdNoeud &rval);

	void AjouterFils(ArbreNdBase * Pnoeud);
	void AjBootstrap();

	double get_val_bootstrap() const;
	void set_force(float force);
	void set_longueur(unsigned int pos, float taille);
	void set_racine(bool oui) {_racine = oui;};
	virtual void oPhylipRec(ostream & fichier) const;//écriture d'arbres au format Phylip
  virtual void oXML(ostream & fichier) const;
	virtual ArbreNdBase * get_Pracine() const;
	virtual unsigned int get_nbbranches() const;
	virtual bool est_racine() const;
	virtual bool ExisteBranche(const ArbreVectUINT & tabInd) const;

	void f_chgt_racine(ArbreNdNoeud * Pracine);
	void f_load_vectind();

	virtual ArbreVectUINT* f_load_id_ind();

	void fCalcValBootstrap(unsigned int total_bootstrap);
	virtual double get_longueur_max() const;
	virtual unsigned int get_nbnoeuds_max()const;

protected:
	void f_chgt_sens(ArbreNdNoeud * Pancracine, ArbreNdNoeud * Pnvsens);

	bool _racine;
	int _force;
//	vector _tabPPind;
	vector _tabP_tab_id_ind;
	unsigned int _accuvalboot;
};

class Arbre {
public:
	Arbre();
//	Arbre(unsigned int nbessais , unsigned int nbind, unsigned int * Ptemp, char * * PPotu);
	Arbre(const Arbre &) {};
	
	virtual ~Arbre();

	virtual ArbreNdOTU * new_ArbreNdOTU(const string & nom);
	virtual ArbreNdOTU * new_ArbreNdOTU(ArbreNdNoeud * PArbreNdNoeudere);
	virtual ArbreNdNoeud * new_ArbreNdNoeud(unsigned int nbbranches);
	virtual ArbreNdNoeud * new_ArbreNdNoeud(ArbreNdNoeud * PArbreNdNoeudere=0);

	void AjBootstrap(Arbre &);

	virtual void iFichier(istream &);

	void iPhylip(istream &);//lecture d'arbres au format Phylip
	void iNimbus(unsigned int nbessais , unsigned int nbind, unsigned int * Ptemp, char * * PPotu);

	void iDistances(MatriceLD &, int);
	void iDistances(MatriceLD & matrice);
	void f_forceiDistances(MatriceLD & distancesRef,int methodeArbre);

	void oFichier(ostream & fichier, unsigned int format=0) const;
//	void iMega(istream &);//lecture d'arbres au format Mega
	void set_Pracine(ArbreNdNoeud * Pracine);

	void f_test();
	void SquizNoeud(ArbreNdNoeud * Pndaeffacer);

	int PositionInd(const char *) const;

	virtual void f_load_vect_id_ind();

	void reset();
	void fCalcValBootstrap();
	bool get_oui_bootstrap() const {return(_oui_bootstrap);};
	bool get_oui_taille_branches() const {return(_oui_taille_branches);};
	void set_oformat(unsigned int nbformat=1) {_oFormat = nbformat;};
	unsigned int get_nbind() const {return(_tabPind.size());};
	void f_tri_ind_alpha();

	void operator>>(ostream& sortie);

	Titre _titre;

protected:
	ArbreNdNoeud * RechercheNoeud(const ArbreVectUINT &) const;
	const ArbreNdOTU * RecherchePOTU(unsigned int id) const;

	void iNeighborJoining(Matrice & distances);
	void iNeighborJoiningTopo(Matrice & distances);
	void iUPGMA(Matrice & distances);

	float iPhylipRecGetTaille(istream & fichier);
	float iPhylipRecGetForce(istream & fichier);
	void i_PhylipRecGetNom(istream & fichier, char *);
	void iPhylipRec(istream & fichier, ArbreNdNoeud * Pnoeud=0 );//lecture d'arbres au format Phylip
	virtual void iPhylipDefGroupe(const string &) {}; //définition d'un groupe
	void oPhylip(ostream &) const;//écriture d'arbres au format Phylip
  void oXML(ostream & fichier) const;
	virtual void oPhylipEcritGroupes(ostream &) const {};

	void iNimbusRec(ArbreNdNoeud * Pnoeud, MatriceLD & tab_nimbus, unsigned int numessai, unsigned int deb, unsigned int fin, unsigned int longueur=0);
//	void iPhylipRecPasser(istream & fichier);
	void f_trishell_ind_alpha(unsigned int lb, unsigned int ub);
	void f_tribulle_ind_alpha();//	void f_tri_ind_alpha();

	ArbreNdNoeud * _Pracine;
	vector _tabPnoeuds;
	vector _tabPind;

	bool _oui_taille_branches;
	bool _oui_bootstrap;
	bool _ind_charge;
	unsigned int _cumulbootstrap;
	unsigned int _oFormat; //format de sortie (1 = phylip/newick)

public:
	struct Anomalie{
		Anomalie (int i):le_pb(i){};

		// 1-> Echec de RechercheNoeud
		int le_pb;
		string _message;

		string& fmessage(int num){
			switch (num) {
			case 1:
				_message = _("Error n°1 in Arbre: leaf not found");
				break;
			case 100:
				_message = _("Error reading treefile");
				break;
				
			default:
				_message = _("Error in Arbre");
				break;
			}
			return(_message);
		}
	};

};


inline bool ArbreNdNoeud::operator== (const ArbreNdNoeud &rval) {
	//=>remplir les vecteurs avant
//cerr << "ArbreNdNoeud::operator==" << endl;		
	unsigned int taille(_tabP_tab_id_ind.size());
	if (taille != rval._tabP_tab_id_ind.size()) return (false);
	if (taille == 0) cerr << "ArbreNdNoeud::operator== vide" << endl;
	if (taille == 1) return (*_tabP_tab_id_ind[0] == *rval._tabP_tab_id_ind[0]);

	unsigned int i,j;
	
	bool ok;

//	bool * tab_dejatrouve;
//	tab_dejatrouve = new bool[taille];
 // for (i = 0; i < taille; i++) tab_dejatrouve[i] = false;

	for (i=0; i < (taille - 1); i++) {
		ok = false;
		for (j=0; ((ok == false) && (j < taille)); j++)
//			if (!tab_dejatrouve[j])
			ok = (*_tabP_tab_id_ind[i] == *rval._tabP_tab_id_ind[j]);
//				if (ok = (*_tabPPind[i] == *rval._tabPPind[j])) tab_dejatrouve[j] = true;
//if (ok) cerr << "ArbreNdNoeud::operator== ok " << this << endl;		
		
		if (!ok) return (false);
	}
//	delete tab_dejatrouve;

	return(true);	
}

}//namespace arbres
}//namespace biolib
#endif


populations-1.2.33+svn0120106.orig/src/fstat.h0000644000175000017500000000364610531115342020733 0ustar  georgeskgeorgesk/***************************************************************************
                          fstat.h  -  bibliotheque permettant de calculer et de
																		présenter les indices de Wright
                             -------------------
    begin                : Wed Oct 11 2000
    copyright            : (C) 2000 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#ifndef FSTAT_H
#define FSTAT_H

#include"jeupop.h"
#include"metapop.h"

// calculs et affichage de Fstat
class Fstat {
public :
	Fstat(MetaPop * Pmetapop);
	~Fstat();

	void f_affparlocus (ostream & sortie) const;
	//void f_calcFstFisFit (MatriceLD & matrice) const {f_calcFstFisFit (matrice, _Pmetapop);};
	void f_calcFstFisFit (JeuMatriceLD & matrices) const;

	void f_rempliVcalcStrucPop (unsigned int niveau) {
		_Pjeupop->f_rempliVcalcStrucPop(niveau);

		_tabPstrucpop = _Pjeupop->_VcalcStrucPop;
	}

private :
	void f_calcFstFisFit (MatriceLD & matrice, const MetaPop * Pmetapop) const;
	void f_calcFstFisFit (JeuMatriceLD & matrices, const MetaPop * Pmetapop) const;
	
	MetaPop * _Pmetapop;
	Jeupop * _Pjeupop;

	vector _tabPstrucpop;

public:

	struct Anomalie{

		int le_pb;
		Anomalie (int i):le_pb(i){};
	};


};
#endif

populations-1.2.33+svn0120106.orig/src/Makefile.am0000644000175000017500000000131610531115342021465 0ustar  georgeskgeorgeskbin_PROGRAMS = populations
populations_SOURCES = populations.cpp applications.cpp applpopulations.cpp \
	arbreplus.cpp arbre.cpp couleur.cpp fstat.cpp jeupop.cpp allele.cpp individu.cpp \
	strucpop.cpp metapop.cpp locus.cpp population.cpp chaineficpop.cpp applpop.cpp \
	jeupopexp.cpp distgnt.cpp matrices.cpp vecteurs.cpp

# set the include path found by configure
INCLUDES= $(all_includes)

# the library search path.
populations_LDFLAGS = $(all_libraries) 
noinst_HEADERS = applpopulations.h internat.h matrices.h vecteurs.h arbreplus.h \
	arbre.h couleur.h fstat.h jeupop.h allele.h individu.h strucpop.h metapop.h \
	metapop.h locus.h population.h chaineficpop.h applpop.h jeupopexp.h distgnt.h \
	applications.h
populations-1.2.33+svn0120106.orig/src/applpop.h0000644000175000017500000000410110531115342021250 0ustar  georgeskgeorgesk/***************************************************************************
                          applpop.h  -  Application dérivée de l'objet ApplPop
                          						spécifique aux populations
                             -------------------
    begin                : ven aug 14 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#ifndef APPLPOP_H
#define APPLPOP_H

#include "jeupopexp.h"
#include "jeupop.h"
#include "arbreplus.h"
#include "distgnt.h"

//#include "matrices.h"
#include "applications.h"

typedef biolib::arbres::ArbrePlus ArbrePlus;

class ApplPop:public Application {
public:

	ApplPop();
	~ApplPop();
  /** Demande à l'utilisateur de choisir une population.
retourne le numéro dans _tabPpop */
  unsigned long DemandePopulation(char []) const;

	void set_groupes_individus();
	void set_groupes_populations();
	void set_groupes_arbre(ArbrePlus & larbre) const;
	void reset_groupes() {_temp.resize(0);_tab_groupes.resize(0);_tab_noms_groupes.resize(0);_tab_couleurs_groupes.resize(0);};
	
protected:
	
	virtual bool litGenepop();

	virtual void affPubEntree() const;
	virtual bool iPopulations();

	Jeupop* _Pjeupop;
	vector _tab_groupes;
	vector _tab_noms_groupes;
	vector _tab_couleurs_groupes;

	unsigned int _niveau;

	Titre _temp;

};

#endif

populations-1.2.33+svn0120106.orig/src/allele.h0000644000175000017500000000551210531115342021042 0ustar  georgeskgeorgesk/***************************************************************************
                          allele.h  -  description
                             -------------------
    begin                : Thu Sep 14 2000
    copyright            : (C) 2000 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#ifndef ALLELE_H
#define ALLELE_H

//#include "arbres.h"
#include "vecteurs.h"

using namespace std;

class Individu;
class Population;
class Allele;
class StrucPop;
class Locus;
class Jeupop;
class ConstGnt;

typedef biolib::vecteurs::ChaineCar ChaineCar;
//allèle
class Allele {
public :
//	Allele();
	Allele(Locus*);
//	Allele(Locus*, const Allele &);
	Allele(const Allele &, Locus * Ploc);//constructeur de sopies
	Allele(Locus*, const char *);
	Allele(Locus*, const string &);
	~Allele();
	bool f_verifnum(int) const;

//	string& get_NomLocus();
	const string& get_Nom() const {return(_nom);};
	Locus * get_Ploc() const {return(_Ploc);};
	const string& get_nom() const {return(_nom);};
	const string& get_NomLocus() const;
	const unsigned int get_nbrepet() const{return(_nbrepet);};
	void set_nbrepet(unsigned int nbrepet) {_nbrepet = nbrepet;};

	void set_Plocus(Locus * Ploc) {_Ploc = Ploc;};
	void set_nom(const char * mot) {_nom = mot;};
	void set_nom(const ChaineCar& mot) {_nom = mot;};
	void set_idXML(const string& id) {_idXML = id;};

	const string& get_idXML() const {return(_idXML);};

  bool r_estnul() const {return(_miss);};
	bool r_nonnul() const {return(!_miss);};

	const Allele& operator= (const Allele &);
	bool operator== (const Allele & rval) const;

	friend class Locus;
	friend class Individu;
	friend class StrucPop;
	friend class Jeupop;
	friend class DistancesGnt;

private :
//	int _occurence; //nb d'occurences de cet allèle dans le jeu de populations
	bool r_ismissingvalue(const string &) const;
	string _nom;
//	char _nomgpop[4];
	Locus * _Ploc;
	bool _miss; //missing value
	unsigned int _nbrepet; //specifique aux microsatellite: nombre de repetitions de motifs
//	int _nbind; //nb d'individus pourvus de cet allèle
//	Individu ** _tabPind;
  string _idXML; //sert à la lecture et à l'écriture en XML

};

#endif
populations-1.2.33+svn0120106.orig/src/arbreplus.cpp0000644000175000017500000001304110531115342022132 0ustar  georgeskgeorgesk/***************************************************************************
                          arbreplus.cpp  -  description
                             -------------------
    begin                : Mon Jun 4 2001
    copyright            : (C) 2001 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#include "arbreplus.h"

namespace biolib {
namespace arbres {

ArbrePlGroupes::ArbrePlGroupes(const ArbrePlus * Parbre): _Parbre(Parbre) {
}
ArbrePlGroupes::~ArbrePlGroupes(){	
//	while (size() > 0) delete back();
}

ArbrePlus::ArbrePlus(): _tabGroupes(this), _couleur_neutre(0,0,0){
}
ArbrePlus::~ArbrePlus(){
}


void ArbrePlGroupes::push_back_groupe(const string & nom, const string & couleur) {
//	push_back(new ArbreVectUINT());
	ArbreVectUINT nouveau;

	push_back(nouveau);

	_tabNom.push_back(nom);
	_tabCouleur.push_back(Couleur(couleur));

}

int ArbrePlGroupes::RechercheGroupeOTU(unsigned int id) const {

	unsigned int i;

	for (i=0 ; i < size(); i++) {
		if (operator[](i).Existe(id)) return(i);
	}
	return (-1);
}


void ArbrePlus::define_outgroup(const ChaineCar & outgroup){
	unsigned int nbmots,i;
	int pos(-1);
	string mot;
	
	if (outgroup == "") return;
	nbmots = outgroup.GetNbMots();
	_Vind_outgroup.resize(0);
	for (i = 0; i < nbmots; i++) {
		outgroup.GetMot(i+1, mot);
		pos = PositionInd(mot.c_str());
		if (pos == -1) {
			cerr << "Erreur TreePlotter::define_outgroup" << endl;
			cerr << mot << _(" was  not found") << endl ;
			return;
		}
//cerr << "TreePlotter::define_outgroup pos" << pos << endl;
		_Vind_outgroup.push_back(_tabPind[pos]->get_id());
	}

	//Recherche du noeud contenant une branche avec _Vind_outgroup
	// => charger les "vecteurs d'individus" de l'arbre
//cerr << "TreePlotter::define_outgroup" << endl;
	_Vind_outgroup.f_tri();
	f_load_vect_id_ind();
//cerr << RechercheNoeud(_Vind_outgroup) << endl;
	set_Pracine(RechercheNoeud(_Vind_outgroup));
//cerr << "TreePlotter::define_outgroup fin"<< endl;
}

void ArbrePlus::ajouter_groupe(const ChaineCar & groupe, const string & couleur, const string & nom){
	unsigned int nbmots,i;
	signed int pos(-1);
	ChaineCar mot;
//cerr << "ArbrePlus::ajouter_groupe " << groupe << endl;
//	Couleur bidon("");

//	if (lacouleur == "") lacouleur.assign(bidon.get_couleur_diff());

	_tabGroupes.push_back_groupe(nom, couleur);
//cerr << "TreePlotter::define_outgroup groupes " << groupe << endl;
	
	if (groupe == "") return;
	nbmots = groupe.GetNbMots();
	_tabGroupes.back().resize(0);
	for (i = 0; i < nbmots; i++) {
		groupe.GetMot(i+1, mot);
		pos = (int) mot;
		if (((mot.EstUnChiffre()) && (pos > 0) && ((unsigned int) pos < _tabPind.size())) || (mot == "0")){
//cerr << "ArbrePlus::ajouter_groupe [" << mot << endl;
			if ((mot == "0") && (_tabPind.size() == 1)) _tabGroupes.back().push_back(0);
			else _tabGroupes.back().push_back(pos);
		}
		else {
			pos = PositionInd(mot.c_str());
//cerr << "TreePlotter::define_outgroup pos" << pos << endl;
			if (pos == -1) {
				cerr << "Erreur" << endl;
				cerr << mot << _(" was  not found") << endl ;
			}
			else if ((unsigned int) pos < _tabPind.size())	_tabGroupes.back().push_back(_tabPind[pos]->get_id());
		}
	}

	//Recherche du noeud contenant une branche avec _Vind_outgroup
	// => charger les "vecteurs d'individus" de l'arbre
//cerr << "TreePlotter::define_outgroup" << endl;
	_tabGroupes.back().f_tri();
}

const Couleur & ArbrePlus::get_couleur_otu (unsigned int id) const {
	int numgroupe(_tabGroupes.RechercheGroupeOTU(id));

	if (numgroupe == -1) return(get_couleur_neutre());
	else return(_tabGroupes.get_couleur((unsigned int)numgroupe));
}

void ArbrePlus::iPhylipDefGroupe(const string & ligne) {
 //définition d'un groupe (lecture de fichier Phylip
	//#G nom couleur 'groupe'
	Titre tabArguments;
cerr << "ArbrePlus::iPhylipDefGroupe(const string & ligne)" << ligne << endl;
	tabArguments.GetArguments(ligne);
cerr << tabArguments[1] << endl;
cerr << tabArguments[2] << endl;
cerr << tabArguments[3] << endl;
	
  if (tabArguments.size() == 4) ajouter_groupe(tabArguments[3], tabArguments[2], tabArguments[1]);
	else if (tabArguments.size() == 3) ajouter_groupe(tabArguments[2], tabArguments[1], "");

}

void ArbrePlus::oPhylipEcritGroupes(ostream & fichier) const {
	//ecrit les groupes au format phylip traffiqué Olivier:
	// #G Couleur 'pop1 pop2 ...popn'
	// dans le fichier
  unsigned int i,j;
	if (_tabGroupes.size() == 0) return;

	if (_titre.size() == 0) fichier << "[";
	else fichier << "\\";

	for (i = 0; i < _tabGroupes.size(); i++) {
		fichier << "#G '" << _tabGroupes.get_nom(i) << "' '" << _tabGroupes.get_couleur(i).get_nom() << "' '";
		
		for (j=0; j < _tabGroupes[i].size(); j++) {
			fichier << _tabGroupes[i][j];
		
			if (j != (_tabGroupes[i].size()-1)) fichier << " ";	
		}
		fichier << "'";
		if (i != (_tabGroupes.size()-1)) fichier << "\\";
	}
	if (_titre.size() == 0) fichier << "]" << endl;
}

} //namespace biolib {
} //namespace arbres {

populations-1.2.33+svn0120106.orig/src/applications.h0000644000175000017500000000513311017776575022316 0ustar  georgeskgeorgesk/***************************************************************************
                          applications.h  -  Librairie d'objets pour creer des applications
                             -------------------
    begin                : ven aug 14 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#ifndef APPLICATIONS_H
#define APPLICATIONS_H

//#define __ENABLE_WSTRING

#include "internat.h"

#include "matrices.h"

# ifndef COMPILATION_MINGW32
//# include "gzstream.h"
# endif

using namespace std;
using namespace biolib::vecteurs;

class Application {
public:

	Application();
	virtual ~Application() {};

	virtual void lancement(int nbcommandes=0, char ** commandes=0);
  /** test si nomfichier existe */
  virtual bool fFichierExiste(const string & nomfichier);
	
protected:
	virtual int menu_principal();
	virtual int menu_formatMatrice();
	virtual void affPubEntree() const;
	virtual void affPubSortie() const;
	virtual void fLigneCommande(char ** commandes, int nbcommandes);

	virtual bool DemandeOuiNon(char laquestion[]) const;
	virtual int DemandeEntier(const string & laquestion, int inf, int sup) const;
	virtual int DemandeEntier(char laquestion[], int inf, int sup, int defaut) const;
	virtual float DemandeReel(char laquestion[], float inf, float sup) const;
	virtual int DemandeChoix(int inf, int sup) const;
	virtual string DemandeString(char laquestion[]) const;
	virtual string DemandeFichier(const string & laquestion);
	bool litMatriceLD(MatriceLD & mat);
	bool litJeuMatriceLD(JeuMatriceLD &jeumat);
	bool ecritMatriceLD(MatriceLD & mat, string nomFichier="", int format=0);
	bool ecritJeuMatriceLD(const JeuMatriceLD & jeumat, string nomFichier="", int format=0);


	string _nomFichier;
	int _choix;
	int _formatMatrice; // 1-> Excel


	ifstream _fichier;

	ofstream _sortie;

	bool _confirmeEcraseFichier;

};

#endif

populations-1.2.33+svn0120106.orig/src/vecteurs.cpp0000644000175000017500000002506711341274043022012 0ustar  georgeskgeorgesk/***************************************************************************
 vecteurs.cpp  -  Librairie d'objets permettant de manipuler des vecteurs
 -------------------
 begin                : ven aug 14 10:25:55 CEST 2000
 copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
 email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

//#include 

//using namespace std;

#include"vecteurs.h"

namespace biolib {
namespace vecteurs {

void GetLigneFlot(istream& entree, string & ligne) {
	char car;
	ligne.assign("");
	car = entree.peek();
	while (((car != 10) & (car != 13)) & (entree.good()) & (entree.eof() == 0)) {
		entree.get(car);
		ligne += car;
		car = entree.peek();
	}
	while (((car == 10) | (car == 12) | (car == 13)) & entree.good()
			& (entree.eof() == 0)) {
		entree.get(car);
		car = entree.peek();
	}
}

void ChaineCar::GetLigneFlot(istream& entree) {
	//cerr << "ChaineCar::GetLigneFlot debut" << endl;

	char car;

	assign("");
	car = entree.peek();
	//cerr << "ChaineCar::GetLigneFlot debut " << car << endl;
	while (((car != 10) && (car != 13)) && (entree.good())) {

		entree.clear();

		entree.get(car);

		//cerr << "ChaineCar::GetLigneFlot car" << car << endl;
		assign(*this + car);
		car = entree.peek();
	}
	while (((car == 10) || (car == 13)) && (entree.good())) {
		entree.get(car);
		car = entree.peek();
	}

	//cerr << "ChaineCar::GetLigneFlot fin" << endl;
}

void ChaineCar::assigner(const string& chorigine, signed long deb,
		signed long fin) {
	//assigne seuleument une partie de la chorigine
	// de deb a fin inclus

	signed long i;

	assign("");
	if (deb < 0)
		deb = 0;

	for (i = deb; i <= fin; i++) {
		if (i >= (signed long) chorigine.size())
			break;
		*this += chorigine[i];
		//		cout << chorigine[i];
	}
	//	cout << endl;
}

bool ChaineCar::EstUnChiffre() const {
	unsigned long i;

	//cerr << "ChaineCar::EstUnChiffre()" << endl;
	for (i = 0; i < size(); i++) {
		if ((operator[](i) < 48) || (operator[](i) > 57))
			return (false);
	}

	//cerr << "ChaineCar::EstUnChiffre() vrai" << endl;
	return (true);
}

ChaineCar& ChaineCar::AjEntier(long i) {
	//conversion automatique en base 10 et concaténation
	int unite;
	long facteur;
	char chiffre;
	bool debut(false);

	if (i == 0) {
		this->string::operator+=("0");
	} else
		for (facteur = 1000000; facteur > 0; facteur = facteur / 10) {

			unite = i / facteur;

			if ((debut) || (unite > 0)) {
				debut = true;
				i = i - (unite * facteur);
				chiffre = unite + 48;
				this->string::operator+=(chiffre);
			}
		}
	return (*this);
}

long ChaineCar::GetNbMots() const {
	//retourne le nombre de mots contenus
	// dans la chaine (séparateur= ' ' ou '/t')
	long resultat(0);
	long i, taille;
	bool change(true);
	bool quote(false);

	taille = this->size();

	//cerr << "ChaineCar::GetNbMots()" << *this <<"Fin" << endl;
	for (i = 0; i < taille; i++) {
		if (this->operator[](i) == '\'')
			quote = !(quote);
		if ((quote == false) && (this->operator[](i) > 32)) {
			if (change) {
				//cerr << this->operator[](i) << endl;
				resultat++;
				change = false;
			}
		} else {
			change = true;
		}
	}

	//cerr << *this << endl;
	//cerr << "ChaineCar::GetNbMots()" << resultat << endl;
	return (resultat);
}

void ChaineCar::GetMot(unsigned int numero, string &mot) const {
	//retourne le numeroième mot contenu
	// dans la chaine (séparateur= ' ' ou '/t')
	if (numero < 1) {
		mot = "";
		return;
	}

	unsigned int resultat(0);
	unsigned int i, taille, debut(0), fin(0);
	bool change(true);
	bool quote(false);

	taille = this->size();

	//cerr << "mot:" << *this <<"Fin" << endl;
	for (i = 0; i < taille; i++) {
		//cerr << this->operator[](i) << endl;
		if (this->operator[](i) == '\'') {
			if ((resultat == numero) && (quote)) {
				fin = (i - 1);
				break;
			}
			quote = !(quote);
			if ((resultat == numero) && (quote)) {
				debut = (i + 1);
				//			break;
			}
		}
		if ((quote) || (this->operator[](i) > 32)) {
			//caractere normal
			if (change) {
				change = false;
				resultat++;
				debut = i;
				if (quote)
					debut++;
			}
			fin = i;
		} else {
			if (resultat == numero)
				break;
			change = true;
		}
	}
	fin++;

	if (resultat != numero) {
		mot = "";
		return;
	}

	mot = substr(debut, (fin - debut));
	//cerr << "mot:" << mot <<"Fin" << endl;

}

const Titre& Titre::operator=(const Titre &rval) {
	unsigned long t(rval.size());
	unsigned long i;

	for (i = 0; i < size(); i++) {
		delete vector::operator[](i);
		//		delete at(i);
	}

	erase(begin(), end());
	reserve(t);
	for (i = 0; i < t; i++) {
		push_back(rval.GetTitre(i));
	}
	return (*this);
}

Titre::~Titre() {
	unsigned long i;

	for (i = 0; i < size(); i++) {
		delete vector::operator[](i);
		//		delete at(i);
	}
}

long Titre::Position(const ChaineCar& chaine) const {
	unsigned long i;
	signed long res(-1);

	for (i = 0; i < size(); i++) {
		if (!(chaine.compare(GetTitre(i)))) {
			//cerr << chaine << GetTitre(i) << "_" << endl;
			//		if (chaine.compare(GetTitre(i)) == 0) {
			res = i;
			break;
		}
	}

	return (res);
}
;

void Titre::GetArguments(const string & ligne) {
	//doit se comporter comme le shell
	// sépare les mots, et accepte les ' ou les "
	unsigned int i;
	bool quote(false), vide(false);

	push_back("");

	for (i = 0; i < ligne.size(); i++) {
		if ((quote == false) && ((back().size() > 0) || vide) && ((ligne[i]
				== ' ') || (ligne[i] == '\t'))) {//séparateur
			push_back("");
			vide = false;
		} else {
			if ((ligne[i] == '"') || (ligne[i] == '\'')) {
				if ((quote) && (back().size() == 0))
					vide = true;
				quote = !(quote);
			} else
				back() += ligne[i];
		}
	}
	/*
	 cerr << "Titre::GetArguments(const string & ligne)" << endl;
	 for (i=0; i < size(); i++) {
	 cerr << get_titre(i) << endl;
	 }
	 */
}

bool Titre::operator==(const Titre &rval) {
	// comparaison de deux titres
	unsigned long i;

	if (rval.size() != size())
		return (false);

	for (i = 0; i < size(); i++) {
		if (GetTitre(i).compare(rval.GetTitre(i)) != 0)
			return (false);
	}

	return (true);
}

Titre::Titre(char ** commandes, int nbcommandes) {
	long i;

	for (i = 0; i < nbcommandes; i++) {
		push_back(commandes[i]);
	}
}

/*
 Titre::Titre(const Titre& rval) {

 *this = rval;

 }
 */

void Titre::resize(long nouvtaille) {
	//on efface:
	long i, taille(size());

	for (i = 0; i < taille; i++)
		delete vector::operator[](i);

	//on réalloue
	vector::resize(nouvtaille);
	for (i = 0; i < nouvtaille; i++)
		vector::operator[](i) = new ChaineCar;

}

Titre Titre::operator+(const Titre &rval) const {
	//marche pas...
	long i, taille(rval.size());
	Titre Resultat;

	Resultat = *this;

	for (i = 0; i < taille; i++) {
		//cerr << rval.GetTitre(i);
		Resultat.push_back(rval.GetTitre(i));
	}

	return Resultat;
}

void ChaineCar::fmajus() {
	//convertit la chaine en majuscules
	// après une lecture par exemple
	int taille(size());
	int i;

	for (i = 0; i < taille; i++) {
		if ((operator[](i) > 96) && (operator[](i) < 124))
			operator[](i) = operator[](i) - 32;
	}
}

void ChaineCar::fsupprchiffres() {
	//supprime les chiffres contenu dans une chaine
	// après une lecture par exemple
	int taille(size() - 1);
	int car, i;

	for (i = taille; i >= 0; i--) {
		car = operator[](i);
		if ((car > 47) && (car < 58))
			erase(i, 1);
	}
}

void ChaineCar::fsupprgauche() {
	//supprime les espaces ou tabulations à gauche
	//	unsigned int i;
	//cerr << "ChaineCar::fsupprgauche() [" << (int) operator[](0) << "]" << *this << endl;

	//	i = 0;
	//	while (((operator[](i) == ' ')||(operator[](i) == '\t')) && (i < size())) {
	while (((operator[](0) == ' ') || (operator[](0) == '\t')) && (size() > 0)) {
		//while ((operator[](i) < 33) && (i < size())) {
		erase(0, 1);
		//		i++;
	}
	//cerr << "ChaineCar::fsupprgauche() [" << *this << endl;
}

void ChaineCar::fsupprdroite() {
	//supprime les espaces ou tabulations à droite
	signed int i;

	i = size() - 1;
	while (((operator[](i) == ' ') || (operator[](i) == '\t')) && (i >= 0)) {
		//while ((operator[](i) < 33) && (i >= 0)) {
		erase(i, 1);
		i--;
	}
}

void ChaineCar::fnettoie(const string & mot) {
	//supprime de la chaine de caractere toutes les occurences de "mot"

	int pos;

	pos = find(mot, 0);
	while (pos != -1) {
		replace(pos, mot.size(), "");
		pos = find(mot, 0);
	}
}

unsigned long ChaineCar::GetNbMots(const string & separateur) const {
	//retourne le nombre de mot separes par separateur

	long pos;
	unsigned long iteration(0);

	if (size() == 0)
		return (0);

	pos = find(separateur, 0);
	while (pos != -1) {
		pos = find(separateur, pos + 1);
		iteration++;
	}

	return (iteration + 1);
}

void ChaineCar::GetMot(unsigned int numero, string &mot,
		const string & separateur) const {
	//retourne le nieme mot separe par separateur

	signed int debut(0);
	int fin(-1);
	unsigned int iteration(1);
	int taillesep(separateur.size());
	mot.assign("");

	fin = find(separateur, 0);
	if ((fin == -1) && (numero < 2)) {
		mot.assign(*this);
		return;
	}
	if (fin == -1)
		fin = size();
	while ((debut != -1) && (iteration < numero)) {
		debut = fin + taillesep;
		//cerr << "debut " << debut << endl;
		fin = find(separateur, debut);
		if (fin == -1)
			fin = size();
		//else fin = pos;
		iteration++;
	}

	if (debut == -1)
		return;
	if (debut > (signed int) size())
		return;
	if (fin > (signed int) size())
		return;
	if (debut > fin)
		return;

	mot = substr(debut, (fin - debut));
}

ChaineCar& Titre::GetTitre(long i) const {
	return (*(vector::operator[](i)));
}

void Titre::Suppr(unsigned long pos) {
	if (pos >= size())
		throw Anomalie(1);
	delete (vector::operator[](pos));
	erase(begin() + pos);
}

/** remplacer les occurences de "couper" par "coller" */
void ChaineCar::Remplacer(const string & couper, const string & coller) {

	int pos;

	pos = find(couper, 0);
	while (pos != -1) {
		replace(pos, couper.size(), coller);
		pos = find(couper, 0);
	}
}

int ChaineCar::Position(const string & motif) const {
	return (find(motif, 0));
}

}//namespace biolib {
}//namespace vecteurs {


populations-1.2.33+svn0120106.orig/src/applpop.cpp0000644000175000017500000001660610531115342021620 0ustar  georgeskgeorgesk/***************************************************************************
                          applpop.cpp  -  Application dérivée de l'objet ApplPop
                          						spécifique aux populations
                             -------------------
    begin                : ven aug 14 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/




//#include "entetepop.h"

#include "applpop.h"

ApplPop::ApplPop ():Application(){
//cerr << _formatMatrice;
	_Pjeupop = 0;
	_niveau = 100; // niveau de structuration des populations (100 => dernier ensemble avant les individus)
}

ApplPop::~ApplPop() {
	if (_Pjeupop != 0) delete _Pjeupop;
}


/*
void ApplPop::fconcatenationpop() {
	// concatenation de jeux de populations
	Jeupop * PjeupopOriginal(_Pjeupop);

	cout << endl << "Lecture des populations a concatener :" <_commentaires[0];
//cerr << _Pjeupop->_commentaires[0];
//cerr << "concat avant" <_commentaires.size(); //<< _Pjeupop->_commentaires[1];
	}
	catch (Jeupop::Anomalie pb) {
		cout << endl << "il y a eu une erreur de type: " << pb.le_pb << endl;

		_Pjeupop = PjeupopOriginal;
	}
}
*/



bool ApplPop::litGenepop() {
	Jeupop * Poldjeupop;
	bool ok(false);

	while (_fichier.is_open() == 0) {
		cout << _("Name of input file (Populations or Genepop format) ?") << endl;
		cin >> _nomFichier;

		_fichier.open(_nomFichier.c_str(), ios::in);
		_fichier.clear();
	}

	try {
		Poldjeupop = _Pjeupop;
//cerr << "ApplPop::litgenepop " <> *(_Pjeupop);
//cerr << "ApplPop::litgenepop fin >>" < _Pjeupop->get_nbpop())) {
		cout << _("Please, choose a population among these ones:") << endl;
		for (i=0; i <  _Pjeupop->get_nbpop(); i++) cout << _Pjeupop->get_nompop(i) << " ";
		cout << endl;

		cout << endl << laquestion << endl;
		cin >> rep;
		try {
			numpop = _Pjeupop->get_numpop(_Pjeupop->get_Ppop(rep));
		}
		catch (Jeupop::Anomalie le_pb) {
			cout << _("the population ") << rep << _(" has not been found.") << endl;		
			numpop = -1;	
		}
	}
	return ((unsigned long) numpop);

}

void ApplPop::set_groupes_individus() {
	// crée des groupes d'individus par Populations
	if (_Pjeupop == 0) return;
	unsigned int nbpop, nbind, i, j;

//cerr << "ApplPop::set_groupes_individus() debut" << endl;
	Titre noms_niveaux;

	try {
//cerr << "ApplPop::set_groupes_individus() rempli" << endl;
		_Pjeupop->f_rempliVcalcStrucPop(_niveau);
//cerr << "ApplPop::set_groupes_individus() noms" << endl;
		//_Pjeupop->get_nomniveauxstruc(noms_niveaux);
	}
	catch (Jeupop::Anomalie pb) {
  	cerr << "ApplPop::set_groupes_individus() anomalie Jeupop " << pb.le_pb << endl;
	}

	nbpop = _Pjeupop->get_nbstrucpopVcalc();

	_tab_groupes.resize(nbpop);
	_tab_noms_groupes.resize(nbpop);
	_tab_couleurs_groupes.resize(nbpop);

	for (i = 0; i < nbpop; i++) {
		_tab_noms_groupes[i] = _Pjeupop->get_PstrucpopVcalc(i)->get_nom();
		_tab_couleurs_groupes[i] = _Pjeupop->get_PstrucpopVcalc(i)->get_couleur();

		nbind = _Pjeupop->get_PstrucpopVcalc(i)->get_nbind();
		_tab_groupes[i] = "";
		for (j = 0; j < nbind; j++) {
			_tab_groupes[i] += "'";
			_tab_groupes[i] += _Pjeupop->get_PstrucpopVcalc(i)->get_nomind(j);
//cerr << "ApplPop::set_groupes_individus() get_nomind" << endl;
			_tab_groupes[i] += "'";
//cerr << _tab_groupes[i] << endl;
			//_tab_couleurs_groupes[i] = Couleur::get_couleur_diff();
			if (j != (nbind -1)) _tab_groupes[i] += " ";
		
    }
	}
//cerr << "ApplPop::set_groupes_individus() fin";
	
}

void ApplPop::set_groupes_populations() {
	// crée des groupes d'individus par Populations
	if (_Pjeupop == 0) return;

	unsigned int nbstrucpop, i,j;
	reset_groupes();
	MetaPop * Pmetapop;
	Vecteur tabPmetapop;

	_Pjeupop->f_rempliVcalcStrucPop(_niveau);

	nbstrucpop = _Pjeupop->get_nbstrucpopVcalc();

	//balayage des strucpop pour voir si il n'existe pas une métastructure
	// => groupe de strucpop
	for (i = 0; i < nbstrucpop; i++) {
		if (_Pjeupop->get_PstrucpopVcalc(i)->get_niveau() < 2) {
			 //pas de metastructure
		}
		else {

			Pmetapop = _Pjeupop->get_PstrucpopVcalc(i)->get_Pmetapop();

			if (!(tabPmetapop.Existe(Pmetapop))) tabPmetapop.push_back(Pmetapop);
		}
	}
	
	_tab_groupes.resize(tabPmetapop.size());
	_tab_noms_groupes.resize(tabPmetapop.size());
	_tab_couleurs_groupes.resize(tabPmetapop.size());

	for (i = 0; i < tabPmetapop.size(); i++) {
		_tab_noms_groupes[i] = tabPmetapop[i]->get_nom();
		_tab_couleurs_groupes[i] = tabPmetapop[i]->get_couleur();

		nbstrucpop = tabPmetapop[i]->get_nbpop();
		_tab_groupes[i] = "";
		for (j = 0; j < nbstrucpop; j++) {
			_tab_groupes[i] += "'";
			_tab_groupes[i] += tabPmetapop[i]->get_nompop(j);
//cerr << "ApplPop::set_groupes_individus() get_nomind" << endl;
			_tab_groupes[i] += "'";
//cerr << _tab_groupes[i] << endl;
			//_tab_couleurs_groupes[i] = Couleur::get_couleur_diff();
			if (j != (nbstrucpop -1)) _tab_groupes[i] += " ";
		
    }

	}
	

}

void ApplPop::set_groupes_arbre(ArbrePlus & larbre) const {
//	larbre._titre = _temp;
	if (_tab_groupes.size() == 0) return;

	unsigned int i, nbgroupes(_tab_groupes.size());

	larbre.f_tri_ind_alpha();

	for (i = 0; i < nbgroupes; i ++) {
    larbre.ajouter_groupe(_tab_groupes[i], _tab_couleurs_groupes[i], _tab_noms_groupes[i]);
	}
}
populations-1.2.33+svn0120106.orig/src/CMakeLists.txt0000644000175000017500000000242511600062131022166 0ustar  georgeskgeorgesk
# this command finds Qt4 libraries and sets all required variables
# note that it's Qt4, not QT4 or qt4
#/usr/share/cmake-2.6/Modules/FindQt4.cmake
SET (QT_USE_QTXML true)
FIND_PACKAGE( Qt4 REQUIRED )

INCLUDE( ${QT_USE_FILE} )

#FIND_PACKAGE(X11 REQUIRED)
#FIND_PACKAGE(FindThreads REQUIRED)

IF(WIN32)
  ADD_DEFINITIONS(-DMINGW32)
ENDIF(WIN32)

#INCLUDE_DIRECTORIES(X11_INCLUDE_DIR)
# X11_FOUND is true if X11 is available.
#    * X11_INCLUDE_DIR contains the include directories to use X11.
#    * X11_LIBRARIES points to the libraries to link against to use X11.
# Make sure the compiler can find include files from our Hello library.
#include_directories (${X11_INCLUDE_DIR})

# -m -pthread FindThreads


# Make sure the linker can find the Hello library once it is built.
#link_directories (${X11_INCLUDE_DIR})

add_executable (populations populations.cpp distgnt.cpp jeupopexp.cpp fstat.cpp jeupop.cpp applpop.cpp applpopulations.cpp matrices.cpp applications.cpp 
arbre.cpp arbreplus.cpp couleur.cpp vecteurs.cpp locus.cpp allele.cpp individu.cpp strucpop.cpp chaineficpop.cpp metapop.cpp population.cpp) 


IF(WIN32)
	target_link_libraries (populations ${QT_LIBRARIES})
ELSE(WIN32)
	target_link_libraries (populations ${QT_LIBRARIES} m)
ENDIF(WIN32)

 populations-1.2.33+svn0120106.orig/src/applpopulations.h0000644000175000017500000000613111326563351023046 0ustar  georgeskgeorgesk/***************************************************************************
 applpopulations.h  -  description
 -------------------
 begin                : Mon Oct 30 2000
 copyright            : (C) 2000 by Olivier Langella
 email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#ifndef APPLPOPULATIONS_H
#define APPLPOPULATIONS_H

#include "config.h"
#define version_populations POPULATIONS_VERSION

#include "arbreplus.h"
#include "fstat.h"
#include "applpop.h"
# ifndef COMPILATION_MINGW32
//# include "olivxml.h"
# endif

//#include "distgnt.h"
/**Objet sp�cifique � l'application "Populations"
 *@author Olivier Langella
 */
typedef biolib::arbres::ArbrePlus ArbrePlus;
typedef biolib::vecteurs::ChaineCar ChaineCar;
//typedef biolib::arbres::Arbre Arbre;

class ApplPopulations: public ApplPop {
public:
	ApplPopulations();
	~ApplPopulations();

	void affPubEntree() const;
	/**  */
	void affVlocus(const Vecteur &) const;
	/** Demande le nom ou le numero d'un locus */
	int DemandeLocus(const char laquestion[] = 0) const;

private:

	int menu_principal();
	void menu_formats();
	int menu_metdistpop();
	//	int menu_metdistind();
	int menu_metconstructarbre();
	void menu_popstructurees();
	void menu_arbrepop();
	void menu_arbreind();
	void menu_calculs();
	/** Choix de locus */
	Vecteur menu_choixlocus() const;

	//traitement en ligne de commande:
	void fLigneCommande(char ** commandes, int nbcommandes);
	void fLiPhylogeny(Titre & tab_commandes);
	void fLiHelp() const;
	void fLiTest(Titre & tab_commandes);

	void fconstructarbre(MatriceLD &distances, string & nomficarbre,
			int methodearbre);
	void fmat2arbre();
	bool fcompdistind(MatriceLD &distances, int metdist = 0);
	void fdistind();
	void ftreeind();
	void ftreeindBootLocus();
	bool fcompdistpop(MatriceLD &distances, int metdist = 0);
	void fdistpop();
	void ftreepop();
	void ftreepopBootLocus();
	void ftreepopBootInd();
	void fintrogresse();
	void frarefaction();
	void fsetniveau();
	void fmicrosatcorrections();

private:

	void ecritGenepop();
	void ecritGenepopCano();
	void ecritPopulations();
	void ecritImmanc();
	void ecritMsat(int);
	void ecritArbre(ArbrePlus & larbre, string nomFichier = "");
	void ecritLea();
	void ecritAdmix();
	void ecritGenetix();
	void ecritFstat();
	void ecritRapportFst();
	void ecritPopulationsXML();

	void AffNiveauxPopStruc(ostream &);

	Vecteur _VcalcLocus;
	bool _square_distance;
};

#endif

populations-1.2.33+svn0120106.orig/src/Makefile.dos0000644000175000017500000000216010754601261021662 0ustar  georgeskgeorgesk#SHELL = /bin/sh

VERSIONNUMBER = 1.2.01
RELEASENUMBER = 1

#UNIX = `wx-config --libs` `wx-config --cflags`

#CC = g++ -DCOMPILATION_MINGW32 -DHAVE_CONFIG_H -I. -I.. -O2 -g3
CC = i586-mingw32msvc-g++ -DCOMPILATION_MINGW32 -I. -I.. -O2 -g3
#CC = i586-mingw32msvc-g++ -DCOMPILATION_MINGW32 -I. -I.. -O2 -g3 -lexpat
#i586-mingw32msvc-strip populations.exe

#g++ -DCOMPILATION_MINGW32 -I. -I.. -O2 -g3

all: populations.cpp
	$(CC) allele.cpp -c
	$(CC) applications.cpp -c
	$(CC) applpop.cpp -c
	$(CC) applpopulations.cpp -c
	$(CC) arbre.cpp -c
	$(CC) arbreplus.cpp -c
	$(CC) chaineficpop.cpp -c
	$(CC) couleur.cpp -c
	$(CC) distgnt.cpp -c
	$(CC) fstat.cpp -c
	$(CC) individu.cpp -c
	$(CC) jeupop.cpp -c
	$(CC) jeupopexp.cpp -c
	$(CC) locus.cpp -c
	$(CC) populations.cpp -c
	$(CC) matrices.cpp -c
	$(CC) metapop.cpp -c
	$(CC) population.cpp -c
	$(CC) strucpop.cpp -c
	$(CC) vecteurs.cpp -c
	$(CC) allele.o applications.o applpop.o applpopulations.o arbre.o arbreplus.o chaineficpop.o couleur.o distgnt.o fstat.o individu.o jeupop.o jeupopexp.o locus.o populations.o matrices.o metapop.o population.o strucpop.o vecteurs.o -o populations.exe
populations-1.2.33+svn0120106.orig/src/metapop.cpp0000644000175000017500000002444010531115342021605 0ustar  georgeskgeorgesk
/***************************************************************************
                          MetaPop.cpp  -  Librairie d'objets permettant de manipuler des donn�es
                          						sp�cifiques aux MetaPops
                             -------------------
    begin                : ven sep 01 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#include "metapop.h"
#include "jeupop.h"

//constructeur du niveau racine
MetaPop::MetaPop(Jeupop * pdonnees):StrucPop(pdonnees) {

//cerr << "MetaPop::MetaPop(Jeupop * pdonnees) constructeur debut" << endl;
	_Pmetapop = NULL;
	_niveau_struc = 0;
	_nom = "TOP_LEVEL";

	_tabPstrucpop.resize(0);
//cerr << "MetaPop::MetaPop(Jeupop * pdonnees) constructeur fin" << endl;
}

//constructeur de niveau interm�diaire
MetaPop::MetaPop(MetaPop * pmetapopsup):StrucPop(pmetapopsup->_Pjeu) {
	_Pmetapop = pmetapopsup;
	_niveau_struc = pmetapopsup->_niveau_struc + 1;
	
	_tabPstrucpop.resize(0);
}

//constructeur de copies
MetaPop::MetaPop (const MetaPop & popori, MetaPop * Pmetapop, Jeupop * Pjeu):StrucPop(popori, Pmetapop, Pjeu){
	unsigned long i, nbpop;
//cerr << "MetaPop::MetaPop construct copie d�but " << endl;

	//seulement pour l'objet MetaPop:
	_niveau_struc = popori.get_niveau();

	nbpop = popori.get_nbpop();

//	MetaPop * Pmetapopori(&popori);

	for (i=0; i < nbpop; i++) {
		if (popori._tabPstrucpop[i]->DuType("Population")) {
			AjouterPopulation(new Population(*(popori._tabPstrucpop[i]), this));
		}
		if (popori._tabPstrucpop[i]->DuType("MetaPop")) {
			AjouterPopulation(new MetaPop(*(popori.get_Ptabmetapop(popori._tabPstrucpop[i])), this, _Pjeu));
		}
	}
//cerr << "MetaPop::MetaPop construct copie fin " << endl;
}

//destructeur
MetaPop::~MetaPop () {
//cerr << "MetaPop::~MetaPop debut" << endl;

	unsigned long i;

	for (i=0;i < _tabPstrucpop.size();i++) delete _tabPstrucpop[i];
//cerr << "MetaPop::~MetaPop fin" << endl;
}

bool MetaPop::DuType(const string & nom) const {
	if (nom == "MetaPop") return(true);
	else return(false);
}

void MetaPop::ifAjouterIndividu(const Individu * Pind) {
}

void MetaPop::AjouterIndividu(Individu * Pind) {
	//ajout d'un individu dans une MetaPopulation

	_tabPind.push_back(Pind);

	if (_niveau_struc !=0) _Pmetapop->AjouterIndividu(Pind);
	
}

void MetaPop::AjouterPopulation(Population * Ppop) {

	_tabPstrucpop.push_back(Ppop);
	_Pjeu->AjouterTabPop(Ppop);
}

void MetaPop::AjouterPopulation(MetaPop * Pmetapop) {
	_tabPstrucpop.push_back(Pmetapop);
	_tabPmetapop.push_back(Pmetapop);
}

MetaPop * MetaPop::NewMetaPop(const biolib::vecteurs::ChaineCar & nom) {
	MetaPop * Pmetapop;
	unsigned long i;

	for (i=0; i < _tabPmetapop.size(); i++) {
		//si ma m�tapop existe d�j�:
		if (_tabPmetapop[i]->get_nom() == nom) return (_tabPmetapop[i]);
	}
	Pmetapop = new MetaPop(this);
	Pmetapop->set_nom(nom);
	AjouterPopulation(Pmetapop);
	return (Pmetapop);
}

void MetaPop::get_nomniveauxstruc(Titre & nom_niveaux) const{

	unsigned long i;

	if (nom_niveaux.size() < (_niveau_struc + 1)) nom_niveaux.push_back(_nom);
	else nom_niveaux[_niveau_struc] = nom_niveaux[_niveau_struc] + " " + _nom;

	for (i = 0; i < _tabPstrucpop.size(); i++) {
		_tabPstrucpop[i]->get_nomniveauxstruc(nom_niveaux);
	}
		
}

void MetaPop::set_nploidie() {
	_nploidie = _Pjeu->get_nploidie();
	_nbloc = _Pjeu->get_nbloc();

	unsigned long i;
//cerr << "MetaPop::set_nploidie() " << _nploidie  << endl;

	for (i=0; i < _tabPstrucpop.size(); i++) {
		_tabPstrucpop[i]->set_nploidie();
	}
//cerr << "MetaPop::set_nploidie() fin" << _nploidie  << endl;
}

void MetaPop::reset() {
	// remise � z�ro
	unsigned long i;

	StrucPop::reset();

	for (i=0 ; i < _tabPstrucpop.size(); i++) {
		delete _tabPstrucpop[i];
	}
	_tabPstrucpop.resize(0);
	_tabPmetapop.resize(0);
	
}

MetaPop * MetaPop::get_Ptabmetapop(const StrucPop * Pstrucpop) const {
	unsigned long i;
	
	for (i=0; i < _tabPmetapop.size(); i++) {
		if (_tabPmetapop[i] == Pstrucpop) return (_tabPmetapop[i]);
	}
//	pos = _tabPmetapop.Position(Pstrucpop);
	return (0);
}

void MetaPop::f_rempliTabStrucPop(Vecteur & tabStrucPop, unsigned int niveau) {
	unsigned long i;

//cerr << "MetaPop::f_rempliTabStrucPop(Vecteur & tabStrucPop, unsigned int niveau)" << endl;
//	if (get_niveau() > niveau) return;

  if (get_niveau() == niveau) {
//cerr <<  get_niveau() << " " << niveau  << endl;
		tabStrucPop.push_back(this);
		return;
	}
	for (i = 0; i < _tabPstrucpop.size(); i++) {
		_tabPstrucpop[i]->f_rempliTabStrucPop(tabStrucPop, niveau);
	}
}

long double MetaPop::f_Mheterozygotieatt(unsigned long locus) const {
//moyenne de l'h�t�rozygotie attendue sur les sous populations
//pour ce locus (Hs barre)
// ok verifie le 11/10/2000

	long unsigned nbpop(get_nbpop()),k, nbpopcalc;
	long double MoyHS(0);

	nbpopcalc = nbpop;
	for (k=0; k < nbpop; k++) {
		MoyHS += _tabPstrucpop[k]->f_heterozygotieatt(locus, &nbpopcalc);
	}
	if ((nbpopcalc == 0) || (nbpopcalc > 100000)) return(0);

	MoyHS /= (long double) nbpopcalc;

	return(MoyHS);

}

long double MetaPop::f_Mheterozygotieobs(unsigned long locus) const {
//moyenne de l'h�t�rozygotie observ�e sur les sous populations
//HI h�t�rozygotie individuelle pour ce locus
// ok verifie le 11/10/2000

	long unsigned nbpop(get_nbpop()),k, nbpopcalc;
	long double MoyHI(0);

	nbpopcalc =  nbpop;
	for (k=0; k < nbpop; k++) {
		MoyHI += _tabPstrucpop[k]->f_heterozygotieobs(locus, &nbpopcalc);
	}
	if ((nbpopcalc == 0) || (nbpopcalc > 100000)) return(0);
	
	MoyHI /= (long double) nbpopcalc;

	return(MoyHI);

}

long double MetaPop::f_Mheterozygotietotale(unsigned long locus) const {
// h�t�rozygotie totale (Ht) attendue, � partir des fr�quences all�liques
// moyennes sur la m�tapopulation pour ce locus
// ok verifie le 11/10/2000

	long unsigned i,nballloc,allnonnuls;
	long double sfreqcarre(0), freq;//, Hs;
	long unsigned nbpop(get_nbpop()),k;
	Allele * Pall;

	nballloc = _Pjeu->get_Plocus(locus)->get_nball();
	for (i=0; i < nballloc; i++) {
		for (freq=0,k=0; k < nbpop; k++) {
			allnonnuls = _tabPstrucpop[k]->r_nballnonnuls(locus);
			if (allnonnuls == 0) continue;

			Pall = _Pjeu->get_Pall(locus,i);
			if (Pall->r_estnul()) continue;
			freq += ((long double) _tabPstrucpop[k]->r_nbcopall(Pall)) / ((long double) allnonnuls);
		}
		freq /= (long double) nbpop; //fr�quence moyenne
		sfreqcarre += (freq * freq);			
	}		
	//Hs += (long double) 1 - sfreqcarre;
	return ((long double) 1 - sfreqcarre);	

	
}

long double MetaPop::f_M_Fis(unsigned long locus) const {
// indice de Wright Fis pour ce locus
// ok verifie le 11/10/2000
// Fis = (Hs barre - Hi) / Hs barre
	if (locus > (unsigned long)get_nbloc()) throw Anomalie(7);

//cerr << "MetaPop::f_M_Fis Hi:" << f_Mheterozygotieobs(locus) << endl;
	long double Hsbarre(f_Mheterozygotieatt(locus));
//cerr << "MetaPop::f_M_Fis Hsbarre:" << Hsbarre << endl;

	return ((Hsbarre - f_Mheterozygotieobs(locus))/ Hsbarre);
}

long double MetaPop::f_M_Fst(unsigned long locus) const {
// indice de Wright Fst pour ce locus
// ok verifie le 11/10/2000
// Fst = (Ht - Hs barre) / Ht
//cerr << "MetaPop::f_M_Fst" << endl;
//cerr << locus << " " << get_nbloc() << endl;
	if (locus > get_nbloc()) throw Anomalie(7);

	long double Ht(f_Mheterozygotietotale(locus));

//cerr << "MetaPop::f_M_Fst Ht " << Ht << endl;
//cerr << "MetaPop::f_M_Fst Hsbarre " << f_Mheterozygotieatt(locus) << endl;

	return ((Ht - f_Mheterozygotieatt(locus))/ Ht);
}


long double MetaPop::f_M_Fit(unsigned long locus) const {
// indice de Wright Fit pour ce locus
// ok verifie le 11/10/2000
// Fit = (Ht - Hi) / Ht
//cerr << "MetaPop::f_M_Fit" << endl;
//cerr << locus << " " << get_nbloc() << endl;

	if (locus > get_nbloc()) throw Anomalie(7);

	long double Ht(f_Mheterozygotietotale(locus));

	return ((Ht - f_Mheterozygotieobs(locus))/ Ht);
}

/** Suppression de la Population Ppop */
void MetaPop::SupprPop(StrucPop * Ppop){
//cerr << "MetaPop::SupprPop debut" << endl;
	unsigned long nbpop(_tabPstrucpop.size()),p;
	bool ok(false);

	for (p=0; p < nbpop; p++) {
		if (Ppop == _tabPstrucpop[p]) {
//cerr << "MetaPop::SupprPop efface" << endl;
			delete Ppop;
			_tabPstrucpop.erase(_tabPstrucpop.begin()+p);
			p--;
			nbpop--;
			ok = true;
		}
	}
//cerr << "MetaPop::SupprPop debut 2" << endl;

	if (ok) {
		nbpop = _tabPmetapop.size();
		for (p=0; p < nbpop; p++) {
			if (Ppop == _tabPmetapop[p]) {
				_tabPmetapop.erase(_tabPmetapop.begin()+p);
			}
		}
//cerr << "MetaPop::SupprPop debut 3 " << "ok" << endl;
	}
	else {
		for (p=0; p < nbpop; p++) _tabPstrucpop[p]->SupprPop(Ppop);
	}
//cerr << "MetaPop::SupprPop fin" << endl;
		
}
/** Retourne vrai, si l'allele n'est pas pr�sent dans MetaPop */
bool MetaPop::r_allelenonpresent(Allele * Pall) const{
	if (r_nbcopall(Pall) > 0) return (false);
	else return(true);
}
/** r�affectation du nombre de locus
 */
void MetaPop::set_nbloc(){
	unsigned int i;
	_nbloc = _Pjeu->get_nbloc();

	for (i = 0; i < _tabPstrucpop.size(); i ++) _tabPstrucpop[i]->set_nbloc();
}

void MetaPop::oPopulationsXML(unsigned int id, ostream & sortie, ostream & infos) {
  unsigned int i, nbpop(_tabPstrucpop.size());
  biolib::vecteurs::ChaineCar idXML;

  sortie << "" << endl;


  for (i=0; i < nbpop; i++) {
    _tabPstrucpop[i]->oPopulationsXML(i, sortie, infos);
  }
  
  sortie << "" << endl;

}

Population * MetaPop::new_population(string & nom) {
  Population * Ppop(new Population(this));

  Ppop->set_nom(nom);
  AjouterPopulation(Ppop);
  return (Ppop);
}

populations-1.2.33+svn0120106.orig/src/metapop.h0000644000175000017500000000625210531115342021253 0ustar  georgeskgeorgesk
/***************************************************************************
                          MetaPop.h  -  Librairie d'objets permettant de manipuler des données
                          						spécifiques aux populations
                             -------------------
    begin                : ven sep 01 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

// population

#ifndef METAPOP_H
#define METAPOP_H

#include "locus.h"
#include "strucpop.h"
#include "population.h"
#include "vecteurs.h"

using namespace biolib::vecteurs;

class MetaPop: public StrucPop {
public:
	MetaPop(Jeupop * pdonnees);
	MetaPop(MetaPop * pmetapopsup);
	MetaPop(const MetaPop & popori, MetaPop * Pmetapop, Jeupop * Pjeu);
	~MetaPop();

	bool DuType(const string & nom) const;
	friend class Jeupop;

	void AjouterIndividu(Individu * Pind);
	void AjouterPopulation(MetaPop * );
	void AjouterPopulation(Population * );

	MetaPop * NewMetaPop(const biolib::vecteurs::ChaineCar & nom);
  Population * new_population(string & nom);

	unsigned long get_nbpop() const {return(_tabPstrucpop.size());};
	unsigned long get_nbmetapop() const {return(_tabPmetapop.size());};
	const MetaPop * get_tabPmetapop(unsigned int i) const {return (_tabPmetapop[i]);};
	const string & get_nompop(unsigned int i) const {return(_tabPstrucpop[i]->get_nom());};
	void get_nomniveauxstruc(Titre & nom_niveaux) const;
	unsigned int get_niveau() const {return (_niveau_struc);};

	void set_nploidie();

	void f_rempliTabStrucPop(Vecteur &, unsigned int);

	long double f_Mheterozygotieobs(unsigned long locus) const;
	long double f_Mheterozygotieatt(unsigned long locus) const;
	long double f_Mheterozygotietotale(unsigned long locus) const;

	long double f_M_Fis(unsigned long locus) const;
	long double f_M_Fst(unsigned long locus) const;
	long double f_M_Fit(unsigned long locus) const;

  void oPopulationsXML(unsigned int id, ostream & sortie, ostream & infos) ;
	
  /** Retourne vrai, si l'allele n'est pas présent dans MetaPop */
  bool r_allelenonpresent(Allele * Pall) const;
protected:
  /** Suppression de la Population Ppop */
  void SupprPop(StrucPop * Ppop);
  MetaPop * get_Ptabmetapop(const StrucPop *) const;

	void ifAjouterIndividu(const Individu * Pind);

	void reset();

  /** réaffectation du nombre de locus
 */
  void set_nbloc();
	unsigned int _niveau_struc;

	vector _tabPstrucpop;

	vector _tabPmetapop;

};

#endif

populations-1.2.33+svn0120106.orig/src/cmake_install.cmake0000644000175000017500000000225711701604740023253 0ustar  georgeskgeorgesk# Install script for directory: /home/georgesk/developpement/populations/populations-1.2.33+svn0120106/src

# Set the install prefix
IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
  SET(CMAKE_INSTALL_PREFIX "/usr")
ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")

# Set the install configuration name.
IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
  IF(BUILD_TYPE)
    STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
           CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
  ELSE(BUILD_TYPE)
    SET(CMAKE_INSTALL_CONFIG_NAME "Release")
  ENDIF(BUILD_TYPE)
  MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)

# Set the component getting installed.
IF(NOT CMAKE_INSTALL_COMPONENT)
  IF(COMPONENT)
    MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
    SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
  ELSE(COMPONENT)
    SET(CMAKE_INSTALL_COMPONENT)
  ENDIF(COMPONENT)
ENDIF(NOT CMAKE_INSTALL_COMPONENT)

# Install shared libraries without execute permission?
IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
  SET(CMAKE_INSTALL_SO_NO_EXE "1")
ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)

populations-1.2.33+svn0120106.orig/src/config.h.cmake0000644000175000017500000000020411701604653022131 0ustar  georgeskgeorgesk#ifndef _CONFIG_H
#define _CONFIG_H

#define POPULATIONS_VERSION "@POPULATIONS_VERSION@"

#include 

#endif /* _CONFIG_H */
populations-1.2.33+svn0120106.orig/src/couleur.cpp0000644000175000017500000000705110531115342021615 0ustar  georgeskgeorgesk/***************************************************************************
                          couleur.cpp  -  description
                             -------------------
    begin                : Mon Jun 4 2001
    copyright            : (C) 2001 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#include "couleur.h"

vector Couleur::_tab_couleurs;
unsigned int Couleur::_pos_tab_couleurs(0);

Couleur::Couleur(unsigned long rouge, unsigned long vert, unsigned long bleu) {
	_boolrgb = true;
	_boolnom = false;

	_rouge = rouge;
	_vert= vert;
	_bleu = bleu;
}

Couleur::Couleur(const biolib::vecteurs::ChaineCar & couleur){
	//couleur peut contenir 3 chiffres (rgb) ou un nom de couleur en Anglais
	biolib::vecteurs::ChaineCar mot, lacouleur(couleur);

	_boolrgb = false;
	_boolnom = false;

	if (lacouleur == "") lacouleur.assign(get_couleur_diff());

	if (lacouleur.GetNbMots() == 3) {
		_boolrgb = true;
		lacouleur.GetMot(1, mot);
		if (mot.EstUnChiffre()) {
			_rouge = (int) mot;
			_rouge *= 256;
		}
		else _boolrgb = false;
		lacouleur.GetMot(2, mot);
		if ((_boolrgb) && (mot.EstUnChiffre())) {
			_vert = (int) mot;
			_vert *= 256;
		}
		else _boolrgb = false;
		lacouleur.GetMot(3, mot);
		if ((_boolrgb) && (mot.EstUnChiffre())) {
			_bleu = (int) mot;
			_bleu *= 256;
		}
		else _boolrgb = false;
		
	}
	if (_boolrgb == false) {//nom de couleur en Anglais
		_boolnom = true;
		_nom.assign(lacouleur);
	}

}

Couleur::~Couleur(){
}

bool Couleur::operator== (const Couleur &rval) const {
	if ((_boolrgb) && (rval._boolrgb) && (_rouge == rval._rouge) && (_vert == rval._vert) && (_bleu == rval._bleu)) return true;

	if ((_boolnom) && (rval._boolnom) && (_nom == rval._nom)) return true;

	return false;
}

const string & Couleur::get_couleur_diff() {
	unsigned int i;

	if ( Couleur::_tab_couleurs.size() == 0 ) Couleur::f_rempli_tab_couleurs();
	i = Couleur::_pos_tab_couleurs;
	Couleur::_pos_tab_couleurs++;
	if (Couleur::_pos_tab_couleurs == Couleur::_tab_couleurs.size()) Couleur::_pos_tab_couleurs = 0;

	return (Couleur::_tab_couleurs[i]);
}


void Couleur::f_rempli_tab_couleurs() {

	_tab_couleurs.push_back("red");
	_tab_couleurs.push_back("green");
	_tab_couleurs.push_back("blue");
	_tab_couleurs.push_back("turquoise");
	_tab_couleurs.push_back("pink");
	_tab_couleurs.push_back("yellow");
	_tab_couleurs.push_back("brown");
	_tab_couleurs.push_back("purple");
	_tab_couleurs.push_back("sea green");
	_tab_couleurs.push_back("salmon");
	_tab_couleurs.push_back("sky blue");
	_tab_couleurs.push_back("yellow green");
	_tab_couleurs.push_back("brown1");
	_tab_couleurs.push_back("aquamarine");
	_tab_couleurs.push_back("orange");
	_tab_couleurs.push_back("brown2");
	_tab_couleurs.push_back("navy blue");
	_tab_couleurs.push_back("goldenrod");
	_tab_couleurs.push_back("tomato");
	_tab_couleurs.push_back("violet");
	_tab_couleurs.push_back("gold");

}
populations-1.2.33+svn0120106.orig/src/applications.cpp0000644000175000017500000002235711326563351022645 0ustar  georgeskgeorgesk/***************************************************************************
 applications.cpp  -  Librairie d'objets pour creer des applications
 -------------------
 begin                : ven aug 14 10:25:55 CEST 2000
 copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
 email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#include"applications.h"

Application::Application() {
#ifndef GZSTREAM_H
	_formatMatrice = 1;
#else
	_formatMatrice = 1; //5 format gnumeric
#endif
	_confirmeEcraseFichier = true;
}
void Application::affPubSortie() const {

	cout << endl << endl;
	cout << "Programmation: Olivier Langella" << endl;
	cout << "" << endl;
	cout << "e-mail: langella@moulon.inra.fr" << endl;
	cout << "" << endl;
	cout << endl << endl;
}

void Application::affPubEntree() const {

	cout << endl << endl;
	cout << "**************************************" << endl;
	//	cout << "*  Populations 1.1.00  CNRS UPR9034  *" << endl;
	cout << "*      langella@moulon.inra.fr      *" << endl;
	cout << "*  *" << endl;
	cout << "**************************************" << endl;
	cout << endl << endl;
}

void Application::lancement(int nbcommandes, char ** commandes) {

	if (nbcommandes > 1) {
		fLigneCommande(commandes, nbcommandes);
	} else {
		affPubEntree();

		while (menu_principal() != 0) {
		}

		affPubSortie();
	}
}

void Application::fLigneCommande(char ** commandes, int nbcommandes) {
	affPubEntree();

}

int Application::menu_principal() {
	int choix;
	cout << endl << endl;
	cout << "0) Quitter" << endl;

	/*	cout << endl << "choix: ";
	 cin >> choix;
	 */
	choix = DemandeChoix(0, 0);

	switch (choix) {
	case 0:
		return (0);
		break;
		//	case 1:
		//		return(1);
		//		break;
	default:
		return (0);
		break;
	}
}

int Application::menu_formatMatrice() {
	int choix;
	cout << endl << endl;
	cout << _("Matrix outputfile format:") << endl;
	cout << "1) " << _("ASCII, (excell or gnumeric compliant)") << endl;
	cout << "2) " << _("NtSys") << endl;
	cout << "3) " << _("Phylip") << endl;
	cout << "4) " << _("xgobi") << endl;
	cout << "5) " << _("Gnumeric spreadsheet") << endl;

	/*	cout << endl << "choix: ";
	 cin >> choix;
	 */
	choix = DemandeChoix(1, 5);

	switch (choix) {
	case 1:
		_formatMatrice = 1;
		return (1);
		break;
	case 2:
		_formatMatrice = 2;
		return (2);
		break;
	case 3:
		_formatMatrice = 4;
		return (3);
		break;
	case 4:
		_formatMatrice = 3;
		return (4);
		break;
	case 5:
		_formatMatrice = 5;
		return (5);
		break;
	default:
		return (0);
		break;
	}
}

bool Application::litMatriceLD(MatriceLD &mat) {
	bool ok(false);

	/*	if (*PPmat != NULL) {
	 delete *PPmat;
	 *PPmat = NULL;
	 }*/

	while (_fichier.is_open() == 0) {
		cout << _("Matrix filename ?") << endl;
		cin >> _nomFichier;

		_fichier.open(_nomFichier.c_str(), ios::in);
		_fichier.clear();
	}

	try {
		//	*PPmat = new MatriceLD();
		cout << _("Reading file...") << endl;

		//cerr << " Application::litMatriceLD(MatriceLD &mat)" << endl;
		//cerr << _fichier;
		//    char c;
		//   while ( _fichier.get(c))
		//	cerr << c;

		mat.iFichier(_fichier);
		_fichier.clear();
		_fichier.close();
		ok = true;
	} catch (MatriceLD::Anomalie pb) {
		_fichier.close();
#ifdef GZSTREAM_H
		igzstream gzfichier;
		gzfichier.open(_nomFichier.c_str(), ios::in);

		try {
			//cerr << " Application::litMatriceLD(MatriceLD &mat) gzfile" << endl;
			//    char c;
			//   while ( _fichier.get(c))
			//	cerr << c;
			mat.iGnumeric(gzfichier);
			ok = true;
			gzfichier.close();
			//cerr << " Application::litMatriceLD(MatriceLD &mat)" << endl;
			//mat.oExcel(cerr);
			return(ok);
		}
		catch (MatriceLD::Anomalie pb) {
			ok = false;
		}
		gzfichier.close();
#else
		ok = false;
#endif
		//	if (*PPmat != NULL) delete *PPmat;


		switch (pb.le_pb) {
		default:
			cout << _("This Matrix file format is not recognized...") << endl;
			break;
		}
	}

	return (ok);
}

bool Application::ecritMatriceLD(MatriceLD &mat, string nomFichier, int format) {
	bool ok(false);
	ofstream sortie;

	if (format == 0)
		format = _formatMatrice;

	/*	if (*PPmat != NULL) {
	 return (false);
	 }*/
	//cerr << format;
	//_sortie << ends;
	//_sortie.close();

	while (nomFichier == "") {
		cout << _("Matrix filename to write into ?") << endl;
		cin >> nomFichier;
	}

	sortie.open(nomFichier.c_str(), ios::out);

	//sortie << "coucou application::ecritMatriceLD";
	// cerr << "coucou pplication::ecritMatriceLD";
	//	_sortie << ends;
	//	_sortie.close();

	try {
		mat.ofFormat(sortie, format, nomFichier);
		//sortie << ends;
		sortie.close();
		ok = true;
	} catch (MatriceLD::Anomalie pb) {
		sortie.close();
		ok = false;

		switch (pb.le_pb) {
		default:
			cout << _("Error writing matrix") << " MatriceLD::Anomalie "
					<< pb.le_pb << endl;
			break;
		}
	}

	return (ok);
}

bool Application::DemandeOuiNon(char laquestion[]) const {
	string rep;

	cout << laquestion << endl;
	cin >> rep;
	//	cout << endl;
	if (rep == "")
		rep.assign("N");

	switch (rep[0]) {
	case 'Y':
		return (true);
		break;
	case 'y':
		return (true);
		break;
	case 'o':
		return (true);
		break;
	case 'O':
		return (true);
		break;
	default:
		return (false);
		break;
	}
}

string Application::DemandeString(char laquestion[]) const {
	string rep("");

	while (rep == "") {
		cout << endl << laquestion << endl;
		cin >> rep;
	}
	return (rep);
}

string Application::DemandeFichier(const string & laquestion) {
	string rep("");
	bool ok(false);

	while ((rep == "") || (ok == false)) {
		ok = false;
		cout << endl << laquestion << endl;
		cin >> rep;
		if ((rep != "") && (_confirmeEcraseFichier) && (fFichierExiste(
				rep.c_str()))) {
			cout << _("The file ") << rep << _(" already exist.") << endl;
			if (DemandeOuiNon(_("Choose Y if you to overwrite it: ")))
				ok = true;
		} else
			ok = true;
	}

	return (rep);
}

float Application::DemandeReel(char laquestion[], float inf, float sup) const {
	float reel(-9999);
	string rep;

	while ((reel < inf) || (reel > sup)) {
		cout << endl << laquestion << endl;
		cin >> rep;
		reel = atof(rep.c_str());
	}
	return (reel);
}

int Application::DemandeEntier(const string & laquestion, int inf, int sup) const {
	int entier(-999);
	string rep;

	while ((entier < inf) || (entier > sup)) {
		cout << endl << laquestion << endl;
		cin >> rep;
		entier = atoi(rep.c_str());
	}
	return (entier);
}

int Application::DemandeEntier(char laquestion[], int inf, int sup, int defaut) const {
	int entier(-999);
	char car;
	string mot;
	if ((defaut < inf) || (defaut > sup))
		cerr << "DemandeEntier defaut ERROR" << endl;

	while ((entier < inf) || (entier > sup)) {
		cout << endl << laquestion << endl;
		cin.get(car);
		cin.get(car);
		//	rep[0] = rep[0]+50;
		//		cout << rep;
		if (car == '\n')
			entier = defaut;
		else {
			cin >> mot;
			mot = car + mot;
			entier = atoi(mot.c_str());
		}
	}
	return (entier);
}

int Application::DemandeChoix(int inf, int sup) const {

	return (DemandeEntier(_("Your choice: "), inf, sup));
}

bool Application::litJeuMatriceLD(JeuMatriceLD &jeumat) {
	bool ok(false);

	/*	if (*PPmat != NULL) {
	 delete *PPmat;
	 *PPmat = NULL;
	 }*/

	while (_fichier.is_open() == 0) {
		cout << _("Filename of the set of matrix ?") << endl;
		cin >> _nomFichier;

		_fichier.open(_nomFichier.c_str(), ios::in);
		_fichier.clear();
	}

	try {
		//	*PPmat = new MatriceLD();
		cout << _("Reading file...") << endl;
		jeumat.iFlux(_fichier);
		_fichier.clear();
		_fichier.close();
		ok = true;
	} catch (MatriceLD::Anomalie pb) {
		_fichier.close();
		ok = false;
		//	if (*PPmat != NULL) delete *PPmat;

		switch (pb.le_pb) {
		default:
			cout << _("This file format is not recognized...") << endl;
			break;
		}
	}

	return (ok);
}

bool Application::ecritJeuMatriceLD(const JeuMatriceLD &jeumat,
		string nomFichier, int format) {
	bool ok(false);
	//string nomFichier;

	if (format == 0)
		format = _formatMatrice;

	/*	if (*PPmat != NULL) {
	 return (false);
	 }*/
	//cerr << format;
	_sortie << ends;
	_sortie.close();

	while (_sortie.is_open() == 0) {
		while (nomFichier == "") {
			cout << _("Name of the file to write the set of matrix ?") << endl;
			cin >> nomFichier;
		}
		_sortie.open(_nomFichier.c_str(), ios::out);
	}

	try {
		nomFichier = _nomFichier;
		jeumat.oFlux(_sortie, format);
		_sortie << ends;
		_sortie.close();
		ok = true;
	} catch (MatriceLD::Anomalie pb) {
		_sortie.close();
		ok = false;

		switch (pb.le_pb) {
		default:
			cout << _("Writing error...") << endl;
			break;
		}
	}

	return (ok);
}
/** test si nomfichier existe */
bool Application::fFichierExiste(const string & nomfichier) {
	_fichier.open(nomfichier.c_str(), ios::in);

	if (_fichier.is_open() == 0) {
		_fichier.clear();
		return (false);
	}
	_fichier.close();
	return (true);
}
populations-1.2.33+svn0120106.orig/src/population.cpp0000644000175000017500000001471610531115342022337 0ustar  georgeskgeorgesk
/***************************************************************************
                          population.cpp  -  Librairie d'objets permettant de manipuler des données
                          						spécifiques aux populations
                             -------------------
    begin                : ven sep 01 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#include "population.h"
#include "jeupop.h"

//constructeur
Population::Population(Jeupop * pdonnees):StrucPop(pdonnees){
	// ********************      Traitement des Metapops ***********
	// *********** 5/9/2000
	_Pmetapop = pdonnees->_Pracinepops;  //par défaut
	// 
	//
	//
	//_Pmetapop->AjouterPopulation(this);

}

//constructeur
Population::Population(MetaPop * Pmetapop):StrucPop(Pmetapop->get_Pjeu()){
	// ********************      Traitement des Metapops ***********
	// *********** 5/9/2000
	_Pmetapop = Pmetapop;
	// 
	// 
	//_Pmetapop->AjouterPopulation(this);

}


//constructeur de copies
Population::Population (const StrucPop & popori, MetaPop * Pmetapop):StrucPop(popori, Pmetapop, Pmetapop->get_Pjeu()){
	unsigned long i;
//cerr << "Population::Population construct copie début " << _nom  << endl;
	Individu * Poriind;

	//seulement pour l'objet Population:
//	_nbind = popori.get_nbind();
//cerr << "Population::Population construct copie _nbind " << popori.get_nbind() << endl;

	for (i=0; i < popori.get_nbind(); i++) {
		Poriind =  popori.get_Pind(i);
//cerr << "Population::Population construct copie _nomind " << Poriind->get_nom() << endl;
		Poriind =  new Individu(*Poriind, this);
//cerr << "Population::Population construct copie _nomind " << Poriind->get_nom() << endl;

		AjouterIndividu(Poriind);
	}
//cerr << "Population::Population construct copie fin " << endl;
}


//destructeur
Population::~Population () {

	while (_tabPind.size() > 0) {
//cerr << "Population::~Population " <<_tabPind[0]->get_nom() << endl;
		SupprIndividu(_tabPind[0]);
	}

}

bool Population::DuType(const string & nom) const {
	if (nom == "Population") return(true);
	else return(false);
}

void Population::AjouterIndividu(Individu * Pind) {
	//ajout d'un individu dans une Population
//cerr << "Population::AjouterIndividu(Individu * Pind) début" << endl;
	_tabPind.push_back(Pind);

	_nbind++;
//cerr << "Population::AjouterIndividu " << _nbind << endl;
	_Pmetapop->AjouterIndividu(Pind);
//cerr << "Population::AjouterIndividu(Individu * Pind) fin" << endl;
	
}

void Population::ifAjouterIndividu(const Individu * Pind) {
	//ajout d'un individu dans une Population, avec les alleles correspondants
	// => recherche d'un individu deja définis
	long i, taille(get_nbind()), nbind(-1);
	const string nomind(Pind->get_nom());

	_nbloc = _Pjeu->get_nbloc();

	for (i = 0 ; i < taille; i++) {
		if (nomind == get_nomind(i)) {
			nbind = i;
			break;
		}
	}

	if (nbind >= 0) { //l'individu existe deja
		//il faut ajouter les locus (les alleles) 
		//     que l'original n'a pas
		// pb à résoudre: incohérence entre alleles d'un meme locus,
		//   d'un meme individu...
		get_Pind(nbind)->ifFusionnerIndividu(*Pind);
	}
	else { //il faut creer un nouvel individu
		_tabPind.push_back(new Individu(this, nomind));
		// et le remplir
		_tabPind.back()->ifFusionnerIndividu(*Pind);
	}
}

void Population::get_nomniveauxstruc(Titre & nom_niveaux) const{

	unsigned long niveau(get_niveau());

	if (nom_niveaux.size() < (niveau + 1)) nom_niveaux.push_back(_nom);
	else nom_niveaux[niveau] = nom_niveaux[niveau] + " " + _nom;
		
}

unsigned int Population::get_niveau() const {
	return (_Pmetapop->get_niveau()+1);
}

void Population::set_nploidie() {
	_nploidie = _Pjeu->get_nploidie();
	_nbloc = _Pjeu->get_nbloc();

	unsigned long i;

//cerr << "Population::set_nploidie() " << _nploidie  << endl;
	for (i=0; i < _tabPind.size(); i++) {
		_tabPind[i]->resize_alleles();
	}
//cerr << "Population::set_nploidie() fin" << _nploidie  << endl;
//cin >> i;
}

void Population::set_nploidie(unsigned int nploidie) {
  if (_nploidie == 0) {
    _nploidie = nploidie;
    _Pjeu->set_nploidie(nploidie);
  }
  else if (_nploidie != nploidie) throw Anomalie(2);
  
}

string Population::get_nom_chemin() const {
	MetaPop * Pmetapop(_Pmetapop);

	string nom_complet(_nom);
	string separateur("/");

	while ((Pmetapop != 0) && (Pmetapop->get_niveau() != 0)) {
		nom_complet = Pmetapop->get_nom() + separateur + nom_complet;
		Pmetapop =  Pmetapop->get_Pmetapop();
	}	

	return (nom_complet);
}

void Population::f_rempliTabStrucPop(Vecteur & tabStrucPop, unsigned int niveau) {
  tabStrucPop.push_back(this);
}
/** Suppression de la Population */
void Population::SupprPop(StrucPop * Ppop){
	if (Ppop != this) return;

	unsigned long nbind (get_nbind()), i;

	for (i = 0; i < nbind; i++) {
		
 	}	
}
/** Suppression d'un individu dans une Population */
void Population::SupprIndividu(Individu * Pind) {
	SupprtabIndividu(Pind);
	delete (Pind);
//cerr << "Population::SupprIndividu fin" << endl;
}

void Population::oPopulationsXML(unsigned int id, ostream & sortie, ostream & infos) {
  unsigned int i, nbind(get_nbind());
  biolib::vecteurs::ChaineCar idXML;

  sortie << "" << endl;


  for (i=0; i < nbind; i++) {
    get_Pind(i)->oPopulationsXML(i, sortie, infos);
  }

  sortie << "" << endl;

}

Individu * Population::new_individual(string & name, unsigned int nploidie) {
  if (get_nploidie() == 0) set_nploidie(nploidie);
  else if (get_nploidie() != nploidie) {
    throw Anomalie(2);
  }

  Individu * Pind(new Individu(this, name));

  AjouterIndividu(Pind);


  return (Pind);
}

populations-1.2.33+svn0120106.orig/src/populations.cpp0000644000175000017500000000360710531115342022517 0ustar  georgeskgeorgesk/***************************************************************************
 *   Copyright (C) 2006 by Olivier Langella   *
 *   olivier.langella@moulon.inra.fr   *
 *                                                                         *
 *   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.,                                       *
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/


#ifdef HAVE_CONFIG_H
#include 
#endif

#include 
#include 
#include "applpopulations.h"

using namespace std;

int main(int argc, char *argv[])
{
	//setlocale (LC_ALL, "");
	//setlocale (LC_NUMERIC, "en_US");
  //bindtextdomain (PACKAGE,LOCALEDIR);
	//bindtextdomain (PACKAGE,"/usr/share/locale");
  //textdomain (PACKAGE);
	//textdomain("populations");
	ApplPopulations application;

//	cout << argc[1] << " " << argv;
	application.lancement(argc, argv);

//	return(0);

  return EXIT_SUCCESS;
}
populations-1.2.33+svn0120106.orig/src/locus.cpp0000644000175000017500000002146210531115342021266 0ustar  georgeskgeorgesk/***************************************************************************
                          locus.cpp  -  Librairie d'objets permettant de manipuler des données
                          						spécifiques aux locus
                             -------------------
    begin                : ven sep 01 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#include"jeupop.h"
#include "locus.h"

//typedef biolib::vecteurs::ChaineCar ChaineCar;

// quelques fonctions mathématiques...

long double fact (int n) {
	long double res (n);
	long double i;

	if (n == 0) return (1);

	for (i = n-1; i > 1 ; i--) {
	//	res = res * i;
		res *= i;
	}

	return (res);
}

long double fact (int n, int m) {
	long double res (1);
	int i;
///equivalent a: fact (n) / fact (m)
	if (n == m) return(1);
	if (n > m) {
		res = n;
		for (i = n-1; i > m ; i--) {
		//	res = res * i;
			res *= i;
		}
		return (res);
	}
	else {
		res = m;
		for (i = m-1; i > n ; i--) {
			res *= i;
		}
		return (1/res);
	}
}
long double comb (int n, int m) {
	long double res;
	int a(m),b(n-m), swap;

	if (b > a) {
		swap = a;
		a = b;
		b = swap;
	}
	res = fact (n,a);
//	res = fact (n) / fact (m);
	res = res / fact (b);

	return (res);
}

/*
//constructeur
Individu::Individu (int nball) {

	_nom.assign("");
	_Ppop = 0;
	_nball = nball;
//	_tabPall = new (Allele*[nball]);
	_tabPall.resize(nball);
//	for (i=0;i < nball;i++) _tabPall.push_back(0);
}
*/

//constructeur de copies
Locus::Locus(const Locus& original, Jeupop * Pjeu) {

	unsigned long i;
	unsigned long nball(original.get_nball());

	_nom = original._nom;
	_Pjeu = Pjeu;

	for (i=0;i < nball;i++) {
		_tabPall.push_back(new Allele(*original._tabPall[i],this));
//		_tabPall[i]->set_Plocus(this);
	}
}

/*//constructeur de copies
Locus::Locus(const Locus& original) {

	long i;
	long nball(original.get_nball());

	_nom = original._nom;
//	_Pjeu = original._Pjeu;

	for (i=0;i < nball;i++) {
		_tabPall.push_back(new Allele(this, original.get_nomall(i)));
//		if (original.getPall(i)->_nul) nul = true;
	}

}
*/

//constructeur
Locus::Locus (long nball) {
	long i;

	_nom.assign("");
	_Pjeu = 0;

	for (i=0;i < nball;i++) _tabPall.push_back(new Allele(this));
}

Locus::Locus (Jeupop * pjeu, long nball) {
	long i;

	_Pjeu = pjeu;

	_nom.assign("");

	for (i=0;i < nball;i++) _tabPall.push_back(new Allele(this));
}

//constructeur

//destructeur
Locus::~Locus () {
//cerr << "Locus::~Locus debut" << endl;
	int i;
	int nball(get_nball());

	for (i=0;i < nball;i++) delete (_tabPall[i]);

//cerr << "Locus::~Locus fin" << endl;
//	delete [] _tabPall;
}



void Locus::reset(Jeupop * Pjeu, long nballnew) {
	long i;
	long nball(get_nball());

	for (i=0;i < nball;i++) delete (_tabPall[i]);

//	delete [] _tabPall;

	_Pjeu = Pjeu;
//	_nball = nball;
//	_tabPall = new (Allele*[nball]);
	_tabPall.resize(nballnew);

	for (i=0;i < nballnew;i++) {
		_tabPall[i] = new Allele(this);
	}

}

//constructeur
/*Population::Population (int nbind) {
	int i;

	_nom.assign("");
	_Pjeu = 0;
	_nbind = nbind;
//	_tabPind = new (Individu*[nbind]);

	_nbloc = 0;
	_nploidie = 0;
//	_tabPall = new (Allele*[0]);

	for (i=0;i < _nbind;i++) _tabPind.push_back(new(Individu));
}*/



/*void Population::sort_all() {
	//tri de _tabPall par loci
	Allele * Pallswap;
	int nbcopies(_nploidie * _nbind);
	int i, j, pos;

	for (i=0;i < _nbloc; i++) {

		for (j=1; j0)) {
					Pallswap = _tabPall[(i * nbcopies) + pos-1];
					_tabPall[(i * nbcopies) + pos-1] = _tabPall[(i * nbcopies) + pos];
					_tabPall[(i * nbcopies) + pos] = Pallswap;
					pos--;
				}
			}
		}
	}
}*/


Allele * Locus::getPallNul() {
	// donne un pointeur sur l'allele nul
	Allele* res;
	unsigned long i;

	res = 0;
	for (i=0; i < _tabPall.size(); i++) {
		if(_tabPall[i]->_miss) {
			res = _tabPall[i];
			break;
		}
	}

	if (res == 0) { //on crée l'allèle nul
		_tabPall.push_back(new Allele(this, "00"));
		res = _tabPall.back();
	}

	return (res);
}

Allele* Locus::getPall(const string & nom) const{
	// donne un pointeur sur l'allele du nom 'nom'
	Allele* res;
	unsigned long i;

	res = 0;
//cerr << "getPall dans Locus debut " << nom << endl;
	for (i=0; i < _tabPall.size(); i++) {
//cerr << "coucou " << _tabPall[i]->_nom << endl;
		if(_tabPall[i]->_nom == nom) {
			res = _tabPall[i];
			break;
		}
	}
//cerr << "getPall dans Locus fin " << res << endl;

	return (res);
}


bool Locus::f_verifnum(int typedenum) const {
	// Vérification du type de numérotation des allèles
//	1 => type Genepop stricte (2digits)
//	2 => nom d'alleles = numéros
//	3 => nom d'alleles = numéros < 999
		//Anomalie 2-> les numéros d'allèles format genepop ne sont pas présents

	long nball(get_nball());
	long i;

	for (i=0; i < nball; i++) {
		if (!(_tabPall[i]->f_verifnum(typedenum))) return(false);
	}

	return(true);
}


void Locus::ifAjouterAllele(const Allele * Pall) {
	//ajout d'un allele dans un locus
	// => recherche un allele preexistant
	// vérifié le 11/09/2000
	unsigned long i, taille(get_nball());
	long nball(-1);

	for (i = 0 ; i < taille; i++) {
		if (*Pall == *getPall(i)) {
			nball = i;
			break;
		}
	}
	if (nball >= 0) { //l'allele existe deja
		return;
	}
	else { //il faut le creer
		_tabPall.push_back(new Allele(*Pall, this));
	}
}

const Locus& Locus::operator= (const Locus & rval) {
	long i;
	long nball(rval.get_nball());

	reset(_Pjeu, nball);
	_nom = rval._nom;

	for (i=0;i < nball;i++) {
		*(_tabPall[i]) = *(rval._tabPall[i]);
	//	_tabPall[i]->set_Plocus(this);
	}

	return(*this);
}

void Locus::f_trad2Gpop(ostream& sortie) {
//transformation des noms d'alleles en chiffres < a 100
	long i;
	long nball(get_nball());
//	char mot[5];
	biolib::vecteurs::ChaineCar mot;

	sortie << endl;
	sortie << "Locus: " << _nom << endl;

	for (i=0; i < nball; i++) {
		mot.assign("");
		
		if (_tabPall[i]->_miss) {
			sortie << _tabPall[i]->_nom << " <--> ";
			_tabPall[i]->set_nom("00");
			sortie << _tabPall[i]->_nom << endl;
		}
		else {
			sortie << _tabPall[i]->_nom << " <--> ";
			
	//		itoa(i+1,mot,10);
	//		mot[2] = '\0';
			if ((i+1) < 10) {
	//			mot[1] = mot[0];
	//			mot[0] = '0';
				mot += '0';
				mot.AjEntier(i+1);
			}
			else if ((i+1) < 100) {
				mot.AjEntier(i+1);
			}
			else cerr <<"erreur..."<< endl;
			_tabPall[i]->set_nom(mot);

			sortie << _tabPall[i]->_nom << endl;
		}
	}
}



void Locus::set_PJeupop(Jeupop * Pjeu) {
	_Pjeu = Pjeu;
}

unsigned long Locus::get_numloc() {
	return(_Pjeu->get_numloc(this));
}
/** Enlève les allèles non représentés dans Jeupop
 */
void Locus::f_nettoieAlleles(){
	unsigned long i;

	for (i = 0; i < _tabPall.size(); ) {
//cerr << i << " " << _tabPall.size() << endl;
    if (_Pjeu->r_allelenonpresent(_tabPall[i])) {
			delete _tabPall[i];
			_tabPall.erase(_tabPall.begin()+i);
		}
		else i++;
	}
}

unsigned long Locus::get_nballnonnuls() const{
/** Retourne le nombre d'allèles non nuls pour ce locus */
	unsigned long nball(0);
	unsigned long i;
	
	for (i=0; i < _tabPall.size(); i++) if (_tabPall[i]->r_nonnul()) nball++;

	return (nball);
}


void Locus::set_microsat_correction(long double valmin, long double valmax, unsigned int value) {
 // corrige la taille des allèles microsats dans l'intervalle valmin<>valmax avec la valeur value

 // 1) trouver les allèles compris entre valmin et valmax
 vector tab_tailles;
 biolib::vecteurs::ChaineCar nom;
 unsigned int i;

 tab_tailles.resize(_tabPall.size());
 for (i=0; i < _tabPall.size(); i++) {
    tab_tailles[i] = (long double) atof(_tabPall[i]->get_nom().c_str());
 }

 for (i=0; i < tab_tailles.size(); i++) {
    if ((tab_tailles[i]>=valmin) && (tab_tailles[i]<=valmax)) {
       _tabPall[i]->set_nbrepet(value);
       nom = "C";
       nom.AjEntier(value);
       _tabPall[i]->set_nom(nom);       
    }
 }
 
 
}

Allele * Locus::new_allele(const string & name, unsigned int nbrepeat) {
  Allele * Pallele(new Allele(this,name));
  //Pallele->set_nom(name);
  Pallele->set_nbrepet(nbrepeat);
  _tabPall.push_back(Pallele);
  return(Pallele);
}
populations-1.2.33+svn0120106.orig/src/population.h0000644000175000017500000000467310531115342022005 0ustar  georgeskgeorgesk
/***************************************************************************
                          population.h  -  Librairie d'objets permettant de manipuler des données
                          						spécifiques aux populations
                             -------------------
    begin                : ven sep 01 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

// population
#ifndef POPULATION_H
#define POPULATION_H

#include "strucpop.h"
#include "metapop.h"
#include "vecteurs.h"

class Population: public StrucPop {
public:
//	Population(Jeupop * pdonnees, long nbind);
//	Population(Jeupop * pdonnees, MetaPop * Pmetapop, long nbind);
	Population(Jeupop * pdonnees);
	Population(MetaPop * Pmetapop);
//	Population(Jeupop * pdonnees, const StrucPop & popori): StrucPop(pdonnees,popori){};
//	Population(Jeupop * pdonnees, const Population & popori);
	Population(const StrucPop & popori, MetaPop * Pmetapop);
	virtual ~Population();

	bool DuType(const string &) const;

	void set_nploidie();
  void set_nploidie(unsigned int nploidie);

  Individu * new_individual(string & name, unsigned int nploidie);
	void AjouterIndividu(Individu * Pind);
	void get_nomniveauxstruc(Titre & nom_niveaux) const;
	unsigned int get_niveau() const;
	string get_nom_chemin() const;

	void f_rempliTabStrucPop(Vecteur &, unsigned int);

  /** Suppression de la Population */
  void SupprPop(StrucPop * Ppop);
	friend class Jeupop;
  /** Suppression d'un individu dans une Population */
  void SupprIndividu(Individu * Pind) ;

  void oPopulationsXML(unsigned int id, ostream & sortie, ostream & infos) ;
	
protected:
	virtual void ifAjouterIndividu(const Individu * Pind);


};

#endif
populations-1.2.33+svn0120106.orig/src/arbreplus.h0000644000175000017500000000470110531115342021602 0ustar  georgeskgeorgesk/***************************************************************************
                          arbreplus.h  -  description
                             -------------------
    begin                : Mon Jun 4 2001
    copyright            : (C) 2001 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#ifndef ARBREPLUS_H
#define ARBREPLUS_H

#include "arbre.h"
#include "couleur.h"

namespace biolib {
namespace arbres {

/**Arbre + informations sur les groupes d'OTUs
  *@author Olivier Langella
  */
class ArbrePlus;

class ArbrePlGroupes : public vector {
// ArbreGroupe contient des groupes d'individus valables pour 1 ArbrePlus
public:
	ArbrePlGroupes(const ArbrePlus * Parbre);
	~ArbrePlGroupes();

	const Couleur & get_couleur(unsigned int i) const {return (_tabCouleur[i]);};
	const string & get_nom(unsigned int i) const {return (_tabNom[i]);};

	void push_back_groupe(const string & nom, const string & couleur);

	int RechercheGroupeOTU(unsigned int id) const;

protected:

	const ArbrePlus * _Parbre;

	vector _tabCouleur;
	vector _tabNom;
//	vector _tabReference;
	
};

class ArbrePlus : public Arbre  {
public: 
	ArbrePlus();
	~ArbrePlus();

	const Couleur & get_couleur_neutre () const {return(_couleur_neutre);};
	const Couleur & get_couleur_otu (unsigned int id) const;

	void define_outgroup(const ChaineCar & outgroup);
	void ajouter_groupe(const ChaineCar & groupe, const string & couleur, const string & nom="");

protected:

	virtual void iPhylipDefGroupe(const string &); //définition d'un groupe
	virtual void oPhylipEcritGroupes(ostream &) const;


	ArbrePlGroupes _tabGroupes;

	ArbreVectUINT _Vind_outgroup;

	Couleur _couleur_neutre;	
};

} //namespace biolib {
} //namespace arbres {


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fDLHHuLHHLHD$8sD$$s:HL(HHHHDŽ$@-LHHp[IH$IH$ IH$@IIHLLD(LH1L(MtLLAt._If8H$I#HHH$IILIL!H{ IHHIvHL$HpI|$$H$xI|$IH{&H{ IHIItZHHDŽ$@HIuHL(HHXHL$HpI|$$L$titKt-I|$I@fDHHxHw jwpHtHH@hfHxgobiName or number of the locus:  was not foundThe locus Output tree file:*     Populations 1.2.33Error n°100 in JeuPopExp:  require diploid populationsError in JeuPopExpWhich level ?level has been set to: Sample size ?Computing...Results matrix output :correspondances.txtStructured PopulationLevel :Structured Populationsback0) Show structure level1) Set level2) 3)  in the object: Error number: JeuPopExpUPGMANeighbor JoiningYour choice: Distance methodsBack) Squared distance: yesSquared distance: no populations inidividuals, ,  bootstraps on individuals bootstraps on locusOnline help missingPlease visit our website :test du jourCopie d'objet Jeupoptoutc2.txtErreur de lecture... Fst, Fis and Fit computationOutput file name ?computing...Allelic frequencies, FstatsFst, Fis, Fit per populationsCompute allelic diversity for reduced sampleTry the linux version.Neighbor-Joiningthe matrix is too smallthe smallest value is: Phylogenetic tree saved in : Reading distance matrix: Locus selection:Select all loci (default)Remove all lociAdd a particular locusRemove a particular locus4) Display selected loci5) Output format:Populations formatPopulations XML formatGenepop formatGenepop modified formatImmanc format6) microsat individuals format7) 8) 9) Admix (G. Bertorelle)10) Genetix11) Fstat (Jerome Goudet)12) vector::_M_fill_insert-output-phylogenyindpop-distDASDmDsneiDccavDadmu2goldsteinFstlatterCpprevostiDrrogerASDDswshriverDRzhivDrureynoldsuDrwreynoldswDrlreynoldsl-constructupgmanj-bootstrap_ind-level-bootstrap_locus individuals--testMain menuExitStructured populationsSHHtHPhH[HT$HHHHH[HHH"8KY+Kiny'&V!=*k8f!E*s3n!=*k8f!E*s3n%:WA:TX-A7BZh<4A7BZh<4-#'7Bs~$*"A7BZhD4(6N\MB8[0
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'1312223734=4}{9)6S[C	P1HHvHf$HHHH@HfDHHH9w`v1HGXH9v(H9vhu	HHHHHHHGxHÿH@HH\$HH8Hl$Ld$HIH{ LHHH?u/HH?u$HHHHl$H$Ld$HJHHH@HName of output file (Phylip tree file) ?**********************************************************                                 **      langella@moulon.inra.fr                           **     http://bioinformatics.org/project/?group_id=84     *Error n°1 in JeuPopExp while exporting to Error n°2 in JeuPopExp: incompatible alleles names to export in Error n°1000 in JeuPopExp: locus names do not exceed 5 caracters in Error n°1001 in JeuPopExp: individual names do not exceed 10 caracters in ApplPopulations::fsetniveau() 1any compute using metapopulation will use this(ex: computing distances or making treesOutput file name (Genepop modified format) ?Genepop format allows only diploid genetic datasetsOutput file name (canonical Genepop format) ?Output file name (Populations format) ?Error writing Populations file...Display Wright indices per lociOutput file format (Immanc format) ?Immanc format allows only diploid genetic datasetsWhat is the name of the population P1 (parental population) ?What is the name of the population P2 (parental population) ?What is the name of the population H (hybrid population)?Output file name (LEA format, M.A. Beaumont, L. Chikhi) ?Output file name (Admix .dat format, G. Bertorelle) ?Output file name (Admix .mtx format, G. Bertorelle) ?Output file (Microsat format) ?Populations is not able to export dataset:Alleles names should be numeric, corresponding to allele size (or number of repetition).Computing distances between populations...Computing distances between individuals...How many times do you want to perform bootstraps ?Populations tree filename (Phylip format):Phylogenetic tree reconstruction aborted, tree file was not writtenCombien de tirages voulez-vous effectuer ?Output file name (Phylip tree format) ?Individuals distance matrix filename :Populations distance matrix filename :http://www.bioinformatics.org/~tryphon/populations/Output file name (Genetix format) ?Output file name (Fstat format) ?Allelic diversity for reduced sampleSorry this version of Populations is unable to read XML files.Output file name (XML Populations format) ?Building phylogenetic tree with UPGMA...Building phylogenetic tree with Neighbor-Joining...Error missing construction method to build phylogenetic treeInconsistant matrix file formatNegative distances in the matrix...to build a tree, you must set negative values to zero.Do you want to set negative values to zero (Y/N) ?The tree file was not written.Individuals tree filename (Phylip format):Error while reading the matrix fileFailure reading matrix file : the matrix is not symetric
Populations only works with euclidian distance matrix
Please check your file and retry

Out of range access in the matrixChoose locus to export (default: all)microsat populations + frequencies formatLEA Likelihood Estimation of AdmixtureDEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) debug output : DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) debug phylogeny : indDEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) debug phylogeny : popDEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) metdist : DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) metconstructarbre : ERROR: Populations is unable to bootstrap on individuals to make a phylogenetic tree of individualsDEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) bootstrap_locus : DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) nb_iterations : DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) phylogeny on individuals DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) Pjeupop->f_distgnt(distances, metdist, _square_distance); DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) larbre.iDistances DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) end larbre.iDistances DEBUG ApplPopulations::fLiPhylogeny(Titre & tab_commandes) set_groupes_arbre(larbre); Input file format seems incorrect...ApplPopulations::fLiPhylogeny(Titre & tab_commandes) ERROR: Negative distances in the matrixReconstructing phylogenetic trees with populationsGet distance matrix between populationsPhylogenetic tree of populationsPhylogenetic tree of populations with bootstraps on locusPhylogenetic tree of populations with bootstraps on individualsChoose locus to compute distances (default: all)Reconstructing phylogenetic trees with individualsGet distance matrix between individualsPhylogenetic tree of individualsPhylogenetic tree of individuals with bootstraps on locusCompute individuals distances + treeCompute populations distances + treeBuild phylogenetic tree with a distance matrixFormated output for other softwaresChoose the output format of matrixmicrosatellites number of repeats correctionsSHHHHxHtH{8H{ HH{[H{ HD$HD$H{HD$HD$HSHHHHxHtH{8H{ H{HH[H{ HD$HD$H{HD$HD$HHHGH+HH9s	HSHHHHxHtH{8H{ HH{[H{ HD$HD$H{HD$HD$HSHHHHxHtH{8H{ H{HH[H{ HD$HD$H{HD$HD$HHl$H\$HLd$Hd~_H]IHLHHHHl$H$Ld$Hf.t[uH]IHLHHHuH롐fffH]IHLHHHuHHHHHHH\$Hl$H_Ld$HIHvHHIt$H}H$Hl$Ld$HHHHSHHH{[HHH\$Hl$HLl$Ld$HLt$L|$HHLoL;otn1MtIEIEH{HGHCHHWH)HHtHHH)H]H\$Hl$ Ld$(Ll$0Lt$8L|$@HHf.HI)IMKL-I9III)ILHT$HT$IKHtHHH3HE1H)HHu]HCO|4E1H)HHu]H;MHtL#MLsLc-f.IAI)ImL4LLL4HLLHH9IIE1I)IH"H\$HHl$Ld$Ll$HLt$L|$HHHH;{t^HtGHGHCHWH)HHtHHH)]H\$Hl$ Ld$(Ll$0Lt$8L|$@HHDH3H)HHH?H9III)ILHT$H3HT$IKHtHE1H)HHtL4LLHCO|4E1H)HHtL4HLLH;MHtL#MLsLc@IAI)ILH?H9(IE1L,I)IH3AWIAVIAUIATIUSHHHoHWHGH)HI9mHHHHH)HH)I9"L9LHCHr	H9LHH)HHT$HHT$(HD$HL$LHHL$H@HtLHHHuI.H\$L9t&fHtHHHHI9uMfJLH\$ M9t'fDHtHHHHI9uMfI.L9tHHL9uI.HtHHD$HT$(I^IHIFHH[]A\A]A^A_H|$0HI^HL)HI9HD$IHHL)HHIM~M)IM~@HHHHIuK\=L9tDHt$0LIL9uH|$0HH[]A\A]A^A_fLH)HHHT$HD$HD$(HD$L+|$txMHHt
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	populations-1.2.33+svn0120106.orig/src/CMakeFiles/CMakeDirectoryInformation.cmake0000644000175000017500000000174611701604740027465 0ustar  georgeskgeorgesk# CMAKE generated file: DO NOT EDIT!
# Generated by "Unix Makefiles" Generator, CMake Version 2.8

# Relative path conversion top directories.
SET(CMAKE_RELATIVE_PATH_TOP_SOURCE "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106")
SET(CMAKE_RELATIVE_PATH_TOP_BINARY "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106")

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SET(CMAKE_FORCE_UNIX_PATHS 1)

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  "/usr/include/qt4/QtGui"
  "/usr/include/qt4/QtXml"
  "/usr/include/qt4/QtCore"
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populations-1.2.33+svn0120106.orig/src/allele.cpp0000644000175000017500000000701710531115342021377 0ustar  georgeskgeorgesk/***************************************************************************
                          allele.cpp  -  description
                             -------------------
    begin                : Thu Sep 14 2000
    copyright            : (C) 2000 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/


//#include "entetepop.h"
#include "allele.h"
#include "locus.h"

//constructeur
Allele::Allele (Locus* Ploc)
{
  _nom.assign("");
  //	strcpy (_nomgpop,_nom.c_str());
  _Ploc = Ploc;

  _miss = r_ismissingvalue(_nom);
  //	if ((_nom == "00") || (_nom == "NULL") || (_nom == "NULL") || (_nom == "NULL")) _nul = true;
  //	else _nul = false;
}


Allele::Allele (const Allele & original, Locus * Ploc)
{
  //constructeur de copies
  _nom.assign(original._nom);

  _Ploc = Ploc;
  _miss = original._miss;
  _nbrepet = original._nbrepet;
}


Allele::Allele (Locus* Ploc,const string & nom)
{
  _nom = nom;
  //	strcpy (_nomgpop,_nom.c_str());
  _Ploc = Ploc;
  _nbrepet = atoi(nom.c_str());

  _miss = r_ismissingvalue(nom);
}

Allele::Allele (Locus* Ploc,const char * nom)
{
  _nom.assign(nom);
  //	strcpy (_nomgpop,_nom.c_str());
  _Ploc = Ploc;
  _nbrepet = atoi(nom);

  _miss = r_ismissingvalue(nom);
}

//destructeur
Allele::~Allele ()
{
  //	delete [] _tabPind;
}

bool Allele::f_verifnum(int typedenum) const
{
  // Vérification du type de numérotation des allèles
  //	1 => type Genepop stricte (2digits)
  //	2 => nom d'alleles = numéros
  //	3 => nom d'alleles = numéros < 999
  //Anomalie 2-> les numéros d'allèles format genepop ne sont pas présents
  unsigned long i;

  switch (typedenum)
  {
  case 1:
    if (_nom.size() != 2) return (false);
    if ((_nom[0] < 48) || ((_nom[0] > 57))) return (false);
    if ((_nom[1] < 48) || ((_nom[1] > 57))) return (false);

    break;
  case 2:
    for (i=0; i < _nom.size();i++)
    {
      if ((_nom[i] < 48) || ((_nom[i] > 57))) return (false);
    }

    break;

  case 3:
    if (_nom.size() > 3) return (false);
    for (i=0; i < _nom.size();i++)
    {
      if ((_nom[i] < 48) || ((_nom[i] > 57))) return (false);
    }

    break;
  }

  return(true);
}

const Allele& Allele::operator= (const Allele & rval)
{

  _nom = rval._nom;
  _miss = rval._miss;
  _nbrepet = rval._nbrepet;
  return(*this);
}

bool Allele::operator== (const Allele & rval) const
{
  //egalité basée sur les noms des allèles et des locus correspondants
  //   PAS sur les pointeurs !!!
  if (rval._Ploc->get_nom() != _Ploc->get_nom()) return (false);

  return((_miss && rval._miss) || (rval._nom == _nom));
}


const string& Allele::get_NomLocus() const
{
  return(_Ploc->get_nom());
}

bool Allele::r_ismissingvalue(const string & nom) const
{
  if ((nom == "0") || (nom == "000") || (nom == "00") || (nom == "null") || (nom == "NULL") || (nom == "miss") || (nom == "missing")) return true;
  else return false;
}

populations-1.2.33+svn0120106.orig/src/jeupopexp.h0000644000175000017500000000603310531115342021622 0ustar  georgeskgeorgesk/***************************************************************************
                          jeupopexp.h  -  Classe dérivée de Jeupop, spécialisée
															dans l'exportation des données
                             -------------------
    begin                : Tue Oct 24 2000
    copyright            : (C) 2000 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

#ifndef JEUPOPEXP_H
#define JEUPOPEXP_H

//#include 
#include 
#include "jeupop.h"
#include "vecteurs.h"

/**
  *@author Olivier Langella
  */

class JeuPopExp {
public: 
	JeuPopExp(Jeupop *);
	~JeuPopExp();

	void oLea(unsigned long P1,unsigned long P2,unsigned long H, ostream & sortie, ostream & infos);
  /** Exportation au format "admix" de G. Bertorelle
voir le site:
http://www.unife.it/genetica/Giorgio/giorgio.html
 */
  void oAdmix_dat(unsigned long P1,unsigned long P2,unsigned long H, ostream & sortie, ostream & infos);
  void oAdmix_mtx(ostream & sortie, ostream & infos);
	void oGenetix(ostream & sortie, ostream & infos);
	void oFstat(ostream & sortie, ostream & infos);
  void oPopulationsXML(ostream & sortie, ostream & infos) const;

private:
	const Jeupop * _Pjeu;
	Jeupop * _Pcopie;
  /** Prépare une copie de jeupop avec 3
populations P1, P2, H (special admixture) */
  void f_prepP1P2H(unsigned long P1,unsigned long P2,unsigned long H, ostream & infos);

public:
	struct Anomalie{

		int le_pb;
		Anomalie (int i, string format):le_pb(i), _format(format){};
		string _message;
		string _format;

		string& fmessage(int num){
			switch (num) {
			case 1:
				_message = _("Error n°1 in JeuPopExp while exporting to ");
				_message += _format;
				break;
			case 2:
				_message = _("Error n°2 in JeuPopExp: incompatible alleles names to export in ");
				_message += _format;
				break;
			case 100:
				_message = _("Error n°100 in JeuPopExp: ");
				_message += _format;
				_message += _(" require diploid populations");
				break;
				
			case 1000:
				_message = _("Error n°1000 in JeuPopExp: locus names do not exceed 5 caracters in ");
				_message += _format;
				break;
			case 1001:
				_message = _("Error n°1001 in JeuPopExp: individual names do not exceed 10 caracters in ");
				_message += _format;
				break;
			default:
				_message = _("Error in JeuPopExp");
				break;
			}
			return(_message);
		}
	};
	
};

#endif

populations-1.2.33+svn0120106.orig/src/chaineficpop.cpp0000644000175000017500000001352410531115342022571 0ustar  georgeskgeorgesk//
// 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 Library 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

//created:
//mer sep 06 14:23:39 CEST 2000 Langella 


/***************************************************************************
                          chaineficpop.cpp  -  Objet pour faciliter la lecture de fichiers genepop/populations
                             -------------------
    begin                : ven sep 06 10:25:55 CEST 2000
    copyright            : (C) 2000 by Olivier Langella CNRS UPR9034
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

#include "chaineficpop.h"

//constructeur
ChaineFicPop::ChaineFicPop(istream & fichier):ChaineCar(""), _fichier(fichier) {
	//_fichier(fichier);
	_fichier.clear();
	_fichier.seekg(0);

	_numeroligne = 0;
	_type_fichier = 0;
	_danspop = false;
	_findefichier = false;
	_boolnompop =  false;
}

//destructeur
ChaineFicPop::~ChaineFicPop() {
	_fichier.clear();
}

int ChaineFicPop::get_titre(biolib::vecteurs::Titre & titres) {
	//lecture des commentaires
//cerr << " ChaineFicPop::get_titre debut" << endl;
//  assign("");
	titres.resize(0);

	if (estuntitre()) titres.push_back(*this);
	
//cerr << " ChaineFicPop::get_titre debut 1" << endl;
	while ((get_ligne()) && (estuntitre())) {
		titres.push_back(*this);
		assign("");
	};
	
//cerr << " ChaineFicPop::get_titre debut 2" << endl;
	if (_fichier.fail()) throw Anomalie(1);

//cerr << " ChaineFicPop::get_titre debut 3" << endl;
	return (0);
}

int ChaineFicPop::get_locus(biolib::vecteurs::Titre & locus) {
	//lecture des locus

	locus.resize(0);

	if ((estunepop()==false) && (*this != "")) ajout_locus(locus);
	
	while ((get_ligne()) && (estunepop()==false)) {
		ajout_locus(locus);
	};
	
	if (_fichier.fail()) throw Anomalie(1);
	if (estunepop()==false) throw Anomalie(2);

	return (0);

}

int ChaineFicPop::get_lignepop() {
	if (_findefichier) return(1);
	get_ligne();
	return(0);
}

int ChaineFicPop::get_nompop(biolib::vecteurs::ChaineCar & nompop) const {

	nompop.assign(_nompop);
//	nompop.Remplacer(" ","_");
/*	if ((GetNbMots()) > 1) GetMot(2, nompop);
	else nompop.assign("");
*/
	return(0);
}

int ChaineFicPop::get_nomind(biolib::vecteurs::ChaineCar & nomind) const {
	if (!(_danspop)) return (1);
	int pos;
	
	pos = find(",", 0);
	if (pos != -1) {
//		ChaineCar mot;
		
		nomind.assign(*this,0, pos);
		nomind.fsupprgauche();
		nomind.fsupprdroite();
//		nomind.assign(mot);
	}
//	nomind.Remplacer(" ","_");

	return(0);
	
}

int ChaineFicPop::get_alleles(biolib::vecteurs::Titre & alleles) const {
//cerr << " ChaineFicPop::get_alleles" << endl;
	if (!(_danspop)) return (1);
	alleles.resize(0);
	int pos;
	
	ChaineCar mots;
	string mot;
	long nbmots, i;
	
	pos = find(",", 0) + 1;
	if (pos != -1) {
		mots.assign(*this,pos, size() - pos);
		
		nbmots = mots.GetNbMots();

		for (i=0; i < nbmots; i++) {
			mots.GetMot(i+1, mot);
			if (mot != "") alleles.push_back(mot);
		}	
	}
	else  return (1);

//cerr << " ChaineFicPop::get_alleles fin 0" << endl;
	return(0);
}

long ChaineFicPop::get_numeroligne() const{
	return(_numeroligne);
}

bool ChaineFicPop::get_ligne() {
//cerr << " ChaineFicPop::get_ligne debut" << endl;
	GetLigneFlot(_fichier);
	_numeroligne++;

	if (_fichier.eof()) _findefichier = true;
	
//cerr << " ChaineFicPop::get_ligne fin" << endl;
	return (_fichier.good());
}

bool ChaineFicPop::estuntitre() {
// détecte les signes d'un titre: """, "Title Line:" ...
	string titre;

  if (size() < 1) return (false);
//cerr << " ChaineFicPop::estuntitre debut" << endl;
	if (operator[](0) == '"') {
//		if (operator[](size()-1) == '"') string titre(*this,1, size() -2);
//cerr << " ChaineFicPop::estuntitre titre " << (size() - 1) << endl;
		titre.assign(*this,1, size() -1);
//cerr << " ChaineFicPop::estuntitre titre " << titre << endl;
		assign(titre);
		return (true);
	}
//cerr << " ChaineFicPop::estuntitre debut 2" << endl;
	int pos;
	string mot("Title line: ");
	
//cerr << " ChaineFicPop::estuntitre debut 3" << endl;
	pos = find(mot, 0);
	if (pos != -1) {
		titre.assign(*this,pos + mot.size(), size() - mot.size() - pos);
		assign(titre);
		return (true);
	}
	
//cerr << " ChaineFicPop::estuntitre debut 4" << endl;
	if (_numeroligne == 1) return(true);

	return (false);
}

bool ChaineFicPop::estunepop() {
// détecte les signes d'un titre: """, "Title Line:" ...
//	string _chainetemp;
	int pos;

	GetMot(1, _chainetemp);
	if ((_chainetemp == "POP")||(_chainetemp == "pop")||(_chainetemp == "Pop")) {
		pos = find(",", 0);
		if (pos > 0) return (false);

		_danspop = true;
		if (size() > 4) {
			_nompop = substr(4, (size() - 4));
			_boolnompop = true; //les noms de pop sont derrière le mot clé pop
		}
		else _nompop.assign("");
		
		return (true);
	}
	return (false);

}

bool ChaineFicPop::estunindividu() const {
// détecte les signes d'un titre: """, "Title Line:" ...
	if (!(_danspop)) return (false);
	
//	string mot;
	
	if (GetNbMots(",") == 2) return (true);
	else return (false);
/*	GetMot(1, mot);
	if (mot[mot.size()-1] == ',') return (true);
	else {
		GetMot(2, mot);
		if (mot == ",") return true;
	}
	return (false);   */
}

void ChaineFicPop::ajout_locus(biolib::vecteurs::Titre & locus) const {
	long nbmots, i;
	string mot;
	
	nbmots = GetNbMots();

	for (i=0; i < nbmots; i++) {
		GetMot(i+1, mot);
		if (mot != "") locus.push_back(mot);
	}

}

bool ChaineFicPop::findefichier() const {
	return (_findefichier);
}

bool ChaineFicPop::get_boolnompop() const {
	return (_boolnompop);
}
populations-1.2.33+svn0120106.orig/src/qtpop/0000755000175000017500000000000011701602133020572 5ustar  georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/src/qtpop/qtpopulations.cpp0000644000175000017500000000063211303771330024225 0ustar  georgeskgeorgesk#include 
#include "mainwindow.h"

int main(int argc, char * * argv) {
	QApplication a(argc, argv);

	abif the_data;
	//string filename("../../doc/test.fsa");
	string filename("");
	//string svgfilename("test.svg");
	if (argc == 2) {
		filename = argv[1];
	}
	MainWindow w;
	w.show();

	if (filename != "") {
		the_data.read_abif_file(filename);

		w.addAbif(the_data);
	}

	return a.exec();
}
populations-1.2.33+svn0120106.orig/src/internat.h0000644000175000017500000000340511142011057021424 0ustar  georgeskgeorgesk /***************************************************************************
                          internat.h  -  description
                             -------------------
    begin                : Thu Sep 21 2000
    copyright            : (C) 2000 by Olivier Langella
    email                : Olivier.Langella@pge.cnrs-gif.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   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.                                   *
 *                                                                         *
 ***************************************************************************/

//internationalisation
#ifndef INTERNAT_H
# define INTERNAT_H
# ifdef MINGW32
#  define OLIV_INTERNAT 0
# endif
# ifdef OLIV_INTERNAT
#   include 
//#   include 
#  define _(String) (String)
#  define gettext(String) (String)
#  define textdomain(String) (String)
#  define setlocale(String1, String2) (String1, String2)
#  define bindtextdomain(String1, String2) (String1, String2)
#  define LOCALEDIR ""
//#  define LC_ALL ""
//#  define LC_NUMERIC ""
#  define PACKAGE ""
# else
#  ifndef _LOCALE_H
#   include 
#   ifndef LOCALEDIR
#    define LOCALEDIR "/usr/share/locale"
#   endif
#  endif
#  ifndef _LIBINTL_H
#   include 
#   ifndef _
#    define _(String) gettext (String)
#   endif
#  endif
# endif
#endif


populations-1.2.33+svn0120106.orig/Makefile0000644000175000017500000001443211701605045020311 0ustar  georgeskgeorgesk# CMAKE generated file: DO NOT EDIT!
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#=============================================================================
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# The shell in which to execute make rules.
SHELL = /bin/sh

# The CMake executable.
CMAKE_COMMAND = /usr/bin/cmake

# The command to remove a file.
RM = /usr/bin/cmake -E remove -f

# The top-level source directory on which CMake was run.
CMAKE_SOURCE_DIR = /home/olivier/eclipse/populations

# The top-level build directory on which CMake was run.
CMAKE_BINARY_DIR = /home/olivier/eclipse/populations

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# Special rule for the target edit_cache
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	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
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.PHONY : install

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	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
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.PHONY : install/strip

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list_install_components:
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.PHONY : list_install_components

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list_install_components/fast: list_install_components
.PHONY : list_install_components/fast

# Special rule for the target package
package: preinstall
	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Run CPack packaging tool..."
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.PHONY : package

# Special rule for the target package
package/fast: package
.PHONY : package/fast

# Special rule for the target package_source
package_source:
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	/usr/bin/cpack --config ./CPackSourceConfig.cmake /home/olivier/eclipse/populations/CPackSourceConfig.cmake
.PHONY : package_source

# Special rule for the target package_source
package_source/fast: package_source
.PHONY : package_source/fast

# Special rule for the target rebuild_cache
rebuild_cache:
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	/usr/bin/cmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
.PHONY : rebuild_cache

# Special rule for the target rebuild_cache
rebuild_cache/fast: rebuild_cache
.PHONY : rebuild_cache/fast

# The main all target
all: cmake_check_build_system
	$(CMAKE_COMMAND) -E cmake_progress_start /home/olivier/eclipse/populations/CMakeFiles /home/olivier/eclipse/populations/CMakeFiles/progress.marks
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	@echo "... depend"
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#=============================================================================
# Special targets to cleanup operation of make.

# Special rule to run CMake to check the build system integrity.
# No rule that depends on this can have commands that come from listfiles
# because they might be regenerated.
cmake_check_build_system:
	$(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
.PHONY : cmake_check_build_system

populations-1.2.33+svn0120106.orig/CMakeLists.txt0000644000175000017500000001222011701605045021402 0ustar  georgeskgeorgesk#http://www.cmake.org/Wiki/CMake:Packaging_With_CPack
cmake_minimum_required(VERSION 2.6)
PROJECT(populations CXX C)

#cpack -G TGZ --config CPackSourceConfig.cmake
# cpack -G TGZ --config CPackSourceConfig.cmake


#.dput.cf
#[olivier-langella]
#fqdn = ppa.launchpad.net
#method = ftp
#incoming = ~olivier-langella/ppa/ubuntu/
#login = olivier-langella
#allow_unsigned_uploads = 0
#
#  debuild -S -sa
# dput -f olivier-langella *changes




message ("compiler : ${CMAKE_BASE_NAME}")


# cross compilation Win32 :
#cd build_win32
#export CC=/usr/bin/i586-mingw32msvc-gcc
#export CXX=/usr/bin/i586-mingw32msvc-g++
#INCLUDE(${populations_SOURCE_DIR}/win32/Toolchain-mingw32.cmake)
#cmake -DCMAKE_TOOLCHAIN_FILE=../win32/Toolchain-mingw32.cmake ..

#IF (MINGW32)
#	ADD_DEFINITIONS(-DCOMPILATION_MINGW32)
#	MESSAGE(coucou)
#	SET( CMAKE_BUILD_TYPE "Debug")
#	SET(CMAKE_CXX_FLAGS_DEBUG "-g")
#ELSE (MINGW32)
#	SET( CMAKE_BUILD_TYPE "Release")
#ENDIF(MINGW32)


IF ( CMAKE_BASE_NAME MATCHES "cl")
	message ("on est sous Windows")
	SET( CMAKE_BUILD_TYPE "Release")
	SET( WIN32 "windows")
ELSE (CMAKE_BASE_NAME MATCHES "cl")
	SET( CMAKE_BUILD_TYPE "Release")
	#SET( CMAKE_BUILD_TYPE "Debug")
ENDIF(CMAKE_BASE_NAME MATCHES "cl")

IF ( CMAKE_BUILD_TYPE MATCHES "Release")
	MESSAGE("compiling as release version")
	ADD_DEFINITIONS("-DQT_NO_DEBUG_OUTPUT")
ELSE ( CMAKE_BUILD_TYPE MATCHES "Release" )
	MESSAGE("compiling as debug version")
ENDIF( CMAKE_BUILD_TYPE MATCHES "Release" )


#CMAKE_CXX_FLAGS
#CMAKE_CXX_FLAGS_DEBUG           -g
#CMAKE_CXX_FLAGS_MINSIZEREL      -Os -DNDEBUG
#CMAKE_CXX_FLAGS_RELEASE         -O3 -DNDEBUG
#CMAKE_CXX_FLAGS_RELWITHDEBINFO  -O2 -g

SET (POPULATIONS_VERSION "1.2.33")

SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
#SET(CPACK_INSTALL_CMAKE_PROJECTS "/tmp;Populations;src;/src")
#SET(CPACK_NSIS_DISPLAY_NAME "CMake 2.5")
SET(CPACK_OUTPUT_CONFIG_FILE "./CPackConfig.cmake")
SET(CPACK_PACKAGE_DESCRIPTION_FILE ${populations_SOURCE_DIR}/COPYING)
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Populations is population genetic software")
SET(CPACK_PACKAGE_EXECUTABLES "populations")
SET(CPACK_PACKAGE_FILE_NAME "populations-${POPULATIONS_VERSION}-Linux-i686")
SET(CPACK_PACKAGE_INSTALL_DIRECTORY "populations ${POPULATIONS_VERSION}")
SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "populations ${POPULATIONS_VERSION}")
SET(CPACK_PACKAGE_NAME "populations")
SET(CPACK_PACKAGE_VENDOR "CNRS")
SET(CPACK_PACKAGE_VERSION ${POPULATIONS_VERSION})
SET(CPACK_PACKAGE_VERSION_MAJOR "1")
SET(CPACK_PACKAGE_VERSION_MINOR "2")
SET(CPACK_PACKAGE_VERSION_PATCH "33")
SET(CPACK_RESOURCE_FILE_LICENSE ${populations_SOURCE_DIR}/COPYING)
SET(CPACK_RESOURCE_FILE_README ${populations_SOURCE_DIR}/README)
SET(CPACK_RESOURCE_FILE_WELCOME ${populations_SOURCE_DIR}/INSTALL)
SET(CPACK_RESOURCE_FILE_LICENSE ${populations_SOURCE_DIR}/ChangeLog)
SET(CPACK_SOURCE_GENERATOR "TGZ;TZ")
SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "./CPackSourceConfig.cmake")
SET(CPACK_SOURCE_PACKAGE_FILE_NAME "populations-${POPULATIONS_VERSION}")
SET(CPACK_SOURCE_STRIP_FILES "")
SET(CPACK_STRIP_FILES "bin/populations")
SET(CPACK_SYSTEM_NAME "Linux-i686")
SET(CPACK_TOPLEVEL_TAG "Linux-i686")


SET(CPACK_SOURCE_IGNORE_FILES 
	"/devel_archives/"
	"/figures/"
	"/Soumis/"
	"Makefile"
	"install_manifest.txt"
	"cmake_install.cmake"
	"cmake_install.cmake"
	"CMakeCache.txt"
	"CPackConfig.cmake"
	"CPackSourceConfig.cmake"
	"install_manifest.txt"
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	"/\\\\.svn/"
	"/\\\\.settings/"
	"Makefile"
	"\\\\.cdtbuild"
	"\\\\.cdtproject"
	"\\\\.project"
	"/win32/"
)
# cpack -G TGZ --config CPackSourceConfig.cmake
# dpkg-buildpackage -rfakeroot
configure_file (${populations_SOURCE_DIR}/src/config.h.cmake ${populations_SOURCE_DIR}/src/config.h)

#SET(CPACK_SOURCE_IGNORE_FILES "/CMakeFiles/;/_CPack_Packages/;/templates/;/debug/;/Debug/;/Release/;/\\\\.svn/;/\\\\.settings/;Makefile;\\\\.cdtbuild;\\\\.cdtproject;\\\\.project")
# cpack -G TGZ --config CPackSourceConfig.cmake
SET(CPACK_PACKAGE_EXECUTABLES "populations" "populations")


SET(CPACK_STRIP_FILES "src/populations")



# for debian package :
SET(CPACK_DEBIAN_PACKAGE_MAINTAINER "Olivier Langella ")
SET(DEBIAN_PACKAGE_BUILDS_DEPENDS "Olivier Langella ")
 


INCLUDE(CPack)

# The name of our project is "HELLO".  CMakeLists files in this project can
# refer to the root source directory of the project as ${HELLO_SOURCE_DIR} and
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project (populations)

# Recurse into the "Hello" and "Demo" subdirectories.  This does not actually
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add_subdirectory (src)
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endif (NOT CMAKE_INSTALL_PREFIX)
INSTALL(PROGRAMS src/populations DESTINATION bin)
#INSTALL(DIRECTORY doc/man1 DESTINATION share/man/man1)
#INSTALL(FILES doc/man1/beads.1 DESTINATION share/man/man1)
populations-1.2.33+svn0120106.orig/obj-x86_64-linux-gnu/0000755000175000017500000000000011701603644022302 5ustar  georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/ChangeLog0000644000175000017500000000000011071407600020402 0ustar  georgeskgeorgeskpopulations-1.2.33+svn0120106.orig/cmake_install.cmake0000644000175000017500000000437211701604740022464 0ustar  georgeskgeorgesk# Install script for directory: /home/georgesk/developpement/populations/populations-1.2.33+svn0120106

# Set the install prefix
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STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")

# Set the install configuration name.
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    SET(CMAKE_INSTALL_CONFIG_NAME "Release")
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  MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)

# Set the component getting installed.
IF(NOT CMAKE_INSTALL_COMPONENT)
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    MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
    SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
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    SET(CMAKE_INSTALL_COMPONENT)
  ENDIF(COMPONENT)
ENDIF(NOT CMAKE_INSTALL_COMPONENT)

# Install shared libraries without execute permission?
IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
  SET(CMAKE_INSTALL_SO_NO_EXE "1")
ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)

IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/bin" TYPE PROGRAM FILES "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106/src/populations")
ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")

IF(NOT CMAKE_INSTALL_LOCAL_ONLY)
  # Include the install script for each subdirectory.
  INCLUDE("/home/georgesk/developpement/populations/populations-1.2.33+svn0120106/src/cmake_install.cmake")

ENDIF(NOT CMAKE_INSTALL_LOCAL_ONLY)

IF(CMAKE_INSTALL_COMPONENT)
  SET(CMAKE_INSTALL_MANIFEST "install_manifest_${CMAKE_INSTALL_COMPONENT}.txt")
ELSE(CMAKE_INSTALL_COMPONENT)
  SET(CMAKE_INSTALL_MANIFEST "install_manifest.txt")
ENDIF(CMAKE_INSTALL_COMPONENT)

FILE(WRITE "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106/${CMAKE_INSTALL_MANIFEST}" "")
FOREACH(file ${CMAKE_INSTALL_MANIFEST_FILES})
  FILE(APPEND "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106/${CMAKE_INSTALL_MANIFEST}" "${file}\n")
ENDFOREACH(file)
populations-1.2.33+svn0120106.orig/CPackConfig.cmake0000644000175000017500000001122711701604740021762 0ustar  georgeskgeorgesk# This file will be configured to contain variables for CPack. These variables
# should be set in the CMake list file of the project before CPack module is
# included. Example variables are:
#   CPACK_GENERATOR                     - Generator used to create package
#   CPACK_INSTALL_CMAKE_PROJECTS        - For each project (path, name, component)
#   CPACK_CMAKE_GENERATOR               - CMake Generator used for the projects
#   CPACK_INSTALL_COMMANDS              - Extra commands to install components
#   CPACK_INSTALL_DIRECTORIES           - Extra directories to install
#   CPACK_PACKAGE_DESCRIPTION_FILE      - Description file for the package
#   CPACK_PACKAGE_DESCRIPTION_SUMMARY   - Summary of the package
#   CPACK_PACKAGE_EXECUTABLES           - List of pairs of executables and labels
#   CPACK_PACKAGE_FILE_NAME             - Name of the package generated
#   CPACK_PACKAGE_ICON                  - Icon used for the package
#   CPACK_PACKAGE_INSTALL_DIRECTORY     - Name of directory for the installer
#   CPACK_PACKAGE_NAME                  - Package project name
#   CPACK_PACKAGE_VENDOR                - Package project vendor
#   CPACK_PACKAGE_VERSION               - Package project version
#   CPACK_PACKAGE_VERSION_MAJOR         - Package project version (major)
#   CPACK_PACKAGE_VERSION_MINOR         - Package project version (minor)
#   CPACK_PACKAGE_VERSION_PATCH         - Package project version (patch)

# There are certain generator specific ones

# NSIS Generator:
#   CPACK_PACKAGE_INSTALL_REGISTRY_KEY  - Name of the registry key for the installer
#   CPACK_NSIS_EXTRA_UNINSTALL_COMMANDS - Extra commands used during uninstall
#   CPACK_NSIS_EXTRA_INSTALL_COMMANDS   - Extra commands used during install


SET(CPACK_BINARY_BUNDLE "")
SET(CPACK_BINARY_CYGWIN "")
SET(CPACK_BINARY_DEB "")
SET(CPACK_BINARY_DRAGNDROP "")
SET(CPACK_BINARY_NSIS "")
SET(CPACK_BINARY_OSXX11 "")
SET(CPACK_BINARY_PACKAGEMAKER "")
SET(CPACK_BINARY_RPM "")
SET(CPACK_BINARY_STGZ "")
SET(CPACK_BINARY_TBZ2 "")
SET(CPACK_BINARY_TGZ "")
SET(CPACK_BINARY_TZ "")
SET(CPACK_BINARY_ZIP "")
SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
SET(CPACK_COMPONENTS_ALL "")
SET(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE")
SET(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE")
SET(CPACK_DEBIAN_PACKAGE_MAINTAINER "Olivier Langella ")
SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
SET(CPACK_INSTALL_CMAKE_PROJECTS "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106;populations;ALL;/")
SET(CPACK_INSTALL_PREFIX "/usr")
SET(CPACK_MODULE_PATH "")
SET(CPACK_NSIS_DISPLAY_NAME "populations 1.2.33")
SET(CPACK_NSIS_INSTALLER_ICON_CODE "")
SET(CPACK_NSIS_INSTALLER_MUI_ICON_CODE "")
SET(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
SET(CPACK_NSIS_PACKAGE_NAME "populations 1.2.33")
SET(CPACK_OUTPUT_CONFIG_FILE "./CPackConfig.cmake")
SET(CPACK_PACKAGE_DEFAULT_LOCATION "/")
SET(CPACK_PACKAGE_DESCRIPTION_FILE "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106/COPYING")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Populations is population genetic software")
SET(CPACK_PACKAGE_EXECUTABLES "populations;populations")
SET(CPACK_PACKAGE_FILE_NAME "populations-1.2.33-Linux-i686")
SET(CPACK_PACKAGE_INSTALL_DIRECTORY "populations 1.2.33")
SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "populations 1.2.33")
SET(CPACK_PACKAGE_NAME "populations")
SET(CPACK_PACKAGE_RELOCATABLE "true")
SET(CPACK_PACKAGE_VENDOR "CNRS")
SET(CPACK_PACKAGE_VERSION "1.2.33")
SET(CPACK_PACKAGE_VERSION_MAJOR "1")
SET(CPACK_PACKAGE_VERSION_MINOR "2")
SET(CPACK_PACKAGE_VERSION_PATCH "33")
SET(CPACK_RESOURCE_FILE_LICENSE "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106/ChangeLog")
SET(CPACK_RESOURCE_FILE_README "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106/README")
SET(CPACK_RESOURCE_FILE_WELCOME "/home/georgesk/developpement/populations/populations-1.2.33+svn0120106/INSTALL")
SET(CPACK_SET_DESTDIR "OFF")
SET(CPACK_SOURCE_CYGWIN "")
SET(CPACK_SOURCE_GENERATOR "TGZ;TZ")
SET(CPACK_SOURCE_IGNORE_FILES "/devel_archives/;/figures/;/Soumis/;Makefile;install_manifest.txt;cmake_install.cmake;cmake_install.cmake;CMakeCache.txt;CPackConfig.cmake;CPackSourceConfig.cmake;install_manifest.txt;/CMakeFiles/;/_CPack_Packages/;/Debug/;/Release/;/\\.externalToolBuilders/;/\\.svn/;/\\.settings/;Makefile;\\.cdtbuild;\\.cdtproject;\\.project;/win32/")
SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "./CPackSourceConfig.cmake")
SET(CPACK_SOURCE_PACKAGE_FILE_NAME "populations-1.2.33")
SET(CPACK_SOURCE_STRIP_FILES "")
SET(CPACK_SOURCE_TBZ2 "")
SET(CPACK_SOURCE_TGZ "")
SET(CPACK_SOURCE_TZ "")
SET(CPACK_SOURCE_ZIP "")
SET(CPACK_STRIP_FILES "src/populations")
SET(CPACK_SYSTEM_NAME "Linux-i686")
SET(CPACK_TOPLEVEL_TAG "Linux-i686")
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	populations
	
	
	
	
		
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SET(CMAKE_AR "/usr/bin/ar")
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