DOMALIGN-0.1.650/0002775000175000017500000000000012171070667010071 500000000000000DOMALIGN-0.1.650/config.sub0000755000175000017500000010532712171070653011773 00000000000000#! /bin/sh # Configuration validation subroutine script. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, # 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, # 2011, 2012 Free Software Foundation, Inc. timestamp='2012-04-18' # This file is (in principle) common to ALL GNU software. # The presence of a machine in this file suggests that SOME GNU software # can handle that machine. It does not imply ALL GNU software can. # # This file 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, see . # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Please send patches to . Submit a context # diff and a properly formatted GNU ChangeLog entry. # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. # You can get the latest version of this script from: # http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. # Each package is responsible for reporting which valid configurations # it does not support. The user should be able to distinguish # a failure to support a valid configuration from a meaningless # configuration. # The goal of this file is to map all the various variations of a given # machine specification into a single specification in the form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM # or in some cases, the newer four-part form: # CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM # It is wrong to echo any other type of specification. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] CPU-MFR-OPSYS $0 [OPTION] ALIAS Canonicalize a configuration name. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.sub ($timestamp) Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" exit 1 ;; *local*) # First pass through any local machine types. echo $1 exit ;; * ) break ;; esac done case $# in 0) echo "$me: missing argument$help" >&2 exit 1;; 1) ;; *) echo "$me: too many arguments$help" >&2 exit 1;; esac # Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). # Here we must recognize all the valid KERNEL-OS combinations. maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \ linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \ knetbsd*-gnu* | netbsd*-gnu* | \ kopensolaris*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` ;; android-linux) os=-linux-android basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown ;; *) basic_machine=`echo $1 | sed 's/-[^-]*$//'` if [ $basic_machine != $1 ] then os=`echo $1 | sed 's/.*-/-/'` else os=; fi ;; esac ### Let's recognize common machines as not being operating systems so ### that things like config.sub decstation-3100 work. We also ### recognize some manufacturers as not being operating systems, so we ### can provide default operating systems below. case $os in -sun*os*) # Prevent following clause from handling this invalid input. ;; -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ -apple | -axis | -knuth | -cray | -microblaze) os= basic_machine=$1 ;; -bluegene*) os=-cnk ;; -sim | -cisco | -oki | -wec | -winbond) os= basic_machine=$1 ;; -scout) ;; -wrs) os=-vxworks basic_machine=$1 ;; -chorusos*) os=-chorusos basic_machine=$1 ;; -chorusrdb) os=-chorusrdb basic_machine=$1 ;; -hiux*) os=-hiuxwe2 ;; -sco6) os=-sco5v6 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco5) os=-sco3.2v5 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco4) os=-sco3.2v4 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2.[4-9]*) os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2v[4-9]*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco5v6*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco*) os=-sco3.2v2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -udk*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -isc) os=-isc2.2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -clix*) basic_machine=clipper-intergraph ;; -isc*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -lynx*178) os=-lynxos178 ;; -lynx*5) os=-lynxos5 ;; -lynx*) os=-lynxos ;; -ptx*) basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` ;; -windowsnt*) os=`echo $os | sed -e 's/windowsnt/winnt/'` ;; -psos*) os=-psos ;; -mint | -mint[0-9]*) basic_machine=m68k-atari os=-mint ;; esac # Decode aliases for certain CPU-COMPANY combinations. case $basic_machine in # Recognize the basic CPU types without company name. # Some are omitted here because they have special meanings below. 1750a | 580 \ | a29k \ | aarch64 | aarch64_be \ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ | am33_2.0 \ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \ | be32 | be64 \ | bfin \ | c4x | clipper \ | d10v | d30v | dlx | dsp16xx \ | epiphany \ | fido | fr30 | frv \ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | hexagon \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ | le32 | le64 \ | lm32 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ | maxq | mb | microblaze | mcore | mep | metag \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ | mips64octeon | mips64octeonel \ | mips64orion | mips64orionel \ | mips64r5900 | mips64r5900el \ | mips64vr | mips64vrel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ | mips64vr5900 | mips64vr5900el \ | mipsisa32 | mipsisa32el \ | mipsisa32r2 | mipsisa32r2el \ | mipsisa64 | mipsisa64el \ | mipsisa64r2 | mipsisa64r2el \ | mipsisa64sb1 | mipsisa64sb1el \ | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ | moxie \ | mt \ | msp430 \ | nds32 | nds32le | nds32be \ | nios | nios2 \ | ns16k | ns32k \ | open8 \ | or32 \ | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle \ | pyramid \ | rl78 | rx \ | score \ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ | spu \ | tahoe | tic4x | tic54x | tic55x | tic6x | tic80 | tron \ | ubicom32 \ | v850 | v850e | v850e1 | v850e2 | v850es | v850e2v3 \ | we32k \ | x86 | xc16x | xstormy16 | xtensa \ | z8k | z80) basic_machine=$basic_machine-unknown ;; c54x) basic_machine=tic54x-unknown ;; c55x) basic_machine=tic55x-unknown ;; c6x) basic_machine=tic6x-unknown ;; m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | picochip) basic_machine=$basic_machine-unknown os=-none ;; m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) ;; ms1) basic_machine=mt-unknown ;; strongarm | thumb | xscale) basic_machine=arm-unknown ;; xgate) basic_machine=$basic_machine-unknown os=-none ;; xscaleeb) basic_machine=armeb-unknown ;; xscaleel) basic_machine=armel-unknown ;; # We use `pc' rather than `unknown' # because (1) that's what they normally are, and # (2) the word "unknown" tends to confuse beginning users. i*86 | x86_64) basic_machine=$basic_machine-pc ;; # Object if more than one company name word. *-*-*) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; # Recognize the basic CPU types with company name. 580-* \ | a29k-* \ | aarch64-* | aarch64_be-* \ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ | avr-* | avr32-* \ | be32-* | be64-* \ | bfin-* | bs2000-* \ | c[123]* | c30-* | [cjt]90-* | c4x-* \ | clipper-* | craynv-* | cydra-* \ | d10v-* | d30v-* | dlx-* \ | elxsi-* \ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \ | h8300-* | h8500-* \ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | hexagon-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ | le32-* | le64-* \ | lm32-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ | mips64octeon-* | mips64octeonel-* \ | mips64orion-* | mips64orionel-* \ | mips64r5900-* | mips64r5900el-* \ | mips64vr-* | mips64vrel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ | mips64vr5900-* | mips64vr5900el-* \ | mipsisa32-* | mipsisa32el-* \ | mipsisa32r2-* | mipsisa32r2el-* \ | mipsisa64-* | mipsisa64el-* \ | mipsisa64r2-* | mipsisa64r2el-* \ | mipsisa64sb1-* | mipsisa64sb1el-* \ | mipsisa64sr71k-* | mipsisa64sr71kel-* \ | mipstx39-* | mipstx39el-* \ | mmix-* \ | mt-* \ | msp430-* \ | nds32-* | nds32le-* | nds32be-* \ | nios-* | nios2-* \ | none-* | np1-* | ns16k-* | ns32k-* \ | open8-* \ | orion-* \ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \ | pyramid-* \ | rl78-* | romp-* | rs6000-* | rx-* \ | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ | sparclite-* \ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | sv1-* | sx?-* \ | tahoe-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ | tile*-* \ | tron-* \ | ubicom32-* \ | v850-* | v850e-* | v850e1-* | v850es-* | v850e2-* | v850e2v3-* \ | vax-* \ | we32k-* \ | x86-* | x86_64-* | xc16x-* | xps100-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ | z8k-* | z80-*) ;; # Recognize the basic CPU types without company name, with glob match. xtensa*) basic_machine=$basic_machine-unknown ;; # Recognize the various machine names and aliases which stand # for a CPU type and a company and sometimes even an OS. 386bsd) basic_machine=i386-unknown os=-bsd ;; 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) basic_machine=m68000-att ;; 3b*) basic_machine=we32k-att ;; a29khif) basic_machine=a29k-amd os=-udi ;; abacus) basic_machine=abacus-unknown ;; adobe68k) basic_machine=m68010-adobe os=-scout ;; alliant | fx80) basic_machine=fx80-alliant ;; altos | altos3068) basic_machine=m68k-altos ;; am29k) basic_machine=a29k-none os=-bsd ;; amd64) basic_machine=x86_64-pc ;; amd64-*) basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; amdahl) basic_machine=580-amdahl os=-sysv ;; amiga | amiga-*) basic_machine=m68k-unknown ;; amigaos | amigados) basic_machine=m68k-unknown os=-amigaos ;; amigaunix | amix) basic_machine=m68k-unknown os=-sysv4 ;; apollo68) basic_machine=m68k-apollo os=-sysv ;; apollo68bsd) basic_machine=m68k-apollo os=-bsd ;; aros) basic_machine=i386-pc os=-aros ;; aux) basic_machine=m68k-apple os=-aux ;; balance) basic_machine=ns32k-sequent os=-dynix ;; blackfin) basic_machine=bfin-unknown os=-linux ;; blackfin-*) basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; bluegene*) basic_machine=powerpc-ibm os=-cnk ;; c54x-*) basic_machine=tic54x-`echo $basic_machine | sed 's/^[^-]*-//'` ;; c55x-*) basic_machine=tic55x-`echo $basic_machine | sed 's/^[^-]*-//'` ;; c6x-*) basic_machine=tic6x-`echo $basic_machine | sed 's/^[^-]*-//'` ;; c90) basic_machine=c90-cray os=-unicos ;; cegcc) basic_machine=arm-unknown os=-cegcc ;; convex-c1) basic_machine=c1-convex os=-bsd ;; convex-c2) basic_machine=c2-convex os=-bsd ;; convex-c32) basic_machine=c32-convex os=-bsd ;; convex-c34) basic_machine=c34-convex os=-bsd ;; convex-c38) basic_machine=c38-convex os=-bsd ;; cray | j90) basic_machine=j90-cray os=-unicos ;; craynv) basic_machine=craynv-cray os=-unicosmp ;; cr16 | cr16-*) basic_machine=cr16-unknown os=-elf ;; crds | unos) basic_machine=m68k-crds ;; crisv32 | crisv32-* | etraxfs*) basic_machine=crisv32-axis ;; cris | cris-* | etrax*) basic_machine=cris-axis ;; crx) basic_machine=crx-unknown os=-elf ;; da30 | da30-*) basic_machine=m68k-da30 ;; decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) basic_machine=mips-dec ;; decsystem10* | dec10*) basic_machine=pdp10-dec os=-tops10 ;; decsystem20* | dec20*) basic_machine=pdp10-dec os=-tops20 ;; delta | 3300 | motorola-3300 | motorola-delta \ | 3300-motorola | delta-motorola) basic_machine=m68k-motorola ;; delta88) basic_machine=m88k-motorola os=-sysv3 ;; dicos) basic_machine=i686-pc os=-dicos ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp ;; dpx20 | dpx20-*) basic_machine=rs6000-bull os=-bosx ;; dpx2* | dpx2*-bull) basic_machine=m68k-bull os=-sysv3 ;; ebmon29k) basic_machine=a29k-amd os=-ebmon ;; elxsi) basic_machine=elxsi-elxsi os=-bsd ;; encore | umax | mmax) basic_machine=ns32k-encore ;; es1800 | OSE68k | ose68k | ose | OSE) basic_machine=m68k-ericsson os=-ose ;; fx2800) basic_machine=i860-alliant ;; genix) basic_machine=ns32k-ns ;; gmicro) basic_machine=tron-gmicro os=-sysv ;; go32) basic_machine=i386-pc os=-go32 ;; h3050r* | hiux*) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; h8300hms) basic_machine=h8300-hitachi os=-hms ;; h8300xray) basic_machine=h8300-hitachi os=-xray ;; h8500hms) basic_machine=h8500-hitachi os=-hms ;; harris) basic_machine=m88k-harris os=-sysv3 ;; hp300-*) basic_machine=m68k-hp ;; hp300bsd) basic_machine=m68k-hp os=-bsd ;; hp300hpux) basic_machine=m68k-hp os=-hpux ;; hp3k9[0-9][0-9] | hp9[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k2[0-9][0-9] | hp9k31[0-9]) basic_machine=m68000-hp ;; hp9k3[2-9][0-9]) basic_machine=m68k-hp ;; hp9k6[0-9][0-9] | hp6[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k7[0-79][0-9] | hp7[0-79][0-9]) basic_machine=hppa1.1-hp ;; hp9k78[0-9] | hp78[0-9]) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[0-9][13679] | hp8[0-9][13679]) basic_machine=hppa1.1-hp ;; hp9k8[0-9][0-9] | hp8[0-9][0-9]) basic_machine=hppa1.0-hp ;; hppa-next) os=-nextstep3 ;; hppaosf) basic_machine=hppa1.1-hp os=-osf ;; hppro) basic_machine=hppa1.1-hp os=-proelf ;; i370-ibm* | ibm*) basic_machine=i370-ibm ;; i*86v32) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv32 ;; i*86v4*) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv4 ;; i*86v) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv ;; i*86sol2) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-solaris2 ;; i386mach) basic_machine=i386-mach os=-mach ;; i386-vsta | vsta) basic_machine=i386-unknown os=-vsta ;; iris | iris4d) basic_machine=mips-sgi case $os in -irix*) ;; *) os=-irix4 ;; esac ;; isi68 | isi) basic_machine=m68k-isi os=-sysv ;; m68knommu) basic_machine=m68k-unknown os=-linux ;; m68knommu-*) basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; m88k-omron*) basic_machine=m88k-omron ;; magnum | m3230) basic_machine=mips-mips os=-sysv ;; merlin) basic_machine=ns32k-utek os=-sysv ;; microblaze) basic_machine=microblaze-xilinx ;; mingw32) basic_machine=i386-pc os=-mingw32 ;; mingw32ce) basic_machine=arm-unknown os=-mingw32ce ;; miniframe) basic_machine=m68000-convergent ;; *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*) basic_machine=m68k-atari os=-mint ;; mips3*-*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'` ;; mips3*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown ;; monitor) basic_machine=m68k-rom68k os=-coff ;; morphos) basic_machine=powerpc-unknown os=-morphos ;; msdos) basic_machine=i386-pc os=-msdos ;; ms1-*) basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'` ;; msys) basic_machine=i386-pc os=-msys ;; mvs) basic_machine=i370-ibm os=-mvs ;; nacl) basic_machine=le32-unknown os=-nacl ;; ncr3000) basic_machine=i486-ncr os=-sysv4 ;; netbsd386) basic_machine=i386-unknown os=-netbsd ;; netwinder) basic_machine=armv4l-rebel os=-linux ;; news | news700 | news800 | news900) basic_machine=m68k-sony os=-newsos ;; news1000) basic_machine=m68030-sony os=-newsos ;; news-3600 | risc-news) basic_machine=mips-sony os=-newsos ;; necv70) basic_machine=v70-nec os=-sysv ;; next | m*-next ) basic_machine=m68k-next case $os in -nextstep* ) ;; -ns2*) os=-nextstep2 ;; *) os=-nextstep3 ;; esac ;; nh3000) basic_machine=m68k-harris os=-cxux ;; nh[45]000) basic_machine=m88k-harris os=-cxux ;; nindy960) basic_machine=i960-intel os=-nindy ;; mon960) basic_machine=i960-intel os=-mon960 ;; nonstopux) basic_machine=mips-compaq os=-nonstopux ;; np1) basic_machine=np1-gould ;; neo-tandem) basic_machine=neo-tandem ;; nse-tandem) basic_machine=nse-tandem ;; nsr-tandem) basic_machine=nsr-tandem ;; op50n-* | op60c-*) basic_machine=hppa1.1-oki os=-proelf ;; openrisc | openrisc-*) basic_machine=or32-unknown ;; os400) basic_machine=powerpc-ibm os=-os400 ;; OSE68000 | ose68000) basic_machine=m68000-ericsson os=-ose ;; os68k) basic_machine=m68k-none os=-os68k ;; pa-hitachi) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; paragon) basic_machine=i860-intel os=-osf ;; parisc) basic_machine=hppa-unknown os=-linux ;; parisc-*) basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; pbd) basic_machine=sparc-tti ;; pbb) basic_machine=m68k-tti ;; pc532 | pc532-*) basic_machine=ns32k-pc532 ;; pc98) basic_machine=i386-pc ;; pc98-*) basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentium | p5 | k5 | k6 | nexgen | viac3) basic_machine=i586-pc ;; pentiumpro | p6 | 6x86 | athlon | athlon_*) basic_machine=i686-pc ;; pentiumii | pentium2 | pentiumiii | pentium3) basic_machine=i686-pc ;; pentium4) basic_machine=i786-pc ;; pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*) basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumpro-* | p6-* | 6x86-* | athlon-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentium4-*) basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'` ;; 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We pick the logical manufacturer. vendor=unknown case $basic_machine in *-unknown) case $os in -riscix*) vendor=acorn ;; -sunos*) vendor=sun ;; -cnk*|-aix*) vendor=ibm ;; -beos*) vendor=be ;; -hpux*) vendor=hp ;; -mpeix*) vendor=hp ;; -hiux*) vendor=hitachi ;; -unos*) vendor=crds ;; -dgux*) vendor=dg ;; -luna*) vendor=omron ;; -genix*) vendor=ns ;; -mvs* | -opened*) vendor=ibm ;; -os400*) vendor=ibm ;; -ptx*) vendor=sequent ;; -tpf*) vendor=ibm ;; -vxsim* | -vxworks* | -windiss*) vendor=wrs ;; -aux*) vendor=apple ;; -hms*) vendor=hitachi ;; -mpw* | -macos*) vendor=apple ;; -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*) vendor=atari ;; -vos*) vendor=stratus ;; esac basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"` ;; esac echo $basic_machine$os exit # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" # End: DOMALIGN-0.1.650/src/0002775000175000017500000000000012171070667010660 500000000000000DOMALIGN-0.1.650/src/domainalign.c0000664000175000017500000012541611741637161013235 00000000000000/* @source domainalign application ** ** Generates DAF files (domain alignment files) of structure-based sequence ** alignments for nodes in a DCF file (domain classification file). ** ** @author: Copyright (C) Ranjeeva Ranasinghe ** @author: Copyright (C) Jon Ison (jison@ebi.ac.uk) ** @@ ** ** 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. ** ******************************************************************************* ** ** DOMAINALIGN documentation ** See http://wwww.emboss.org ** ** Please cite the authors and EMBOSS. ** ** Rice P, Bleasby A.J. 2000. EMBOSS - The European Molecular Biology Open ** Software Suite. Trends in Genetics, 15:276-278. ** See also http://www.uk.embnet.org/Software/EMBOSS ** ** Email jison@ebi.ac.uk. ** ** NOTES ** Implement futher alignment options, e.g. TCOFFEE. ** Implement proper residue number positions in alignment ('0' is given on ** each side of the sequence currently). ******************************************************************************/ #include #include "emboss.h" #define MODE_STAMP 1 #define MODE_TCOFFEE 2 /****************************************************************************** ** ** PROTOTYPES ** ******************************************************************************/ static void domainalign_ProcessStampFile(AjPStr in, AjPStr out, AjPDomain domain, ajint noden, AjPFile logf); static void domainalign_writelast(AjPDomain domain, ajint noden, AjPStr *last_node, ajint *last_nodeid); static void domainalign_writeid(AjPDomain domain, ajint noden, AjPDirout daf, AjPDirout super, AjPStr *align, AjPStr *alignc); static void domainalign_writesid(AjPDomain domain, ajint noden, AjPStr *id); static void domainalign_stamp(AjPDomain prevdomain, AjPDomain domain, AjPDirout daf, AjPDirout super, AjPDirout singlets, AjPStr align, AjPStr alignc, AjPStr dom, AjPStr name, AjPStr set, AjPStr scan, AjPStr sort, AjPStr log, AjPStr out, AjBool keepsinglets, ajint moden, ajint noden, ajint nset, AjPFile logf); static void domainalign_keepsinglets(AjPDomain domain, ajint noden, AjPDirout singlets, AjPFile logf); static void domainalign_ProcessTcoffeeFile(AjPStr in, AjPStr out, AjPDomain domain, ajint noden, AjPFile logf); static void domainalign_tcoffee(AjPDomain domain, AjPStr in, AjPStr align, AjPStr alignc, AjPStr pdbnames, ajint noden, AjPFile logf); /* @prog domainalign ********************************************************** ** ** Generates DAF files (domain alignment files) structure-based sequence ** alignments for nodes in a DCF file (domain classification file). ** ******************************************************************************/ int main(int argc, char **argv) { ajint famn = 0; /* Counter for the families. */ ajint nset = 0; /* No. entries in family. */ ajint last_nodeid = 0; /* SCOP Sunid of last family that was processed. */ AjPStr last_node = NULL; /* Last family that was processed. */ AjPStr exec = NULL; /* The UNIX command line to be executed. */ AjPStr out = NULL; /* Name of stamp alignment file. */ AjPStr align = NULL; /* Name of sequence alignment file. */ AjPStr alignc = NULL; /* Name of structure alignment file. */ AjPStr log = NULL; /* Name of STAMP log file. */ AjPStr dom = NULL; /* Name of file containing single domain. */ AjPStr set = NULL; /* Name of file containing set of domains. */ AjPStr scan = NULL; /* Name of temp. file used by STAMP. */ AjPStr sort = NULL; /* Name of temp. file used by STAMP. */ AjPStr name = NULL; /* Base name of STAMP temp files. */ AjPStr pdbnames = NULL; /* Names of domain pdb files to be passed to TCOFFEEE. */ AjPDir pdb = NULL; /* Path of domain coordinate files (pdb format input). */ AjPDirout daf = NULL; /* Path of sequence alignment files for output. */ AjPDirout super = NULL; /* Path of structure alignment files for output. */ AjPDirout singlets = NULL; /* Path of FASTA singlet sequence files for output. */ AjPStr temp1 = NULL; /* A temporary string. */ AjPFile dcfin = NULL; /* File pointer for original Escop.dat file.*/ AjPFile domf = NULL; /* File pointer for single domain file. */ AjPFile setf = NULL; /* File pointer for domain set file. */ AjPFile logf = NULL; /* Log file. */ AjPDomain domain = NULL; /* Pointer to domain structure. */ AjPDomain prevdomain = NULL; /* Pointer to previous domain structure. */ AjEDomainType type = ajEDomainTypeNULL; /* AJAX Domain Type enumeration ** (ajEDomainTypeSCOP or ** ajEDomainTypeCATH) in the ** DCF file. */ AjPStr *node = NULL; /* Node of alignment . */ ajint noden = 0; /*1: Class (SCOP), 2: Fold (SCOP) etc, see ACD file. */ AjPStr *mode = NULL; /* Mode of operation from acd*/ ajint moden = 0; /* Program mode, 1: MODE_STAMP, 2: MODE_TCOFFEE (not yet implemented). */ AjBool keepsinglets= ajFalse; /*Whether to retain sequences of singlet families and write them to an output file. */ AjPStr temp = NULL; /* A temporary string. */ /* Initialise strings etc*/ last_node = ajStrNew(); exec = ajStrNew(); out = ajStrNew(); align = ajStrNew(); alignc = ajStrNew(); log = ajStrNew(); dom = ajStrNew(); set = ajStrNew(); scan = ajStrNew(); sort = ajStrNew(); name = ajStrNew(); temp = ajStrNew(); temp1 = ajStrNew(); pdbnames = ajStrNew(); /* Read data from acd. */ embInitPV("domainalign",argc,argv,"DOMALIGN",VERSION); dcfin = ajAcdGetInfile("dcfinfile"); pdb = ajAcdGetDirectory("pdbdir"); daf = ajAcdGetOutdir("dafoutdir"); super = ajAcdGetOutdir("superoutdir"); singlets = ajAcdGetOutdir("singletsoutdir"); node = ajAcdGetList("node"); mode = ajAcdGetList("mode"); keepsinglets = ajAcdGetToggle("keepsinglets"); logf = ajAcdGetOutfile("logfile"); /* Convert the selected node and mode to an integer. */ if(!(ajStrToInt(node[0], &noden))) ajFatal("Could not parse ACD node option"); if(!(ajStrToInt(mode[0], &moden))) ajFatal("Could not parse ACD node option"); /* Initialise random number generator for naming of temp. files. */ ajRandomSeed(); ajFilenameSetTempname(&name); /* Create names for temp. files. */ ajStrAssignS(&log, name); ajStrAppendC(&log, ".log"); ajStrAssignS(&dom, name); ajStrAppendC(&dom, ".dom"); ajStrAssignS(&set, name); ajStrAppendC(&set, ".set"); ajStrAssignS(&scan, name); ajStrAppendC(&scan, ".scan"); ajStrAssignS(&sort, name); ajStrAppendC(&sort, ".sort"); ajStrAssignS(&out, name); ajStrAppendC(&out, ".out"); /* Initialise last_node with something that is not in SCOP. */ ajStrAssignC(&last_node,"!!!!!"); /* Open STAMP domain set file. */ if(moden == MODE_STAMP) { if(!(setf=ajFileNewOutNameS(set))) ajFatal("Could not open domain set file\n"); } /* Get domain type. */ type = ajDomainDCFType(dcfin); /* Start of main application loop. */ while((domain=(ajDomainReadCNew(dcfin, "*", type)))) { /* A new family. */ if(((domain->Type == ajEDomainTypeSCOP) && (((noden==1) && (last_nodeid != domain->Scop->Sunid_Class)) || ((noden==2) && (last_nodeid != domain->Scop->Sunid_Fold)) || ((noden==3) && (last_nodeid != domain->Scop->Sunid_Superfamily))|| ((noden==4) && (last_nodeid != domain->Scop->Sunid_Family)))) || ((domain->Type == ajEDomainTypeCATH) && (((noden==5) && (last_nodeid != domain->Cath->Class_Id)) || ((noden==6) && (last_nodeid != domain->Cath->Arch_Id)) || ((noden==7) && (last_nodeid != domain->Cath->Topology_Id)) || ((noden==8) && (last_nodeid != domain->Cath->Superfamily_Id)) || ((noden==9) && (last_nodeid != domain->Cath->Family_Id))))) { /* If we have done the first family. */ if(famn) { /* Create the output file for the alignment - the name will be the same as the Sunid for the DOMAIN family. */ domainalign_writeid(prevdomain, noden, daf, super, &align, &alignc); if(moden == MODE_STAMP) { /* Close domain set file. */ ajFileClose(&setf); /* Call STAMP. */ /* Family with 2 or more entries. */ if(nset > 1) { domainalign_stamp(prevdomain, domain, daf, super, singlets, align, alignc, dom, name, set, scan, sort, log, out, keepsinglets, moden, noden, nset, logf); } else if(keepsinglets) /* Singlet family. */ domainalign_keepsinglets(prevdomain, noden, singlets, logf); /* Open STAMP domain set file. */ if(!(setf=ajFileNewOutNameS(set))) ajFatal("Could not open domain set file\n"); } else { /* Call TCOFEE. */ if(nset > 1) domainalign_tcoffee(prevdomain, out, align, alignc, pdbnames, noden, logf); else if(keepsinglets) /* Singlet family. */ domainalign_keepsinglets(prevdomain, noden, singlets, logf); } /* Set the number of members of the new family to zero. */ nset = 0; /* Clear TCOFFEE argument. */ ajStrSetClear(&pdbnames); } /* Open, write and close STAMP domain file. */ if(moden == MODE_STAMP) { if(!(domf=ajFileNewOutNameS(dom))) ajFatal("Could not open domain file\n"); ajStrAssignS(&temp, ajDomainGetId(domain)); ajStrFmtLower(&temp); ajFmtPrintF(domf, "%S %S { ALL }\n", temp, temp); ajFileClose(&domf); } /* Copy current family name to last_node. */ domainalign_writelast(domain, noden, &last_node, &last_nodeid); /* Copy current domain pointer to prevdomain. */ ajDomainDel(&prevdomain); prevdomain=NULL; ajDomainCopy(&prevdomain, domain); /* Increment family counter. */ famn++; } ajStrAssignS(&temp, ajDomainGetId(domain)); ajStrFmtLower(&temp); /* Write STAMP domain set file. */ if(moden == MODE_STAMP) ajFmtPrintF(setf, "%S %S { ALL }\n", temp, temp); /* Write TCOFFEE argument. */ else { ajStrAppendS(&pdbnames, ajDirGetPath(pdb)); ajStrAppendS(&pdbnames, temp); ajStrAppendC(&pdbnames, "."); ajStrAppendS(&pdbnames, ajDirGetExt(pdb)); ajStrAppendC(&pdbnames, " "); } ajDomainDel(&domain); /* Increment number of members in family. */ nset++; } /* End of main application loop. */ domain=prevdomain; ajFmtPrint("\nProcessing node %d\n", last_nodeid); /* Create the output file for the alignment - the name will be the same as the Sunid for the DOMAIN family. */ domainalign_writeid(prevdomain, noden, daf, super, &align, &alignc); /* Code to process last family. */ if(moden == MODE_STAMP) { /*Close domain set file. */ ajFileClose(&setf); /* ajFmtPrint("\n***** SECOND CALL\n");. */ if(nset > 1) { domainalign_stamp(prevdomain, domain, daf, super, singlets, align, alignc, dom, name, set, scan, sort, log, out, keepsinglets, moden, noden, nset, logf); } else if(keepsinglets) /* Singlet family. */ domainalign_keepsinglets(prevdomain, noden, singlets, logf); } else { /* Call TCOFEE. */ if(nset > 1) domainalign_tcoffee(prevdomain, out, align, alignc, pdbnames, noden, logf); else if(keepsinglets) /* Singlet family. */ domainalign_keepsinglets(prevdomain, noden, singlets, logf); } /* Remove all temporary files. */ ajSysFileUnlinkS(log); ajSysFileUnlinkS(dom); ajSysFileUnlinkS(set); ajSysFileUnlinkS(scan); ajSysFileUnlinkS(sort); ajSysFileUnlinkS(out); ajStrAssignS(&temp, name); ajStrAppendC(&temp, ".mat"); ajSysFileUnlinkS(temp); /* Tidy up*/ ajDomainDel(&domain); ajFileClose(&dcfin); ajStrDel(&last_node); ajStrDel(&exec); ajStrDel(&log); ajStrDel(&dom); ajStrDel(&set); ajStrDel(&scan); ajStrDel(&sort); ajStrDel(&name); ajStrDel(&out); ajStrDel(&align); ajStrDel(&alignc); ajStrDel(&pdbnames); ajDirDel(&pdb); ajDiroutDel(&daf); ajDiroutDel(&super); ajDiroutDel(&singlets); ajStrDel(&temp); ajStrDel(&temp1); ajStrDel(&node[0]); AJFREE(node); ajStrDel(&mode[0]); AJFREE(mode); ajFileClose(&logf); ajExit(); return 0; } /* @funcstatic domainalign_ProcessStampFile *********************************** ** ** This function is very specific to domainalign, hence it is not library code. ** This function reads the output of ver2hor, i.e. a stamp alignment (Figure ** 1 below) and creates an output file which is annotated with DOMAIN records ** (Figure 2 below). ** ** ** Figure 1 ** ** VER2HOR R.B. Russell, 1995 ** Prints STAMP alignments in horizontal format ** for quick viewing ** Reading Alignment... ** Getting STAMP information... ** 6 STAMP fields read in for 547 positions ** Processing the alignment... ** Output: ** Very reliable => Pij' >=6 for stretches of >=3 ** Less reliable => Pij' >=4.5 for stretches of >=3 ** Post reliable => All Pij' > stamp_post parameter for stretches >=3 ** ** Number 10 20 30 40 50 ** d1maac_ egrEDPQLLVRVRGGQLRGIRLKAPGGPVSAFLGIPFAEPPVGSRRFMPPEPKRPWS ** d1maad__1 EDPQLLVRVRGGQLRGIRLKAPGGPVSAFLGIPFAEPPVGSRRFMPPEPKRPWS ** ** d1maac__ds ????????????????????????????????????????????????????????? ** d1maad__1_ ?????????????????????????????????????????????????????? ** ** Very similar ---111111111111111111111111111111111111111111111111111111 ** Less similar ---111111111111111111111111111111111111111111111111111111 ** Post similar ---111111111111111111111111111111111111111111111111111111 ** ** Number 60 70 80 90 100 110 ** d1maac_ GVLDATTFQNVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPASPTPV ** d1maad__1 GVLDATTFQNVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPASPTPV ** ** d1maac__ds ????????????????????????????????????????????????????????? ** d1maad__1_ ????????????????????????????????????????????????????????? ** ** Very similar 111111111111111111111111111111111111111111111111111111111 ** Less similar 111111111111111111111111111111111111111111111111111111111 ** Post similar 111111111111111111111111111111111111111111111111111111111 ** ** Number 120 130 140 150 160 170 ** d1maac_ LIWIYGGGFYSGAASLDVYDGRFLAQVEGAVLVSMNYRVGTFGFLALPGSREAPGNV ** d1maad__1 LIWIYGGGFYSGAASLDVYDGRFLAQVEGAVLVSMNYRVGTFGFLALPGSREAPGNV ** ** d1maac__ds ????????????????????????????????????????????????????????? ** d1maad__1_ ????????????????????????????????????????????????????????? ** ** Very similar 111111111111111111111111111111111111111111111111111111111 ** Less similar 111111111111111111111111111111111111111111111111111111111 ** Post similar 111111111111111111111111111111111111111111111111111111111 ** ** ** ** Figure 2 ** ** # CL Alpha and beta proteins (a/b) ** # XX ** # FO alpha/beta-Hydrolases ** # XX ** # SF alpha/beta-Hydrolases ** # XX ** # FA Acetylcholinesterase-like ** # XX ** # SI 1321321 ** # XX ** # Number 10 20 30 40 50 ** d1maac_ egrEDPQLLVRVRGGQLRGIRLKAPGGPVSAFLGIPFAEPPVGSRRFMPPEPKRPWS ** d1maad_ EDPQLLVRVRGGQLRGIRLKAPGGPVSAFLGIPFAEPPVGSRRFMPPEPKRPWS ** # Post similar ---111111111111111111111111111111111111111111111111111111 ** ** # Number 60 70 80 90 100 110 ** d1maac_ GVLDATTFQNVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPASPTPV ** d1maad_ GVLDATTFQNVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTPYPRPASPTPV ** # Post similar 111111111111111111111111111111111111111111111111111111111 ** ** # Number 120 130 140 150 160 170 ** d1maac_ LIWIYGGGFYSGAASLDVYDGRFLAQVEGAVLVSMNYRVGTFGFLALPGSREAPGNV ** d1maad_ LIWIYGGGFYSGAASLDVYDGRFLAQVEGAVLVSMNYRVGTFGFLALPGSREAPGNV ** # Post similar 111111111111111111111111111111111111111111111111111111111 ** ** ** @param [r] in [AjPStr] Name of input file ** @param [r] out [AjPStr] Name of output file ** @param [r] domain [AjPDomain] DOMAIN structure with DOMAIN classification ** records ** @param [r] noden [ajint] Node number. ** @param [r] logf [AjPFile] Log file. ** ** @return [void] ** @@ ******************************************************************************/ static void domainalign_ProcessStampFile(AjPStr in, AjPStr out, AjPDomain domain, ajint noden, AjPFile logf) { AjPFile outf = NULL; /* Output file pointer. */ AjPFile inf = NULL; /* Input file pointer. */ AjPStr temp1 = NULL; /* Temporary string. */ AjPStr temp2 = NULL; /* Temporary string. */ AjPStr temp3 = NULL; /* Temporary string. */ AjPStr line = NULL; /* Line of text from input file. */ ajint blk = 1; /* Count of the current block in the input file. Block 1 is the numbering and protein sequences, Block 2 is the secondary structure, Block 3 is the Very/Less/Post similar records*/ AjBool ok = ajFalse; /* Initialise strings. */ line = ajStrNew(); temp1 = ajStrNew(); temp2 = ajStrNew(); temp3 = ajStrNew(); /* Open input and output files. */ if(!(inf=ajFileNewInNameS(in))) ajFatal("Could not open input file in domainalign_ProcessStampFile"); /* Start of code for reading input file. Ignore everything up to first line beginning with 'Number'. */ while((ajReadlineTrim(inf,&line))) { /* ajFileReadLine will trim the tailing \n. */ if((ajStrGetCharPos(line, 1)=='\0')) { ok = ajTrue; break; } } /* Read rest of input file. */ if(ok) { /* Write DOMAIN classification records to file. */ if(!(outf=ajFileNewOutNameS(out))) ajFatal("Could not open output file in domainalign_ProcessStampFile"); if((domain->Type == ajEDomainTypeSCOP)) { ajFmtPrintF(outf,"# TY SCOP\n# XX\n"); ajFmtPrintF(outf,"# CL %S",domain->Scop->Class); ajFmtPrintSplit(outf,domain->Scop->Fold,"\n# XX\n# FO ", 75," \t\n\r"); ajFmtPrintSplit(outf,domain->Scop->Superfamily,"# XX\n# SF ", 75," \t\n\r"); ajFmtPrintSplit(outf,domain->Scop->Family,"# XX\n# FA ", 75," \t\n\r"); ajFmtPrintF(outf,"# XX\n"); } else { ajFmtPrintF(outf,"# TY CATH\n# XX\n"); ajFmtPrintF(outf,"# CL %S",domain->Cath->Class); ajFmtPrintSplit(outf,domain->Cath->Architecture,"\n# XX\n# AR ", 75," \t\n\r"); ajFmtPrintSplit(outf,domain->Cath->Topology,"# XX\n# TP ",75, " \t\n\r"); ajFmtPrintSplit(outf,domain->Cath->Superfamily,"# XX\n# SF ",75, " \t\n\r"); ajFmtPrintF(outf,"# XX\n"); } if((domain->Type == ajEDomainTypeSCOP)) { if(noden==1) ajFmtPrintF(outf,"# SI %d\n# XX",domain->Scop->Sunid_Class); else if(noden==2) ajFmtPrintF(outf,"# SI %d\n# XX",domain->Scop->Sunid_Fold); else if(noden==3) ajFmtPrintF(outf,"# SI %d\n# XX", domain->Scop->Sunid_Superfamily); else if(noden==4) ajFmtPrintF(outf,"# SI %d\n# XX", domain->Scop->Sunid_Family); else ajFatal("Node number error in domainalign_ProcessStampFile"); } else { if(noden==5) ajFmtPrintF(outf,"# SI %d\n# XX", domain->Cath->Class_Id); else if(noden==6) ajFmtPrintF(outf,"# SI %d\n# XX", domain->Cath->Arch_Id); else if(noden==7) ajFmtPrintF(outf,"# SI %d\n# XX",domain->Cath->Topology_Id); else if(noden==8) ajFmtPrintF(outf,"# SI %d\n# XX", domain->Cath->Superfamily_Id); else if(noden==9) ajFmtPrintF(outf,"# SI %d\n# XX",domain->Cath->Family_Id); else ajFatal("Node number error in domainalign_ProcessStampFile"); } while((ajReadlineTrim(inf,&line))) { /* Increment counter for block of file. */ if((ajStrGetCharPos(line, 1)=='\0')) { blk++; if(blk==4) blk=1; continue; } /* Block of numbering line and protein sequences. */ if(blk==1) { /* Print the number line out as it is. */ if(ajStrPrefixC(line,"Number")) ajFmtPrintF(outf,"\n# %7s %S\n"," ", line); else { /* Read only the 7 characters of the domain identifier code in. */ ajFmtScanS(line, "%S", &temp1); ajStrAssignSubS(&temp2, temp1, 0, 6); /* Read the sequence. */ ajStrAssignSubS(&temp3, line, 13, 69); ajStrExchangeSetCC(&temp3, " ", "X"); ajFmtPrintF(logf, "Replaced ' ' in STAMP alignment " "with 'X'\n"); ajStrFmtUpper(&temp3); /* Write domain id code and sequence out. */ ajFmtPrintF(outf,"%-15S%7d %S%7d\n", temp2, 0, temp3, 0); } } /* Secondary structure filled with '????' (unwanted). */ else if(blk==2) { continue; } /* Similarity lines. */ else { if(ajStrPrefixC(line,"Post")) { /* Read the sequence. */ ajStrAssignSubS(&temp3, line, 13, 69); /* Write post similar line out. */ ajFmtPrintF(outf,"%-15s%7s %S\n","# Post_similar", " ", temp3); } /* Ignore Very and Less similar lines. */ else continue; } } } else /* ok == ajFalse. */ { ajWarn("\n***********************************************\n" "* STAMP was called but output file was EMPTY! *\n" "* NO OUTPUT FILE GENERATED FOR THIS NODE. *\n" "***********************************************\n"); ajFmtPrintF(logf, "STAMP called but output file empty. " "No output file for this node!"); } /* Clean up and close input and output files. */ ajFileClose(&outf); ajFileClose(&inf); ajStrDel(&line); ajStrDel(&temp1); ajStrDel(&temp2); ajStrDel(&temp3); /* All done. */ return; } /* @funcstatic domainalign_writelast ****************************************** ** ** House-keeping function. ** ** @param [r] domain [AjPDomain] Domain. ** @param [r] noden [ajint] Node number. ** @param [r] last_node [AjPStr *] Last node. ** @param [r] last_nodeid [ajint *] Id of last node. ** ** @return [void] ** ** @@ ****************************************************************************/ static void domainalign_writelast(AjPDomain domain, ajint noden, AjPStr *last_node, ajint *last_nodeid) { if(noden==1) { ajStrAssignS(last_node, domain->Scop->Class); *last_nodeid = domain->Scop->Sunid_Class; } else if (noden==2) { ajStrAssignS(last_node, domain->Scop->Fold); *last_nodeid = domain->Scop->Sunid_Fold; } else if (noden==3) { ajStrAssignS(last_node, domain->Scop->Superfamily); *last_nodeid = domain->Scop->Sunid_Superfamily; } else if (noden==4) { ajStrAssignS(last_node, domain->Scop->Family); *last_nodeid = domain->Scop->Sunid_Family; } else if (noden==5) { ajStrAssignS(last_node, domain->Cath->Class); *last_nodeid = domain->Cath->Class_Id ; } else if (noden==6) { ajStrAssignS(last_node, domain->Cath->Architecture); *last_nodeid = domain->Cath->Arch_Id; } else if (noden==7) { ajStrAssignS(last_node, domain->Cath->Topology); *last_nodeid = domain->Cath->Topology_Id; } else if (noden==8) { ajStrAssignS(last_node, domain->Cath->Superfamily); *last_nodeid = domain->Cath->Superfamily_Id; } else if (noden==9) { /* There is no text describing the CATH families. */ ajFmtPrintS(last_node, "%d", domain->Cath->Family_Id); *last_nodeid = domain->Cath->Family_Id; } } /* @funcstatic domainalign_writeid ******************************************** ** ** House-keeping function. ** ** @param [r] domain [AjPDomain] Domain. ** @param [r] noden [ajint] Node number. ** @param [r] daf [AjPDirout] Domain alignment files. ** @param [r] super [AjPDirout] Structural superimposition files. ** @param [r] align [AjPStr *] Align. ** @param [r] alignc [AjPStr *] Alignc. ** ** @return [void] ** ** @@ ****************************************************************************/ static void domainalign_writeid(AjPDomain domain, ajint noden, AjPDirout daf, AjPDirout super, AjPStr *align, AjPStr *alignc) { AjPStr temp=NULL; temp=ajStrNew(); if(noden==1) ajStrFromInt(&temp, domain->Scop->Sunid_Class); else if (noden==2) ajStrFromInt(&temp, domain->Scop->Sunid_Fold); else if (noden==3) ajStrFromInt(&temp, domain->Scop->Sunid_Superfamily); else if (noden==4) ajStrFromInt(&temp, domain->Scop->Sunid_Family); else if (noden==5) ajStrFromInt(&temp, domain->Cath->Class_Id ); else if (noden==6) ajStrFromInt(&temp, domain->Cath->Arch_Id); else if (noden==7) ajStrFromInt(&temp, domain->Cath->Topology_Id); else if (noden==8) ajStrFromInt(&temp, domain->Cath->Superfamily_Id); else if (noden==9) ajStrFromInt(&temp, domain->Cath->Family_Id); ajStrAssignS(align, temp); ajStrInsertS(align, 0, ajDiroutGetPath(daf)); ajStrAppendC(align, "."); ajStrAppendS(align, ajDiroutGetExt(daf)); ajStrAssignS(alignc, temp); ajStrInsertS(alignc, 0, ajDiroutGetPath(super)); ajStrAppendC(alignc, "."); ajStrAppendS(alignc, ajDiroutGetExt(super)); ajDebug("daf file '%S' super file '%S'\n", *align, *alignc); ajStrDel(&temp); return; } /* @funcstatic domainalign_writesid ******************************************* ** ** House-keeping function. ** ** @param [r] domain [AjPDomain] Domain. ** @param [r] noden [ajint] Node number. ** @param [r] id [AjPStr *] Id. ** ** @return [void] ** ** @@ ****************************************************************************/ static void domainalign_writesid(AjPDomain domain, ajint noden, AjPStr *id) { if(noden==1) ajStrFromInt(id, domain->Scop->Sunid_Class); else if (noden==2) ajStrFromInt(id, domain->Scop->Sunid_Fold); else if (noden==3) ajStrFromInt(id, domain->Scop->Sunid_Superfamily); else if (noden==4) ajStrFromInt(id, domain->Scop->Sunid_Family); else if (noden==5) ajStrFromInt(id, domain->Cath->Class_Id ); else if (noden==6) ajStrFromInt(id, domain->Cath->Arch_Id); else if (noden==7) ajStrFromInt(id, domain->Cath->Topology_Id); else if (noden==8) ajStrFromInt(id, domain->Cath->Superfamily_Id); else if (noden==9) ajStrFromInt(id, domain->Cath->Family_Id); return; } /* @funcstatic domainalign_stamp ********************************************** ** ** Call STAMP and process files. ** ** @param [r] prevdomain [AjPDomain] Previous domain. ** @param [r] domain [AjPDomain] This domain. ** @param [r] daf [AjPDirout] Domain alignment files. ** @param [r] super [AjPDirout] Superimposition files. ** @param [r] singlets [AjPDirout] Singlet files. ** @param [r] align [AjPStr] Align. ** @param [r] alignc [AjPStr] Alignc. ** @param [r] dom [AjPStr] Dom. ** @param [r] name [AjPStr] Name. ** @param [r] set [AjPStr] Name of set file. ** @param [r] scan [AjPStr] Name of scan file. ** @param [r] sort [AjPStr] Name of sort file. ** @param [r] log [AjPStr] Log file name. ** @param [r] out [AjPStr] Out file name. ** @param [r] keepsinglets [AjBool] Keep singlet sequences or not. ** @param [r] moden [ajint] Mode number. ** @param [r] noden [ajint] Node number. ** @param [r] nset [ajint] Number in set. ** @param [r] logf [AjPFile] Lof file. ** ** ** @return [void] True on success ** @@ ****************************************************************************/ static void domainalign_stamp(AjPDomain prevdomain, AjPDomain domain, AjPDirout daf, AjPDirout super, AjPDirout singlets, AjPStr align, AjPStr alignc, AjPStr dom, AjPStr name, AjPStr set, AjPStr scan, AjPStr sort, AjPStr log, AjPStr out, AjBool keepsinglets, ajint moden, ajint noden, ajint nset, AjPFile logf) { AjPStr exec = NULL; /* The UNIX command line to be executed. */ AjPFile clusterf = NULL; /* File pointer for log file. */ ajint ncluster = 0; /* Counter for the number of clusters. */ AjPStr line = NULL; /* Holds a line from the log file. */ AjPRegexp rexp = NULL; /* For parsing no. of clusters in log file */ AjPStr temp = NULL; /* A temporary string. */ ajint x = 0; /* Loop counter. */ /* TODO: The following parameters are unused. */ (void) domain; (void) daf; (void) super; (void) singlets; (void) keepsinglets; (void) moden; (void) nset; exec = ajStrNew(); line = ajStrNew(); temp = ajStrNew(); rexp = ajRegCompC("^(Cluster:)"); ajDebug("domainalign_stamp name: '%S'\n", name); /* Call STAMP. */ ajFmtPrintS(&exec, "%S -l %S -s -n 2 -slide 5 -prefix %S -d %S", ajAcdGetpathC("stamp"), dom, name, set); ajFmtPrint("\n%S\n\n", exec); ajSysExecS(exec); ajFmtPrintS(&exec, "%S -f %S -s Sc 2.5", ajAcdGetpathC("sorttrans"), scan); ajFmtPrint("\n%S > %S\n\n", exec, sort); ajSysExecOutnameS(exec, sort); ajFmtPrintS(&exec, "%S -l %S -prefix %S", ajAcdGetpathC("stamp"), sort, name); ajFmtPrint("\n%S > %S\n\n", exec, log); ajSysExecOutnameS(exec, log); ajFmtPrintS(&exec, "%S -f %S -g -o %S", ajAcdGetpathC("transform"), sort, alignc); ajFmtPrint("\n%S\n\n", exec); ajSysExecS(exec); /* Count the number of clusters in the log file. */ if(!(clusterf=ajFileNewInNameS(log))) ajFatal("Could not open log file '%S'\n", log); ncluster=0; while(ajReadlineTrim(clusterf,&line)) if(ajRegExec(rexp,line)) ncluster++; ajFileClose(&clusterf); ajDebug("ncluster: %d\n", ncluster); /* Call STAMP ... calculate two fields for structural equivalence using threshold Pij value of 0.5, see stamp manual v4.1 pg 27. */ ajFmtPrintS(&exec,"%S -f %S.%d -min 0.5", ajAcdGetpathC("poststamp"), name, ncluster); ajFmtPrint("%S\n\n", exec); ajSysExecS(exec); /* Call STAMP ... convert block format alignment into clustal format. */ ajFmtPrintS(&exec,"%S -f %S.%d.post", ajAcdGetpathC("ver2hor"), name, ncluster); ajFmtPrint("%S > %S\n\n", exec, out); ajSysExecOutnameS(exec, out); /* Process STAMP alignment file and generate alignment file for output. */ domainalign_ProcessStampFile(out, align, prevdomain, noden, logf); /* Remove all temporary files. */ for(x=1;x %S\n", exec, in); ajSysExecOutnameS(exec, in); /* Process tcoffee alignment file and generate alignment file for output. */ domainalign_ProcessTcoffeeFile(in, align, domain, noden, logf); ajStrDel(&exec); return; } /* @funcstatic domainalign_ProcessTcoffeeFile ********************************* ** ** Parses tcoffee output. ** ** @param [r] in [AjPStr] Name of TCOFFEE input file ** @param [r] align [AjPStr] Name of sequence alignment file for output ** @param [r] domain [AjPDomain] Domain being aligned ** @param [r] noden [ajint] Node-level of alignment** ** @param [r] logf [AjPFile] Log file ** ** @return [void] True on success ** @@ ****************************************************************************/ static void domainalign_ProcessTcoffeeFile(AjPStr in, AjPStr align, AjPDomain domain, ajint noden, AjPFile logf) { AjPFile outf = NULL; /* Output file pointer. */ AjPFile inf = NULL; /* Input file pointer. */ AjPStr temp1 = NULL; /* Temporary string. */ AjPStr temp2 = NULL; /* Temporary string. */ AjPStr temp3 = NULL; /* Temporary string. */ AjPStr line = NULL; /* Line of text from input file. */ /* TODO: The following parameters are unused. */ (void) logf; /* Initialise strings. */ line = ajStrNew(); temp1 = ajStrNew(); temp2 = ajStrNew(); temp3 = ajStrNew(); /* Open input and output files. */ if(!(inf=ajFileNewInNameS(in))) ajFatal("Could not open input file in domainalign_ProcessTcoffeeFile"); if(!(outf=ajFileNewOutNameS(align))) ajFatal("Could not open output file in domainalign_ProcessTcoffeeFile"); /*Write DOMAIN classification records to file*/ if((domain->Type == ajEDomainTypeSCOP)) { ajFmtPrintF(outf,"# TY SCOP\n# XX\n"); ajFmtPrintF(outf,"# CL %S",domain->Scop->Class); ajFmtPrintSplit(outf,domain->Scop->Fold,"\n# XX\n# FO ",75," \t\n\r"); ajFmtPrintSplit(outf,domain->Scop->Superfamily,"# XX\n# SF ",75," \t\n\r"); ajFmtPrintSplit(outf,domain->Scop->Family,"# XX\n# FA ",75," \t\n\r"); ajFmtPrintF(outf,"# XX\n"); } else { ajFmtPrintF(outf,"# TY CATH\n# XX\n"); ajFmtPrintF(outf,"# CL %S",domain->Cath->Class); ajFmtPrintSplit(outf,domain->Cath->Architecture,"\n# XX\n# AR ",75," \t\n\r"); ajFmtPrintSplit(outf,domain->Cath->Topology,"# XX\n# TP ",75," \t\n\r"); ajFmtPrintSplit(outf,domain->Cath->Superfamily,"# XX\n# SF ",75," \t\n\r"); ajFmtPrintF(outf,"# XX\n"); } if((domain->Type == ajEDomainTypeSCOP)) { if(noden==1) ajFmtPrintF(outf,"# SI %d\n# XX\n",domain->Scop->Sunid_Class); else if(noden==2) ajFmtPrintF(outf,"# SI %d\n# XX\n",domain->Scop->Sunid_Fold); else if(noden==3) ajFmtPrintF(outf,"# SI %d\n# XX\n",domain->Scop->Sunid_Superfamily); else if(noden==4) ajFmtPrintF(outf,"# SI %d\n# XX\n", domain->Scop->Sunid_Family); else ajFatal("Node number error in domainalign_ProcessStampFile"); } else { if(noden==5) ajFmtPrintF(outf,"# SI %d\n# XX\n", domain->Cath->Class_Id); else if(noden==6) ajFmtPrintF(outf,"# SI %d\n# XX\n", domain->Cath->Arch_Id); else if(noden==7) ajFmtPrintF(outf,"# SI %d\n# XX\n",domain->Cath->Topology_Id); else if(noden==8) ajFmtPrintF(outf,"# SI %d\n# XX\n",domain->Cath->Superfamily_Id); else if(noden==9) ajFmtPrintF(outf,"# SI %d\n# XX\n",domain->Cath->Family_Id); else ajFatal("Node number error in domainalign_ProcessStampFile"); } /* Start of code for reading input file. */ /*Ignore everything up to first line beginning with 'Number'*/ while((ajReadlineTrim(inf,&line))) /* ajFileReadLine will trim the tailing \n. */ if((ajStrGetCharPos(line, 1)=='\0')) break; /* Read rest of input file. */ while((ajReadlineTrim(inf,&line))) { if((ajStrGetCharPos(line, 1)=='\0')) continue; /* Print the number line out as it is. */ else if(ajStrPrefixC(line,"CLUSTAL")) continue; else if(ajStrPrefixC(line," ")) ajFmtPrintF(outf,"\n"); /* write out a block of protein sequences. */ else { /* Read only the 7 characters of the domain identifier code in. */ ajFmtScanS(line, "%S %S", &temp1,&temp3); ajStrAssignSubS(&temp2, temp1, 0, 6); /* Read the sequence ajStrAssignSubS(&temp3, line, 13, 69); ajStrExchangeSetCC(&temp3, " ", "X"); ajStrFmtUpper(&temp3);*/ /* Write domain id code and sequence out. */ ajFmtPrintF(outf,"%-13S%S\n",temp2, temp3); } } /* Clean up and close input and output files. */ ajFileClose(&outf); ajFileClose(&inf); ajStrDel(&line); ajStrDel(&temp1); ajStrDel(&temp2); ajStrDel(&temp3); /* All done. */ return; } /* @funcstatic domainalign_keepsinglets *************************************** ** ** Write singlet sequences to file. ** ** @param [r] domain [AjPDomain] ** @param [r] noden [ajint] ** @param [r] singlets [AjPDirout] ** @param [r] logf [AjPFile] ** ** @return [void] True on success ** @@ ****************************************************************************/ static void domainalign_keepsinglets(AjPDomain domain, ajint noden, AjPDirout singlets, AjPFile logf) { AjPStr temp2 = NULL; /* A temporary string. */ AjPFile singf = NULL; /* File pointer for singlets file. */ EmbPHitlist hitlist = NULL; /* Hitlist object for output of data. */ temp2 = ajStrNew(); domainalign_writesid(domain, noden, &temp2); if(MAJSTRGETLEN(ajDomainGetSeqPdb(domain))) { /* Write Hit object. */ hitlist = embHitlistNew(1); hitlist->Type = domain->Type; ajStrAssignS(&hitlist->hits[0]->Seq, ajDomainGetSeqPdb(domain)); ajStrAssignS(&hitlist->hits[0]->Acc, ajDomainGetAcc(domain)); ajStrAssignS(&hitlist->hits[0]->Spr, ajDomainGetSpr(domain)); ajStrAssignS(&hitlist->hits[0]->Dom, ajDomainGetId(domain)); if((domain->Type == ajEDomainTypeSCOP)) { ajStrAssignS(&hitlist->Class, domain->Scop->Class); ajStrAssignS(&hitlist->Fold, domain->Scop->Fold); ajStrAssignS(&hitlist->Superfamily, domain->Scop->Superfamily); ajStrAssignS(&hitlist->Family, domain->Scop->Family); if(noden==4) hitlist->Sunid_Family = domain->Scop->Sunid_Family; else if(noden==3) hitlist->Sunid_Family = domain->Scop->Sunid_Superfamily; else if(noden==2) hitlist->Sunid_Family = domain->Scop->Sunid_Fold; else if(noden==1) hitlist->Sunid_Family = domain->Scop->Sunid_Class; } else { ajStrAssignS(&hitlist->Class, domain->Cath->Class); ajStrAssignS(&hitlist->Architecture, domain->Cath->Architecture); ajStrAssignS(&hitlist->Topology, domain->Cath->Topology); ajStrAssignS(&hitlist->Superfamily, domain->Cath->Superfamily); if(noden==9) hitlist->Sunid_Family = domain->Cath->Family_Id; if(noden==8) hitlist->Sunid_Family = domain->Cath->Superfamily_Id; else if(noden==7) hitlist->Sunid_Family = domain->Cath->Topology_Id; else if(noden==6) hitlist->Sunid_Family = domain->Cath->Arch_Id; else if(noden==5) hitlist->Sunid_Family = domain->Cath->Class_Id; } singf = ajFileNewOutNameDirS(temp2, singlets); embHitlistWriteFasta(singf, hitlist); /* ajFmtPrintF(singf, ">%S\n%S\n", temp2, ajDomainGetSeqPdb(domain)); */ ajFileClose(&singf); } else { ajWarn("No sequence found (no 'DS' record in DCF file) for singlet %S " "despite configuring to save singlets. " "NO file written!", ajDomainGetId(domain)); ajFmtPrintF(logf, "No sequence found (no 'DS' record in DCF file) for " "singlet %S despite configuring to save singlets. " "NO file written!", ajDomainGetId(domain)); } ajStrDel(&temp2); return; } DOMALIGN-0.1.650/src/domainrep.c0000664000175000017500000005211411741637230012720 00000000000000/* @source domainrep application ** ** Reorder DCF file (domain classification file) so that the representative ** structure of each user-specified node is given first. ** ** ** @author: Copyright (C) Mathew Blades ** @author: Copyright (C) Jon Ison (jison@ebi.ac.uk) ** @@ ** ** 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. ** ******************************************************************************* ** ** DOMAINREP documentation ** See http://wwww.emboss.org ** ** Please cite the authors and EMBOSS. ** ** Rice P, Bleasby A.J. 2000. EMBOSS - The European Molecular Biology Open ** Software Suite. Trends in Genetics, 15:276-278. ** See also http://www.uk.embnet.org/Software/EMBOSS ** ** Email jison@ebi.ac.uk. ** ** NOTES ** The stamp application must be installed on the system that is running ** domainrep and correctly configured (see DOMAINREP documentation). ******************************************************************************/ #include #include "emboss.h" /****************************************************************************** ** ** PROTOTYPES ** ******************************************************************************/ static AjBool domainrep_WriteRmsd(ajint x, ajint y, AjPFloat2d *scores, AjPFile fptr); static void domainrep_writelast(AjPDomain domain, ajint noden, AjPStr *last_node, ajint *last_nodeid); /* @prog domainrep ************************************************************ ** ** Reorder scop classificaiton file so that the representative ** structure of each family is given first. ** ******************************************************************************/ int main(int argc, char **argv) { ajint nfam = 0; /* Counter for the families */ ajint x = 0; /* Counter */ ajint y = 0; /* Counter */ ajint last_nodeid= 0; /* SCOP Sunid of last family that was processed */ AjPStr last_node = NULL; /* Last node that was processed */ AjPStr exec = NULL; /* The UNIX command line to be executed*/ AjPStr dom = NULL; /* Name of file containing single domain*/ AjPStr set = NULL; /* Name of file containing set of domains*/ AjPStr out = NULL; /* Name of file containing pairwise rmsd values */ AjPStr scan = NULL; /* Name of temp. file used by STAMP. */ AjPStr name = NULL; /* Base name of STAMP temp files */ AjPStr temp = NULL; /* A temporary string */ AjPFile dcfin = NULL; /* File pointer for Escop.dat file (input)*/ AjPFile dcfout = NULL; /* File pointer for Escop.dat file (output)*/ AjPFile domf = NULL; /* File pointer for single domain file */ AjPFile setf = NULL; /* File pointer for domain set file */ AjPFile outf = NULL; /* File pointer for file containing pairwise rmsd values */ AjPDomain domain = NULL; /* Pointer to domain structure */ AjPList famlist = NULL; /* List of Scopobjects for current family */ AjPDomain *arr = NULL; /* Array of pointers to the famlist data */ AjPDomain tmp = NULL; /* Temp. pointer for freeing famlist*/ ajint famsize = 0; /* No. domains in the family */ AjPFloat2d scores = NULL; /* Array of pairwise rmsd values */ AjPFloat means = NULL; /* Array of average pairwise rmsd values */ float reso_cnt = 0.0F; /* Used to calculate means array */ ajint divisor = 0; /* Used to calculate means array */ ajint ignore = 0; /* Used for writing ordered scop output file */ float min = 0.0F; /* Used for writing ordered scop output file */ AjPStr node = NULL; /* Node of redundancy removal */ ajint noden = 0; /*1: Class (SCOP), 2: Fold (SCOP) etc, see ACD file */ AjEDomainType type = ajEDomainTypeNULL; /* AJAX Domain Type enumeration ** of domain (ajEDomainTypeSCOP or ** ajEDomainTypeCATH) in the ** DCF file. */ /* Initialise strings etc*/ last_node = ajStrNew(); exec = ajStrNew(); dom = ajStrNew(); set = ajStrNew(); name = ajStrNew(); temp = ajStrNew(); scan = ajStrNew(); famlist = ajListNew(); /* Read data from acd */ embInitPV("domainrep",argc,argv,"DOMALIGN",VERSION); dcfin = ajAcdGetInfile("dcfinfile"); dcfout = ajAcdGetOutfile("dcfoutfile"); node = ajAcdGetListSingle("node"); /* Convert the selected node to an integer. */ if(!(ajStrToInt(node, &noden))) ajFatal("Could not parse ACD node option"); /* Initialise random number generator for naming of temp. files*/ ajRandomSeed(); ajFilenameSetTempname(&name); /* Create names for temp. files*/ ajStrAssignS(&dom, name); ajStrAppendC(&dom, ".dom"); ajStrAssignS(&set, name); ajStrAppendC(&set, ".set"); ajStrAssignS(&out, name); ajStrAppendC(&out, ".out"); ajStrAssignS(&scan, name); ajStrAppendC(&scan, ".scan"); /* Initialise last_node with something that is not in SCOP. */ ajStrAssignC(&last_node,"!!!!!"); type = ajDomainDCFType(dcfin); /* Start of main application loop. */ while((domain=(ajDomainReadCNew(dcfin, "*", type)))) { /* A new family. */ if(((domain->Type == ajEDomainTypeSCOP) && (((noden == 1) && (last_nodeid != domain->Scop->Sunid_Class)) || ((noden == 2) && (last_nodeid != domain->Scop->Sunid_Fold)) || ((noden == 3) && (last_nodeid != domain->Scop->Sunid_Superfamily))|| ((noden == 4) && (last_nodeid != domain->Scop->Sunid_Family)))) || ((domain->Type == ajEDomainTypeCATH) && (((noden == 5) && (last_nodeid != domain->Cath->Class_Id)) || ((noden == 6) && (last_nodeid != domain->Cath->Arch_Id)) || ((noden == 7) && (last_nodeid != domain->Cath->Topology_Id)) || ((noden == 8) && (last_nodeid != domain->Cath->Superfamily_Id)) || ((noden == 9) && (last_nodeid != domain->Cath->Family_Id))))) { /* If we have done the first family*/ if(nfam) { /* Get family size. */ famsize = ajListGetLength(famlist); if(famsize>2) { /* Create an array of pointers to the famlist data. */ ajListToarray(famlist, (void ***) &(arr)); /* Allocate & initialise scores and mean arrays. */ scores = ajFloat2dNewRes(famsize); for(x=0;x2) { /* Create an array of pointers to the famlist data. */ ajListToarray(famlist, (void ***) &(arr)); /* Allocate & initialise scores and mean arrays. */ scores = ajFloat2dNewRes(famsize); for(x=0;xScop->Class); *last_nodeid = domain->Scop->Sunid_Class; } else if (noden==2) { ajStrAssignS(last_node, domain->Scop->Fold); *last_nodeid = domain->Scop->Sunid_Fold; } else if (noden==3) { ajStrAssignS(last_node, domain->Scop->Superfamily); *last_nodeid = domain->Scop->Sunid_Superfamily; } else if (noden==4) { ajStrAssignS(last_node, domain->Scop->Family); *last_nodeid = domain->Scop->Sunid_Family; } else if (noden==5) { ajStrAssignS(last_node, domain->Cath->Class); *last_nodeid = domain->Cath->Class_Id ; } else if (noden==6) { ajStrAssignS(last_node, domain->Cath->Architecture); *last_nodeid = domain->Cath->Arch_Id; } else if (noden==7) { ajStrAssignS(last_node, domain->Cath->Topology); *last_nodeid = domain->Cath->Topology_Id; } else if (noden==8) { ajStrAssignS(last_node, domain->Cath->Superfamily); *last_nodeid = domain->Cath->Superfamily_Id; } else if (noden==9) { /* There is no text describing the CATH families. */ ajFmtPrintS(last_node, "%d", domain->Cath->Family_Id); *last_nodeid = domain->Cath->Family_Id; } } DOMALIGN-0.1.650/src/seqalign.c0000664000175000017500000004425111741637252012554 00000000000000/* @source seqalign application ** ** Reads a DAF file (domain alignment file) and a DHF (domain hits file) and ** writes a DAF file extended with the hits. ** ** @author: Copyright (C) Ranjeeva Ranasinghe ** @author: Copyright (C) Jon Ison (jison@ebi.ac.uk) ** @@ ** ** 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. ** ******************************************************************************* ** ** SEQALIGN Documentation ** See http://wwww.emboss.org ** ** Please cite the authors and EMBOSS. ** ** Rice P, Bleasby A.J. 2000. EMBOSS - The European Molecular Biology Open ** Software Suite. Trends in Genetics, 15:276-278. ** See also http://www.uk.embnet.org/Software/EMBOSS ** ** Email jison@ebi.mrc.ac.uk. ** ** NOTES ** seqalign writes a temporary clustalw input file in fasta format (via a call ** to embDmxScopalgWriteFasta) rather than clustal format. This is to ensure ** it will work on input alignments that have been hand-edited by Jalview. ** (Jalview writes a deviant "clustal" format file that causes clustalw to fail). ** ****************************************************************************/ #include #include "emboss.h" /* @prog seqalign ************************************************************* ** ** Reads a DAF file (domain alignment file) and a DHF (domain hits file) and ** writes a DAF file extended with the hits. ** ******************************************************************************/ int main(int argc, char **argv) { AjPList inseqs = NULL; /* Directory of input sequences. Is made to point to inseqsdhf or inseqsdaf. */ AjPList inseqsdhf = NULL; /* Directory of DAF file (domain alignment file) or singlet sequence files (input). */ AjPList inseqsdaf = NULL; /* Directory of DAF file (domain alignment file) or singlet sequence files (input). */ AjPStr inname = NULL; /* Full name of current DAF or singlet file */ AjPFile inf = NULL; /* DAF or singlet file (input) */ AjPDir dhfin = NULL; /* Directory of domain hits files (input). */ AjPFile hitsinf = NULL; /* Current domain hits file. */ AjPStr hitsname = NULL; /* Name of current domain hits file. */ AjPDirout dafout = NULL; /* Directory of domain alignment outfiles */ AjPStr tmp_name = NULL; /* Random name for temp. files. */ AjPStr clustin1 = NULL; /* Name of clustalw input alignment file. */ AjPFile clustinf1 = NULL; /* Clustalw input align file (CLUSTAL fmt) */ AjPStr clustin2 = NULL; /* Name of clustalw input sequence file. */ AjPFile clustinf2 = NULL; /* Clustalw input sequence file */ AjPStr clustout = NULL; /* Name of clustalw file that will be created, will be reformated into domain alignment format */ AjPStr clustdnd = NULL; /* the name of the Clustal tree file (delete)*/ AjPFile logf = NULL; /* Log file pointer */ ajuint x=0; /* Loop counter */ AjPStr cmd = NULL; /* Executable command */ AjPFile alg_in = NULL; /* the alignment file for reading */ AjPFile alg_out = NULL; /* the alignment file for writing */ AjPStr outname = NULL; /* Name of domain alignment file (output). */ AjPStr line = NULL; AjPScopalg scopalign = NULL; /* Scopalg object for input alignmennt (domain alignment file) */ AjPSeqset seqset_a = NULL; /* Seqset for input alignment */ AjPSeqin seqin_a = NULL; /* Seqin for input alignment */ AjPScophit hit_sing = NULL; /* Hit for input hit sequences (domain hits file) */ AjPSeq seq_sing = NULL; /* Seq for input singlet sequence */ AjPSeqin seqin_sing = NULL; /* Seqin for input singlet sequence */ EmbPHitlist hitlist_h = NULL; /* Hitlist for input hit sequences (domain hits file) */ AjPSeqset seqset_h = NULL; /* Seqset for input hit sequences */ AjPSeqin seqin_h = NULL; /* Seqin for input hit sequences */ AjPStr *amode = NULL; /* Mode of operation from acd */ ajint amoden = 0; /* Program mode, 1: MODE_STAMP, 2: MODE_TCOFFEE (not yet implemented) */ AjPStr *mode = NULL; /* ** Mode of operation from ACD: ** 1: Single sequences, ** 2: Sequence sets */ ajint modei = 0; /* ACD mode as int */ AjPStr tmp1 = NULL; AjPStr tmp2 = NULL; AjBool ok = ajFalse; AjBool ok2 = ajFalse; AjBool forcetype = ajFalse; /* ACD variable */ /* Memory allocation */ line = ajStrNew(); inname = ajStrNew(); hitsname = ajStrNew(); cmd = ajStrNew(); tmp_name = ajStrNew(); clustin1 = ajStrNew(); clustin2 = ajStrNew(); clustout = ajStrNew(); clustdnd = ajStrNew(); tmp1 = ajStrNew(); tmp2 = ajStrNew(); /* ACD processing */ embInitPV("seqalign",argc,argv,"DOMALIGN",VERSION); inseqsdhf = ajAcdGetDirlist("dhfinpath"); inseqsdaf = ajAcdGetDirlist("dafinpath"); dhfin = ajAcdGetDirectory("dhfindir"); dafout = ajAcdGetOutdir("dafoutdir"); logf = ajAcdGetOutfile("logfile"); amode = ajAcdGetList("amode"); mode = ajAcdGetList("mode"); forcetype = ajAcdGetBoolean("forcetype"); /* Convert the selected amode to an integer */ if(!(ajStrToInt(amode[0], &amoden))) ajFatal("Could not parse ACD node option"); modei = (ajint) ajStrGetCharFirst(*mode)-48; /* Create name for temp. clustalw input files. */ ajRandomSeed(); ajFilenameSetTempname(&tmp_name); /* Read each domain alignment file */ if(modei==1) inseqs = inseqsdhf; else if(modei==2) inseqs = inseqsdaf; else ajFatal("Unrecognised mode"); while(ajListPop(inseqs,(void **)&inname)) { ajFmtPrint("Processing %S\n", inname); ajFmtPrintF(logf, "//\n%S\n", inname); /* Open domain alignment file */ if((inf = ajFileNewInNameS(inname)) == NULL) { ajWarn("Could not open seed alignment file %S", inname); ajFmtPrintF(logf, "//\nCould not open seed alignment file %S\n", inname); continue; } /* Create file name for clustal .dnd tree file (deleted later) and clustal output file. */ ajStrAssignS(&clustdnd,tmp_name); ajStrAppendC(&clustdnd,".dnd"); ajStrAssignS(&clustout,tmp_name); ajStrAppendC(&clustout,".out"); /* Input sequences are seed alignment. */ if(modei==2) { /* Read the domain seed alignment file. */ ok = ajFalse; if(!ajDmxScopalgRead(inf,&scopalign)) { ajWarn("ajDmxScopalgRead call failed in seqsearch_psialigned"); /* Read sequence set instead. */ seqset_a = ajSeqsetNew(); seqin_a = ajSeqinNew(); /* Set the filename via the USA. ajSeqsetRead interprets it to find the filename. */ ajSeqinUsa(&seqin_a, inname); if(!(ajSeqsetRead(seqset_a, seqin_a))) ajFatal("SeqsetRead failed in seqsearch_psialigned"); if(ajSeqsetGetSize(seqset_a)) ok = ajTrue; } else if(scopalign->Number) ok = ajTrue; ajFileClose(&inf); if(!ok) { ajWarn("Empty alignment in %S\n", inname); ajFmtPrintF(logf, "Empty alignment in %S\n", inname); if(scopalign) ajDmxScopalgDel(&scopalign); if(seqset_a) ajSeqsetDel(&seqset_a); if(seqin_a) ajSeqinDel(&seqin_a); continue; } /* Create clustal input alignment in CLUSTAL format. */ ajStrAssignS(&clustin1,tmp_name); ajStrAppendC(&clustin1,".aln"); if((clustinf1 = ajFileNewOutNameS(clustin1))==NULL) ajFatal("Could not open %S for writing\n", clustin1); if(scopalign) ajDmxScopalgWriteFasta(scopalign,clustinf1); else { for(x=0;x%S_%d\n%S\n", ajSeqsetGetseqNameS(seqset_a, x), x, ajSeqsetGetseqSeqS(seqset_a, x)); ajFmtPrintF(clustinf1,"\n"); } ajFileClose(&clustinf1); } /* Input sequences are singlets. */ else if(modei==1) { ok = ajFalse; if(!((hit_sing = ajDmxScophitReadFasta(inf)))) { ajWarn("embHitReadFasta call failed in seqsearch_psialigned for %F", inf); /* Read sequence set instead. */ seq_sing = ajSeqNew(); seqin_sing = ajSeqinNew(); /* Set the filename via the USA. ajSeqsetRead interprets it to find the filename. */ ajSeqinUsa(&seqin_sing, inname); if(!(ajSeqRead(seq_sing, seqin_sing))) ajFatal("SeqRead failed in seqsearch_psialigned"); if(MAJSTRGETLEN(ajSeqGetSeqS(seq_sing))) ok = ajTrue; } else if(MAJSTRGETLEN(hit_sing->Seq)) ok = ajTrue; ajFileClose(&inf); if(!ok) { ajWarn("Empty singlet sequence in %S\n", inname); ajFmtPrintF(logf, "Empty singlet sequence for %S\n", inname); if(hit_sing) ajDmxScophitDel(&hit_sing); if(seqset_a) ajSeqDel(&seq_sing); if(seqin_a) ajSeqinDel(&seqin_sing); continue; } } else ajFatal("Unrecognised mode in SEQALIGN"); /* Open domain hits file (input). */ ajStrAssignS(&hitsname, inname); ajFilenameTrimPathExt(&hitsname); ajStrInsertS(&hitsname, 0, ajDirGetPath(dhfin)); ajStrAppendC(&hitsname, "."); ajStrAppendS(&hitsname, ajDirGetExt(dhfin)); if(!(hitsinf = ajFileNewInNameS(hitsname))) { ajWarn("Could not open domain hits file %S", hitsname); ajFmtPrintF(logf, "Could not open domain hits file %S", hitsname); if(scopalign) ajDmxScopalgDel(&scopalign); if(seqset_a) ajSeqsetDel(&seqset_a); if(seqin_a) ajSeqinDel(&seqin_a); if(hit_sing) ajDmxScophitDel(&hit_sing); continue; } else { if(!ajReadlineTrim(hitsinf, &line)) { ajWarn("Empty domain hits file %S", hitsname); ajFmtPrintF(logf, "Empty domain hits file %S", hitsname); if(scopalign) ajDmxScopalgDel(&scopalign); if(seqset_a) ajSeqsetDel(&seqset_a); if(seqin_a) ajSeqinDel(&seqin_a); if(hit_sing) ajDmxScophitDel(&hit_sing); continue; } else /* rewind file */ ajFileSeek(hitsinf, 0, 0); } /* Create Hitlist from domain hits file. */ ok2=ajFalse; if((!(hitlist_h = embHitlistReadFasta(hitsinf)))) { /* Read sequence set instead. */ seqset_h = ajSeqsetNew(); seqin_h = ajSeqinNew(); /* Set the filename via the USA. ajSeqsetRead interprets it to find the filename. */ ajSeqinUsa(&seqin_h, hitsname); if(!(ajSeqsetRead(seqset_h, seqin_h))) ajFatal("SeqsetRead failed in seqsearch_psialigned"); if(ajSeqsetGetSize(seqset_h) >= 1) ok2 = ajTrue; } else if((hitlist_h->N >= 1)) ok2 = ajTrue; if(!ok2) { ajWarn("Not enough sequences found in domain hits file"); ajFmtPrintF(logf, "Not enough sequences found in domain hits file"); if(scopalign) ajDmxScopalgDel(&scopalign); if(seqset_a) ajSeqsetDel(&seqset_a); if(seqin_a) ajSeqinDel(&seqin_a); if(hitsinf) ajFileClose(&hitsinf); if(hit_sing) ajDmxScophitDel(&hit_sing); continue; } /* Create file of clustal input sequences. */ ajStrAssignS(&clustin2,tmp_name); ajStrAppendC(&clustin2,".seqs"); clustinf2 = ajFileNewOutNameS(clustin2); /* ajFmtPrint("hit_sing->Dom: %S\nhit_sing->Acc: %S\n", hit_sing->Dom, hit_sing->Acc); */ /* Singlet sequence input rather than seed alignment. Add this sequence to the file of hits. */ if(modei==1) { if(hit_sing) { if((MAJSTRGETLEN(hit_sing->Dom))) /* The start and end may just be zero for domain sequences but include them for consistency with the other inputs */ ajFmtPrintF(clustinf2,">%S_%d_%d\n", hit_sing->Dom, hit_sing->Start, hit_sing->End); else if((MAJSTRGETLEN(hit_sing->Acc))) ajFmtPrintF(clustinf2,">%S_%d_%d\n", hit_sing->Acc, hit_sing->Start, hit_sing->End); else ajFmtPrintF(clustinf2,">._%d_%d\n", hit_sing->Start, hit_sing->End); ajFmtPrintF(clustinf2,"%S\n",hit_sing->Seq); } else { /* The '0' is just for consistency with the other inputs. */ ajFmtPrintF(clustinf2,">%s_0\n", ajSeqGetNameC(seq_sing)); ajFmtPrintF(clustinf2,"%S\n", ajSeqGetSeqS(seq_sing)); } } if(hitlist_h) { for(x=0;xN;x++) { if((MAJSTRGETLEN(hitlist_h->hits[x]->Dom))) ajFmtPrintF(clustinf2,">%S_%d_%d\n", hitlist_h->hits[x]->Dom, hitlist_h->hits[x]->Start, hitlist_h->hits[x]->End); else if((MAJSTRGETLEN(hitlist_h->hits[x]->Acc))) ajFmtPrintF(clustinf2,">%S_%d_%d\n", hitlist_h->hits[x]->Acc, hitlist_h->hits[x]->Start, hitlist_h->hits[x]->End); else ajFmtPrintF(clustinf2,">._%d_%d\n", hitlist_h->hits[x]->Start, hitlist_h->hits[x]->End); ajFmtPrintF(clustinf2,"%S\n",hitlist_h->hits[x]->Seq); } } else { for(x=0;x%S_%d\n", ajSeqsetGetseqNameS(seqset_h, x), x); ajFmtPrintF(clustinf2,"%S\n", ajSeqsetGetseqSeqC(seqset_h, x)); } } ajFileClose(&clustinf2); embHitlistDel(&hitlist_h); /* Call clustalw. */ if(modei==2) { /* Alignment is available: do profile to sequence mode. */ ajFmtPrintS(&cmd,"%S -type=protein -profile1=%S -sequences" " -profile2=%S -MATRIX=BLOSUM -GAPOPEN=10" " -GAPEXT=0.5 -outfile=%S\n", ajAcdGetpathC("clustalw"), clustin1,clustin2,clustout); } /* Such cases will now no longer occur ... but keep here for time being. */ else if(modei==1) { /* Alignment is NOT available: multiple sequence mode. */ ajFmtPrintS(&cmd,"%S -infile=%S -align" " -MATRIX=BLOSUM -GAPOPEN=10" " -GAPEXT=0.5 -outfile=%S\n", ajAcdGetpathC("clustalw"), clustin2,clustout); } ajFmtPrint("\n%S\n", cmd); ajSysExecS(cmd); /* Reformat output file into domain alignment format. */ if((alg_in = ajFileNewInNameS(clustout))==NULL) ajFatal("Could not read clustal output file %S", clustout); /* Open domain alignment file (output). */ ajStrAssignS(&outname, inname); ajFilenameTrimPathExt(&outname); ajStrInsertS(&outname, 0, ajDiroutGetPath(dafout)); ajStrAppendC(&outname, "."); ajStrAppendS(&outname, ajDiroutGetExt(dafout)); if((alg_out = ajFileNewOutNameS(outname))==NULL) ajFatal("Could not write clustal output file"); /* Then write domain classification data. */ if((modei==2)) { if(scopalign) { if(scopalign->Type == ajEDomainTypeSCOP) ajFmtPrintF(alg_out,"# TY SCOP\n# XX\n"); else ajFmtPrintF(alg_out,"# TY CATH\n# XX\n"); ajFmtPrintF(alg_out,"# CL %S\n# XX\n",scopalign->Class); ajFmtPrintF(alg_out,"# FO %S\n# XX\n",scopalign->Fold); ajFmtPrintF(alg_out,"# SF %S\n# XX\n",scopalign->Superfamily); ajFmtPrintF(alg_out,"# FA %S\n# XX\n",scopalign->Family); ajFmtPrintF(alg_out,"# SI %d\n# XX\n",scopalign->Sunid_Family); } else if(forcetype) ajFmtPrintF(alg_out,"# TY SCOP\n# XX\n"); } else if(modei==1) { if(hit_sing) { if(hit_sing->Type == ajEDomainTypeSCOP) ajFmtPrintF(alg_out,"# TY SCOP\n# XX\n"); else ajFmtPrintF(alg_out,"# TY CATH\n# XX\n"); ajFmtPrintF(alg_out,"# CL %S\n# XX\n",hit_sing->Class); ajFmtPrintF(alg_out,"# FO %S\n# XX\n",hit_sing->Fold); ajFmtPrintF(alg_out,"# SF %S\n# XX\n",hit_sing->Superfamily); ajFmtPrintF(alg_out,"# FA %S\n# XX\n",hit_sing->Family); ajFmtPrintF(alg_out,"# SI %d\n# XX\n",hit_sing->Sunid_Family); } else if(forcetype) ajFmtPrintF(alg_out,"# TY SCOP\n# XX\n"); } /* Then parse the clustal file and write the alignment. */ while(ajReadlineTrim(alg_in,&line)) { if(ajStrPrefixC(line, "CLUSTAL")) continue; if(MAJSTRGETLEN(line)==0) continue; if(line->Ptr[0]==' ') ajFmtPrintF(alg_out, "\n"); else { /* Add bogus index numbers (of 0) to conform to EMBOSS simple / srs format. */ ajFmtScanS(line, "%S %S", &tmp1, &tmp2); if(MAJSTRGETLEN(tmp1)>25) ajFatal("Code longer than permissible width in seqalign"); ajFmtPrintF(alg_out, "%-25S 0 %S 0\n", tmp1, tmp2); } } ajFileClose(&alg_in); ajFileClose(&alg_out); if(hitsinf) ajFileClose(&hitsinf); /* Clean up directory. */ if(modei==2) if(scopalign->Number !=0) ajSysFileUnlinkS(clustin1); ajSysFileUnlinkS(clustin2); ajSysFileUnlinkS(clustout); ajSysFileUnlinkS(clustdnd); /* Free memory. */ if(scopalign) ajDmxScopalgDel(&scopalign); if(seqset_a) ajSeqsetDel(&seqset_a); if(seqin_a) ajSeqinDel(&seqin_a); if(hit_sing) ajDmxScophitDel(&hit_sing); if(seq_sing) ajSeqDel(&seq_sing); if(seqin_sing) ajSeqinDel(&seqin_sing); ajStrDel(&inname); } /* Memory management. */ ajStrDel(&hitsname); ajStrDel(&line); ajStrDel(&cmd); ajListstrFree(&inseqsdhf); ajListstrFree(&inseqsdaf); ajDirDel(&dhfin); ajDiroutDel(&dafout); ajStrDel(&tmp_name); ajStrDel(&outname); ajStrDel(&clustin1); ajStrDel(&clustin2); ajStrDel(&clustout); ajStrDel(&clustdnd); ajFileClose(&logf); ajStrDel(&amode[0]); AJFREE(amode); ajStrDel(&mode[0]); AJFREE(mode); ajStrDel(&tmp1); ajStrDel(&tmp2); ajExit(); return 0; } DOMALIGN-0.1.650/src/config.h.in0000664000175000017500000001213112171070652012611 00000000000000/* src/config.h.in. Generated from configure.in by autoheader. */ /* Define if building universal (internal helper macro) */ #undef AC_APPLE_UNIVERSAL_BUILD /* Define to 1 to compile all deprecated functions */ #undef AJ_COMPILE_DEPRECATED /* Define to 1 to compile deprecated functions used in book texts for 6.2.0 */ #undef AJ_COMPILE_DEPRECATED_BOOK /* Define to 1 to collect AJAX library usage statistics. */ #undef AJ_SAVESTATS /* Define to 1 if the `getpgrp' function requires zero arguments. */ #undef GETPGRP_VOID /* Define to 1 if you have the header file, and it defines `DIR'. */ #undef HAVE_DIRENT_H /* Define to 1 if you have the header file. */ #undef HAVE_DLFCN_H /* Define to 1 if you don't have `vprintf' but do have `_doprnt.' */ #undef HAVE_DOPRNT /* Define to 1 if you have the `erand48' function. */ #undef HAVE_ERAND48 /* Define to 1 if you have the `fork' function. */ #undef HAVE_FORK /* Define to 1 if you have the header file. */ #undef HAVE_INTTYPES_H /* Define to 1 if the Java Native Interface (JNI) is available. */ #undef HAVE_JAVA /* Define to 1 if you have the `m' library (-lm). */ #undef HAVE_LIBM /* Define to 1 if you have the `mcheck' function. */ #undef HAVE_MCHECK /* Define to 1 if you have the `memmove' function. */ #undef HAVE_MEMMOVE /* Define to 1 if you have the header file. */ #undef HAVE_MEMORY_H /* Define to 1 if MySQL libraries are available. */ #undef HAVE_MYSQL /* Define to 1 if you have the header file, and it defines `DIR'. */ #undef HAVE_NDIR_H /* Define to 1 if PostgreSQL libraries are available. */ #undef HAVE_POSTGRESQL /* Define to 1 if you have the header file. */ #undef HAVE_STDINT_H /* Define to 1 if you have the header file. */ #undef HAVE_STDLIB_H /* Define to 1 if you have the `strchr' function. */ #undef HAVE_STRCHR /* Define to 1 if you have the `strdup' function. */ #undef HAVE_STRDUP /* Define to 1 if you have the `strftime' function. */ #undef HAVE_STRFTIME /* Define to 1 if you have the header file. */ #undef HAVE_STRINGS_H /* Define to 1 if you have the header file. */ #undef HAVE_STRING_H /* Define to 1 if you have the `strstr' function. */ #undef HAVE_STRSTR /* Define to 1 if you have the header file, and it defines `DIR'. */ #undef HAVE_SYS_DIR_H /* Define to 1 if you have the header file, and it defines `DIR'. */ #undef HAVE_SYS_NDIR_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_STAT_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_TARGETCONFIG_H /* Define to 1 if you have the header file. */ #undef HAVE_UNISTD_H /* Define to 1 if you have the `vfork' function. */ #undef HAVE_VFORK /* Define to 1 if you have the header file. */ #undef HAVE_VFORK_H /* Define to 1 if you have the `vprintf' function. */ #undef HAVE_VPRINTF /* Define to 1 if `fork' works. */ #undef HAVE_WORKING_FORK /* Define to 1 if `vfork' works. */ #undef HAVE_WORKING_VFORK /* Set to 1 if HPUX 64bit ptrs on 32 bit m/c */ #undef HPUX64PTRS /* Define to the sub-directory in which libtool stores uninstalled libraries. */ #undef LT_OBJDIR /* Name of package */ #undef PACKAGE /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the home page for this package. */ #undef PACKAGE_URL /* Define to the version of this package. */ #undef PACKAGE_VERSION /* Define to 1 if PDF support is available */ #undef PLD_pdf /* Define to 1 is PNG support is available */ #undef PLD_png /* Define to 1 if X11 support is available */ #undef PLD_xwin /* Define to 1 if you have the ANSI C header files. */ #undef STDC_HEADERS /* Define to 1 if your declares `struct tm'. */ #undef TM_IN_SYS_TIME /* Version number of package */ #undef VERSION /* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most significant byte first (like Motorola and SPARC, unlike Intel). */ #if defined AC_APPLE_UNIVERSAL_BUILD # if defined __BIG_ENDIAN__ # define WORDS_BIGENDIAN 1 # endif #else # ifndef WORDS_BIGENDIAN # undef WORDS_BIGENDIAN # endif #endif /* Define to 1 if the X Window System is missing or not being used. */ #undef X_DISPLAY_MISSING /* Set to 2 for open args */ #undef _FORTIFY_SOURCE /* Define to empty if `const' does not conform to ANSI C. */ #undef const /* Define to `__inline__' or `__inline' if that's what the C compiler calls it, or to nothing if 'inline' is not supported under any name. */ #ifndef __cplusplus #undef inline #endif /* Define to `int' if does not define. */ #undef pid_t /* Define to `unsigned int' if does not define. */ #undef size_t /* Define as `fork' if `vfork' does not work. */ #undef vfork DOMALIGN-0.1.650/src/allversusall.c0000664000175000017500000001405111741637135013455 00000000000000/* @Source allversusall application ** ** Does an all-versus-all global alignment for each set of sequences in an ** input directory and writes files of sequence similarity values. ** ** @author: Copyright (C) Jon Ison (jison@ebi.ac.uk) ** @@ ** ** 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. ** ******************************************************************************* ** ** ALLVERSUSALL Documentation ** See http://wwww.emboss.org ** ** Please cite the authors and EMBOSS. ** ** Rice P, Bleasby A.J. 2000. EMBOSS - The European Molecular Biology Open ** Software Suite. Trends in Genetics, 15:276-278. ** See also http://www.uk.embnet.org/Software/EMBOSS ** ** Email jison@ebi.mrc.ac.uk. ** ** NOTES ** ****************************************************************************/ #include #include "emboss.h" /* @prog allversusall ******************************************************* ** ** Does an all-versus-all global alignment for each set of sequences in an ** input directory and writes files of sequence similarity values. ** ****************************************************************************/ int main(int argc, char **argv) { /* Variable declarations */ AjPList in = NULL; /* Names of domain hits files (input). */ AjPStr inname = NULL; /* Full name of the current DHF file. */ AjPFile inf = NULL; /* Current DHF file. */ AjPMatrixf matrix = NULL; /* Substitution matrix. */ float gapopen = 0.0F; /* Gap insertion penalty. */ float gapextend = 0.0F; /* Gap extension penalty. */ AjPDirout out = NULL; /* Domain hits files (output). */ AjPFile outf = NULL; /* Current DHF file (output). */ AjPStr outname = NULL; /* Name of output file (re-used). */ AjPFile logf = NULL; /* log file pointer. */ AjBool ok = ajFalse; /* Housekeeping */ AjPSeqset seqset = NULL; /* Seqset (re-used) */ AjPSeqin seqin = NULL; /* Seqin (re-used) */ AjPList seq_list = NULL; /* Main list for redundancy removal. */ ajuint seq_list_siz = 0; /* Size of seq_list */ AjPSeq seq_tmp = NULL; /* Temp. pointer for making seq_list. */ AjPFloat2d scores = NULL; /* 1: Sequence in seq_list was classed as non-redundant, 0: redundant. */ ajuint x = 0; /* Housekeeping. */ ajuint y = 0; /* Housekeeping. */ /* Read data from acd */ embInitPV("allversusall",argc,argv,"DOMALIGN",VERSION); in = ajAcdGetDirlist("seqinpath"); matrix = ajAcdGetMatrixf("matrix"); gapopen = ajAcdGetFloat("gapopen"); gapextend = ajAcdGetFloat("gapextend"); out = ajAcdGetOutdir("datoutdir"); logf = ajAcdGetOutfile("logfile"); /* Housekeeping */ outname = ajStrNew(); /* Process each DHF (input) in turn */ while(ajListPop(in,(void **)&inname)) { ajFmtPrint("Processing %S\n", inname); ajFmtPrintF(logf, "//\n%S\n", inname); seq_list = ajListNew(); /* Open & read sequence file. */ if((inf = ajFileNewInNameS(inname)) == NULL) ajFatal("Could not open DHF file %S", inname); seqset = ajSeqsetNew(); seqin = ajSeqinNew(); ajSeqinUsa(&seqin, inname); if(!(ajSeqsetRead(seqset, seqin))) ajFatal("SeqsetRead failed in seqsearch_psialigned"); ok = ajFalse; if(ajSeqsetGetSize(seqset)) ok = ajTrue; ajFileClose(&inf); /* Process empty sequence files (should never occur). */ if(!ok) { ajWarn("Empty input file %S\n", inname); ajFmtPrintF(logf, "Empty input file %S\n", inname); if(seqset) ajSeqsetDel(&seqset); if(seqin) ajSeqinDel(&seqin); continue; } /* 1. Create list of sequences from the main input directory. */ for(x = 0U; x < ajSeqsetGetSize(seqset); x++) { seq_tmp = ajSeqNew(); ajStrAssignS(&seq_tmp->Acc, ajSeqsetGetseqAccS(seqset, x)); ajStrAssignC(&seq_tmp->Seq, ajSeqsetGetseqSeqC(seqset, x)); ajListPushAppend(seq_list,seq_tmp); } /* 4. Identify redundant domains. */ if((!embDmxSeqCompall(seq_list, &scores, matrix, gapopen, gapextend))) ajFatal("embDmxSeqCompall failure in allversusall"); /* Create output files. */ ajStrAssignS(&outname, inname); ajFilenameTrimPathExt(&outname); outf = ajFileNewOutNameDirS(outname, out); /* 5. Write sequence similarity values to output directory. */ seq_list_siz = ajListGetLength(seq_list); for(x = 0U; x < seq_list_siz; x++) for(y = x + 1U; y < seq_list_siz; y++) ajFmtPrintF(outf, "%u %S : %u %S : %.2f\n", x + 1U, ajSeqsetGetseqNameS(seqset, x), y + 1U, ajSeqsetGetseqNameS(seqset, y), ajFloat2dGet(scores, x, y)); ajSeqsetDel(&seqset); ajSeqinDel(&seqin); ajFileClose(&outf); ajStrDel(&inname); while(ajListPop(seq_list, (void **) &seq_tmp)) ajSeqDel(&seq_tmp); ajListFree(&seq_list); ajFloat2dDel(&scores); } /* Memory management. */ ajListFree(&in); ajDiroutDel(&out); ajFileClose(&logf); ajStrDel(&outname); ajMatrixfDel(&matrix); embExit(); return 0; } DOMALIGN-0.1.650/src/Makefile.am0000664000175000017500000000412611430502104012614 00000000000000## Process this file with automake to produce Makefile.in if !ESYSTEMLIBS LLINCLUDES = -I../../../ajax/expat -I../../../ajax/zlib NLINCLUDES = -I${embprefix}/include/ezlib -I${embprefix}/include/eexpat LLAIXLIBS = -L../../../ajax/expat/.libs -L../../../ajax/zlib/.libs NLAIXLIBS = -leexpat -lezlib LLADD = ../../../ajax/expat/libeexpat.la ../../../ajax/zlib/libezlib.la NLADD = -leexpat -lezlib endif if LOCALLINK AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ $(LLINCLUDES) \ -I../../../ajax/core -I../../../ajax/graphics \ -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ -I../../../ajax/acd -I../../../plplot else AM_CPPFLAGS = -I../include -I${embprefix}/include \ -I${embprefix}/include/eplplot \ $(NLINCLUDES) \ -I${embprefix}/include/epcre endif if ISSHARED if ISAIXIA64 if LOCALLINK AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L../../../plplot/.libs \ -L../../../ajax/pcre/.libs $(LLAIXLIBS) \ -L../../../ajax/core/.libs \ -L../../../ajax/graphics/.libs -L../../../ajax/ensembl/.libs \ -L../../../ajax/ajaxdb/.libs -L../../../ajax/acd/.libs \ -L../../../nucleus/.libs \ -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre \ $(NLAIXLIBS) -leplplot else AIX_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lacd \ -lajaxdb -lensembl -lajaxg -lajax -lepcre $(NLAIXLIBS) -leplplot endif endif endif AM_CFLAGS = $(AIX_CFLAGS) $(WARN_CFLAGS) $(DEVWARN_CFLAGS) bin_PROGRAMS = allversusall domainalign domainrep \ seqalign allversusall_SOURCES = allversusall.c domainalign_SOURCES = domainalign.c domainrep_SOURCES = domainrep.c seqalign_SOURCES = seqalign.c if LOCALLINK LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ ../../../ajax/ajaxdb/libajaxdb.la \ ../../../ajax/ensembl/libensembl.la \ ../../../ajax/graphics/libajaxg.la \ ../../../ajax/core/libajax.la \ ../../../ajax/expat/libeexpat.la \ ../../../ajax/pcre/libepcre.la \ ../../../ajax/zlib/libezlib.la \ ../../../plplot/libeplplot.la $(XLIB) else LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -lajax -lepcre $(NLADD) -leplplot $(XLIB) endif DOMALIGN-0.1.650/src/Makefile.in0000664000175000017500000006236012171070654012646 00000000000000# Makefile.in generated by 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There is NO # warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # GNU Libtool 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. # # As a special exception to the GNU General Public License, # if you distribute this file as part of a program or library that # is built using GNU Libtool, you may include this file under the # same distribution terms that you use for the rest of that program. # # GNU Libtool 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 GNU Libtool; see the file COPYING. If not, a copy # can be downloaded from http://www.gnu.org/licenses/gpl.html, # or obtained by writing to the Free Software Foundation, Inc., # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # Usage: $progname [OPTION]... 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Use a colon delimited # list incase some portion of path contains whitespace. my_dir_list="$my_directory_path:$my_dir_list" # If the last portion added has no slash in it, the list is done case $my_directory_path in */*) ;; *) break ;; esac # ...otherwise throw away the child directory and loop my_directory_path=`$ECHO "$my_directory_path" | $SED -e "$dirname"` done my_dir_list=`$ECHO "$my_dir_list" | $SED 's,:*$,,'` save_mkdir_p_IFS="$IFS"; IFS=':' for my_dir in $my_dir_list; do IFS="$save_mkdir_p_IFS" # mkdir can fail with a `File exist' error if two processes # try to create one of the directories concurrently. Don't # stop in that case! $MKDIR "$my_dir" 2>/dev/null || : done IFS="$save_mkdir_p_IFS" # Bail out if we (or some other process) failed to create a directory. test -d "$my_directory_path" || \ func_fatal_error "Failed to create \`$1'" fi } # func_mktempdir [string] # Make a temporary directory that won't clash with other running # libtool processes, and avoids race conditions if possible. If # given, STRING is the basename for that directory. func_mktempdir () { my_template="${TMPDIR-/tmp}/${1-$progname}" if test "$opt_dry_run" = ":"; then # Return a directory name, but don't create it in dry-run mode my_tmpdir="${my_template}-$$" else # If mktemp works, use that first and foremost my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null` if test ! -d "$my_tmpdir"; then # Failing that, at least try and use $RANDOM to avoid a race my_tmpdir="${my_template}-${RANDOM-0}$$" save_mktempdir_umask=`umask` umask 0077 $MKDIR "$my_tmpdir" umask $save_mktempdir_umask fi # If we're not in dry-run mode, bomb out on failure test -d "$my_tmpdir" || \ func_fatal_error "cannot create temporary directory \`$my_tmpdir'" fi $ECHO "$my_tmpdir" } # func_quote_for_eval arg # Aesthetically quote ARG to be evaled later. # This function returns two values: FUNC_QUOTE_FOR_EVAL_RESULT # is double-quoted, suitable for a subsequent eval, whereas # FUNC_QUOTE_FOR_EVAL_UNQUOTED_RESULT has merely all characters # which are still active within double quotes backslashified. func_quote_for_eval () { case $1 in *[\\\`\"\$]*) func_quote_for_eval_unquoted_result=`$ECHO "$1" | $SED "$sed_quote_subst"` ;; *) func_quote_for_eval_unquoted_result="$1" ;; esac case $func_quote_for_eval_unquoted_result in # Double-quote args containing shell metacharacters to delay # word splitting, command substitution and and variable # expansion for a subsequent eval. # Many Bourne shells cannot handle close brackets correctly # in scan sets, so we specify it separately. *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") func_quote_for_eval_result="\"$func_quote_for_eval_unquoted_result\"" ;; *) func_quote_for_eval_result="$func_quote_for_eval_unquoted_result" esac } # func_quote_for_expand arg # Aesthetically quote ARG to be evaled later; same as above, # but do not quote variable references. func_quote_for_expand () { case $1 in *[\\\`\"]*) my_arg=`$ECHO "$1" | $SED \ -e "$double_quote_subst" -e "$sed_double_backslash"` ;; *) my_arg="$1" ;; esac case $my_arg in # Double-quote args containing shell metacharacters to delay # word splitting and command substitution for a subsequent eval. # Many Bourne shells cannot handle close brackets correctly # in scan sets, so we specify it separately. *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") my_arg="\"$my_arg\"" ;; esac func_quote_for_expand_result="$my_arg" } # func_show_eval cmd [fail_exp] # Unless opt_silent is true, then output CMD. Then, if opt_dryrun is # not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP # is given, then evaluate it. func_show_eval () { my_cmd="$1" my_fail_exp="${2-:}" ${opt_silent-false} || { func_quote_for_expand "$my_cmd" eval "func_echo $func_quote_for_expand_result" } if ${opt_dry_run-false}; then :; else eval "$my_cmd" my_status=$? if test "$my_status" -eq 0; then :; else eval "(exit $my_status); $my_fail_exp" fi fi } # func_show_eval_locale cmd [fail_exp] # Unless opt_silent is true, then output CMD. Then, if opt_dryrun is # not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP # is given, then evaluate it. Use the saved locale for evaluation. func_show_eval_locale () { my_cmd="$1" my_fail_exp="${2-:}" ${opt_silent-false} || { func_quote_for_expand "$my_cmd" eval "func_echo $func_quote_for_expand_result" } if ${opt_dry_run-false}; then :; else eval "$lt_user_locale $my_cmd" my_status=$? eval "$lt_safe_locale" if test "$my_status" -eq 0; then :; else eval "(exit $my_status); $my_fail_exp" fi fi } # func_tr_sh # Turn $1 into a string suitable for a shell variable name. # Result is stored in $func_tr_sh_result. All characters # not in the set a-zA-Z0-9_ are replaced with '_'. Further, # if $1 begins with a digit, a '_' is prepended as well. func_tr_sh () { case $1 in [0-9]* | *[!a-zA-Z0-9_]*) func_tr_sh_result=`$ECHO "$1" | $SED 's/^\([0-9]\)/_\1/; s/[^a-zA-Z0-9_]/_/g'` ;; * ) func_tr_sh_result=$1 ;; esac } # func_version # Echo version message to standard output and exit. func_version () { $opt_debug $SED -n '/(C)/!b go :more /\./!{ N s/\n# / / b more } :go /^# '$PROGRAM' (GNU /,/# warranty; / { s/^# // s/^# *$// s/\((C)\)[ 0-9,-]*\( [1-9][0-9]*\)/\1\2/ p }' < "$progpath" exit $? } # func_usage # Echo short help message to standard output and exit. func_usage () { $opt_debug $SED -n '/^# Usage:/,/^# *.*--help/ { s/^# // s/^# *$// s/\$progname/'$progname'/ p }' < "$progpath" echo $ECHO "run \`$progname --help | more' for full usage" exit $? } # func_help [NOEXIT] # Echo long help message to standard output and exit, # unless 'noexit' is passed as argument. func_help () { $opt_debug $SED -n '/^# Usage:/,/# Report bugs to/ { :print s/^# // s/^# *$// s*\$progname*'$progname'* s*\$host*'"$host"'* s*\$SHELL*'"$SHELL"'* s*\$LTCC*'"$LTCC"'* s*\$LTCFLAGS*'"$LTCFLAGS"'* s*\$LD*'"$LD"'* s/\$with_gnu_ld/'"$with_gnu_ld"'/ s/\$automake_version/'"`(${AUTOMAKE-automake} --version) 2>/dev/null |$SED 1q`"'/ s/\$autoconf_version/'"`(${AUTOCONF-autoconf} --version) 2>/dev/null |$SED 1q`"'/ p d } /^# .* home page:/b print /^# General help using/b print ' < "$progpath" ret=$? if test -z "$1"; then exit $ret fi } # func_missing_arg argname # Echo program name prefixed message to standard error and set global # exit_cmd. func_missing_arg () { $opt_debug func_error "missing argument for $1." exit_cmd=exit } # func_split_short_opt shortopt # Set func_split_short_opt_name and func_split_short_opt_arg shell # variables after splitting SHORTOPT after the 2nd character. func_split_short_opt () { my_sed_short_opt='1s/^\(..\).*$/\1/;q' my_sed_short_rest='1s/^..\(.*\)$/\1/;q' func_split_short_opt_name=`$ECHO "$1" | $SED "$my_sed_short_opt"` func_split_short_opt_arg=`$ECHO "$1" | $SED "$my_sed_short_rest"` } # func_split_short_opt may be replaced by extended shell implementation # func_split_long_opt longopt # Set func_split_long_opt_name and func_split_long_opt_arg shell # variables after splitting LONGOPT at the `=' sign. func_split_long_opt () { my_sed_long_opt='1s/^\(--[^=]*\)=.*/\1/;q' my_sed_long_arg='1s/^--[^=]*=//' func_split_long_opt_name=`$ECHO "$1" | $SED "$my_sed_long_opt"` func_split_long_opt_arg=`$ECHO "$1" | $SED "$my_sed_long_arg"` } # func_split_long_opt may be replaced by extended shell implementation exit_cmd=: magic="%%%MAGIC variable%%%" magic_exe="%%%MAGIC EXE variable%%%" # Global variables. nonopt= preserve_args= lo2o="s/\\.lo\$/.${objext}/" o2lo="s/\\.${objext}\$/.lo/" extracted_archives= extracted_serial=0 # If this variable is set in any of the actions, the command in it # will be execed at the end. This prevents here-documents from being # left over by shells. exec_cmd= # func_append var value # Append VALUE to the end of shell variable VAR. func_append () { eval "${1}=\$${1}\${2}" } # func_append may be replaced by extended shell implementation # func_append_quoted var value # Quote VALUE and append to the end of shell variable VAR, separated # by a space. func_append_quoted () { func_quote_for_eval "${2}" eval "${1}=\$${1}\\ \$func_quote_for_eval_result" } # func_append_quoted may be replaced by extended shell implementation # func_arith arithmetic-term... func_arith () { func_arith_result=`expr "${@}"` } # func_arith may be replaced by extended shell implementation # func_len string # STRING may not start with a hyphen. func_len () { func_len_result=`expr "${1}" : ".*" 2>/dev/null || echo $max_cmd_len` } # func_len may be replaced by extended shell implementation # func_lo2o object func_lo2o () { func_lo2o_result=`$ECHO "${1}" | $SED "$lo2o"` } # func_lo2o may be replaced by extended shell implementation # func_xform libobj-or-source func_xform () { func_xform_result=`$ECHO "${1}" | $SED 's/\.[^.]*$/.lo/'` } # func_xform may be replaced by extended shell implementation # func_fatal_configuration arg... # Echo program name prefixed message to standard error, followed by # a configuration failure hint, and exit. func_fatal_configuration () { func_error ${1+"$@"} func_error "See the $PACKAGE documentation for more information." func_fatal_error "Fatal configuration error." } # func_config # Display the configuration for all the tags in this script. func_config () { re_begincf='^# ### BEGIN LIBTOOL' re_endcf='^# ### END LIBTOOL' # Default configuration. $SED "1,/$re_begincf CONFIG/d;/$re_endcf CONFIG/,\$d" < "$progpath" # Now print the configurations for the tags. for tagname in $taglist; do $SED -n "/$re_begincf TAG CONFIG: $tagname\$/,/$re_endcf TAG CONFIG: $tagname\$/p" < "$progpath" done exit $? } # func_features # Display the features supported by this script. func_features () { echo "host: $host" if test "$build_libtool_libs" = yes; then echo "enable shared libraries" else echo "disable shared libraries" fi if test "$build_old_libs" = yes; then echo "enable static libraries" else echo "disable static libraries" fi exit $? } # func_enable_tag tagname # Verify that TAGNAME is valid, and either flag an error and exit, or # enable the TAGNAME tag. We also add TAGNAME to the global $taglist # variable here. func_enable_tag () { # Global variable: tagname="$1" re_begincf="^# ### BEGIN LIBTOOL TAG CONFIG: $tagname\$" re_endcf="^# ### END LIBTOOL TAG CONFIG: $tagname\$" sed_extractcf="/$re_begincf/,/$re_endcf/p" # Validate tagname. case $tagname in *[!-_A-Za-z0-9,/]*) func_fatal_error "invalid tag name: $tagname" ;; esac # Don't test for the "default" C tag, as we know it's # there but not specially marked. case $tagname in CC) ;; *) if $GREP "$re_begincf" "$progpath" >/dev/null 2>&1; then taglist="$taglist $tagname" # Evaluate the configuration. Be careful to quote the path # and the sed script, to avoid splitting on whitespace, but # also don't use non-portable quotes within backquotes within # quotes we have to do it in 2 steps: extractedcf=`$SED -n -e "$sed_extractcf" < "$progpath"` eval "$extractedcf" else func_error "ignoring unknown tag $tagname" fi ;; esac } # func_check_version_match # Ensure that we are using m4 macros, and libtool script from the same # release of libtool. func_check_version_match () { if test "$package_revision" != "$macro_revision"; then if test "$VERSION" != "$macro_version"; then if test -z "$macro_version"; then cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from an older release. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from $PACKAGE $macro_version. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF fi else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, revision $package_revision, $progname: but the definition of this LT_INIT comes from revision $macro_revision. $progname: You should recreate aclocal.m4 with macros from revision $package_revision $progname: of $PACKAGE $VERSION and run autoconf again. _LT_EOF fi exit $EXIT_MISMATCH fi } # Shorthand for --mode=foo, only valid as the first argument case $1 in clean|clea|cle|cl) shift; set dummy --mode clean ${1+"$@"}; shift ;; compile|compil|compi|comp|com|co|c) shift; set dummy --mode compile ${1+"$@"}; shift ;; execute|execut|execu|exec|exe|ex|e) shift; set dummy --mode execute ${1+"$@"}; shift ;; finish|finis|fini|fin|fi|f) shift; set dummy --mode finish ${1+"$@"}; shift ;; install|instal|insta|inst|ins|in|i) shift; set dummy --mode install ${1+"$@"}; shift ;; link|lin|li|l) shift; set dummy --mode link ${1+"$@"}; shift ;; uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u) shift; set dummy --mode uninstall ${1+"$@"}; shift ;; esac # Option defaults: opt_debug=: opt_dry_run=false opt_config=false opt_preserve_dup_deps=false opt_features=false opt_finish=false opt_help=false opt_help_all=false opt_silent=: opt_warning=: opt_verbose=: opt_silent=false opt_verbose=false # Parse options once, thoroughly. This comes as soon as possible in the # script to make things like `--version' happen as quickly as we can. { # this just eases exit handling while test $# -gt 0; do opt="$1" shift case $opt in --debug|-x) opt_debug='set -x' func_echo "enabling shell trace mode" $opt_debug ;; --dry-run|--dryrun|-n) opt_dry_run=: ;; --config) opt_config=: func_config ;; --dlopen|-dlopen) optarg="$1" opt_dlopen="${opt_dlopen+$opt_dlopen }$optarg" shift ;; --preserve-dup-deps) opt_preserve_dup_deps=: ;; --features) opt_features=: func_features ;; --finish) opt_finish=: set dummy --mode finish ${1+"$@"}; shift ;; --help) opt_help=: ;; --help-all) opt_help_all=: opt_help=': help-all' ;; --mode) test $# = 0 && func_missing_arg $opt && break optarg="$1" opt_mode="$optarg" case $optarg in # Valid mode arguments: clean|compile|execute|finish|install|link|relink|uninstall) ;; # Catch anything else as an error *) func_error "invalid argument for $opt" exit_cmd=exit break ;; esac shift ;; --no-silent|--no-quiet) opt_silent=false func_append preserve_args " $opt" ;; --no-warning|--no-warn) opt_warning=false func_append preserve_args " $opt" ;; --no-verbose) opt_verbose=false func_append preserve_args " $opt" ;; --silent|--quiet) opt_silent=: func_append preserve_args " $opt" opt_verbose=false ;; --verbose|-v) opt_verbose=: func_append preserve_args " $opt" opt_silent=false ;; --tag) test $# = 0 && func_missing_arg $opt && break optarg="$1" opt_tag="$optarg" func_append preserve_args " $opt $optarg" func_enable_tag "$optarg" shift ;; -\?|-h) func_usage ;; --help) func_help ;; --version) func_version ;; # Separate optargs to long options: --*=*) func_split_long_opt "$opt" set dummy "$func_split_long_opt_name" "$func_split_long_opt_arg" ${1+"$@"} shift ;; # Separate non-argument short options: -\?*|-h*|-n*|-v*) func_split_short_opt "$opt" set dummy "$func_split_short_opt_name" "-$func_split_short_opt_arg" ${1+"$@"} shift ;; --) break ;; -*) func_fatal_help "unrecognized option \`$opt'" ;; *) set dummy "$opt" ${1+"$@"}; shift; break ;; esac done # Validate options: # save first non-option argument if test "$#" -gt 0; then nonopt="$opt" shift fi # preserve --debug test "$opt_debug" = : || func_append preserve_args " --debug" case $host in *cygwin* | *mingw* | *pw32* | *cegcc*) # don't eliminate duplications in $postdeps and $predeps opt_duplicate_compiler_generated_deps=: ;; *) opt_duplicate_compiler_generated_deps=$opt_preserve_dup_deps ;; esac $opt_help || { # Sanity checks first: func_check_version_match if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then func_fatal_configuration "not configured to build any kind of library" fi # Darwin sucks eval std_shrext=\"$shrext_cmds\" # Only execute mode is allowed to have -dlopen flags. if test -n "$opt_dlopen" && test "$opt_mode" != execute; then func_error "unrecognized option \`-dlopen'" $ECHO "$help" 1>&2 exit $EXIT_FAILURE fi # Change the help message to a mode-specific one. generic_help="$help" help="Try \`$progname --help --mode=$opt_mode' for more information." } # Bail if the options were screwed $exit_cmd $EXIT_FAILURE } ## ----------- ## ## Main. ## ## ----------- ## # func_lalib_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_lalib_p () { test -f "$1" && $SED -e 4q "$1" 2>/dev/null \ | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1 } # func_lalib_unsafe_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function implements the same check as func_lalib_p without # resorting to external programs. To this end, it redirects stdin and # closes it afterwards, without saving the original file descriptor. # As a safety measure, use it only where a negative result would be # fatal anyway. Works if `file' does not exist. func_lalib_unsafe_p () { lalib_p=no if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then for lalib_p_l in 1 2 3 4 do read lalib_p_line case "$lalib_p_line" in \#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;; esac done exec 0<&5 5<&- fi test "$lalib_p" = yes } # func_ltwrapper_script_p file # True iff FILE is a libtool wrapper script # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_script_p () { func_lalib_p "$1" } # func_ltwrapper_executable_p file # True iff FILE is a libtool wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_executable_p () { func_ltwrapper_exec_suffix= case $1 in *.exe) ;; *) func_ltwrapper_exec_suffix=.exe ;; esac $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1 } # func_ltwrapper_scriptname file # Assumes file is an ltwrapper_executable # uses $file to determine the appropriate filename for a # temporary ltwrapper_script. func_ltwrapper_scriptname () { func_dirname_and_basename "$1" "" "." func_stripname '' '.exe' "$func_basename_result" func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper" } # func_ltwrapper_p file # True iff FILE is a libtool wrapper script or wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_p () { func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1" } # func_execute_cmds commands fail_cmd # Execute tilde-delimited COMMANDS. # If FAIL_CMD is given, eval that upon failure. # FAIL_CMD may read-access the current command in variable CMD! func_execute_cmds () { $opt_debug save_ifs=$IFS; IFS='~' for cmd in $1; do IFS=$save_ifs eval cmd=\"$cmd\" func_show_eval "$cmd" "${2-:}" done IFS=$save_ifs } # func_source file # Source FILE, adding directory component if necessary. # Note that it is not necessary on cygwin/mingw to append a dot to # FILE even if both FILE and FILE.exe exist: automatic-append-.exe # behavior happens only for exec(3), not for open(2)! Also, sourcing # `FILE.' does not work on cygwin managed mounts. func_source () { $opt_debug case $1 in */* | *\\*) . "$1" ;; *) . "./$1" ;; esac } # func_resolve_sysroot PATH # Replace a leading = in PATH with a sysroot. Store the result into # func_resolve_sysroot_result func_resolve_sysroot () { func_resolve_sysroot_result=$1 case $func_resolve_sysroot_result in =*) func_stripname '=' '' "$func_resolve_sysroot_result" func_resolve_sysroot_result=$lt_sysroot$func_stripname_result ;; esac } # func_replace_sysroot PATH # If PATH begins with the sysroot, replace it with = and # store the result into func_replace_sysroot_result. func_replace_sysroot () { case "$lt_sysroot:$1" in ?*:"$lt_sysroot"*) func_stripname "$lt_sysroot" '' "$1" func_replace_sysroot_result="=$func_stripname_result" ;; *) # Including no sysroot. func_replace_sysroot_result=$1 ;; esac } # func_infer_tag arg # Infer tagged configuration to use if any are available and # if one wasn't chosen via the "--tag" command line option. # Only attempt this if the compiler in the base compile # command doesn't match the default compiler. # arg is usually of the form 'gcc ...' func_infer_tag () { $opt_debug if test -n "$available_tags" && test -z "$tagname"; then CC_quoted= for arg in $CC; do func_append_quoted CC_quoted "$arg" done CC_expanded=`func_echo_all $CC` CC_quoted_expanded=`func_echo_all $CC_quoted` case $@ in # Blanks in the command may have been stripped by the calling shell, # but not from the CC environment variable when configure was run. " $CC "* | "$CC "* | " $CC_expanded "* | "$CC_expanded "* | \ " $CC_quoted"* | "$CC_quoted "* | " $CC_quoted_expanded "* | "$CC_quoted_expanded "*) ;; # Blanks at the start of $base_compile will cause this to fail # if we don't check for them as well. *) for z in $available_tags; do if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then # Evaluate the configuration. eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`" CC_quoted= for arg in $CC; do # Double-quote args containing other shell metacharacters. func_append_quoted CC_quoted "$arg" done CC_expanded=`func_echo_all $CC` CC_quoted_expanded=`func_echo_all $CC_quoted` case "$@ " in " $CC "* | "$CC "* | " $CC_expanded "* | "$CC_expanded "* | \ " $CC_quoted"* | "$CC_quoted "* | " $CC_quoted_expanded "* | "$CC_quoted_expanded "*) # The compiler in the base compile command matches # the one in the tagged configuration. # Assume this is the tagged configuration we want. tagname=$z break ;; esac fi done # If $tagname still isn't set, then no tagged configuration # was found and let the user know that the "--tag" command # line option must be used. if test -z "$tagname"; then func_echo "unable to infer tagged configuration" func_fatal_error "specify a tag with \`--tag'" # else # func_verbose "using $tagname tagged configuration" fi ;; esac fi } # func_write_libtool_object output_name pic_name nonpic_name # Create a libtool object file (analogous to a ".la" file), # but don't create it if we're doing a dry run. func_write_libtool_object () { write_libobj=${1} if test "$build_libtool_libs" = yes; then write_lobj=\'${2}\' else write_lobj=none fi if test "$build_old_libs" = yes; then write_oldobj=\'${3}\' else write_oldobj=none fi $opt_dry_run || { cat >${write_libobj}T </dev/null` if test "$?" -eq 0 && test -n "${func_convert_core_file_wine_to_w32_tmp}"; then func_convert_core_file_wine_to_w32_result=`$ECHO "$func_convert_core_file_wine_to_w32_tmp" | $SED -e "$lt_sed_naive_backslashify"` else func_convert_core_file_wine_to_w32_result= fi fi } # end: func_convert_core_file_wine_to_w32 # func_convert_core_path_wine_to_w32 ARG # Helper function used by path conversion functions when $build is *nix, and # $host is mingw, cygwin, or some other w32 environment. Relies on a correctly # configured wine environment available, with the winepath program in $build's # $PATH. Assumes ARG has no leading or trailing path separator characters. # # ARG is path to be converted from $build format to win32. # Result is available in $func_convert_core_path_wine_to_w32_result. # Unconvertible file (directory) names in ARG are skipped; if no directory names # are convertible, then the result may be empty. func_convert_core_path_wine_to_w32 () { $opt_debug # unfortunately, winepath doesn't convert paths, only file names func_convert_core_path_wine_to_w32_result="" if test -n "$1"; then oldIFS=$IFS IFS=: for func_convert_core_path_wine_to_w32_f in $1; do IFS=$oldIFS func_convert_core_file_wine_to_w32 "$func_convert_core_path_wine_to_w32_f" if test -n "$func_convert_core_file_wine_to_w32_result" ; then if test -z "$func_convert_core_path_wine_to_w32_result"; then func_convert_core_path_wine_to_w32_result="$func_convert_core_file_wine_to_w32_result" else func_append func_convert_core_path_wine_to_w32_result ";$func_convert_core_file_wine_to_w32_result" fi fi done IFS=$oldIFS fi } # end: func_convert_core_path_wine_to_w32 # func_cygpath ARGS... # Wrapper around calling the cygpath program via LT_CYGPATH. This is used when # when (1) $build is *nix and Cygwin is hosted via a wine environment; or (2) # $build is MSYS and $host is Cygwin, or (3) $build is Cygwin. In case (1) or # (2), returns the Cygwin file name or path in func_cygpath_result (input # file name or path is assumed to be in w32 format, as previously converted # from $build's *nix or MSYS format). In case (3), returns the w32 file name # or path in func_cygpath_result (input file name or path is assumed to be in # Cygwin format). Returns an empty string on error. # # ARGS are passed to cygpath, with the last one being the file name or path to # be converted. # # Specify the absolute *nix (or w32) name to cygpath in the LT_CYGPATH # environment variable; do not put it in $PATH. func_cygpath () { $opt_debug if test -n "$LT_CYGPATH" && test -f "$LT_CYGPATH"; then func_cygpath_result=`$LT_CYGPATH "$@" 2>/dev/null` if test "$?" -ne 0; then # on failure, ensure result is empty func_cygpath_result= fi else func_cygpath_result= func_error "LT_CYGPATH is empty or specifies non-existent file: \`$LT_CYGPATH'" fi } #end: func_cygpath # func_convert_core_msys_to_w32 ARG # Convert file name or path ARG from MSYS format to w32 format. Return # result in func_convert_core_msys_to_w32_result. func_convert_core_msys_to_w32 () { $opt_debug # awkward: cmd appends spaces to result func_convert_core_msys_to_w32_result=`( cmd //c echo "$1" ) 2>/dev/null | $SED -e 's/[ ]*$//' -e "$lt_sed_naive_backslashify"` } #end: func_convert_core_msys_to_w32 # func_convert_file_check ARG1 ARG2 # Verify that ARG1 (a file name in $build format) was converted to $host # format in ARG2. Otherwise, emit an error message, but continue (resetting # func_to_host_file_result to ARG1). func_convert_file_check () { $opt_debug if test -z "$2" && test -n "$1" ; then func_error "Could not determine host file name corresponding to" func_error " \`$1'" func_error "Continuing, but uninstalled executables may not work." # Fallback: func_to_host_file_result="$1" fi } # end func_convert_file_check # func_convert_path_check FROM_PATHSEP TO_PATHSEP FROM_PATH TO_PATH # Verify that FROM_PATH (a path in $build format) was converted to $host # format in TO_PATH. Otherwise, emit an error message, but continue, resetting # func_to_host_file_result to a simplistic fallback value (see below). func_convert_path_check () { $opt_debug if test -z "$4" && test -n "$3"; then func_error "Could not determine the host path corresponding to" func_error " \`$3'" func_error "Continuing, but uninstalled executables may not work." # Fallback. This is a deliberately simplistic "conversion" and # should not be "improved". See libtool.info. if test "x$1" != "x$2"; then lt_replace_pathsep_chars="s|$1|$2|g" func_to_host_path_result=`echo "$3" | $SED -e "$lt_replace_pathsep_chars"` else func_to_host_path_result="$3" fi fi } # end func_convert_path_check # func_convert_path_front_back_pathsep FRONTPAT BACKPAT REPL ORIG # Modifies func_to_host_path_result by prepending REPL if ORIG matches FRONTPAT # and appending REPL if ORIG matches BACKPAT. func_convert_path_front_back_pathsep () { $opt_debug case $4 in $1 ) func_to_host_path_result="$3$func_to_host_path_result" ;; esac case $4 in $2 ) func_append func_to_host_path_result "$3" ;; esac } # end func_convert_path_front_back_pathsep ################################################## # $build to $host FILE NAME CONVERSION FUNCTIONS # ################################################## # invoked via `$to_host_file_cmd ARG' # # In each case, ARG is the path to be converted from $build to $host format. # Result will be available in $func_to_host_file_result. # func_to_host_file ARG # Converts the file name ARG from $build format to $host format. Return result # in func_to_host_file_result. func_to_host_file () { $opt_debug $to_host_file_cmd "$1" } # end func_to_host_file # func_to_tool_file ARG LAZY # converts the file name ARG from $build format to toolchain format. Return # result in func_to_tool_file_result. If the conversion in use is listed # in (the comma separated) LAZY, no conversion takes place. func_to_tool_file () { $opt_debug case ,$2, in *,"$to_tool_file_cmd",*) func_to_tool_file_result=$1 ;; *) $to_tool_file_cmd "$1" func_to_tool_file_result=$func_to_host_file_result ;; esac } # end func_to_tool_file # func_convert_file_noop ARG # Copy ARG to func_to_host_file_result. func_convert_file_noop () { func_to_host_file_result="$1" } # end func_convert_file_noop # func_convert_file_msys_to_w32 ARG # Convert file name ARG from (mingw) MSYS to (mingw) w32 format; automatic # conversion to w32 is not available inside the cwrapper. Returns result in # func_to_host_file_result. func_convert_file_msys_to_w32 () { $opt_debug func_to_host_file_result="$1" if test -n "$1"; then func_convert_core_msys_to_w32 "$1" func_to_host_file_result="$func_convert_core_msys_to_w32_result" fi func_convert_file_check "$1" "$func_to_host_file_result" } # end func_convert_file_msys_to_w32 # func_convert_file_cygwin_to_w32 ARG # Convert file name ARG from Cygwin to w32 format. Returns result in # func_to_host_file_result. func_convert_file_cygwin_to_w32 () { $opt_debug func_to_host_file_result="$1" if test -n "$1"; then # because $build is cygwin, we call "the" cygpath in $PATH; no need to use # LT_CYGPATH in this case. func_to_host_file_result=`cygpath -m "$1"` fi func_convert_file_check "$1" "$func_to_host_file_result" } # end func_convert_file_cygwin_to_w32 # func_convert_file_nix_to_w32 ARG # Convert file name ARG from *nix to w32 format. Requires a wine environment # and a working winepath. Returns result in func_to_host_file_result. func_convert_file_nix_to_w32 () { $opt_debug func_to_host_file_result="$1" if test -n "$1"; then func_convert_core_file_wine_to_w32 "$1" func_to_host_file_result="$func_convert_core_file_wine_to_w32_result" fi func_convert_file_check "$1" "$func_to_host_file_result" } # end func_convert_file_nix_to_w32 # func_convert_file_msys_to_cygwin ARG # Convert file name ARG from MSYS to Cygwin format. Requires LT_CYGPATH set. # Returns result in func_to_host_file_result. func_convert_file_msys_to_cygwin () { $opt_debug func_to_host_file_result="$1" if test -n "$1"; then func_convert_core_msys_to_w32 "$1" func_cygpath -u "$func_convert_core_msys_to_w32_result" func_to_host_file_result="$func_cygpath_result" fi func_convert_file_check "$1" "$func_to_host_file_result" } # end func_convert_file_msys_to_cygwin # func_convert_file_nix_to_cygwin ARG # Convert file name ARG from *nix to Cygwin format. Requires Cygwin installed # in a wine environment, working winepath, and LT_CYGPATH set. Returns result # in func_to_host_file_result. func_convert_file_nix_to_cygwin () { $opt_debug func_to_host_file_result="$1" if test -n "$1"; then # convert from *nix to w32, then use cygpath to convert from w32 to cygwin. func_convert_core_file_wine_to_w32 "$1" func_cygpath -u "$func_convert_core_file_wine_to_w32_result" func_to_host_file_result="$func_cygpath_result" fi func_convert_file_check "$1" "$func_to_host_file_result" } # end func_convert_file_nix_to_cygwin ############################################# # $build to $host PATH CONVERSION FUNCTIONS # ############################################# # invoked via `$to_host_path_cmd ARG' # # In each case, ARG is the path to be converted from $build to $host format. # The result will be available in $func_to_host_path_result. # # Path separators are also converted from $build format to $host format. If # ARG begins or ends with a path separator character, it is preserved (but # converted to $host format) on output. # # All path conversion functions are named using the following convention: # file name conversion function : func_convert_file_X_to_Y () # path conversion function : func_convert_path_X_to_Y () # where, for any given $build/$host combination the 'X_to_Y' value is the # same. If conversion functions are added for new $build/$host combinations, # the two new functions must follow this pattern, or func_init_to_host_path_cmd # will break. # func_init_to_host_path_cmd # Ensures that function "pointer" variable $to_host_path_cmd is set to the # appropriate value, based on the value of $to_host_file_cmd. to_host_path_cmd= func_init_to_host_path_cmd () { $opt_debug if test -z "$to_host_path_cmd"; then func_stripname 'func_convert_file_' '' "$to_host_file_cmd" to_host_path_cmd="func_convert_path_${func_stripname_result}" fi } # func_to_host_path ARG # Converts the path ARG from $build format to $host format. Return result # in func_to_host_path_result. func_to_host_path () { $opt_debug func_init_to_host_path_cmd $to_host_path_cmd "$1" } # end func_to_host_path # func_convert_path_noop ARG # Copy ARG to func_to_host_path_result. func_convert_path_noop () { func_to_host_path_result="$1" } # end func_convert_path_noop # func_convert_path_msys_to_w32 ARG # Convert path ARG from (mingw) MSYS to (mingw) w32 format; automatic # conversion to w32 is not available inside the cwrapper. Returns result in # func_to_host_path_result. func_convert_path_msys_to_w32 () { $opt_debug func_to_host_path_result="$1" if test -n "$1"; then # Remove leading and trailing path separator characters from ARG. MSYS # behavior is inconsistent here; cygpath turns them into '.;' and ';.'; # and winepath ignores them completely. func_stripname : : "$1" func_to_host_path_tmp1=$func_stripname_result func_convert_core_msys_to_w32 "$func_to_host_path_tmp1" func_to_host_path_result="$func_convert_core_msys_to_w32_result" func_convert_path_check : ";" \ "$func_to_host_path_tmp1" "$func_to_host_path_result" func_convert_path_front_back_pathsep ":*" "*:" ";" "$1" fi } # end func_convert_path_msys_to_w32 # func_convert_path_cygwin_to_w32 ARG # Convert path ARG from Cygwin to w32 format. Returns result in # func_to_host_file_result. func_convert_path_cygwin_to_w32 () { $opt_debug func_to_host_path_result="$1" if test -n "$1"; then # See func_convert_path_msys_to_w32: func_stripname : : "$1" func_to_host_path_tmp1=$func_stripname_result func_to_host_path_result=`cygpath -m -p "$func_to_host_path_tmp1"` func_convert_path_check : ";" \ "$func_to_host_path_tmp1" "$func_to_host_path_result" func_convert_path_front_back_pathsep ":*" "*:" ";" "$1" fi } # end func_convert_path_cygwin_to_w32 # func_convert_path_nix_to_w32 ARG # Convert path ARG from *nix to w32 format. Requires a wine environment and # a working winepath. Returns result in func_to_host_file_result. func_convert_path_nix_to_w32 () { $opt_debug func_to_host_path_result="$1" if test -n "$1"; then # See func_convert_path_msys_to_w32: func_stripname : : "$1" func_to_host_path_tmp1=$func_stripname_result func_convert_core_path_wine_to_w32 "$func_to_host_path_tmp1" func_to_host_path_result="$func_convert_core_path_wine_to_w32_result" func_convert_path_check : ";" \ "$func_to_host_path_tmp1" "$func_to_host_path_result" func_convert_path_front_back_pathsep ":*" "*:" ";" "$1" fi } # end func_convert_path_nix_to_w32 # func_convert_path_msys_to_cygwin ARG # Convert path ARG from MSYS to Cygwin format. Requires LT_CYGPATH set. # Returns result in func_to_host_file_result. func_convert_path_msys_to_cygwin () { $opt_debug func_to_host_path_result="$1" if test -n "$1"; then # See func_convert_path_msys_to_w32: func_stripname : : "$1" func_to_host_path_tmp1=$func_stripname_result func_convert_core_msys_to_w32 "$func_to_host_path_tmp1" func_cygpath -u -p "$func_convert_core_msys_to_w32_result" func_to_host_path_result="$func_cygpath_result" func_convert_path_check : : \ "$func_to_host_path_tmp1" "$func_to_host_path_result" func_convert_path_front_back_pathsep ":*" "*:" : "$1" fi } # end func_convert_path_msys_to_cygwin # func_convert_path_nix_to_cygwin ARG # Convert path ARG from *nix to Cygwin format. Requires Cygwin installed in a # a wine environment, working winepath, and LT_CYGPATH set. Returns result in # func_to_host_file_result. func_convert_path_nix_to_cygwin () { $opt_debug func_to_host_path_result="$1" if test -n "$1"; then # Remove leading and trailing path separator characters from # ARG. msys behavior is inconsistent here, cygpath turns them # into '.;' and ';.', and winepath ignores them completely. func_stripname : : "$1" func_to_host_path_tmp1=$func_stripname_result func_convert_core_path_wine_to_w32 "$func_to_host_path_tmp1" func_cygpath -u -p "$func_convert_core_path_wine_to_w32_result" func_to_host_path_result="$func_cygpath_result" func_convert_path_check : : \ "$func_to_host_path_tmp1" "$func_to_host_path_result" func_convert_path_front_back_pathsep ":*" "*:" : "$1" fi } # end func_convert_path_nix_to_cygwin # func_mode_compile arg... func_mode_compile () { $opt_debug # Get the compilation command and the source file. base_compile= srcfile="$nonopt" # always keep a non-empty value in "srcfile" suppress_opt=yes suppress_output= arg_mode=normal libobj= later= pie_flag= for arg do case $arg_mode in arg ) # do not "continue". Instead, add this to base_compile lastarg="$arg" arg_mode=normal ;; target ) libobj="$arg" arg_mode=normal continue ;; normal ) # Accept any command-line options. case $arg in -o) test -n "$libobj" && \ func_fatal_error "you cannot specify \`-o' more than once" arg_mode=target continue ;; -pie | -fpie | -fPIE) func_append pie_flag " $arg" continue ;; -shared | -static | -prefer-pic | -prefer-non-pic) func_append later " $arg" continue ;; -no-suppress) suppress_opt=no continue ;; -Xcompiler) arg_mode=arg # the next one goes into the "base_compile" arg list continue # The current "srcfile" will either be retained or ;; # replaced later. I would guess that would be a bug. -Wc,*) func_stripname '-Wc,' '' "$arg" args=$func_stripname_result lastarg= save_ifs="$IFS"; IFS=',' for arg in $args; do IFS="$save_ifs" func_append_quoted lastarg "$arg" done IFS="$save_ifs" func_stripname ' ' '' "$lastarg" lastarg=$func_stripname_result # Add the arguments to base_compile. func_append base_compile " $lastarg" continue ;; *) # Accept the current argument as the source file. # The previous "srcfile" becomes the current argument. # lastarg="$srcfile" srcfile="$arg" ;; esac # case $arg ;; esac # case $arg_mode # Aesthetically quote the previous argument. func_append_quoted base_compile "$lastarg" done # for arg case $arg_mode in arg) func_fatal_error "you must specify an argument for -Xcompile" ;; target) func_fatal_error "you must specify a target with \`-o'" ;; *) # Get the name of the library object. test -z "$libobj" && { func_basename "$srcfile" libobj="$func_basename_result" } ;; esac # Recognize several different file suffixes. # If the user specifies -o file.o, it is replaced with file.lo case $libobj in *.[cCFSifmso] | \ *.ada | *.adb | *.ads | *.asm | \ *.c++ | *.cc | *.ii | *.class | *.cpp | *.cxx | \ *.[fF][09]? | *.for | *.java | *.go | *.obj | *.sx | *.cu | *.cup) func_xform "$libobj" libobj=$func_xform_result ;; esac case $libobj in *.lo) func_lo2o "$libobj"; obj=$func_lo2o_result ;; *) func_fatal_error "cannot determine name of library object from \`$libobj'" ;; esac func_infer_tag $base_compile for arg in $later; do case $arg in -shared) test "$build_libtool_libs" != yes && \ func_fatal_configuration "can not build a shared library" build_old_libs=no continue ;; -static) build_libtool_libs=no build_old_libs=yes continue ;; -prefer-pic) pic_mode=yes continue ;; -prefer-non-pic) pic_mode=no continue ;; esac done func_quote_for_eval "$libobj" test "X$libobj" != "X$func_quote_for_eval_result" \ && $ECHO "X$libobj" | $GREP '[]~#^*{};<>?"'"'"' &()|`$[]' \ && func_warning "libobj name \`$libobj' may not contain shell special characters." func_dirname_and_basename "$obj" "/" "" objname="$func_basename_result" xdir="$func_dirname_result" lobj=${xdir}$objdir/$objname test -z "$base_compile" && \ func_fatal_help "you must specify a compilation command" # Delete any leftover library objects. if test "$build_old_libs" = yes; then removelist="$obj $lobj $libobj ${libobj}T" else removelist="$lobj $libobj ${libobj}T" fi # On Cygwin there's no "real" PIC flag so we must build both object types case $host_os in cygwin* | mingw* | pw32* | os2* | cegcc*) pic_mode=default ;; esac if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then # non-PIC code in shared libraries is not supported pic_mode=default fi # Calculate the filename of the output object if compiler does # not support -o with -c if test "$compiler_c_o" = no; then output_obj=`$ECHO "$srcfile" | $SED 's%^.*/%%; s%\.[^.]*$%%'`.${objext} lockfile="$output_obj.lock" else output_obj= need_locks=no lockfile= fi # Lock this critical section if it is needed # We use this script file to make the link, it avoids creating a new file if test "$need_locks" = yes; then until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do func_echo "Waiting for $lockfile to be removed" sleep 2 done elif test "$need_locks" = warn; then if test -f "$lockfile"; then $ECHO "\ *** ERROR, $lockfile exists and contains: `cat $lockfile 2>/dev/null` This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi func_append removelist " $output_obj" $ECHO "$srcfile" > "$lockfile" fi $opt_dry_run || $RM $removelist func_append removelist " $lockfile" trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15 func_to_tool_file "$srcfile" func_convert_file_msys_to_w32 srcfile=$func_to_tool_file_result func_quote_for_eval "$srcfile" qsrcfile=$func_quote_for_eval_result # Only build a PIC object if we are building libtool libraries. if test "$build_libtool_libs" = yes; then # Without this assignment, base_compile gets emptied. fbsd_hideous_sh_bug=$base_compile if test "$pic_mode" != no; then command="$base_compile $qsrcfile $pic_flag" else # Don't build PIC code command="$base_compile $qsrcfile" fi func_mkdir_p "$xdir$objdir" if test -z "$output_obj"; then # Place PIC objects in $objdir func_append command " -o $lobj" fi func_show_eval_locale "$command" \ 'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed, then go on to compile the next one if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then func_show_eval '$MV "$output_obj" "$lobj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi # Allow error messages only from the first compilation. if test "$suppress_opt" = yes; then suppress_output=' >/dev/null 2>&1' fi fi # Only build a position-dependent object if we build old libraries. if test "$build_old_libs" = yes; then if test "$pic_mode" != yes; then # Don't build PIC code command="$base_compile $qsrcfile$pie_flag" else command="$base_compile $qsrcfile $pic_flag" fi if test "$compiler_c_o" = yes; then func_append command " -o $obj" fi # Suppress compiler output if we already did a PIC compilation. func_append command "$suppress_output" func_show_eval_locale "$command" \ '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then func_show_eval '$MV "$output_obj" "$obj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi fi $opt_dry_run || { func_write_libtool_object "$libobj" "$objdir/$objname" "$objname" # Unlock the critical section if it was locked if test "$need_locks" != no; then removelist=$lockfile $RM "$lockfile" fi } exit $EXIT_SUCCESS } $opt_help || { test "$opt_mode" = compile && func_mode_compile ${1+"$@"} } func_mode_help () { # We need to display help for each of the modes. case $opt_mode in "") # Generic help is extracted from the usage comments # at the start of this file. func_help ;; clean) $ECHO \ "Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE... Remove files from the build directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, object or program, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; compile) $ECHO \ "Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE Compile a source file into a libtool library object. This mode accepts the following additional options: -o OUTPUT-FILE set the output file name to OUTPUT-FILE -no-suppress do not suppress compiler output for multiple passes -prefer-pic try to build PIC objects only -prefer-non-pic try to build non-PIC objects only -shared do not build a \`.o' file suitable for static linking -static only build a \`.o' file suitable for static linking -Wc,FLAG pass FLAG directly to the compiler COMPILE-COMMAND is a command to be used in creating a \`standard' object file from the given SOURCEFILE. The output file name is determined by removing the directory component from SOURCEFILE, then substituting the C source code suffix \`.c' with the library object suffix, \`.lo'." ;; execute) $ECHO \ "Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]... Automatically set library path, then run a program. This mode accepts the following additional options: -dlopen FILE add the directory containing FILE to the library path This mode sets the library path environment variable according to \`-dlopen' flags. If any of the ARGS are libtool executable wrappers, then they are translated into their corresponding uninstalled binary, and any of their required library directories are added to the library path. Then, COMMAND is executed, with ARGS as arguments." ;; finish) $ECHO \ "Usage: $progname [OPTION]... --mode=finish [LIBDIR]... Complete the installation of libtool libraries. Each LIBDIR is a directory that contains libtool libraries. The commands that this mode executes may require superuser privileges. Use the \`--dry-run' option if you just want to see what would be executed." ;; install) $ECHO \ "Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND... Install executables or libraries. INSTALL-COMMAND is the installation command. The first component should be either the \`install' or \`cp' program. The following components of INSTALL-COMMAND are treated specially: -inst-prefix-dir PREFIX-DIR Use PREFIX-DIR as a staging area for installation The rest of the components are interpreted as arguments to that command (only BSD-compatible install options are recognized)." ;; link) $ECHO \ "Usage: $progname [OPTION]... --mode=link LINK-COMMAND... Link object files or libraries together to form another library, or to create an executable program. LINK-COMMAND is a command using the C compiler that you would use to create a program from several object files. The following components of LINK-COMMAND are treated specially: -all-static do not do any dynamic linking at all -avoid-version do not add a version suffix if possible -bindir BINDIR specify path to binaries directory (for systems where libraries must be found in the PATH setting at runtime) -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols -export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3) -export-symbols SYMFILE try to export only the symbols listed in SYMFILE -export-symbols-regex REGEX try to export only the symbols matching REGEX -LLIBDIR search LIBDIR for required installed libraries -lNAME OUTPUT-FILE requires the installed library libNAME -module build a library that can dlopened -no-fast-install disable the fast-install mode -no-install link a not-installable executable -no-undefined declare that a library does not refer to external symbols -o OUTPUT-FILE create OUTPUT-FILE from the specified objects -objectlist FILE Use a list of object files found in FILE to specify objects -precious-files-regex REGEX don't remove output files matching REGEX -release RELEASE specify package release information -rpath LIBDIR the created library will eventually be installed in LIBDIR -R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries -shared only do dynamic linking of libtool libraries -shrext SUFFIX override the standard shared library file extension -static do not do any dynamic linking of uninstalled libtool libraries -static-libtool-libs do not do any dynamic linking of libtool libraries -version-info CURRENT[:REVISION[:AGE]] specify library version info [each variable defaults to 0] -weak LIBNAME declare that the target provides the LIBNAME interface -Wc,FLAG -Xcompiler FLAG pass linker-specific FLAG directly to the compiler -Wl,FLAG -Xlinker FLAG pass linker-specific FLAG directly to the linker -XCClinker FLAG pass link-specific FLAG to the compiler driver (CC) All other options (arguments beginning with \`-') are ignored. Every other argument is treated as a filename. Files ending in \`.la' are treated as uninstalled libtool libraries, other files are standard or library object files. If the OUTPUT-FILE ends in \`.la', then a libtool library is created, only library objects (\`.lo' files) may be specified, and \`-rpath' is required, except when creating a convenience library. If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created using \`ar' and \`ranlib', or on Windows using \`lib'. If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file is created, otherwise an executable program is created." ;; uninstall) $ECHO \ "Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE... Remove libraries from an installation directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; *) func_fatal_help "invalid operation mode \`$opt_mode'" ;; esac echo $ECHO "Try \`$progname --help' for more information about other modes." } # Now that we've collected a possible --mode arg, show help if necessary if $opt_help; then if test "$opt_help" = :; then func_mode_help else { func_help noexit for opt_mode in compile link execute install finish uninstall clean; do func_mode_help done } | sed -n '1p; 2,$s/^Usage:/ or: /p' { func_help noexit for opt_mode in compile link execute install finish uninstall clean; do echo func_mode_help done } | sed '1d /^When reporting/,/^Report/{ H d } $x /information about other modes/d /more detailed .*MODE/d s/^Usage:.*--mode=\([^ ]*\) .*/Description of \1 mode:/' fi exit $? fi # func_mode_execute arg... func_mode_execute () { $opt_debug # The first argument is the command name. cmd="$nonopt" test -z "$cmd" && \ func_fatal_help "you must specify a COMMAND" # Handle -dlopen flags immediately. for file in $opt_dlopen; do test -f "$file" \ || func_fatal_help "\`$file' is not a file" dir= case $file in *.la) func_resolve_sysroot "$file" file=$func_resolve_sysroot_result # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$lib' is not a valid libtool archive" # Read the libtool library. dlname= library_names= func_source "$file" # Skip this library if it cannot be dlopened. if test -z "$dlname"; then # Warn if it was a shared library. test -n "$library_names" && \ func_warning "\`$file' was not linked with \`-export-dynamic'" continue fi func_dirname "$file" "" "." dir="$func_dirname_result" if test -f "$dir/$objdir/$dlname"; then func_append dir "/$objdir" else if test ! -f "$dir/$dlname"; then func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'" fi fi ;; *.lo) # Just add the directory containing the .lo file. func_dirname "$file" "" "." dir="$func_dirname_result" ;; *) func_warning "\`-dlopen' is ignored for non-libtool libraries and objects" continue ;; esac # Get the absolute pathname. absdir=`cd "$dir" && pwd` test -n "$absdir" && dir="$absdir" # Now add the directory to shlibpath_var. if eval "test -z \"\$$shlibpath_var\""; then eval "$shlibpath_var=\"\$dir\"" else eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\"" fi done # This variable tells wrapper scripts just to set shlibpath_var # rather than running their programs. libtool_execute_magic="$magic" # Check if any of the arguments is a wrapper script. args= for file do case $file in -* | *.la | *.lo ) ;; *) # Do a test to see if this is really a libtool program. if func_ltwrapper_script_p "$file"; then func_source "$file" # Transform arg to wrapped name. file="$progdir/$program" elif func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" func_source "$func_ltwrapper_scriptname_result" # Transform arg to wrapped name. file="$progdir/$program" fi ;; esac # Quote arguments (to preserve shell metacharacters). func_append_quoted args "$file" done if test "X$opt_dry_run" = Xfalse; then if test -n "$shlibpath_var"; then # Export the shlibpath_var. eval "export $shlibpath_var" fi # Restore saved environment variables for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES do eval "if test \"\${save_$lt_var+set}\" = set; then $lt_var=\$save_$lt_var; export $lt_var else $lt_unset $lt_var fi" done # Now prepare to actually exec the command. exec_cmd="\$cmd$args" else # Display what would be done. if test -n "$shlibpath_var"; then eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\"" echo "export $shlibpath_var" fi $ECHO "$cmd$args" exit $EXIT_SUCCESS fi } test "$opt_mode" = execute && func_mode_execute ${1+"$@"} # func_mode_finish arg... func_mode_finish () { $opt_debug libs= libdirs= admincmds= for opt in "$nonopt" ${1+"$@"} do if test -d "$opt"; then func_append libdirs " $opt" elif test -f "$opt"; then if func_lalib_unsafe_p "$opt"; then func_append libs " $opt" else func_warning "\`$opt' is not a valid libtool archive" fi else func_fatal_error "invalid argument \`$opt'" fi done if test -n "$libs"; then if test -n "$lt_sysroot"; then sysroot_regex=`$ECHO "$lt_sysroot" | $SED "$sed_make_literal_regex"` sysroot_cmd="s/\([ ']\)$sysroot_regex/\1/g;" else sysroot_cmd= fi # Remove sysroot references if $opt_dry_run; then for lib in $libs; do echo "removing references to $lt_sysroot and \`=' prefixes from $lib" done else tmpdir=`func_mktempdir` for lib in $libs; do sed -e "${sysroot_cmd} s/\([ ']-[LR]\)=/\1/g; s/\([ ']\)=/\1/g" $lib \ > $tmpdir/tmp-la mv -f $tmpdir/tmp-la $lib done ${RM}r "$tmpdir" fi fi if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then for libdir in $libdirs; do if test -n "$finish_cmds"; then # Do each command in the finish commands. func_execute_cmds "$finish_cmds" 'admincmds="$admincmds '"$cmd"'"' fi if test -n "$finish_eval"; then # Do the single finish_eval. eval cmds=\"$finish_eval\" $opt_dry_run || eval "$cmds" || func_append admincmds " $cmds" fi done fi # Exit here if they wanted silent mode. $opt_silent && exit $EXIT_SUCCESS if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then echo "----------------------------------------------------------------------" echo "Libraries have been installed in:" for libdir in $libdirs; do $ECHO " $libdir" done echo echo "If you ever happen to want to link against installed libraries" echo "in a given directory, LIBDIR, you must either use libtool, and" echo "specify the full pathname of the library, or use the \`-LLIBDIR'" echo "flag during linking and do at least one of the following:" if test -n "$shlibpath_var"; then echo " - add LIBDIR to the \`$shlibpath_var' environment variable" echo " during execution" fi if test -n "$runpath_var"; then echo " - add LIBDIR to the \`$runpath_var' environment variable" echo " during linking" fi if test -n "$hardcode_libdir_flag_spec"; then libdir=LIBDIR eval flag=\"$hardcode_libdir_flag_spec\" $ECHO " - use the \`$flag' linker flag" fi if test -n "$admincmds"; then $ECHO " - have your system administrator run these commands:$admincmds" fi if test -f /etc/ld.so.conf; then echo " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'" fi echo echo "See any operating system documentation about shared libraries for" case $host in solaris2.[6789]|solaris2.1[0-9]) echo "more information, such as the ld(1), crle(1) and ld.so(8) manual" echo "pages." ;; *) echo "more information, such as the ld(1) and ld.so(8) manual pages." ;; esac echo "----------------------------------------------------------------------" fi exit $EXIT_SUCCESS } test "$opt_mode" = finish && func_mode_finish ${1+"$@"} # func_mode_install arg... func_mode_install () { $opt_debug # There may be an optional sh(1) argument at the beginning of # install_prog (especially on Windows NT). if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh || # Allow the use of GNU shtool's install command. case $nonopt in *shtool*) :;; *) false;; esac; then # Aesthetically quote it. func_quote_for_eval "$nonopt" install_prog="$func_quote_for_eval_result " arg=$1 shift else install_prog= arg=$nonopt fi # The real first argument should be the name of the installation program. # Aesthetically quote it. func_quote_for_eval "$arg" func_append install_prog "$func_quote_for_eval_result" install_shared_prog=$install_prog case " $install_prog " in *[\\\ /]cp\ *) install_cp=: ;; *) install_cp=false ;; esac # We need to accept at least all the BSD install flags. dest= files= opts= prev= install_type= isdir=no stripme= no_mode=: for arg do arg2= if test -n "$dest"; then func_append files " $dest" dest=$arg continue fi case $arg in -d) isdir=yes ;; -f) if $install_cp; then :; else prev=$arg fi ;; -g | -m | -o) prev=$arg ;; -s) stripme=" -s" continue ;; -*) ;; *) # If the previous option needed an argument, then skip it. if test -n "$prev"; then if test "x$prev" = x-m && test -n "$install_override_mode"; then arg2=$install_override_mode no_mode=false fi prev= else dest=$arg continue fi ;; esac # Aesthetically quote the argument. func_quote_for_eval "$arg" func_append install_prog " $func_quote_for_eval_result" if test -n "$arg2"; then func_quote_for_eval "$arg2" fi func_append install_shared_prog " $func_quote_for_eval_result" done test -z "$install_prog" && \ func_fatal_help "you must specify an install program" test -n "$prev" && \ func_fatal_help "the \`$prev' option requires an argument" if test -n "$install_override_mode" && $no_mode; then if $install_cp; then :; else func_quote_for_eval "$install_override_mode" func_append install_shared_prog " -m $func_quote_for_eval_result" fi fi if test -z "$files"; then if test -z "$dest"; then func_fatal_help "no file or destination specified" else func_fatal_help "you must specify a destination" fi fi # Strip any trailing slash from the destination. func_stripname '' '/' "$dest" dest=$func_stripname_result # Check to see that the destination is a directory. test -d "$dest" && isdir=yes if test "$isdir" = yes; then destdir="$dest" destname= else func_dirname_and_basename "$dest" "" "." destdir="$func_dirname_result" destname="$func_basename_result" # Not a directory, so check to see that there is only one file specified. set dummy $files; shift test "$#" -gt 1 && \ func_fatal_help "\`$dest' is not a directory" fi case $destdir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) for file in $files; do case $file in *.lo) ;; *) func_fatal_help "\`$destdir' must be an absolute directory name" ;; esac done ;; esac # This variable tells wrapper scripts just to set variables rather # than running their programs. libtool_install_magic="$magic" staticlibs= future_libdirs= current_libdirs= for file in $files; do # Do each installation. case $file in *.$libext) # Do the static libraries later. func_append staticlibs " $file" ;; *.la) func_resolve_sysroot "$file" file=$func_resolve_sysroot_result # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$file' is not a valid libtool archive" library_names= old_library= relink_command= func_source "$file" # Add the libdir to current_libdirs if it is the destination. if test "X$destdir" = "X$libdir"; then case "$current_libdirs " in *" $libdir "*) ;; *) func_append current_libdirs " $libdir" ;; esac else # Note the libdir as a future libdir. case "$future_libdirs " in *" $libdir "*) ;; *) func_append future_libdirs " $libdir" ;; esac fi func_dirname "$file" "/" "" dir="$func_dirname_result" func_append dir "$objdir" if test -n "$relink_command"; then # Determine the prefix the user has applied to our future dir. inst_prefix_dir=`$ECHO "$destdir" | $SED -e "s%$libdir\$%%"` # Don't allow the user to place us outside of our expected # location b/c this prevents finding dependent libraries that # are installed to the same prefix. # At present, this check doesn't affect windows .dll's that # are installed into $libdir/../bin (currently, that works fine) # but it's something to keep an eye on. test "$inst_prefix_dir" = "$destdir" && \ func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir" if test -n "$inst_prefix_dir"; then # Stick the inst_prefix_dir data into the link command. relink_command=`$ECHO "$relink_command" | $SED "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"` else relink_command=`$ECHO "$relink_command" | $SED "s%@inst_prefix_dir@%%"` fi func_warning "relinking \`$file'" func_show_eval "$relink_command" \ 'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"' fi # See the names of the shared library. set dummy $library_names; shift if test -n "$1"; then realname="$1" shift srcname="$realname" test -n "$relink_command" && srcname="$realname"T # Install the shared library and build the symlinks. func_show_eval "$install_shared_prog $dir/$srcname $destdir/$realname" \ 'exit $?' tstripme="$stripme" case $host_os in cygwin* | mingw* | pw32* | cegcc*) case $realname in *.dll.a) tstripme="" ;; esac ;; esac if test -n "$tstripme" && test -n "$striplib"; then func_show_eval "$striplib $destdir/$realname" 'exit $?' fi if test "$#" -gt 0; then # Delete the old symlinks, and create new ones. # Try `ln -sf' first, because the `ln' binary might depend on # the symlink we replace! Solaris /bin/ln does not understand -f, # so we also need to try rm && ln -s. for linkname do test "$linkname" != "$realname" \ && func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })" done fi # Do each command in the postinstall commands. lib="$destdir/$realname" func_execute_cmds "$postinstall_cmds" 'exit $?' fi # Install the pseudo-library for information purposes. func_basename "$file" name="$func_basename_result" instname="$dir/$name"i func_show_eval "$install_prog $instname $destdir/$name" 'exit $?' # Maybe install the static library, too. test -n "$old_library" && func_append staticlibs " $dir/$old_library" ;; *.lo) # Install (i.e. copy) a libtool object. # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # Deduce the name of the destination old-style object file. case $destfile in *.lo) func_lo2o "$destfile" staticdest=$func_lo2o_result ;; *.$objext) staticdest="$destfile" destfile= ;; *) func_fatal_help "cannot copy a libtool object to \`$destfile'" ;; esac # Install the libtool object if requested. test -n "$destfile" && \ func_show_eval "$install_prog $file $destfile" 'exit $?' # Install the old object if enabled. if test "$build_old_libs" = yes; then # Deduce the name of the old-style object file. func_lo2o "$file" staticobj=$func_lo2o_result func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?' fi exit $EXIT_SUCCESS ;; *) # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # If the file is missing, and there is a .exe on the end, strip it # because it is most likely a libtool script we actually want to # install stripped_ext="" case $file in *.exe) if test ! -f "$file"; then func_stripname '' '.exe' "$file" file=$func_stripname_result stripped_ext=".exe" fi ;; esac # Do a test to see if this is really a libtool program. case $host in *cygwin* | *mingw*) if func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" wrapper=$func_ltwrapper_scriptname_result else func_stripname '' '.exe' "$file" wrapper=$func_stripname_result fi ;; *) wrapper=$file ;; esac if func_ltwrapper_script_p "$wrapper"; then notinst_deplibs= relink_command= func_source "$wrapper" # Check the variables that should have been set. test -z "$generated_by_libtool_version" && \ func_fatal_error "invalid libtool wrapper script \`$wrapper'" finalize=yes for lib in $notinst_deplibs; do # Check to see that each library is installed. libdir= if test -f "$lib"; then func_source "$lib" fi libfile="$libdir/"`$ECHO "$lib" | $SED 's%^.*/%%g'` ### testsuite: skip nested quoting test if test -n "$libdir" && test ! -f "$libfile"; then func_warning "\`$lib' has not been installed in \`$libdir'" finalize=no fi done relink_command= func_source "$wrapper" outputname= if test "$fast_install" = no && test -n "$relink_command"; then $opt_dry_run || { if test "$finalize" = yes; then tmpdir=`func_mktempdir` func_basename "$file$stripped_ext" file="$func_basename_result" outputname="$tmpdir/$file" # Replace the output file specification. relink_command=`$ECHO "$relink_command" | $SED 's%@OUTPUT@%'"$outputname"'%g'` $opt_silent || { func_quote_for_expand "$relink_command" eval "func_echo $func_quote_for_expand_result" } if eval "$relink_command"; then : else func_error "error: relink \`$file' with the above command before installing it" $opt_dry_run || ${RM}r "$tmpdir" continue fi file="$outputname" else func_warning "cannot relink \`$file'" fi } else # Install the binary that we compiled earlier. file=`$ECHO "$file$stripped_ext" | $SED "s%\([^/]*\)$%$objdir/\1%"` fi fi # remove .exe since cygwin /usr/bin/install will append another # one anyway case $install_prog,$host in */usr/bin/install*,*cygwin*) case $file:$destfile in *.exe:*.exe) # this is ok ;; *.exe:*) destfile=$destfile.exe ;; *:*.exe) func_stripname '' '.exe' "$destfile" destfile=$func_stripname_result ;; esac ;; esac func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?' $opt_dry_run || if test -n "$outputname"; then ${RM}r "$tmpdir" fi ;; esac done for file in $staticlibs; do func_basename "$file" name="$func_basename_result" # Set up the ranlib parameters. oldlib="$destdir/$name" func_to_tool_file "$oldlib" func_convert_file_msys_to_w32 tool_oldlib=$func_to_tool_file_result func_show_eval "$install_prog \$file \$oldlib" 'exit $?' if test -n "$stripme" && test -n "$old_striplib"; then func_show_eval "$old_striplib $tool_oldlib" 'exit $?' fi # Do each command in the postinstall commands. func_execute_cmds "$old_postinstall_cmds" 'exit $?' done test -n "$future_libdirs" && \ func_warning "remember to run \`$progname --finish$future_libdirs'" if test -n "$current_libdirs"; then # Maybe just do a dry run. $opt_dry_run && current_libdirs=" -n$current_libdirs" exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs' else exit $EXIT_SUCCESS fi } test "$opt_mode" = install && func_mode_install ${1+"$@"} # func_generate_dlsyms outputname originator pic_p # Extract symbols from dlprefiles and create ${outputname}S.o with # a dlpreopen symbol table. func_generate_dlsyms () { $opt_debug my_outputname="$1" my_originator="$2" my_pic_p="${3-no}" my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'` my_dlsyms= if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then if test -n "$NM" && test -n "$global_symbol_pipe"; then my_dlsyms="${my_outputname}S.c" else func_error "not configured to extract global symbols from dlpreopened files" fi fi if test -n "$my_dlsyms"; then case $my_dlsyms in "") ;; *.c) # Discover the nlist of each of the dlfiles. nlist="$output_objdir/${my_outputname}.nm" func_show_eval "$RM $nlist ${nlist}S ${nlist}T" # Parse the name list into a source file. func_verbose "creating $output_objdir/$my_dlsyms" $opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\ /* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */ /* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */ #ifdef __cplusplus extern \"C\" { #endif #if defined(__GNUC__) && (((__GNUC__ == 4) && (__GNUC_MINOR__ >= 4)) || (__GNUC__ > 4)) #pragma GCC diagnostic ignored \"-Wstrict-prototypes\" #endif /* Keep this code in sync between libtool.m4, ltmain, lt_system.h, and tests. */ #if defined(_WIN32) || defined(__CYGWIN__) || defined(_WIN32_WCE) /* DATA imports from DLLs on WIN32 con't be const, because runtime relocations are performed -- see ld's documentation on pseudo-relocs. */ # define LT_DLSYM_CONST #elif defined(__osf__) /* This system does not cope well with relocations in const data. */ # define LT_DLSYM_CONST #else # define LT_DLSYM_CONST const #endif /* External symbol declarations for the compiler. */\ " if test "$dlself" = yes; then func_verbose "generating symbol list for \`$output'" $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist" # Add our own program objects to the symbol list. progfiles=`$ECHO "$objs$old_deplibs" | $SP2NL | $SED "$lo2o" | $NL2SP` for progfile in $progfiles; do func_to_tool_file "$progfile" func_convert_file_msys_to_w32 func_verbose "extracting global C symbols from \`$func_to_tool_file_result'" $opt_dry_run || eval "$NM $func_to_tool_file_result | $global_symbol_pipe >> '$nlist'" done if test -n "$exclude_expsyms"; then $opt_dry_run || { eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi if test -n "$export_symbols_regex"; then $opt_dry_run || { eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi # Prepare the list of exported symbols if test -z "$export_symbols"; then export_symbols="$output_objdir/$outputname.exp" $opt_dry_run || { $RM $export_symbols eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"' case $host in *cygwin* | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"' ;; esac } else $opt_dry_run || { eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"' eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' case $host in *cygwin* | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$nlist" >> "$output_objdir/$outputname.def"' ;; esac } fi fi for dlprefile in $dlprefiles; do func_verbose "extracting global C symbols from \`$dlprefile'" func_basename "$dlprefile" name="$func_basename_result" case $host in *cygwin* | *mingw* | *cegcc* ) # if an import library, we need to obtain dlname if func_win32_import_lib_p "$dlprefile"; then func_tr_sh "$dlprefile" eval "curr_lafile=\$libfile_$func_tr_sh_result" dlprefile_dlbasename="" if test -n "$curr_lafile" && func_lalib_p "$curr_lafile"; then # Use subshell, to avoid clobbering current variable values dlprefile_dlname=`source "$curr_lafile" && echo "$dlname"` if test -n "$dlprefile_dlname" ; then func_basename "$dlprefile_dlname" dlprefile_dlbasename="$func_basename_result" else # no lafile. user explicitly requested -dlpreopen . $sharedlib_from_linklib_cmd "$dlprefile" dlprefile_dlbasename=$sharedlib_from_linklib_result fi fi $opt_dry_run || { if test -n "$dlprefile_dlbasename" ; then eval '$ECHO ": $dlprefile_dlbasename" >> "$nlist"' else func_warning "Could not compute DLL name from $name" eval '$ECHO ": $name " >> "$nlist"' fi func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32 eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe | $SED -e '/I __imp/d' -e 's/I __nm_/D /;s/_nm__//' >> '$nlist'" } else # not an import lib $opt_dry_run || { eval '$ECHO ": $name " >> "$nlist"' func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32 eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe >> '$nlist'" } fi ;; *) $opt_dry_run || { eval '$ECHO ": $name " >> "$nlist"' func_to_tool_file "$dlprefile" func_convert_file_msys_to_w32 eval "$NM \"$func_to_tool_file_result\" 2>/dev/null | $global_symbol_pipe >> '$nlist'" } ;; esac done $opt_dry_run || { # Make sure we have at least an empty file. test -f "$nlist" || : > "$nlist" if test -n "$exclude_expsyms"; then $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T $MV "$nlist"T "$nlist" fi # Try sorting and uniquifying the output. if $GREP -v "^: " < "$nlist" | if sort -k 3 /dev/null 2>&1; then sort -k 3 else sort +2 fi | uniq > "$nlist"S; then : else $GREP -v "^: " < "$nlist" > "$nlist"S fi if test -f "$nlist"S; then eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"' else echo '/* NONE */' >> "$output_objdir/$my_dlsyms" fi echo >> "$output_objdir/$my_dlsyms" "\ /* The mapping between symbol names and symbols. */ typedef struct { const char *name; void *address; } lt_dlsymlist; extern LT_DLSYM_CONST lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[]; LT_DLSYM_CONST lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[] = {\ { \"$my_originator\", (void *) 0 }," case $need_lib_prefix in no) eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; *) eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; esac echo >> "$output_objdir/$my_dlsyms" "\ {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt_${my_prefix}_LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif\ " } # !$opt_dry_run pic_flag_for_symtable= case "$compile_command " in *" -static "*) ;; *) case $host in # compiling the symbol table file with pic_flag works around # a FreeBSD bug that causes programs to crash when -lm is # linked before any other PIC object. But we must not use # pic_flag when linking with -static. The problem exists in # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1. *-*-freebsd2.*|*-*-freebsd3.0*|*-*-freebsdelf3.0*) pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;; *-*-hpux*) pic_flag_for_symtable=" $pic_flag" ;; *) if test "X$my_pic_p" != Xno; then pic_flag_for_symtable=" $pic_flag" fi ;; esac ;; esac symtab_cflags= for arg in $LTCFLAGS; do case $arg in -pie | -fpie | -fPIE) ;; *) func_append symtab_cflags " $arg" ;; esac done # Now compile the dynamic symbol file. func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?' # Clean up the generated files. func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"' # Transform the symbol file into the correct name. symfileobj="$output_objdir/${my_outputname}S.$objext" case $host in *cygwin* | *mingw* | *cegcc* ) if test -f "$output_objdir/$my_outputname.def"; then compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` else compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$symfileobj%"` fi ;; *) compile_command=`$ECHO "$compile_command" | $SED "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "$finalize_command" | $SED "s%@SYMFILE@%$symfileobj%"` ;; esac ;; *) func_fatal_error "unknown suffix for \`$my_dlsyms'" ;; esac else # We keep going just in case the user didn't refer to # lt_preloaded_symbols. The linker will fail if global_symbol_pipe # really was required. # Nullify the symbol file. compile_command=`$ECHO "$compile_command" | $SED "s% @SYMFILE@%%"` finalize_command=`$ECHO "$finalize_command" | $SED "s% @SYMFILE@%%"` fi } # func_win32_libid arg # return the library type of file 'arg' # # Need a lot of goo to handle *both* DLLs and import libs # Has to be a shell function in order to 'eat' the argument # that is supplied when $file_magic_command is called. # Despite the name, also deal with 64 bit binaries. func_win32_libid () { $opt_debug win32_libid_type="unknown" win32_fileres=`file -L $1 2>/dev/null` case $win32_fileres in *ar\ archive\ import\ library*) # definitely import win32_libid_type="x86 archive import" ;; *ar\ archive*) # could be an import, or static # Keep the egrep pattern in sync with the one in _LT_CHECK_MAGIC_METHOD. if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null | $EGREP 'file format (pei*-i386(.*architecture: i386)?|pe-arm-wince|pe-x86-64)' >/dev/null; then func_to_tool_file "$1" func_convert_file_msys_to_w32 win32_nmres=`eval $NM -f posix -A \"$func_to_tool_file_result\" | $SED -n -e ' 1,100{ / I /{ s,.*,import, p q } }'` case $win32_nmres in import*) win32_libid_type="x86 archive import";; *) win32_libid_type="x86 archive static";; esac fi ;; *DLL*) win32_libid_type="x86 DLL" ;; *executable*) # but shell scripts are "executable" too... case $win32_fileres in *MS\ Windows\ PE\ Intel*) win32_libid_type="x86 DLL" ;; esac ;; esac $ECHO "$win32_libid_type" } # func_cygming_dll_for_implib ARG # # Platform-specific function to extract the # name of the DLL associated with the specified # import library ARG. # Invoked by eval'ing the libtool variable # $sharedlib_from_linklib_cmd # Result is available in the variable # $sharedlib_from_linklib_result func_cygming_dll_for_implib () { $opt_debug sharedlib_from_linklib_result=`$DLLTOOL --identify-strict --identify "$1"` } # func_cygming_dll_for_implib_fallback_core SECTION_NAME LIBNAMEs # # The is the core of a fallback implementation of a # platform-specific function to extract the name of the # DLL associated with the specified import library LIBNAME. # # SECTION_NAME is either .idata$6 or .idata$7, depending # on the platform and compiler that created the implib. # # Echos the name of the DLL associated with the # specified import library. func_cygming_dll_for_implib_fallback_core () { $opt_debug match_literal=`$ECHO "$1" | $SED "$sed_make_literal_regex"` $OBJDUMP -s --section "$1" "$2" 2>/dev/null | $SED '/^Contents of section '"$match_literal"':/{ # Place marker at beginning of archive member dllname section s/.*/====MARK====/ p d } # These lines can sometimes be longer than 43 characters, but # are always uninteresting /:[ ]*file format pe[i]\{,1\}-/d /^In archive [^:]*:/d # Ensure marker is printed /^====MARK====/p # Remove all lines with less than 43 characters /^.\{43\}/!d # From remaining lines, remove first 43 characters s/^.\{43\}//' | $SED -n ' # Join marker and all lines until next marker into a single line /^====MARK====/ b para H $ b para b :para x s/\n//g # Remove the marker s/^====MARK====// # Remove trailing dots and whitespace s/[\. \t]*$// # Print /./p' | # we now have a list, one entry per line, of the stringified # contents of the appropriate section of all members of the # archive which possess that section. Heuristic: eliminate # all those which have a first or second character that is # a '.' (that is, objdump's representation of an unprintable # character.) This should work for all archives with less than # 0x302f exports -- but will fail for DLLs whose name actually # begins with a literal '.' or a single character followed by # a '.'. # # Of those that remain, print the first one. $SED -e '/^\./d;/^.\./d;q' } # func_cygming_gnu_implib_p ARG # This predicate returns with zero status (TRUE) if # ARG is a GNU/binutils-style import library. Returns # with nonzero status (FALSE) otherwise. func_cygming_gnu_implib_p () { $opt_debug func_to_tool_file "$1" func_convert_file_msys_to_w32 func_cygming_gnu_implib_tmp=`$NM "$func_to_tool_file_result" | eval "$global_symbol_pipe" | $EGREP ' (_head_[A-Za-z0-9_]+_[ad]l*|[A-Za-z0-9_]+_[ad]l*_iname)$'` test -n "$func_cygming_gnu_implib_tmp" } # func_cygming_ms_implib_p ARG # This predicate returns with zero status (TRUE) if # ARG is an MS-style import library. Returns # with nonzero status (FALSE) otherwise. func_cygming_ms_implib_p () { $opt_debug func_to_tool_file "$1" func_convert_file_msys_to_w32 func_cygming_ms_implib_tmp=`$NM "$func_to_tool_file_result" | eval "$global_symbol_pipe" | $GREP '_NULL_IMPORT_DESCRIPTOR'` test -n "$func_cygming_ms_implib_tmp" } # func_cygming_dll_for_implib_fallback ARG # Platform-specific function to extract the # name of the DLL associated with the specified # import library ARG. # # This fallback implementation is for use when $DLLTOOL # does not support the --identify-strict option. # Invoked by eval'ing the libtool variable # $sharedlib_from_linklib_cmd # Result is available in the variable # $sharedlib_from_linklib_result func_cygming_dll_for_implib_fallback () { $opt_debug if func_cygming_gnu_implib_p "$1" ; then # binutils import library sharedlib_from_linklib_result=`func_cygming_dll_for_implib_fallback_core '.idata$7' "$1"` elif func_cygming_ms_implib_p "$1" ; then # ms-generated import library sharedlib_from_linklib_result=`func_cygming_dll_for_implib_fallback_core '.idata$6' "$1"` else # unknown sharedlib_from_linklib_result="" fi } # func_extract_an_archive dir oldlib func_extract_an_archive () { $opt_debug f_ex_an_ar_dir="$1"; shift f_ex_an_ar_oldlib="$1" if test "$lock_old_archive_extraction" = yes; then lockfile=$f_ex_an_ar_oldlib.lock until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do func_echo "Waiting for $lockfile to be removed" sleep 2 done fi func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" \ 'stat=$?; rm -f "$lockfile"; exit $stat' if test "$lock_old_archive_extraction" = yes; then $opt_dry_run || rm -f "$lockfile" fi if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then : else func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib" fi } # func_extract_archives gentop oldlib ... func_extract_archives () { $opt_debug my_gentop="$1"; shift my_oldlibs=${1+"$@"} my_oldobjs="" my_xlib="" my_xabs="" my_xdir="" for my_xlib in $my_oldlibs; do # Extract the objects. case $my_xlib in [\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;; *) my_xabs=`pwd`"/$my_xlib" ;; esac func_basename "$my_xlib" my_xlib="$func_basename_result" my_xlib_u=$my_xlib while :; do case " $extracted_archives " in *" $my_xlib_u "*) func_arith $extracted_serial + 1 extracted_serial=$func_arith_result my_xlib_u=lt$extracted_serial-$my_xlib ;; *) break ;; esac done extracted_archives="$extracted_archives $my_xlib_u" my_xdir="$my_gentop/$my_xlib_u" func_mkdir_p "$my_xdir" case $host in *-darwin*) func_verbose "Extracting $my_xabs" # Do not bother doing anything if just a dry run $opt_dry_run || { darwin_orig_dir=`pwd` cd $my_xdir || exit $? darwin_archive=$my_xabs darwin_curdir=`pwd` darwin_base_archive=`basename "$darwin_archive"` darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true` if test -n "$darwin_arches"; then darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'` darwin_arch= func_verbose "$darwin_base_archive has multiple architectures $darwin_arches" for darwin_arch in $darwin_arches ; do func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}" $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}" cd "unfat-$$/${darwin_base_archive}-${darwin_arch}" func_extract_an_archive "`pwd`" "${darwin_base_archive}" cd "$darwin_curdir" $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" done # $darwin_arches ## Okay now we've a bunch of thin objects, gotta fatten them up :) darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u` darwin_file= darwin_files= for darwin_file in $darwin_filelist; do darwin_files=`find unfat-$$ -name $darwin_file -print | sort | $NL2SP` $LIPO -create -output "$darwin_file" $darwin_files done # $darwin_filelist $RM -rf unfat-$$ cd "$darwin_orig_dir" else cd $darwin_orig_dir func_extract_an_archive "$my_xdir" "$my_xabs" fi # $darwin_arches } # !$opt_dry_run ;; *) func_extract_an_archive "$my_xdir" "$my_xabs" ;; esac my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | sort | $NL2SP` done func_extract_archives_result="$my_oldobjs" } # func_emit_wrapper [arg=no] # # Emit a libtool wrapper script on stdout. # Don't directly open a file because we may want to # incorporate the script contents within a cygwin/mingw # wrapper executable. Must ONLY be called from within # func_mode_link because it depends on a number of variables # set therein. # # ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR # variable will take. If 'yes', then the emitted script # will assume that the directory in which it is stored is # the $objdir directory. This is a cygwin/mingw-specific # behavior. func_emit_wrapper () { func_emit_wrapper_arg1=${1-no} $ECHO "\ #! $SHELL # $output - temporary wrapper script for $objdir/$outputname # Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION # # The $output program cannot be directly executed until all the libtool # libraries that it depends on are installed. # # This wrapper script should never be moved out of the build directory. # If it is, it will not operate correctly. # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. sed_quote_subst='$sed_quote_subst' # Be Bourne compatible if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which # is contrary to our usage. Disable this feature. alias -g '\${1+\"\$@\"}'='\"\$@\"' setopt NO_GLOB_SUBST else case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac fi BIN_SH=xpg4; export BIN_SH # for Tru64 DUALCASE=1; export DUALCASE # for MKS sh # The HP-UX ksh and POSIX shell print the target directory to stdout # if CDPATH is set. (unset CDPATH) >/dev/null 2>&1 && unset CDPATH relink_command=\"$relink_command\" # This environment variable determines our operation mode. if test \"\$libtool_install_magic\" = \"$magic\"; then # install mode needs the following variables: generated_by_libtool_version='$macro_version' notinst_deplibs='$notinst_deplibs' else # When we are sourced in execute mode, \$file and \$ECHO are already set. if test \"\$libtool_execute_magic\" != \"$magic\"; then file=\"\$0\"" qECHO=`$ECHO "$ECHO" | $SED "$sed_quote_subst"` $ECHO "\ # A function that is used when there is no print builtin or printf. func_fallback_echo () { eval 'cat <<_LTECHO_EOF \$1 _LTECHO_EOF' } ECHO=\"$qECHO\" fi # Very basic option parsing. These options are (a) specific to # the libtool wrapper, (b) are identical between the wrapper # /script/ and the wrapper /executable/ which is used only on # windows platforms, and (c) all begin with the string "--lt-" # (application programs are unlikely to have options which match # this pattern). # # There are only two supported options: --lt-debug and # --lt-dump-script. There is, deliberately, no --lt-help. # # The first argument to this parsing function should be the # script's $0 value, followed by "$@". lt_option_debug= func_parse_lt_options () { lt_script_arg0=\$0 shift for lt_opt do case \"\$lt_opt\" in --lt-debug) lt_option_debug=1 ;; --lt-dump-script) lt_dump_D=\`\$ECHO \"X\$lt_script_arg0\" | $SED -e 's/^X//' -e 's%/[^/]*$%%'\` test \"X\$lt_dump_D\" = \"X\$lt_script_arg0\" && lt_dump_D=. lt_dump_F=\`\$ECHO \"X\$lt_script_arg0\" | $SED -e 's/^X//' -e 's%^.*/%%'\` cat \"\$lt_dump_D/\$lt_dump_F\" exit 0 ;; --lt-*) \$ECHO \"Unrecognized --lt- option: '\$lt_opt'\" 1>&2 exit 1 ;; esac done # Print the debug banner immediately: if test -n \"\$lt_option_debug\"; then echo \"${outputname}:${output}:\${LINENO}: libtool wrapper (GNU $PACKAGE$TIMESTAMP) $VERSION\" 1>&2 fi } # Used when --lt-debug. Prints its arguments to stdout # (redirection is the responsibility of the caller) func_lt_dump_args () { lt_dump_args_N=1; for lt_arg do \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[\$lt_dump_args_N]: \$lt_arg\" lt_dump_args_N=\`expr \$lt_dump_args_N + 1\` done } # Core function for launching the target application func_exec_program_core () { " case $host in # Backslashes separate directories on plain windows *-*-mingw | *-*-os2* | *-cegcc*) $ECHO "\ if test -n \"\$lt_option_debug\"; then \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[0]: \$progdir\\\\\$program\" 1>&2 func_lt_dump_args \${1+\"\$@\"} 1>&2 fi exec \"\$progdir\\\\\$program\" \${1+\"\$@\"} " ;; *) $ECHO "\ if test -n \"\$lt_option_debug\"; then \$ECHO \"${outputname}:${output}:\${LINENO}: newargv[0]: \$progdir/\$program\" 1>&2 func_lt_dump_args \${1+\"\$@\"} 1>&2 fi exec \"\$progdir/\$program\" \${1+\"\$@\"} " ;; esac $ECHO "\ \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2 exit 1 } # A function to encapsulate launching the target application # Strips options in the --lt-* namespace from \$@ and # launches target application with the remaining arguments. func_exec_program () { case \" \$* \" in *\\ --lt-*) for lt_wr_arg do case \$lt_wr_arg in --lt-*) ;; *) set x \"\$@\" \"\$lt_wr_arg\"; shift;; esac shift done ;; esac func_exec_program_core \${1+\"\$@\"} } # Parse options func_parse_lt_options \"\$0\" \${1+\"\$@\"} # Find the directory that this script lives in. thisdir=\`\$ECHO \"\$file\" | $SED 's%/[^/]*$%%'\` test \"x\$thisdir\" = \"x\$file\" && thisdir=. # Follow symbolic links until we get to the real thisdir. file=\`ls -ld \"\$file\" | $SED -n 's/.*-> //p'\` while test -n \"\$file\"; do destdir=\`\$ECHO \"\$file\" | $SED 's%/[^/]*\$%%'\` # If there was a directory component, then change thisdir. if test \"x\$destdir\" != \"x\$file\"; then case \"\$destdir\" in [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;; *) thisdir=\"\$thisdir/\$destdir\" ;; esac fi file=\`\$ECHO \"\$file\" | $SED 's%^.*/%%'\` file=\`ls -ld \"\$thisdir/\$file\" | $SED -n 's/.*-> //p'\` done # Usually 'no', except on cygwin/mingw when embedded into # the cwrapper. WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_arg1 if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then # special case for '.' if test \"\$thisdir\" = \".\"; then thisdir=\`pwd\` fi # remove .libs from thisdir case \"\$thisdir\" in *[\\\\/]$objdir ) thisdir=\`\$ECHO \"\$thisdir\" | $SED 's%[\\\\/][^\\\\/]*$%%'\` ;; $objdir ) thisdir=. ;; esac fi # Try to get the absolute directory name. absdir=\`cd \"\$thisdir\" && pwd\` test -n \"\$absdir\" && thisdir=\"\$absdir\" " if test "$fast_install" = yes; then $ECHO "\ program=lt-'$outputname'$exeext progdir=\"\$thisdir/$objdir\" if test ! -f \"\$progdir/\$program\" || { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\ test \"X\$file\" != \"X\$progdir/\$program\"; }; then file=\"\$\$-\$program\" if test ! -d \"\$progdir\"; then $MKDIR \"\$progdir\" else $RM \"\$progdir/\$file\" fi" $ECHO "\ # relink executable if necessary if test -n \"\$relink_command\"; then if relink_command_output=\`eval \$relink_command 2>&1\`; then : else $ECHO \"\$relink_command_output\" >&2 $RM \"\$progdir/\$file\" exit 1 fi fi $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null || { $RM \"\$progdir/\$program\"; $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; } $RM \"\$progdir/\$file\" fi" else $ECHO "\ program='$outputname' progdir=\"\$thisdir/$objdir\" " fi $ECHO "\ if test -f \"\$progdir/\$program\"; then" # fixup the dll searchpath if we need to. # # Fix the DLL searchpath if we need to. Do this before prepending # to shlibpath, because on Windows, both are PATH and uninstalled # libraries must come first. if test -n "$dllsearchpath"; then $ECHO "\ # Add the dll search path components to the executable PATH PATH=$dllsearchpath:\$PATH " fi # Export our shlibpath_var if we have one. if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then $ECHO "\ # Add our own library path to $shlibpath_var $shlibpath_var=\"$temp_rpath\$$shlibpath_var\" # Some systems cannot cope with colon-terminated $shlibpath_var # The second colon is a workaround for a bug in BeOS R4 sed $shlibpath_var=\`\$ECHO \"\$$shlibpath_var\" | $SED 's/::*\$//'\` export $shlibpath_var " fi $ECHO "\ if test \"\$libtool_execute_magic\" != \"$magic\"; then # Run the actual program with our arguments. func_exec_program \${1+\"\$@\"} fi else # The program doesn't exist. \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2 \$ECHO \"This script is just a wrapper for \$program.\" 1>&2 \$ECHO \"See the $PACKAGE documentation for more information.\" 1>&2 exit 1 fi fi\ " } # func_emit_cwrapperexe_src # emit the source code for a wrapper executable on stdout # Must ONLY be called from within func_mode_link because # it depends on a number of variable set therein. func_emit_cwrapperexe_src () { cat < #include #ifdef _MSC_VER # include # include # include #else # include # include # ifdef __CYGWIN__ # include # endif #endif #include #include #include #include #include #include #include #include /* declarations of non-ANSI functions */ #if defined(__MINGW32__) # ifdef __STRICT_ANSI__ int _putenv (const char *); # endif #elif defined(__CYGWIN__) # ifdef __STRICT_ANSI__ char *realpath (const char *, char *); int putenv (char *); int setenv (const char *, const char *, int); # endif /* #elif defined (other platforms) ... */ #endif /* portability defines, excluding path handling macros */ #if defined(_MSC_VER) # define setmode _setmode # define stat _stat # define chmod _chmod # define getcwd _getcwd # define putenv _putenv # define S_IXUSR _S_IEXEC # ifndef _INTPTR_T_DEFINED # define _INTPTR_T_DEFINED # define intptr_t int # endif #elif defined(__MINGW32__) # define setmode _setmode # define stat _stat # define chmod _chmod # define getcwd _getcwd # define putenv _putenv #elif defined(__CYGWIN__) # define HAVE_SETENV # define FOPEN_WB "wb" /* #elif defined (other platforms) ... */ #endif #if defined(PATH_MAX) # define LT_PATHMAX PATH_MAX #elif defined(MAXPATHLEN) # define LT_PATHMAX MAXPATHLEN #else # define LT_PATHMAX 1024 #endif #ifndef S_IXOTH # define S_IXOTH 0 #endif #ifndef S_IXGRP # define S_IXGRP 0 #endif /* path handling portability macros */ #ifndef DIR_SEPARATOR # define DIR_SEPARATOR '/' # define PATH_SEPARATOR ':' #endif #if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \ defined (__OS2__) # define HAVE_DOS_BASED_FILE_SYSTEM # define FOPEN_WB "wb" # ifndef DIR_SEPARATOR_2 # define DIR_SEPARATOR_2 '\\' # endif # ifndef PATH_SEPARATOR_2 # define PATH_SEPARATOR_2 ';' # endif #endif #ifndef DIR_SEPARATOR_2 # define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR) #else /* DIR_SEPARATOR_2 */ # define IS_DIR_SEPARATOR(ch) \ (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2)) #endif /* DIR_SEPARATOR_2 */ #ifndef PATH_SEPARATOR_2 # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR) #else /* PATH_SEPARATOR_2 */ # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2) #endif /* PATH_SEPARATOR_2 */ #ifndef FOPEN_WB # define FOPEN_WB "w" #endif #ifndef _O_BINARY # define _O_BINARY 0 #endif #define XMALLOC(type, num) ((type *) xmalloc ((num) * sizeof(type))) #define XFREE(stale) do { \ if (stale) { free ((void *) stale); stale = 0; } \ } while (0) #if defined(LT_DEBUGWRAPPER) static int lt_debug = 1; #else static int lt_debug = 0; #endif const char *program_name = "libtool-wrapper"; /* in case xstrdup fails */ void *xmalloc (size_t num); char *xstrdup (const char *string); const char *base_name (const char *name); char *find_executable (const char *wrapper); char *chase_symlinks (const char *pathspec); int make_executable (const char *path); int check_executable (const char *path); char *strendzap (char *str, const char *pat); void lt_debugprintf (const char *file, int line, const char *fmt, ...); void lt_fatal (const char *file, int line, const char *message, ...); static const char *nonnull (const char *s); static const char *nonempty (const char *s); void lt_setenv (const char *name, const char *value); char *lt_extend_str (const char *orig_value, const char *add, int to_end); void lt_update_exe_path (const char *name, const char *value); void lt_update_lib_path (const char *name, const char *value); char **prepare_spawn (char **argv); void lt_dump_script (FILE *f); EOF cat <= 0) && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH))) return 1; else return 0; } int make_executable (const char *path) { int rval = 0; struct stat st; lt_debugprintf (__FILE__, __LINE__, "(make_executable): %s\n", nonempty (path)); if ((!path) || (!*path)) return 0; if (stat (path, &st) >= 0) { rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR); } return rval; } /* Searches for the full path of the wrapper. Returns newly allocated full path name if found, NULL otherwise Does not chase symlinks, even on platforms that support them. */ char * find_executable (const char *wrapper) { int has_slash = 0; const char *p; const char *p_next; /* static buffer for getcwd */ char tmp[LT_PATHMAX + 1]; int tmp_len; char *concat_name; lt_debugprintf (__FILE__, __LINE__, "(find_executable): %s\n", nonempty (wrapper)); if ((wrapper == NULL) || (*wrapper == '\0')) return NULL; /* Absolute path? */ #if defined (HAVE_DOS_BASED_FILE_SYSTEM) if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':') { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } else { #endif if (IS_DIR_SEPARATOR (wrapper[0])) { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } #if defined (HAVE_DOS_BASED_FILE_SYSTEM) } #endif for (p = wrapper; *p; p++) if (*p == '/') { has_slash = 1; break; } if (!has_slash) { /* no slashes; search PATH */ const char *path = getenv ("PATH"); if (path != NULL) { for (p = path; *p; p = p_next) { const char *q; size_t p_len; for (q = p; *q; q++) if (IS_PATH_SEPARATOR (*q)) break; p_len = q - p; p_next = (*q == '\0' ? q : q + 1); if (p_len == 0) { /* empty path: current directory */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal (__FILE__, __LINE__, "getcwd failed: %s", nonnull (strerror (errno))); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); } else { concat_name = XMALLOC (char, p_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, p, p_len); concat_name[p_len] = '/'; strcpy (concat_name + p_len + 1, wrapper); } if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } } /* not found in PATH; assume curdir */ } /* Relative path | not found in path: prepend cwd */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal (__FILE__, __LINE__, "getcwd failed: %s", nonnull (strerror (errno))); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); return NULL; } char * chase_symlinks (const char *pathspec) { #ifndef S_ISLNK return xstrdup (pathspec); #else char buf[LT_PATHMAX]; struct stat s; char *tmp_pathspec = xstrdup (pathspec); char *p; int has_symlinks = 0; while (strlen (tmp_pathspec) && !has_symlinks) { lt_debugprintf (__FILE__, __LINE__, "checking path component for symlinks: %s\n", tmp_pathspec); if (lstat (tmp_pathspec, &s) == 0) { if (S_ISLNK (s.st_mode) != 0) { has_symlinks = 1; break; } /* search backwards for last DIR_SEPARATOR */ p = tmp_pathspec + strlen (tmp_pathspec) - 1; while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) p--; if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) { /* no more DIR_SEPARATORS left */ break; } *p = '\0'; } else { lt_fatal (__FILE__, __LINE__, "error accessing file \"%s\": %s", tmp_pathspec, nonnull (strerror (errno))); } } XFREE (tmp_pathspec); if (!has_symlinks) { return xstrdup (pathspec); } tmp_pathspec = realpath (pathspec, buf); if (tmp_pathspec == 0) { lt_fatal (__FILE__, __LINE__, "could not follow symlinks for %s", pathspec); } return xstrdup (tmp_pathspec); #endif } char * strendzap (char *str, const char *pat) { size_t len, patlen; assert (str != NULL); assert (pat != NULL); len = strlen (str); patlen = strlen (pat); if (patlen <= len) { str += len - patlen; if (strcmp (str, pat) == 0) *str = '\0'; } return str; } void lt_debugprintf (const char *file, int line, const char *fmt, ...) { va_list args; if (lt_debug) { (void) fprintf (stderr, "%s:%s:%d: ", program_name, file, line); va_start (args, fmt); (void) vfprintf (stderr, fmt, args); va_end (args); } } static void lt_error_core (int exit_status, const char *file, int line, const char *mode, const char *message, va_list ap) { fprintf (stderr, "%s:%s:%d: %s: ", program_name, file, line, mode); vfprintf (stderr, message, ap); fprintf (stderr, ".\n"); if (exit_status >= 0) exit (exit_status); } void lt_fatal (const char *file, int line, const char *message, ...) { va_list ap; va_start (ap, message); lt_error_core (EXIT_FAILURE, file, line, "FATAL", message, ap); va_end (ap); } static const char * nonnull (const char *s) { return s ? s : "(null)"; } static const char * nonempty (const char *s) { return (s && !*s) ? "(empty)" : nonnull (s); } void lt_setenv (const char *name, const char *value) { lt_debugprintf (__FILE__, __LINE__, "(lt_setenv) setting '%s' to '%s'\n", nonnull (name), nonnull (value)); { #ifdef HAVE_SETENV /* always make a copy, for consistency with !HAVE_SETENV */ char *str = xstrdup (value); setenv (name, str, 1); #else int len = strlen (name) + 1 + strlen (value) + 1; char *str = XMALLOC (char, len); sprintf (str, "%s=%s", name, value); if (putenv (str) != EXIT_SUCCESS) { XFREE (str); } #endif } } char * lt_extend_str (const char *orig_value, const char *add, int to_end) { char *new_value; if (orig_value && *orig_value) { int orig_value_len = strlen (orig_value); int add_len = strlen (add); new_value = XMALLOC (char, add_len + orig_value_len + 1); if (to_end) { strcpy (new_value, orig_value); strcpy (new_value + orig_value_len, add); } else { strcpy (new_value, add); strcpy (new_value + add_len, orig_value); } } else { new_value = xstrdup (add); } return new_value; } void lt_update_exe_path (const char *name, const char *value) { lt_debugprintf (__FILE__, __LINE__, "(lt_update_exe_path) modifying '%s' by prepending '%s'\n", nonnull (name), nonnull (value)); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); /* some systems can't cope with a ':'-terminated path #' */ int len = strlen (new_value); while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1])) { new_value[len-1] = '\0'; } lt_setenv (name, new_value); XFREE (new_value); } } void lt_update_lib_path (const char *name, const char *value) { lt_debugprintf (__FILE__, __LINE__, "(lt_update_lib_path) modifying '%s' by prepending '%s'\n", nonnull (name), nonnull (value)); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); lt_setenv (name, new_value); XFREE (new_value); } } EOF case $host_os in mingw*) cat <<"EOF" /* Prepares an argument vector before calling spawn(). Note that spawn() does not by itself call the command interpreter (getenv ("COMSPEC") != NULL ? getenv ("COMSPEC") : ({ OSVERSIONINFO v; v.dwOSVersionInfoSize = sizeof(OSVERSIONINFO); GetVersionEx(&v); v.dwPlatformId == VER_PLATFORM_WIN32_NT; }) ? "cmd.exe" : "command.com"). Instead it simply concatenates the arguments, separated by ' ', and calls CreateProcess(). We must quote the arguments since Win32 CreateProcess() interprets characters like ' ', '\t', '\\', '"' (but not '<' and '>') in a special way: - Space and tab are interpreted as delimiters. They are not treated as delimiters if they are surrounded by double quotes: "...". - Unescaped double quotes are removed from the input. Their only effect is that within double quotes, space and tab are treated like normal characters. - Backslashes not followed by double quotes are not special. - But 2*n+1 backslashes followed by a double quote become n backslashes followed by a double quote (n >= 0): \" -> " \\\" -> \" \\\\\" -> \\" */ #define SHELL_SPECIAL_CHARS "\"\\ \001\002\003\004\005\006\007\010\011\012\013\014\015\016\017\020\021\022\023\024\025\026\027\030\031\032\033\034\035\036\037" #define SHELL_SPACE_CHARS " \001\002\003\004\005\006\007\010\011\012\013\014\015\016\017\020\021\022\023\024\025\026\027\030\031\032\033\034\035\036\037" char ** prepare_spawn (char **argv) { size_t argc; char **new_argv; size_t i; /* Count number of arguments. */ for (argc = 0; argv[argc] != NULL; argc++) ; /* Allocate new argument vector. */ new_argv = XMALLOC (char *, argc + 1); /* Put quoted arguments into the new argument vector. */ for (i = 0; i < argc; i++) { const char *string = argv[i]; if (string[0] == '\0') new_argv[i] = xstrdup ("\"\""); else if (strpbrk (string, SHELL_SPECIAL_CHARS) != NULL) { int quote_around = (strpbrk (string, SHELL_SPACE_CHARS) != NULL); size_t length; unsigned int backslashes; const char *s; char *quoted_string; char *p; length = 0; backslashes = 0; if (quote_around) length++; for (s = string; *s != '\0'; s++) { char c = *s; if (c == '"') length += backslashes + 1; length++; if (c == '\\') backslashes++; else backslashes = 0; } if (quote_around) length += backslashes + 1; quoted_string = XMALLOC (char, length + 1); p = quoted_string; backslashes = 0; if (quote_around) *p++ = '"'; for (s = string; *s != '\0'; s++) { char c = *s; if (c == '"') { unsigned int j; for (j = backslashes + 1; j > 0; j--) *p++ = '\\'; } *p++ = c; if (c == '\\') backslashes++; else backslashes = 0; } if (quote_around) { unsigned int j; for (j = backslashes; j > 0; j--) *p++ = '\\'; *p++ = '"'; } *p = '\0'; new_argv[i] = quoted_string; } else new_argv[i] = (char *) string; } new_argv[argc] = NULL; return new_argv; } EOF ;; esac cat <<"EOF" void lt_dump_script (FILE* f) { EOF func_emit_wrapper yes | $SED -n -e ' s/^\(.\{79\}\)\(..*\)/\1\ \2/ h s/\([\\"]\)/\\\1/g s/$/\\n/ s/\([^\n]*\).*/ fputs ("\1", f);/p g D' cat <<"EOF" } EOF } # end: func_emit_cwrapperexe_src # func_win32_import_lib_p ARG # True if ARG is an import lib, as indicated by $file_magic_cmd func_win32_import_lib_p () { $opt_debug case `eval $file_magic_cmd \"\$1\" 2>/dev/null | $SED -e 10q` in *import*) : ;; *) false ;; esac } # func_mode_link arg... func_mode_link () { $opt_debug case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) # It is impossible to link a dll without this setting, and # we shouldn't force the makefile maintainer to figure out # which system we are compiling for in order to pass an extra # flag for every libtool invocation. # allow_undefined=no # FIXME: Unfortunately, there are problems with the above when trying # to make a dll which has undefined symbols, in which case not # even a static library is built. For now, we need to specify # -no-undefined on the libtool link line when we can be certain # that all symbols are satisfied, otherwise we get a static library. allow_undefined=yes ;; *) allow_undefined=yes ;; esac libtool_args=$nonopt base_compile="$nonopt $@" compile_command=$nonopt finalize_command=$nonopt compile_rpath= finalize_rpath= compile_shlibpath= finalize_shlibpath= convenience= old_convenience= deplibs= old_deplibs= compiler_flags= linker_flags= dllsearchpath= lib_search_path=`pwd` inst_prefix_dir= new_inherited_linker_flags= avoid_version=no bindir= dlfiles= dlprefiles= dlself=no export_dynamic=no export_symbols= export_symbols_regex= generated= libobjs= ltlibs= module=no no_install=no objs= non_pic_objects= precious_files_regex= prefer_static_libs=no preload=no prev= prevarg= release= rpath= xrpath= perm_rpath= temp_rpath= thread_safe=no vinfo= vinfo_number=no weak_libs= single_module="${wl}-single_module" func_infer_tag $base_compile # We need to know -static, to get the right output filenames. for arg do case $arg in -shared) test "$build_libtool_libs" != yes && \ func_fatal_configuration "can not build a shared library" build_old_libs=no break ;; -all-static | -static | -static-libtool-libs) case $arg in -all-static) if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then func_warning "complete static linking is impossible in this configuration" fi if test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; -static) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=built ;; -static-libtool-libs) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; esac build_libtool_libs=no build_old_libs=yes break ;; esac done # See if our shared archives depend on static archives. test -n "$old_archive_from_new_cmds" && build_old_libs=yes # Go through the arguments, transforming them on the way. while test "$#" -gt 0; do arg="$1" shift func_quote_for_eval "$arg" qarg=$func_quote_for_eval_unquoted_result func_append libtool_args " $func_quote_for_eval_result" # If the previous option needs an argument, assign it. if test -n "$prev"; then case $prev in output) func_append compile_command " @OUTPUT@" func_append finalize_command " @OUTPUT@" ;; esac case $prev in bindir) bindir="$arg" prev= continue ;; dlfiles|dlprefiles) if test "$preload" = no; then # Add the symbol object into the linking commands. func_append compile_command " @SYMFILE@" func_append finalize_command " @SYMFILE@" preload=yes fi case $arg in *.la | *.lo) ;; # We handle these cases below. force) if test "$dlself" = no; then dlself=needless export_dynamic=yes fi prev= continue ;; self) if test "$prev" = dlprefiles; then dlself=yes elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then dlself=yes else dlself=needless export_dynamic=yes fi prev= continue ;; *) if test "$prev" = dlfiles; then func_append dlfiles " $arg" else func_append dlprefiles " $arg" fi prev= continue ;; esac ;; expsyms) export_symbols="$arg" test -f "$arg" \ || func_fatal_error "symbol file \`$arg' does not exist" prev= continue ;; expsyms_regex) export_symbols_regex="$arg" prev= continue ;; framework) case $host in *-*-darwin*) case "$deplibs " in *" $qarg.ltframework "*) ;; *) func_append deplibs " $qarg.ltframework" # this is fixed later ;; esac ;; esac prev= continue ;; inst_prefix) inst_prefix_dir="$arg" prev= continue ;; objectlist) if test -f "$arg"; then save_arg=$arg moreargs= for fil in `cat "$save_arg"` do # func_append moreargs " $fil" arg=$fil # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then func_append dlfiles " $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. func_append dlprefiles " $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi done else func_fatal_error "link input file \`$arg' does not exist" fi arg=$save_arg prev= continue ;; precious_regex) precious_files_regex="$arg" prev= continue ;; release) release="-$arg" prev= continue ;; rpath | xrpath) # We need an absolute path. case $arg in [\\/]* | [A-Za-z]:[\\/]*) ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac if test "$prev" = rpath; then case "$rpath " in *" $arg "*) ;; *) func_append rpath " $arg" ;; esac else case "$xrpath " in *" $arg "*) ;; *) func_append xrpath " $arg" ;; esac fi prev= continue ;; shrext) shrext_cmds="$arg" prev= continue ;; weak) func_append weak_libs " $arg" prev= continue ;; xcclinker) func_append linker_flags " $qarg" func_append compiler_flags " $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xcompiler) func_append compiler_flags " $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xlinker) func_append linker_flags " $qarg" func_append compiler_flags " $wl$qarg" prev= func_append compile_command " $wl$qarg" func_append finalize_command " $wl$qarg" continue ;; *) eval "$prev=\"\$arg\"" prev= continue ;; esac fi # test -n "$prev" prevarg="$arg" case $arg in -all-static) if test -n "$link_static_flag"; then # See comment for -static flag below, for more details. func_append compile_command " $link_static_flag" func_append finalize_command " $link_static_flag" fi continue ;; -allow-undefined) # FIXME: remove this flag sometime in the future. func_fatal_error "\`-allow-undefined' must not be used because it is the default" ;; -avoid-version) avoid_version=yes continue ;; -bindir) prev=bindir continue ;; -dlopen) prev=dlfiles continue ;; -dlpreopen) prev=dlprefiles continue ;; -export-dynamic) export_dynamic=yes continue ;; -export-symbols | -export-symbols-regex) if test -n "$export_symbols" || test -n "$export_symbols_regex"; then func_fatal_error "more than one -exported-symbols argument is not allowed" fi if test "X$arg" = "X-export-symbols"; then prev=expsyms else prev=expsyms_regex fi continue ;; -framework) prev=framework continue ;; -inst-prefix-dir) prev=inst_prefix continue ;; # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:* # so, if we see these flags be careful not to treat them like -L -L[A-Z][A-Z]*:*) case $with_gcc/$host in no/*-*-irix* | /*-*-irix*) func_append compile_command " $arg" func_append finalize_command " $arg" ;; esac continue ;; -L*) func_stripname "-L" '' "$arg" if test -z "$func_stripname_result"; then if test "$#" -gt 0; then func_fatal_error "require no space between \`-L' and \`$1'" else func_fatal_error "need path for \`-L' option" fi fi func_resolve_sysroot "$func_stripname_result" dir=$func_resolve_sysroot_result # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) absdir=`cd "$dir" && pwd` test -z "$absdir" && \ func_fatal_error "cannot determine absolute directory name of \`$dir'" dir="$absdir" ;; esac case "$deplibs " in *" -L$dir "* | *" $arg "*) # Will only happen for absolute or sysroot arguments ;; *) # Preserve sysroot, but never include relative directories case $dir in [\\/]* | [A-Za-z]:[\\/]* | =*) func_append deplibs " $arg" ;; *) func_append deplibs " -L$dir" ;; esac func_append lib_search_path " $dir" ;; esac case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) testbindir=`$ECHO "$dir" | $SED 's*/lib$*/bin*'` case :$dllsearchpath: in *":$dir:"*) ;; ::) dllsearchpath=$dir;; *) func_append dllsearchpath ":$dir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; *) func_append dllsearchpath ":$testbindir";; esac ;; esac continue ;; -l*) if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc* | *-*-haiku*) # These systems don't actually have a C or math library (as such) continue ;; *-*-os2*) # These systems don't actually have a C library (as such) test "X$arg" = "X-lc" && continue ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. test "X$arg" = "X-lc" && continue ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C and math libraries are in the System framework func_append deplibs " System.ltframework" continue ;; *-*-sco3.2v5* | *-*-sco5v6*) # Causes problems with __ctype test "X$arg" = "X-lc" && continue ;; *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) # Compiler inserts libc in the correct place for threads to work test "X$arg" = "X-lc" && continue ;; esac elif test "X$arg" = "X-lc_r"; then case $host in *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc_r directly, use -pthread flag. continue ;; esac fi func_append deplibs " $arg" continue ;; -module) module=yes continue ;; # Tru64 UNIX uses -model [arg] to determine the layout of C++ # classes, name mangling, and exception handling. # Darwin uses the -arch flag to determine output architecture. -model|-arch|-isysroot|--sysroot) func_append compiler_flags " $arg" func_append compile_command " $arg" func_append finalize_command " $arg" prev=xcompiler continue ;; -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe \ |-threads|-fopenmp|-openmp|-mp|-xopenmp|-omp|-qsmp=*) func_append compiler_flags " $arg" func_append compile_command " $arg" func_append finalize_command " $arg" case "$new_inherited_linker_flags " in *" $arg "*) ;; * ) func_append new_inherited_linker_flags " $arg" ;; esac continue ;; -multi_module) single_module="${wl}-multi_module" continue ;; -no-fast-install) fast_install=no continue ;; -no-install) case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*) # The PATH hackery in wrapper scripts is required on Windows # and Darwin in order for the loader to find any dlls it needs. func_warning "\`-no-install' is ignored for $host" func_warning "assuming \`-no-fast-install' instead" fast_install=no ;; *) no_install=yes ;; esac continue ;; -no-undefined) allow_undefined=no continue ;; -objectlist) prev=objectlist continue ;; -o) prev=output ;; -precious-files-regex) prev=precious_regex continue ;; -release) prev=release continue ;; -rpath) prev=rpath continue ;; -R) prev=xrpath continue ;; -R*) func_stripname '-R' '' "$arg" dir=$func_stripname_result # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; =*) func_stripname '=' '' "$dir" dir=$lt_sysroot$func_stripname_result ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac case "$xrpath " in *" $dir "*) ;; *) func_append xrpath " $dir" ;; esac continue ;; -shared) # The effects of -shared are defined in a previous loop. continue ;; -shrext) prev=shrext continue ;; -static | -static-libtool-libs) # The effects of -static are defined in a previous loop. # We used to do the same as -all-static on platforms that # didn't have a PIC flag, but the assumption that the effects # would be equivalent was wrong. It would break on at least # Digital Unix and AIX. continue ;; -thread-safe) thread_safe=yes continue ;; -version-info) prev=vinfo continue ;; -version-number) prev=vinfo vinfo_number=yes continue ;; -weak) prev=weak continue ;; -Wc,*) func_stripname '-Wc,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" func_append arg " $func_quote_for_eval_result" func_append compiler_flags " $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Wl,*) func_stripname '-Wl,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" func_append arg " $wl$func_quote_for_eval_result" func_append compiler_flags " $wl$func_quote_for_eval_result" func_append linker_flags " $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Xcompiler) prev=xcompiler continue ;; -Xlinker) prev=xlinker continue ;; -XCClinker) prev=xcclinker continue ;; # -msg_* for osf cc -msg_*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; # Flags to be passed through unchanged, with rationale: # -64, -mips[0-9] enable 64-bit mode for the SGI compiler # -r[0-9][0-9]* specify processor for the SGI compiler # -xarch=*, -xtarget=* enable 64-bit mode for the Sun compiler # +DA*, +DD* enable 64-bit mode for the HP compiler # -q* compiler args for the IBM compiler # -m*, -t[45]*, -txscale* architecture-specific flags for GCC # -F/path path to uninstalled frameworks, gcc on darwin # -p, -pg, --coverage, -fprofile-* profiling flags for GCC # @file GCC response files # -tp=* Portland pgcc target processor selection # --sysroot=* for sysroot support # -O*, -flto*, -fwhopr*, -fuse-linker-plugin GCC link-time optimization -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \ -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*|-tp=*|--sysroot=*| \ -O*|-flto*|-fwhopr*|-fuse-linker-plugin) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" func_append compile_command " $arg" func_append finalize_command " $arg" func_append compiler_flags " $arg" continue ;; # Some other compiler flag. -* | +*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; *.$objext) # A standard object. func_append objs " $arg" ;; *.lo) # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then func_append dlfiles " $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. func_append dlprefiles " $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi ;; *.$libext) # An archive. func_append deplibs " $arg" func_append old_deplibs " $arg" continue ;; *.la) # A libtool-controlled library. func_resolve_sysroot "$arg" if test "$prev" = dlfiles; then # This library was specified with -dlopen. func_append dlfiles " $func_resolve_sysroot_result" prev= elif test "$prev" = dlprefiles; then # The library was specified with -dlpreopen. func_append dlprefiles " $func_resolve_sysroot_result" prev= else func_append deplibs " $func_resolve_sysroot_result" fi continue ;; # Some other compiler argument. *) # Unknown arguments in both finalize_command and compile_command need # to be aesthetically quoted because they are evaled later. func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; esac # arg # Now actually substitute the argument into the commands. if test -n "$arg"; then func_append compile_command " $arg" func_append finalize_command " $arg" fi done # argument parsing loop test -n "$prev" && \ func_fatal_help "the \`$prevarg' option requires an argument" if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then eval arg=\"$export_dynamic_flag_spec\" func_append compile_command " $arg" func_append finalize_command " $arg" fi oldlibs= # calculate the name of the file, without its directory func_basename "$output" outputname="$func_basename_result" libobjs_save="$libobjs" if test -n "$shlibpath_var"; then # get the directories listed in $shlibpath_var eval shlib_search_path=\`\$ECHO \"\${$shlibpath_var}\" \| \$SED \'s/:/ /g\'\` else shlib_search_path= fi eval sys_lib_search_path=\"$sys_lib_search_path_spec\" eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\" func_dirname "$output" "/" "" output_objdir="$func_dirname_result$objdir" func_to_tool_file "$output_objdir/" tool_output_objdir=$func_to_tool_file_result # Create the object directory. func_mkdir_p "$output_objdir" # Determine the type of output case $output in "") func_fatal_help "you must specify an output file" ;; *.$libext) linkmode=oldlib ;; *.lo | *.$objext) linkmode=obj ;; *.la) linkmode=lib ;; *) linkmode=prog ;; # Anything else should be a program. esac specialdeplibs= libs= # Find all interdependent deplibs by searching for libraries # that are linked more than once (e.g. -la -lb -la) for deplib in $deplibs; do if $opt_preserve_dup_deps ; then case "$libs " in *" $deplib "*) func_append specialdeplibs " $deplib" ;; esac fi func_append libs " $deplib" done if test "$linkmode" = lib; then libs="$predeps $libs $compiler_lib_search_path $postdeps" # Compute libraries that are listed more than once in $predeps # $postdeps and mark them as special (i.e., whose duplicates are # not to be eliminated). pre_post_deps= if $opt_duplicate_compiler_generated_deps; then for pre_post_dep in $predeps $postdeps; do case "$pre_post_deps " in *" $pre_post_dep "*) func_append specialdeplibs " $pre_post_deps" ;; esac func_append pre_post_deps " $pre_post_dep" done fi pre_post_deps= fi deplibs= newdependency_libs= newlib_search_path= need_relink=no # whether we're linking any uninstalled libtool libraries notinst_deplibs= # not-installed libtool libraries notinst_path= # paths that contain not-installed libtool libraries case $linkmode in lib) passes="conv dlpreopen link" for file in $dlfiles $dlprefiles; do case $file in *.la) ;; *) func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file" ;; esac done ;; prog) compile_deplibs= finalize_deplibs= alldeplibs=no newdlfiles= newdlprefiles= passes="conv scan dlopen dlpreopen link" ;; *) passes="conv" ;; esac for pass in $passes; do # The preopen pass in lib mode reverses $deplibs; put it back here # so that -L comes before libs that need it for instance... if test "$linkmode,$pass" = "lib,link"; then ## FIXME: Find the place where the list is rebuilt in the wrong ## order, and fix it there properly tmp_deplibs= for deplib in $deplibs; do tmp_deplibs="$deplib $tmp_deplibs" done deplibs="$tmp_deplibs" fi if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan"; then libs="$deplibs" deplibs= fi if test "$linkmode" = prog; then case $pass in dlopen) libs="$dlfiles" ;; dlpreopen) libs="$dlprefiles" ;; link) libs="$deplibs %DEPLIBS% $dependency_libs" ;; esac fi if test "$linkmode,$pass" = "lib,dlpreopen"; then # Collect and forward deplibs of preopened libtool libs for lib in $dlprefiles; do # Ignore non-libtool-libs dependency_libs= func_resolve_sysroot "$lib" case $lib in *.la) func_source "$func_resolve_sysroot_result" ;; esac # Collect preopened libtool deplibs, except any this library # has declared as weak libs for deplib in $dependency_libs; do func_basename "$deplib" deplib_base=$func_basename_result case " $weak_libs " in *" $deplib_base "*) ;; *) func_append deplibs " $deplib" ;; esac done done libs="$dlprefiles" fi if test "$pass" = dlopen; then # Collect dlpreopened libraries save_deplibs="$deplibs" deplibs= fi for deplib in $libs; do lib= found=no case $deplib in -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe \ |-threads|-fopenmp|-openmp|-mp|-xopenmp|-omp|-qsmp=*) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else func_append compiler_flags " $deplib" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) func_append new_inherited_linker_flags " $deplib" ;; esac fi fi continue ;; -l*) if test "$linkmode" != lib && test "$linkmode" != prog; then func_warning "\`-l' is ignored for archives/objects" continue fi func_stripname '-l' '' "$deplib" name=$func_stripname_result if test "$linkmode" = lib; then searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path" else searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path" fi for searchdir in $searchdirs; do for search_ext in .la $std_shrext .so .a; do # Search the libtool library lib="$searchdir/lib${name}${search_ext}" if test -f "$lib"; then if test "$search_ext" = ".la"; then found=yes else found=no fi break 2 fi done done if test "$found" != yes; then # deplib doesn't seem to be a libtool library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue else # deplib is a libtool library # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib, # We need to do some special things here, and not later. if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then case " $predeps $postdeps " in *" $deplib "*) if func_lalib_p "$lib"; then library_names= old_library= func_source "$lib" for l in $old_library $library_names; do ll="$l" done if test "X$ll" = "X$old_library" ; then # only static version available found=no func_dirname "$lib" "" "." ladir="$func_dirname_result" lib=$ladir/$old_library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue fi fi ;; *) ;; esac fi fi ;; # -l *.ltframework) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) func_append new_inherited_linker_flags " $deplib" ;; esac fi fi continue ;; -L*) case $linkmode in lib) deplibs="$deplib $deplibs" test "$pass" = conv && continue newdependency_libs="$deplib $newdependency_libs" func_stripname '-L' '' "$deplib" func_resolve_sysroot "$func_stripname_result" func_append newlib_search_path " $func_resolve_sysroot_result" ;; prog) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi if test "$pass" = scan; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi func_stripname '-L' '' "$deplib" func_resolve_sysroot "$func_stripname_result" func_append newlib_search_path " $func_resolve_sysroot_result" ;; *) func_warning "\`-L' is ignored for archives/objects" ;; esac # linkmode continue ;; # -L -R*) if test "$pass" = link; then func_stripname '-R' '' "$deplib" func_resolve_sysroot "$func_stripname_result" dir=$func_resolve_sysroot_result # Make sure the xrpath contains only unique directories. case "$xrpath " in *" $dir "*) ;; *) func_append xrpath " $dir" ;; esac fi deplibs="$deplib $deplibs" continue ;; *.la) func_resolve_sysroot "$deplib" lib=$func_resolve_sysroot_result ;; *.$libext) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi case $linkmode in lib) # Linking convenience modules into shared libraries is allowed, # but linking other static libraries is non-portable. case " $dlpreconveniencelibs " in *" $deplib "*) ;; *) valid_a_lib=no case $deplibs_check_method in match_pattern*) set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` if eval "\$ECHO \"$deplib\"" 2>/dev/null | $SED 10q \ | $EGREP "$match_pattern_regex" > /dev/null; then valid_a_lib=yes fi ;; pass_all) valid_a_lib=yes ;; esac if test "$valid_a_lib" != yes; then echo $ECHO "*** Warning: Trying to link with static lib archive $deplib." echo "*** I have the capability to make that library automatically link in when" echo "*** you link to this library. But I can only do this if you have a" echo "*** shared version of the library, which you do not appear to have" echo "*** because the file extensions .$libext of this argument makes me believe" echo "*** that it is just a static archive that I should not use here." else echo $ECHO "*** Warning: Linking the shared library $output against the" $ECHO "*** static library $deplib is not portable!" deplibs="$deplib $deplibs" fi ;; esac continue ;; prog) if test "$pass" != link; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi continue ;; esac # linkmode ;; # *.$libext *.lo | *.$objext) if test "$pass" = conv; then deplibs="$deplib $deplibs" elif test "$linkmode" = prog; then if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlopen support or we're linking statically, # we need to preload. func_append newdlprefiles " $deplib" compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else func_append newdlfiles " $deplib" fi fi continue ;; %DEPLIBS%) alldeplibs=yes continue ;; esac # case $deplib if test "$found" = yes || test -f "$lib"; then : else func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'" fi # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$lib" \ || func_fatal_error "\`$lib' is not a valid libtool archive" func_dirname "$lib" "" "." ladir="$func_dirname_result" dlname= dlopen= dlpreopen= libdir= library_names= old_library= inherited_linker_flags= # If the library was installed with an old release of libtool, # it will not redefine variables installed, or shouldnotlink installed=yes shouldnotlink=no avoidtemprpath= # Read the .la file func_source "$lib" # Convert "-framework foo" to "foo.ltframework" if test -n "$inherited_linker_flags"; then tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'` for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do case " $new_inherited_linker_flags " in *" $tmp_inherited_linker_flag "*) ;; *) func_append new_inherited_linker_flags " $tmp_inherited_linker_flag";; esac done fi dependency_libs=`$ECHO " $dependency_libs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan" || { test "$linkmode" != prog && test "$linkmode" != lib; }; then test -n "$dlopen" && func_append dlfiles " $dlopen" test -n "$dlpreopen" && func_append dlprefiles " $dlpreopen" fi if test "$pass" = conv; then # Only check for convenience libraries deplibs="$lib $deplibs" if test -z "$libdir"; then if test -z "$old_library"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # It is a libtool convenience library, so add in its objects. func_append convenience " $ladir/$objdir/$old_library" func_append old_convenience " $ladir/$objdir/$old_library" elif test "$linkmode" != prog && test "$linkmode" != lib; then func_fatal_error "\`$lib' is not a convenience library" fi tmp_libs= for deplib in $dependency_libs; do deplibs="$deplib $deplibs" if $opt_preserve_dup_deps ; then case "$tmp_libs " in *" $deplib "*) func_append specialdeplibs " $deplib" ;; esac fi func_append tmp_libs " $deplib" done continue fi # $pass = conv # Get the name of the library we link against. linklib= if test -n "$old_library" && { test "$prefer_static_libs" = yes || test "$prefer_static_libs,$installed" = "built,no"; }; then linklib=$old_library else for l in $old_library $library_names; do linklib="$l" done fi if test -z "$linklib"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # This library was specified with -dlopen. if test "$pass" = dlopen; then if test -z "$libdir"; then func_fatal_error "cannot -dlopen a convenience library: \`$lib'" fi if test -z "$dlname" || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlname, no dlopen support or we're linking # statically, we need to preload. We also need to preload any # dependent libraries so libltdl's deplib preloader doesn't # bomb out in the load deplibs phase. func_append dlprefiles " $lib $dependency_libs" else func_append newdlfiles " $lib" fi continue fi # $pass = dlopen # We need an absolute path. case $ladir in [\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;; *) abs_ladir=`cd "$ladir" && pwd` if test -z "$abs_ladir"; then func_warning "cannot determine absolute directory name of \`$ladir'" func_warning "passing it literally to the linker, although it might fail" abs_ladir="$ladir" fi ;; esac func_basename "$lib" laname="$func_basename_result" # Find the relevant object directory and library name. if test "X$installed" = Xyes; then if test ! -f "$lt_sysroot$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then func_warning "library \`$lib' was moved." dir="$ladir" absdir="$abs_ladir" libdir="$abs_ladir" else dir="$lt_sysroot$libdir" absdir="$lt_sysroot$libdir" fi test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes else if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then dir="$ladir" absdir="$abs_ladir" # Remove this search path later func_append notinst_path " $abs_ladir" else dir="$ladir/$objdir" absdir="$abs_ladir/$objdir" # Remove this search path later func_append notinst_path " $abs_ladir" fi fi # $installed = yes func_stripname 'lib' '.la' "$laname" name=$func_stripname_result # This library was specified with -dlpreopen. if test "$pass" = dlpreopen; then if test -z "$libdir" && test "$linkmode" = prog; then func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'" fi case "$host" in # special handling for platforms with PE-DLLs. *cygwin* | *mingw* | *cegcc* ) # Linker will automatically link against shared library if both # static and shared are present. Therefore, ensure we extract # symbols from the import library if a shared library is present # (otherwise, the dlopen module name will be incorrect). We do # this by putting the import library name into $newdlprefiles. # We recover the dlopen module name by 'saving' the la file # name in a special purpose variable, and (later) extracting the # dlname from the la file. if test -n "$dlname"; then func_tr_sh "$dir/$linklib" eval "libfile_$func_tr_sh_result=\$abs_ladir/\$laname" func_append newdlprefiles " $dir/$linklib" else func_append newdlprefiles " $dir/$old_library" # Keep a list of preopened convenience libraries to check # that they are being used correctly in the link pass. test -z "$libdir" && \ func_append dlpreconveniencelibs " $dir/$old_library" fi ;; * ) # Prefer using a static library (so that no silly _DYNAMIC symbols # are required to link). if test -n "$old_library"; then func_append newdlprefiles " $dir/$old_library" # Keep a list of preopened convenience libraries to check # that they are being used correctly in the link pass. test -z "$libdir" && \ func_append dlpreconveniencelibs " $dir/$old_library" # Otherwise, use the dlname, so that lt_dlopen finds it. elif test -n "$dlname"; then func_append newdlprefiles " $dir/$dlname" else func_append newdlprefiles " $dir/$linklib" fi ;; esac fi # $pass = dlpreopen if test -z "$libdir"; then # Link the convenience library if test "$linkmode" = lib; then deplibs="$dir/$old_library $deplibs" elif test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$dir/$old_library $compile_deplibs" finalize_deplibs="$dir/$old_library $finalize_deplibs" else deplibs="$lib $deplibs" # used for prog,scan pass fi continue fi if test "$linkmode" = prog && test "$pass" != link; then func_append newlib_search_path " $ladir" deplibs="$lib $deplibs" linkalldeplibs=no if test "$link_all_deplibs" != no || test -z "$library_names" || test "$build_libtool_libs" = no; then linkalldeplibs=yes fi tmp_libs= for deplib in $dependency_libs; do case $deplib in -L*) func_stripname '-L' '' "$deplib" func_resolve_sysroot "$func_stripname_result" func_append newlib_search_path " $func_resolve_sysroot_result" ;; esac # Need to link against all dependency_libs? if test "$linkalldeplibs" = yes; then deplibs="$deplib $deplibs" else # Need to hardcode shared library paths # or/and link against static libraries newdependency_libs="$deplib $newdependency_libs" fi if $opt_preserve_dup_deps ; then case "$tmp_libs " in *" $deplib "*) func_append specialdeplibs " $deplib" ;; esac fi func_append tmp_libs " $deplib" done # for deplib continue fi # $linkmode = prog... if test "$linkmode,$pass" = "prog,link"; then if test -n "$library_names" && { { test "$prefer_static_libs" = no || test "$prefer_static_libs,$installed" = "built,yes"; } || test -z "$old_library"; }; then # We need to hardcode the library path if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then # Make sure the rpath contains only unique directories. case "$temp_rpath:" in *"$absdir:"*) ;; *) func_append temp_rpath "$absdir:" ;; esac fi # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) func_append compile_rpath " $absdir" ;; esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) func_append finalize_rpath " $libdir" ;; esac ;; esac fi # $linkmode,$pass = prog,link... if test "$alldeplibs" = yes && { test "$deplibs_check_method" = pass_all || { test "$build_libtool_libs" = yes && test -n "$library_names"; }; }; then # We only need to search for static libraries continue fi fi link_static=no # Whether the deplib will be linked statically use_static_libs=$prefer_static_libs if test "$use_static_libs" = built && test "$installed" = yes; then use_static_libs=no fi if test -n "$library_names" && { test "$use_static_libs" = no || test -z "$old_library"; }; then case $host in *cygwin* | *mingw* | *cegcc*) # No point in relinking DLLs because paths are not encoded func_append notinst_deplibs " $lib" need_relink=no ;; *) if test "$installed" = no; then func_append notinst_deplibs " $lib" need_relink=yes fi ;; esac # This is a shared library # Warn about portability, can't link against -module's on some # systems (darwin). Don't bleat about dlopened modules though! dlopenmodule="" for dlpremoduletest in $dlprefiles; do if test "X$dlpremoduletest" = "X$lib"; then dlopenmodule="$dlpremoduletest" break fi done if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then echo if test "$linkmode" = prog; then $ECHO "*** Warning: Linking the executable $output against the loadable module" else $ECHO "*** Warning: Linking the shared library $output against the loadable module" fi $ECHO "*** $linklib is not portable!" fi if test "$linkmode" = lib && test "$hardcode_into_libs" = yes; then # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) func_append compile_rpath " $absdir" ;; esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) func_append finalize_rpath " $libdir" ;; esac ;; esac fi if test -n "$old_archive_from_expsyms_cmds"; then # figure out the soname set dummy $library_names shift realname="$1" shift libname=`eval "\\$ECHO \"$libname_spec\""` # use dlname if we got it. it's perfectly good, no? if test -n "$dlname"; then soname="$dlname" elif test -n "$soname_spec"; then # bleh windows case $host in *cygwin* | mingw* | *cegcc*) func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; esac eval soname=\"$soname_spec\" else soname="$realname" fi # Make a new name for the extract_expsyms_cmds to use soroot="$soname" func_basename "$soroot" soname="$func_basename_result" func_stripname 'lib' '.dll' "$soname" newlib=libimp-$func_stripname_result.a # If the library has no export list, then create one now if test -f "$output_objdir/$soname-def"; then : else func_verbose "extracting exported symbol list from \`$soname'" func_execute_cmds "$extract_expsyms_cmds" 'exit $?' fi # Create $newlib if test -f "$output_objdir/$newlib"; then :; else func_verbose "generating import library for \`$soname'" func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?' fi # make sure the library variables are pointing to the new library dir=$output_objdir linklib=$newlib fi # test -n "$old_archive_from_expsyms_cmds" if test "$linkmode" = prog || test "$opt_mode" != relink; then add_shlibpath= add_dir= add= lib_linked=yes case $hardcode_action in immediate | unsupported) if test "$hardcode_direct" = no; then add="$dir/$linklib" case $host in *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;; *-*-sysv4*uw2*) add_dir="-L$dir" ;; *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \ *-*-unixware7*) add_dir="-L$dir" ;; *-*-darwin* ) # if the lib is a (non-dlopened) module then we can not # link against it, someone is ignoring the earlier warnings if /usr/bin/file -L $add 2> /dev/null | $GREP ": [^:]* bundle" >/dev/null ; then if test "X$dlopenmodule" != "X$lib"; then $ECHO "*** Warning: lib $linklib is a module, not a shared library" if test -z "$old_library" ; then echo echo "*** And there doesn't seem to be a static archive available" echo "*** The link will probably fail, sorry" else add="$dir/$old_library" fi elif test -n "$old_library"; then add="$dir/$old_library" fi fi esac elif test "$hardcode_minus_L" = no; then case $host in *-*-sunos*) add_shlibpath="$dir" ;; esac add_dir="-L$dir" add="-l$name" elif test "$hardcode_shlibpath_var" = no; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; relink) if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$dir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$absdir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) func_append add_dir " -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; *) lib_linked=no ;; esac if test "$lib_linked" != yes; then func_fatal_configuration "unsupported hardcode properties" fi if test -n "$add_shlibpath"; then case :$compile_shlibpath: in *":$add_shlibpath:"*) ;; *) func_append compile_shlibpath "$add_shlibpath:" ;; esac fi if test "$linkmode" = prog; then test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs" test -n "$add" && compile_deplibs="$add $compile_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" if test "$hardcode_direct" != yes && test "$hardcode_minus_L" != yes && test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) func_append finalize_shlibpath "$libdir:" ;; esac fi fi fi if test "$linkmode" = prog || test "$opt_mode" = relink; then add_shlibpath= add_dir= add= # Finalize command for both is simple: just hardcode it. if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$libdir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$libdir" add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) func_append finalize_shlibpath "$libdir:" ;; esac add="-l$name" elif test "$hardcode_automatic" = yes; then if test -n "$inst_prefix_dir" && test -f "$inst_prefix_dir$libdir/$linklib" ; then add="$inst_prefix_dir$libdir/$linklib" else add="$libdir/$linklib" fi else # We cannot seem to hardcode it, guess we'll fake it. add_dir="-L$libdir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) func_append add_dir " -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" fi if test "$linkmode" = prog; then test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs" test -n "$add" && finalize_deplibs="$add $finalize_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" fi fi elif test "$linkmode" = prog; then # Here we assume that one of hardcode_direct or hardcode_minus_L # is not unsupported. This is valid on all known static and # shared platforms. if test "$hardcode_direct" != unsupported; then test -n "$old_library" && linklib="$old_library" compile_deplibs="$dir/$linklib $compile_deplibs" finalize_deplibs="$dir/$linklib $finalize_deplibs" else compile_deplibs="-l$name -L$dir $compile_deplibs" finalize_deplibs="-l$name -L$dir $finalize_deplibs" fi elif test "$build_libtool_libs" = yes; then # Not a shared library if test "$deplibs_check_method" != pass_all; then # We're trying link a shared library against a static one # but the system doesn't support it. # Just print a warning and add the library to dependency_libs so # that the program can be linked against the static library. echo $ECHO "*** Warning: This system can not link to static lib archive $lib." echo "*** I have the capability to make that library automatically link in when" echo "*** you link to this library. But I can only do this if you have a" echo "*** shared version of the library, which you do not appear to have." if test "$module" = yes; then echo "*** But as you try to build a module library, libtool will still create " echo "*** a static module, that should work as long as the dlopening application" echo "*** is linked with the -dlopen flag to resolve symbols at runtime." if test -z "$global_symbol_pipe"; then echo echo "*** However, this would only work if libtool was able to extract symbol" echo "*** lists from a program, using \`nm' or equivalent, but libtool could" echo "*** not find such a program. So, this module is probably useless." echo "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi else deplibs="$dir/$old_library $deplibs" link_static=yes fi fi # link shared/static library? if test "$linkmode" = lib; then if test -n "$dependency_libs" && { test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes || test "$link_static" = yes; }; then # Extract -R from dependency_libs temp_deplibs= for libdir in $dependency_libs; do case $libdir in -R*) func_stripname '-R' '' "$libdir" temp_xrpath=$func_stripname_result case " $xrpath " in *" $temp_xrpath "*) ;; *) func_append xrpath " $temp_xrpath";; esac;; *) func_append temp_deplibs " $libdir";; esac done dependency_libs="$temp_deplibs" fi func_append newlib_search_path " $absdir" # Link against this library test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs" # ... and its dependency_libs tmp_libs= for deplib in $dependency_libs; do newdependency_libs="$deplib $newdependency_libs" case $deplib in -L*) func_stripname '-L' '' "$deplib" func_resolve_sysroot "$func_stripname_result";; *) func_resolve_sysroot "$deplib" ;; esac if $opt_preserve_dup_deps ; then case "$tmp_libs " in *" $func_resolve_sysroot_result "*) func_append specialdeplibs " $func_resolve_sysroot_result" ;; esac fi func_append tmp_libs " $func_resolve_sysroot_result" done if test "$link_all_deplibs" != no; then # Add the search paths of all dependency libraries for deplib in $dependency_libs; do path= case $deplib in -L*) path="$deplib" ;; *.la) func_resolve_sysroot "$deplib" deplib=$func_resolve_sysroot_result func_dirname "$deplib" "" "." dir=$func_dirname_result # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;; *) absdir=`cd "$dir" && pwd` if test -z "$absdir"; then func_warning "cannot determine absolute directory name of \`$dir'" absdir="$dir" fi ;; esac if $GREP "^installed=no" $deplib > /dev/null; then case $host in *-*-darwin*) depdepl= eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib` if test -n "$deplibrary_names" ; then for tmp in $deplibrary_names ; do depdepl=$tmp done if test -f "$absdir/$objdir/$depdepl" ; then depdepl="$absdir/$objdir/$depdepl" darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` if test -z "$darwin_install_name"; then darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` fi func_append compiler_flags " ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}" func_append linker_flags " -dylib_file ${darwin_install_name}:${depdepl}" path= fi fi ;; *) path="-L$absdir/$objdir" ;; esac else eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib` test -z "$libdir" && \ func_fatal_error "\`$deplib' is not a valid libtool archive" test "$absdir" != "$libdir" && \ func_warning "\`$deplib' seems to be moved" path="-L$absdir" fi ;; esac case " $deplibs " in *" $path "*) ;; *) deplibs="$path $deplibs" ;; esac done fi # link_all_deplibs != no fi # linkmode = lib done # for deplib in $libs if test "$pass" = link; then if test "$linkmode" = "prog"; then compile_deplibs="$new_inherited_linker_flags $compile_deplibs" finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs" else compiler_flags="$compiler_flags "`$ECHO " $new_inherited_linker_flags" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` fi fi dependency_libs="$newdependency_libs" if test "$pass" = dlpreopen; then # Link the dlpreopened libraries before other libraries for deplib in $save_deplibs; do deplibs="$deplib $deplibs" done fi if test "$pass" != dlopen; then if test "$pass" != conv; then # Make sure lib_search_path contains only unique directories. lib_search_path= for dir in $newlib_search_path; do case "$lib_search_path " in *" $dir "*) ;; *) func_append lib_search_path " $dir" ;; esac done newlib_search_path= fi if test "$linkmode,$pass" != "prog,link"; then vars="deplibs" else vars="compile_deplibs finalize_deplibs" fi for var in $vars dependency_libs; do # Add libraries to $var in reverse order eval tmp_libs=\"\$$var\" new_libs= for deplib in $tmp_libs; do # FIXME: Pedantically, this is the right thing to do, so # that some nasty dependency loop isn't accidentally # broken: #new_libs="$deplib $new_libs" # Pragmatically, this seems to cause very few problems in # practice: case $deplib in -L*) new_libs="$deplib $new_libs" ;; -R*) ;; *) # And here is the reason: when a library appears more # than once as an explicit dependence of a library, or # is implicitly linked in more than once by the # compiler, it is considered special, and multiple # occurrences thereof are not removed. Compare this # with having the same library being listed as a # dependency of multiple other libraries: in this case, # we know (pedantically, we assume) the library does not # need to be listed more than once, so we keep only the # last copy. This is not always right, but it is rare # enough that we require users that really mean to play # such unportable linking tricks to link the library # using -Wl,-lname, so that libtool does not consider it # for duplicate removal. case " $specialdeplibs " in *" $deplib "*) new_libs="$deplib $new_libs" ;; *) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$deplib $new_libs" ;; esac ;; esac ;; esac done tmp_libs= for deplib in $new_libs; do case $deplib in -L*) case " $tmp_libs " in *" $deplib "*) ;; *) func_append tmp_libs " $deplib" ;; esac ;; *) func_append tmp_libs " $deplib" ;; esac done eval $var=\"$tmp_libs\" done # for var fi # Last step: remove runtime libs from dependency_libs # (they stay in deplibs) tmp_libs= for i in $dependency_libs ; do case " $predeps $postdeps $compiler_lib_search_path " in *" $i "*) i="" ;; esac if test -n "$i" ; then func_append tmp_libs " $i" fi done dependency_libs=$tmp_libs done # for pass if test "$linkmode" = prog; then dlfiles="$newdlfiles" fi if test "$linkmode" = prog || test "$linkmode" = lib; then dlprefiles="$newdlprefiles" fi case $linkmode in oldlib) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for archives" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for archives" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for archives" test -n "$xrpath" && \ func_warning "\`-R' is ignored for archives" test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for archives" test -n "$release" && \ func_warning "\`-release' is ignored for archives" test -n "$export_symbols$export_symbols_regex" && \ func_warning "\`-export-symbols' is ignored for archives" # Now set the variables for building old libraries. build_libtool_libs=no oldlibs="$output" func_append objs "$old_deplibs" ;; lib) # Make sure we only generate libraries of the form `libNAME.la'. case $outputname in lib*) func_stripname 'lib' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" ;; *) test "$module" = no && \ func_fatal_help "libtool library \`$output' must begin with \`lib'" if test "$need_lib_prefix" != no; then # Add the "lib" prefix for modules if required func_stripname '' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" else func_stripname '' '.la' "$outputname" libname=$func_stripname_result fi ;; esac if test -n "$objs"; then if test "$deplibs_check_method" != pass_all; then func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs" else echo $ECHO "*** Warning: Linking the shared library $output against the non-libtool" $ECHO "*** objects $objs is not portable!" func_append libobjs " $objs" fi fi test "$dlself" != no && \ func_warning "\`-dlopen self' is ignored for libtool libraries" set dummy $rpath shift test "$#" -gt 1 && \ func_warning "ignoring multiple \`-rpath's for a libtool library" install_libdir="$1" oldlibs= if test -z "$rpath"; then if test "$build_libtool_libs" = yes; then # Building a libtool convenience library. # Some compilers have problems with a `.al' extension so # convenience libraries should have the same extension an # archive normally would. oldlibs="$output_objdir/$libname.$libext $oldlibs" build_libtool_libs=convenience build_old_libs=yes fi test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for convenience libraries" test -n "$release" && \ func_warning "\`-release' is ignored for convenience libraries" else # Parse the version information argument. save_ifs="$IFS"; IFS=':' set dummy $vinfo 0 0 0 shift IFS="$save_ifs" test -n "$7" && \ func_fatal_help "too many parameters to \`-version-info'" # convert absolute version numbers to libtool ages # this retains compatibility with .la files and attempts # to make the code below a bit more comprehensible case $vinfo_number in yes) number_major="$1" number_minor="$2" number_revision="$3" # # There are really only two kinds -- those that # use the current revision as the major version # and those that subtract age and use age as # a minor version. But, then there is irix # which has an extra 1 added just for fun # case $version_type in # correct linux to gnu/linux during the next big refactor darwin|linux|osf|windows|none) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_revision" ;; freebsd-aout|freebsd-elf|qnx|sunos) current="$number_major" revision="$number_minor" age="0" ;; irix|nonstopux) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_minor" lt_irix_increment=no ;; esac ;; no) current="$1" revision="$2" age="$3" ;; esac # Check that each of the things are valid numbers. case $current in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "CURRENT \`$current' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $revision in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "REVISION \`$revision' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $age in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "AGE \`$age' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac if test "$age" -gt "$current"; then func_error "AGE \`$age' is greater than the current interface number \`$current'" func_fatal_error "\`$vinfo' is not valid version information" fi # Calculate the version variables. major= versuffix= verstring= case $version_type in none) ;; darwin) # Like Linux, but with the current version available in # verstring for coding it into the library header func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" # Darwin ld doesn't like 0 for these options... func_arith $current + 1 minor_current=$func_arith_result xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision" verstring="-compatibility_version $minor_current -current_version $minor_current.$revision" ;; freebsd-aout) major=".$current" versuffix=".$current.$revision"; ;; freebsd-elf) major=".$current" versuffix=".$current" ;; irix | nonstopux) if test "X$lt_irix_increment" = "Xno"; then func_arith $current - $age else func_arith $current - $age + 1 fi major=$func_arith_result case $version_type in nonstopux) verstring_prefix=nonstopux ;; *) verstring_prefix=sgi ;; esac verstring="$verstring_prefix$major.$revision" # Add in all the interfaces that we are compatible with. loop=$revision while test "$loop" -ne 0; do func_arith $revision - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring_prefix$major.$iface:$verstring" done # Before this point, $major must not contain `.'. major=.$major versuffix="$major.$revision" ;; linux) # correct to gnu/linux during the next big refactor func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" ;; osf) func_arith $current - $age major=.$func_arith_result versuffix=".$current.$age.$revision" verstring="$current.$age.$revision" # Add in all the interfaces that we are compatible with. loop=$age while test "$loop" -ne 0; do func_arith $current - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring:${iface}.0" done # Make executables depend on our current version. func_append verstring ":${current}.0" ;; qnx) major=".$current" versuffix=".$current" ;; sunos) major=".$current" versuffix=".$current.$revision" ;; windows) # Use '-' rather than '.', since we only want one # extension on DOS 8.3 filesystems. func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; *) func_fatal_configuration "unknown library version type \`$version_type'" ;; esac # Clear the version info if we defaulted, and they specified a release. if test -z "$vinfo" && test -n "$release"; then major= case $version_type in darwin) # we can't check for "0.0" in archive_cmds due to quoting # problems, so we reset it completely verstring= ;; *) verstring="0.0" ;; esac if test "$need_version" = no; then versuffix= else versuffix=".0.0" fi fi # Remove version info from name if versioning should be avoided if test "$avoid_version" = yes && test "$need_version" = no; then major= versuffix= verstring="" fi # Check to see if the archive will have undefined symbols. if test "$allow_undefined" = yes; then if test "$allow_undefined_flag" = unsupported; then func_warning "undefined symbols not allowed in $host shared libraries" build_libtool_libs=no build_old_libs=yes fi else # Don't allow undefined symbols. allow_undefined_flag="$no_undefined_flag" fi fi func_generate_dlsyms "$libname" "$libname" "yes" func_append libobjs " $symfileobj" test "X$libobjs" = "X " && libobjs= if test "$opt_mode" != relink; then # Remove our outputs, but don't remove object files since they # may have been created when compiling PIC objects. removelist= tempremovelist=`$ECHO "$output_objdir/*"` for p in $tempremovelist; do case $p in *.$objext | *.gcno) ;; $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*) if test "X$precious_files_regex" != "X"; then if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1 then continue fi fi func_append removelist " $p" ;; *) ;; esac done test -n "$removelist" && \ func_show_eval "${RM}r \$removelist" fi # Now set the variables for building old libraries. if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then func_append oldlibs " $output_objdir/$libname.$libext" # Transform .lo files to .o files. oldobjs="$objs "`$ECHO "$libobjs" | $SP2NL | $SED "/\.${libext}$/d; $lo2o" | $NL2SP` fi # Eliminate all temporary directories. #for path in $notinst_path; do # lib_search_path=`$ECHO "$lib_search_path " | $SED "s% $path % %g"` # deplibs=`$ECHO "$deplibs " | $SED "s% -L$path % %g"` # dependency_libs=`$ECHO "$dependency_libs " | $SED "s% -L$path % %g"` #done if test -n "$xrpath"; then # If the user specified any rpath flags, then add them. temp_xrpath= for libdir in $xrpath; do func_replace_sysroot "$libdir" func_append temp_xrpath " -R$func_replace_sysroot_result" case "$finalize_rpath " in *" $libdir "*) ;; *) func_append finalize_rpath " $libdir" ;; esac done if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then dependency_libs="$temp_xrpath $dependency_libs" fi fi # Make sure dlfiles contains only unique files that won't be dlpreopened old_dlfiles="$dlfiles" dlfiles= for lib in $old_dlfiles; do case " $dlprefiles $dlfiles " in *" $lib "*) ;; *) func_append dlfiles " $lib" ;; esac done # Make sure dlprefiles contains only unique files old_dlprefiles="$dlprefiles" dlprefiles= for lib in $old_dlprefiles; do case "$dlprefiles " in *" $lib "*) ;; *) func_append dlprefiles " $lib" ;; esac done if test "$build_libtool_libs" = yes; then if test -n "$rpath"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc* | *-*-haiku*) # these systems don't actually have a c library (as such)! ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C library is in the System framework func_append deplibs " System.ltframework" ;; *-*-netbsd*) # Don't link with libc until the a.out ld.so is fixed. ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. ;; *-*-sco3.2v5* | *-*-sco5v6*) # Causes problems with __ctype ;; *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) # Compiler inserts libc in the correct place for threads to work ;; *) # Add libc to deplibs on all other systems if necessary. if test "$build_libtool_need_lc" = "yes"; then func_append deplibs " -lc" fi ;; esac fi # Transform deplibs into only deplibs that can be linked in shared. name_save=$name libname_save=$libname release_save=$release versuffix_save=$versuffix major_save=$major # I'm not sure if I'm treating the release correctly. I think # release should show up in the -l (ie -lgmp5) so we don't want to # add it in twice. Is that correct? release="" versuffix="" major="" newdeplibs= droppeddeps=no case $deplibs_check_method in pass_all) # Don't check for shared/static. Everything works. # This might be a little naive. We might want to check # whether the library exists or not. But this is on # osf3 & osf4 and I'm not really sure... Just # implementing what was already the behavior. newdeplibs=$deplibs ;; test_compile) # This code stresses the "libraries are programs" paradigm to its # limits. Maybe even breaks it. We compile a program, linking it # against the deplibs as a proxy for the library. Then we can check # whether they linked in statically or dynamically with ldd. $opt_dry_run || $RM conftest.c cat > conftest.c </dev/null` $nocaseglob else potential_libs=`ls $i/$libnameglob[.-]* 2>/dev/null` fi for potent_lib in $potential_libs; do # Follow soft links. if ls -lLd "$potent_lib" 2>/dev/null | $GREP " -> " >/dev/null; then continue fi # The statement above tries to avoid entering an # endless loop below, in case of cyclic links. # We might still enter an endless loop, since a link # loop can be closed while we follow links, # but so what? potlib="$potent_lib" while test -h "$potlib" 2>/dev/null; do potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'` case $potliblink in [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";; *) potlib=`$ECHO "$potlib" | $SED 's,[^/]*$,,'`"$potliblink";; esac done if eval $file_magic_cmd \"\$potlib\" 2>/dev/null | $SED -e 10q | $EGREP "$file_magic_regex" > /dev/null; then func_append newdeplibs " $a_deplib" a_deplib="" break 2 fi done done fi if test -n "$a_deplib" ; then droppeddeps=yes echo $ECHO "*** Warning: linker path does not have real file for library $a_deplib." echo "*** I have the capability to make that library automatically link in when" echo "*** you link to this library. But I can only do this if you have a" echo "*** shared version of the library, which you do not appear to have" echo "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for file magic test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a file magic. Last file checked: $potlib" fi fi ;; *) # Add a -L argument. func_append newdeplibs " $a_deplib" ;; esac done # Gone through all deplibs. ;; match_pattern*) set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` for a_deplib in $deplibs; do case $a_deplib in -l*) func_stripname -l '' "$a_deplib" name=$func_stripname_result if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then case " $predeps $postdeps " in *" $a_deplib "*) func_append newdeplibs " $a_deplib" a_deplib="" ;; esac fi if test -n "$a_deplib" ; then libname=`eval "\\$ECHO \"$libname_spec\""` for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do potential_libs=`ls $i/$libname[.-]* 2>/dev/null` for potent_lib in $potential_libs; do potlib="$potent_lib" # see symlink-check above in file_magic test if eval "\$ECHO \"$potent_lib\"" 2>/dev/null | $SED 10q | \ $EGREP "$match_pattern_regex" > /dev/null; then func_append newdeplibs " $a_deplib" a_deplib="" break 2 fi done done fi if test -n "$a_deplib" ; then droppeddeps=yes echo $ECHO "*** Warning: linker path does not have real file for library $a_deplib." echo "*** I have the capability to make that library automatically link in when" echo "*** you link to this library. But I can only do this if you have a" echo "*** shared version of the library, which you do not appear to have" echo "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a regex pattern. Last file checked: $potlib" fi fi ;; *) # Add a -L argument. func_append newdeplibs " $a_deplib" ;; esac done # Gone through all deplibs. ;; none | unknown | *) newdeplibs="" tmp_deplibs=`$ECHO " $deplibs" | $SED 's/ -lc$//; s/ -[LR][^ ]*//g'` if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then for i in $predeps $postdeps ; do # can't use Xsed below, because $i might contain '/' tmp_deplibs=`$ECHO " $tmp_deplibs" | $SED "s,$i,,"` done fi case $tmp_deplibs in *[!\ \ ]*) echo if test "X$deplibs_check_method" = "Xnone"; then echo "*** Warning: inter-library dependencies are not supported in this platform." else echo "*** Warning: inter-library dependencies are not known to be supported." fi echo "*** All declared inter-library dependencies are being dropped." droppeddeps=yes ;; esac ;; esac versuffix=$versuffix_save major=$major_save release=$release_save libname=$libname_save name=$name_save case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library with the System framework newdeplibs=`$ECHO " $newdeplibs" | $SED 's/ -lc / System.ltframework /'` ;; esac if test "$droppeddeps" = yes; then if test "$module" = yes; then echo echo "*** Warning: libtool could not satisfy all declared inter-library" $ECHO "*** dependencies of module $libname. Therefore, libtool will create" echo "*** a static module, that should work as long as the dlopening" echo "*** application is linked with the -dlopen flag." if test -z "$global_symbol_pipe"; then echo echo "*** However, this would only work if libtool was able to extract symbol" echo "*** lists from a program, using \`nm' or equivalent, but libtool could" echo "*** not find such a program. So, this module is probably useless." echo "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi else echo "*** The inter-library dependencies that have been dropped here will be" echo "*** automatically added whenever a program is linked with this library" echo "*** or is declared to -dlopen it." if test "$allow_undefined" = no; then echo echo "*** Since this library must not contain undefined symbols," echo "*** because either the platform does not support them or" echo "*** it was explicitly requested with -no-undefined," echo "*** libtool will only create a static version of it." if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi fi fi # Done checking deplibs! deplibs=$newdeplibs fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" case $host in *-*-darwin*) newdeplibs=`$ECHO " $newdeplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` deplibs=`$ECHO " $deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $deplibs " in *" -L$path/$objdir "*) func_append new_libs " -L$path/$objdir" ;; esac ;; esac done for deplib in $deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) func_append new_libs " $deplib" ;; esac ;; *) func_append new_libs " $deplib" ;; esac done deplibs="$new_libs" # All the library-specific variables (install_libdir is set above). library_names= old_library= dlname= # Test again, we may have decided not to build it any more if test "$build_libtool_libs" = yes; then # Remove ${wl} instances when linking with ld. # FIXME: should test the right _cmds variable. case $archive_cmds in *\$LD\ *) wl= ;; esac if test "$hardcode_into_libs" = yes; then # Hardcode the library paths hardcode_libdirs= dep_rpath= rpath="$finalize_rpath" test "$opt_mode" != relink && rpath="$compile_rpath$rpath" for libdir in $rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then func_replace_sysroot "$libdir" libdir=$func_replace_sysroot_result if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) func_append hardcode_libdirs "$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" func_append dep_rpath " $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) func_append perm_rpath " $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval "dep_rpath=\"$hardcode_libdir_flag_spec\"" fi if test -n "$runpath_var" && test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do func_append rpath "$dir:" done eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var" fi test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs" fi shlibpath="$finalize_shlibpath" test "$opt_mode" != relink && shlibpath="$compile_shlibpath$shlibpath" if test -n "$shlibpath"; then eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var" fi # Get the real and link names of the library. eval shared_ext=\"$shrext_cmds\" eval library_names=\"$library_names_spec\" set dummy $library_names shift realname="$1" shift if test -n "$soname_spec"; then eval soname=\"$soname_spec\" else soname="$realname" fi if test -z "$dlname"; then dlname=$soname fi lib="$output_objdir/$realname" linknames= for link do func_append linknames " $link" done # Use standard objects if they are pic test -z "$pic_flag" && libobjs=`$ECHO "$libobjs" | $SP2NL | $SED "$lo2o" | $NL2SP` test "X$libobjs" = "X " && libobjs= delfiles= if test -n "$export_symbols" && test -n "$include_expsyms"; then $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp" export_symbols="$output_objdir/$libname.uexp" func_append delfiles " $export_symbols" fi orig_export_symbols= case $host_os in cygwin* | mingw* | cegcc*) if test -n "$export_symbols" && test -z "$export_symbols_regex"; then # exporting using user supplied symfile if test "x`$SED 1q $export_symbols`" != xEXPORTS; then # and it's NOT already a .def file. Must figure out # which of the given symbols are data symbols and tag # them as such. So, trigger use of export_symbols_cmds. # export_symbols gets reassigned inside the "prepare # the list of exported symbols" if statement, so the # include_expsyms logic still works. orig_export_symbols="$export_symbols" export_symbols= always_export_symbols=yes fi fi ;; esac # Prepare the list of exported symbols if test -z "$export_symbols"; then if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols cmds=$export_symbols_cmds save_ifs="$IFS"; IFS='~' for cmd1 in $cmds; do IFS="$save_ifs" # Take the normal branch if the nm_file_list_spec branch # doesn't work or if tool conversion is not needed. case $nm_file_list_spec~$to_tool_file_cmd in *~func_convert_file_noop | *~func_convert_file_msys_to_w32 | ~*) try_normal_branch=yes eval cmd=\"$cmd1\" func_len " $cmd" len=$func_len_result ;; *) try_normal_branch=no ;; esac if test "$try_normal_branch" = yes \ && { test "$len" -lt "$max_cmd_len" \ || test "$max_cmd_len" -le -1; } then func_show_eval "$cmd" 'exit $?' skipped_export=false elif test -n "$nm_file_list_spec"; then func_basename "$output" output_la=$func_basename_result save_libobjs=$libobjs save_output=$output output=${output_objdir}/${output_la}.nm func_to_tool_file "$output" libobjs=$nm_file_list_spec$func_to_tool_file_result func_append delfiles " $output" func_verbose "creating $NM input file list: $output" for obj in $save_libobjs; do func_to_tool_file "$obj" $ECHO "$func_to_tool_file_result" done > "$output" eval cmd=\"$cmd1\" func_show_eval "$cmd" 'exit $?' output=$save_output libobjs=$save_libobjs skipped_export=false else # The command line is too long to execute in one step. func_verbose "using reloadable object file for export list..." skipped_export=: # Break out early, otherwise skipped_export may be # set to false by a later but shorter cmd. break fi done IFS="$save_ifs" if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi fi if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "$include_expsyms" | $SP2NL >> "$tmp_export_symbols"' fi if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter func_append delfiles " $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi tmp_deplibs= for test_deplib in $deplibs; do case " $convenience " in *" $test_deplib "*) ;; *) func_append tmp_deplibs " $test_deplib" ;; esac done deplibs="$tmp_deplibs" if test -n "$convenience"; then if test -n "$whole_archive_flag_spec" && test "$compiler_needs_object" = yes && test -z "$libobjs"; then # extract the archives, so we have objects to list. # TODO: could optimize this to just extract one archive. whole_archive_flag_spec= fi if test -n "$whole_archive_flag_spec"; then save_libobjs=$libobjs eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= else gentop="$output_objdir/${outputname}x" func_append generated " $gentop" func_extract_archives $gentop $convenience func_append libobjs " $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi fi if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then eval flag=\"$thread_safe_flag_spec\" func_append linker_flags " $flag" fi # Make a backup of the uninstalled library when relinking if test "$opt_mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $? fi # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then eval test_cmds=\"$module_expsym_cmds\" cmds=$module_expsym_cmds else eval test_cmds=\"$module_cmds\" cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then eval test_cmds=\"$archive_expsym_cmds\" cmds=$archive_expsym_cmds else eval test_cmds=\"$archive_cmds\" cmds=$archive_cmds fi fi if test "X$skipped_export" != "X:" && func_len " $test_cmds" && len=$func_len_result && test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then : else # The command line is too long to link in one step, link piecewise # or, if using GNU ld and skipped_export is not :, use a linker # script. # Save the value of $output and $libobjs because we want to # use them later. If we have whole_archive_flag_spec, we # want to use save_libobjs as it was before # whole_archive_flag_spec was expanded, because we can't # assume the linker understands whole_archive_flag_spec. # This may have to be revisited, in case too many # convenience libraries get linked in and end up exceeding # the spec. if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then save_libobjs=$libobjs fi save_output=$output func_basename "$output" output_la=$func_basename_result # Clear the reloadable object creation command queue and # initialize k to one. test_cmds= concat_cmds= objlist= last_robj= k=1 if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then output=${output_objdir}/${output_la}.lnkscript func_verbose "creating GNU ld script: $output" echo 'INPUT (' > $output for obj in $save_libobjs do func_to_tool_file "$obj" $ECHO "$func_to_tool_file_result" >> $output done echo ')' >> $output func_append delfiles " $output" func_to_tool_file "$output" output=$func_to_tool_file_result elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then output=${output_objdir}/${output_la}.lnk func_verbose "creating linker input file list: $output" : > $output set x $save_libobjs shift firstobj= if test "$compiler_needs_object" = yes; then firstobj="$1 " shift fi for obj do func_to_tool_file "$obj" $ECHO "$func_to_tool_file_result" >> $output done func_append delfiles " $output" func_to_tool_file "$output" output=$firstobj\"$file_list_spec$func_to_tool_file_result\" else if test -n "$save_libobjs"; then func_verbose "creating reloadable object files..." output=$output_objdir/$output_la-${k}.$objext eval test_cmds=\"$reload_cmds\" func_len " $test_cmds" len0=$func_len_result len=$len0 # Loop over the list of objects to be linked. for obj in $save_libobjs do func_len " $obj" func_arith $len + $func_len_result len=$func_arith_result if test "X$objlist" = X || test "$len" -lt "$max_cmd_len"; then func_append objlist " $obj" else # The command $test_cmds is almost too long, add a # command to the queue. if test "$k" -eq 1 ; then # The first file doesn't have a previous command to add. reload_objs=$objlist eval concat_cmds=\"$reload_cmds\" else # All subsequent reloadable object files will link in # the last one created. reload_objs="$objlist $last_robj" eval concat_cmds=\"\$concat_cmds~$reload_cmds~\$RM $last_robj\" fi last_robj=$output_objdir/$output_la-${k}.$objext func_arith $k + 1 k=$func_arith_result output=$output_objdir/$output_la-${k}.$objext objlist=" $obj" func_len " $last_robj" func_arith $len0 + $func_len_result len=$func_arith_result fi done # Handle the remaining objects by creating one last # reloadable object file. All subsequent reloadable object # files will link in the last one created. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ reload_objs="$objlist $last_robj" eval concat_cmds=\"\${concat_cmds}$reload_cmds\" if test -n "$last_robj"; then eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\" fi func_append delfiles " $output" else output= fi if ${skipped_export-false}; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols libobjs=$output # Append the command to create the export file. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\" if test -n "$last_robj"; then eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\" fi fi test -n "$save_libobjs" && func_verbose "creating a temporary reloadable object file: $output" # Loop through the commands generated above and execute them. save_ifs="$IFS"; IFS='~' for cmd in $concat_cmds; do IFS="$save_ifs" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$opt_mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" if test -n "$export_symbols_regex" && ${skipped_export-false}; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi if ${skipped_export-false}; then if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "$include_expsyms" | $SP2NL >> "$tmp_export_symbols"' fi if test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter func_append delfiles " $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi fi libobjs=$output # Restore the value of output. output=$save_output if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= fi # Expand the library linking commands again to reset the # value of $libobjs for piecewise linking. # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then cmds=$module_expsym_cmds else cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then cmds=$archive_expsym_cmds else cmds=$archive_cmds fi fi fi if test -n "$delfiles"; then # Append the command to remove temporary files to $cmds. eval cmds=\"\$cmds~\$RM $delfiles\" fi # Add any objects from preloaded convenience libraries if test -n "$dlprefiles"; then gentop="$output_objdir/${outputname}x" func_append generated " $gentop" func_extract_archives $gentop $dlprefiles func_append libobjs " $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$opt_mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" # Restore the uninstalled library and exit if test "$opt_mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $? if test -n "$convenience"; then if test -z "$whole_archive_flag_spec"; then func_show_eval '${RM}r "$gentop"' fi fi exit $EXIT_SUCCESS fi # Create links to the real library. for linkname in $linknames; do if test "$realname" != "$linkname"; then func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?' fi done # If -module or -export-dynamic was specified, set the dlname. if test "$module" = yes || test "$export_dynamic" = yes; then # On all known operating systems, these are identical. dlname="$soname" fi fi ;; obj) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for objects" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for objects" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for objects" test -n "$xrpath" && \ func_warning "\`-R' is ignored for objects" test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for objects" test -n "$release" && \ func_warning "\`-release' is ignored for objects" case $output in *.lo) test -n "$objs$old_deplibs" && \ func_fatal_error "cannot build library object \`$output' from non-libtool objects" libobj=$output func_lo2o "$libobj" obj=$func_lo2o_result ;; *) libobj= obj="$output" ;; esac # Delete the old objects. $opt_dry_run || $RM $obj $libobj # Objects from convenience libraries. This assumes # single-version convenience libraries. Whenever we create # different ones for PIC/non-PIC, this we'll have to duplicate # the extraction. reload_conv_objs= gentop= # reload_cmds runs $LD directly, so let us get rid of # -Wl from whole_archive_flag_spec and hope we can get by with # turning comma into space.. wl= if test -n "$convenience"; then if test -n "$whole_archive_flag_spec"; then eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\" reload_conv_objs=$reload_objs\ `$ECHO "$tmp_whole_archive_flags" | $SED 's|,| |g'` else gentop="$output_objdir/${obj}x" func_append generated " $gentop" func_extract_archives $gentop $convenience reload_conv_objs="$reload_objs $func_extract_archives_result" fi fi # If we're not building shared, we need to use non_pic_objs test "$build_libtool_libs" != yes && libobjs="$non_pic_objects" # Create the old-style object. reload_objs="$objs$old_deplibs "`$ECHO "$libobjs" | $SP2NL | $SED "/\.${libext}$/d; /\.lib$/d; $lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test output="$obj" func_execute_cmds "$reload_cmds" 'exit $?' # Exit if we aren't doing a library object file. if test -z "$libobj"; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS fi if test "$build_libtool_libs" != yes; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi # Create an invalid libtool object if no PIC, so that we don't # accidentally link it into a program. # $show "echo timestamp > $libobj" # $opt_dry_run || eval "echo timestamp > $libobj" || exit $? exit $EXIT_SUCCESS fi if test -n "$pic_flag" || test "$pic_mode" != default; then # Only do commands if we really have different PIC objects. reload_objs="$libobjs $reload_conv_objs" output="$libobj" func_execute_cmds "$reload_cmds" 'exit $?' fi if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS ;; prog) case $host in *cygwin*) func_stripname '' '.exe' "$output" output=$func_stripname_result.exe;; esac test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for programs" test -n "$release" && \ func_warning "\`-release' is ignored for programs" test "$preload" = yes \ && test "$dlopen_support" = unknown \ && test "$dlopen_self" = unknown \ && test "$dlopen_self_static" = unknown && \ func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support." case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library is the System framework compile_deplibs=`$ECHO " $compile_deplibs" | $SED 's/ -lc / System.ltframework /'` finalize_deplibs=`$ECHO " $finalize_deplibs" | $SED 's/ -lc / System.ltframework /'` ;; esac case $host in *-*-darwin*) # Don't allow lazy linking, it breaks C++ global constructors # But is supposedly fixed on 10.4 or later (yay!). if test "$tagname" = CXX ; then case ${MACOSX_DEPLOYMENT_TARGET-10.0} in 10.[0123]) func_append compile_command " ${wl}-bind_at_load" func_append finalize_command " ${wl}-bind_at_load" ;; esac fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" compile_deplibs=`$ECHO " $compile_deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` finalize_deplibs=`$ECHO " $finalize_deplibs" | $SED 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $compile_deplibs " in *" -L$path/$objdir "*) func_append new_libs " -L$path/$objdir" ;; esac ;; esac done for deplib in $compile_deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) func_append new_libs " $deplib" ;; esac ;; *) func_append new_libs " $deplib" ;; esac done compile_deplibs="$new_libs" func_append compile_command " $compile_deplibs" func_append finalize_command " $finalize_deplibs" if test -n "$rpath$xrpath"; then # If the user specified any rpath flags, then add them. for libdir in $rpath $xrpath; do # This is the magic to use -rpath. case "$finalize_rpath " in *" $libdir "*) ;; *) func_append finalize_rpath " $libdir" ;; esac done fi # Now hardcode the library paths rpath= hardcode_libdirs= for libdir in $compile_rpath $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) func_append hardcode_libdirs "$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" func_append rpath " $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) func_append perm_rpath " $libdir" ;; esac fi case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'` case :$dllsearchpath: in *":$libdir:"*) ;; ::) dllsearchpath=$libdir;; *) func_append dllsearchpath ":$libdir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; *) func_append dllsearchpath ":$testbindir";; esac ;; esac done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi compile_rpath="$rpath" rpath= hardcode_libdirs= for libdir in $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) func_append hardcode_libdirs "$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" func_append rpath " $flag" fi elif test -n "$runpath_var"; then case "$finalize_perm_rpath " in *" $libdir "*) ;; *) func_append finalize_perm_rpath " $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi finalize_rpath="$rpath" if test -n "$libobjs" && test "$build_old_libs" = yes; then # Transform all the library objects into standard objects. compile_command=`$ECHO "$compile_command" | $SP2NL | $SED "$lo2o" | $NL2SP` finalize_command=`$ECHO "$finalize_command" | $SP2NL | $SED "$lo2o" | $NL2SP` fi func_generate_dlsyms "$outputname" "@PROGRAM@" "no" # template prelinking step if test -n "$prelink_cmds"; then func_execute_cmds "$prelink_cmds" 'exit $?' fi wrappers_required=yes case $host in *cegcc* | *mingw32ce*) # Disable wrappers for cegcc and mingw32ce hosts, we are cross compiling anyway. wrappers_required=no ;; *cygwin* | *mingw* ) if test "$build_libtool_libs" != yes; then wrappers_required=no fi ;; *) if test "$need_relink" = no || test "$build_libtool_libs" != yes; then wrappers_required=no fi ;; esac if test "$wrappers_required" = no; then # Replace the output file specification. compile_command=`$ECHO "$compile_command" | $SED 's%@OUTPUT@%'"$output"'%g'` link_command="$compile_command$compile_rpath" # We have no uninstalled library dependencies, so finalize right now. exit_status=0 func_show_eval "$link_command" 'exit_status=$?' if test -n "$postlink_cmds"; then func_to_tool_file "$output" postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'` func_execute_cmds "$postlink_cmds" 'exit $?' fi # Delete the generated files. if test -f "$output_objdir/${outputname}S.${objext}"; then func_show_eval '$RM "$output_objdir/${outputname}S.${objext}"' fi exit $exit_status fi if test -n "$compile_shlibpath$finalize_shlibpath"; then compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command" fi if test -n "$finalize_shlibpath"; then finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command" fi compile_var= finalize_var= if test -n "$runpath_var"; then if test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do func_append rpath "$dir:" done compile_var="$runpath_var=\"$rpath\$$runpath_var\" " fi if test -n "$finalize_perm_rpath"; then # We should set the runpath_var. rpath= for dir in $finalize_perm_rpath; do func_append rpath "$dir:" done finalize_var="$runpath_var=\"$rpath\$$runpath_var\" " fi fi if test "$no_install" = yes; then # We don't need to create a wrapper script. link_command="$compile_var$compile_command$compile_rpath" # Replace the output file specification. link_command=`$ECHO "$link_command" | $SED 's%@OUTPUT@%'"$output"'%g'` # Delete the old output file. $opt_dry_run || $RM $output # Link the executable and exit func_show_eval "$link_command" 'exit $?' if test -n "$postlink_cmds"; then func_to_tool_file "$output" postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'` func_execute_cmds "$postlink_cmds" 'exit $?' fi exit $EXIT_SUCCESS fi if test "$hardcode_action" = relink; then # Fast installation is not supported link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" func_warning "this platform does not like uninstalled shared libraries" func_warning "\`$output' will be relinked during installation" else if test "$fast_install" != no; then link_command="$finalize_var$compile_command$finalize_rpath" if test "$fast_install" = yes; then relink_command=`$ECHO "$compile_var$compile_command$compile_rpath" | $SED 's%@OUTPUT@%\$progdir/\$file%g'` else # fast_install is set to needless relink_command= fi else link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" fi fi # Replace the output file specification. link_command=`$ECHO "$link_command" | $SED 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'` # Delete the old output files. $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname func_show_eval "$link_command" 'exit $?' if test -n "$postlink_cmds"; then func_to_tool_file "$output_objdir/$outputname" postlink_cmds=`func_echo_all "$postlink_cmds" | $SED -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g' -e 's%@TOOL_OUTPUT@%'"$func_to_tool_file_result"'%g'` func_execute_cmds "$postlink_cmds" 'exit $?' fi # Now create the wrapper script. func_verbose "creating $output" # Quote the relink command for shipping. if test -n "$relink_command"; then # Preserve any variables that may affect compiler behavior for var in $variables_saved_for_relink; do if eval test -z \"\${$var+set}\"; then relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" elif eval var_value=\$$var; test -z "$var_value"; then relink_command="$var=; export $var; $relink_command" else func_quote_for_eval "$var_value" relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command" fi done relink_command="(cd `pwd`; $relink_command)" relink_command=`$ECHO "$relink_command" | $SED "$sed_quote_subst"` fi # Only actually do things if not in dry run mode. $opt_dry_run || { # win32 will think the script is a binary if it has # a .exe suffix, so we strip it off here. case $output in *.exe) func_stripname '' '.exe' "$output" output=$func_stripname_result ;; esac # test for cygwin because mv fails w/o .exe extensions case $host in *cygwin*) exeext=.exe func_stripname '' '.exe' "$outputname" outputname=$func_stripname_result ;; *) exeext= ;; esac case $host in *cygwin* | *mingw* ) func_dirname_and_basename "$output" "" "." output_name=$func_basename_result output_path=$func_dirname_result cwrappersource="$output_path/$objdir/lt-$output_name.c" cwrapper="$output_path/$output_name.exe" $RM $cwrappersource $cwrapper trap "$RM $cwrappersource $cwrapper; exit $EXIT_FAILURE" 1 2 15 func_emit_cwrapperexe_src > $cwrappersource # The wrapper executable is built using the $host compiler, # because it contains $host paths and files. If cross- # compiling, it, like the target executable, must be # executed on the $host or under an emulation environment. $opt_dry_run || { $LTCC $LTCFLAGS -o $cwrapper $cwrappersource $STRIP $cwrapper } # Now, create the wrapper script for func_source use: func_ltwrapper_scriptname $cwrapper $RM $func_ltwrapper_scriptname_result trap "$RM $func_ltwrapper_scriptname_result; exit $EXIT_FAILURE" 1 2 15 $opt_dry_run || { # note: this script will not be executed, so do not chmod. if test "x$build" = "x$host" ; then $cwrapper --lt-dump-script > $func_ltwrapper_scriptname_result else func_emit_wrapper no > $func_ltwrapper_scriptname_result fi } ;; * ) $RM $output trap "$RM $output; exit $EXIT_FAILURE" 1 2 15 func_emit_wrapper no > $output chmod +x $output ;; esac } exit $EXIT_SUCCESS ;; esac # See if we need to build an old-fashioned archive. for oldlib in $oldlibs; do if test "$build_libtool_libs" = convenience; then oldobjs="$libobjs_save $symfileobj" addlibs="$convenience" build_libtool_libs=no else if test "$build_libtool_libs" = module; then oldobjs="$libobjs_save" build_libtool_libs=no else oldobjs="$old_deplibs $non_pic_objects" if test "$preload" = yes && test -f "$symfileobj"; then func_append oldobjs " $symfileobj" fi fi addlibs="$old_convenience" fi if test -n "$addlibs"; then gentop="$output_objdir/${outputname}x" func_append generated " $gentop" func_extract_archives $gentop $addlibs func_append oldobjs " $func_extract_archives_result" fi # Do each command in the archive commands. if test -n "$old_archive_from_new_cmds" && test "$build_libtool_libs" = yes; then cmds=$old_archive_from_new_cmds else # Add any objects from preloaded convenience libraries if test -n "$dlprefiles"; then gentop="$output_objdir/${outputname}x" func_append generated " $gentop" func_extract_archives $gentop $dlprefiles func_append oldobjs " $func_extract_archives_result" fi # POSIX demands no paths to be encoded in archives. We have # to avoid creating archives with duplicate basenames if we # might have to extract them afterwards, e.g., when creating a # static archive out of a convenience library, or when linking # the entirety of a libtool archive into another (currently # not supported by libtool). if (for obj in $oldobjs do func_basename "$obj" $ECHO "$func_basename_result" done | sort | sort -uc >/dev/null 2>&1); then : else echo "copying selected object files to avoid basename conflicts..." gentop="$output_objdir/${outputname}x" func_append generated " $gentop" func_mkdir_p "$gentop" save_oldobjs=$oldobjs oldobjs= counter=1 for obj in $save_oldobjs do func_basename "$obj" objbase="$func_basename_result" case " $oldobjs " in " ") oldobjs=$obj ;; *[\ /]"$objbase "*) while :; do # Make sure we don't pick an alternate name that also # overlaps. newobj=lt$counter-$objbase func_arith $counter + 1 counter=$func_arith_result case " $oldobjs " in *[\ /]"$newobj "*) ;; *) if test ! -f "$gentop/$newobj"; then break; fi ;; esac done func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj" func_append oldobjs " $gentop/$newobj" ;; *) func_append oldobjs " $obj" ;; esac done fi func_to_tool_file "$oldlib" func_convert_file_msys_to_w32 tool_oldlib=$func_to_tool_file_result eval cmds=\"$old_archive_cmds\" func_len " $cmds" len=$func_len_result if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then cmds=$old_archive_cmds elif test -n "$archiver_list_spec"; then func_verbose "using command file archive linking..." for obj in $oldobjs do func_to_tool_file "$obj" $ECHO "$func_to_tool_file_result" done > $output_objdir/$libname.libcmd func_to_tool_file "$output_objdir/$libname.libcmd" oldobjs=" $archiver_list_spec$func_to_tool_file_result" cmds=$old_archive_cmds else # the command line is too long to link in one step, link in parts func_verbose "using piecewise archive linking..." save_RANLIB=$RANLIB RANLIB=: objlist= concat_cmds= save_oldobjs=$oldobjs oldobjs= # Is there a better way of finding the last object in the list? for obj in $save_oldobjs do last_oldobj=$obj done eval test_cmds=\"$old_archive_cmds\" func_len " $test_cmds" len0=$func_len_result len=$len0 for obj in $save_oldobjs do func_len " $obj" func_arith $len + $func_len_result len=$func_arith_result func_append objlist " $obj" if test "$len" -lt "$max_cmd_len"; then : else # the above command should be used before it gets too long oldobjs=$objlist if test "$obj" = "$last_oldobj" ; then RANLIB=$save_RANLIB fi test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\" objlist= len=$len0 fi done RANLIB=$save_RANLIB oldobjs=$objlist if test "X$oldobjs" = "X" ; then eval cmds=\"\$concat_cmds\" else eval cmds=\"\$concat_cmds~\$old_archive_cmds\" fi fi fi func_execute_cmds "$cmds" 'exit $?' done test -n "$generated" && \ func_show_eval "${RM}r$generated" # Now create the libtool archive. case $output in *.la) old_library= test "$build_old_libs" = yes && old_library="$libname.$libext" func_verbose "creating $output" # Preserve any variables that may affect compiler behavior for var in $variables_saved_for_relink; do if eval test -z \"\${$var+set}\"; then relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" elif eval var_value=\$$var; test -z "$var_value"; then relink_command="$var=; export $var; $relink_command" else func_quote_for_eval "$var_value" relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command" fi done # Quote the link command for shipping. relink_command="(cd `pwd`; $SHELL $progpath $preserve_args --mode=relink $libtool_args @inst_prefix_dir@)" relink_command=`$ECHO "$relink_command" | $SED "$sed_quote_subst"` if test "$hardcode_automatic" = yes ; then relink_command= fi # Only create the output if not a dry run. $opt_dry_run || { for installed in no yes; do if test "$installed" = yes; then if test -z "$install_libdir"; then break fi output="$output_objdir/$outputname"i # Replace all uninstalled libtool libraries with the installed ones newdependency_libs= for deplib in $dependency_libs; do case $deplib in *.la) func_basename "$deplib" name="$func_basename_result" func_resolve_sysroot "$deplib" eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $func_resolve_sysroot_result` test -z "$libdir" && \ func_fatal_error "\`$deplib' is not a valid libtool archive" func_append newdependency_libs " ${lt_sysroot:+=}$libdir/$name" ;; -L*) func_stripname -L '' "$deplib" func_replace_sysroot "$func_stripname_result" func_append newdependency_libs " -L$func_replace_sysroot_result" ;; -R*) func_stripname -R '' "$deplib" func_replace_sysroot "$func_stripname_result" func_append newdependency_libs " -R$func_replace_sysroot_result" ;; *) func_append newdependency_libs " $deplib" ;; esac done dependency_libs="$newdependency_libs" newdlfiles= for lib in $dlfiles; do case $lib in *.la) func_basename "$lib" name="$func_basename_result" eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib` test -z "$libdir" && \ func_fatal_error "\`$lib' is not a valid libtool archive" func_append newdlfiles " ${lt_sysroot:+=}$libdir/$name" ;; *) func_append newdlfiles " $lib" ;; esac done dlfiles="$newdlfiles" newdlprefiles= for lib in $dlprefiles; do case $lib in *.la) # Only pass preopened files to the pseudo-archive (for # eventual linking with the app. that links it) if we # didn't already link the preopened objects directly into # the library: func_basename "$lib" name="$func_basename_result" eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib` test -z "$libdir" && \ func_fatal_error "\`$lib' is not a valid libtool archive" func_append newdlprefiles " ${lt_sysroot:+=}$libdir/$name" ;; esac done dlprefiles="$newdlprefiles" else newdlfiles= for lib in $dlfiles; do case $lib in [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;; *) abs=`pwd`"/$lib" ;; esac func_append newdlfiles " $abs" done dlfiles="$newdlfiles" newdlprefiles= for lib in $dlprefiles; do case $lib in [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;; *) abs=`pwd`"/$lib" ;; esac func_append newdlprefiles " $abs" done dlprefiles="$newdlprefiles" fi $RM $output # place dlname in correct position for cygwin # In fact, it would be nice if we could use this code for all target # systems that can't hard-code library paths into their executables # and that have no shared library path variable independent of PATH, # but it turns out we can't easily determine that from inspecting # libtool variables, so we have to hard-code the OSs to which it # applies here; at the moment, that means platforms that use the PE # object format with DLL files. See the long comment at the top of # tests/bindir.at for full details. tdlname=$dlname case $host,$output,$installed,$module,$dlname in *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll | *cegcc*,*lai,yes,no,*.dll) # If a -bindir argument was supplied, place the dll there. if test "x$bindir" != x ; then func_relative_path "$install_libdir" "$bindir" tdlname=$func_relative_path_result$dlname else # Otherwise fall back on heuristic. tdlname=../bin/$dlname fi ;; esac $ECHO > $output "\ # $outputname - a libtool library file # Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION # # Please DO NOT delete this file! # It is necessary for linking the library. # The name that we can dlopen(3). dlname='$tdlname' # Names of this library. library_names='$library_names' # The name of the static archive. old_library='$old_library' # Linker flags that can not go in dependency_libs. inherited_linker_flags='$new_inherited_linker_flags' # Libraries that this one depends upon. dependency_libs='$dependency_libs' # Names of additional weak libraries provided by this library weak_library_names='$weak_libs' # Version information for $libname. current=$current age=$age revision=$revision # Is this an already installed library? installed=$installed # Should we warn about portability when linking against -modules? shouldnotlink=$module # Files to dlopen/dlpreopen dlopen='$dlfiles' dlpreopen='$dlprefiles' # Directory that this library needs to be installed in: libdir='$install_libdir'" if test "$installed" = no && test "$need_relink" = yes; then $ECHO >> $output "\ relink_command=\"$relink_command\"" fi done } # Do a symbolic link so that the libtool archive can be found in # LD_LIBRARY_PATH before the program is installed. func_show_eval '( cd "$output_objdir" && $RM "$outputname" && $LN_S "../$outputname" "$outputname" )' 'exit $?' ;; esac exit $EXIT_SUCCESS } { test "$opt_mode" = link || test "$opt_mode" = relink; } && func_mode_link ${1+"$@"} # func_mode_uninstall arg... func_mode_uninstall () { $opt_debug RM="$nonopt" files= rmforce= exit_status=0 # This variable tells wrapper scripts just to set variables rather # than running their programs. libtool_install_magic="$magic" for arg do case $arg in -f) func_append RM " $arg"; rmforce=yes ;; -*) func_append RM " $arg" ;; *) func_append files " $arg" ;; esac done test -z "$RM" && \ func_fatal_help "you must specify an RM program" rmdirs= for file in $files; do func_dirname "$file" "" "." dir="$func_dirname_result" if test "X$dir" = X.; then odir="$objdir" else odir="$dir/$objdir" fi func_basename "$file" name="$func_basename_result" test "$opt_mode" = uninstall && odir="$dir" # Remember odir for removal later, being careful to avoid duplicates if test "$opt_mode" = clean; then case " $rmdirs " in *" $odir "*) ;; *) func_append rmdirs " $odir" ;; esac fi # Don't error if the file doesn't exist and rm -f was used. if { test -L "$file"; } >/dev/null 2>&1 || { test -h "$file"; } >/dev/null 2>&1 || test -f "$file"; then : elif test -d "$file"; then exit_status=1 continue elif test "$rmforce" = yes; then continue fi rmfiles="$file" case $name in *.la) # Possibly a libtool archive, so verify it. if func_lalib_p "$file"; then func_source $dir/$name # Delete the libtool libraries and symlinks. for n in $library_names; do func_append rmfiles " $odir/$n" done test -n "$old_library" && func_append rmfiles " $odir/$old_library" case "$opt_mode" in clean) case " $library_names " in *" $dlname "*) ;; *) test -n "$dlname" && func_append rmfiles " $odir/$dlname" ;; esac test -n "$libdir" && func_append rmfiles " $odir/$name $odir/${name}i" ;; uninstall) if test -n "$library_names"; then # Do each command in the postuninstall commands. func_execute_cmds "$postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1' fi if test -n "$old_library"; then # Do each command in the old_postuninstall commands. func_execute_cmds "$old_postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1' fi # FIXME: should reinstall the best remaining shared library. ;; esac fi ;; *.lo) # Possibly a libtool object, so verify it. if func_lalib_p "$file"; then # Read the .lo file func_source $dir/$name # Add PIC object to the list of files to remove. if test -n "$pic_object" && test "$pic_object" != none; then func_append rmfiles " $dir/$pic_object" fi # Add non-PIC object to the list of files to remove. if test -n "$non_pic_object" && test "$non_pic_object" != none; then func_append rmfiles " $dir/$non_pic_object" fi fi ;; *) if test "$opt_mode" = clean ; then noexename=$name case $file in *.exe) func_stripname '' '.exe' "$file" file=$func_stripname_result func_stripname '' '.exe' "$name" noexename=$func_stripname_result # $file with .exe has already been added to rmfiles, # add $file without .exe func_append rmfiles " $file" ;; esac # Do a test to see if this is a libtool program. if func_ltwrapper_p "$file"; then if func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" relink_command= func_source $func_ltwrapper_scriptname_result func_append rmfiles " $func_ltwrapper_scriptname_result" else relink_command= func_source $dir/$noexename fi # note $name still contains .exe if it was in $file originally # as does the version of $file that was added into $rmfiles func_append rmfiles " $odir/$name $odir/${name}S.${objext}" if test "$fast_install" = yes && test -n "$relink_command"; then func_append rmfiles " $odir/lt-$name" fi if test "X$noexename" != "X$name" ; then func_append rmfiles " $odir/lt-${noexename}.c" fi fi fi ;; esac func_show_eval "$RM $rmfiles" 'exit_status=1' done # Try to remove the ${objdir}s in the directories where we deleted files for dir in $rmdirs; do if test -d "$dir"; then func_show_eval "rmdir $dir >/dev/null 2>&1" fi done exit $exit_status } { test "$opt_mode" = uninstall || test "$opt_mode" = clean; } && func_mode_uninstall ${1+"$@"} test -z "$opt_mode" && { help="$generic_help" func_fatal_help "you must specify a MODE" } test -z "$exec_cmd" && \ func_fatal_help "invalid operation mode \`$opt_mode'" if test -n "$exec_cmd"; then eval exec "$exec_cmd" exit $EXIT_FAILURE fi exit $exit_status # The TAGs below are defined such that we never get into a situation # in which we disable both kinds of libraries. Given conflicting # choices, we go for a static library, that is the most portable, # since we can't tell whether shared libraries were disabled because # the user asked for that or because the platform doesn't support # them. This is particularly important on AIX, because we don't # support having both static and shared libraries enabled at the same # time on that platform, so we default to a shared-only configuration. # If a disable-shared tag is given, we'll fallback to a static-only # configuration. But we'll never go from static-only to shared-only. # ### BEGIN LIBTOOL TAG CONFIG: disable-shared build_libtool_libs=no build_old_libs=yes # ### END LIBTOOL TAG CONFIG: disable-shared # ### BEGIN LIBTOOL TAG CONFIG: disable-static build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac` # ### END LIBTOOL TAG CONFIG: disable-static # Local Variables: # mode:shell-script # sh-indentation:2 # End: # vi:sw=2 DOMALIGN-0.1.650/install-sh0000755000175000017500000003325512171070653012014 00000000000000#!/bin/sh # install - install a program, script, or datafile scriptversion=2011-11-20.07; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the # following copyright and license. # # Copyright (C) 1994 X Consortium # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to # deal in the Software without restriction, including without limitation the # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or # sell copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN # AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC- # TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # # Except as contained in this notice, the name of the X Consortium shall not # be used in advertising or otherwise to promote the sale, use or other deal- # ings in this Software without prior written authorization from the X Consor- # tium. # # # FSF changes to this file are in the public domain. # # Calling this script install-sh is preferred over install.sh, to prevent # 'make' implicit rules from creating a file called install from it # when there is no Makefile. # # This script is compatible with the BSD install script, but was written # from scratch. nl=' ' IFS=" "" $nl" # set DOITPROG to echo to test this script # Don't use :- since 4.3BSD and earlier shells don't like it. doit=${DOITPROG-} if test -z "$doit"; then doit_exec=exec else doit_exec=$doit fi # Put in absolute file names if you don't have them in your path; # or use environment vars. chgrpprog=${CHGRPPROG-chgrp} chmodprog=${CHMODPROG-chmod} chownprog=${CHOWNPROG-chown} cmpprog=${CMPPROG-cmp} cpprog=${CPPROG-cp} mkdirprog=${MKDIRPROG-mkdir} mvprog=${MVPROG-mv} rmprog=${RMPROG-rm} stripprog=${STRIPPROG-strip} posix_glob='?' initialize_posix_glob=' test "$posix_glob" != "?" || { if (set -f) 2>/dev/null; then posix_glob= else posix_glob=: fi } ' posix_mkdir= # Desired mode of installed file. mode=0755 chgrpcmd= chmodcmd=$chmodprog chowncmd= mvcmd=$mvprog rmcmd="$rmprog -f" stripcmd= src= dst= dir_arg= dst_arg= copy_on_change=false no_target_directory= usage="\ Usage: $0 [OPTION]... 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(umask $mkdir_umask && eval "\$doit_exec \$mkdirprog $prefixes") || test -d "$dstdir" || exit 1 obsolete_mkdir_used=true fi fi fi if test -n "$dir_arg"; then { test -z "$chowncmd" || $doit $chowncmd "$dst"; } && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } && { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false || test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1 else # Make a couple of temp file names in the proper directory. dsttmp=$dstdir/_inst.$$_ rmtmp=$dstdir/_rm.$$_ # Trap to clean up those temp files at exit. trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0 # Copy the file name to the temp name. (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") && # and set any options; do chmod last to preserve setuid bits. # # If any of these fail, we abort the whole thing. If we want to # ignore errors from any of these, just make sure not to ignore # errors from the above "$doit $cpprog $src $dsttmp" command. # { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } && { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } && { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } && # If -C, don't bother to copy if it wouldn't change the file. if $copy_on_change && old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` && new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` && eval "$initialize_posix_glob" && $posix_glob set -f && set X $old && old=:$2:$4:$5:$6 && set X $new && new=:$2:$4:$5:$6 && $posix_glob set +f && test "$old" = "$new" && $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1 then rm -f "$dsttmp" else # Rename the file to the real destination. $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null || # The rename failed, perhaps because mv can't rename something else # to itself, or perhaps because mv is so ancient that it does not # support -f. { # Now remove or move aside any old file at destination location. # We try this two ways since rm can't unlink itself on some # systems and the destination file might be busy for other # reasons. In this case, the final cleanup might fail but the new # file should still install successfully. { test ! -f "$dst" || $doit $rmcmd -f "$dst" 2>/dev/null || { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null && { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; } } || { echo "$0: cannot unlink or rename $dst" >&2 (exit 1); exit 1 } } && # Now rename the file to the real destination. $doit $mvcmd "$dsttmp" "$dst" } fi || exit 1 trap '' 0 fi done # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-time-zone: "UTC" # time-stamp-end: "; # UTC" # End: DOMALIGN-0.1.650/INSTALL0000644000175000017500000003660512171070653011043 00000000000000Installation Instructions ************************* Copyright (C) 1994-1996, 1999-2002, 2004-2012 Free Software Foundation, Inc. Copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright notice and this notice are preserved. This file is offered as-is, without warranty of any kind. Basic Installation ================== Briefly, the shell commands `./configure; make; make install' should configure, build, and install this package. The following more-detailed instructions are generic; see the `README' file for instructions specific to this package. Some packages provide this `INSTALL' file but do not implement all of the features documented below. The lack of an optional feature in a given package is not necessarily a bug. More recommendations for GNU packages can be found in *note Makefile Conventions: (standards)Makefile Conventions. 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, and a file `config.log' containing compiler output (useful mainly for debugging `configure'). It can also use an optional file (typically called `config.cache' and enabled with `--cache-file=config.cache' or simply `-C') that saves the results of its tests to speed up reconfiguring. Caching is disabled by default to prevent problems with accidental use of stale cache files. 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 you are using the cache, and at some point `config.cache' contains results you don't want to keep, you may remove or edit it. The file `configure.ac' (or `configure.in') is used to create `configure' by a program called `autoconf'. You need `configure.ac' 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. Running `configure' might take a while. While running, it prints some messages telling which features it is checking for. 2. Type `make' to compile the package. 3. Optionally, type `make check' to run any self-tests that come with the package, generally using the just-built uninstalled binaries. 4. Type `make install' to install the programs and any data files and documentation. When installing into a prefix owned by root, it is recommended that the package be configured and built as a regular user, and only the `make install' phase executed with root privileges. 5. 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In practice, not all packages have tested that uninstallation works correctly, even though it is required by the GNU Coding Standards. 8. Some packages, particularly those that use Automake, provide `make distcheck', which can by used by developers to test that all other targets like `make install' and `make uninstall' work correctly. This target is generally not run by end users. Compilers and Options ===================== Some systems require unusual options for compilation or linking that the `configure' script does not know about. Run `./configure --help' for details on some of the pertinent environment variables. You can give `configure' initial values for configuration parameters by setting variables in the command line or in the environment. Here is an example: ./configure CC=c99 CFLAGS=-g LIBS=-lposix *Note Defining Variables::, for more details. 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On MacOS X 10.5 and later systems, you can create libraries and executables that work on multiple system types--known as "fat" or "universal" binaries--by specifying multiple `-arch' options to the compiler but only a single `-arch' option to the preprocessor. Like this: ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \ CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \ CPP="gcc -E" CXXCPP="g++ -E" This is not guaranteed to produce working output in all cases, you may have to build one architecture at a time and combine the results using the `lipo' tool if you have problems. Installation Names ================== By default, `make install' installs the package's commands under `/usr/local/bin', include files under `/usr/local/include', etc. You can specify an installation prefix other than `/usr/local' by giving `configure' the option `--prefix=PREFIX', where PREFIX must be an absolute file name. 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DOMALIGN-0.1.650/emboss_acd/0002775000175000017500000000000012171070667012170 500000000000000DOMALIGN-0.1.650/emboss_acd/domainalign.acd0000664000175000017500000001367111727433152015047 00000000000000application: domainalign [ documentation: "Generate alignments (DAF file) for nodes in a DCF file." groups: "Protein:Domains, Alignment:Local" gui: "yes" batch: "yes" cpu: "medium" embassy: "domalign" external: "stamp STAMP package http://www.compbio.dundee.ac.uk/" external: "sorttrans STAMP package http://www.compbio.dundee.ac.uk/" external: "transform STAMP package http://www.compbio.dundee.ac.uk/" external: "poststamp STAMP package http://www.compbio.dundee.ac.uk/" external: "ver2hor STAMP package http://www.compbio.dundee.ac.uk/" relations: "EDAM_topic:0182 Sequence alignment" relations: "EDAM_topic:0736 Protein domains and folds" relations: "EDAM_operation:0292 Sequence alignment construction" ] section: input [ information: "Input section" type: "page" ] infile: dcfinfile [ parameter: "Y" information: "Domain classification file" help: "This option specifies the name of DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS." knowntype: "Domain classification" relations: "EDAM_data:0900 Protein domain classification" ] directory: pdbdir [ parameter: "Y" information: "Domain pdb directory" help: "This option specifies the location of domain PDB files (input). A 'domain PDB file' contains coordinate data for a single domain from SCOP or CATH, in PDB format. The files are generated by using DOMAINER." default: "./" extension: "ent" knowntype: "domain pdb" relations: "EDAM_data:1468 Protein domain" relations: "EDAM_identifier:1049 Directory name" ] endsection: input section: required [ information: "Required section" type: "page" ] list: node [ standard: "Y" default: "1" minimum: "1" maximum: "1" values: "1: Class (SCOP), 2: Fold (SCOP), 3: Superfamily (SCOP), 4: Family (SCOP), 5: Class (CATH), 6: Architecture (CATH), 7: Topology (CATH), 8: Homologous Superfamily (CATH), 9: Family (CATH)" help: "This option specifies the node for redundancy removal. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies. For example by selecting 'Class' entries belonging to the same Class will be non-redundant." delimiter: "," codedelimiter: ":" header: "Node at which to remove redundancy" information: "Select number." relations: "EDAM_data:2527 Parameter" ] list: mode [ standard: "Y" default: "1" minimum: "1" maximum: "1" values: "1: STAMP, 2: TCOFFEE" help: "This option specifies the alignment algorithm to use." delimiter: "," codedelimiter: ":" header: "Alignment algorithm option" information: "Select number." relations: "EDAM_identifier:1190 Tool name" ] toggle: keepsinglets [ standard: "Y" information: "Write sequences of singlet families to file." help: "This option specifies whether to write sequences of singlet families to file. If you specify this option, the sequence for each singlet family are written to file (output)." default: "Y" relations: "EDAM_data:2527 Parameter" ] endsection: required section: output [ information: "Output section" type: "page" ] outdir: dafoutdir [ parameter: "Y" information: "Domain alignment file output directory" help: "This option specifies the location of DAF files (domain alignment files) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The files are in clustal format and are annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN." default: "./" extension: "daf" knowntype: "domain alignment" relations: "EDAM_identifier:1049 Directory name" relations: "EDAM_data:1384 Sequence alignment (protein)" ] outdir: singletsoutdir [ standard: "$(keepsinglets)" information: "Domain hits file output directory" help: "This option specifies the location of DHF files (domain hits files) for singlet sequences (output). The singlets are written out as a 'domain hits file' - which contains database hits (sequences) with domain classification information, in FASTA format." default: "./" extension: "dhf" knowntype: "domain hits" relations: "EDAM_identifier:1049 Directory name" relations: "EDAM_data:0849 Sequence record" relations: "EDAM_format:1219 pure protein" ] outdir: superoutdir [ standard: "@($(mode)==1)" information: "Pdb entry file output directory" help: "This option specifies the location of structural superimposition files (output). A file in PDB format of the structural superimposition is generated for each family if the STAMP algorithm is used." default: "./" extension: "ent" knowntype: "pdb" relations: "EDAM_identifier:1049 Directory name" relations: "EDAM_data:1481 Structure alignment (protein)" ] outfile: logfile [ standard: "Y" information: "Domainatrix log output file" help: "This option specifies the name of log file (output). The log file contains messages about any errors arising while domainalign ran." default: "domainalign.log" knowntype: "domainatrix log" relations: "EDAM_data:1678 Tool log" ] endsection: output DOMALIGN-0.1.650/emboss_acd/domainrep.acd0000664000175000017500000000540511727433152014537 00000000000000application: domainrep [ documentation: "Reorder DCF file to identify representative structures." groups: "Protein:3D Structure, Protein:Domains, Alignment:Local" gui: "yes" batch: "yes" cpu: "medium" embassy: "domalign" external: "stamp Modified stamp - contact Jon Ison jison@ebi.ac.uk" relations: "EDAM_topic:0182 Sequence alignment" relations: "EDAM_topic:0164 Sequence clustering" relations: "EDAM_topic:0736 Protein domains and folds" relations: "EDAM_operation:2233 Representative sequence identification" ] section: input [ information: "Input section" type: "page" ] infile: dcfinfile [ parameter: "Y" information: "Domain classification file" help: "This option specifies the name of DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS." knowntype: "Domain classification" relations: "EDAM_data:0900 Protein domain classification" ] endsection: input section: required [ information: "Required section" type: "page" ] list: node [ standard: "Y" default: "1" minimum: "1" maximum: "1" values: "1: Class (SCOP), 2: Fold (SCOP), 3: Superfamily (SCOP), 4: Family (SCOP), 5: Class (CATH), 6: Architecture (CATH), 7: Topology (CATH), 8: Homologous Superfamily (CATH), 9: Family (CATH)" help: "This option specifies the node fore reordering the file. Reordering can be done for any specified node in the SCOP or CATH hierarchies. For example by selecting 'Class' entries belonging to the same Class will be reordered in turn." delimiter: "," codedelimiter: ":" header: "Node at which to reorder" information: "Select number." relations: "EDAM_data:2527 Parameter" ] endsection: required section: output [ information: "Output section" type: "page" ] outfile: dcfoutfile [ parameter: "Y" information: "Domain classification output file" help: "This option specifies the name of DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS." default: "test.scop" knowntype: "domain classification" relations: "EDAM_data:0900 Protein domain classification" ] endsection: output DOMALIGN-0.1.650/emboss_acd/seqalign.acd0000664000175000017500000001467011727433152014370 00000000000000application: seqalign [ documentation: "Extend alignments (DAF file) with sequences (DHF file)." groups: "Protein:Domains, Alignment:Local" gui: "yes" batch: "yes" cpu: "high" embassy: "domalign" external: "clustalw" relations: "EDAM_topic:0182 Sequence alignment" relations: "EDAM_topic:0736 Protein domains and folds" relations: "EDAM_operation:0292 Sequence alignment construction" ] section: input [ information: "Input section" type: "page" ] list: mode [ standard: "Y" default: "1" minimum: "1" maximum: "1" delimiter: "," codedelimiter: ":" values: "1: Single sequences, 2: Multiple sequences (e.g. sequence set or alignment)" header: "Input mode" information: "Select mode of operation." button: "Y" help: "This option specifies the mode of SEQALIGN operation. SEQALIGN takes as input a directory of either i. single sequences, ii. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file)). The user has to specify which." relations: "EDAM_data:2527 Parameter" ] dirlist: dhfinpath [ standard: "@($(mode)==1)" information: "Program seqalign input directories" help: "This option specifies the location of sequences, e.g. DHF files (domain hits files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN." default: "./" extension: "dhf" knowntype: "seqalign input" nullok: "Y" relations: "EDAM_identifier:1049 Directory name" relations: "EDAM_data:0849 Sequence record" relations: "EDAM_format:1219 pure protein" ] dirlist: dafinpath [ standard: "@($(mode)==2)" information: "Domain alignment directories" help: "This option specifies the location of sequences, e.g. DAF files (domain alignment files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN." default: "./" extension: "daf" knowntype: "domain alignment" nullok: "Y" relations: "EDAM_identifier:1049 Directory name" relations: "EDAM_data:1384 Sequence alignment (protein)" ] directory: dhfindir [ parameter: "Y" information: "Domain hits directory" help: "This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH." default: "./" extension: "dhf" knowntype: "domain hits" relations: "EDAM_identifier:1049 Directory name" relations: "EDAM_data:0849 Sequence record" relations: "EDAM_format:1219 pure protein" ] endsection: input section: required [ information: "Required section" type: "page" ] list: amode [ standard: "Y" default: "1" minimum: "1" maximum: "1" values: "1: CLUSTALW, 2: TCOFFEE (not yet implemented)" help: "This option specifies which alignment algorithm to use." delimiter: "," codedelimiter: ":" header: "Alignment algorithm option" information: "Select number." relations: "EDAM_identifier:1190 Tool name" ] endsection: required section: additional [ information: "Additional section" type: "page" ] boolean: forcetype [ additional: "Y" information: "Force output of minimal domain classification data." help: "This option specifies whether to force minimal domain classification data to be written to the output file in cases where singlet sequences were given as input file and no classification data was available" default: "N" relations: "EDAM_data:2527 Parameter" ] endsection: additional section: output [ information: "Output section" type: "page" ] outdir: dafoutdir [ parameter: "Y" information: "Domain alignment file output directory" help: "This option specifies the location of DAF files (domain alignment files) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN." default: "./" extension: "daf" knowntype: "domain alignment" relations: "EDAM_identifier:1049 Directory name" relations: "EDAM_data:1384 Sequence alignment (protein)" ] outfile: logfile [ standard: "Y" information: "Domainatrix log output file" default: "seqalign.log" help: "This option specifies the name of log file for the build. The log file contains messages about any errors arising while SEQALIGN ran." knowntype: "domainatrix log" relations: "EDAM_data:1678 Tool log" ] endsection: output DOMALIGN-0.1.650/emboss_acd/allversusall.acd0000664000175000017500000000734311727433152015275 00000000000000application: allversusall [ documentation: "Sequence similarity data from all-versus-all comparison." groups: "Utils:Database creation" gui: "yes" batch: "yes" cpu: "medium" embassy: "domalign" relations: "EDAM_topic:0091 Data handling" relations: "EDAM_topic:0182 Sequence alignment" relations: "EDAM_operation:0292 Sequence alignment construction" relations: "EDAM_operation:0289 Sequence distance matrix generation" ] section: input [ information: "Input section" type: "page" ] dirlist: seqinpath [ parameter: "Y" default: "./" extension: "fasta" information: "Sequence directories" knowntype: "protein sequence" relations: "EDAM_data:2886 Sequence record (protein)" ] matrixf: matrix [ additional: "Y" information: "Residue substitution matrix" help: "This option specifies the residue substitution matrix that is used for sequence comparison." default: "EBLOSUM62" relations: "EDAM_data:1449 Comparison matrix (amino acid)" ] endsection: input section: required [ information: "Required section" type: "page" ] endsection: required section: additional [ information: "Additional section" type: "page" ] float: gapopen [ additional: "Y" information: "Gap insertion penalty" minimum: "1.0" maximum: "100.0" default: "10" valid: "Floating point number from 1.0 to 100.0" expected: "10.0 for any sequence" help: "This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences." relations: "EDAM_data:1397 Gap opening penalty" ] float: gapextend [ additional: "Y" information: "Gap extension penalty" minimum: "0.0" maximum: "10.0" default: "0.5" valid: "Floating point number from 0.0 to 10.0" expected: "0.5 for any sequence" help: "This option specifies the gap extension penalty. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring." relations: "EDAM_data:1398 Gap extension penalty" ] endsection: additional section: output [ information: "Output section" type: "page" ] outdir: datoutdir [ parameter: "Y" information: "Location of sequence similarity data files (output)" help: "This option specifies the location of sequence similarity data files (output)." default: "./" extension: "out" knowntype: "allversusall output" relations: "EDAM_identifier:1049 Directory name" relations: "EDAM_data:1413 Sequence similarity" ] outfile: logfile [ standard: "Y" information: "Domainatrix log output file" default: "allversusall.log" help: "This option specifies the name of ALLVERSUSALL log file (output). The log file contains messages about any errors arising while ALLVERSUSALL ran." knowntype: "domainatrix log" relations: "EDAM_data:1678 Tool log" ] endsection: output DOMALIGN-0.1.650/emboss_acd/Makefile0000664000175000017500000003426012171070665013551 00000000000000# Makefile.in generated by automake 1.12.2 from Makefile.am. # emboss_acd/Makefile. 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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, see . # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Per Bothner. Please send patches (context # diff format) to and include a ChangeLog # entry. # # This script attempts to guess a canonical system name similar to # config.sub. If it succeeds, it prints the system name on stdout, and # exits with 0. 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We always set it to "unknown". sysctl="sysctl -n hw.machine_arch" UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \ /usr/sbin/$sysctl 2>/dev/null || echo unknown)` case "${UNAME_MACHINE_ARCH}" in armeb) machine=armeb-unknown ;; arm*) machine=arm-unknown ;; sh3el) machine=shl-unknown ;; sh3eb) machine=sh-unknown ;; sh5el) machine=sh5le-unknown ;; *) machine=${UNAME_MACHINE_ARCH}-unknown ;; esac # The Operating System including object format, if it has switched # to ELF recently, or will in the future. case "${UNAME_MACHINE_ARCH}" in arm*|i386|m68k|ns32k|sh3*|sparc|vax) eval $set_cc_for_build if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ELF__ then # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). # Return netbsd for either. FIX? os=netbsd else os=netbsdelf fi ;; *) os=netbsd ;; esac # The OS release # Debian GNU/NetBSD machines have a different userland, and # thus, need a distinct triplet. However, they do not need # kernel version information, so it can be replaced with a # suitable tag, in the style of linux-gnu. case "${UNAME_VERSION}" in Debian*) release='-gnu' ;; *) release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'` ;; esac # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM: # contains redundant information, the shorter form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. echo "${machine}-${os}${release}" exit ;; *:OpenBSD:*:*) UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'` echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE} exit ;; *:ekkoBSD:*:*) echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE} exit ;; *:SolidBSD:*:*) echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE} exit ;; macppc:MirBSD:*:*) echo powerpc-unknown-mirbsd${UNAME_RELEASE} exit ;; *:MirBSD:*:*) echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE} exit ;; alpha:OSF1:*:*) case $UNAME_RELEASE in *4.0) UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'` ;; *5.*) UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'` ;; esac # According to Compaq, /usr/sbin/psrinfo has been available on # OSF/1 and Tru64 systems produced since 1995. I hope that # covers most systems running today. This code pipes the CPU # types through head -n 1, so we only detect the type of CPU 0. ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1` case "$ALPHA_CPU_TYPE" in "EV4 (21064)") UNAME_MACHINE="alpha" ;; "EV4.5 (21064)") UNAME_MACHINE="alpha" ;; "LCA4 (21066/21068)") UNAME_MACHINE="alpha" ;; "EV5 (21164)") UNAME_MACHINE="alphaev5" ;; "EV5.6 (21164A)") UNAME_MACHINE="alphaev56" ;; "EV5.6 (21164PC)") UNAME_MACHINE="alphapca56" ;; "EV5.7 (21164PC)") UNAME_MACHINE="alphapca57" ;; "EV6 (21264)") UNAME_MACHINE="alphaev6" ;; "EV6.7 (21264A)") UNAME_MACHINE="alphaev67" ;; "EV6.8CB (21264C)") UNAME_MACHINE="alphaev68" ;; "EV6.8AL (21264B)") UNAME_MACHINE="alphaev68" ;; "EV6.8CX (21264D)") UNAME_MACHINE="alphaev68" ;; "EV6.9A (21264/EV69A)") UNAME_MACHINE="alphaev69" ;; "EV7 (21364)") UNAME_MACHINE="alphaev7" ;; "EV7.9 (21364A)") UNAME_MACHINE="alphaev79" ;; esac # A Pn.n version is a patched version. # A Vn.n version is a released version. # A Tn.n version is a released field test version. # A Xn.n version is an unreleased experimental baselevel. # 1.2 uses "1.2" for uname -r. echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` # Reset EXIT trap before exiting to avoid spurious non-zero exit code. exitcode=$? trap '' 0 exit $exitcode ;; Alpha\ *:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # Should we change UNAME_MACHINE based on the output of uname instead # of the specific Alpha model? echo alpha-pc-interix exit ;; 21064:Windows_NT:50:3) echo alpha-dec-winnt3.5 exit ;; Amiga*:UNIX_System_V:4.0:*) echo m68k-unknown-sysv4 exit ;; *:[Aa]miga[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-amigaos exit ;; *:[Mm]orph[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-morphos exit ;; *:OS/390:*:*) echo i370-ibm-openedition exit ;; *:z/VM:*:*) echo s390-ibm-zvmoe exit ;; *:OS400:*:*) echo powerpc-ibm-os400 exit ;; arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) echo arm-acorn-riscix${UNAME_RELEASE} exit ;; arm:riscos:*:*|arm:RISCOS:*:*) echo arm-unknown-riscos exit ;; SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) echo hppa1.1-hitachi-hiuxmpp exit ;; Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. if test "`(/bin/universe) 2>/dev/null`" = att ; then echo pyramid-pyramid-sysv3 else echo pyramid-pyramid-bsd fi exit ;; NILE*:*:*:dcosx) echo pyramid-pyramid-svr4 exit ;; DRS?6000:unix:4.0:6*) echo sparc-icl-nx6 exit ;; DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) case `/usr/bin/uname -p` in sparc) echo sparc-icl-nx7; exit ;; esac ;; s390x:SunOS:*:*) echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4H:SunOS:5.*:*) echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*) echo i386-pc-auroraux${UNAME_RELEASE} exit ;; i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) eval $set_cc_for_build SUN_ARCH="i386" # If there is a compiler, see if it is configured for 64-bit objects. # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. # This test works for both compilers. if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ grep IS_64BIT_ARCH >/dev/null then SUN_ARCH="x86_64" fi fi echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:6*:*) # According to config.sub, this is the proper way to canonicalize # SunOS6. Hard to guess exactly what SunOS6 will be like, but # it's likely to be more like Solaris than SunOS4. echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:*:*) case "`/usr/bin/arch -k`" in Series*|S4*) UNAME_RELEASE=`uname -v` ;; esac # Japanese Language versions have a version number like `4.1.3-JL'. echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'` exit ;; sun3*:SunOS:*:*) echo m68k-sun-sunos${UNAME_RELEASE} exit ;; sun*:*:4.2BSD:*) UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null` test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3 case "`/bin/arch`" in sun3) echo m68k-sun-sunos${UNAME_RELEASE} ;; sun4) echo sparc-sun-sunos${UNAME_RELEASE} ;; esac exit ;; aushp:SunOS:*:*) echo sparc-auspex-sunos${UNAME_RELEASE} exit ;; # The situation for MiNT is a little confusing. The machine name # can be virtually everything (everything which is not # "atarist" or "atariste" at least should have a processor # > m68000). The system name ranges from "MiNT" over "FreeMiNT" # to the lowercase version "mint" (or "freemint"). Finally # the system name "TOS" denotes a system which is actually not # MiNT. But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) echo m68k-milan-mint${UNAME_RELEASE} exit ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) echo m68k-hades-mint${UNAME_RELEASE} exit ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) echo m68k-unknown-mint${UNAME_RELEASE} exit ;; m68k:machten:*:*) echo m68k-apple-machten${UNAME_RELEASE} exit ;; powerpc:machten:*:*) echo powerpc-apple-machten${UNAME_RELEASE} exit ;; RISC*:Mach:*:*) echo mips-dec-mach_bsd4.3 exit ;; RISC*:ULTRIX:*:*) echo mips-dec-ultrix${UNAME_RELEASE} exit ;; VAX*:ULTRIX*:*:*) echo vax-dec-ultrix${UNAME_RELEASE} exit ;; 2020:CLIX:*:* | 2430:CLIX:*:*) echo clipper-intergraph-clix${UNAME_RELEASE} exit ;; mips:*:*:UMIPS | mips:*:*:RISCos) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #ifdef __cplusplus #include /* for printf() prototype */ int main (int argc, char *argv[]) { #else int main (argc, argv) int argc; char *argv[]; { #endif #if defined (host_mips) && defined (MIPSEB) #if defined (SYSTYPE_SYSV) printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_SVR4) printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); #endif #endif exit (-1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` && SYSTEM_NAME=`$dummy $dummyarg` && { echo "$SYSTEM_NAME"; exit; } echo mips-mips-riscos${UNAME_RELEASE} exit ;; Motorola:PowerMAX_OS:*:*) echo powerpc-motorola-powermax exit ;; Motorola:*:4.3:PL8-*) echo powerpc-harris-powermax exit ;; Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) echo powerpc-harris-powermax exit ;; Night_Hawk:Power_UNIX:*:*) echo powerpc-harris-powerunix exit ;; m88k:CX/UX:7*:*) echo m88k-harris-cxux7 exit ;; m88k:*:4*:R4*) echo m88k-motorola-sysv4 exit ;; m88k:*:3*:R3*) echo m88k-motorola-sysv3 exit ;; AViiON:dgux:*:*) # DG/UX returns AViiON for all architectures UNAME_PROCESSOR=`/usr/bin/uname -p` if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] then if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ [ ${TARGET_BINARY_INTERFACE}x = x ] then echo m88k-dg-dgux${UNAME_RELEASE} else echo m88k-dg-dguxbcs${UNAME_RELEASE} fi else echo i586-dg-dgux${UNAME_RELEASE} fi exit ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) echo m88k-dolphin-sysv3 exit ;; M88*:*:R3*:*) # Delta 88k system running SVR3 echo m88k-motorola-sysv3 exit ;; XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) echo m88k-tektronix-sysv3 exit ;; Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) echo m68k-tektronix-bsd exit ;; *:IRIX*:*:*) echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` exit ;; ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id exit ;; # Note that: echo "'`uname -s`'" gives 'AIX ' i*86:AIX:*:*) echo i386-ibm-aix exit ;; ia64:AIX:*:*) if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} exit ;; *:AIX:2:3) if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include main() { if (!__power_pc()) exit(1); puts("powerpc-ibm-aix3.2.5"); exit(0); } EOF if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` then echo "$SYSTEM_NAME" else echo rs6000-ibm-aix3.2.5 fi elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then echo rs6000-ibm-aix3.2.4 else echo rs6000-ibm-aix3.2 fi exit ;; *:AIX:*:[4567]) IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then IBM_ARCH=rs6000 else IBM_ARCH=powerpc fi if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${IBM_ARCH}-ibm-aix${IBM_REV} exit ;; *:AIX:*:*) echo rs6000-ibm-aix exit ;; ibmrt:4.4BSD:*|romp-ibm:BSD:*) echo romp-ibm-bsd4.4 exit ;; ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to exit ;; # report: romp-ibm BSD 4.3 *:BOSX:*:*) echo rs6000-bull-bosx exit ;; DPX/2?00:B.O.S.:*:*) echo m68k-bull-sysv3 exit ;; 9000/[34]??:4.3bsd:1.*:*) echo m68k-hp-bsd exit ;; hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) echo m68k-hp-bsd4.4 exit ;; 9000/[34678]??:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` case "${UNAME_MACHINE}" in 9000/31? ) HP_ARCH=m68000 ;; 9000/[34]?? ) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) if [ -x /usr/bin/getconf ]; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` case "${sc_cpu_version}" in 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 532) # CPU_PA_RISC2_0 case "${sc_kernel_bits}" in 32) HP_ARCH="hppa2.0n" ;; 64) HP_ARCH="hppa2.0w" ;; '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 esac ;; esac fi if [ "${HP_ARCH}" = "" ]; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #define _HPUX_SOURCE #include #include int main () { #if defined(_SC_KERNEL_BITS) long bits = sysconf(_SC_KERNEL_BITS); #endif long cpu = sysconf (_SC_CPU_VERSION); switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0"); break; case CPU_PA_RISC1_1: puts ("hppa1.1"); break; case CPU_PA_RISC2_0: #if defined(_SC_KERNEL_BITS) switch (bits) { case 64: puts ("hppa2.0w"); break; case 32: puts ("hppa2.0n"); break; default: puts ("hppa2.0"); break; } break; #else /* !defined(_SC_KERNEL_BITS) */ puts ("hppa2.0"); break; #endif default: puts ("hppa1.0"); break; } exit (0); } EOF (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` test -z "$HP_ARCH" && HP_ARCH=hppa fi ;; esac if [ ${HP_ARCH} = "hppa2.0w" ] then eval $set_cc_for_build # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler # generating 64-bit code. GNU and HP use different nomenclature: # # $ CC_FOR_BUILD=cc ./config.guess # => hppa2.0w-hp-hpux11.23 # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | grep -q __LP64__ then HP_ARCH="hppa2.0w" else HP_ARCH="hppa64" fi fi echo ${HP_ARCH}-hp-hpux${HPUX_REV} exit ;; ia64:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` echo ia64-hp-hpux${HPUX_REV} exit ;; 3050*:HI-UX:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include int main () { long cpu = sysconf (_SC_CPU_VERSION); /* The order matters, because CPU_IS_HP_MC68K erroneously returns true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct results, however. */ if (CPU_IS_PA_RISC (cpu)) { switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; default: puts ("hppa-hitachi-hiuxwe2"); break; } } else if (CPU_IS_HP_MC68K (cpu)) puts ("m68k-hitachi-hiuxwe2"); else puts ("unknown-hitachi-hiuxwe2"); exit (0); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } echo unknown-hitachi-hiuxwe2 exit ;; 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) echo hppa1.1-hp-bsd exit ;; 9000/8??:4.3bsd:*:*) echo hppa1.0-hp-bsd exit ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) echo hppa1.0-hp-mpeix exit ;; hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) echo hppa1.1-hp-osf exit ;; hp8??:OSF1:*:*) echo hppa1.0-hp-osf exit ;; i*86:OSF1:*:*) if [ -x /usr/sbin/sysversion ] ; then echo ${UNAME_MACHINE}-unknown-osf1mk else echo ${UNAME_MACHINE}-unknown-osf1 fi exit ;; parisc*:Lites*:*:*) echo hppa1.1-hp-lites exit ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) echo c1-convex-bsd exit ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) echo c34-convex-bsd exit ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) echo c38-convex-bsd exit ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) echo c4-convex-bsd exit ;; CRAY*Y-MP:*:*:*) echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*[A-Z]90:*:*:*) echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ -e 's/\.[^.]*$/.X/' exit ;; CRAY*TS:*:*:*) echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*T3E:*:*:*) echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*SV1:*:*:*) echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; *:UNICOS/mp:*:*) echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; 5000:UNIX_System_V:4.*:*) FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} exit ;; sparc*:BSD/OS:*:*) echo sparc-unknown-bsdi${UNAME_RELEASE} exit ;; *:BSD/OS:*:*) echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} exit ;; *:FreeBSD:*:*) UNAME_PROCESSOR=`/usr/bin/uname -p` case ${UNAME_PROCESSOR} in amd64) echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; *) echo ${UNAME_PROCESSOR}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; esac exit ;; i*:CYGWIN*:*) echo ${UNAME_MACHINE}-pc-cygwin exit ;; *:MINGW*:*) echo ${UNAME_MACHINE}-pc-mingw32 exit ;; i*:MSYS*:*) echo ${UNAME_MACHINE}-pc-msys exit ;; i*:windows32*:*) # uname -m includes "-pc" on this system. echo ${UNAME_MACHINE}-mingw32 exit ;; i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; *:Interix*:*) case ${UNAME_MACHINE} in x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; authenticamd | genuineintel | EM64T) echo x86_64-unknown-interix${UNAME_RELEASE} exit ;; IA64) echo ia64-unknown-interix${UNAME_RELEASE} exit ;; esac ;; [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; 8664:Windows_NT:*) echo x86_64-pc-mks exit ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. 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EV56) UNAME_MACHINE=alphaev56 ;; PCA56) UNAME_MACHINE=alphapca56 ;; PCA57) UNAME_MACHINE=alphapca56 ;; EV6) UNAME_MACHINE=alphaev6 ;; EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; esac objdump --private-headers /bin/sh | grep -q ld.so.1 if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} exit ;; arm*:Linux:*:*) eval $set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_EABI__ then echo ${UNAME_MACHINE}-unknown-linux-gnu else if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_PCS_VFP then echo ${UNAME_MACHINE}-unknown-linux-gnueabi else echo ${UNAME_MACHINE}-unknown-linux-gnueabihf fi fi exit ;; avr32*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; cris:Linux:*:*) echo ${UNAME_MACHINE}-axis-linux-gnu exit ;; crisv32:Linux:*:*) echo ${UNAME_MACHINE}-axis-linux-gnu exit ;; frv:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; hexagon:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; i*86:Linux:*:*) LIBC=gnu eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #ifdef __dietlibc__ LIBC=dietlibc #endif EOF eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'` echo "${UNAME_MACHINE}-pc-linux-${LIBC}" exit ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m32r*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; mips:Linux:*:* | mips64:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU #undef ${UNAME_MACHINE} #undef ${UNAME_MACHINE}el #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) CPU=${UNAME_MACHINE}el #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) CPU=${UNAME_MACHINE} #else CPU= #endif #endif EOF eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'` test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } ;; or32:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; padre:Linux:*:*) echo sparc-unknown-linux-gnu exit ;; parisc64:Linux:*:* | hppa64:Linux:*:*) echo hppa64-unknown-linux-gnu exit ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in PA7*) echo hppa1.1-unknown-linux-gnu ;; PA8*) echo hppa2.0-unknown-linux-gnu ;; *) echo hppa-unknown-linux-gnu ;; esac exit ;; ppc64:Linux:*:*) echo powerpc64-unknown-linux-gnu exit ;; ppc:Linux:*:*) echo powerpc-unknown-linux-gnu exit ;; s390:Linux:*:* | s390x:Linux:*:*) echo ${UNAME_MACHINE}-ibm-linux exit ;; sh64*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; sh*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; sparc:Linux:*:* | sparc64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; tile*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; vax:Linux:*:*) echo ${UNAME_MACHINE}-dec-linux-gnu exit ;; x86_64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; xtensa*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both # sysname and nodename. echo i386-sequent-sysv4 exit ;; i*86:UNIX_SV:4.2MP:2.*) # Unixware is an offshoot of SVR4, but it has its own version # number series starting with 2... # I am not positive that other SVR4 systems won't match this, # I just have to hope. -- rms. # Use sysv4.2uw... so that sysv4* matches it. echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} exit ;; i*86:OS/2:*:*) # If we were able to find `uname', then EMX Unix compatibility # is probably installed. echo ${UNAME_MACHINE}-pc-os2-emx exit ;; i*86:XTS-300:*:STOP) echo ${UNAME_MACHINE}-unknown-stop exit ;; i*86:atheos:*:*) echo ${UNAME_MACHINE}-unknown-atheos exit ;; i*86:syllable:*:*) echo ${UNAME_MACHINE}-pc-syllable exit ;; i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit ;; i*86:*DOS:*:*) echo ${UNAME_MACHINE}-pc-msdosdjgpp exit ;; i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} else echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} fi exit ;; i*86:*:5:[678]*) # UnixWare 7.x, OpenUNIX and OpenServer 6. case `/bin/uname -X | grep "^Machine"` in *486*) UNAME_MACHINE=i486 ;; *Pentium) UNAME_MACHINE=i586 ;; *Pent*|*Celeron) UNAME_MACHINE=i686 ;; esac echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} exit ;; i*86:*:3.2:*) if test -f /usr/options/cb.name; then UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ && UNAME_MACHINE=i586 (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ && UNAME_MACHINE=i686 (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ && UNAME_MACHINE=i686 echo ${UNAME_MACHINE}-pc-sco$UNAME_REL else echo ${UNAME_MACHINE}-pc-sysv32 fi exit ;; pc:*:*:*) # Left here for compatibility: # uname -m prints for DJGPP always 'pc', but it prints nothing about # the processor, so we play safe by assuming i586. # Note: whatever this is, it MUST be the same as what config.sub # prints for the "djgpp" host, or else GDB configury will decide that # this is a cross-build. echo i586-pc-msdosdjgpp exit ;; Intel:Mach:3*:*) echo i386-pc-mach3 exit ;; paragon:*:*:*) echo i860-intel-osf1 exit ;; i860:*:4.*:*) # i860-SVR4 if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4 else # Add other i860-SVR4 vendors below as they are discovered. echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4 fi exit ;; mini*:CTIX:SYS*5:*) # "miniframe" echo m68010-convergent-sysv exit ;; mc68k:UNIX:SYSTEM5:3.51m) echo m68k-convergent-sysv exit ;; M680?0:D-NIX:5.3:*) echo m68k-diab-dnix exit ;; M68*:*:R3V[5678]*:*) test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) OS_REL='' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4; exit; } ;; NCR*:*:4.2:* | MPRAS*:*:4.2:*) OS_REL='.3' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) echo m68k-unknown-lynxos${UNAME_RELEASE} exit ;; mc68030:UNIX_System_V:4.*:*) echo m68k-atari-sysv4 exit ;; TSUNAMI:LynxOS:2.*:*) echo sparc-unknown-lynxos${UNAME_RELEASE} exit ;; rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit ;; PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit ;; SM[BE]S:UNIX_SV:*:*) echo mips-dde-sysv${UNAME_RELEASE} exit ;; RM*:ReliantUNIX-*:*:*) echo mips-sni-sysv4 exit ;; RM*:SINIX-*:*:*) echo mips-sni-sysv4 exit ;; *:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` echo ${UNAME_MACHINE}-sni-sysv4 else echo ns32k-sni-sysv fi exit ;; PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort # says echo i586-unisys-sysv4 exit ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm echo hppa1.1-stratus-sysv4 exit ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. echo i860-stratus-sysv4 exit ;; i*86:VOS:*:*) # From Paul.Green@stratus.com. echo ${UNAME_MACHINE}-stratus-vos exit ;; *:VOS:*:*) # From Paul.Green@stratus.com. echo hppa1.1-stratus-vos exit ;; mc68*:A/UX:*:*) echo m68k-apple-aux${UNAME_RELEASE} exit ;; news*:NEWS-OS:6*:*) echo mips-sony-newsos6 exit ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then echo mips-nec-sysv${UNAME_RELEASE} else echo mips-unknown-sysv${UNAME_RELEASE} fi exit ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. echo powerpc-apple-beos exit ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; BePC:Haiku:*:*) # Haiku running on Intel PC compatible. echo i586-pc-haiku exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; SX-5:SUPER-UX:*:*) echo sx5-nec-superux${UNAME_RELEASE} exit ;; SX-6:SUPER-UX:*:*) echo sx6-nec-superux${UNAME_RELEASE} exit ;; SX-7:SUPER-UX:*:*) echo sx7-nec-superux${UNAME_RELEASE} exit ;; SX-8:SUPER-UX:*:*) echo sx8-nec-superux${UNAME_RELEASE} exit ;; SX-8R:SUPER-UX:*:*) echo sx8r-nec-superux${UNAME_RELEASE} exit ;; Power*:Rhapsody:*:*) echo powerpc-apple-rhapsody${UNAME_RELEASE} exit ;; *:Rhapsody:*:*) echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} exit ;; *:Darwin:*:*) UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown case $UNAME_PROCESSOR in i386) eval $set_cc_for_build if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ grep IS_64BIT_ARCH >/dev/null then UNAME_PROCESSOR="x86_64" fi fi ;; unknown) UNAME_PROCESSOR=powerpc ;; esac echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} exit ;; *:procnto*:*:* | *:QNX:[0123456789]*:*) UNAME_PROCESSOR=`uname -p` if test "$UNAME_PROCESSOR" = "x86"; then UNAME_PROCESSOR=i386 UNAME_MACHINE=pc fi echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE} exit ;; *:QNX:*:4*) echo i386-pc-qnx exit ;; NEO-?:NONSTOP_KERNEL:*:*) echo neo-tandem-nsk${UNAME_RELEASE} exit ;; NSE-*:NONSTOP_KERNEL:*:*) echo nse-tandem-nsk${UNAME_RELEASE} exit ;; NSR-?:NONSTOP_KERNEL:*:*) echo nsr-tandem-nsk${UNAME_RELEASE} exit ;; *:NonStop-UX:*:*) echo mips-compaq-nonstopux exit ;; BS2000:POSIX*:*:*) echo bs2000-siemens-sysv exit ;; DS/*:UNIX_System_V:*:*) echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} exit ;; *:Plan9:*:*) # "uname -m" is not consistent, so use $cputype instead. 386 # is converted to i386 for consistency with other x86 # operating systems. if test "$cputype" = "386"; then UNAME_MACHINE=i386 else UNAME_MACHINE="$cputype" fi echo ${UNAME_MACHINE}-unknown-plan9 exit ;; *:TOPS-10:*:*) echo pdp10-unknown-tops10 exit ;; *:TENEX:*:*) echo pdp10-unknown-tenex exit ;; KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) echo pdp10-dec-tops20 exit ;; XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) echo pdp10-xkl-tops20 exit ;; *:TOPS-20:*:*) echo pdp10-unknown-tops20 exit ;; *:ITS:*:*) echo pdp10-unknown-its exit ;; SEI:*:*:SEIUX) echo mips-sei-seiux${UNAME_RELEASE} exit ;; *:DragonFly:*:*) echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` exit ;; *:*VMS:*:*) UNAME_MACHINE=`(uname -p) 2>/dev/null` case "${UNAME_MACHINE}" in A*) echo alpha-dec-vms ; exit ;; I*) echo ia64-dec-vms ; exit ;; V*) echo vax-dec-vms ; exit ;; esac ;; *:XENIX:*:SysV) echo i386-pc-xenix exit ;; i*86:skyos:*:*) echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//' exit ;; i*86:rdos:*:*) echo ${UNAME_MACHINE}-pc-rdos exit ;; i*86:AROS:*:*) echo ${UNAME_MACHINE}-pc-aros exit ;; x86_64:VMkernel:*:*) echo ${UNAME_MACHINE}-unknown-esx exit ;; esac #echo '(No uname command or uname output not recognized.)' 1>&2 #echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 eval $set_cc_for_build cat >$dummy.c < # include #endif main () { #if defined (sony) #if defined (MIPSEB) /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, I don't know.... */ printf ("mips-sony-bsd\n"); exit (0); #else #include printf ("m68k-sony-newsos%s\n", #ifdef NEWSOS4 "4" #else "" #endif ); exit (0); #endif #endif #if defined (__arm) && defined (__acorn) && defined (__unix) printf ("arm-acorn-riscix\n"); exit (0); #endif #if defined (hp300) && !defined (hpux) printf ("m68k-hp-bsd\n"); exit (0); #endif #if defined (NeXT) #if !defined (__ARCHITECTURE__) #define __ARCHITECTURE__ "m68k" #endif int version; version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; if (version < 4) printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); else printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); exit (0); #endif #if defined (MULTIMAX) || defined (n16) #if defined (UMAXV) printf ("ns32k-encore-sysv\n"); exit (0); #else #if defined (CMU) printf ("ns32k-encore-mach\n"); exit (0); #else printf ("ns32k-encore-bsd\n"); exit (0); #endif #endif #endif #if defined (__386BSD__) printf ("i386-pc-bsd\n"); exit (0); #endif #if defined (sequent) #if defined (i386) printf ("i386-sequent-dynix\n"); exit (0); #endif #if defined (ns32000) printf ("ns32k-sequent-dynix\n"); exit (0); #endif #endif #if defined (_SEQUENT_) struct utsname un; uname(&un); if (strncmp(un.version, "V2", 2) == 0) { printf ("i386-sequent-ptx2\n"); exit (0); } if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ printf ("i386-sequent-ptx1\n"); exit (0); } printf ("i386-sequent-ptx\n"); exit (0); #endif #if defined (vax) # if !defined (ultrix) # include # if defined (BSD) # if BSD == 43 printf ("vax-dec-bsd4.3\n"); exit (0); # else # if BSD == 199006 printf ("vax-dec-bsd4.3reno\n"); exit (0); # else printf ("vax-dec-bsd\n"); exit (0); # endif # endif # else printf ("vax-dec-bsd\n"); exit (0); # endif # else printf ("vax-dec-ultrix\n"); exit (0); # endif #endif #if defined (alliant) && defined (i860) printf ("i860-alliant-bsd\n"); exit (0); #endif exit (1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } # Apollos put the system type in the environment. test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; } # Convex versions that predate uname can use getsysinfo(1) if [ -x /usr/convex/getsysinfo ] then case `getsysinfo -f cpu_type` in c1*) echo c1-convex-bsd exit ;; c2*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; c34*) echo c34-convex-bsd exit ;; c38*) echo c38-convex-bsd exit ;; c4*) echo c4-convex-bsd exit ;; esac fi cat >&2 < in order to provide the needed information to handle your system. config.guess timestamp = $timestamp uname -m = `(uname -m) 2>/dev/null || echo unknown` uname -r = `(uname -r) 2>/dev/null || echo unknown` uname -s = `(uname -s) 2>/dev/null || echo unknown` uname -v = `(uname -v) 2>/dev/null || echo unknown` /usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` /bin/uname -X = `(/bin/uname -X) 2>/dev/null` hostinfo = `(hostinfo) 2>/dev/null` /bin/universe = `(/bin/universe) 2>/dev/null` /usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` /bin/arch = `(/bin/arch) 2>/dev/null` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` UNAME_MACHINE = ${UNAME_MACHINE} UNAME_RELEASE = ${UNAME_RELEASE} UNAME_SYSTEM = ${UNAME_SYSTEM} UNAME_VERSION = ${UNAME_VERSION} EOF exit 1 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" # End: DOMALIGN-0.1.650/README0000664000175000017500000000000010231743376010654 00000000000000DOMALIGN-0.1.650/ChangeLog0000664000175000017500000000000010231743376011546 00000000000000DOMALIGN-0.1.650/COPYING0000664000175000017500000004311010231743376011040 00000000000000 GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) 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 this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) 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 Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. DOMALIGN-0.1.650/depcomp0000755000175000017500000005055212171070654011365 00000000000000#! /bin/sh # depcomp - compile a program generating dependencies as side-effects scriptversion=2012-03-27.16; # UTC # Copyright (C) 1999-2012 Free Software Foundation, Inc. # 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, 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, see . # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Alexandre Oliva . case $1 in '') echo "$0: No command. Try '$0 --help' for more information." 1>&2 exit 1; ;; -h | --h*) cat <<\EOF Usage: depcomp [--help] [--version] PROGRAM [ARGS] Run PROGRAMS ARGS to compile a file, generating dependencies as side-effects. Environment variables: depmode Dependency tracking mode. source Source file read by 'PROGRAMS ARGS'. object Object file output by 'PROGRAMS ARGS'. DEPDIR directory where to store dependencies. depfile Dependency file to output. tmpdepfile Temporary file to use when outputting dependencies. libtool Whether libtool is used (yes/no). Report bugs to . EOF exit $? ;; -v | --v*) echo "depcomp $scriptversion" exit $? ;; esac # A tabulation character. tab=' ' # A newline character. nl=' ' if test -z "$depmode" || test -z "$source" || test -z "$object"; then echo "depcomp: Variables source, object and depmode must be set" 1>&2 exit 1 fi # Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po. depfile=${depfile-`echo "$object" | sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`} tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} rm -f "$tmpdepfile" # Some modes work just like other modes, but use different flags. We # parameterize here, but still list the modes in the big case below, # to make depend.m4 easier to write. Note that we *cannot* use a case # here, because this file can only contain one case statement. if test "$depmode" = hp; then # HP compiler uses -M and no extra arg. gccflag=-M depmode=gcc fi if test "$depmode" = dashXmstdout; then # This is just like dashmstdout with a different argument. dashmflag=-xM depmode=dashmstdout fi cygpath_u="cygpath -u -f -" if test "$depmode" = msvcmsys; then # This is just like msvisualcpp but w/o cygpath translation. # Just convert the backslash-escaped backslashes to single forward # slashes to satisfy depend.m4 cygpath_u='sed s,\\\\,/,g' depmode=msvisualcpp fi if test "$depmode" = msvc7msys; then # This is just like msvc7 but w/o cygpath translation. # Just convert the backslash-escaped backslashes to single forward # slashes to satisfy depend.m4 cygpath_u='sed s,\\\\,/,g' depmode=msvc7 fi if test "$depmode" = xlc; then # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency informations. gccflag=-qmakedep=gcc,-MF depmode=gcc fi case "$depmode" in gcc3) ## gcc 3 implements dependency tracking that does exactly what ## we want. Yay! Note: for some reason libtool 1.4 doesn't like ## it if -MD -MP comes after the -MF stuff. Hmm. ## Unfortunately, FreeBSD c89 acceptance of flags depends upon ## the command line argument order; so add the flags where they ## appear in depend2.am. Note that the slowdown incurred here ## affects only configure: in makefiles, %FASTDEP% shortcuts this. for arg do case $arg in -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;; *) set fnord "$@" "$arg" ;; esac shift # fnord shift # $arg done "$@" stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi mv "$tmpdepfile" "$depfile" ;; gcc) ## There are various ways to get dependency output from gcc. Here's ## why we pick this rather obscure method: ## - Don't want to use -MD because we'd like the dependencies to end ## up in a subdir. Having to rename by hand is ugly. ## (We might end up doing this anyway to support other compilers.) ## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like ## -MM, not -M (despite what the docs say). ## - Using -M directly means running the compiler twice (even worse ## than renaming). if test -z "$gccflag"; then gccflag=-MD, fi "$@" -Wp,"$gccflag$tmpdepfile" stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" echo "$object : \\" > "$depfile" alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz ## The second -e expression handles DOS-style file names with drive letters. sed -e 's/^[^:]*: / /' \ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile" ## This next piece of magic avoids the "deleted header file" problem. ## The problem is that when a header file which appears in a .P file ## is deleted, the dependency causes make to die (because there is ## typically no way to rebuild the header). We avoid this by adding ## dummy dependencies for each header file. Too bad gcc doesn't do ## this for us directly. tr ' ' "$nl" < "$tmpdepfile" | ## Some versions of gcc put a space before the ':'. On the theory ## that the space means something, we add a space to the output as ## well. hp depmode also adds that space, but also prefixes the VPATH ## to the object. Take care to not repeat it in the output. ## Some versions of the HPUX 10.20 sed can't process this invocation ## correctly. Breaking it into two sed invocations is a workaround. sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \ | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; hp) # This case exists only to let depend.m4 do its work. It works by # looking at the text of this script. This case will never be run, # since it is checked for above. exit 1 ;; sgi) if test "$libtool" = yes; then "$@" "-Wp,-MDupdate,$tmpdepfile" else "$@" -MDupdate "$tmpdepfile" fi stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files echo "$object : \\" > "$depfile" # Clip off the initial element (the dependent). Don't try to be # clever and replace this with sed code, as IRIX sed won't handle # lines with more than a fixed number of characters (4096 in # IRIX 6.2 sed, 8192 in IRIX 6.5). 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"$@" || exit $? # Remove the call to Libtool. if test "$libtool" = yes; then while test "X$1" != 'X--mode=compile'; do shift done shift fi IFS=" " for arg do case "$arg" in -o) shift ;; $object) shift ;; "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") set fnord "$@" shift shift ;; *) set fnord "$@" "$arg" shift shift ;; esac done "$@" -E 2>/dev/null | sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::'"$tab"'\1 \\:p' >> "$depfile" echo "$tab" >> "$depfile" sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile" rm -f "$tmpdepfile" ;; msvcmsys) # This case exists only to let depend.m4 do its work. It works by # looking at the text of this script. This case will never be run, # since it is checked for above. exit 1 ;; none) exec "$@" ;; *) echo "Unknown depmode $depmode" 1>&2 exit 1 ;; esac exit 0 # Local Variables: # mode: shell-script # sh-indentation: 2 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-time-zone: "UTC" # time-stamp-end: "; # UTC" # End: DOMALIGN-0.1.650/m4/0002775000175000017500000000000012171070667010411 500000000000000DOMALIGN-0.1.650/m4/ltsugar.m40000644000175000017500000001042412171070647012247 00000000000000# ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*- # # Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc. # Written by Gary V. Vaughan, 2004 # # This file is free software; the Free Software Foundation gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # serial 6 ltsugar.m4 # This is to help aclocal find these macros, as it can't see m4_define. AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])]) # lt_join(SEP, ARG1, [ARG2...]) # ----------------------------- # Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their # associated separator. # Needed until we can rely on m4_join from Autoconf 2.62, since all earlier # versions in m4sugar had bugs. m4_define([lt_join], [m4_if([$#], [1], [], [$#], [2], [[$2]], [m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])]) m4_define([_lt_join], [m4_if([$#$2], [2], [], [m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])]) # lt_car(LIST) # lt_cdr(LIST) # ------------ # Manipulate m4 lists. # These macros are necessary as long as will still need to support # Autoconf-2.59 which quotes differently. m4_define([lt_car], [[$1]]) m4_define([lt_cdr], [m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])], [$#], 1, [], [m4_dquote(m4_shift($@))])]) m4_define([lt_unquote], $1) # lt_append(MACRO-NAME, STRING, [SEPARATOR]) # ------------------------------------------ # Redefine MACRO-NAME to hold its former content plus `SEPARATOR'`STRING'. # Note that neither SEPARATOR nor STRING are expanded; they are appended # to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked). # No SEPARATOR is output if MACRO-NAME was previously undefined (different # than defined and empty). # # This macro is needed until we can rely on Autoconf 2.62, since earlier # versions of m4sugar mistakenly expanded SEPARATOR but not STRING. m4_define([lt_append], [m4_define([$1], m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])]) # lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...]) # ---------------------------------------------------------- # Produce a SEP delimited list of all paired combinations of elements of # PREFIX-LIST with SUFFIX1 through SUFFIXn. Each element of the list # has the form PREFIXmINFIXSUFFIXn. # Needed until we can rely on m4_combine added in Autoconf 2.62. m4_define([lt_combine], [m4_if(m4_eval([$# > 3]), [1], [m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl [[m4_foreach([_Lt_prefix], [$2], [m4_foreach([_Lt_suffix], ]m4_dquote(m4_dquote(m4_shift(m4_shift(m4_shift($@)))))[, [_Lt_sep([$1])[]m4_defn([_Lt_prefix])[$3]m4_defn([_Lt_suffix])])])])]) # lt_if_append_uniq(MACRO-NAME, VARNAME, [SEPARATOR], [UNIQ], [NOT-UNIQ]) # ----------------------------------------------------------------------- # Iff MACRO-NAME does not yet contain VARNAME, then append it (delimited # by SEPARATOR if supplied) and expand UNIQ, else NOT-UNIQ. m4_define([lt_if_append_uniq], [m4_ifdef([$1], [m4_if(m4_index([$3]m4_defn([$1])[$3], [$3$2$3]), [-1], [lt_append([$1], [$2], [$3])$4], [$5])], [lt_append([$1], [$2], [$3])$4])]) # lt_dict_add(DICT, KEY, VALUE) # ----------------------------- m4_define([lt_dict_add], [m4_define([$1($2)], [$3])]) # lt_dict_add_subkey(DICT, KEY, SUBKEY, VALUE) # -------------------------------------------- m4_define([lt_dict_add_subkey], [m4_define([$1($2:$3)], [$4])]) # lt_dict_fetch(DICT, KEY, [SUBKEY]) # ---------------------------------- m4_define([lt_dict_fetch], [m4_ifval([$3], m4_ifdef([$1($2:$3)], [m4_defn([$1($2:$3)])]), m4_ifdef([$1($2)], [m4_defn([$1($2)])]))]) # lt_if_dict_fetch(DICT, KEY, [SUBKEY], VALUE, IF-TRUE, [IF-FALSE]) # ----------------------------------------------------------------- m4_define([lt_if_dict_fetch], [m4_if(lt_dict_fetch([$1], [$2], [$3]), [$4], [$5], [$6])]) # lt_dict_filter(DICT, [SUBKEY], VALUE, [SEPARATOR], KEY, [...]) # -------------------------------------------------------------- m4_define([lt_dict_filter], [m4_if([$5], [], [], [lt_join(m4_quote(m4_default([$4], [[, ]])), lt_unquote(m4_split(m4_normalize(m4_foreach(_Lt_key, lt_car([m4_shiftn(4, $@)]), [lt_if_dict_fetch([$1], _Lt_key, [$2], [$3], [_Lt_key ])])))))])[]dnl ]) DOMALIGN-0.1.650/m4/lf_x11.m40000664000175000017500000000547311546377050011675 00000000000000dnl Copyright (C) 1988 Eleftherios Gkioulekas dnl dnl This program is free software; you can redistribute it and/or modify dnl it under the terms of the GNU General Public License as published by dnl the Free Software Foundation; either version 2 of the License, or dnl (at your option) any later version. dnl dnl This program is distributed in the hope that it will be useful, dnl but WITHOUT ANY WARRANTY; without even the implied warranty of dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the dnl GNU General Public License for more details. dnl dnl You should have received a copy of the GNU General Public License dnl along with this program; if not, write to the Free Software dnl Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. dnl dnl As a special exception to the GNU General Public License, if you dnl distribute this file as part of a program that contains a configuration dnl script generated by Autoconf, you may include it under the same dnl distribution terms that you use for the rest of that program. #----------------------------------------------------------------------- # This macro searches for Xlib and when it finds it it adds the # appropriate flags to CFLAGS and export the link sequence to # the variable XLIB. # In your configure.in file add: # LF_PATH_XLIB # In your Makefile.am add # program_LDADD = .... $(XLIB) #------------------------------------------------------------------------ # # Just added EMBOSS into LF_PATH_XLIB so that on the systems where # LF_PATH_XLIB exists there are no duplication errors. AC_DEFUN([LF_EMBOSS_PATH_XLIB],[ CFLAGS="$CFLAGS $X_CFLAGS" case $host_os in irix*) XLIB="-lX11 $X_EXTRA_LIBS" ;; *) XLIB="$X_LIBS -lX11 $X_EXTRA_LIBS" ;; esac AC_SUBST([XLIB]) AC_CHECK_HEADER(X11/Xlib.h, [ AC_DEFINE([PLD_xwin], [1], [Define to 1 if X11 support is available]) ], [ echo "" echo "X11 graphics have been selected but no X11 header files" echo "have been found." echo "" echo "This error usually happens on Linux/MacOSX distributions" echo "where the optional X11 development files have not been installed." echo "On Linux RPM systems this package is usually called something" echo "like xorg-x11-proto-devel whereas on Debian/Ubuntu it may" echo "be called x-dev. On MacOSX installation DVDs the X11 files" echo "can usually be found as an explicitly named optional" echo "installation." echo "" echo "After installing the X11 development files you should do a" echo "'make clean' and perform the configure stage again." echo "" echo "Alternatively, to install EMBOSS without X11 support, you can add" echo "the --without-x switch to the configure command." echo "" exit $? ]) ]) DOMALIGN-0.1.650/m4/pngdriver.m40000664000175000017500000000641211430325236012564 00000000000000dnl @synopsis CHECK_PNGDRIVER() dnl dnl This macro searches for an installed png/gd/zlib library. If nothing dnl was specified when calling configure, it searches first in /usr/local dnl and then in /usr. If the --with-pngdriver=DIR is specified, it will try dnl to find it in DIR/include/zlib.h and DIR/lib/libz.a. If --without-pngdriver dnl is specified, the library is not searched at all. dnl dnl It defines the symbol PLD_png if the librarys are found. You should dnl use autoheader to include a definition for this symbol in a config.h dnl file. dnl dnl Sources files should then use something like dnl dnl #ifdef PLD_png dnl #include dnl #endif /* PLD_png */ dnl dnl @author Ian Longden dnl Modified: Alan Bleasby. Corrected library order dnl AC_DEFUN([CHECK_PNGDRIVER], # # Handle user hints # [AC_MSG_CHECKING([if png driver is wanted]) AC_ARG_WITH([pngdriver], [AS_HELP_STRING([--with-pngdriver=@<:@DIR@:>@], [root directory path of png/gd/zlib installation (defaults to /usr)])], [if test "$withval" != no ; then AC_MSG_RESULT([yes]) ALT_HOME="$withval" else AC_MSG_RESULT([no]) fi], [ AC_MSG_RESULT([yes]) ALT_HOME=/usr ]) # # Locate png/gd/zlib, if wanted # if test -d "${ALT_HOME}" then # # Keep a copy if it fails # ALT_LDFLAGS="$LDFLAGS" ALT_CPPFLAGS="$CPPFLAGS" # # Set # LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib" CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include" ICCHECK=0 case $host_os in solaris*) AC_CHECK_LIB(iconv, libiconv_close, ICCHECK=1, ICCHECK=0, -L${ALT_HOME}/lib -liconv) if test $ICCHECK = "1" ; then LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib -liconv" fi LDFLAGS="$LDFLAGS -R$ALT_HOME/lib" ;; esac # # Check for zlib in ALT_HOME # AC_CHECK_LIB(z, inflateEnd, CHECK=1, CHECK=0, -L${ALT_HOME}/lib -lz) # # # Check for png # if test $CHECK = "1" ; then AC_CHECK_LIB(png, png_destroy_read_struct, CHECK=1, CHECK=0 , -L${ALT_HOME}/lib -lz) fi # # Check for gd # if test $CHECK = "1"; then AC_CHECK_LIB(gd, gdImageCreateFromPng, CHECK=1, CHECK=0 , -L${ALT_HOME}/lib -lgd -lpng -lz -lm) if test $CHECK = "0"; then echo need to upgrade gd for png driver for plplot fi fi # # If everything found okay then proceed to include png driver in config. # if test $CHECK = "1" ; then LIBS="$LIBS -lgd -lpng -lz -lm" if test $ICCHECK = "1" ; then LIBS="$LIBS -liconv" fi case $host_os in solaris*) LDFLAGS="$LDFLAGS -R$ALT_HOME/lib" ;; esac AC_DEFINE([PLD_png], [1], [Define to 1 is PNG support is available]) AM_CONDITIONAL(AMPNG, true) echo PNG libraries found if test $ALT_HOME = "/usr" ; then LDFLAGS="$ALT_LDFLAGS" CPPFLAGS="$ALT_CPPFLAGS" fi else # # If not okay then reset FLAGS. # AM_CONDITIONAL(AMPNG, false) LDFLAGS="$ALT_LDFLAGS" CPPFLAGS="$ALT_CPPFLAGS" echo No png driver will be made due to librarys missing/old. fi # echo PNG STUFF FOLLOWS!!! # echo CHECK = $CHECK # echo LIBS = $LIBS # echo LDFLAGS = $LDFLAGS # echo CPPFLAGS = $CPPFLAGS else if test $withval != "no"; then echo "Directory $ALT_HOME does not exist" exit 0 fi fi ]) DOMALIGN-0.1.650/m4/postgresql.m40000664000175000017500000001334311732713445013000 00000000000000dnl -*- Autoconf -*- ##### http://autoconf-archive.cryp.to/ax_lib_postgresql.html # # SYNOPSIS # # AX_LIB_POSTGRESQL([MINIMUM-VERSION]) # # DESCRIPTION # # This macro provides tests of availability of PostgreSQL 'libpq' # library of particular version or newer. # # AX_LIB_POSTGRESQL macro takes only one argument which is optional. # If there is no required version passed, then macro does not run # version test. # # The --with-postgresql option takes one of three possible values: # # no - do not check for PostgreSQL client library # # yes - do check for PostgreSQL library in standard locations # (pg_config should be in the PATH) # # path - complete path to pg_config utility, use this option if # pg_config can't be found in the PATH # # This macro calls: # # AC_SUBST([POSTGRESQL_CFLAGS]) # AC_SUBST([POSTGRESQL_CPPFLAGS]) # AC_SUBST([POSTGRESQL_LDFLAGS]) # AC_SUBST([POSTGRESQL_VERSION]) # # And sets: # # HAVE_POSTGRESQL # # LAST MODIFICATION # # 2006-07-16 # 2010-05-14 MKS: Added POSTGRESQL_CPPFLAGS # 2011-06-21 AJB: Added workaround for Fedora pg_config oddity # 2011-08-01 MKS: Changed PG_CONFIG to POSTGRESQL_CONFIG # Made test constructs more portable # # COPYLEFT # # Copyright (c) 2006 Mateusz Loskot # # Copying and distribution of this file, with or without # modification, are permitted in any medium without royalty provided # the copyright notice and this notice are preserved. AC_DEFUN([AX_LIB_POSTGRESQL], [ POSTGRESQL_CFLAGS="" POSTGRESQL_CPPFLAGS="" POSTGRESQL_LDFLAGS="" POSTGRESQL_CONFIG="" POSTGRESQL_VERSION="" AC_ARG_WITH([postgresql], [AS_HELP_STRING([--with-postgresql@<:=@ARG@:>@], [use PostgreSQL library @<:@default=yes@:>@, optionally specify path to pg_config])], [ AS_IF([test "x${withval}" = "xno"], [want_postgresql="no"], [test "x${withval}" = "xyes"], [want_postgresql="yes"], [ want_postgresql="yes" POSTGRESQL_CONFIG="${withval}" ]) ], [want_postgresql="yes"]) dnl dnl Check PostgreSQL libraries (libpq) dnl AS_IF([test "x${want_postgresql}" = "xyes"], [ AS_IF([test -z "${POSTGRESQL_CONFIG}" -o test], [AC_PATH_PROG([POSTGRESQL_CONFIG], [pg_config], [no])]) AS_IF([test "x${POSTGRESQL_CONFIG}" != "xno"], [ AC_MSG_CHECKING([for PostgreSQL libraries]) POSTGRESQL_CFLAGS="-I`${POSTGRESQL_CONFIG} --includedir`" POSTGRESQL_CPPFLAGS="-I`${POSTGRESQL_CONFIG} --includedir`" POSTGRESQL_LDFLAGS="-L`${POSTGRESQL_CONFIG} --libdir` -lpq" POSTGRESQL_VERSION=`${POSTGRESQL_CONFIG} --version | sed -e 's#PostgreSQL ##'` dnl It isn't enough to just test for pg_config as Fedora dnl provides it in the postgresql RPM even though postgresql-devel may dnl not be installed EMBCPPFLAGS="${CPPFLAGS}" EMBLDFLAGS="${LDFLAGS}" CPPFLAGS="${POSTGRESQL_CPPFLAGS} ${EMBCPPFLAGS}" LDFLAGS="${POSTGRESQL_LDFLAGS} ${EMBLDFLAGS}" AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include #include "libpq-fe.h"]], [[PQconnectdb(NULL)]])], [havepostgresql="yes"], [havepostgresql="no"]) CPPFLAGS="${EMBCPPFLAGS}" LDFLAGS="${EMBLDFLAGS}" AS_IF([test "x${havepostgresql}" = "xyes"], [ AC_DEFINE([HAVE_POSTGRESQL], [1], [Define to 1 if PostgreSQL libraries are available.]) found_postgresql="yes" AC_MSG_RESULT([yes]) ], [ POSTGRESQL_CFLAGS="" POSTGRESQL_CPPFLAGS="" POSTGRESQL_LDFLAGS="" found_postgresql="no" AC_MSG_RESULT([no]) ]) ], [ found_postgresql="no" ]) ]) dnl dnl Check if required version of PostgreSQL is available dnl postgresql_version_req=ifelse([$1], [], [], [$1]) AS_IF([test "x${found_postgresql}" = "xyes" -a -n "${postgresql_version_req}"], [ AC_MSG_CHECKING([if PostgreSQL version is >= ${postgresql_version_req}]) dnl Decompose required version string of PostgreSQL dnl and calculate its number representation postgresql_version_req_major=`expr ${postgresql_version_req} : '\([[0-9]]*\)'` postgresql_version_req_minor=`expr ${postgresql_version_req} : '[[0-9]]*\.\([[0-9]]*\)'` postgresql_version_req_micro=`expr ${postgresql_version_req} : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'` AS_IF([test "x${postgresql_version_req_micro}" = "x"], [postgresql_version_req_micro="0"]) postgresql_version_req_number=`expr ${postgresql_version_req_major} \* 1000000 \ \+ ${postgresql_version_req_minor} \* 1000 \ \+ ${postgresql_version_req_micro}` dnl Decompose version string of installed PostgreSQL dnl and calculate its number representation postgresql_version_major=`expr ${POSTGRESQL_VERSION} : '\([[0-9]]*\)'` postgresql_version_minor=`expr ${POSTGRESQL_VERSION} : '[[0-9]]*\.\([[0-9]]*\)'` postgresql_version_micro=`expr ${POSTGRESQL_VERSION} : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'` AS_IF([test "x${postgresql_version_micro}" = "x"], [postgresql_version_micro="0"]) postgresql_version_number=`expr ${postgresql_version_major} \* 1000000 \ \+ ${postgresql_version_minor} \* 1000 \ \+ ${postgresql_version_micro}` postgresql_version_check=`expr ${postgresql_version_number} \>\= ${postgresql_version_req_number}` AS_IF([test "x${postgresql_version_check}" = "x1"], [AC_MSG_RESULT([yes])], [AC_MSG_RESULT([no])]) ]) AC_SUBST([POSTGRESQL_CFLAGS]) AC_SUBST([POSTGRESQL_CPPFLAGS]) AC_SUBST([POSTGRESQL_LDFLAGS]) AC_SUBST([POSTGRESQL_VERSION]) ]) DOMALIGN-0.1.650/m4/libtool.m40000644000175000017500000105743212171070647012245 00000000000000# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*- # # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, # 2006, 2007, 2008, 2009, 2010, 2011 Free Software # Foundation, Inc. # Written by Gordon Matzigkeit, 1996 # # This file is free software; 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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 GNU Libtool; see the file COPYING. If not, a copy # can be downloaded from http://www.gnu.org/licenses/gpl.html, or # obtained by writing to the Free Software Foundation, Inc., # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. ]) # serial 57 LT_INIT # LT_PREREQ(VERSION) # ------------------ # Complain and exit if this libtool version is less that VERSION. m4_defun([LT_PREREQ], [m4_if(m4_version_compare(m4_defn([LT_PACKAGE_VERSION]), [$1]), -1, [m4_default([$3], [m4_fatal([Libtool version $1 or higher is required], 63)])], [$2])]) # _LT_CHECK_BUILDDIR # ------------------ # Complain if the absolute build directory name contains unusual characters m4_defun([_LT_CHECK_BUILDDIR], [case `pwd` in *\ * | *\ *) AC_MSG_WARN([Libtool does not cope well with whitespace in `pwd`]) ;; esac ]) # LT_INIT([OPTIONS]) # ------------------ AC_DEFUN([LT_INIT], [AC_PREREQ([2.58])dnl We use AC_INCLUDES_DEFAULT AC_REQUIRE([AC_CONFIG_AUX_DIR_DEFAULT])dnl AC_BEFORE([$0], [LT_LANG])dnl AC_BEFORE([$0], [LT_OUTPUT])dnl AC_BEFORE([$0], [LTDL_INIT])dnl m4_require([_LT_CHECK_BUILDDIR])dnl dnl Autoconf doesn't catch unexpanded LT_ macros by default: m4_pattern_forbid([^_?LT_[A-Z_]+$])dnl m4_pattern_allow([^(_LT_EOF|LT_DLGLOBAL|LT_DLLAZY_OR_NOW|LT_MULTI_MODULE)$])dnl dnl aclocal doesn't pull ltoptions.m4, ltsugar.m4, or ltversion.m4 dnl unless we require an AC_DEFUNed macro: AC_REQUIRE([LTOPTIONS_VERSION])dnl AC_REQUIRE([LTSUGAR_VERSION])dnl AC_REQUIRE([LTVERSION_VERSION])dnl AC_REQUIRE([LTOBSOLETE_VERSION])dnl m4_require([_LT_PROG_LTMAIN])dnl _LT_SHELL_INIT([SHELL=${CONFIG_SHELL-/bin/sh}]) dnl Parse OPTIONS _LT_SET_OPTIONS([$0], [$1]) # This can be used to rebuild libtool when needed LIBTOOL_DEPS="$ltmain" # Always use our own libtool. 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It is not # nice to cause kernel panics so lets avoid the loop below. # First set a reasonable default. lt_cv_sys_max_cmd_len=16384 # if test -x /sbin/sysconfig; then case `/sbin/sysconfig -q proc exec_disable_arg_limit` in *1*) lt_cv_sys_max_cmd_len=-1 ;; esac fi ;; sco3.2v5*) lt_cv_sys_max_cmd_len=102400 ;; sysv5* | sco5v6* | sysv4.2uw2*) kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null` if test -n "$kargmax"; then lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[[ ]]//'` else lt_cv_sys_max_cmd_len=32768 fi ;; *) lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null` if test -n "$lt_cv_sys_max_cmd_len"; then lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` else # Make teststring a little bigger before we do anything with it. # a 1K string should be a reasonable start. for i in 1 2 3 4 5 6 7 8 ; do teststring=$teststring$teststring done SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}} # If test is not a shell built-in, we'll probably end up computing a # maximum length that is only half of the actual maximum length, but # we can't tell. while { test "X"`env echo "$teststring$teststring" 2>/dev/null` \ = "X$teststring$teststring"; } >/dev/null 2>&1 && test $i != 17 # 1/2 MB should be enough do i=`expr $i + 1` teststring=$teststring$teststring done # Only check the string length outside the loop. lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1` teststring= # Add a significant safety factor because C++ compilers can tack on # massive amounts of additional arguments before passing them to the # linker. It appears as though 1/2 is a usable value. lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2` fi ;; esac ]) if test -n $lt_cv_sys_max_cmd_len ; then AC_MSG_RESULT($lt_cv_sys_max_cmd_len) else AC_MSG_RESULT(none) fi max_cmd_len=$lt_cv_sys_max_cmd_len _LT_DECL([], [max_cmd_len], [0], [What is the maximum length of a command?]) ])# LT_CMD_MAX_LEN # Old name: AU_ALIAS([AC_LIBTOOL_SYS_MAX_CMD_LEN], [LT_CMD_MAX_LEN]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_LIBTOOL_SYS_MAX_CMD_LEN], []) # _LT_HEADER_DLFCN # ---------------- m4_defun([_LT_HEADER_DLFCN], [AC_CHECK_HEADERS([dlfcn.h], [], [], [AC_INCLUDES_DEFAULT])dnl ])# _LT_HEADER_DLFCN # _LT_TRY_DLOPEN_SELF (ACTION-IF-TRUE, ACTION-IF-TRUE-W-USCORE, # ACTION-IF-FALSE, ACTION-IF-CROSS-COMPILING) # ---------------------------------------------------------------- m4_defun([_LT_TRY_DLOPEN_SELF], [m4_require([_LT_HEADER_DLFCN])dnl if test "$cross_compiling" = yes; then : [$4] else lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2 lt_status=$lt_dlunknown cat > conftest.$ac_ext <<_LT_EOF [#line $LINENO "configure" #include "confdefs.h" #if HAVE_DLFCN_H #include #endif #include #ifdef RTLD_GLOBAL # define LT_DLGLOBAL RTLD_GLOBAL #else # ifdef DL_GLOBAL # define LT_DLGLOBAL DL_GLOBAL # else # define LT_DLGLOBAL 0 # endif #endif /* We may have to define LT_DLLAZY_OR_NOW in the command line if we find out it does not work in some platform. */ #ifndef LT_DLLAZY_OR_NOW # ifdef RTLD_LAZY # define LT_DLLAZY_OR_NOW RTLD_LAZY # else # ifdef DL_LAZY # define LT_DLLAZY_OR_NOW DL_LAZY # else # ifdef RTLD_NOW # define LT_DLLAZY_OR_NOW RTLD_NOW # else # ifdef DL_NOW # define LT_DLLAZY_OR_NOW DL_NOW # else # define LT_DLLAZY_OR_NOW 0 # endif # endif # endif # endif #endif /* When -fvisbility=hidden is used, assume the code has been annotated correspondingly for the symbols needed. */ #if defined(__GNUC__) && (((__GNUC__ == 3) && (__GNUC_MINOR__ >= 3)) || (__GNUC__ > 3)) int fnord () __attribute__((visibility("default"))); #endif int fnord () { return 42; } int main () { void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW); int status = $lt_dlunknown; if (self) { if (dlsym (self,"fnord")) status = $lt_dlno_uscore; else { if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore; else puts (dlerror ()); } /* dlclose (self); */ } else puts (dlerror ()); return status; }] _LT_EOF if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext} 2>/dev/null; then (./conftest; exit; ) >&AS_MESSAGE_LOG_FD 2>/dev/null lt_status=$? case x$lt_status in x$lt_dlno_uscore) $1 ;; x$lt_dlneed_uscore) $2 ;; x$lt_dlunknown|x*) $3 ;; esac else : # compilation failed $3 fi fi rm -fr conftest* ])# _LT_TRY_DLOPEN_SELF # LT_SYS_DLOPEN_SELF # ------------------ AC_DEFUN([LT_SYS_DLOPEN_SELF], [m4_require([_LT_HEADER_DLFCN])dnl if test "x$enable_dlopen" != xyes; then enable_dlopen=unknown enable_dlopen_self=unknown enable_dlopen_self_static=unknown else lt_cv_dlopen=no lt_cv_dlopen_libs= case $host_os in beos*) lt_cv_dlopen="load_add_on" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ;; mingw* | pw32* | cegcc*) lt_cv_dlopen="LoadLibrary" lt_cv_dlopen_libs= ;; cygwin*) lt_cv_dlopen="dlopen" lt_cv_dlopen_libs= ;; darwin*) # if libdl is installed we need to link against it AC_CHECK_LIB([dl], [dlopen], [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],[ lt_cv_dlopen="dyld" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ]) ;; *) AC_CHECK_FUNC([shl_load], [lt_cv_dlopen="shl_load"], [AC_CHECK_LIB([dld], [shl_load], [lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld"], [AC_CHECK_FUNC([dlopen], [lt_cv_dlopen="dlopen"], [AC_CHECK_LIB([dl], [dlopen], [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"], [AC_CHECK_LIB([svld], [dlopen], [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"], [AC_CHECK_LIB([dld], [dld_link], [lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld"]) ]) ]) ]) ]) ]) ;; esac if test "x$lt_cv_dlopen" != xno; then enable_dlopen=yes else enable_dlopen=no fi case $lt_cv_dlopen in dlopen) save_CPPFLAGS="$CPPFLAGS" test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H" save_LDFLAGS="$LDFLAGS" wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\" save_LIBS="$LIBS" LIBS="$lt_cv_dlopen_libs $LIBS" AC_CACHE_CHECK([whether a program can dlopen itself], lt_cv_dlopen_self, [dnl _LT_TRY_DLOPEN_SELF( lt_cv_dlopen_self=yes, lt_cv_dlopen_self=yes, lt_cv_dlopen_self=no, lt_cv_dlopen_self=cross) ]) if test "x$lt_cv_dlopen_self" = xyes; then wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\" AC_CACHE_CHECK([whether a statically linked program can dlopen itself], lt_cv_dlopen_self_static, [dnl _LT_TRY_DLOPEN_SELF( lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=no, lt_cv_dlopen_self_static=cross) ]) fi CPPFLAGS="$save_CPPFLAGS" LDFLAGS="$save_LDFLAGS" LIBS="$save_LIBS" ;; esac case $lt_cv_dlopen_self in yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;; *) enable_dlopen_self=unknown ;; esac case $lt_cv_dlopen_self_static in yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;; *) enable_dlopen_self_static=unknown ;; esac fi _LT_DECL([dlopen_support], [enable_dlopen], [0], [Whether dlopen is supported]) _LT_DECL([dlopen_self], [enable_dlopen_self], [0], [Whether dlopen of programs is supported]) _LT_DECL([dlopen_self_static], [enable_dlopen_self_static], [0], [Whether dlopen of statically linked programs is supported]) ])# LT_SYS_DLOPEN_SELF # Old name: AU_ALIAS([AC_LIBTOOL_DLOPEN_SELF], [LT_SYS_DLOPEN_SELF]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_LIBTOOL_DLOPEN_SELF], []) # _LT_COMPILER_C_O([TAGNAME]) # --------------------------- # Check to see if options -c and -o are simultaneously supported by compiler. # This macro does not hard code the compiler like AC_PROG_CC_C_O. m4_defun([_LT_COMPILER_C_O], [m4_require([_LT_DECL_SED])dnl m4_require([_LT_FILEUTILS_DEFAULTS])dnl m4_require([_LT_TAG_COMPILER])dnl AC_CACHE_CHECK([if $compiler supports -c -o file.$ac_objext], [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)], [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=no $RM -r conftest 2>/dev/null mkdir conftest cd conftest mkdir out echo "$lt_simple_compile_test_code" > conftest.$ac_ext lt_compiler_flag="-o out/conftest2.$ac_objext" # Insert the option either (1) after the last *FLAGS variable, or # (2) before a word containing "conftest.", or (3) at the end. # Note that $ac_compile itself does not contain backslashes and begins # with a dollar sign (not a hyphen), so the echo should work correctly. lt_compile=`echo "$ac_compile" | $SED \ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; 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then # do not overwrite the value of need_locks provided by the user AC_MSG_CHECKING([if we can lock with hard links]) hard_links=yes $RM conftest* ln conftest.a conftest.b 2>/dev/null && hard_links=no touch conftest.a ln conftest.a conftest.b 2>&5 || hard_links=no ln conftest.a conftest.b 2>/dev/null && hard_links=no AC_MSG_RESULT([$hard_links]) if test "$hard_links" = no; then AC_MSG_WARN([`$CC' does not support `-c -o', so `make -j' may be unsafe]) need_locks=warn fi else need_locks=no fi _LT_DECL([], [need_locks], [1], [Must we lock files when doing compilation?]) ])# _LT_COMPILER_FILE_LOCKS # _LT_CHECK_OBJDIR # ---------------- m4_defun([_LT_CHECK_OBJDIR], [AC_CACHE_CHECK([for objdir], [lt_cv_objdir], [rm -f .libs 2>/dev/null mkdir .libs 2>/dev/null if test -d .libs; then lt_cv_objdir=.libs else # MS-DOS does not allow filenames that begin with a dot. lt_cv_objdir=_libs fi rmdir .libs 2>/dev/null]) objdir=$lt_cv_objdir _LT_DECL([], [objdir], [0], [The name of the directory that contains temporary libtool files])dnl m4_pattern_allow([LT_OBJDIR])dnl AC_DEFINE_UNQUOTED(LT_OBJDIR, "$lt_cv_objdir/", [Define to the sub-directory in which libtool stores uninstalled libraries.]) ])# _LT_CHECK_OBJDIR # _LT_LINKER_HARDCODE_LIBPATH([TAGNAME]) # -------------------------------------- # Check hardcoding attributes. m4_defun([_LT_LINKER_HARDCODE_LIBPATH], [AC_MSG_CHECKING([how to hardcode library paths into programs]) _LT_TAGVAR(hardcode_action, $1)= if test -n "$_LT_TAGVAR(hardcode_libdir_flag_spec, $1)" || test -n "$_LT_TAGVAR(runpath_var, $1)" || test "X$_LT_TAGVAR(hardcode_automatic, $1)" = "Xyes" ; then # We can hardcode non-existent directories. if test "$_LT_TAGVAR(hardcode_direct, $1)" != no && # If the only mechanism to avoid hardcoding is shlibpath_var, we # have to relink, otherwise we might link with an installed library # when we should be linking with a yet-to-be-installed one ## test "$_LT_TAGVAR(hardcode_shlibpath_var, $1)" != no && test "$_LT_TAGVAR(hardcode_minus_L, $1)" != no; then # Linking always hardcodes the temporary library directory. _LT_TAGVAR(hardcode_action, $1)=relink else # We can link without hardcoding, and we can hardcode nonexisting dirs. _LT_TAGVAR(hardcode_action, $1)=immediate fi else # We cannot hardcode anything, or else we can only hardcode existing # directories. _LT_TAGVAR(hardcode_action, $1)=unsupported fi AC_MSG_RESULT([$_LT_TAGVAR(hardcode_action, $1)]) if test "$_LT_TAGVAR(hardcode_action, $1)" = relink || test "$_LT_TAGVAR(inherit_rpath, $1)" = yes; then # Fast installation is not supported enable_fast_install=no elif test "$shlibpath_overrides_runpath" = yes || test "$enable_shared" = no; then # Fast installation is not necessary enable_fast_install=needless fi _LT_TAGDECL([], [hardcode_action], [0], [How to hardcode a shared library path into an executable]) ])# _LT_LINKER_HARDCODE_LIBPATH # _LT_CMD_STRIPLIB # ---------------- m4_defun([_LT_CMD_STRIPLIB], [m4_require([_LT_DECL_EGREP]) striplib= old_striplib= AC_MSG_CHECKING([whether stripping libraries is possible]) if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then test -z "$old_striplib" && old_striplib="$STRIP --strip-debug" test -z "$striplib" && striplib="$STRIP --strip-unneeded" AC_MSG_RESULT([yes]) else # FIXME - insert some real tests, host_os isn't really good enough case $host_os in darwin*) if test -n "$STRIP" ; then striplib="$STRIP -x" old_striplib="$STRIP -S" AC_MSG_RESULT([yes]) else AC_MSG_RESULT([no]) fi ;; *) AC_MSG_RESULT([no]) ;; esac fi _LT_DECL([], [old_striplib], [1], [Commands to strip libraries]) _LT_DECL([], [striplib], [1]) ])# _LT_CMD_STRIPLIB # _LT_SYS_DYNAMIC_LINKER([TAG]) # ----------------------------- # PORTME Fill in your ld.so characteristics m4_defun([_LT_SYS_DYNAMIC_LINKER], [AC_REQUIRE([AC_CANONICAL_HOST])dnl m4_require([_LT_DECL_EGREP])dnl m4_require([_LT_FILEUTILS_DEFAULTS])dnl m4_require([_LT_DECL_OBJDUMP])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_CHECK_SHELL_FEATURES])dnl AC_MSG_CHECKING([dynamic linker characteristics]) m4_if([$1], [], [ if test "$GCC" = yes; 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esac ;; gnu*) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; haiku*) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no dynamic_linker="$host_os runtime_loader" library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LIBRARY_PATH shlibpath_overrides_runpath=yes sys_lib_dlsearch_path_spec='/boot/home/config/lib /boot/common/lib /boot/system/lib' hardcode_into_libs=yes ;; hpux9* | hpux10* | hpux11*) # Give a soname corresponding to the major version so that dld.sl refuses to # link against other versions. version_type=sunos need_lib_prefix=no need_version=no case $host_cpu in ia64*) shrext_cmds='.so' hardcode_into_libs=yes dynamic_linker="$host_os dld.so" shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' if test "X$HPUX_IA64_MODE" = X32; then sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" else sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" fi sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; hppa*64*) shrext_cmds='.sl' hardcode_into_libs=yes dynamic_linker="$host_os dld.sl" shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64" sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; *) shrext_cmds='.sl' dynamic_linker="$host_os dld.sl" shlibpath_var=SHLIB_PATH shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' ;; esac # HP-UX runs *really* slowly unless shared libraries are mode 555, ... postinstall_cmds='chmod 555 $lib' # or fails outright, so override atomically: install_override_mode=555 ;; interix[[3-9]]*) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; irix5* | irix6* | nonstopux*) case $host_os in nonstopux*) version_type=nonstopux ;; *) if test "$lt_cv_prog_gnu_ld" = yes; then version_type=linux # correct to gnu/linux during the next big refactor else version_type=irix fi ;; esac need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}' case $host_os in irix5* | nonstopux*) libsuff= shlibsuff= ;; *) case $LD in # libtool.m4 will add one of these switches to LD *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") libsuff= shlibsuff= libmagic=32-bit;; *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") libsuff=32 shlibsuff=N32 libmagic=N32;; *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") libsuff=64 shlibsuff=64 libmagic=64-bit;; *) libsuff= shlibsuff= libmagic=never-match;; esac ;; esac shlibpath_var=LD_LIBRARY${shlibsuff}_PATH shlibpath_overrides_runpath=no sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" hardcode_into_libs=yes ;; # No shared lib support for Linux oldld, aout, or coff. linux*oldld* | linux*aout* | linux*coff*) dynamic_linker=no ;; # This must be glibc/ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no # Some binutils ld are patched to set DT_RUNPATH AC_CACHE_VAL([lt_cv_shlibpath_overrides_runpath], [lt_cv_shlibpath_overrides_runpath=no save_LDFLAGS=$LDFLAGS save_libdir=$libdir eval "libdir=/foo; wl=\"$_LT_TAGVAR(lt_prog_compiler_wl, $1)\"; \ LDFLAGS=\"\$LDFLAGS $_LT_TAGVAR(hardcode_libdir_flag_spec, $1)\"" AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])], [AS_IF([ ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null], [lt_cv_shlibpath_overrides_runpath=yes])]) LDFLAGS=$save_LDFLAGS libdir=$save_libdir ]) shlibpath_overrides_runpath=$lt_cv_shlibpath_overrides_runpath # This implies no fast_install, which is unacceptable. # Some rework will be needed to allow for fast_install # before this can be enabled. hardcode_into_libs=yes # Add ABI-specific directories to the system library path. sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /lib /usr/lib" # Append ld.so.conf contents to the search path if test -f /etc/ld.so.conf; then lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;s/"//g;/^$/d' | tr '\n' ' '` sys_lib_dlsearch_path_spec="$sys_lib_dlsearch_path_spec $lt_ld_extra" fi # We used to test for /lib/ld.so.1 and disable shared libraries on # powerpc, because MkLinux only supported shared libraries with the # GNU dynamic linker. Since this was broken with cross compilers, # most powerpc-linux boxes support dynamic linking these days and # people can always --disable-shared, the test was removed, and we # assume the GNU/Linux dynamic linker is in use. dynamic_linker='GNU/Linux ld.so' ;; netbsd*) version_type=sunos need_lib_prefix=no need_version=no if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' dynamic_linker='NetBSD (a.out) ld.so' else library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' dynamic_linker='NetBSD ld.elf_so' fi shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes ;; newsos6) version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes ;; *nto* | *qnx*) version_type=qnx need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes dynamic_linker='ldqnx.so' ;; openbsd*) version_type=sunos sys_lib_dlsearch_path_spec="/usr/lib" need_lib_prefix=no # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. case $host_os in openbsd3.3 | openbsd3.3.*) need_version=yes ;; *) need_version=no ;; esac library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' shlibpath_var=LD_LIBRARY_PATH if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then case $host_os in openbsd2.[[89]] | openbsd2.[[89]].*) shlibpath_overrides_runpath=no ;; *) shlibpath_overrides_runpath=yes ;; esac else shlibpath_overrides_runpath=yes fi ;; os2*) libname_spec='$name' shrext_cmds=".dll" need_lib_prefix=no library_names_spec='$libname${shared_ext} $libname.a' dynamic_linker='OS/2 ld.exe' shlibpath_var=LIBPATH ;; osf3* | osf4* | osf5*) version_type=osf need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" ;; rdos*) dynamic_linker=no ;; solaris*) version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes # ldd complains unless libraries are executable postinstall_cmds='chmod +x $lib' ;; sunos4*) version_type=sunos library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes if test "$with_gnu_ld" = yes; then need_lib_prefix=no fi need_version=yes ;; sysv4 | sysv4.3*) version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH case $host_vendor in sni) shlibpath_overrides_runpath=no need_lib_prefix=no runpath_var=LD_RUN_PATH ;; siemens) need_lib_prefix=no ;; motorola) need_lib_prefix=no need_version=no shlibpath_overrides_runpath=no sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib' ;; esac ;; sysv4*MP*) if test -d /usr/nec ;then version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}' soname_spec='$libname${shared_ext}.$major' shlibpath_var=LD_LIBRARY_PATH fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) version_type=freebsd-elf need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes if test "$with_gnu_ld" = yes; then sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' else sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' case $host_os in sco3.2v5*) sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" ;; esac fi sys_lib_dlsearch_path_spec='/usr/lib' ;; tpf*) # TPF is a cross-target only. Preferred cross-host = GNU/Linux. version_type=linux # correct to gnu/linux during the next big refactor need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; uts4*) version_type=linux # correct to gnu/linux during the next big refactor library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH ;; *) dynamic_linker=no ;; esac AC_MSG_RESULT([$dynamic_linker]) test "$dynamic_linker" = no && can_build_shared=no variables_saved_for_relink="PATH $shlibpath_var $runpath_var" if test "$GCC" = yes; then variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" fi if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec" fi if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec" fi _LT_DECL([], [variables_saved_for_relink], [1], [Variables whose values should be saved in libtool wrapper scripts and restored at link time]) _LT_DECL([], [need_lib_prefix], [0], [Do we need the "lib" prefix for modules?]) _LT_DECL([], [need_version], [0], [Do we need a version for libraries?]) _LT_DECL([], [version_type], [0], [Library versioning type]) _LT_DECL([], [runpath_var], [0], [Shared library runtime path variable]) _LT_DECL([], [shlibpath_var], [0],[Shared library path variable]) _LT_DECL([], [shlibpath_overrides_runpath], [0], [Is shlibpath searched before the hard-coded library search path?]) _LT_DECL([], [libname_spec], [1], [Format of library name prefix]) _LT_DECL([], [library_names_spec], [1], [[List of archive names. First name is the real one, the rest are links. The last name is the one that the linker finds with -lNAME]]) _LT_DECL([], [soname_spec], [1], [[The coded name of the library, if different from the real name]]) _LT_DECL([], [install_override_mode], [1], [Permission mode override for installation of shared libraries]) _LT_DECL([], [postinstall_cmds], [2], [Command to use after installation of a shared archive]) _LT_DECL([], [postuninstall_cmds], [2], [Command to use after uninstallation of a shared archive]) _LT_DECL([], [finish_cmds], [2], [Commands used to finish a libtool library installation in a directory]) _LT_DECL([], [finish_eval], [1], [[As "finish_cmds", except a single script fragment to be evaled but not shown]]) _LT_DECL([], [hardcode_into_libs], [0], [Whether we should hardcode library paths into libraries]) _LT_DECL([], [sys_lib_search_path_spec], [2], [Compile-time system search path for libraries]) _LT_DECL([], [sys_lib_dlsearch_path_spec], [2], [Run-time system search path for libraries]) ])# _LT_SYS_DYNAMIC_LINKER # _LT_PATH_TOOL_PREFIX(TOOL) # -------------------------- # find a file program which can recognize shared library AC_DEFUN([_LT_PATH_TOOL_PREFIX], [m4_require([_LT_DECL_EGREP])dnl AC_MSG_CHECKING([for $1]) AC_CACHE_VAL(lt_cv_path_MAGIC_CMD, [case $MAGIC_CMD in [[\\/*] | ?:[\\/]*]) lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path. ;; *) lt_save_MAGIC_CMD="$MAGIC_CMD" lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR dnl $ac_dummy forces splitting on constant user-supplied paths. dnl POSIX.2 word splitting is done only on the output of word expansions, dnl not every word. 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Nevertheless, you *** may want to report the problem to your system manager and/or to *** bug-libtool@gnu.org _LT_EOF fi ;; esac fi break fi done IFS="$lt_save_ifs" MAGIC_CMD="$lt_save_MAGIC_CMD" ;; esac]) MAGIC_CMD="$lt_cv_path_MAGIC_CMD" if test -n "$MAGIC_CMD"; then AC_MSG_RESULT($MAGIC_CMD) else AC_MSG_RESULT(no) fi _LT_DECL([], [MAGIC_CMD], [0], [Used to examine libraries when file_magic_cmd begins with "file"])dnl ])# _LT_PATH_TOOL_PREFIX # Old name: AU_ALIAS([AC_PATH_TOOL_PREFIX], [_LT_PATH_TOOL_PREFIX]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_PATH_TOOL_PREFIX], []) # _LT_PATH_MAGIC # -------------- # find a file program which can recognize a shared library m4_defun([_LT_PATH_MAGIC], [_LT_PATH_TOOL_PREFIX(${ac_tool_prefix}file, /usr/bin$PATH_SEPARATOR$PATH) if test -z "$lt_cv_path_MAGIC_CMD"; then if test -n "$ac_tool_prefix"; then _LT_PATH_TOOL_PREFIX(file, /usr/bin$PATH_SEPARATOR$PATH) else MAGIC_CMD=: fi fi ])# _LT_PATH_MAGIC # LT_PATH_LD # ---------- # find the pathname to the GNU or non-GNU linker AC_DEFUN([LT_PATH_LD], [AC_REQUIRE([AC_PROG_CC])dnl AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_CANONICAL_BUILD])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_DECL_EGREP])dnl m4_require([_LT_PROG_ECHO_BACKSLASH])dnl AC_ARG_WITH([gnu-ld], [AS_HELP_STRING([--with-gnu-ld], [assume the C compiler uses GNU ld @<:@default=no@:>@])], [test "$withval" = no || with_gnu_ld=yes], [with_gnu_ld=no])dnl ac_prog=ld if test "$GCC" = yes; then # Check if gcc -print-prog-name=ld gives a path. 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hppa*64*) [lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF[ -][0-9][0-9])(-bit)?( [LM]SB)? shared object( file)?[, -]* PA-RISC [0-9]\.[0-9]'] lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|PA-RISC[[0-9]]\.[[0-9]]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[[3-9]]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be glibc/ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) lt_cv_deplibs_check_method=pass_all ;; netbsd*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|_pic\.a)$' fi ;; 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ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac ]) file_magic_glob= want_nocaseglob=no if test "$build" = "$host"; then case $host_os in mingw* | pw32*) if ( shopt | grep nocaseglob ) >/dev/null 2>&1; then want_nocaseglob=yes else file_magic_glob=`echo aAbBcCdDeEfFgGhHiIjJkKlLmMnNoOpPqQrRsStTuUvVwWxXyYzZ | $SED -e "s/\(..\)/s\/[[\1]]\/[[\1]]\/g;/g"` fi ;; esac fi file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown _LT_DECL([], [deplibs_check_method], [1], [Method to check whether dependent libraries are shared objects]) _LT_DECL([], [file_magic_cmd], [1], [Command to use when deplibs_check_method = "file_magic"]) _LT_DECL([], [file_magic_glob], [1], [How to find potential files when deplibs_check_method = "file_magic"]) _LT_DECL([], [want_nocaseglob], [1], [Find potential files using nocaseglob when deplibs_check_method = "file_magic"]) ])# _LT_CHECK_MAGIC_METHOD # LT_PATH_NM # ---------- # find the pathname to a BSD- or MS-compatible name lister AC_DEFUN([LT_PATH_NM], [AC_REQUIRE([AC_PROG_CC])dnl AC_CACHE_CHECK([for BSD- or MS-compatible name lister (nm)], lt_cv_path_NM, [if test -n "$NM"; then # Let the user override the test. lt_cv_path_NM="$NM" else lt_nm_to_check="${ac_tool_prefix}nm" if test -n "$ac_tool_prefix" && test "$build" = "$host"; then lt_nm_to_check="$lt_nm_to_check nm" fi for lt_tmp_nm in $lt_nm_to_check; do lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. tmp_nm="$ac_dir/$lt_tmp_nm" if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then # Check to see if the nm accepts a BSD-compat flag. # Adding the `sed 1q' prevents false positives on HP-UX, which says: # nm: unknown option "B" ignored # Tru64's nm complains that /dev/null is an invalid object file case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in */dev/null* | *'Invalid file or object type'*) lt_cv_path_NM="$tmp_nm -B" break ;; *) case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in */dev/null*) lt_cv_path_NM="$tmp_nm -p" break ;; *) lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but continue # so that we can try to find one that supports BSD flags ;; esac ;; esac fi done IFS="$lt_save_ifs" done : ${lt_cv_path_NM=no} fi]) if test "$lt_cv_path_NM" != "no"; then NM="$lt_cv_path_NM" else # Didn't find any BSD compatible name lister, look for dumpbin. if test -n "$DUMPBIN"; then : # Let the user override the test. else AC_CHECK_TOOLS(DUMPBIN, [dumpbin "link -dump"], :) case `$DUMPBIN -symbols /dev/null 2>&1 | sed '1q'` in *COFF*) DUMPBIN="$DUMPBIN -symbols" ;; *) DUMPBIN=: ;; esac fi AC_SUBST([DUMPBIN]) if test "$DUMPBIN" != ":"; then NM="$DUMPBIN" fi fi test -z "$NM" && NM=nm AC_SUBST([NM]) _LT_DECL([], [NM], [1], [A BSD- or MS-compatible name lister])dnl AC_CACHE_CHECK([the name lister ($NM) interface], [lt_cv_nm_interface], [lt_cv_nm_interface="BSD nm" echo "int some_variable = 0;" > conftest.$ac_ext (eval echo "\"\$as_me:$LINENO: $ac_compile\"" >&AS_MESSAGE_LOG_FD) (eval "$ac_compile" 2>conftest.err) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:$LINENO: $NM \\\"conftest.$ac_objext\\\"\"" >&AS_MESSAGE_LOG_FD) (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:$LINENO: output\"" >&AS_MESSAGE_LOG_FD) cat conftest.out >&AS_MESSAGE_LOG_FD if $GREP 'External.*some_variable' conftest.out > /dev/null; then lt_cv_nm_interface="MS dumpbin" fi rm -f conftest*]) ])# LT_PATH_NM # Old names: AU_ALIAS([AM_PROG_NM], [LT_PATH_NM]) AU_ALIAS([AC_PROG_NM], [LT_PATH_NM]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AM_PROG_NM], []) dnl AC_DEFUN([AC_PROG_NM], []) # _LT_CHECK_SHAREDLIB_FROM_LINKLIB # -------------------------------- # how to determine the name of the shared library # associated with a specific link library. # -- PORTME fill in with the dynamic library characteristics m4_defun([_LT_CHECK_SHAREDLIB_FROM_LINKLIB], [m4_require([_LT_DECL_EGREP]) m4_require([_LT_DECL_OBJDUMP]) m4_require([_LT_DECL_DLLTOOL]) AC_CACHE_CHECK([how to associate runtime and link libraries], lt_cv_sharedlib_from_linklib_cmd, [lt_cv_sharedlib_from_linklib_cmd='unknown' case $host_os in cygwin* | mingw* | pw32* | cegcc*) # two different shell functions defined in ltmain.sh # decide which to use based on capabilities of $DLLTOOL case `$DLLTOOL --help 2>&1` in *--identify-strict*) lt_cv_sharedlib_from_linklib_cmd=func_cygming_dll_for_implib ;; *) lt_cv_sharedlib_from_linklib_cmd=func_cygming_dll_for_implib_fallback ;; esac ;; *) # fallback: assume linklib IS sharedlib lt_cv_sharedlib_from_linklib_cmd="$ECHO" ;; esac ]) sharedlib_from_linklib_cmd=$lt_cv_sharedlib_from_linklib_cmd test -z "$sharedlib_from_linklib_cmd" && sharedlib_from_linklib_cmd=$ECHO _LT_DECL([], [sharedlib_from_linklib_cmd], [1], [Command to associate shared and link libraries]) ])# _LT_CHECK_SHAREDLIB_FROM_LINKLIB # _LT_PATH_MANIFEST_TOOL # ---------------------- # locate the manifest tool m4_defun([_LT_PATH_MANIFEST_TOOL], [AC_CHECK_TOOL(MANIFEST_TOOL, mt, :) test -z "$MANIFEST_TOOL" && MANIFEST_TOOL=mt AC_CACHE_CHECK([if $MANIFEST_TOOL is a manifest tool], [lt_cv_path_mainfest_tool], [lt_cv_path_mainfest_tool=no echo "$as_me:$LINENO: $MANIFEST_TOOL '-?'" >&AS_MESSAGE_LOG_FD $MANIFEST_TOOL '-?' 2>conftest.err > conftest.out cat conftest.err >&AS_MESSAGE_LOG_FD if $GREP 'Manifest Tool' conftest.out > /dev/null; then lt_cv_path_mainfest_tool=yes fi rm -f conftest*]) if test "x$lt_cv_path_mainfest_tool" != xyes; then MANIFEST_TOOL=: fi _LT_DECL([], [MANIFEST_TOOL], [1], [Manifest tool])dnl ])# _LT_PATH_MANIFEST_TOOL # LT_LIB_M # -------- # check for math library AC_DEFUN([LT_LIB_M], [AC_REQUIRE([AC_CANONICAL_HOST])dnl LIBM= case $host in *-*-beos* | *-*-cegcc* | *-*-cygwin* | *-*-haiku* | *-*-pw32* | *-*-darwin*) # These system don't have libm, or don't need it ;; *-ncr-sysv4.3*) AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw") AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm") ;; *) AC_CHECK_LIB(m, cos, LIBM="-lm") ;; esac AC_SUBST([LIBM]) ])# LT_LIB_M # Old name: AU_ALIAS([AC_CHECK_LIBM], [LT_LIB_M]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_CHECK_LIBM], []) # _LT_COMPILER_NO_RTTI([TAGNAME]) # ------------------------------- m4_defun([_LT_COMPILER_NO_RTTI], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)= if test "$GCC" = yes; then case $cc_basename in nvcc*) _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -Xcompiler -fno-builtin' ;; *) _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin' ;; esac _LT_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions], lt_cv_prog_compiler_rtti_exceptions, [-fno-rtti -fno-exceptions], [], [_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"]) fi _LT_TAGDECL([no_builtin_flag], [lt_prog_compiler_no_builtin_flag], [1], [Compiler flag to turn off builtin functions]) ])# _LT_COMPILER_NO_RTTI # _LT_CMD_GLOBAL_SYMBOLS # ---------------------- m4_defun([_LT_CMD_GLOBAL_SYMBOLS], [AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_PROG_CC])dnl AC_REQUIRE([AC_PROG_AWK])dnl AC_REQUIRE([LT_PATH_NM])dnl AC_REQUIRE([LT_PATH_LD])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_DECL_EGREP])dnl m4_require([_LT_TAG_COMPILER])dnl # Check for command to grab the raw symbol name followed by C symbol from nm. AC_MSG_CHECKING([command to parse $NM output from $compiler object]) AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe], [ # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[[BCDEGRST]]' # Regexp to match symbols that can be accessed directly from C. sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[[BCDT]]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[[ABCDGISTW]]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[[ABCDEGRST]]' fi ;; irix* | nonstopux*) symcode='[[BCDEGRST]]' ;; osf*) symcode='[[BCDEGQRST]]' ;; solaris*) symcode='[[BDRT]]' ;; sco3.2v5*) symcode='[[DT]]' ;; sysv4.2uw2*) symcode='[[DT]]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[[ABDT]]' ;; sysv4) symcode='[[DFNSTU]]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[[ABCDGIRSTW]]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\)[[ ]]*$/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([[^ ]]*\)[[ ]]*$/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \(lib[[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK ['"\ " {last_section=section; section=\$ 3};"\ " /^COFF SYMBOL TABLE/{for(i in hide) delete hide[i]};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx]" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ ]]\($symcode$symcode*\)[[ ]][[ ]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi lt_cv_sys_global_symbol_pipe="$lt_cv_sys_global_symbol_pipe | sed '/ __gnu_lto/d'" # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if AC_TRY_EVAL(ac_compile); then # Now try to grab the symbols. nlist=conftest.nm if AC_TRY_EVAL(NM conftest.$ac_objext \| "$lt_cv_sys_global_symbol_pipe" \> $nlist) && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext /* Keep this code in sync between libtool.m4, ltmain, lt_system.h, and tests. */ #if defined(_WIN32) || defined(__CYGWIN__) || defined(_WIN32_WCE) /* DATA imports from DLLs on WIN32 con't be const, because runtime relocations are performed -- see ld's documentation on pseudo-relocs. */ # define LT@&t@_DLSYM_CONST #elif defined(__osf__) /* This system does not cope well with relocations in const data. */ # define LT@&t@_DLSYM_CONST #else # define LT@&t@_DLSYM_CONST const #endif #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ LT@&t@_DLSYM_CONST struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[[]] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_globsym_save_LIBS=$LIBS lt_globsym_save_CFLAGS=$CFLAGS LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)" if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS=$lt_globsym_save_LIBS CFLAGS=$lt_globsym_save_CFLAGS else echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD fi else echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done ]) if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then AC_MSG_RESULT(failed) else AC_MSG_RESULT(ok) fi # Response file support. if test "$lt_cv_nm_interface" = "MS dumpbin"; then nm_file_list_spec='@' elif $NM --help 2>/dev/null | grep '[[@]]FILE' >/dev/null; then nm_file_list_spec='@' fi _LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1], [Take the output of nm and produce a listing of raw symbols and C names]) _LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1], [Transform the output of nm in a proper C declaration]) _LT_DECL([global_symbol_to_c_name_address], [lt_cv_sys_global_symbol_to_c_name_address], [1], [Transform the output of nm in a C name address pair]) _LT_DECL([global_symbol_to_c_name_address_lib_prefix], [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1], [Transform the output of nm in a C name address pair when lib prefix is needed]) _LT_DECL([], [nm_file_list_spec], [1], [Specify filename containing input files for $NM]) ]) # _LT_CMD_GLOBAL_SYMBOLS # _LT_COMPILER_PIC([TAGNAME]) # --------------------------- m4_defun([_LT_COMPILER_PIC], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_wl, $1)= _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)= m4_if([$1], [CXX], [ # C++ specific cases for pic, static, wl, etc. if test "$GXX" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | os2* | pw32* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; *djgpp*) # DJGPP does not support shared libraries at all _LT_TAGVAR(lt_prog_compiler_pic, $1)= ;; haiku*) # PIC is the default for Haiku. # The "-static" flag exists, but is broken. _LT_TAGVAR(lt_prog_compiler_static, $1)= ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac else case $host_os in aix[[4-9]]*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; chorus*) case $cc_basename in cxch68*) # Green Hills C++ Compiler # _LT_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a" ;; esac ;; mingw* | cygwin* | os2* | pw32* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; dgux*) case $cc_basename in ec++*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; ghcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; freebsd* | dragonfly*) # FreeBSD uses GNU C++ ;; hpux9* | hpux10* | hpux11*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' if test "$host_cpu" != ia64; then _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' fi ;; aCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac ;; *) ;; esac ;; interix*) # This is c89, which is MS Visual C++ (no shared libs) # Anyone wants to do a port? ;; irix5* | irix6* | nonstopux*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' # CC pic flag -KPIC is the default. ;; *) ;; esac ;; linux* | k*bsd*-gnu | kopensolaris*-gnu) case $cc_basename in KCC*) # KAI C++ Compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; ecpc* ) # old Intel C++ for x86_64 which still supported -KPIC. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; icpc* ) # Intel C++, used to be incompatible with GCC. # ICC 10 doesn't accept -KPIC any more. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; pgCC* | pgcpp*) # Portland Group C++ compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; cxx*) # Compaq C++ # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; xlc* | xlC* | bgxl[[cC]]* | mpixl[[cC]]*) # IBM XL 8.0, 9.0 on PPC and BlueGene _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' ;; *) case `$CC -V 2>&1 | sed 5q` in *Sun\ C*) # Sun C++ 5.9 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; esac ;; esac ;; lynxos*) ;; m88k*) ;; mvs*) case $cc_basename in cxx*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall' ;; *) ;; esac ;; netbsd*) ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; osf3* | osf4* | osf5*) case $cc_basename in KCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' ;; RCC*) # Rational C++ 2.4.1 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; cxx*) # Digital/Compaq C++ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; *) ;; esac ;; psos*) ;; solaris*) case $cc_basename in CC* | sunCC*) # Sun C++ 4.2, 5.x and Centerline C++ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; gcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' ;; *) ;; esac ;; sunos4*) case $cc_basename in CC*) # Sun C++ 4.x _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; lcc*) # Lucid _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; esac ;; tandem*) case $cc_basename in NCC*) # NonStop-UX NCC 3.20 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; *) ;; esac ;; vxworks*) ;; *) _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no ;; esac fi ], [ if test "$GCC" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; haiku*) # PIC is the default for Haiku. # The "-static" flag exists, but is broken. _LT_TAGVAR(lt_prog_compiler_static, $1)= ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; msdosdjgpp*) # Just because we use GCC doesn't mean we suddenly get shared libraries # on systems that don't support them. _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no enable_shared=no ;; *nto* | *qnx*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac case $cc_basename in nvcc*) # Cuda Compiler Driver 2.2 _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Xlinker ' if test -n "$_LT_TAGVAR(lt_prog_compiler_pic, $1)"; then _LT_TAGVAR(lt_prog_compiler_pic, $1)="-Xcompiler $_LT_TAGVAR(lt_prog_compiler_pic, $1)" fi ;; esac else # PORTME Check for flag to pass linker flags through the system compiler. case $host_os in aix*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; hpux9* | hpux10* | hpux11*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but # not for PA HP-UX. case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac # Is there a better lt_prog_compiler_static that works with the bundled CC? _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' ;; irix5* | irix6* | nonstopux*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC (with -KPIC) is the default. _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; linux* | k*bsd*-gnu | kopensolaris*-gnu) case $cc_basename in # old Intel for x86_64 which still supported -KPIC. ecc*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; # icc used to be incompatible with GCC. # ICC 10 doesn't accept -KPIC any more. icc* | ifort*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; # Lahey Fortran 8.1. lf95*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='--shared' _LT_TAGVAR(lt_prog_compiler_static, $1)='--static' ;; nagfor*) # NAG Fortran compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,-Wl,,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; pgcc* | pgf77* | pgf90* | pgf95* | pgfortran*) # Portland Group compilers (*not* the Pentium gcc compiler, # which looks to be a dead project) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; ccc*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # All Alpha code is PIC. _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; xl* | bgxl* | bgf* | mpixl*) # IBM XL C 8.0/Fortran 10.1, 11.1 on PPC and BlueGene _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' ;; *) case `$CC -V 2>&1 | sed 5q` in *Sun\ Ceres\ Fortran* | *Sun*Fortran*\ [[1-7]].* | *Sun*Fortran*\ 8.[[0-3]]*) # Sun Fortran 8.3 passes all unrecognized flags to the linker _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='' ;; *Sun\ F* | *Sun*Fortran*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; 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amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' _LT_TAGVAR(archive_expsym_cmds, $1)='' ;; m68k) _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_TAGVAR(hardcode_minus_L, $1)=yes ;; esac ;; bsdi[[45]]*) _LT_TAGVAR(export_dynamic_flag_spec, $1)=-rdynamic ;; cygwin* | mingw* | pw32* | cegcc*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. case $cc_basename in cl*) # Native MSVC _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=' ' _LT_TAGVAR(allow_undefined_flag, $1)=unsupported _LT_TAGVAR(always_export_symbols, $1)=yes _LT_TAGVAR(file_list_spec, $1)='@' # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. _LT_TAGVAR(archive_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $compiler_flags $deplibs -Wl,-dll~linknames=' _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then sed -n -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' -e '1\\\!p' < $export_symbols > $output_objdir/$soname.exp; else sed -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp; fi~ $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~ linknames=' # The linker will not automatically build a static lib if we build a DLL. # _LT_TAGVAR(old_archive_from_new_cmds, $1)='true' _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes _LT_TAGVAR(exclude_expsyms, $1)='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*' _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1,DATA/'\'' | $SED -e '\''/^[[AITW]][[ ]]/s/.*[[ ]]//'\'' | sort | uniq > $export_symbols' # Don't use ranlib _LT_TAGVAR(old_postinstall_cmds, $1)='chmod 644 $oldlib' _LT_TAGVAR(postlink_cmds, $1)='lt_outputfile="@OUTPUT@"~ lt_tool_outputfile="@TOOL_OUTPUT@"~ case $lt_outputfile in *.exe|*.EXE) ;; *) lt_outputfile="$lt_outputfile.exe" lt_tool_outputfile="$lt_tool_outputfile.exe" ;; esac~ if test "$MANIFEST_TOOL" != ":" && test -f "$lt_outputfile.manifest"; then $MANIFEST_TOOL -manifest "$lt_tool_outputfile.manifest" -outputresource:"$lt_tool_outputfile" || exit 1; $RM "$lt_outputfile.manifest"; fi' ;; *) # Assume MSVC wrapper _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=' ' _LT_TAGVAR(allow_undefined_flag, $1)=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. _LT_TAGVAR(archive_cmds, $1)='$CC -o $lib $libobjs $compiler_flags `func_echo_all "$deplibs" | $SED '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. _LT_TAGVAR(old_archive_from_new_cmds, $1)='true' # FIXME: Should let the user specify the lib program. _LT_TAGVAR(old_archive_cmds, $1)='lib -OUT:$oldlib$oldobjs$old_deplibs' _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes ;; esac ;; darwin* | rhapsody*) _LT_DARWIN_LINKER_FEATURES($1) ;; dgux*) _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor # support. 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hpux9*) if test "$GCC" = yes; then _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared $pic_flag ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' fi _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: _LT_TAGVAR(hardcode_direct, $1)=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. _LT_TAGVAR(hardcode_minus_L, $1)=yes _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' ;; hpux10*) if test "$GCC" = yes && test "$with_gnu_ld" = no; then _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else _LT_TAGVAR(archive_cmds, $1)='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi if test "$with_gnu_ld" = no; then _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_direct_absolute, $1)=yes _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. _LT_TAGVAR(hardcode_minus_L, $1)=yes fi ;; hpux11*) if test "$GCC" = yes && test "$with_gnu_ld" = no; then case $host_cpu in hppa*64*) _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac else case $host_cpu in hppa*64*) _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) m4_if($1, [], [ # Older versions of the 11.00 compiler do not understand -b yet # (HP92453-01 A.11.01.20 doesn't, HP92453-01 B.11.X.35175-35176.GP does) _LT_LINKER_OPTION([if $CC understands -b], _LT_TAGVAR(lt_cv_prog_compiler__b, $1), [-b], [_LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'], [_LT_TAGVAR(archive_cmds, $1)='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'])], [_LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags']) ;; esac fi if test "$with_gnu_ld" = no; then _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: case $host_cpu in hppa*64*|ia64*) _LT_TAGVAR(hardcode_direct, $1)=no _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; *) _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_direct_absolute, $1)=yes _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. _LT_TAGVAR(hardcode_minus_L, $1)=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' # Try to use the -exported_symbol ld option, if it does not # work, assume that -exports_file does not work either and # implicitly export all symbols. # This should be the same for all languages, so no per-tag cache variable. 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*) _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' ;; esac fi else _LT_TAGVAR(ld_shlibs, $1)=no fi ;; os2*) _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_TAGVAR(hardcode_minus_L, $1)=yes _LT_TAGVAR(allow_undefined_flag, $1)=unsupported _LT_TAGVAR(archive_cmds, $1)='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~echo DATA >> $output_objdir/$libname.def~echo " SINGLE NONSHARED" >> $output_objdir/$libname.def~echo EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' _LT_TAGVAR(old_archive_from_new_cmds, $1)='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*' _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*' _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib' fi _LT_TAGVAR(archive_cmds_need_lc, $1)='no' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: ;; 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FIXME _LT_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' else _LT_TAGVAR(ld_shlibs, $1)=no fi ;; chorus*) case $cc_basename in *) # FIXME: insert proper C++ library support _LT_TAGVAR(ld_shlibs, $1)=no ;; esac ;; cygwin* | mingw* | pw32* | cegcc*) case $GXX,$cc_basename in ,cl* | no,cl*) # Native MSVC # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=' ' _LT_TAGVAR(allow_undefined_flag, $1)=unsupported _LT_TAGVAR(always_export_symbols, $1)=yes _LT_TAGVAR(file_list_spec, $1)='@' # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. _LT_TAGVAR(archive_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $compiler_flags $deplibs -Wl,-dll~linknames=' _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; 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To avoid this, we pick a random, # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link # time. 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These are needed # for certain cross-compile configurations and native mingw. m4_defun([_LT_PATH_CONVERSION_FUNCTIONS], [AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_CANONICAL_BUILD])dnl AC_MSG_CHECKING([how to convert $build file names to $host format]) AC_CACHE_VAL(lt_cv_to_host_file_cmd, [case $host in *-*-mingw* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_host_file_cmd=func_convert_file_msys_to_w32 ;; *-*-cygwin* ) lt_cv_to_host_file_cmd=func_convert_file_cygwin_to_w32 ;; * ) # otherwise, assume *nix lt_cv_to_host_file_cmd=func_convert_file_nix_to_w32 ;; esac ;; *-*-cygwin* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_host_file_cmd=func_convert_file_msys_to_cygwin ;; *-*-cygwin* ) lt_cv_to_host_file_cmd=func_convert_file_noop ;; * ) # otherwise, assume *nix lt_cv_to_host_file_cmd=func_convert_file_nix_to_cygwin ;; esac ;; * ) # unhandled hosts (and "normal" native builds) lt_cv_to_host_file_cmd=func_convert_file_noop ;; esac ]) to_host_file_cmd=$lt_cv_to_host_file_cmd AC_MSG_RESULT([$lt_cv_to_host_file_cmd]) _LT_DECL([to_host_file_cmd], [lt_cv_to_host_file_cmd], [0], [convert $build file names to $host format])dnl AC_MSG_CHECKING([how to convert $build file names to toolchain format]) AC_CACHE_VAL(lt_cv_to_tool_file_cmd, [#assume ordinary cross tools, or native build. lt_cv_to_tool_file_cmd=func_convert_file_noop case $host in *-*-mingw* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_tool_file_cmd=func_convert_file_msys_to_w32 ;; esac ;; esac ]) to_tool_file_cmd=$lt_cv_to_tool_file_cmd AC_MSG_RESULT([$lt_cv_to_tool_file_cmd]) _LT_DECL([to_tool_file_cmd], [lt_cv_to_tool_file_cmd], [0], [convert $build files to toolchain format])dnl ])# _LT_PATH_CONVERSION_FUNCTIONS DOMALIGN-0.1.650/m4/java.m40000664000175000017500000001505511732713220011507 00000000000000dnl -*- Autoconf -*- dnl @synopsis CHECK_JAVA() dnl dnl Need to specify --with-java and --with-javaos dnl @author Alan Bleasby dnl dnl This macro calls: dnl dnl AC_SUBST([JAVA_CFLAGS]) dnl AC_SUBST([JAVA_CPPFLAGS]) dnl AC_SUBST([JAVA_LDFLAGS]) dnl dnl AM_CONDITIONAL([JAVA_BUILD], ...) dnl dnl And sets: dnl dnl AC_DEFINE([HAVE_JAVA], ...) dnl dnl AC_PATH_PROG([ANT], ...) dnl AC_PATH_PROG([JAR], ...) dnl AC_PATH_PROG([JAVA], ...) dnl AC_PATH_PROG([JAVAC], ...) AC_DEFUN([CHECK_JAVA], [ JAVA_CFLAGS="" JAVA_CPPFLAGS="" JAVA_LDFLAGS="" have_java="yes" auth_java="" AC_MSG_CHECKING([for Java JNI]) AC_ARG_WITH([java], [AS_HELP_STRING([--with-java@<:@=ARG@:>@], [root directory path of Java installation])], [ AC_MSG_RESULT([${withval}]) AS_IF([test "x${withval}" = "xno"], [have_java="no"]) ], [ AC_MSG_RESULT([no]) have_java="no" ]) AS_IF([test "x${have_java}" = "xyes"], [ # If specified, the Java JNI include directory has to exist. AS_IF([test -d ${with_java}], [AS_VAR_SET([JAVA_CPPFLAGS], ["-I${withval}"])], [ have_java="no" AC_MSG_ERROR([Java include directory ${withval} does not exist]) ]) ]) AC_MSG_CHECKING([for Java JNI OS]) AC_ARG_WITH([javaos], [AS_HELP_STRING([--with-javaos@<:@=ARG@:>@], [root directory path of Java OS include])], [ AC_MSG_RESULT([${withval}]) AS_IF([test "x${withval}" != "xno"], [ # If specified, the Java JNI OS include directory has to exist. AS_IF([test "x${have_java}" = "xyes" && test -d ${withval}], [AS_VAR_APPEND([JAVA_CPPFLAGS], [" -I${withval}"])], [ have_java="no" AC_MSG_ERROR([Java OS include directory ${withval} does not exist]) ]) ]) ], [ AC_MSG_RESULT([no]) ]) # Authorisation type AC_MSG_CHECKING([for authorisation type]) AC_ARG_WITH([auth], [AS_HELP_STRING([--with-auth@<:@=ARG@:>@], [authorisation mechanism for Jemboss server @<:@default=PAM@:>@])], [ AS_IF([test "x${withval}" != "xno"], [ AC_MSG_RESULT([yes]) AS_CASE([${withval}], [yes], [ auth_java="PAM" AC_CHECK_LIB([pam], [main], [AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpam"])]) ], [pam], [ auth_java="PAM" AC_CHECK_LIB([pam], [main], [AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpam"])]) ], [shadow], [ auth_java="N_SHADOW" AC_CHECK_LIB([crypy], [main], [AS_VAR_APPEND([JAVA_LDFLAGS], [" -lcrypt"])]) ], [rshadow], [ auth_java="R_SHADOW" AC_CHECK_LIB([crypy], [main], [AS_VAR_APPEND([JAVA_LDFLAGS], [" -lcrypt"])]) ], [noshadow], [auth_java="NO_SHADOW"], [rnoshadow], [auth_java="RNO_SHADOW"], [aixshadow], [auth_java="AIX_SHADOW"], [hpuxshadow], [auth_java="HPUX_SHADOW"]) ], [AC_MSG_RESULT([no])]) ], [AC_MSG_RESULT([no])]) AS_IF([test -n "${auth_java}"], [AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D${auth_java}"])], [AS_VAR_APPEND([JAVA_CPPFLAGS], [" -DNO_AUTH"])]) # Threading type AC_MSG_CHECKING([for threading type]) AC_ARG_WITH([thread], [AS_HELP_STRING([--with-thread@<:@=ARG@:>@], [thread type @<:@default=linux@:>@])], [ AS_IF([test "x${withval}" != "xno"], [ AC_MSG_RESULT([yes]) AS_CASE([${withval}], [yes], [ AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_REENTRANT"]) AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"]) # AS_VAR_APPEND([LIBS], [" -lpthread"]) ], [freebsd], [ AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_THREAD_SAFE"]) AS_VAR_APPEND([JAVA_LDFLAGS], [" -pthread"]) # AS_VAR_APPEND([LIBS], [" -lc_r"]) ], [linux], [ AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_REENTRANT"]) AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"]) # AS_VAR_APPEND([LIBS], [" -lpthread"]) ], [solaris], [ AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_POSIX_C_SOURCE=199506L"]) AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"]) # AS_VAR_APPEND([LIBS], [" -lpthread"]) ], [macos], [ # AS_VAR_APPEND([JAVA_CPPFLAGS], [""]) # AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"]) # AS_VAR_APPEND([LIBS], [" -lpthread"]) ], [hpux], [ AS_VAR_APPEND([JAVA_CFLAGS], [" -Ae +z"]) AS_VAR_APPEND([JAVA CPPFLAGS], [" -DNATIVE -D_POSIX_C_SOURCE=199506L"]) AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"]) # AS_VAR_APPEND([LIBS], [" -lpthread"]) ], [irix], [ # AS_VAR_APPEND([JAVA_CFLAGS], [""]) AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"]) AS_VAR_APPEND([LIBS], [" -lpthread"]) ], [aix], [ AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_REENTRANT"]) AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"]) AS_VAR_APPEND([LIBS], [" -lpthread"]) ], [osf], [ AS_VAR_APPEND([JAVA_CPPFLAGS], [" -D_REENTRANT -D_OSF_SOURCE"]) AS_VAR_APPEND([JAVA_LDFLAGS], [" -lpthread"]) AS_VAR_APPEND([LIBS], [" -lpthread"]) ]) ], [AC_MSG_RESULT([no])]) ], [AC_MSG_RESULT([no])]) # Test for programs ant, jar, java and javac. AS_IF([test "x${have_java}" = "xyes"], [ AC_PATH_PROG([ANT], [ant], [no]) AS_IF([test "x${ANT}" = "xno"], [have_java="no"]) AC_PATH_PROG([JAR], [jar], [no]) AS_IF([test "x${JAR}" = "xno"], [have_java="no"]) AC_PATH_PROG([JAVA], [java], [no]) AS_IF([test "x${JAVA}" = "xno"], [have_java="no"]) AC_PATH_PROG([JAVAC], [javac], [no]) AS_IF([test "x${JAVAC}" = "xno"], [have_java="no"]) ]) AS_IF([test "x${have_java}" = "xyes"], [ AC_DEFINE([HAVE_JAVA], [1], [Define to 1 if the Java Native Interface (JNI) is available.]) ### FIXME: Append -DDEBIAN for the moment. # Debian uses PAM service "ssh" instead of "login", see ajjava.c # This could use AC_DEFINE() if no better option was avialable. # Ultimately, this should be configurable via server configuration # files. AS_IF([test -f "/etc/debian_release" || test -f /etc/debian_version], [AS_VAR_APPEND([JAVA_CPPFLAGS], [" -DDEBIAN"])]) ]) AC_ARG_VAR([ANT], [Path to the Apache Ant make tool]) AC_ARG_VAR([JAR], [Path to the Java archive tool]) AC_ARG_VAR([JAVA], [Path to the Java application launcher]) AC_ARG_VAR([JAVAC], [Path to the Java compiler]) AC_SUBST([JAVA_CFLAGS]) AC_SUBST([JAVA_CPPFLAGS]) AC_SUBST([JAVA_LDFLAGS]) AM_CONDITIONAL([JAVA_BUILD], [test "x${have_java}" = "xyes"]) ]) DOMALIGN-0.1.650/m4/ltversion.m40000644000175000017500000000126212171070647012613 00000000000000# ltversion.m4 -- version numbers -*- Autoconf -*- # # Copyright (C) 2004 Free Software Foundation, Inc. # Written by Scott James Remnant, 2004 # # This file 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. # @configure_input@ # serial 3337 ltversion.m4 # This file is part of GNU Libtool m4_define([LT_PACKAGE_VERSION], [2.4.2]) m4_define([LT_PACKAGE_REVISION], [1.3337]) AC_DEFUN([LTVERSION_VERSION], [macro_version='2.4.2' macro_revision='1.3337' _LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?]) _LT_DECL(, macro_revision, 0) ]) DOMALIGN-0.1.650/m4/general.m40000664000175000017500000000125311374607600012204 00000000000000AC_DEFUN([CHECK_GENERAL], # # Handle general setup e.g. documentation directory # [AC_MSG_CHECKING(if docroot is given) AC_ARG_WITH([docroot], [AS_HELP_STRING([--with-docroot=DIR], [root directory path of documentation (defaults to none)])], [if test "$withval" != no ; then AC_MSG_RESULT(yes) CPPFLAGS="$CPPFLAGS -DDOC_ROOT=\\\"$withval\\\"" fi], [ AC_MSG_RESULT(no) ]) ] # GCC profiling [AC_MSG_CHECKING(if gcc profiling is selected) AC_ARG_WITH([gccprofile], [AS_HELP_STRING([--with-gccprofile], [selects profiling])], [if test "$withval" != no ; then AC_MSG_RESULT(yes) CFLAGS="$CFLAGS -g -pg" LDFLAGS="$LDFLAGS -pg" fi], [ AC_MSG_RESULT(no) ]) ] ) DOMALIGN-0.1.650/m4/mysql.m40000664000175000017500000001266311732713347011747 00000000000000dnl -*- Autoconf -*- ##### http://autoconf-archive.cryp.to/ax_lib_mysql.html # # SYNOPSIS # # AX_LIB_MYSQL([MINIMUM-VERSION]) # # DESCRIPTION # # This macro provides tests of availability of MySQL 'libmysqlclient' # library of particular version or newer. # # AX_LIB_MYSQL macro takes only one argument which is optional. # If there is no required version passed, then macro does not run # version test. # # The --with-mysql option takes one of three possible values: # # no - do not check for MySQL client library # # yes - do check for MySQL library in standard locations # (mysql_config should be in the PATH) # # path - complete path to mysql_config utility, use this option if # mysql_config can't be found in the PATH # # This macro calls: # # AC_SUBST([MYSQL_CFLAGS]) # AC_SUBST([MYSQL_CPPFLAGS]) # AC_SUBST([MYSQL_LDFLAGS]) # AC_SUBST([MYSQL_VERSION]) # # And sets: # # HAVE_MYSQL # # LAST MODIFICATION # # 2006-07-16 # 2007-01-09 MKS: mysql_config --cflags may set gcc -fomit-frame-pointers, # which prevents gdb from displaying stack traces. # Changed mysql_config --cflags to mysql_config --include # 2009-09-23 AJB: Checking for availability of both, include files and # library files. # 2010-06-14 MKS: Added MYSQL_CPPFLAGS # 2011-08-01 MKS: Made test constructs more portable # # COPYLEFT # # Copyright (c) 2006 Mateusz Loskot # # Copying and distribution of this file, with or without # modification, are permitted in any medium without royalty provided # the copyright notice and this notice are preserved. AC_DEFUN([AX_LIB_MYSQL], [ MYSQL_CFLAGS="" MYSQL_CPPFLAGS="" MYSQL_LDFLAGS="" MYSQL_CONFIG="" MYSQL_VERSION="" AC_ARG_WITH([mysql], [AS_HELP_STRING([--with-mysql@<:@=ARG@:>@], [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config])], [ AS_IF([test "x${withval}" = "xno"], [want_mysql="no"], [test "x${withval}" = "xyes"], [want_mysql="yes"], [ want_mysql="yes" MYSQL_CONFIG="${withval}" ]) ], [want_mysql="yes"]) dnl dnl Check MySQL libraries (libmysqlclient) dnl AS_IF([test "x${want_mysql}" = "xyes"], [ AS_IF([test -z "${MYSQL_CONFIG}" -o test], [AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no])]) AS_IF([test "x${MYSQL_CONFIG}" != "xno"], [ AC_MSG_CHECKING([for MySQL libraries]) MYSQL_CFLAGS="`${MYSQL_CONFIG} --cflags`" MYSQL_CPPFLAGS="`${MYSQL_CONFIG} --include`" MYSQL_LDFLAGS="`${MYSQL_CONFIG} --libs`" MYSQL_VERSION=`${MYSQL_CONFIG} --version` dnl It isn't enough to just test for mysql_config as Fedora dnl provides it in the mysql RPM even though mysql-devel may dnl not be installed EMBCPPFLAGS="${CPPFLAGS}" EMBLDFLAGS="${LDFLAGS}" CPPFLAGS="${MYSQL_CPPFLAGS} ${EMBCPPFLAGS}" LDFLAGS="${MYSQL_LDFLAGS} ${EMBLDFLAGS}" AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include #include "mysql.h"]], [[mysql_info(NULL)]])], [havemysql="yes"], [havemysql="no"]) CPPFLAGS="${EMBCPPFLAGS}" LDFLAGS="${EMBLDFLAGS}" AS_IF([test "x${havemysql}" = "xyes"], [ AC_DEFINE([HAVE_MYSQL], [1], [Define to 1 if MySQL libraries are available.]) found_mysql="yes" AC_MSG_RESULT([yes]) ], [ MYSQL_CFLAGS="" MYSQL_CPPFLAGS="" MYSQL_LDFLAGS="" found_mysql="no" AC_MSG_RESULT([no]) ]) ], [ found_mysql="no" ]) ]) dnl dnl Check if required version of MySQL is available dnl mysql_version_req=ifelse([$1], [], [], [$1]) AS_IF([test "x${found_mysql}" = "xyes" -a -n "${mysql_version_req}"], [ AC_MSG_CHECKING([if MySQL version is >= ${mysql_version_req}]) dnl Decompose required version string of MySQL dnl and calculate its number representation mysql_version_req_major=`expr ${mysql_version_req} : '\([[0-9]]*\)'` mysql_version_req_minor=`expr ${mysql_version_req} : '[[0-9]]*\.\([[0-9]]*\)'` mysql_version_req_micro=`expr ${mysql_version_req} : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'` AS_IF([test "x${mysql_version_req_micro}" = "x"], [mysql_version_req_micro="0"]) mysql_version_req_number=`expr ${mysql_version_req_major} \* 1000000 \ \+ ${mysql_version_req_minor} \* 1000 \ \+ ${mysql_version_req_micro}` dnl Decompose version string of installed MySQL dnl and calculate its number representation mysql_version_major=`expr ${MYSQL_VERSION} : '\([[0-9]]*\)'` mysql_version_minor=`expr ${MYSQL_VERSION} : '[[0-9]]*\.\([[0-9]]*\)'` mysql_version_micro=`expr ${MYSQL_VERSION} : '[[0-9]]*\.[[0-9]]*\.\([[0-9]]*\)'` AS_IF([test "x${mysql_version_micro}" = "x"], [mysql_version_micro="0"]) mysql_version_number=`expr ${mysql_version_major} \* 1000000 \ \+ ${mysql_version_minor} \* 1000 \ \+ ${mysql_version_micro}` mysql_version_check=`expr ${mysql_version_number} \>\= ${mysql_version_req_number}` AS_IF([test "x${mysql_version_check}" = "x1"], [AC_MSG_RESULT([yes])], [AC_MSG_RESULT([no])]) ]) AC_SUBST([MYSQL_CFLAGS]) AC_SUBST([MYSQL_CPPFLAGS]) AC_SUBST([MYSQL_LDFLAGS]) AC_SUBST([MYSQL_VERSION]) ]) DOMALIGN-0.1.650/m4/hpdf.m40000664000175000017500000000353011430325236011503 00000000000000dnl @synopsis CHECK_HPDF() dnl dnl This macro searches for an installed libhpdf (libharu) library. If nothing dnl was specified when calling configure, it first searches in /usr/local dnl and then in /usr. If the --with-hpdf=DIR is specified, it will try dnl to find it in DIR/include and DIR/lib. dnl dnl It defines the symbol PLD_pdf if the library is found. dnl AC_DEFUN([CHECK_HPDF], # # Handle user hints # [AC_MSG_CHECKING([whether to look for pdf support]) AC_ARG_WITH([hpdf], [AS_HELP_STRING([--with-hpdf=DIR], [root directory path of hpdf installation @<:@defaults to /usr@:>@])], [if test "$withval" != no ; then AC_MSG_RESULT(yes) ALT_HOME="$withval" else AC_MSG_RESULT([no]) fi], [ AC_MSG_RESULT([yes]) ALT_HOME=/usr ]) # # Locate hpdf # if test -d "${ALT_HOME}" then # # Keep a copy if it fails # ALT_LDFLAGS="$LDFLAGS" ALT_CPPFLAGS="$CPPFLAGS" # # Set # LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib" CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include" # # Check for libharu in ALT_HOME # AC_CHECK_LIB(hpdf, HPDF_New, CHECK=1, CHECK=0, -L${ALT_HOME}/lib) # # # If everything found okay then proceed to include png driver in config. # if test $CHECK = "1" ; then LIBS="$LIBS -lhpdf" case $host_os in solaris*) LDFLAGS="$LDFLAGS -R$ALT_HOME/lib" ;; esac AC_DEFINE([PLD_pdf], [1], [Define to 1 if PDF support is available]) AM_CONDITIONAL(AMPDF, true) echo PDF support found if test $ALT_HOME = "/usr" ; then LDFLAGS="$ALT_LDFLAGS" CPPFLAGS="$ALT_CPPFLAGS" fi else # # If not okay then reset FLAGS. # AM_CONDITIONAL(AMPDF, false) LDFLAGS="$ALT_LDFLAGS" CPPFLAGS="$ALT_CPPFLAGS" echo "No pdf support (libhpdf) found." fi else if test $withval != "no"; then echo "Directory $ALT_HOME does not exist" exit 0 fi fi ]) DOMALIGN-0.1.650/m4/lt~obsolete.m40000644000175000017500000001375612171070647013153 00000000000000# lt~obsolete.m4 -- aclocal satisfying obsolete definitions. -*-Autoconf-*- # # Copyright (C) 2004, 2005, 2007, 2009 Free Software Foundation, Inc. # Written by Scott James Remnant, 2004. # # This file 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. # serial 5 lt~obsolete.m4 # These exist entirely to fool aclocal when bootstrapping libtool. # # In the past libtool.m4 has provided macros via AC_DEFUN (or AU_DEFUN) # which have later been changed to m4_define as they aren't part of the # exported API, or moved to Autoconf or Automake where they belong. # # The trouble is, aclocal is a bit thick. It'll see the old AC_DEFUN # in /usr/share/aclocal/libtool.m4 and remember it, then when it sees us # using a macro with the same name in our local m4/libtool.m4 it'll # pull the old libtool.m4 in (it doesn't see our shiny new m4_define # and doesn't know about Autoconf macros at all.) # # So we provide this file, which has a silly filename so it's always # included after everything else. This provides aclocal with the # AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything # because those macros already exist, or will be overwritten later. # We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6. # # Anytime we withdraw an AC_DEFUN or AU_DEFUN, remember to add it here. # Yes, that means every name once taken will need to remain here until # we give up compatibility with versions before 1.7, at which point # we need to keep only those names which we still refer to. # This is to help aclocal find these macros, as it can't see m4_define. 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You may also peek at any GNU archive site, in case some other package would contain this missing '$1' program." exit 1 ;; esac exit 0 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-time-zone: "UTC" # time-stamp-end: "; # UTC" # End: DOMALIGN-0.1.650/Makefile.am0000664000175000017500000000062011614226107012032 00000000000000# ACLOCAL_AMFLAGS = -I m4 SUBDIRS = src emboss_acd emboss_doc EXTRA_DIST = depcomp ltmain.sh install-sh config.sub config.guess dist-hook: tar cBf - emboss_acd | ( cd $(distdir); tar xBf - ; cd emboss_acd; rm -rf CVS) tar cBf - emboss_doc | ( cd $(distdir); tar xBf - ; cd emboss_doc; rm -rf CVS; rm -rf master) tar cBf - test | ( cd $(distdir); tar xBf - ; cd test; rm -rf CVS) DOMALIGN-0.1.650/emboss_doc/0002775000175000017500000000000012171070667012206 500000000000000DOMALIGN-0.1.650/emboss_doc/text/0002775000175000017500000000000012171070665013170 500000000000000DOMALIGN-0.1.650/emboss_doc/text/CVS/0002775000175000017500000000000012171064326013620 500000000000000DOMALIGN-0.1.650/emboss_doc/text/CVS/Entries0000664000175000017500000000043412171064326015073 00000000000000/.cvsignore/1.1/Thu Jan 21 17:58:07 2010/-kk/ /Makefile.am/1.1/Tue Mar 7 12:47:55 2006// /allversusall.txt/1.22/Mon Jul 15 21:25:42 2013// /domainalign.txt/1.15/Mon Jul 15 21:25:42 2013// /domainrep.txt/1.14/Mon Jul 15 21:25:42 2013// /seqalign.txt/1.21/Mon Jul 15 21:25:42 2013// D DOMALIGN-0.1.650/emboss_doc/text/CVS/Root0000664000175000017500000000005612000651453014377 00000000000000rice@dev.open-bio.org:/home/repository/emboss DOMALIGN-0.1.650/emboss_doc/text/CVS/Repository0000664000175000017500000000005712000651453015634 00000000000000emboss/emboss/embassy/domalign/emboss_doc/text DOMALIGN-0.1.650/emboss_doc/text/seqalign.txt0000664000175000017500000005622212171064326015456 00000000000000 SEQALIGN documentation CONTENTS 1.0 SUMMARY 2.0 INPUTS & OUTPUTS 3.0 INPUT FILE FORMAT 4.0 OUTPUT FILE FORMAT 5.0 DATA FILES 6.0 USAGE 7.0 KNOWN BUGS & WARNINGS 8.0 NOTES 9.0 DESCRIPTION 10.0 ALGORITHM 11.0 RELATED APPLICATIONS 12.0 DIAGNOSTIC ERROR MESSAGES 13.0 AUTHORS 14.0 REFERENCES 1.0 SUMMARY Extend alignments (DAF file) with sequences (DHF file) 2.0 INPUTS & OUTPUTS SEQALIGN reads a directory of "seed" alignments and a directory of sets of protein sequences and writes a directory of "extended" alignments. An extended alignment is a seed alignment that is extended with sequences from the appropriate sequence set. The sets directory must contain a sequence set for each seed alignment directory and the files must have the same base name. For example, sequences from "family.sets" are used to extend the seed alignment "family.aln". Typically, the inputs are (i) DAF files (domain alignment files) containing structure-based sequence alignments and (ii) DHF files (domain hits files) containing sequence relatives (of unknown structure) of these alignments, and the output are DAF files containing the extended alignments. The base names of the output alignments are the same as the input alignments. The paths for input and output files are specified by the user and the file extensions are set in the ACD file. 3.0 INPUT FILE FORMAT The format of the domain alignment file is described in DOMAINALIGN documentation. If other alignment files are used as input, all of the common file formats are supported. The format of the domain hits file is described in SEQSEARCH documentation. If other sequence sets are used as input, all of the common file formats are supported. 4.0 OUTPUT FILE FORMAT The format of the domain alignment file is described in DOMAINALIGN documentation. Note however that the file will never contain 'Number' or 'Post_similar' records. Futhermore, the code before each sequence is of the form Acc_Start_End (where domain hits files were used as input sequences) or Acc_n (where other sequences were used as input), where 'Acc' is the accession number of the sequence, 'Start' and 'End' are the start and end point of the sequence in the full length sequence respectively, and 'n' is a sequential count of the sequence in the alignment. Output files for usage example File: 54894.daf # TY SCOP # XX # CL Alpha and beta proteins (a+b) # XX # FO Ferredoxin-like # XX # SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain # XX # FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain # XX # SI 54894 # XX d4at1b1_0 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPXSGEMG RKDLIKIE 0 d4at1d1_1 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSGXEMG RKDLIKIE 0 P00478_1_92 0 -VEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSG-EMG RKDLIKIE 0 Q83IL8_1_92 0 -VEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSG-EMG RKDLIKIE 0 P08421_1_92 0 -VEAIKCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSG-EMG RKDLIKIE 0 Q8Z130_1_92 0 -VEAIKCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSG-EMG RKDLIKIE 0 Q8ZB38_1_92 0 -VEAIKCGTVIDHIPAQIGFKLLSLFKLTATD----QRITIGLNLPSK-RSG RKDLIKIE 0 P19936_1_92 0 -VEAIKCGTVIDHIPAQIGFKLLTLFKLTATD----QRITIGLNLPSN-ELG RKDLIKIE 0 Q7MZ14_1_92 0 -VEAIRCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSN-RLG KKDLIKIE 0 Q8K9H8_1_92 0 -VEAIKSGSVIDHIPAHIGFKLLSLFRFTETE----KRITIGLNLPSQ-KLD KKDIIKIE 0 P57451_1_92 0 -VEAIKSGSVIDHIPEYIGFKLLSLFRFTETE----KRITIGLNLPSK-KLG RKDIIKIE 0 Q9KP65_1_92 0 -VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSA----QRVTIGLNLPSS-ALG SKDLLKIE 0 Q87LF7_1_92 0 -VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALG HKDLLKIE 0 Q8DCF7_1_92 0 -VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALG NKDLLKIE 0 Q7MHF0_1_92 0 -VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALG NKDLLKIE 0 Q8D1W6_1_92 0 -VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTK----ERITMGLNLPSN-QQK KKDLIKLE 0 Q7P144_1_92 0 -VEALKQGTVIDHIPAGEGVKILRLFKLTETG----ERVTVGLNLVSR-HMG SKDLIKVE 0 P96175_1_92 0 -VEAICNGYVIDHIPSGQGVKILRLFSLTDTK----QRVTVGFNLPSH-DGT TKDLIKVE 0 Q9K1K9_1_92 0 -VEAIEKGTVIDHIPAGRGLTILRQFKLLHYG----NAVTVGFNLPSK-TQG SKDIIKIK 0 Q9JWY6_1_92 0 -VEAIEKGTVIDHIPAGRGLTILRQFKLLHYG----NAVTVGFNLPSK-TQG SKDIIKIK 0 Q970X3_1_91 0 -VSKIKNGTVIDHIPAGRALAVLRILKIAEG-----YRIALVMNVESK-KMG KKDIVKIE 0 Q9UX07_1_93 0 -VSKIRNGTVIDHIPAGRALAVLRILGIRGSEG---YRVALVMNVESK-KIG RKDIVKIE 0 P74766_1_93 0 -VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEG---FRIALVINVDSK-KMG KKDIVKIE 0 Q8ZTG2_1_93 0 -VSKIENGTVIDHIPAGRALTVLRILGISGKEG---LRVALVMNVESK-KLG KKDIVKIE 0 O58452_1_94 0 -VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNG--GSVLLAMNVPSK-KLG RKDIVKVE 0 Q8U374_1_94 0 -VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNG--GAVLLAMNVPSK-KLG RKDIVKVE 0 P77919_1_94 0 -VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNG--GAVLLAMNVPSK-KLG RKDIVKVE 0 O30129_1_93 0 -VSKIKEGTVIDHINAGKALLVLKILKIQPGTD---LTVSMAMNVPSS-KMG KKDIVKVE 0 Q8TVB1_1_92 0 -VKRIEMGTVLDHLPPGTAPQIMRILDIDPTET----TLLVAINVESS-KMG RKDILKIE 0 Q8THL3_1_92 0 -IQAIENGTVIDHITAGQALNVLRILRISSAFR---ATVSFVMNAPGA--RG KKDVVKIE 0 Q8PXK6_1_92 0 -VQAIESGTVIDHIKSGQALNVLRILGISSAFR---ATISFVMNAPGA--GG KKDVVKIE 0 Q9HHN3_1_93 0 -VSKIQAGTVIDHIPAGQALQVLQILGTNGASD---DQITVGMNVTSE-RHH RKDIVKIE 0 Q58801_1_91 0 -VKKITNGTVIDHIDAGKALMVFKVLNVPKETS-----VMIAINVPSK-KKG KKDILKIE 0 O26938_1_91 0 -VKPIKNGTVIDHITANRSLNVLNILGLPDGRS----KVTVAMNMDSS-QLG SKDIVKIE 0 Q97B28_1_93 0 -ISKIKDGTVIDHIPSGKALRVLSILGIRDDVD---YTVSVGMHVPSS-KME YKDVIKIE 0 Q9HKM3_1_93 0 -ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVN---YTVSLAIHVPSN-KMG FKDVIKIE 0 Q9YBD5_1_95 0 -VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGY-RWRIAVVINAESS-KLG RKDILKIE 0 Q7MX57_1_92 0 -VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDK----RITIGNNLRSR-SHG SKGVIKIE 0 Q8A9S4_1_92 0 -VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCN----ITIGFNLDSK-KLG KKGIIKIA 0 Q891I9_1_91 0 -ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYS----VALIMNVFSS-KLG KKDIIKIA 0 Q97FS4_1_90 0 -INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFP----TALIMNAISK-KNK AKDIIKIE 0 P96111_1_98 0 GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGS FKGYISLP 0 d4at1b1_0 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0 d4at1d1_1 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0 P00478_1_92 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0 Q83IL8_1_92 0 NTFLSEEQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0 P08421_1_92 0 NTFLTEEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 0 Q8Z130_1_92 0 NTFLTDEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 0 Q8ZB38_1_92 0 NTFLTEQQANQLAMYAPDATVNRIDNYEVVKKLTLSLP 0 P19936_1_92 0 NTFLTEQQANQLAMYAPKATVNRIDNYEVVRKLTLSLP 0 Q7MZ14_1_92 0 NTFLTEQQANQLAMYAPNATVNCIENYEVVKKLPINLP 0 Q8K9H8_1_92 0 NTFLSDDQINQLAIYAPCATVNYIEKYNLVGKIFPSLP 0 P57451_1_92 0 NTFLSDEQINQLAIYAPHATVNYINEYNLVRKVFPTLP 0 Q9KP65_1_92 0 NVFISEAQANKLALYAPHATVNQIENYEVVKKLALQLP 0 Q87LF7_1_92 0 NVFINEEQASKLALYAPHATVNQIENYEVVKKLALELP 0 Q8DCF7_1_92 0 NVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP 0 Q7MHF0_1_92 0 NVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP 0 Q8D1W6_1_92 0 NVLLNEDQANQLSIYAPLATVNQIKNYIVIKKQKLKLP 0 Q7P144_1_92 0 NVALTEEQANELALFAPKATVNVIDNFEVVKKHKLTLP 0 P96175_1_92 0 NTEITKSQANQLALLAPNATVNIIENFKVTDKHSLALP 0 Q9K1K9_1_92 0 GVCLDDKAADRLALFAPEAVVNTIDNFKVVQKRHLNLP 0 Q9JWY6_1_92 0 GVCLDDKAADRLALFAPEAVVNTIDHFKVVQKRHLNLP 0 Q970X3_1_91 0 NKEVDEKEANLITLIAPTATINIIRDYEVVEKKKLKIP 0 Q9UX07_1_93 0 DRVIDEKEASLITLIAPSATINIIRDYVVTEKRHLEVP 0 P74766_1_93 0 DKEISDTEANLITLIAPTATINIVREYEVVKKTKLEVP 0 Q8ZTG2_1_93 0 GRELTPEEVNIISAVAPTATINIIRNFAVVKKFKVTPP 0 O58452_1_94 0 GKFLSEEEVNKIALVAPTATVNIIRNYKVVEKFKVEVP 0 Q8U374_1_94 0 GKFLSEEEVNKIALVAPTATVNIIREYKVVEKFKVEIP 0 P77919_1_94 0 GRFLSEEEVNKIALVAPNATVNIIRDYKVVEKFKVEVP 0 O30129_1_93 0 GMFIRDEELNKIALISPNATINLIRDYEIERKFKVSPP 0 Q8TVB1_1_92 0 GKILSEEEANKVALVAPNATVNIVRDYSVAEKFQVKPP 0 Q8THL3_1_92 0 GKELSVEELNRIALISPKATINIIRDFEVVQKNKVVLP 0 Q8PXK6_1_92 0 GKELSVEELNRIALISPKATINIIRDFVVVQKNNVVLP 0 Q9HHN3_1_93 0 GRELSQDEVDVLSLIAPDATINIVRDYEVDEKRRVDRP 0 Q58801_1_91 0 GIELKKEDVDKISLISPDVTINIIRNGKVVEKLKPQIP 0 O26938_1_91 0 NRELKPSEVDQIALIAPRATINIVRDYKIVEKAKVRL- 0 Q97B28_1_93 0 NRSLDKNELDMISLTAPNATISIIKNYEISEKFKVELP 0 Q9HKM3_1_93 0 NRFLDRNELDMISLIAPNATISIIKNYEISEKFQVELP 0 Q9YBD5_1_95 0 GYKPRQRDLEVLGIIAPGATFNVIEDYKVVEKVKLKLP 0 Q7MX57_1_92 0 DKTFEEEELNRIALIAPNVRLNIIRDYEVVEKRQVEVP 0 Q8A9S4_1_92 0 DKFFCDEEINRISVVAPYVKLNIIRDYEVVEKKEVRMP 0 Q891I9_1_91 0 NKEIDID-FTVLGLIDPTITINIIEDEKIKEKLNLELP 0 Q97FS4_1_90 0 N--VMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP 0 P96111_1_98 0 DRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP 0 File: 55074.daf # TY SCOP # XX # CL Alpha and beta proteins (a+b) # XX # FO Ferredoxin-like # XX # SF Adenylyl and guanylyl cyclase catalytic domain # XX # FA Adenylyl and guanylyl cyclase catalytic domain # XX # SI 55074 # XX d1cs4a__0 0 MMFHKIYIQKXHXDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR FDKLAAE- 0 d1fx2a__1 0 XXNNNRAPXKEPTDPVTLIFTDIESSTALWAAX----HPDLMPDAVAAHHRM VRSLIGR- 0 Q04400_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR FDKLAAE- 0 P40144_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR FDKLAAE- 0 P30803_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR FDKLAAE- 0 O95622_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR FDKLAAE- 0 Q03343_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR FDKLAAE- 0 O43306_1_189 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR FDKLAAE- 0 Q01341_1_188 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR FDKLAAE- 0 P30804_1_188 0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFAR FDKLAAE- 0 Q99279_1_218 0 --NNNRAPKE-PTDPVTLIFTDIESSTALWAA-----HPDLMPDAVAAHHRM VRSLIGR- 0 Q99280_6_216 0 ---------KEPTGPVTLIFTDIESSTALWAA-----HPDLMPDAVATHHRL IRSLITR- 0 P26338_1_216 0 ----NNLAPKELTDPVTLIFTDIESSTALWAA-----HPELMPDAVATHHRL IRSLIGR- 0 Q26721_1_206 0 --------------PVTLIFTDIESSTALWAA-----HPEVMPDAVATHHRL IRTLISK- 0 Q99396_1_212 0 ---------KELADPVTLIFTDIESSTAQWAT-----QPELMPDAVATHHSM VRSLIEN- 0 Q08828_1_186 0 --FHKIYIQR--HDNVSILFADIVGFTGLASQC----TAQELVKLLNELFGK FDELATE- 0 P19754_1_186 0 --FHKIYIQR--HDNVSILFADIVGFTGLASQC----TAQELVKLLNELFGK FDELATE- 0 P32870_1_186 0 --FHRIYIQK--HENVSILFADIVGFTVLSSQC----SAQELVRLLNELFGR FDQLAHD- 0 Q26896_6_216 0 ---------KEFTDPVTLIFTDIESSTALWAA-----HPGMMADAVATHHRL IRSLIAL- 0 P97490_1_186 0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFAR FDRLAHE- 0 P40146_1_186 0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFAR FDRLAHE- 0 P40145_1_186 0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFAR FDRLAHE- 0 Q8VHH7_1_186 0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFAR FDKLAAK- 0 P21932_1_186 0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFAR FDKLAAK- 0 O60266_1_186 0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFAR FDKLAAK- 0 Q27675_1_217 0 ---NNDAAPKDGDEPVTLLFTDIESSTALWAA-----LPQLMSDAIAAHHRV IRQLVKK- 0 Q25263_1_217 0 ---NNDAAPKDGDEPVTLLFTDIESSTALWAA-----LPQLMSDAIAAHHRV IRQLVKK- 0 Q91WF3_1_158 0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGK FDQIAKE- 0 Q8NFM4_1_158 0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGK FDQIAKE- 0 P26770_1_158 0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGK FDQIAKE- 0 Q08462_1_186 0 --FHNLYVKR--HTNVSILYADIVGFTRLASDC----SPGELVHMLNELFGK FDQIAKE- 0 P26769_1_186 0 --FHNLYVKR--HTNVSILYADIVGFTRLASDC----SPGELVHMLNELFGK FDQIAKE- 0 Q29450_1_186 0 --FHNLYVKR--HQNVSILYADIVGFTRLASDC----SPKELVVVLNELFGK FDQIAKA- 0 P51829_1_186 0 --FHSLYVKR--HQNVSILYADIVGFTRLASDC----SPKELVVVLNELFGK FDQIAKA- 0 P51828_1_186 0 --FHSLYVKR--HQNVSILYADIVGFTQLASDC----SPKELVVVLNELFGK FDQIAKA- 0 P98999_1_150 0 -------------EQVSILFADIVGFTKMSANK----SAHALVGLLNDLFGR FDRLCEE- 0 Q9DGG6_1_181 0 -------------EQVSILFADIVGFTKMSANK----SAHALVGLLNDLFGR FDRLCED- 0 P51830_1_179 0 ---------------VSILFADIVGFTKMSANK----SAHALVGLLNDLFGR FDRLCEQ- 0 [Part of this file has been deleted for brevity] P40144_1_159 0 ---------------------- 0 P30803_1_159 0 ---------------------- 0 O95622_1_159 0 ---------------------- 0 Q03343_1_159 0 ---------------------- 0 Q01341_1_159 0 ---------------------- 0 P30804_1_159 0 ---------------------- 0 O43306_1_159 0 ---------------------- 0 P97490_1_162 0 ---------------------- 0 P40146_1_162 0 ---------------------- 0 P40145_1_162 0 ---------------------- 0 O30820_1_149 0 ---------------------- 0 Q03101_1_149 0 ---------------------- 0 P16065_1_143 0 ---------------------- 0 P46197_1_168 0 ---------------------- 0 P20594_1_168 0 ---------------------- 0 P16067_1_168 0 ---------------------- 0 P18293_1_168 0 ---------------------- 0 P18910_1_168 0 ---------------------- 0 P16066_1_168 0 ---------------------- 0 P55202_1_154 0 ---------------------- 0 Q07553_1_152 0 ---------------------- 0 Q02846_1_152 0 ---------------------- 0 P52785_1_150 0 ---------------------- 0 P51840_1_150 0 ---------------------- 0 O19179_1_150 0 ---------------------- 0 P55203_1_151 0 ---------------------- 0 P51842_1_152 0 ---------------------- 0 P51841_1_152 0 ---------------------- 0 O02740_1_162 0 ---------------------- 0 P51839_1_163 0 ---------------------- 0 P55204_1_150 0 ---------------------- 0 P25092_1_150 0 ---------------------- 0 P70106_1_150 0 ---------------------- 0 P23897_1_150 0 ---------------------- 0 P55205_1_154 0 ---------------------- 0 Q09435_1_161 0 ---------------------- 0 P22717_1_147 0 ---------------------- 0 O75343_1_147 0 ---------------------- 0 Q9WVI4_1_149 0 ---------------------- 0 P33402_1_149 0 ---------------------- 0 Q9ERL9_1_152 0 ---------------------- 0 P19686_1_160 0 ---------------------- 0 Q02108_1_160 0 ---------------------- 0 P19687_1_161 0 ---------------------- 0 Q07093_1_158 0 ---------------------- 0 Q02153_1_165 0 ---------------------- 0 P20595_1_165 0 ---------------------- 0 P16068_1_165 0 ---------------------- 0 P40137_1_139 0 ---------------------- 0 P23466_1_154 0 ---------------------- 0 File: seqalign.log // /homes/user/test/qa/domainalign-keep/daf/54894.daf // /homes/user/test/qa/domainalign-keep/daf/55074.daf 5.0 DATA FILES SEQALIGN does not use a data file. 6.0 USAGE 6.1 COMMAND LINE ARGUMENTS Extend alignments (DAF file) with sequences (DHF file). Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers (* if not always prompted): -mode menu [1] This option specifies the mode of SEQALIGN operation. SEQALIGN takes as input a directory of either i. single sequences, ii. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file)). The user has to specify which. (Values: 1 (Single sequences); 2 (Multiple sequences (e.g. sequence set or alignment))) * -dhfinpath dirlist [./] This option specifies the location of sequences, e.g. DHF files (domain hits files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. * -dafinpath dirlist [./] This option specifies the location of sequences, e.g. DAF files (domain alignment files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. [-dhfindir] directory [./] This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. -amode menu [1] This option specifies which alignment algorithm to use. (Values: 1 (CLUSTALW); 2 (TCOFFEE (not yet implemented))) [-dafoutdir] outdir [./] This option specifies the location of DAF files (domain alignment files) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. -logfile outfile [seqalign.log] This option specifies the name of log file for the build. The log file contains messages about any errors arising while SEQALIGN ran. Additional (Optional) qualifiers: -forcetype boolean [N] This option specifies whether to force minimal domain classification data to be written to the output file in cases where singlet sequences were given as input file and no classification data was available Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-dhfinpath" associated qualifiers -extension string Default file extension "-dafinpath" associated qualifiers -extension string Default file extension "-dhfindir" associated qualifiers -extension1 string Default file extension "-dafoutdir" associated qualifiers -extension2 string Default file extension "-logfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit DOMALIGN-0.1.650/emboss_doc/text/domainalign.txt0000664000175000017500000007367212171064326016145 00000000000000 DOMAINALIGN documentation CONTENTS 1.0 SUMMARY 2.0 INPUTS & OUTPUTS 3.0 INPUT FILE FORMAT 4.0 OUTPUT FILE FORMAT 5.0 DATA FILES 6.0 USAGE 7.0 KNOWN BUGS & WARNINGS 8.0 NOTES 9.0 DESCRIPTION 10.0 ALGORITHM 11.0 RELATED APPLICATIONS 12.0 DIAGNOSTIC ERROR MESSAGES 13.0 AUTHORS 14.0 REFERENCES 1.0 SUMMARY Generate alignments (DAF file) for nodes in a DCF file 2.0 INPUTS & OUTPUTS DOMAINALIGN generates a DAF file (domain alignment file) for each user-defined node (e.g. family or superfamily) in a DCF file (domain classification file) that is read. Each DAF file contains a structure-based sequence alignment annotated with domain classification data. If the STAMP algorithm is used, structural superimpositions are also generated and saved to file (PDB format). The alignments are calculated by using STAMP or TCOFFEE and these applications must be installed on the system that is running DOMAINALIGN (see 'Notes' below). Clearly no alignment can be generated for nodes with a single entry (domain) only: sequences for such domains are (optionally) written to file (fasta format). DOMAINALIGN requires a directory of domain PDB files; the path and extension of these must be set by the user (via the ACD file) and also specified in the STAMP "pdb.directories" file (see 'Notes' below) A log file of diagnostic messages is written. The identifier (e.g SCOP Sunid) of the nodes from the DCF file are used to name the output files. The user also specifies the input file, paths for the two types of alignment files (output), path of singlet sequence files (if output) and name of log file. 3.0 INPUT FILE FORMAT The format of the DCF (domain classification file) is described in SCOPPARSE documentation Input files for usage example File: all.scop2 ID D1CS4A_ XX EN 1CS4 XX TY SCOP XX SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Adenylyl and guanylyl cyclase catalytic domain XX FA Adenylyl and guanylyl cyclase catalytic domain XX DO Adenylyl cyclase VC1, domain C1a XX OS Dog (Canis familiaris) XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // ID D1FX2A_ XX EN 1FX2 XX TY SCOP XX SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Adenylyl and guanylyl cyclase catalytic domain XX FA Adenylyl and guanylyl cyclase catalytic domain XX DO Receptor-type monomeric adenylyl cyclase XX OS Trypanosome (Trypanosoma brucei), different isoform XX NC 1 XX CN [1] XX [Part of this file has been deleted for brevity] XX EN 4AT1 XX TY SCOP XX SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX DO Aspartate carbamoyltransferase XX OS Escherichia coli XX NC 1 XX CN [1] XX CH B CHAIN; 8 START; 100 END; // ID D4AT1D1 XX EN 4AT1 XX TY SCOP XX SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX DO Aspartate carbamoyltransferase XX OS Escherichia coli XX NC 1 XX CN [1] XX CH D CHAIN; 8 START; 100 END; // 4.0 OUTPUT FILE FORMAT Structure-based sequence alignment The DAF (domain alignment file) format (Figure 1) consists of an alignment in EMBOSS "simple" multiple sequence alignment format with domain classification records. All lines other than sequence lines begin with '#' to denote a comment. The domain classification records for the appopriate node from the DCF file are given at the top of the file above the alignment. The records shown are TY (domain type, either SCOP or CATH), CL (class), FO (fold), SF (superfamily) and FA (family). For CATH domains, AR (architecture) and TP (topology) may also be given. Regardless of which node (family, superfamily etc) is represented, a unique identifier for the node is given after SI. Below the classification records, there are blocks that contain the sequence names, positions and aligned sequences. The names are the 7 character domain identifier codes taken from the DCF file. The positions are the start and end residue positions of the appropriate section of sequence. The sequence uses '-' as a gap character. The STAMP 'Post similar' line is given as a markup line underneath the sequence but no dssp assignments are written. Output files for usage example File: 54894.ent REMARK Output from transform REMARK STAMP Package (Russell and Barton Proteins, 14, 309-323, 1992) REMARK Domains were read from the file ./domainalign-1234567890.1234.sort REMARK Chains are labelled sequentially starting with 'A' and REMARK after the order given in the file ./domainalign-1234567890.1234.sort REMARK The domains in this file are: REMARK d4at1b1 chain A REMARK d4at1d1_1 chain B REMARK Does not include heteroatoms REMARK Does not include DNA/RNA REMARK Does not include waters ATOM 1 N GLY A 8 13.557 82.383 35.829 1.00 92.06 N ATOM 2 CA GLY A 8 14.363 82.355 34.620 1.00 92.63 C ATOM 3 C GLY A 8 14.480 83.797 34.150 1.00 91.80 C ATOM 4 O GLY A 8 13.625 84.596 34.527 1.00 93.34 O ATOM 5 N VAL A 9 15.499 84.132 33.352 1.00 90.04 N ATOM 6 CA VAL A 9 15.799 85.525 33.008 1.00 89.55 C ATOM 7 C VAL A 9 15.294 86.094 31.646 1.00 90.94 C ATOM 8 O VAL A 9 14.395 85.528 31.008 1.00 91.46 O ATOM 9 CB VAL A 9 17.381 85.731 33.167 1.00 88.13 C ATOM 10 CG1 VAL A 9 17.571 86.421 34.506 1.00 86.27 C ATOM 11 CG2 VAL A 9 18.232 84.456 33.191 1.00 86.95 C ATOM 12 N GLU A 10 15.892 87.223 31.201 1.00 89.98 N ATOM 13 CA GLU A 10 15.543 87.988 30.004 1.00 87.19 C ATOM 14 C GLU A 10 16.748 88.251 29.055 1.00 83.25 C ATOM 15 O GLU A 10 17.879 87.817 29.318 1.00 81.89 O ATOM 16 CB GLU A 10 14.876 89.324 30.474 1.00 89.77 C ATOM 17 CG GLU A 10 15.390 90.058 31.748 1.00 93.53 C ATOM 18 CD GLU A 10 16.862 90.513 31.791 1.00 96.84 C ATOM 19 OE1 GLU A 10 17.570 90.129 32.731 1.00 98.75 O ATOM 20 OE2 GLU A 10 17.306 91.258 30.905 1.00 97.00 O ATOM 21 N ALA A 11 16.471 89.023 27.987 1.00 77.76 N ATOM 22 CA ALA A 11 17.315 89.379 26.829 1.00 71.32 C ATOM 23 C ALA A 11 18.829 89.525 26.622 1.00 65.96 C ATOM 24 O ALA A 11 19.605 90.124 27.370 1.00 64.35 O ATOM 25 CB ALA A 11 16.692 90.608 26.193 1.00 70.48 C ATOM 26 N ILE A 12 19.133 88.956 25.457 1.00 62.08 N ATOM 27 CA ILE A 12 20.419 88.929 24.778 1.00 60.99 C ATOM 28 C ILE A 12 19.984 89.116 23.325 1.00 61.87 C ATOM 29 O ILE A 12 18.841 88.755 22.999 1.00 62.16 O ATOM 30 CB ILE A 12 21.198 87.545 24.850 1.00 59.43 C ATOM 31 CG1 ILE A 12 20.354 86.363 24.347 1.00 55.38 C ATOM 32 CG2 ILE A 12 21.619 87.298 26.290 1.00 59.29 C ATOM 33 CD1 ILE A 12 21.107 85.072 24.029 1.00 50.25 C ATOM 34 N LYS A 13 20.745 89.683 22.389 1.00 62.88 N ATOM 35 CA LYS A 13 20.307 89.668 20.991 1.00 63.76 C ATOM 36 C LYS A 13 21.229 88.611 20.439 1.00 63.26 C ATOM 37 O LYS A 13 22.425 88.631 20.755 1.00 63.54 O ATOM 38 CB LYS A 13 20.570 90.941 20.133 1.00 65.83 C ATOM 39 CG LYS A 13 21.100 92.232 20.765 1.00 68.73 C [Part of this file has been deleted for brevity] ATOM 675 O LYS B 94 12.694 74.659 17.436 1.00 60.00 O ATOM 676 CB LYS B 94 11.414 76.090 20.144 1.00 54.56 C ATOM 677 CG LYS B 94 10.901 77.252 20.962 1.00 56.83 C ATOM 678 CD LYS B 94 9.923 76.671 21.990 1.00 59.11 C ATOM 679 CE LYS B 94 9.043 77.717 22.641 1.00 60.10 C ATOM 680 NZ LYS B 94 9.890 78.702 23.259 1.00 64.17 N ATOM 681 N SER B 95 13.444 74.034 19.484 1.00 54.16 N ATOM 682 CA SER B 95 13.785 72.651 19.195 1.00 49.80 C ATOM 683 C SER B 95 13.767 71.904 20.531 1.00 49.50 C ATOM 684 O SER B 95 13.715 72.494 21.617 1.00 50.66 O ATOM 685 CB SER B 95 15.186 72.559 18.595 1.00 49.06 C ATOM 686 OG SER B 95 15.488 73.550 17.615 1.00 48.30 O ATOM 687 N ARG B 96 13.817 70.590 20.497 1.00 50.27 N ATOM 688 CA ARG B 96 13.868 69.771 21.694 1.00 49.58 C ATOM 689 C ARG B 96 14.839 68.647 21.295 1.00 47.31 C ATOM 690 O ARG B 96 15.006 68.414 20.088 1.00 44.69 O ATOM 691 CB ARG B 96 12.426 69.305 21.983 1.00 53.09 C ATOM 692 CG ARG B 96 12.197 68.404 23.200 1.00 58.05 C ATOM 693 CD ARG B 96 10.794 68.557 23.787 1.00 61.70 C ATOM 694 NE ARG B 96 10.618 69.895 24.354 1.00 66.11 N ATOM 695 CZ ARG B 96 9.772 70.814 23.850 1.00 69.37 C ATOM 696 NH1 ARG B 96 9.702 72.024 24.422 1.00 71.16 N ATOM 697 NH2 ARG B 96 8.988 70.558 22.790 1.00 70.99 N ATOM 698 N PRO B 97 15.591 68.002 22.198 1.00 47.31 N ATOM 699 CA PRO B 97 16.438 66.853 21.917 1.00 47.03 C ATOM 700 C PRO B 97 15.755 65.610 21.357 1.00 46.69 C ATOM 701 O PRO B 97 14.800 65.056 21.929 1.00 47.44 O ATOM 702 CB PRO B 97 17.138 66.581 23.238 1.00 48.99 C ATOM 703 CG PRO B 97 17.256 67.940 23.887 1.00 49.17 C ATOM 704 CD PRO B 97 15.868 68.473 23.559 1.00 49.45 C ATOM 705 N SER B 98 16.313 65.239 20.191 1.00 45.02 N ATOM 706 CA SER B 98 16.016 64.022 19.436 1.00 41.65 C ATOM 707 C SER B 98 17.197 63.101 19.711 1.00 39.46 C ATOM 708 O SER B 98 18.327 63.608 19.718 1.00 38.78 O ATOM 709 CB SER B 98 15.952 64.291 17.940 1.00 42.24 C ATOM 710 OG SER B 98 14.657 64.744 17.586 1.00 46.01 O ATOM 711 N LEU B 99 16.992 61.793 19.950 1.00 36.31 N ATOM 712 CA LEU B 99 18.078 60.869 20.273 1.00 33.04 C ATOM 713 C LEU B 99 19.004 60.692 19.051 1.00 33.65 C ATOM 714 O LEU B 99 18.467 60.339 17.994 1.00 35.86 O ATOM 715 CB LEU B 99 17.420 59.573 20.697 1.00 29.39 C ATOM 716 CG LEU B 99 18.126 58.649 21.690 1.00 28.47 C ATOM 717 CD1 LEU B 99 18.261 59.352 23.048 1.00 27.24 C ATOM 718 CD2 LEU B 99 17.332 57.342 21.817 1.00 25.66 C ATOM 719 N PRO B 100 20.325 60.971 19.041 1.00 33.12 N ATOM 720 CA PRO B 100 21.146 60.885 17.830 1.00 35.17 C ATOM 721 C PRO B 100 21.517 59.413 17.592 1.00 38.22 C ATOM 722 O PRO B 100 21.547 58.620 18.542 1.00 36.98 O ATOM 723 CB PRO B 100 22.317 61.776 18.143 1.00 34.28 C ATOM 724 CG PRO B 100 22.530 61.464 19.626 1.00 33.62 C ATOM 725 CD PRO B 100 21.124 61.360 20.204 1.00 31.93 C Directory: daf This directory contains output files, for example 54894.daf and 55074.daf. File: daf/54894.daf # TY SCOP # XX # CL Alpha and beta proteins (a+b) # XX # FO Ferredoxin-like # XX # SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain # XX # FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain # XX # SI 54894 # XX # Number 10 20 30 40 50 d4at1b1 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPXSGEMGRKDLIKIEN 0 d4at1d1 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGXEMGRKDLIKIEN 0 # Post_similar 111111111111111111111111111111111111111111-0-111111111111 # Number 60 70 80 90 d4at1b1 0 TFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0 d4at1d1 0 TFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0 # Post_similar 1111111111111111111111111111111111111 File: daf/55074.daf # TY SCOP # XX # CL Alpha and beta proteins (a+b) # XX # FO Ferredoxin-like # XX # SF Adenylyl and guanylyl cyclase catalytic domain # XX # FA Adenylyl and guanylyl cyclase catalytic domain # XX # SI 55074 # XX # Number 10 20 30 40 50 d1cs4a_ 0 MMFHKIYIQKXHXDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENH 0 d1fx2a_ 0 XXNNNRAPXKEPTDPVTLIFTDIESSTALWAAXHPDLMPDAVAAHHRMVRSLIGRYK 0 # Post_similar --000000-0-0-1111111111111111111-000111111111111111111111 # Number 60 70 80 90 100 110 d1cs4a_ 0 CLRIKILGDCYYCVSGLPEARADHAHCCVEMGMDMIEAISLVREMXTXGXXXXXXXX 0 d1fx2a_ 0 CYEVKTVGDSFMIAXXXXSKXXXSPFAAVQLAQELQLCFLHXHDWGTNALDDSYREF 0 # Post_similar 11111111111111----00---111111111111111111-000-0-0-------- # Number 120 130 140 150 160 170 d1cs4a_ 0 XXXXXXXXXXXXXXXXXXXXXXXXXXXVNVNMRVGIHSGRVHXCGVLGLRKWQFDVW 0 d1fx2a_ 0 EEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRHDXEXVTKGYDYY 0 # Post_similar ---------------------------011111111111111-111-0-00001111 # Number 180 190 200 210 220 d1cs4a_ 0 SNDVTLANHMEAGGKAGRIHITKATLSYLNXXXGXDYEVEPGCGGERNXAYLKEHSI 0 d1fx2a_ 0 GRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALXGDXVALRGXVSDPV 0 # Post_similar 111111111111111111111111111111---0-1111111-00-00-00-00111 # Number 230 240 250 d1cs4a_ 0 ETFLILXXXXXXXXXXXXXXXXXX 0 d1fx2a_ 0 KMYQLNTVPSRNFAALRLDREYFD 0 # Post_similar 111111------------------ File: 55074.ent REMARK Output from transform REMARK STAMP Package (Russell and Barton Proteins, 14, 309-323, 1992) REMARK Domains were read from the file ./domainalign-1234567890.1234.sort REMARK Chains are labelled sequentially starting with 'A' and REMARK after the order given in the file ./domainalign-1234567890.1234.sort REMARK The domains in this file are: REMARK d1cs4a_ chain A REMARK d1fx2a__1 chain B REMARK Does not include heteroatoms REMARK Does not include DNA/RNA REMARK Does not include waters ATOM 1 N MET A 377 28.568 -27.770 32.255 1.00 73.77 N ATOM 2 CA MET A 377 28.292 -26.443 32.794 1.00 72.28 C ATOM 3 C MET A 377 29.325 -25.377 32.396 1.00 69.48 C ATOM 4 O MET A 377 30.485 -25.687 32.098 1.00 67.04 O ATOM 5 CB MET A 377 28.075 -26.504 34.312 1.00 74.79 C ATOM 6 CG MET A 377 29.171 -27.205 35.092 1.00 78.73 C ATOM 7 SD MET A 377 28.708 -27.446 36.824 1.00 83.74 S ATOM 8 CE MET A 377 28.745 -25.745 37.440 1.00 81.94 C ATOM 9 N MET A 378 28.883 -24.120 32.395 1.00 66.44 N ATOM 10 CA MET A 378 29.698 -22.969 32.011 1.00 62.94 C ATOM 11 C MET A 378 30.928 -22.727 32.886 1.00 59.70 C ATOM 12 O MET A 378 32.059 -22.739 32.400 1.00 57.00 O ATOM 13 CB MET A 378 28.824 -21.715 31.966 1.00 64.01 C ATOM 14 CG MET A 378 27.551 -21.872 31.137 1.00 64.35 C ATOM 15 SD MET A 378 27.897 -22.219 29.403 1.00 67.83 S ATOM 16 CE MET A 378 27.844 -24.014 29.357 1.00 65.41 C ATOM 17 N PHE A 379 30.697 -22.474 34.167 1.00 56.03 N ATOM 18 CA PHE A 379 31.763 -22.225 35.123 1.00 53.16 C ATOM 19 C PHE A 379 32.157 -23.501 35.837 1.00 51.53 C ATOM 20 O PHE A 379 31.372 -24.440 35.914 1.00 53.09 O ATOM 21 CB PHE A 379 31.296 -21.227 36.186 1.00 54.14 C ATOM 22 CG PHE A 379 31.091 -19.832 35.671 1.00 51.13 C ATOM 23 CD1 PHE A 379 29.927 -19.493 34.986 1.00 50.12 C ATOM 24 CD2 PHE A 379 32.049 -18.846 35.907 1.00 49.63 C ATOM 25 CE1 PHE A 379 29.716 -18.196 34.546 1.00 51.63 C ATOM 26 CE2 PHE A 379 31.852 -17.545 35.474 1.00 50.16 C ATOM 27 CZ PHE A 379 30.682 -17.216 34.792 1.00 51.72 C ATOM 28 N HIS A 380 33.371 -23.529 36.372 1.00 50.09 N ATOM 29 CA HIS A 380 33.830 -24.687 37.120 1.00 49.62 C ATOM 30 C HIS A 380 33.046 -24.672 38.431 1.00 49.26 C ATOM 31 O HIS A 380 32.579 -23.623 38.866 1.00 50.30 O ATOM 32 CB HIS A 380 35.327 -24.574 37.439 1.00 52.29 C ATOM 33 CG HIS A 380 36.235 -24.929 36.299 1.00 53.66 C ATOM 34 ND1 HIS A 380 36.782 -23.983 35.457 1.00 53.12 N ATOM 35 CD2 HIS A 380 36.737 -26.122 35.898 1.00 52.37 C ATOM 36 CE1 HIS A 380 37.581 -24.576 34.588 1.00 50.60 C ATOM 37 NE2 HIS A 380 37.572 -25.873 34.833 1.00 52.60 N ATOM 38 N LYS A 381 32.879 -25.832 39.051 1.00 50.19 N ATOM 39 CA LYS A 381 32.167 -25.897 40.318 1.00 51.93 C [Part of this file has been deleted for brevity] ATOM 1806 CG ASP B1117 55.881 2.260 56.337 1.00 70.08 C ATOM 1807 OD1 ASP B1117 55.414 2.017 55.197 1.00 73.38 O ATOM 1808 OD2 ASP B1117 57.084 2.059 56.637 1.00 70.53 O ATOM 1809 N ARG B1118 52.764 0.077 56.474 1.00 66.61 N ATOM 1810 CA ARG B1118 52.481 -1.377 56.573 1.00 68.20 C ATOM 1811 C ARG B1118 53.212 -2.511 55.828 1.00 68.77 C ATOM 1812 O ARG B1118 54.421 -2.488 55.587 1.00 70.57 O ATOM 1813 CB ARG B1118 51.033 -1.596 56.196 1.00 71.02 C ATOM 1814 CG ARG B1118 49.988 -0.730 56.780 1.00 66.89 C ATOM 1815 CD ARG B1118 48.805 -0.985 55.855 1.00 69.79 C ATOM 1816 NE ARG B1118 47.548 -0.457 56.346 1.00 65.16 N ATOM 1817 CZ ARG B1118 47.350 0.805 56.714 1.00 67.30 C ATOM 1818 NH1 ARG B1118 48.318 1.717 56.649 1.00 62.67 N ATOM 1819 NH2 ARG B1118 46.198 1.137 57.253 1.00 60.83 N ATOM 1820 N GLU B1119 52.370 -3.490 55.468 1.00 74.62 N ATOM 1821 CA GLU B1119 52.576 -4.775 54.756 1.00 71.44 C ATOM 1822 C GLU B1119 51.216 -5.345 55.152 1.00 68.30 C ATOM 1823 O GLU B1119 50.787 -5.071 56.255 1.00 70.28 O ATOM 1824 CB GLU B1119 53.628 -5.683 55.451 1.00 72.63 C ATOM 1825 CG GLU B1119 53.056 -6.991 56.217 1.00 68.78 C ATOM 1826 CD GLU B1119 52.428 -6.728 57.622 1.00 67.37 C ATOM 1827 OE1 GLU B1119 52.888 -5.743 58.270 1.00 63.79 O ATOM 1828 OE2 GLU B1119 51.452 -7.444 58.067 1.00 24.30 O ATOM 1829 N TYR B1120 50.504 -6.074 54.309 1.00 69.56 N ATOM 1830 CA TYR B1120 49.237 -6.679 54.769 1.00 66.82 C ATOM 1831 C TYR B1120 49.096 -7.992 54.006 1.00 69.41 C ATOM 1832 O TYR B1120 49.547 -8.082 52.863 1.00 60.86 O ATOM 1833 CB TYR B1120 48.062 -5.721 54.629 1.00 64.84 C ATOM 1834 CG TYR B1120 46.960 -6.107 53.681 1.00 72.65 C ATOM 1835 CD1 TYR B1120 47.056 -5.809 52.324 1.00 69.04 C ATOM 1836 CD2 TYR B1120 45.764 -6.658 54.154 1.00 72.45 C ATOM 1837 CE1 TYR B1120 45.996 -6.038 51.461 1.00 74.31 C ATOM 1838 CE2 TYR B1120 44.688 -6.892 53.292 1.00 74.14 C ATOM 1839 CZ TYR B1120 44.815 -6.576 51.947 1.00 77.01 C ATOM 1840 OH TYR B1120 43.765 -6.791 51.087 1.00 73.74 O ATOM 1841 N PHE B1121 48.537 -9.016 54.663 1.00 67.32 N ATOM 1842 CA PHE B1121 48.401 -10.387 54.120 1.00 68.14 C ATOM 1843 C PHE B1121 48.561 -10.745 52.626 1.00 68.72 C ATOM 1844 O PHE B1121 49.618 -11.228 52.233 1.00 71.84 O ATOM 1845 CB PHE B1121 47.210 -11.123 54.717 1.00 64.05 C ATOM 1846 CG PHE B1121 47.408 -12.619 54.794 1.00 61.04 C ATOM 1847 CD1 PHE B1121 48.271 -13.164 55.734 1.00 58.84 C ATOM 1848 CD2 PHE B1121 46.737 -13.479 53.925 1.00 63.12 C ATOM 1849 CE1 PHE B1121 48.466 -14.540 55.815 1.00 60.74 C ATOM 1850 CE2 PHE B1121 46.925 -14.859 53.999 1.00 59.31 C ATOM 1851 CZ PHE B1121 47.788 -15.392 54.941 1.00 64.18 C ATOM 1852 N ASP B1122 47.527 -10.585 51.805 1.00 72.82 N ATOM 1853 CA ASP B1122 47.656 -10.920 50.374 1.00 73.64 C ATOM 1854 C ASP B1122 46.520 -10.365 49.515 1.00 74.17 C ATOM 1855 O ASP B1122 46.464 -10.761 48.332 1.00 75.01 O ATOM 1856 CB ASP B1122 47.790 -12.446 50.171 1.00 73.22 C File: domainalign.log Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' Replaced ' ' in STAMP alignment with 'X' 5.0 DATA FILES DOMAINALIGN does not use any data files but uses the STAMP "pdb.directories" file which specifies the permissible prefix, extension and path of PDB files used by STAMP. This file should look like : test_data/ - .dent /data/pdb - - /data/pdb _ .ent /data/pdb _ .pdb /data/pdb pdb .ent /data/pdbscop _ _ /data/pdbscop _ .ent /data/pdbscop _ .pdb /data/pdbscop pdb .ent ./ _ _ ./ _ .ent ./ _ .ent.z ./ _ .ent.gz ./ _ .pdb ./ _ .pdb.Z ./ _ .pdb.gz ./ pdb .ent ./ pdb .ent.Z ./ pdb .ent.gz /data/CASS1/pdb/coords/ _ .pdb /data/CASS1/pdb/coords/ _ .pdb.Z /data/CASS1/pdb/coords/ _ .pdb.gz 6.0 USAGE 6.1 COMMAND LINE ARGUMENTS Generate alignments (DAF file) for nodes in a DCF file. Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers (* if not always prompted): [-dcfinfile] infile This option specifies the name of DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. [-pdbdir] directory [./] This option specifies the location of domain PDB files (input). A 'domain PDB file' contains coordinate data for a single domain from SCOP or CATH, in PDB format. The files are generated by using DOMAINER. -node menu [1] This option specifies the node for redundancy removal. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies. For example by selecting 'Class' entries belonging to the same Class will be non-redundant. (Values: 1 (Class (SCOP)); 2 (Fold (SCOP)); 3 (Superfamily (SCOP)); 4 (Family (SCOP)); 5 (Class (CATH)); 6 (Architecture (CATH)); 7 (Topology (CATH)); 8 (Homologous Superfamily (CATH)); 9 (Family (CATH))) -mode menu [1] This option specifies the alignment algorithm to use. (Values: 1 (STAMP); 2 (TCOFFEE)) -[no]keepsinglets toggle [Y] This option specifies whether to write sequences of singlet families to file. If you specify this option, the sequence for each singlet family are written to file (output). [-dafoutdir] outdir [./] This option specifies the location of DAF files (domain alignment files) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The files are in clustal format and are annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. * -singletsoutdir outdir [./] This option specifies the location of DHF files (domain hits files) for singlet sequences (output). The singlets are written out as a 'domain hits file' - which contains database hits (sequences) with domain classification information, in FASTA format. * -superoutdir outdir [./] This option specifies the location of structural superimposition files (output). A file in PDB format of the structural superimposition is generated for each family if the STAMP algorithm is used. -logfile outfile [domainalign.log] This option specifies the name of log file (output). The log file contains messages about any errors arising while domainalign ran. Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-pdbdir" associated qualifiers -extension2 string Default file extension "-dafoutdir" associated qualifiers -extension3 string Default file extension "-singletsoutdir" associated qualifiers -extension string Default file extension "-superoutdir" associated qualifiers -extension string Default file extension "-logfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit DOMALIGN-0.1.650/emboss_doc/text/domainrep.txt0000664000175000017500000002110512171064326015621 00000000000000 DOMAINREP documentation CONTENTS 1.0 SUMMARY 2.0 INPUTS & OUTPUTS 3.0 INPUT FILE FORMAT 4.0 OUTPUT FILE FORMAT 5.0 DATA FILES 6.0 USAGE 7.0 KNOWN BUGS & WARNINGS 8.0 NOTES 9.0 DESCRIPTION 10.0 ALGORITHM 11.0 RELATED APPLICATIONS 12.0 DIAGNOSTIC ERROR MESSAGES 13.0 AUTHORS 14.0 REFERENCES 1.0 SUMMARY Reorder DCF file to identify representative structures 2.0 INPUTS & OUTPUTS DOMAINREP reads a DCF file (domain classification file) and writes a DCF file containing the same data except that the order of domains within each user-specified node (e.g. family) in the hierarchy may be changed so that the representative structure of each node is given first. The representative structure is found by using stamp and this application must be installed on the system that is running DOMAINREP and correctly configured (see 'Notes' below). A 'domain PDB file' for each domain in the DCF file must exist in a directory specified in the stamp "pdb.directories" file (see 'Notes' below). The domain PDB file contains coordinate data for a single domain from SCOP or CATH, in PDB format. The input and output files are specified by the user. 3.0 INPUT FILE FORMAT The format of the DCF file is described in the SCOPPARSE documentation. Input files for usage example File: all.scop2 ID D1CS4A_ XX EN 1CS4 XX TY SCOP XX SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Adenylyl and guanylyl cyclase catalytic domain XX FA Adenylyl and guanylyl cyclase catalytic domain XX DO Adenylyl cyclase VC1, domain C1a XX OS Dog (Canis familiaris) XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // ID D1FX2A_ XX EN 1FX2 XX TY SCOP XX SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Adenylyl and guanylyl cyclase catalytic domain XX FA Adenylyl and guanylyl cyclase catalytic domain XX DO Receptor-type monomeric adenylyl cyclase XX OS Trypanosome (Trypanosoma brucei), different isoform XX NC 1 XX CN [1] XX [Part of this file has been deleted for brevity] XX EN 4AT1 XX TY SCOP XX SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX DO Aspartate carbamoyltransferase XX OS Escherichia coli XX NC 1 XX CN [1] XX CH B CHAIN; 8 START; 100 END; // ID D4AT1D1 XX EN 4AT1 XX TY SCOP XX SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX DO Aspartate carbamoyltransferase XX OS Escherichia coli XX NC 1 XX CN [1] XX CH D CHAIN; 8 START; 100 END; // 4.0 OUTPUT FILE FORMAT The format of the DCF file is described in the SCOPPARSE documentation. Output files for usage example File: all_rep1st.scop ID D4AT1B1 XX EN 4AT1 XX TY SCOP XX SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX DO Aspartate carbamoyltransferase XX OS Escherichia coli XX NC 1 XX CN [1] XX CH B CHAIN; 8 START; 100 END; // ID D1CS4A_ XX EN 1CS4 XX TY SCOP XX SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Adenylyl and guanylyl cyclase catalytic domain XX FA Adenylyl and guanylyl cyclase catalytic domain XX DO Adenylyl cyclase VC1, domain C1a XX OS Dog (Canis familiaris) XX NC 1 XX CN [1] XX [Part of this file has been deleted for brevity] XX EN 1FX2 XX TY SCOP XX SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Adenylyl and guanylyl cyclase catalytic domain XX FA Adenylyl and guanylyl cyclase catalytic domain XX DO Receptor-type monomeric adenylyl cyclase XX OS Trypanosome (Trypanosoma brucei), different isoform XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // ID D4AT1D1 XX EN 4AT1 XX TY SCOP XX SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX DO Aspartate carbamoyltransferase XX OS Escherichia coli XX NC 1 XX CN [1] XX CH D CHAIN; 8 START; 100 END; // 5.0 DATA FILES DOMAINREP does not use any data files but does make use of the stamp "pdb.directories" file (see 'Notes'). 6.0 USAGE 6.1 COMMAND LINE ARGUMENTS Reorder DCF file to identify representative structures. Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-dcfinfile] infile This option specifies the name of DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. -node menu [1] This option specifies the node fore reordering the file. Reordering can be done for any specified node in the SCOP or CATH hierarchies. For example by selecting 'Class' entries belonging to the same Class will be reordered in turn. (Values: 1 (Class (SCOP)); 2 (Fold (SCOP)); 3 (Superfamily (SCOP)); 4 (Family (SCOP)); 5 (Class (CATH)); 6 (Architecture (CATH)); 7 (Topology (CATH)); 8 (Homologous Superfamily (CATH)); 9 (Family (CATH))) [-dcfoutfile] outfile [test.scop] This option specifies the name of DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. 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The output files have the same base name as the input files. The path and extension of the input and output files are specified by the user in the ACD file. 3.0 INPUT FILE FORMAT All common sequence format are supported. 4.0 OUTPUT FILE FORMAT The output file contains 7 columns as follows: * (1) Sequence number (sequential order in input file) of first sequence of a pair. * (2) Accesion number of first sequence of a pair. * (3) A ':' is always given. * (4) Sequence number of second sequence. * (5) Accesion number of second sequence. * (6) A ':' is always given. * (7) Sequence similarity value (2dp). Output files for usage example File: swtiny1.out 1 Q9WVI4 : 2 Q9ERL9 : 90.48 1 Q9WVI4 : 3 Q9DGG6 : 55.70 1 Q9WVI4 : 4 Q99396 : 54.74 1 Q9WVI4 : 5 Q99280 : 57.66 2 Q9ERL9 : 3 Q9DGG6 : 58.28 2 Q9ERL9 : 4 Q99396 : 56.39 2 Q9ERL9 : 5 Q99280 : 62.31 3 Q9DGG6 : 4 Q99396 : 52.26 3 Q9DGG6 : 5 Q99280 : 53.99 4 Q99396 : 5 Q99280 : 83.41 File: swtiny2.out 1 O58452 : 2 O30129 : 82.42 1 O58452 : 3 O26938 : 75.56 2 O30129 : 3 O26938 : 71.43 File: allversusall.log // /homes/user/test/data/structure/allversusall/swtiny1.fasta // /homes/user/test/data/structure/allversusall/swtiny2.fasta 5.0 DATA FILES ALLVERSUSALL uses a residue substitution matrix. 6.0 USAGE 6.1 COMMAND LINE ARGUMENTS Sequence similarity data from all-versus-all comparison. Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-seqinpath] dirlist [./] Sequence directories [-datoutdir] outdir [./] This option specifies the location of sequence similarity data files (output). -logfile outfile [allversusall.log] This option specifies the name of ALLVERSUSALL log file (output). The log file contains messages about any errors arising while ALLVERSUSALL ran. Additional (Optional) qualifiers: -matrix matrixf [EBLOSUM62] This option specifies the residue substitution matrix that is used for sequence comparison. -gapopen float [10.0 for any sequence] This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. (Floating point number from 1.0 to 100.0) -gapextend float [0.5 for any sequence] This option specifies the gap extension penalty. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. (Floating point number from 0.0 to 10.0) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-seqinpath" associated qualifiers -extension1 string Default file extension "-datoutdir" associated qualifiers -extension2 string Default file extension "-logfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit DOMALIGN-0.1.650/emboss_doc/text/.cvsignore0000664000175000017500000000002511326112657015102 00000000000000Makefile.in Makefile DOMALIGN-0.1.650/emboss_doc/html/0002775000175000017500000000000012171070665013150 500000000000000DOMALIGN-0.1.650/emboss_doc/html/CVS/0002775000175000017500000000000012171064326013600 500000000000000DOMALIGN-0.1.650/emboss_doc/html/CVS/Entries0000664000175000017500000000051312171064326015051 00000000000000/.cvsignore/1.1/Thu Jan 21 17:58:07 2010/-kk/ /Makefile.am/1.1/Tue Mar 7 12:47:55 2006// /index.html/1.2/Wed Jul 12 15:50:44 2006// /allversusall.html/1.30/Mon Jul 15 21:25:42 2013// /domainalign.html/1.33/Mon Jul 15 21:25:42 2013// /domainrep.html/1.24/Mon Jul 15 21:25:42 2013// /seqalign.html/1.31/Mon Jul 15 21:25:42 2013// D DOMALIGN-0.1.650/emboss_doc/html/CVS/Root0000664000175000017500000000005612000651452014356 00000000000000rice@dev.open-bio.org:/home/repository/emboss DOMALIGN-0.1.650/emboss_doc/html/CVS/Repository0000664000175000017500000000005712000651452015613 00000000000000emboss/emboss/embassy/domalign/emboss_doc/html DOMALIGN-0.1.650/emboss_doc/html/domainalign.html0000664000175000017500000021603212171064326016237 00000000000000 EMBASSY: DOMAINALIGN documentation.

DOMAINALIGN documentation


 


CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES



1.0 SUMMARY

Generate alignments (DAF file) for nodes in a DCF file


2.0 INPUTS & OUTPUTS

DOMAINALIGN generates a DAF file (domain alignment file) for each user-defined node (e.g. family or superfamily) in a DCF file (domain classification file) that is read. Each DAF file contains a structure-based sequence alignment annotated with domain classification data. If the STAMP algorithm is used, structural superimpositions are also generated and saved to file (PDB format). The alignments are calculated by using STAMP or TCOFFEE and these applications must be installed on the system that is running DOMAINALIGN (see 'Notes' below).
Clearly no alignment can be generated for nodes with a single entry (domain) only: sequences for such domains are (optionally) written to file (fasta format).
DOMAINALIGN requires a directory of domain PDB files; the path and extension of these must be set by the user (via the ACD file) and also specified in the STAMP "pdb.directories" file (see 'Notes' below)
A log file of diagnostic messages is written. The identifier (e.g SCOP Sunid) of the nodes from the DCF file are used to name the output files. The user also specifies the input file, paths for the two types of alignment files (output), path of singlet sequence files (if output) and name of log file.


3.0 INPUT FILE FORMAT

The format of the DCF (domain classification file) is described in SCOPPARSE documentation

Input files for usage example

File: all.scop2

ID   D1CS4A_
XX
EN   1CS4
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Adenylyl cyclase VC1, domain C1a
XX
OS   Dog (Canis familiaris)
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1FX2A_
XX
EN   1FX2
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Receptor-type monomeric adenylyl cyclase
XX
OS   Trypanosome (Trypanosoma brucei), different isoform
XX
NC   1
XX
CN   [1]
XX


  [Part of this file has been deleted for brevity]

XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   B CHAIN; 8 START; 100 END;
//
ID   D4AT1D1
XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   D CHAIN; 8 START; 100 END;
//




4.0 OUTPUT FILE FORMAT

Structure-based sequence alignment
The DAF (domain alignment file) format (Figure 1) consists of an alignment in EMBOSS "simple" multiple sequence alignment format with domain classification records. All lines other than sequence lines begin with '#' to denote a comment. The domain classification records for the appopriate node from the DCF file are given at the top of the file above the alignment. The records shown are TY (domain type, either SCOP or CATH), CL (class), FO (fold), SF (superfamily) and FA (family). For CATH domains, AR (architecture) and TP (topology) may also be given. Regardless of which node (family, superfamily etc) is represented, a unique identifier for the node is given after SI. Below the classification records, there are blocks that contain the sequence names, positions and aligned sequences. The names are the 7 character domain identifier codes taken from the DCF file. The positions are the start and end residue positions of the appropriate section of sequence. The sequence uses '-' as a gap character. The STAMP 'Post similar' line is given as a markup line underneath the sequence but no dssp assignments are written.

Output files for usage example

File: 54894.ent

REMARK Output from transform
REMARK  STAMP Package (Russell and Barton Proteins, 14, 309-323, 1992)
REMARK Domains were read from the file ./domainalign-1234567890.1234.sort
REMARK Chains are labelled sequentially starting with 'A' and
REMARK  after the order given in the file ./domainalign-1234567890.1234.sort
REMARK The domains in this file are:
REMARK       d4at1b1  chain A 
REMARK       d4at1d1_1  chain B 
REMARK Does not include heteroatoms
REMARK  Does not include DNA/RNA 
REMARK Does not include waters
ATOM      1  N   GLY A   8      13.557  82.383  35.829  1.00 92.06           N  
ATOM      2  CA  GLY A   8      14.363  82.355  34.620  1.00 92.63           C  
ATOM      3  C   GLY A   8      14.480  83.797  34.150  1.00 91.80           C  
ATOM      4  O   GLY A   8      13.625  84.596  34.527  1.00 93.34           O  
ATOM      5  N   VAL A   9      15.499  84.132  33.352  1.00 90.04           N  
ATOM      6  CA  VAL A   9      15.799  85.525  33.008  1.00 89.55           C  
ATOM      7  C   VAL A   9      15.294  86.094  31.646  1.00 90.94           C  
ATOM      8  O   VAL A   9      14.395  85.528  31.008  1.00 91.46           O  
ATOM      9  CB  VAL A   9      17.381  85.731  33.167  1.00 88.13           C  
ATOM     10  CG1 VAL A   9      17.571  86.421  34.506  1.00 86.27           C  
ATOM     11  CG2 VAL A   9      18.232  84.456  33.191  1.00 86.95           C  
ATOM     12  N   GLU A  10      15.892  87.223  31.201  1.00 89.98           N  
ATOM     13  CA  GLU A  10      15.543  87.988  30.004  1.00 87.19           C  
ATOM     14  C   GLU A  10      16.748  88.251  29.055  1.00 83.25           C  
ATOM     15  O   GLU A  10      17.879  87.817  29.318  1.00 81.89           O  
ATOM     16  CB  GLU A  10      14.876  89.324  30.474  1.00 89.77           C  
ATOM     17  CG  GLU A  10      15.390  90.058  31.748  1.00 93.53           C  
ATOM     18  CD  GLU A  10      16.862  90.513  31.791  1.00 96.84           C  
ATOM     19  OE1 GLU A  10      17.570  90.129  32.731  1.00 98.75           O  
ATOM     20  OE2 GLU A  10      17.306  91.258  30.905  1.00 97.00           O  
ATOM     21  N   ALA A  11      16.471  89.023  27.987  1.00 77.76           N  
ATOM     22  CA  ALA A  11      17.315  89.379  26.829  1.00 71.32           C  
ATOM     23  C   ALA A  11      18.829  89.525  26.622  1.00 65.96           C  
ATOM     24  O   ALA A  11      19.605  90.124  27.370  1.00 64.35           O  
ATOM     25  CB  ALA A  11      16.692  90.608  26.193  1.00 70.48           C  
ATOM     26  N   ILE A  12      19.133  88.956  25.457  1.00 62.08           N  
ATOM     27  CA  ILE A  12      20.419  88.929  24.778  1.00 60.99           C  
ATOM     28  C   ILE A  12      19.984  89.116  23.325  1.00 61.87           C  
ATOM     29  O   ILE A  12      18.841  88.755  22.999  1.00 62.16           O  
ATOM     30  CB  ILE A  12      21.198  87.545  24.850  1.00 59.43           C  
ATOM     31  CG1 ILE A  12      20.354  86.363  24.347  1.00 55.38           C  
ATOM     32  CG2 ILE A  12      21.619  87.298  26.290  1.00 59.29           C  
ATOM     33  CD1 ILE A  12      21.107  85.072  24.029  1.00 50.25           C  
ATOM     34  N   LYS A  13      20.745  89.683  22.389  1.00 62.88           N  
ATOM     35  CA  LYS A  13      20.307  89.668  20.991  1.00 63.76           C  
ATOM     36  C   LYS A  13      21.229  88.611  20.439  1.00 63.26           C  
ATOM     37  O   LYS A  13      22.425  88.631  20.755  1.00 63.54           O  
ATOM     38  CB  LYS A  13      20.570  90.941  20.133  1.00 65.83           C  
ATOM     39  CG  LYS A  13      21.100  92.232  20.765  1.00 68.73           C  


  [Part of this file has been deleted for brevity]

ATOM    675  O   LYS B  94      12.694  74.659  17.436  1.00 60.00           O  
ATOM    676  CB  LYS B  94      11.414  76.090  20.144  1.00 54.56           C  
ATOM    677  CG  LYS B  94      10.901  77.252  20.962  1.00 56.83           C  
ATOM    678  CD  LYS B  94       9.923  76.671  21.990  1.00 59.11           C  
ATOM    679  CE  LYS B  94       9.043  77.717  22.641  1.00 60.10           C  
ATOM    680  NZ  LYS B  94       9.890  78.702  23.259  1.00 64.17           N  
ATOM    681  N   SER B  95      13.444  74.034  19.484  1.00 54.16           N  
ATOM    682  CA  SER B  95      13.785  72.651  19.195  1.00 49.80           C  
ATOM    683  C   SER B  95      13.767  71.904  20.531  1.00 49.50           C  
ATOM    684  O   SER B  95      13.715  72.494  21.617  1.00 50.66           O  
ATOM    685  CB  SER B  95      15.186  72.559  18.595  1.00 49.06           C  
ATOM    686  OG  SER B  95      15.488  73.550  17.615  1.00 48.30           O  
ATOM    687  N   ARG B  96      13.817  70.590  20.497  1.00 50.27           N  
ATOM    688  CA  ARG B  96      13.868  69.771  21.694  1.00 49.58           C  
ATOM    689  C   ARG B  96      14.839  68.647  21.295  1.00 47.31           C  
ATOM    690  O   ARG B  96      15.006  68.414  20.088  1.00 44.69           O  
ATOM    691  CB  ARG B  96      12.426  69.305  21.983  1.00 53.09           C  
ATOM    692  CG  ARG B  96      12.197  68.404  23.200  1.00 58.05           C  
ATOM    693  CD  ARG B  96      10.794  68.557  23.787  1.00 61.70           C  
ATOM    694  NE  ARG B  96      10.618  69.895  24.354  1.00 66.11           N  
ATOM    695  CZ  ARG B  96       9.772  70.814  23.850  1.00 69.37           C  
ATOM    696  NH1 ARG B  96       9.702  72.024  24.422  1.00 71.16           N  
ATOM    697  NH2 ARG B  96       8.988  70.558  22.790  1.00 70.99           N  
ATOM    698  N   PRO B  97      15.591  68.002  22.198  1.00 47.31           N  
ATOM    699  CA  PRO B  97      16.438  66.853  21.917  1.00 47.03           C  
ATOM    700  C   PRO B  97      15.755  65.610  21.357  1.00 46.69           C  
ATOM    701  O   PRO B  97      14.800  65.056  21.929  1.00 47.44           O  
ATOM    702  CB  PRO B  97      17.138  66.581  23.238  1.00 48.99           C  
ATOM    703  CG  PRO B  97      17.256  67.940  23.887  1.00 49.17           C  
ATOM    704  CD  PRO B  97      15.868  68.473  23.559  1.00 49.45           C  
ATOM    705  N   SER B  98      16.313  65.239  20.191  1.00 45.02           N  
ATOM    706  CA  SER B  98      16.016  64.022  19.436  1.00 41.65           C  
ATOM    707  C   SER B  98      17.197  63.101  19.711  1.00 39.46           C  
ATOM    708  O   SER B  98      18.327  63.608  19.718  1.00 38.78           O  
ATOM    709  CB  SER B  98      15.952  64.291  17.940  1.00 42.24           C  
ATOM    710  OG  SER B  98      14.657  64.744  17.586  1.00 46.01           O  
ATOM    711  N   LEU B  99      16.992  61.793  19.950  1.00 36.31           N  
ATOM    712  CA  LEU B  99      18.078  60.869  20.273  1.00 33.04           C  
ATOM    713  C   LEU B  99      19.004  60.692  19.051  1.00 33.65           C  
ATOM    714  O   LEU B  99      18.467  60.339  17.994  1.00 35.86           O  
ATOM    715  CB  LEU B  99      17.420  59.573  20.697  1.00 29.39           C  
ATOM    716  CG  LEU B  99      18.126  58.649  21.690  1.00 28.47           C  
ATOM    717  CD1 LEU B  99      18.261  59.352  23.048  1.00 27.24           C  
ATOM    718  CD2 LEU B  99      17.332  57.342  21.817  1.00 25.66           C  
ATOM    719  N   PRO B 100      20.325  60.971  19.041  1.00 33.12           N  
ATOM    720  CA  PRO B 100      21.146  60.885  17.830  1.00 35.17           C  
ATOM    721  C   PRO B 100      21.517  59.413  17.592  1.00 38.22           C  
ATOM    722  O   PRO B 100      21.547  58.620  18.542  1.00 36.98           O  
ATOM    723  CB  PRO B 100      22.317  61.776  18.143  1.00 34.28           C  
ATOM    724  CG  PRO B 100      22.530  61.464  19.626  1.00 33.62           C  
ATOM    725  CD  PRO B 100      21.124  61.360  20.204  1.00 31.93           C  

Directory: daf

This directory contains output files, for example 54894.daf and 55074.daf.

File: daf/54894.daf

# TY   SCOP
# XX
# CL   Alpha and beta proteins (a+b)
# XX
# FO   Ferredoxin-like
# XX
# SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# SI   54894
# XX
#         Number               10        20        30        40        50    
d4at1b1              0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPXSGEMGRKDLIKIEN      0
d4at1d1              0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGXEMGRKDLIKIEN      0
# Post_similar         111111111111111111111111111111111111111111-0-111111111111

#         Number        60        70        80        90 
d4at1b1              0 TFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP      0
d4at1d1              0 TFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP      0
# Post_similar         1111111111111111111111111111111111111

File: daf/55074.daf

# TY   SCOP
# XX
# CL   Alpha and beta proteins (a+b)
# XX
# FO   Ferredoxin-like
# XX
# SF   Adenylyl and guanylyl cyclase catalytic domain
# XX
# FA   Adenylyl and guanylyl cyclase catalytic domain
# XX
# SI   55074
# XX
#         Number               10        20        30        40        50    
d1cs4a_              0 MMFHKIYIQKXHXDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENH      0
d1fx2a_              0 XXNNNRAPXKEPTDPVTLIFTDIESSTALWAAXHPDLMPDAVAAHHRMVRSLIGRYK      0
# Post_similar         --000000-0-0-1111111111111111111-000111111111111111111111

#         Number        60        70        80        90       100       110 
d1cs4a_              0 CLRIKILGDCYYCVSGLPEARADHAHCCVEMGMDMIEAISLVREMXTXGXXXXXXXX      0
d1fx2a_              0 CYEVKTVGDSFMIAXXXXSKXXXSPFAAVQLAQELQLCFLHXHDWGTNALDDSYREF      0
# Post_similar         11111111111111----00---111111111111111111-000-0-0--------

#         Number          120       130       140       150       160       170
d1cs4a_              0 XXXXXXXXXXXXXXXXXXXXXXXXXXXVNVNMRVGIHSGRVHXCGVLGLRKWQFDVW      0
d1fx2a_              0 EEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRHDXEXVTKGYDYY      0
# Post_similar         ---------------------------011111111111111-111-0-00001111

#         Number             180       190       200       210       220     
d1cs4a_              0 SNDVTLANHMEAGGKAGRIHITKATLSYLNXXXGXDYEVEPGCGGERNXAYLKEHSI      0
d1fx2a_              0 GRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALXGDXVALRGXVSDPV      0
# Post_similar         111111111111111111111111111111---0-1111111-00-00-00-00111

#         Number      230       240       250
d1cs4a_              0 ETFLILXXXXXXXXXXXXXXXXXX      0
d1fx2a_              0 KMYQLNTVPSRNFAALRLDREYFD      0
# Post_similar         111111------------------

File: 55074.ent

REMARK Output from transform
REMARK  STAMP Package (Russell and Barton Proteins, 14, 309-323, 1992)
REMARK Domains were read from the file ./domainalign-1234567890.1234.sort
REMARK Chains are labelled sequentially starting with 'A' and
REMARK  after the order given in the file ./domainalign-1234567890.1234.sort
REMARK The domains in this file are:
REMARK       d1cs4a_  chain A 
REMARK       d1fx2a__1  chain B 
REMARK Does not include heteroatoms
REMARK  Does not include DNA/RNA 
REMARK Does not include waters
ATOM      1  N   MET A 377      28.568 -27.770  32.255  1.00 73.77           N  
ATOM      2  CA  MET A 377      28.292 -26.443  32.794  1.00 72.28           C  
ATOM      3  C   MET A 377      29.325 -25.377  32.396  1.00 69.48           C  
ATOM      4  O   MET A 377      30.485 -25.687  32.098  1.00 67.04           O  
ATOM      5  CB  MET A 377      28.075 -26.504  34.312  1.00 74.79           C  
ATOM      6  CG  MET A 377      29.171 -27.205  35.092  1.00 78.73           C  
ATOM      7  SD  MET A 377      28.708 -27.446  36.824  1.00 83.74           S  
ATOM      8  CE  MET A 377      28.745 -25.745  37.440  1.00 81.94           C  
ATOM      9  N   MET A 378      28.883 -24.120  32.395  1.00 66.44           N  
ATOM     10  CA  MET A 378      29.698 -22.969  32.011  1.00 62.94           C  
ATOM     11  C   MET A 378      30.928 -22.727  32.886  1.00 59.70           C  
ATOM     12  O   MET A 378      32.059 -22.739  32.400  1.00 57.00           O  
ATOM     13  CB  MET A 378      28.824 -21.715  31.966  1.00 64.01           C  
ATOM     14  CG  MET A 378      27.551 -21.872  31.137  1.00 64.35           C  
ATOM     15  SD  MET A 378      27.897 -22.219  29.403  1.00 67.83           S  
ATOM     16  CE  MET A 378      27.844 -24.014  29.357  1.00 65.41           C  
ATOM     17  N   PHE A 379      30.697 -22.474  34.167  1.00 56.03           N  
ATOM     18  CA  PHE A 379      31.763 -22.225  35.123  1.00 53.16           C  
ATOM     19  C   PHE A 379      32.157 -23.501  35.837  1.00 51.53           C  
ATOM     20  O   PHE A 379      31.372 -24.440  35.914  1.00 53.09           O  
ATOM     21  CB  PHE A 379      31.296 -21.227  36.186  1.00 54.14           C  
ATOM     22  CG  PHE A 379      31.091 -19.832  35.671  1.00 51.13           C  
ATOM     23  CD1 PHE A 379      29.927 -19.493  34.986  1.00 50.12           C  
ATOM     24  CD2 PHE A 379      32.049 -18.846  35.907  1.00 49.63           C  
ATOM     25  CE1 PHE A 379      29.716 -18.196  34.546  1.00 51.63           C  
ATOM     26  CE2 PHE A 379      31.852 -17.545  35.474  1.00 50.16           C  
ATOM     27  CZ  PHE A 379      30.682 -17.216  34.792  1.00 51.72           C  
ATOM     28  N   HIS A 380      33.371 -23.529  36.372  1.00 50.09           N  
ATOM     29  CA  HIS A 380      33.830 -24.687  37.120  1.00 49.62           C  
ATOM     30  C   HIS A 380      33.046 -24.672  38.431  1.00 49.26           C  
ATOM     31  O   HIS A 380      32.579 -23.623  38.866  1.00 50.30           O  
ATOM     32  CB  HIS A 380      35.327 -24.574  37.439  1.00 52.29           C  
ATOM     33  CG  HIS A 380      36.235 -24.929  36.299  1.00 53.66           C  
ATOM     34  ND1 HIS A 380      36.782 -23.983  35.457  1.00 53.12           N  
ATOM     35  CD2 HIS A 380      36.737 -26.122  35.898  1.00 52.37           C  
ATOM     36  CE1 HIS A 380      37.581 -24.576  34.588  1.00 50.60           C  
ATOM     37  NE2 HIS A 380      37.572 -25.873  34.833  1.00 52.60           N  
ATOM     38  N   LYS A 381      32.879 -25.832  39.051  1.00 50.19           N  
ATOM     39  CA  LYS A 381      32.167 -25.897  40.318  1.00 51.93           C  


  [Part of this file has been deleted for brevity]

ATOM   1806  CG  ASP B1117      55.881   2.260  56.337  1.00 70.08           C  
ATOM   1807  OD1 ASP B1117      55.414   2.017  55.197  1.00 73.38           O  
ATOM   1808  OD2 ASP B1117      57.084   2.059  56.637  1.00 70.53           O  
ATOM   1809  N   ARG B1118      52.764   0.077  56.474  1.00 66.61           N  
ATOM   1810  CA  ARG B1118      52.481  -1.377  56.573  1.00 68.20           C  
ATOM   1811  C   ARG B1118      53.212  -2.511  55.828  1.00 68.77           C  
ATOM   1812  O   ARG B1118      54.421  -2.488  55.587  1.00 70.57           O  
ATOM   1813  CB  ARG B1118      51.033  -1.596  56.196  1.00 71.02           C  
ATOM   1814  CG  ARG B1118      49.988  -0.730  56.780  1.00 66.89           C  
ATOM   1815  CD  ARG B1118      48.805  -0.985  55.855  1.00 69.79           C  
ATOM   1816  NE  ARG B1118      47.548  -0.457  56.346  1.00 65.16           N  
ATOM   1817  CZ  ARG B1118      47.350   0.805  56.714  1.00 67.30           C  
ATOM   1818  NH1 ARG B1118      48.318   1.717  56.649  1.00 62.67           N  
ATOM   1819  NH2 ARG B1118      46.198   1.137  57.253  1.00 60.83           N  
ATOM   1820  N   GLU B1119      52.370  -3.490  55.468  1.00 74.62           N  
ATOM   1821  CA  GLU B1119      52.576  -4.775  54.756  1.00 71.44           C  
ATOM   1822  C   GLU B1119      51.216  -5.345  55.152  1.00 68.30           C  
ATOM   1823  O   GLU B1119      50.787  -5.071  56.255  1.00 70.28           O  
ATOM   1824  CB  GLU B1119      53.628  -5.683  55.451  1.00 72.63           C  
ATOM   1825  CG  GLU B1119      53.056  -6.991  56.217  1.00 68.78           C  
ATOM   1826  CD  GLU B1119      52.428  -6.728  57.622  1.00 67.37           C  
ATOM   1827  OE1 GLU B1119      52.888  -5.743  58.270  1.00 63.79           O  
ATOM   1828  OE2 GLU B1119      51.452  -7.444  58.067  1.00 24.30           O  
ATOM   1829  N   TYR B1120      50.504  -6.074  54.309  1.00 69.56           N  
ATOM   1830  CA  TYR B1120      49.237  -6.679  54.769  1.00 66.82           C  
ATOM   1831  C   TYR B1120      49.096  -7.992  54.006  1.00 69.41           C  
ATOM   1832  O   TYR B1120      49.547  -8.082  52.863  1.00 60.86           O  
ATOM   1833  CB  TYR B1120      48.062  -5.721  54.629  1.00 64.84           C  
ATOM   1834  CG  TYR B1120      46.960  -6.107  53.681  1.00 72.65           C  
ATOM   1835  CD1 TYR B1120      47.056  -5.809  52.324  1.00 69.04           C  
ATOM   1836  CD2 TYR B1120      45.764  -6.658  54.154  1.00 72.45           C  
ATOM   1837  CE1 TYR B1120      45.996  -6.038  51.461  1.00 74.31           C  
ATOM   1838  CE2 TYR B1120      44.688  -6.892  53.292  1.00 74.14           C  
ATOM   1839  CZ  TYR B1120      44.815  -6.576  51.947  1.00 77.01           C  
ATOM   1840  OH  TYR B1120      43.765  -6.791  51.087  1.00 73.74           O  
ATOM   1841  N   PHE B1121      48.537  -9.016  54.663  1.00 67.32           N  
ATOM   1842  CA  PHE B1121      48.401 -10.387  54.120  1.00 68.14           C  
ATOM   1843  C   PHE B1121      48.561 -10.745  52.626  1.00 68.72           C  
ATOM   1844  O   PHE B1121      49.618 -11.228  52.233  1.00 71.84           O  
ATOM   1845  CB  PHE B1121      47.210 -11.123  54.717  1.00 64.05           C  
ATOM   1846  CG  PHE B1121      47.408 -12.619  54.794  1.00 61.04           C  
ATOM   1847  CD1 PHE B1121      48.271 -13.164  55.734  1.00 58.84           C  
ATOM   1848  CD2 PHE B1121      46.737 -13.479  53.925  1.00 63.12           C  
ATOM   1849  CE1 PHE B1121      48.466 -14.540  55.815  1.00 60.74           C  
ATOM   1850  CE2 PHE B1121      46.925 -14.859  53.999  1.00 59.31           C  
ATOM   1851  CZ  PHE B1121      47.788 -15.392  54.941  1.00 64.18           C  
ATOM   1852  N   ASP B1122      47.527 -10.585  51.805  1.00 72.82           N  
ATOM   1853  CA  ASP B1122      47.656 -10.920  50.374  1.00 73.64           C  
ATOM   1854  C   ASP B1122      46.520 -10.365  49.515  1.00 74.17           C  
ATOM   1855  O   ASP B1122      46.464 -10.761  48.332  1.00 75.01           O  
ATOM   1856  CB  ASP B1122      47.790 -12.446  50.171  1.00 73.22           C  

File: domainalign.log

Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'




5.0 DATA FILES

DOMAINALIGN does not use any data files but uses the STAMP "pdb.directories" file which specifies the permissible prefix, extension and path of PDB files used by STAMP. This file should look like :
 test_data/ - .dent
 /data/pdb - -
 /data/pdb _ .ent
 /data/pdb _ .pdb
 /data/pdb pdb .ent
 /data/pdbscop _ _
 /data/pdbscop _ .ent
 /data/pdbscop _ .pdb
 /data/pdbscop pdb .ent
 ./ _ _
 ./ _ .ent
 ./ _ .ent.z
 ./ _ .ent.gz
 ./ _ .pdb
 ./ _ .pdb.Z
 ./ _ .pdb.gz
 ./ pdb .ent
 ./ pdb .ent.Z
 ./ pdb .ent.gz
 /data/CASS1/pdb/coords/ _ .pdb
 /data/CASS1/pdb/coords/ _ .pdb.Z
 /data/CASS1/pdb/coords/ _ .pdb.gz




6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Generate alignments (DAF file) for nodes in a DCF file.
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-dcfinfile]         infile     This option specifies the name of DCF file
                                  (domain classification file) (input). A
                                  'domain classification file' contains
                                  classification and other data for domains
                                  from SCOP or CATH, in DCF format
                                  (EMBL-like). The files are generated by
                                  using SCOPPARSE and CATHPARSE. Domain
                                  sequence information can be added to the
                                  file by using DOMAINSEQS.
  [-pdbdir]            directory  [./] This option specifies the location of
                                  domain PDB files (input). A 'domain PDB
                                  file' contains coordinate data for a single
                                  domain from SCOP or CATH, in PDB format. The
                                  files are generated by using DOMAINER.
   -node               menu       [1] This option specifies the node for
                                  redundancy removal. Redundancy can be
                                  removed at any specified node in the SCOP or
                                  CATH hierarchies. For example by selecting
                                  'Class' entries belonging to the same Class
                                  will be non-redundant. (Values: 1 (Class
                                  (SCOP)); 2 (Fold (SCOP)); 3 (Superfamily
                                  (SCOP)); 4 (Family (SCOP)); 5 (Class
                                  (CATH)); 6 (Architecture (CATH)); 7
                                  (Topology (CATH)); 8 (Homologous Superfamily
                                  (CATH)); 9 (Family (CATH)))
   -mode               menu       [1] This option specifies the alignment
                                  algorithm to use. (Values: 1 (STAMP); 2
                                  (TCOFFEE))
   -[no]keepsinglets   toggle     [Y] This option specifies whether to write
                                  sequences of singlet families to file. If
                                  you specify this option, the sequence for
                                  each singlet family are written to file
                                  (output).
  [-dafoutdir]         outdir     [./] This option specifies the location of
                                  DAF files (domain alignment files) (output).
                                  A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The files are
                                  in clustal format and are annotated with
                                  domain family classification information.
                                  The files generated by using SCOPALIGN will
                                  contain a structure-based sequence alignment
                                  of domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
*  -singletsoutdir     outdir     [./] This option specifies the location of
                                  DHF files (domain hits files) for singlet
                                  sequences (output). The singlets are written
                                  out as a 'domain hits file' - which
                                  contains database hits (sequences) with
                                  domain classification information, in FASTA
                                  format.
*  -superoutdir        outdir     [./] This option specifies the location of
                                  structural superimposition files (output). A
                                  file in PDB format of the structural
                                  superimposition is generated for each family
                                  if the STAMP algorithm is used.
   -logfile            outfile    [domainalign.log] This option specifies the
                                  name of log file (output). The log file
                                  contains messages about any errors arising
                                  while domainalign ran.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-pdbdir" associated qualifiers
   -extension2         string     Default file extension

   "-dafoutdir" associated qualifiers
   -extension3         string     Default file extension

   "-singletsoutdir" associated qualifiers
   -extension          string     Default file extension

   "-superoutdir" associated qualifiers
   -extension          string     Default file extension

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-dcfinfile]
(Parameter 1)
infile This option specifies the name of DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. Input file Required
[-pdbdir]
(Parameter 2)
directory This option specifies the location of domain PDB files (input). A 'domain PDB file' contains coordinate data for a single domain from SCOP or CATH, in PDB format. The files are generated by using DOMAINER. Directory ./
-node list This option specifies the node for redundancy removal. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies. For example by selecting 'Class' entries belonging to the same Class will be non-redundant.
1 (Class (SCOP))
2 (Fold (SCOP))
3 (Superfamily (SCOP))
4 (Family (SCOP))
5 (Class (CATH))
6 (Architecture (CATH))
7 (Topology (CATH))
8 (Homologous Superfamily (CATH))
9 (Family (CATH))
1
-mode list This option specifies the alignment algorithm to use.
1 (STAMP)
2 (TCOFFEE)
1
-[no]keepsinglets toggle This option specifies whether to write sequences of singlet families to file. If you specify this option, the sequence for each singlet family are written to file (output). Toggle value Yes/No Yes
[-dafoutdir]
(Parameter 3)
outdir This option specifies the location of DAF files (domain alignment files) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The files are in clustal format and are annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Output directory ./
-singletsoutdir outdir This option specifies the location of DHF files (domain hits files) for singlet sequences (output). The singlets are written out as a 'domain hits file' - which contains database hits (sequences) with domain classification information, in FASTA format. Output directory ./
-superoutdir outdir This option specifies the location of structural superimposition files (output). A file in PDB format of the structural superimposition is generated for each family if the STAMP algorithm is used. Output directory ./
-logfile outfile This option specifies the name of log file (output). The log file contains messages about any errors arising while domainalign ran. Output file domainalign.log
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-pdbdir" associated directory qualifiers
-extension2
-extension_pdbdir
string Default file extension Any string ent
"-dafoutdir" associated outdir qualifiers
-extension3
-extension_dafoutdir
string Default file extension Any string daf
"-singletsoutdir" associated outdir qualifiers
-extension string Default file extension Any string dhf
"-superoutdir" associated outdir qualifiers
-extension string Default file extension Any string ent
"-logfile" associated outfile qualifiers
-odirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

6.2 EXAMPLE SESSION

An example of interactive use of DOMAINALIGN is shown below. Here is a sample session with domainalign


% domainalign 
Generate alignments (DAF file) for nodes in a DCF file.
Domain classification file: all.scop2
Domain pdb directory [./]: 
Node at which to remove redundancy
         1 : Class (SCOP)
         2 : Fold (SCOP)
         3 : Superfamily (SCOP)
         4 : Family (SCOP)
         5 : Class (CATH)
         6 : Architecture (CATH)
         7 : Topology (CATH)
         8 : Homologous Superfamily (CATH)
         9 : Family (CATH)
Select number. [1]: 4
Alignment algorithm option
         1 : STAMP
         2 : TCOFFEE
Select number. [1]: 1
Write sequences of singlet families to file. [Y]: N
Domain alignment file output directory [./]: daf
Pdb entry file output directory [./]: 
Domainatrix log output file [domainalign.log]: 


STAMP Structural Alignment of Multiple Proteins
 by Robert B. Russell & Geoffrey J. Barton 
 Please cite PROTEINS, v14, 309-323, 1992

Results of scan will be written to file ./domainalign-1234567890.1234.scan
Fits  = no. of fits performed, Sc = STAMP score, RMS = RMS deviation
Align = alignment length, Nfit = residues fitted, Eq. = equivalent residues
Secs  = no. equiv. secondary structures, %I = seq. identity, %S = sec. str. identity
P(m)  = P value (p=1/10) calculated after Murzin (1993), JMB, 230, 689-694

     Domain1         Domain2          Fits  Sc      RMS   Len1 Len2 Align Fit   Eq. Secs    %I    %S     P(m)
Scan d1cs4a_         d1cs4a_            1   9.799   0.001  189  189  189  189  188    0 100.00 100.00 0.00e+00
Scan d1cs4a_         d1fx2a_            1   6.522   1.343  189  235  225  135  133    0  20.30 100.00 0.00017
See the file ./domainalign-1234567890.1234.scan

/shared/software/bin/stamp -l ./domainalign-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainalign-1234567890.1234 -d ./domainalign-1234567890.1234.set


/shared/software/bin/sorttrans -f ./domainalign-1234567890.1234.scan -s Sc 2.5 > ./domainalign-1234567890.1234.sort


/shared/software/bin/stamp -l ./domainalign-1234567890.1234.sort -prefix ./domainalign-1234567890.1234 > ./domainalign-1234567890.1234.log

TRANSFORM R.B. Russell, 1995
 Using PDB files
 Files will not include heteroatoms
 Files will not include DNA/RNA 
 Files will not include waters
 All coordinates will be in file ./55074.ent
 Domain   1, d1cs4a_ => to ./55074.ent (chain A)
 Domain   2, d1fx2a__1 => to ./55074.ent (chain B)
POSTSTAMP, R.B. Russell 1995
 New output will be in file ./domainalign-1234567890.1234.1
 E1 =   3.800, E2 =   3.800
 Minimum Pij set to 0.500
 Reading domain descriptors/transformations from the file ./domainalign-1234567890.1234.1
 Reading alignment...
  Reading coordinates...
 Domain   1 /homes/user/test/qa/domainer-keep2//d1cs4a_.ent d1cs4a_
        all residues 189 CAs =>  189 CAs in total
 Transforming coordinates...
 Domain   2 /homes/user/test/qa/domainer-keep2//d1fx2a_.ent d1fx2a__1
        all residues 235 CAs =>  235 CAs in total
 Transforming coordinates...
 ...done.

/shared/software/bin/transform -f ./domainalign-1234567890.1234.sort -g  -o ./55074.ent

/shared/software/bin/poststamp -f ./domainalign-1234567890.1234.1 -min 0.5

/shared/software/bin/ver2hor -f ./domainalign-1234567890.1234.1.post > ./domainalign-1234567890.1234.out


STAMP Structural Alignment of Multiple Proteins
 by Robert B. Russell & Geoffrey J. Barton 
 Please cite PROTEINS, v14, 309-323, 1992

Results of scan will be written to file ./domainalign-1234567890.1234.scan
Fits  = no. of fits performed, Sc = STAMP score, RMS = RMS deviation
Align = alignment length, Nfit = residues fitted, Eq. = equivalent residues
Secs  = no. equiv. secondary structures, %I = seq. identity, %S = sec. str. identity
P(m)  = P value (p=1/10) calculated after Murzin (1993), JMB, 230, 689-694

     Domain1         Domain2          Fits  Sc      RMS   Len1 Len2 Align Fit   Eq. Secs    %I    %S     P(m)
Scan d4at1b1         d4at1b1            1   9.799   0.001   93   93   93   93   92    0 100.00 100.00 1.00e-92
Scan d4at1b1         d4at1d1            1   9.251   0.588   93   93   94   89   88    0 100.00 100.00 1.00e-88
See the file ./domainalign-1234567890.1234.scan

Processing node 54894

/shared/software/bin/stamp -l ./domainalign-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainalign-1234567890.1234 -d ./domainalign-1234567890.1234.set


/shared/software/bin/sorttrans -f ./domainalign-1234567890.1234.scan -s Sc 2.5 > ./domainalign-1234567890.1234.sort


/shared/software/bin/stamp -l ./domainalign-1234567890.1234.sort -prefix ./domainalign-1234567890.1234 > ./domainalign-1234567890.1234.log

TRANSFORM R.B. Russell, 1995
 Using PDB files
 Files will not include heteroatoms
 Files will not include DNA/RNA 
 Files will not include waters
 All coordinates will be in file ./54894.ent
 Domain   1, d4at1b1 => to ./54894.ent (chain A)
 Domain   2, d4at1d1_1 => to ./54894.ent (chain B)
POSTSTAMP, R.B. Russell 1995
 New output will be in file ./domainalign-1234567890.1234.1
 E1 =   3.800, E2 =   3.800
 Minimum Pij set to 0.500
 Reading domain descriptors/transformations from the file ./domainalign-1234567890.1234.1
 Reading alignment...
  Reading coordinates...
 Domain   1 /homes/user/test/qa/domainer-keep2//d4at1b1.ent d4at1b1
        all residues  93 CAs =>   93 CAs in total
 Transforming coordinates...
 Domain   2 /homes/user/test/qa/domainer-keep2//d4at1d1.ent d4at1d1_1
        all residues  93 CAs =>   93 CAs in total
 Transforming coordinates...
 ...done.

/shared/software/bin/transform -f ./domainalign-1234567890.1234.sort -g  -o ./54894.ent

/shared/software/bin/poststamp -f ./domainalign-1234567890.1234.1 -min 0.5

/shared/software/bin/ver2hor -f ./domainalign-1234567890.1234.1.post > ./domainalign-1234567890.1234.out


Go to the input files for this example
Go to the output files for this example



The following command line would achieve the same result.
 
 domainalign /test_data/all.scop2 /test_data/ /test_data/ /test_data/domainalign -keepsinglets Y 
-singlets /test_data/domainalign -node 4 -mode 1
-->


7.0 KNOWN BUGS & WARNINGS

1. Use of stamp
DOMAINALIGN requires a modified version of STAMP (see Notes below). The modified STAMP application must be installed on the system that is running DOMAINALIGN.

2. Strange STAMP behaviour
STAMP will ignore (omit from the alignment and *not* replace with '-' or any other symbol) ANY residues or groups in a PDB file that

(i) are not structured (i.e. do not appear in the ATOM records) or
(ii) lack a CA atom, regardless of whether it is a known amino acid or not.

This means that the position (column) in the alignment cannot reliably be used as the basis for an index into arrays representing the full length sequences. STAMP will however include in the alignment residues with a single atom only, so long as it is the CA atom.

3. Handling of singlet nodes
No sequence alignment or structural superimposition files are generated for nodes that contain a single domain only. Sequences for such domains can be saved to file (see 2.0 INPUTS & OUTPUTS).

4. Alignment numbering
Residue number positions in alignment are not implemented (zero's are given).


8.0 NOTES

1. Adaption of STAMP for domain codes
DOMAINALIGN will only run with with a version of STAMP which has been modified so that PDB id codes of length greater than 4 characters are acceptable. This involves a trivial change to the STAMP module getdomain.c (around line number 155), a 4 must be changed to a 7 as follows:
 temp=getfile(domain[0].id,dirfile,4,OUTPUT); 
 temp=getfile(domain[0].id,dirfile,7,OUTPUT); 

2. Adaption of STAMP for larger datasets
STAMP fails to align a large dataset of all the available V set Ig domains. The ver2hor module generates the following error:
 Transforming coordinates...
  ...done.
 ver2hor -f ./domainalign-1022069396.11280.76.post > ./domainalign-1022069396.11280.out
 error: something wrong with STAMP file
          STAMP length is 370, Alignment length is 422
          STAMP nseq is 155, Alignment nseq is 155

This is fixed by the following change in alignfit.h.
#define MAXtlen 200 
#define MAXtlen 2000

At the same time the following may be changed as a safety measure:
 gstamp.c  : #define MAX_SEQ_LEN 10000    (was 2000)
 pdbseq.c  : #define MAX_SEQ_LEN 10000    (was 3000)
 defaults.h: #define MAX_SEQ_LEN 10000    (was 8000)
 defaults.h: #define MAX_NSEQ 10000       (was 1000)
 defaults.h: #define MAX_BLOC_SEQ 5000    (was 500)
 dstamp.h  : #define MAX_N_SEQ 10000      (was 1000)
 ver2hor.h : #define MAX_N_SEQ 10000      (was 1000)


3. pdb.directories file
STAMP (and therefore DOMAINALIGN) uses a "pdb.directories" file: see 5.0 DATA FILES

4. Choice of alignment algorithm
Future versions of DOMAINALIGN will implement a larger choice of alignment algorithms.

5. Getting the best alignment
DOMAINALIGN will produce better alignments if the DCF file is reordered so that the representative structure of each node (e.g. family) is given first. This is achieved by using DOMAINREP.

6. Whitespace in alignment
STAMP can insert non-sensical whitespaces into its alignments, e.g. instead of a residue character where that residue was missing electron density in the PDB file. DOMAINALIGN replaces each whitespace within a STAMP alignment with an "X".

8.1 GLOSSARY OF FILE TYPES

FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
Domain classification file (for SCOP) DCF format (EMBL-like format for domain classification data). Classification and other data for domains from SCOP. SCOPPARSE Domain sequence information can be added to the file by using DOMAINSEQS.
Domain classification file (for CATH) DCF format (EMBL-like format for domain classification data). Classification and other data for domains from CATH. CATHPARSE Domain sequence information can be added to the file by using DOMAINSEQS.
Domain PDB file PDB format for domain coordinate data. Coordinate data for a single domain from SCOP or CATH. DOMAINER N.A.
Domain alignment file DAF format (clustal format with domain classification information). Contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is annotated with domain family classification information. DOMAINALIGN (structure-based sequence alignment of domains of known structure). DOMAINALIGN alignments can be extended with sequence relatives (of unknown structure) to the family in question by using SEQALIGN.
None


9.0 DESCRIPTION

The generation of alignments for large datasets such as SCOP and CATH potentially requires a lot of time for preparation of datasets, writing of scripts, running individual jobs and so on, in addition to the compute time required for the alignments themselves. DOMAINALIGN automates this process: it reads a domain classification file and generates alignments for each user-specified node in turn.


10.0 ALGORITHM

More information on STAMP can be found at http://www.compbio.dundee.ac.uk/manuals/stamp.4.2
More information on TCOFFEE can be found at http://www.ch.embnet.org/software/TCoffee.html


11.0 RELATED APPLICATIONS

See also

Program name Description
cathparse Generate DCF file from raw CATH files
domainnr Remove redundant domains from a DCF file
domainrep Reorder DCF file to identify representative structures
domainseqs Add sequence records to a DCF file
domainsse Add secondary structure records to a DCF file
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
libgen Generate discriminating elements from alignments
matcher Waterman-Eggert local alignment of two sequences
matgen3d Generate a 3D-1D scoring matrix from CCF files
oalistat Statistics for multiple alignment files
pepcoil Predict coiled coil regions in protein sequences
rocon Generate a hits file from comparing two DHF files
rocplot Perform ROC analysis on hits files
scopparse Generate DCF file from raw SCOP files
seqalign Extend alignments (DAF file) with sequences (DHF file)
seqfraggle Remove fragment sequences from DHF files
seqmatchall All-against-all word comparison of a sequence set
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generate DHF files from keyword search of UniProt
ssematch Search a DCF file for secondary structure matches
supermatcher Calculate approximate local pair-wise alignments of larger sequences
water Smith-Waterman local alignment of sequences
wordfinder Match large sequences against one or more other sequences
wordmatch Find regions of identity (exact matches) of two sequences



12.0 DIAGNOSTIC ERROR MESSAGES

The following message may appear in the log file.

Replaced ' ' in STAMP alignment with 'X' (STAMP can insert non-sensical whitespaces into its alignments, e.g. instead of a residue character where that residue was missing electron density in the PDB file. DOMAINALIGN replaces each whitespace within a STAMP alignment with an "X").


13.0 AUTHORS

Ranjeeva Ranasinghe

Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK


14.0 REFERENCES

Please cite the authors and EMBOSS.

Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

14.1 Other useful references


Russell, R. B. & Barton, G. J. (1992), Multiple Sequence Alignment from Tertiary Structure Comparison: Assignment of Global and Residue Confidence Levels, PROTEINS: Struct. Funct. Genet., 14, 309-323.
C. Notredame, D. Higgins, J. Heringa. T-Coffee: A novel method for multiple sequence alignments. Journal of Molecular Biology, 302, 205-217, (2000)

More information on STAMP can be found at http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/
More information on TCOFFEE can be found at http://www.ch.embnet.org/software/TCoffee.html
DOMALIGN-0.1.650/emboss_doc/html/seqalign.html0000664000175000017500000105027212171064326015563 00000000000000 EMBASSY: SEQALIGN documentation.

SEQALIGN documentation


 


CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES



1.0 SUMMARY

Extend alignments (DAF file) with sequences (DHF file)


2.0 INPUTS & OUTPUTS

SEQALIGN reads a directory of "seed" alignments and a directory of sets of protein sequences and writes a directory of "extended" alignments. An extended alignment is a seed alignment that is extended with sequences from the appropriate sequence set. The sets directory must contain a sequence set for each seed alignment directory and the files must have the same base name. For example, sequences from "family.sets" are used to extend the seed alignment "family.aln".
Typically, the inputs are (i) DAF files (domain alignment files) containing structure-based sequence alignments and (ii) DHF files (domain hits files) containing sequence relatives (of unknown structure) of these alignments, and the output are DAF files containing the extended alignments.
The base names of the output alignments are the same as the input alignments. The paths for input and output files are specified by the user and the file extensions are set in the ACD file.


3.0 INPUT FILE FORMAT

The format of the domain alignment file is described in DOMAINALIGN documentation.
If other alignment files are used as input, all of the common file formats are supported.

The format of the domain hits file is described in SEQSEARCH documentation.
If other sequence sets are used as input, all of the common file formats are supported.


4.0 OUTPUT FILE FORMAT

The format of the domain alignment file is described in DOMAINALIGN documentation. Note however that the file will never contain 'Number' or 'Post_similar' records. Futhermore, the code before each sequence is of the form Acc_Start_End (where domain hits files were used as input sequences) or Acc_n (where other sequences were used as input), where 'Acc' is the accession number of the sequence, 'Start' and 'End' are the start and end point of the sequence in the full length sequence respectively, and 'n' is a sequential count of the sequence in the alignment.

Output files for usage example

File: 54894.daf

# TY   SCOP
# XX
# CL   Alpha and beta proteins (a+b)
# XX
# FO   Ferredoxin-like
# XX
# SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
# XX
# SI   54894
# XX
d4at1b1_0                 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPXSGEMGRKDLIKIE 0
d4at1d1_1                 0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSGXEMGRKDLIKIE 0
P00478_1_92               0 -VEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSG-EMGRKDLIKIE 0
Q83IL8_1_92               0 -VEAIKRGTVIDHIPAQIGFKLLSLFKLTETD----QRITIGLNLPSG-EMGRKDLIKIE 0
P08421_1_92               0 -VEAIKCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSG-EMGRKDLIKIE 0
Q8Z130_1_92               0 -VEAIKCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSG-EMGRKDLIKIE 0
Q8ZB38_1_92               0 -VEAIKCGTVIDHIPAQIGFKLLSLFKLTATD----QRITIGLNLPSK-RSGRKDLIKIE 0
P19936_1_92               0 -VEAIKCGTVIDHIPAQIGFKLLTLFKLTATD----QRITIGLNLPSN-ELGRKDLIKIE 0
Q7MZ14_1_92               0 -VEAIRCGTVIDHIPAQVGFKLLSLFKLTETD----QRITIGLNLPSN-RLGKKDLIKIE 0
Q8K9H8_1_92               0 -VEAIKSGSVIDHIPAHIGFKLLSLFRFTETE----KRITIGLNLPSQ-KLDKKDIIKIE 0
P57451_1_92               0 -VEAIKSGSVIDHIPEYIGFKLLSLFRFTETE----KRITIGLNLPSK-KLGRKDIIKIE 0
Q9KP65_1_92               0 -VEAIKNGTVIDHIPAKVGIKVLKLFDMHNSA----QRVTIGLNLPSS-ALGSKDLLKIE 0
Q87LF7_1_92               0 -VEAIKNGTVIDHIPAQIGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALGHKDLLKIE 0
Q8DCF7_1_92               0 -VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALGNKDLLKIE 0
Q7MHF0_1_92               0 -VEAIKNGTVIDHIPAQVGIKVLKLFDMHNSS----QRVTIGLNLPSS-ALGNKDLLKIE 0
Q8D1W6_1_92               0 -VEAIFGGTVIDHIPAQVGLKLLSLFKWLHTK----ERITMGLNLPSN-QQKKKDLIKLE 0
Q7P144_1_92               0 -VEALKQGTVIDHIPAGEGVKILRLFKLTETG----ERVTVGLNLVSR-HMGSKDLIKVE 0
P96175_1_92               0 -VEAICNGYVIDHIPSGQGVKILRLFSLTDTK----QRVTVGFNLPSH-DGTTKDLIKVE 0
Q9K1K9_1_92               0 -VEAIEKGTVIDHIPAGRGLTILRQFKLLHYG----NAVTVGFNLPSK-TQGSKDIIKIK 0
Q9JWY6_1_92               0 -VEAIEKGTVIDHIPAGRGLTILRQFKLLHYG----NAVTVGFNLPSK-TQGSKDIIKIK 0
Q970X3_1_91               0 -VSKIKNGTVIDHIPAGRALAVLRILKIAEG-----YRIALVMNVESK-KMGKKDIVKIE 0
Q9UX07_1_93               0 -VSKIRNGTVIDHIPAGRALAVLRILGIRGSEG---YRVALVMNVESK-KIGRKDIVKIE 0
P74766_1_93               0 -VSKIKNGTVIDHIPAGRAFAVLNVLGIKGHEG---FRIALVINVDSK-KMGKKDIVKIE 0
Q8ZTG2_1_93               0 -VSKIENGTVIDHIPAGRALTVLRILGISGKEG---LRVALVMNVESK-KLGKKDIVKIE 0
O58452_1_94               0 -VSAIKEGTVIDHIPAGKGLKVIEILGLSKLSNG--GSVLLAMNVPSK-KLGRKDIVKVE 0
Q8U374_1_94               0 -VSAIKEGTVIDHIPAGKGLKVIQILGLGELKNG--GAVLLAMNVPSK-KLGRKDIVKVE 0
P77919_1_94               0 -VSAIKEGTVIDHIPAGKGLKVIEILKLGKLTNG--GAVLLAMNVPSK-KLGRKDIVKVE 0
O30129_1_93               0 -VSKIKEGTVIDHINAGKALLVLKILKIQPGTD---LTVSMAMNVPSS-KMGKKDIVKVE 0
Q8TVB1_1_92               0 -VKRIEMGTVLDHLPPGTAPQIMRILDIDPTET----TLLVAINVESS-KMGRKDILKIE 0
Q8THL3_1_92               0 -IQAIENGTVIDHITAGQALNVLRILRISSAFR---ATVSFVMNAPGA--RGKKDVVKIE 0
Q8PXK6_1_92               0 -VQAIESGTVIDHIKSGQALNVLRILGISSAFR---ATISFVMNAPGA--GGKKDVVKIE 0
Q9HHN3_1_93               0 -VSKIQAGTVIDHIPAGQALQVLQILGTNGASD---DQITVGMNVTSE-RHHRKDIVKIE 0
Q58801_1_91               0 -VKKITNGTVIDHIDAGKALMVFKVLNVPKETS-----VMIAINVPSK-KKGKKDILKIE 0
O26938_1_91               0 -VKPIKNGTVIDHITANRSLNVLNILGLPDGRS----KVTVAMNMDSS-QLGSKDIVKIE 0
Q97B28_1_93               0 -ISKIKDGTVIDHIPSGKALRVLSILGIRDDVD---YTVSVGMHVPSS-KMEYKDVIKIE 0
Q9HKM3_1_93               0 -ISKIRDGTVIDHVPSGKGIRVIGVLGVHEDVN---YTVSLAIHVPSN-KMGFKDVIKIE 0
Q9YBD5_1_95               0 -VRKIRSGVVIDHIPPGRAFTMLKALGLLPPRGY-RWRIAVVINAESS-KLGRKDILKIE 0
Q7MX57_1_92               0 -VAAIRNGIVIDHIPPTKLFKVATLLQLDDLDK----RITIGNNLRSR-SHGSKGVIKIE 0
Q8A9S4_1_92               0 -VAALKNGTVIDHIPSEKLFTVVQLLGVEQMKCN----ITIGFNLDSK-KLGKKGIIKIA 0
Q891I9_1_91               0 -ITSIKDGIVIDHIKSGYGIKIFNYLNLKNVEYS----VALIMNVFSS-KLGKKDIIKIA 0
Q97FS4_1_90               0 -INSIKNGIVIDHIKAGHGIKIYNYLKLGEAEFP----TALIMNAISK-KNKAKDIIKIE 0
P96111_1_98               0 GIKPIENGTVIDHIAKGKTPEEIYSTILKIRKILRLYDVDSADGIFRSSDGSFKGYISLP 0

d4at1b1_0                 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
d4at1d1_1                 0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
P00478_1_92               0 NTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
Q83IL8_1_92               0 NTFLSEEQVDQLALYAPQATVNRIDNYEVVGKSRPSLP 0
P08421_1_92               0 NTFLTEEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 0
Q8Z130_1_92               0 NTFLTDEQVNQLALYAPQATVNRIDNYDVVGKSRPSLP 0
Q8ZB38_1_92               0 NTFLTEQQANQLAMYAPDATVNRIDNYEVVKKLTLSLP 0
P19936_1_92               0 NTFLTEQQANQLAMYAPKATVNRIDNYEVVRKLTLSLP 0
Q7MZ14_1_92               0 NTFLTEQQANQLAMYAPNATVNCIENYEVVKKLPINLP 0
Q8K9H8_1_92               0 NTFLSDDQINQLAIYAPCATVNYIEKYNLVGKIFPSLP 0
P57451_1_92               0 NTFLSDEQINQLAIYAPHATVNYINEYNLVRKVFPTLP 0
Q9KP65_1_92               0 NVFISEAQANKLALYAPHATVNQIENYEVVKKLALQLP 0
Q87LF7_1_92               0 NVFINEEQASKLALYAPHATVNQIENYEVVKKLALELP 0
Q8DCF7_1_92               0 NVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP 0
Q7MHF0_1_92               0 NVFINEEQASKLALYAPHATVNQIEDYQVVKKLALELP 0
Q8D1W6_1_92               0 NVLLNEDQANQLSIYAPLATVNQIKNYIVIKKQKLKLP 0
Q7P144_1_92               0 NVALTEEQANELALFAPKATVNVIDNFEVVKKHKLTLP 0
P96175_1_92               0 NTEITKSQANQLALLAPNATVNIIENFKVTDKHSLALP 0
Q9K1K9_1_92               0 GVCLDDKAADRLALFAPEAVVNTIDNFKVVQKRHLNLP 0
Q9JWY6_1_92               0 GVCLDDKAADRLALFAPEAVVNTIDHFKVVQKRHLNLP 0
Q970X3_1_91               0 NKEVDEKEANLITLIAPTATINIIRDYEVVEKKKLKIP 0
Q9UX07_1_93               0 DRVIDEKEASLITLIAPSATINIIRDYVVTEKRHLEVP 0
P74766_1_93               0 DKEISDTEANLITLIAPTATINIVREYEVVKKTKLEVP 0
Q8ZTG2_1_93               0 GRELTPEEVNIISAVAPTATINIIRNFAVVKKFKVTPP 0
O58452_1_94               0 GKFLSEEEVNKIALVAPTATVNIIRNYKVVEKFKVEVP 0
Q8U374_1_94               0 GKFLSEEEVNKIALVAPTATVNIIREYKVVEKFKVEIP 0
P77919_1_94               0 GRFLSEEEVNKIALVAPNATVNIIRDYKVVEKFKVEVP 0
O30129_1_93               0 GMFIRDEELNKIALISPNATINLIRDYEIERKFKVSPP 0
Q8TVB1_1_92               0 GKILSEEEANKVALVAPNATVNIVRDYSVAEKFQVKPP 0
Q8THL3_1_92               0 GKELSVEELNRIALISPKATINIIRDFEVVQKNKVVLP 0
Q8PXK6_1_92               0 GKELSVEELNRIALISPKATINIIRDFVVVQKNNVVLP 0
Q9HHN3_1_93               0 GRELSQDEVDVLSLIAPDATINIVRDYEVDEKRRVDRP 0
Q58801_1_91               0 GIELKKEDVDKISLISPDVTINIIRNGKVVEKLKPQIP 0
O26938_1_91               0 NRELKPSEVDQIALIAPRATINIVRDYKIVEKAKVRL- 0
Q97B28_1_93               0 NRSLDKNELDMISLTAPNATISIIKNYEISEKFKVELP 0
Q9HKM3_1_93               0 NRFLDRNELDMISLIAPNATISIIKNYEISEKFQVELP 0
Q9YBD5_1_95               0 GYKPRQRDLEVLGIIAPGATFNVIEDYKVVEKVKLKLP 0
Q7MX57_1_92               0 DKTFEEEELNRIALIAPNVRLNIIRDYEVVEKRQVEVP 0
Q8A9S4_1_92               0 DKFFCDEEINRISVVAPYVKLNIIRDYEVVEKKEVRMP 0
Q891I9_1_91               0 NKEIDID-FTVLGLIDPTITINIIEDEKIKEKLNLELP 0
Q97FS4_1_90               0 N--VMDLDLAVLGFLDPNITVNIIEDEKIRQKIQLKLP 0
P96111_1_98               0 DRYLSKKEIKKLSAISPNTTVNIIKNSTVVEKYRIKLP 0

File: 55074.daf

# TY   SCOP
# XX
# CL   Alpha and beta proteins (a+b)
# XX
# FO   Ferredoxin-like
# XX
# SF   Adenylyl and guanylyl cyclase catalytic domain
# XX
# FA   Adenylyl and guanylyl cyclase catalytic domain
# XX
# SI   55074
# XX
d1cs4a__0                 0 MMFHKIYIQKXHXDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
d1fx2a__1                 0 XXNNNRAPXKEPTDPVTLIFTDIESSTALWAAX----HPDLMPDAVAAHHRMVRSLIGR- 0
Q04400_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
P40144_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
P30803_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
O95622_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
Q03343_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
O43306_1_189              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
Q01341_1_188              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
P30804_1_188              0 MMFHKIYIQK--HDNVSILFADIEGFTSLASQC----TAQELVMTLNELFARFDKLAAE- 0
Q99279_1_218              0 --NNNRAPKE-PTDPVTLIFTDIESSTALWAA-----HPDLMPDAVAAHHRMVRSLIGR- 0
Q99280_6_216              0 ---------KEPTGPVTLIFTDIESSTALWAA-----HPDLMPDAVATHHRLIRSLITR- 0
P26338_1_216              0 ----NNLAPKELTDPVTLIFTDIESSTALWAA-----HPELMPDAVATHHRLIRSLIGR- 0
Q26721_1_206              0 --------------PVTLIFTDIESSTALWAA-----HPEVMPDAVATHHRLIRTLISK- 0
Q99396_1_212              0 ---------KELADPVTLIFTDIESSTAQWAT-----QPELMPDAVATHHSMVRSLIEN- 0
Q08828_1_186              0 --FHKIYIQR--HDNVSILFADIVGFTGLASQC----TAQELVKLLNELFGKFDELATE- 0
P19754_1_186              0 --FHKIYIQR--HDNVSILFADIVGFTGLASQC----TAQELVKLLNELFGKFDELATE- 0
P32870_1_186              0 --FHRIYIQK--HENVSILFADIVGFTVLSSQC----SAQELVRLLNELFGRFDQLAHD- 0
Q26896_6_216              0 ---------KEFTDPVTLIFTDIESSTALWAA-----HPGMMADAVATHHRLIRSLIAL- 0
P97490_1_186              0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFARFDRLAHE- 0
P40146_1_186              0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFARFDRLAHE- 0
P40145_1_186              0 --FHRIYIHR--YENVSILFADVKGFTNLSTTL----SAQELVRMLNELFARFDRLAHE- 0
Q8VHH7_1_186              0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFARFDKLAAK- 0
P21932_1_186              0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFARFDKLAAK- 0
O60266_1_186              0 --FNTMYMYR--HENVSILFADIVGFTQLSSAC----SAQELVKLLNELFARFDKLAAK- 0
Q27675_1_217              0 ---NNDAAPKDGDEPVTLLFTDIESSTALWAA-----LPQLMSDAIAAHHRVIRQLVKK- 0
Q25263_1_217              0 ---NNDAAPKDGDEPVTLLFTDIESSTALWAA-----LPQLMSDAIAAHHRVIRQLVKK- 0
Q91WF3_1_158              0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGKFDQIAKE- 0
Q8NFM4_1_158              0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGKFDQIAKE- 0
P26770_1_158              0 --FHSLYVKR--HQGVSVLYADIVGFTRLASEC----SPKELVLMLNELFGKFDQIAKE- 0
Q08462_1_186              0 --FHNLYVKR--HTNVSILYADIVGFTRLASDC----SPGELVHMLNELFGKFDQIAKE- 0
P26769_1_186              0 --FHNLYVKR--HTNVSILYADIVGFTRLASDC----SPGELVHMLNELFGKFDQIAKE- 0
Q29450_1_186              0 --FHNLYVKR--HQNVSILYADIVGFTRLASDC----SPKELVVVLNELFGKFDQIAKA- 0
P51829_1_186              0 --FHSLYVKR--HQNVSILYADIVGFTRLASDC----SPKELVVVLNELFGKFDQIAKA- 0
P51828_1_186              0 --FHSLYVKR--HQNVSILYADIVGFTQLASDC----SPKELVVVLNELFGKFDQIAKA- 0
P98999_1_150              0 -------------EQVSILFADIVGFTKMSANK----SAHALVGLLNDLFGRFDRLCEE- 0
Q9DGG6_1_181              0 -------------EQVSILFADIVGFTKMSANK----SAHALVGLLNDLFGRFDRLCED- 0
P51830_1_179              0 ---------------VSILFADIVGFTKMSANK----SAHALVGLLNDLFGRFDRLCEQ- 0


  [Part of this file has been deleted for brevity]

P40144_1_159              0 ---------------------- 0
P30803_1_159              0 ---------------------- 0
O95622_1_159              0 ---------------------- 0
Q03343_1_159              0 ---------------------- 0
Q01341_1_159              0 ---------------------- 0
P30804_1_159              0 ---------------------- 0
O43306_1_159              0 ---------------------- 0
P97490_1_162              0 ---------------------- 0
P40146_1_162              0 ---------------------- 0
P40145_1_162              0 ---------------------- 0
O30820_1_149              0 ---------------------- 0
Q03101_1_149              0 ---------------------- 0
P16065_1_143              0 ---------------------- 0
P46197_1_168              0 ---------------------- 0
P20594_1_168              0 ---------------------- 0
P16067_1_168              0 ---------------------- 0
P18293_1_168              0 ---------------------- 0
P18910_1_168              0 ---------------------- 0
P16066_1_168              0 ---------------------- 0
P55202_1_154              0 ---------------------- 0
Q07553_1_152              0 ---------------------- 0
Q02846_1_152              0 ---------------------- 0
P52785_1_150              0 ---------------------- 0
P51840_1_150              0 ---------------------- 0
O19179_1_150              0 ---------------------- 0
P55203_1_151              0 ---------------------- 0
P51842_1_152              0 ---------------------- 0
P51841_1_152              0 ---------------------- 0
O02740_1_162              0 ---------------------- 0
P51839_1_163              0 ---------------------- 0
P55204_1_150              0 ---------------------- 0
P25092_1_150              0 ---------------------- 0
P70106_1_150              0 ---------------------- 0
P23897_1_150              0 ---------------------- 0
P55205_1_154              0 ---------------------- 0
Q09435_1_161              0 ---------------------- 0
P22717_1_147              0 ---------------------- 0
O75343_1_147              0 ---------------------- 0
Q9WVI4_1_149              0 ---------------------- 0
P33402_1_149              0 ---------------------- 0
Q9ERL9_1_152              0 ---------------------- 0
P19686_1_160              0 ---------------------- 0
Q02108_1_160              0 ---------------------- 0
P19687_1_161              0 ---------------------- 0
Q07093_1_158              0 ---------------------- 0
Q02153_1_165              0 ---------------------- 0
P20595_1_165              0 ---------------------- 0
P16068_1_165              0 ---------------------- 0
P40137_1_139              0 ---------------------- 0
P23466_1_154              0 ---------------------- 0

File: seqalign.log

//
/homes/user/test/qa/domainalign-keep/daf/54894.daf
//
/homes/user/test/qa/domainalign-keep/daf/55074.daf




5.0 DATA FILES

SEQALIGN does not use a data file.


6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Extend alignments (DAF file) with sequences (DHF file).
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
   -mode               menu       [1] This option specifies the mode of
                                  SEQALIGN operation. SEQALIGN takes as input
                                  a directory of either i. single sequences,
                                  ii. set of sequences (unaligned or aligned,
                                  but typically aligned sequences within a
                                  domain alignment file)). The user has to
                                  specify which. (Values: 1 (Single
                                  sequences); 2 (Multiple sequences (e.g.
                                  sequence set or alignment)))
*  -dhfinpath          dirlist    [./] This option specifies the location of
                                  sequences, e.g. DHF files (domain hits
                                  files) (input). SEQALIGN takes as input a
                                  database of either i. single sequences, ii.
                                  sets of unaligned sequences or iii. sets of
                                  aligned sequences, e.g. a domain alignment
                                  file. A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The file is in
                                  clustal format annotated with domain family
                                  classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
*  -dafinpath          dirlist    [./] This option specifies the location of
                                  sequences, e.g. DAF files (domain alignment
                                  files) (input). SEQALIGN takes as input a
                                  database of either i. single sequences, ii.
                                  sets of unaligned sequences or iii. sets of
                                  aligned sequences, e.g. a domain alignment
                                  file. A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The file is in
                                  clustal format annotated with domain family
                                  classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
  [-dhfindir]          directory  [./] This option specifies the location of
                                  DHF files (domain hits files) (input). A
                                  'domain hits file' contains database hits
                                  (sequences) with domain classification
                                  information, in the DHF format (FASTA or
                                  EMBL-like). The hits are relatives to a SCOP
                                  or CATH family and are found from a search
                                  of a sequence database. Files containing
                                  hits retrieved by PSIBLAST are generated by
                                  using SEQSEARCH.
   -amode              menu       [1] This option specifies which alignment
                                  algorithm to use. (Values: 1 (CLUSTALW); 2
                                  (TCOFFEE (not yet implemented)))
  [-dafoutdir]         outdir     [./] This option specifies the location of
                                  DAF files (domain alignment files) (output).
                                  A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The file is in
                                  clustal format annotated with domain family
                                  classification information. The files
                                  generated by using SCOPALIGN will contain a
                                  structure-based sequence alignment of
                                  domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
   -logfile            outfile    [seqalign.log] This option specifies the
                                  name of log file for the build. The log file
                                  contains messages about any errors arising
                                  while SEQALIGN ran.

   Additional (Optional) qualifiers:
   -forcetype          boolean    [N] This option specifies whether to force
                                  minimal domain classification data to be
                                  written to the output file in cases where
                                  singlet sequences were given as input file
                                  and no classification data was available

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-dhfinpath" associated qualifiers
   -extension          string     Default file extension

   "-dafinpath" associated qualifiers
   -extension          string     Default file extension

   "-dhfindir" associated qualifiers
   -extension1         string     Default file extension

   "-dafoutdir" associated qualifiers
   -extension2         string     Default file extension

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
-mode list This option specifies the mode of SEQALIGN operation. SEQALIGN takes as input a directory of either i. single sequences, ii. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file)). The user has to specify which.
1 (Single sequences)
2 (Multiple sequences (e.g. sequence set or alignment))
1
-dhfinpath dirlist This option specifies the location of sequences, e.g. DHF files (domain hits files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Directory with files ./
-dafinpath dirlist This option specifies the location of sequences, e.g. DAF files (domain alignment files) (input). SEQALIGN takes as input a database of either i. single sequences, ii. sets of unaligned sequences or iii. sets of aligned sequences, e.g. a domain alignment file. A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Directory with files ./
[-dhfindir]
(Parameter 1)
directory This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. Directory ./
-amode list This option specifies which alignment algorithm to use.
1 (CLUSTALW)
2 (TCOFFEE (not yet implemented))
1
[-dafoutdir]
(Parameter 2)
outdir This option specifies the location of DAF files (domain alignment files) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is in clustal format annotated with domain family classification information. The files generated by using SCOPALIGN will contain a structure-based sequence alignment of domains of known structure only. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN. Output directory ./
-logfile outfile This option specifies the name of log file for the build. The log file contains messages about any errors arising while SEQALIGN ran. Output file seqalign.log
Additional (Optional) qualifiers
-forcetype boolean This option specifies whether to force minimal domain classification data to be written to the output file in cases where singlet sequences were given as input file and no classification data was available Boolean value Yes/No No
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-dhfinpath" associated dirlist qualifiers
-extension string Default file extension Any string dhf
"-dafinpath" associated dirlist qualifiers
-extension string Default file extension Any string daf
"-dhfindir" associated directory qualifiers
-extension1
-extension_dhfindir
string Default file extension Any string dhf
"-dafoutdir" associated outdir qualifiers
-extension2
-extension_dafoutdir
string Default file extension Any string daf
"-logfile" associated outfile qualifiers
-odirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

6.2 EXAMPLE SESSION

An example of interactive use of SEQALIGN is shown below. Here is a sample session with seqalign


% seqalign 
Extend alignments (DAF file) with sequences (DHF file).
Input mode
         1 : Single sequences
         2 : Multiple sequences (e.g. sequence set or alignment)
Select mode of operation. [1]: 2
Domain alignment directories [./]: ../domainalign-keep/daf
Domain hits directory [./]: ../seqsearch-domalign
Alignment algorithm option
         1 : CLUSTALW
         2 : TCOFFEE (not yet implemented)
Select number. [1]: 1
Domain alignment file output directory [./]: 
Domainatrix log output file [seqalign.log]: 




 CLUSTAL 2.1 Multiple Sequence Alignments


Sequence type explicitly set to Protein
Sequence format is Pearson
No. of seqs = 2
Sequences assumed to be PROTEIN
Sequence 1: d4at1b1_0     94 aa
Sequence 2: d4at1d1_1     94 aa
before profileInput
Sequence format is Pearson
No. of seqs in profile=40
Total no. of seqs     =42
Sequences assumed to be PROTEIN
Sequence 3: Q9YBD5_1_95    95 aa
Sequence 4: Q9UX07_1_93    93 aa
Sequence 5: Q9KP65_1_92    92 aa
Sequence 6: Q9K1K9_1_92    92 aa
Sequence 7: Q9JWY6_1_92    92 aa
Sequence 8: Q9HKM3_1_93    93 aa
Sequence 9: Q9HHN3_1_93    93 aa
Sequence 10: Q97FS4_1_90    90 aa
Sequence 11: Q97B28_1_93    93 aa
Sequence 12: Q970X3_1_91    91 aa
Sequence 13: Q8ZTG2_1_93    93 aa
Sequence 14: Q8ZB38_1_92    92 aa
Sequence 15: Q8Z130_1_92    92 aa
Sequence 16: Q8U374_1_94    94 aa
Sequence 17: Q8TVB1_1_92    92 aa
Sequence 18: Q8THL3_1_92    92 aa
Sequence 19: Q8PXK6_1_92    92 aa
Sequence 20: Q8K9H8_1_92    92 aa
Sequence 21: Q8DCF7_1_92    92 aa
Sequence 22: Q8D1W6_1_92    92 aa
Sequence 23: Q8A9S4_1_92    92 aa
Sequence 24: Q891I9_1_91    91 aa
Sequence 25: Q87LF7_1_92    92 aa
Sequence 26: Q83IL8_1_92    92 aa
Sequence 27: Q7P144_1_92    92 aa
Sequence 28: Q7MZ14_1_92    92 aa
Sequence 29: Q7MX57_1_92    92 aa
Sequence 30: Q7MHF0_1_92    92 aa
Sequence 31: Q58801_1_91    91 aa
Sequence 32: P96175_1_92    92 aa
Sequence 33: P96111_1_98    98 aa
Sequence 34: P77919_1_94    94 aa
Sequence 35: P74766_1_93    93 aa
Sequence 36: P57451_1_92    92 aa
Sequence 37: P19936_1_92    92 aa
Sequence 38: P08421_1_92    92 aa
Sequence 39: P00478_1_92    92 aa
Sequence 40: O58452_1_94    94 aa
Sequence 41: O30129_1_93    93 aa
Sequence 42: O26938_1_91    91 aa
after profileInput
Start of Pairwise alignments
Aligning...

Sequences (1:3) Aligned. Score:  35
Sequences (1:4) Aligned. Score:  34
Sequences (1:5) Aligned. Score:  65
Sequences (1:6) Aligned. Score:  51
Sequences (1:7) Aligned. Score:  50
Sequences (1:8) Aligned. Score:  37
Sequences (1:9) Aligned. Score:  45
Sequences (1:10) Aligned. Score:  35
Sequences (1:11) Aligned. Score:  40
Sequences (1:12) Aligned. Score:  45
Sequences (1:13) Aligned. Score:  34
Sequences (1:14) Aligned. Score:  83
Sequences (1:15) Aligned. Score:  92
Sequences (1:16) Aligned. Score:  46
Sequences (1:17) Aligned. Score:  36
Sequences (1:18) Aligned. Score:  38
Sequences (1:19) Aligned. Score:  38
Sequences (1:20) Aligned. Score:  72
Sequences (1:21) Aligned. Score:  63
Sequences (1:22) Aligned. Score:  64
Sequences (1:23) Aligned. Score:  39
Sequences (1:24) Aligned. Score:  32
Sequences (1:25) Aligned. Score:  66
Sequences (1:26) Aligned. Score:  98
Sequences (1:27) Aligned. Score:  65
Sequences (1:28) Aligned. Score:  78
Sequences (1:29) Aligned. Score:  45
Sequences (1:30) Aligned. Score:  63
Sequences (1:31) Aligned. Score:  37
Sequences (1:32) Aligned. Score:  56
Sequences (1:33) Aligned. Score:  32
Sequences (1:34) Aligned. Score:  46
Sequences (1:35) Aligned. Score:  37
Sequences (1:36) Aligned. Score:  70
Sequences (1:37) Aligned. Score:  83
Sequences (1:38) Aligned. Score:  93
Sequences (1:39) Aligned. Score:  100
Sequences (1:40) Aligned. Score:  46
Sequences (1:41) Aligned. Score:  35
Sequences (1:42) Aligned. Score:  41
Sequences (2:3) Aligned. Score:  37
Sequences (2:4) Aligned. Score:  33
Sequences (2:5) Aligned. Score:  65
Sequences (2:6) Aligned. Score:  52
Sequences (2:7) Aligned. Score:  51
Sequences (2:8) Aligned. Score:  36
Sequences (2:9) Aligned. Score:  45
Sequences (2:10) Aligned. Score:  35
Sequences (2:11) Aligned. Score:  40
Sequences (2:12) Aligned. Score:  45
Sequences (2:13) Aligned. Score:  33
Sequences (2:14) Aligned. Score:  83
Sequences (2:15) Aligned. Score:  92
Sequences (2:16) Aligned. Score:  45
Sequences (2:17) Aligned. Score:  36
Sequences (2:18) Aligned. Score:  36
Sequences (2:19) Aligned. Score:  36
Sequences (2:20) Aligned. Score:  72
Sequences (2:21) Aligned. Score:  63
Sequences (2:22) Aligned. Score:  64
Sequences (2:23) Aligned. Score:  39
Sequences (2:24) Aligned. Score:  32
Sequences (2:25) Aligned. Score:  66
Sequences (2:26) Aligned. Score:  98
Sequences (2:27) Aligned. Score:  65
Sequences (2:28) Aligned. Score:  78
Sequences (2:29) Aligned. Score:  45
Sequences (2:30) Aligned. Score:  63
Sequences (2:31) Aligned. Score:  37
Sequences (2:32) Aligned. Score:  56
Sequences (2:33) Aligned. Score:  31
Sequences (2:34) Aligned. Score:  45
Sequences (2:35) Aligned. Score:  36
Sequences (2:36) Aligned. Score:  70
Sequences (2:37) Aligned. Score:  83
Sequences (2:38) Aligned. Score:  93
Sequences (2:39) Aligned. Score:  100
Sequences (2:40) Aligned. Score:  45
Sequences (2:41) Aligned. Score:  34
Sequences (2:42) Aligned. Score:  41
Sequences (3:4) Aligned. Score:  51
Sequences (3:5) Aligned. Score:  41
Sequences (3:6) Aligned. Score:  42
Sequences (3:7) Aligned. Score:  42
Sequences (3:8) Aligned. Score:  36
Sequences (3:9) Aligned. Score:  45
Sequences (3:10) Aligned. Score:  42
Sequences (3:11) Aligned. Score:  38
Sequences (3:12) Aligned. Score:  51
Sequences (3:13) Aligned. Score:  48
Sequences (3:14) Aligned. Score:  40
Sequences (3:15) Aligned. Score:  39
Sequences (3:16) Aligned. Score:  41
Sequences (3:17) Aligned. Score:  44
Sequences (3:18) Aligned. Score:  39
Sequences (3:19) Aligned. Score:  42
Sequences (3:20) Aligned. Score:  41
Sequences (3:21) Aligned. Score:  42
Sequences (3:22) Aligned. Score:  38
Sequences (3:23) Aligned. Score:  35
Sequences (3:24) Aligned. Score:  43
Sequences (3:25) Aligned. Score:  41
Sequences (3:26) Aligned. Score:  39
Sequences (3:27) Aligned. Score:  38
Sequences (3:28) Aligned. Score:  41
Sequences (3:29) Aligned. Score:  40
Sequences (3:30) Aligned. Score:  42
Sequences (3:31) Aligned. Score:  42
Sequences (3:32) Aligned. Score:  36
Sequences (3:33) Aligned. Score:  26
Sequences (3:34) Aligned. Score:  41
Sequences (3:35) Aligned. Score:  49
Sequences (3:36) Aligned. Score:  43
Sequences (3:37) Aligned. Score:  41
Sequences (3:38) Aligned. Score:  39
Sequences (3:39) Aligned. Score:  39
Sequences (3:40) Aligned. Score:  41
Sequences (3:41) Aligned. Score:  43
Sequences (3:42) Aligned. Score:  43
Sequences (4:5) Aligned. Score:  43
Sequences (4:6) Aligned. Score:  45
Sequences (4:7) Aligned. Score:  45
Sequences (4:8) Aligned. Score:  48
Sequences (4:9) Aligned. Score:  56
Sequences (4:10) Aligned. Score:  37
Sequences (4:11) Aligned. Score:  52
Sequences (4:12) Aligned. Score:  80
Sequences (4:13) Aligned. Score:  67
Sequences (4:14) Aligned. Score:  39
Sequences (4:15) Aligned. Score:  35
Sequences (4:16) Aligned. Score:  56
Sequences (4:17) Aligned. Score:  48
Sequences (4:18) Aligned. Score:  50
Sequences (4:19) Aligned. Score:  50
Sequences (4:20) Aligned. Score:  33
Sequences (4:21) Aligned. Score:  46
Sequences (4:22) Aligned. Score:  35
Sequences (4:23) Aligned. Score:  40
Sequences (4:24) Aligned. Score:  45
Sequences (4:25) Aligned. Score:  45
Sequences (4:26) Aligned. Score:  36
Sequences (4:27) Aligned. Score:  39
Sequences (4:28) Aligned. Score:  36
Sequences (4:29) Aligned. Score:  45
Sequences (4:30) Aligned. Score:  46
Sequences (4:31) Aligned. Score:  48
Sequences (4:32) Aligned. Score:  39
Sequences (4:33) Aligned. Score:  31
Sequences (4:34) Aligned. Score:  59
Sequences (4:35) Aligned. Score:  72
Sequences (4:36) Aligned. Score:  35
Sequences (4:37) Aligned. Score:  38
Sequences (4:38) Aligned. Score:  36
Sequences (4:39) Aligned. Score:  36
Sequences (4:40) Aligned. Score:  59
Sequences (4:41) Aligned. Score:  52
Sequences (4:42) Aligned. Score:  51
Sequences (5:6) Aligned. Score:  51
Sequences (5:7) Aligned. Score:  50
Sequences (5:8) Aligned. Score:  38
Sequences (5:9) Aligned. Score:  38
Sequences (5:10) Aligned. Score:  36
Sequences (5:11) Aligned. Score:  38
Sequences (5:12) Aligned. Score:  46
Sequences (5:13) Aligned. Score:  41
Sequences (5:14) Aligned. Score:  68
Sequences (5:15) Aligned. Score:  64
Sequences (5:16) Aligned. Score:  48
Sequences (5:17) Aligned. Score:  39
Sequences (5:18) Aligned. Score:  38
Sequences (5:19) Aligned. Score:  35
Sequences (5:20) Aligned. Score:  58
Sequences (5:21) Aligned. Score:  90
Sequences (5:22) Aligned. Score:  60
Sequences (5:23) Aligned. Score:  40
Sequences (5:24) Aligned. Score:  39
Sequences (5:25) Aligned. Score:  91
Sequences (5:26) Aligned. Score:  65
Sequences (5:27) Aligned. Score:  63
Sequences (5:28) Aligned. Score:  69
Sequences (5:29) Aligned. Score:  44
Sequences (5:30) Aligned. Score:  90
Sequences (5:31) Aligned. Score:  41
Sequences (5:32) Aligned. Score:  57
Sequences (5:33) Aligned. Score:  31
Sequences (5:34) Aligned. Score:  48
Sequences (5:35) Aligned. Score:  45
Sequences (5:36) Aligned. Score:  58
Sequences (5:37) Aligned. Score:  68
Sequences (5:38) Aligned. Score:  65
Sequences (5:39) Aligned. Score:  65
Sequences (5:40) Aligned. Score:  50
Sequences (5:41) Aligned. Score:  42
Sequences (5:42) Aligned. Score:  42
Sequences (6:7) Aligned. Score:  98
Sequences (6:8) Aligned. Score:  33
Sequences (6:9) Aligned. Score:  40
Sequences (6:10) Aligned. Score:  38
Sequences (6:11) Aligned. Score:  36
Sequences (6:12) Aligned. Score:  45
Sequences (6:13) Aligned. Score:  45
Sequences (6:14) Aligned. Score:  53
Sequences (6:15) Aligned. Score:  52
Sequences (6:16) Aligned. Score:  47
Sequences (6:17) Aligned. Score:  36
Sequences (6:18) Aligned. Score:  40
Sequences (6:19) Aligned. Score:  40
Sequences (6:20) Aligned. Score:  44
Sequences (6:21) Aligned. Score:  48
Sequences (6:22) Aligned. Score:  51
Sequences (6:23) Aligned. Score:  36
Sequences (6:24) Aligned. Score:  35
Sequences (6:25) Aligned. Score:  50
Sequences (6:26) Aligned. Score:  52
Sequences (6:27) Aligned. Score:  60
Sequences (6:28) Aligned. Score:  51
Sequences (6:29) Aligned. Score:  36
Sequences (6:30) Aligned. Score:  48
Sequences (6:31) Aligned. Score:  39
Sequences (6:32) Aligned. Score:  53
Sequences (6:33) Aligned. Score:  33
Sequences (6:34) Aligned. Score:  48
Sequences (6:35) Aligned. Score:  40
Sequences (6:36) Aligned. Score:  45
Sequences (6:37) Aligned. Score:  52
Sequences (6:38) Aligned. Score:  51
Sequences (6:39) Aligned. Score:  52
Sequences (6:40) Aligned. Score:  47
Sequences (6:41) Aligned. Score:  35
Sequences (6:42) Aligned. Score:  41
Sequences (7:8) Aligned. Score:  32
Sequences (7:9) Aligned. Score:  40
Sequences (7:10) Aligned. Score:  38
Sequences (7:11) Aligned. Score:  35
Sequences (7:12) Aligned. Score:  45
Sequences (7:13) Aligned. Score:  44
Sequences (7:14) Aligned. Score:  52
Sequences (7:15) Aligned. Score:  51
Sequences (7:16) Aligned. Score:  47
Sequences (7:17) Aligned. Score:  36
Sequences (7:18) Aligned. Score:  40
Sequences (7:19) Aligned. Score:  40
Sequences (7:20) Aligned. Score:  44
Sequences (7:21) Aligned. Score:  48
Sequences (7:22) Aligned. Score:  50
Sequences (7:23) Aligned. Score:  36
Sequences (7:24) Aligned. Score:  35
Sequences (7:25) Aligned. Score:  48
Sequences (7:26) Aligned. Score:  51
Sequences (7:27) Aligned. Score:  59
Sequences (7:28) Aligned. Score:  50
Sequences (7:29) Aligned. Score:  36
Sequences (7:30) Aligned. Score:  48
Sequences (7:31) Aligned. Score:  38
Sequences (7:32) Aligned. Score:  52
Sequences (7:33) Aligned. Score:  32
Sequences (7:34) Aligned. Score:  48
Sequences (7:35) Aligned. Score:  40
Sequences (7:36) Aligned. Score:  45
Sequences (7:37) Aligned. Score:  51
Sequences (7:38) Aligned. Score:  50
Sequences (7:39) Aligned. Score:  51
Sequences (7:40) Aligned. Score:  46
Sequences (7:41) Aligned. Score:  35
Sequences (7:42) Aligned. Score:  41
Sequences (8:9) Aligned. Score:  43
Sequences (8:10) Aligned. Score:  36
Sequences (8:11) Aligned. Score:  77
Sequences (8:12) Aligned. Score:  48
Sequences (8:13) Aligned. Score:  45
Sequences (8:14) Aligned. Score:  34
Sequences (8:15) Aligned. Score:  36
Sequences (8:16) Aligned. Score:  50
Sequences (8:17) Aligned. Score:  41
Sequences (8:18) Aligned. Score:  42
Sequences (8:19) Aligned. Score:  41
Sequences (8:20) Aligned. Score:  32
Sequences (8:21) Aligned. Score:  36
Sequences (8:22) Aligned. Score:  33
Sequences (8:23) Aligned. Score:  38
Sequences (8:24) Aligned. Score:  45
Sequences (8:25) Aligned. Score:  39
Sequences (8:26) Aligned. Score:  39
Sequences (8:27) Aligned. Score:  34
Sequences (8:28) Aligned. Score:  39
Sequences (8:29) Aligned. Score:  41
Sequences (8:30) Aligned. Score:  36
Sequences (8:31) Aligned. Score:  46
Sequences (8:32) Aligned. Score:  34
Sequences (8:33) Aligned. Score:  36
Sequences (8:34) Aligned. Score:  51
Sequences (8:35) Aligned. Score:  45
Sequences (8:36) Aligned. Score:  33
Sequences (8:37) Aligned. Score:  35
Sequences (8:38) Aligned. Score:  36
Sequences (8:39) Aligned. Score:  39
Sequences (8:40) Aligned. Score:  51
Sequences (8:41) Aligned. Score:  49
Sequences (8:42) Aligned. Score:  42
Sequences (9:10) Aligned. Score:  32
Sequences (9:11) Aligned. Score:  51
Sequences (9:12) Aligned. Score:  57
Sequences (9:13) Aligned. Score:  55
Sequences (9:14) Aligned. Score:  42
Sequences (9:15) Aligned. Score:  41
Sequences (9:16) Aligned. Score:  52
Sequences (9:17) Aligned. Score:  47
Sequences (9:18) Aligned. Score:  51
Sequences (9:19) Aligned. Score:  51
Sequences (9:20) Aligned. Score:  34
Sequences (9:21) Aligned. Score:  38
Sequences (9:22) Aligned. Score:  38
Sequences (9:23) Aligned. Score:  40
Sequences (9:24) Aligned. Score:  36
Sequences (9:25) Aligned. Score:  38
Sequences (9:26) Aligned. Score:  44
Sequences (9:27) Aligned. Score:  35
Sequences (9:28) Aligned. Score:  39
Sequences (9:29) Aligned. Score:  42
Sequences (9:30) Aligned. Score:  38
Sequences (9:31) Aligned. Score:  49
Sequences (9:32) Aligned. Score:  35
Sequences (9:33) Aligned. Score:  31
Sequences (9:34) Aligned. Score:  52
Sequences (9:35) Aligned. Score:  53
Sequences (9:36) Aligned. Score:  34
Sequences (9:37) Aligned. Score:  40
Sequences (9:38) Aligned. Score:  41
Sequences (9:39) Aligned. Score:  45
Sequences (9:40) Aligned. Score:  52
Sequences (9:41) Aligned. Score:  49
Sequences (9:42) Aligned. Score:  54
Sequences (10:11) Aligned. Score:  34
Sequences (10:12) Aligned. Score:  43
Sequences (10:13) Aligned. Score:  35
Sequences (10:14) Aligned. Score:  36
Sequences (10:15) Aligned. Score:  36
Sequences (10:16) Aligned. Score:  40
Sequences (10:17) Aligned. Score:  32
Sequences (10:18) Aligned. Score:  33
Sequences (10:19) Aligned. Score:  31
Sequences (10:20) Aligned. Score:  40
Sequences (10:21) Aligned. Score:  37
Sequences (10:22) Aligned. Score:  35
Sequences (10:23) Aligned. Score:  28
Sequences (10:24) Aligned. Score:  63
Sequences (10:25) Aligned. Score:  36
Sequences (10:26) Aligned. Score:  35
Sequences (10:27) Aligned. Score:  37
Sequences (10:28) Aligned. Score:  36
Sequences (10:29) Aligned. Score:  32
Sequences (10:30) Aligned. Score:  37
Sequences (10:31) Aligned. Score:  34
Sequences (10:32) Aligned. Score:  40
Sequences (10:33) Aligned. Score:  28
Sequences (10:34) Aligned. Score:  42
Sequences (10:35) Aligned. Score:  38
Sequences (10:36) Aligned. Score:  37
Sequences (10:37) Aligned. Score:  35
Sequences (10:38) Aligned. Score:  35
Sequences (10:39) Aligned. Score:  35
Sequences (10:40) Aligned. Score:  36
Sequences (10:41) Aligned. Score:  35
Sequences (10:42) Aligned. Score:  35
Sequences (11:12) Aligned. Score:  53
Sequences (11:13) Aligned. Score:  51
Sequences (11:14) Aligned. Score:  38
Sequences (11:15) Aligned. Score:  39
Sequences (11:16) Aligned. Score:  49
Sequences (11:17) Aligned. Score:  43
Sequences (11:18) Aligned. Score:  48
Sequences (11:19) Aligned. Score:  46
Sequences (11:20) Aligned. Score:  34
Sequences (11:21) Aligned. Score:  36
Sequences (11:22) Aligned. Score:  38
Sequences (11:23) Aligned. Score:  36
Sequences (11:24) Aligned. Score:  43
Sequences (11:25) Aligned. Score:  39
Sequences (11:26) Aligned. Score:  41
Sequences (11:27) Aligned. Score:  38
Sequences (11:28) Aligned. Score:  38
Sequences (11:29) Aligned. Score:  41
Sequences (11:30) Aligned. Score:  36
Sequences (11:31) Aligned. Score:  45
Sequences (11:32) Aligned. Score:  39
Sequences (11:33) Aligned. Score:  38
Sequences (11:34) Aligned. Score:  50
Sequences (11:35) Aligned. Score:  46
Sequences (11:36) Aligned. Score:  34
Sequences (11:37) Aligned. Score:  36
Sequences (11:38) Aligned. Score:  39
Sequences (11:39) Aligned. Score:  41
Sequences (11:40) Aligned. Score:  50
Sequences (11:41) Aligned. Score:  56
Sequences (11:42) Aligned. Score:  50
Sequences (12:13) Aligned. Score:  71
Sequences (12:14) Aligned. Score:  47
Sequences (12:15) Aligned. Score:  43
Sequences (12:16) Aligned. Score:  62
Sequences (12:17) Aligned. Score:  53
Sequences (12:18) Aligned. Score:  54
Sequences (12:19) Aligned. Score:  51
Sequences (12:20) Aligned. Score:  40
Sequences (12:21) Aligned. Score:  45
Sequences (12:22) Aligned. Score:  43
Sequences (12:23) Aligned. Score:  47
Sequences (12:24) Aligned. Score:  47
Sequences (12:25) Aligned. Score:  45
Sequences (12:26) Aligned. Score:  45
Sequences (12:27) Aligned. Score:  48
Sequences (12:28) Aligned. Score:  45
Sequences (12:29) Aligned. Score:  46
Sequences (12:30) Aligned. Score:  45
Sequences (12:31) Aligned. Score:  52
Sequences (12:32) Aligned. Score:  39
Sequences (12:33) Aligned. Score:  34
Sequences (12:34) Aligned. Score:  60
Sequences (12:35) Aligned. Score:  79
Sequences (12:36) Aligned. Score:  40
Sequences (12:37) Aligned. Score:  46
Sequences (12:38) Aligned. Score:  45
Sequences (12:39) Aligned. Score:  45
Sequences (12:40) Aligned. Score:  61
Sequences (12:41) Aligned. Score:  60
Sequences (12:42) Aligned. Score:  54
Sequences (13:14) Aligned. Score:  40
Sequences (13:15) Aligned. Score:  40
Sequences (13:16) Aligned. Score:  64
Sequences (13:17) Aligned. Score:  51
Sequences (13:18) Aligned. Score:  59
Sequences (13:19) Aligned. Score:  57
Sequences (13:20) Aligned. Score:  38
Sequences (13:21) Aligned. Score:  40
Sequences (13:22) Aligned. Score:  39
Sequences (13:23) Aligned. Score:  45
Sequences (13:24) Aligned. Score:  39
Sequences (13:25) Aligned. Score:  41
Sequences (13:26) Aligned. Score:  38
Sequences (13:27) Aligned. Score:  45
Sequences (13:28) Aligned. Score:  41
Sequences (13:29) Aligned. Score:  38
Sequences (13:30) Aligned. Score:  40
Sequences (13:31) Aligned. Score:  56
Sequences (13:32) Aligned. Score:  39
Sequences (13:33) Aligned. Score:  33
Sequences (13:34) Aligned. Score:  62
Sequences (13:35) Aligned. Score:  66
Sequences (13:36) Aligned. Score:  40
Sequences (13:37) Aligned. Score:  39
Sequences (13:38) Aligned. Score:  40
Sequences (13:39) Aligned. Score:  36
Sequences (13:40) Aligned. Score:  65
Sequences (13:41) Aligned. Score:  56
Sequences (13:42) Aligned. Score:  54
Sequences (14:15) Aligned. Score:  83
Sequences (14:16) Aligned. Score:  46
Sequences (14:17) Aligned. Score:  35
Sequences (14:18) Aligned. Score:  33
Sequences (14:19) Aligned. Score:  32
Sequences (14:20) Aligned. Score:  68
Sequences (14:21) Aligned. Score:  66
Sequences (14:22) Aligned. Score:  67
Sequences (14:23) Aligned. Score:  41
Sequences (14:24) Aligned. Score:  32
Sequences (14:25) Aligned. Score:  69
Sequences (14:26) Aligned. Score:  83
Sequences (14:27) Aligned. Score:  67
Sequences (14:28) Aligned. Score:  86
Sequences (14:29) Aligned. Score:  45
Sequences (14:30) Aligned. Score:  66
Sequences (14:31) Aligned. Score:  36
Sequences (14:32) Aligned. Score:  59
Sequences (14:33) Aligned. Score:  30
Sequences (14:34) Aligned. Score:  47
Sequences (14:35) Aligned. Score:  43
Sequences (14:36) Aligned. Score:  69
Sequences (14:37) Aligned. Score:  93
Sequences (14:38) Aligned. Score:  84
Sequences (14:39) Aligned. Score:  83
Sequences (14:40) Aligned. Score:  47
Sequences (14:41) Aligned. Score:  39
Sequences (14:42) Aligned. Score:  38
Sequences (15:16) Aligned. Score:  48
Sequences (15:17) Aligned. Score:  36
Sequences (15:18) Aligned. Score:  35
Sequences (15:19) Aligned. Score:  35
Sequences (15:20) Aligned. Score:  71
Sequences (15:21) Aligned. Score:  64
Sequences (15:22) Aligned. Score:  64
Sequences (15:23) Aligned. Score:  41
Sequences (15:24) Aligned. Score:  32
Sequences (15:25) Aligned. Score:  64
Sequences (15:26) Aligned. Score:  93
Sequences (15:27) Aligned. Score:  66
Sequences (15:28) Aligned. Score:  80
Sequences (15:29) Aligned. Score:  45
Sequences (15:30) Aligned. Score:  64
Sequences (15:31) Aligned. Score:  37
Sequences (15:32) Aligned. Score:  58
Sequences (15:33) Aligned. Score:  30
Sequences (15:34) Aligned. Score:  48
Sequences (15:35) Aligned. Score:  41
Sequences (15:36) Aligned. Score:  71
Sequences (15:37) Aligned. Score:  83
Sequences (15:38) Aligned. Score:  98
Sequences (15:39) Aligned. Score:  92
Sequences (15:40) Aligned. Score:  48
Sequences (15:41) Aligned. Score:  42
Sequences (15:42) Aligned. Score:  40
Sequences (16:17) Aligned. Score:  55
Sequences (16:18) Aligned. Score:  47
Sequences (16:19) Aligned. Score:  51
Sequences (16:20) Aligned. Score:  44
Sequences (16:21) Aligned. Score:  48
Sequences (16:22) Aligned. Score:  41
Sequences (16:23) Aligned. Score:  50
Sequences (16:24) Aligned. Score:  42
Sequences (16:25) Aligned. Score:  48
Sequences (16:26) Aligned. Score:  50
Sequences (16:27) Aligned. Score:  48
Sequences (16:28) Aligned. Score:  45
Sequences (16:29) Aligned. Score:  47
Sequences (16:30) Aligned. Score:  48
Sequences (16:31) Aligned. Score:  54
Sequences (16:32) Aligned. Score:  42
Sequences (16:33) Aligned. Score:  34
Sequences (16:34) Aligned. Score:  91
Sequences (16:35) Aligned. Score:  56
Sequences (16:36) Aligned. Score:  48
Sequences (16:37) Aligned. Score:  46
Sequences (16:38) Aligned. Score:  50
Sequences (16:39) Aligned. Score:  48
Sequences (16:40) Aligned. Score:  92
Sequences (16:41) Aligned. Score:  60
Sequences (16:42) Aligned. Score:  54
Sequences (17:18) Aligned. Score:  42
Sequences (17:19) Aligned. Score:  43
Sequences (17:20) Aligned. Score:  33
Sequences (17:21) Aligned. Score:  39
Sequences (17:22) Aligned. Score:  32
Sequences (17:23) Aligned. Score:  35
Sequences (17:24) Aligned. Score:  32
Sequences (17:25) Aligned. Score:  38
Sequences (17:26) Aligned. Score:  38
Sequences (17:27) Aligned. Score:  39
Sequences (17:28) Aligned. Score:  35
Sequences (17:29) Aligned. Score:  41
Sequences (17:30) Aligned. Score:  39
Sequences (17:31) Aligned. Score:  46
Sequences (17:32) Aligned. Score:  35
Sequences (17:33) Aligned. Score:  34
Sequences (17:34) Aligned. Score:  56
Sequences (17:35) Aligned. Score:  47
Sequences (17:36) Aligned. Score:  36
Sequences (17:37) Aligned. Score:  35
Sequences (17:38) Aligned. Score:  38
Sequences (17:39) Aligned. Score:  36
Sequences (17:40) Aligned. Score:  55
Sequences (17:41) Aligned. Score:  52
Sequences (17:42) Aligned. Score:  42
Sequences (18:19) Aligned. Score:  90
Sequences (18:20) Aligned. Score:  32
Sequences (18:21) Aligned. Score:  36
Sequences (18:22) Aligned. Score:  31
Sequences (18:23) Aligned. Score:  36
Sequences (18:24) Aligned. Score:  32
Sequences (18:25) Aligned. Score:  36
Sequences (18:26) Aligned. Score:  36
Sequences (18:27) Aligned. Score:  39
Sequences (18:28) Aligned. Score:  34
Sequences (18:29) Aligned. Score:  42
Sequences (18:30) Aligned. Score:  36
Sequences (18:31) Aligned. Score:  46
Sequences (18:32) Aligned. Score:  34
Sequences (18:33) Aligned. Score:  33
Sequences (18:34) Aligned. Score:  47
Sequences (18:35) Aligned. Score:  51
Sequences (18:36) Aligned. Score:  32
Sequences (18:37) Aligned. Score:  34
Sequences (18:38) Aligned. Score:  35
Sequences (18:39) Aligned. Score:  35
Sequences (18:40) Aligned. Score:  53
Sequences (18:41) Aligned. Score:  57
Sequences (18:42) Aligned. Score:  48
Sequences (19:20) Aligned. Score:  32
Sequences (19:21) Aligned. Score:  35
Sequences (19:22) Aligned. Score:  30
Sequences (19:23) Aligned. Score:  38
Sequences (19:24) Aligned. Score:  35
Sequences (19:25) Aligned. Score:  34
Sequences (19:26) Aligned. Score:  35
Sequences (19:27) Aligned. Score:  36
Sequences (19:28) Aligned. Score:  33
Sequences (19:29) Aligned. Score:  41
Sequences (19:30) Aligned. Score:  35
Sequences (19:31) Aligned. Score:  45
Sequences (19:32) Aligned. Score:  36
Sequences (19:33) Aligned. Score:  32
Sequences (19:34) Aligned. Score:  50
Sequences (19:35) Aligned. Score:  50
Sequences (19:36) Aligned. Score:  33
Sequences (19:37) Aligned. Score:  33
Sequences (19:38) Aligned. Score:  35
Sequences (19:39) Aligned. Score:  34
Sequences (19:40) Aligned. Score:  52
Sequences (19:41) Aligned. Score:  54
Sequences (19:42) Aligned. Score:  46
Sequences (20:21) Aligned. Score:  56
Sequences (20:22) Aligned. Score:  59
Sequences (20:23) Aligned. Score:  42
Sequences (20:24) Aligned. Score:  36
Sequences (20:25) Aligned. Score:  57
Sequences (20:26) Aligned. Score:  71
Sequences (20:27) Aligned. Score:  53
Sequences (20:28) Aligned. Score:  69
Sequences (20:29) Aligned. Score:  40
Sequences (20:30) Aligned. Score:  56
Sequences (20:31) Aligned. Score:  34
Sequences (20:32) Aligned. Score:  52
Sequences (20:33) Aligned. Score:  28
Sequences (20:34) Aligned. Score:  43
Sequences (20:35) Aligned. Score:  41
Sequences (20:36) Aligned. Score:  86
Sequences (20:37) Aligned. Score:  68
Sequences (20:38) Aligned. Score:  70
Sequences (20:39) Aligned. Score:  72
Sequences (20:40) Aligned. Score:  43
Sequences (20:41) Aligned. Score:  38
Sequences (20:42) Aligned. Score:  36
Sequences (21:22) Aligned. Score:  60
Sequences (21:23) Aligned. Score:  40
Sequences (21:24) Aligned. Score:  41
Sequences (21:25) Aligned. Score:  95
Sequences (21:26) Aligned. Score:  64
Sequences (21:27) Aligned. Score:  59
Sequences (21:28) Aligned. Score:  67
Sequences (21:29) Aligned. Score:  44
Sequences (21:30) Aligned. Score:  100
Sequences (21:31) Aligned. Score:  40
Sequences (21:32) Aligned. Score:  55
Sequences (21:33) Aligned. Score:  29
Sequences (21:34) Aligned. Score:  50
Sequences (21:35) Aligned. Score:  43
Sequences (21:36) Aligned. Score:  57
Sequences (21:37) Aligned. Score:  66
Sequences (21:38) Aligned. Score:  65
Sequences (21:39) Aligned. Score:  63
Sequences (21:40) Aligned. Score:  50
Sequences (21:41) Aligned. Score:  42
Sequences (21:42) Aligned. Score:  42
Sequences (22:23) Aligned. Score:  34
Sequences (22:24) Aligned. Score:  29
Sequences (22:25) Aligned. Score:  60
Sequences (22:26) Aligned. Score:  63
Sequences (22:27) Aligned. Score:  60
Sequences (22:28) Aligned. Score:  69
Sequences (22:29) Aligned. Score:  35
Sequences (22:30) Aligned. Score:  60
Sequences (22:31) Aligned. Score:  32
Sequences (22:32) Aligned. Score:  54
Sequences (22:33) Aligned. Score:  33
Sequences (22:34) Aligned. Score:  42
Sequences (22:35) Aligned. Score:  39
Sequences (22:36) Aligned. Score:  56
Sequences (22:37) Aligned. Score:  66
Sequences (22:38) Aligned. Score:  65
Sequences (22:39) Aligned. Score:  64
Sequences (22:40) Aligned. Score:  42
Sequences (22:41) Aligned. Score:  34
Sequences (22:42) Aligned. Score:  35
Sequences (23:24) Aligned. Score:  34
Sequences (23:25) Aligned. Score:  40
Sequences (23:26) Aligned. Score:  40
Sequences (23:27) Aligned. Score:  35
Sequences (23:28) Aligned. Score:  41
Sequences (23:29) Aligned. Score:  59
Sequences (23:30) Aligned. Score:  40
Sequences (23:31) Aligned. Score:  41
Sequences (23:32) Aligned. Score:  33
Sequences (23:33) Aligned. Score:  30
Sequences (23:34) Aligned. Score:  46
Sequences (23:35) Aligned. Score:  47
Sequences (23:36) Aligned. Score:  44
Sequences (23:37) Aligned. Score:  41
Sequences (23:38) Aligned. Score:  40
Sequences (23:39) Aligned. Score:  39
Sequences (23:40) Aligned. Score:  47
Sequences (23:41) Aligned. Score:  39
Sequences (23:42) Aligned. Score:  40
Sequences (24:25) Aligned. Score:  40
Sequences (24:26) Aligned. Score:  31
Sequences (24:27) Aligned. Score:  34
Sequences (24:28) Aligned. Score:  34
Sequences (24:29) Aligned. Score:  32
Sequences (24:30) Aligned. Score:  41
Sequences (24:31) Aligned. Score:  43
Sequences (24:32) Aligned. Score:  39
Sequences (24:33) Aligned. Score:  25
Sequences (24:34) Aligned. Score:  41
Sequences (24:35) Aligned. Score:  46
Sequences (24:36) Aligned. Score:  35
Sequences (24:37) Aligned. Score:  34
Sequences (24:38) Aligned. Score:  31
Sequences (24:39) Aligned. Score:  32
Sequences (24:40) Aligned. Score:  43
Sequences (24:41) Aligned. Score:  39
Sequences (24:42) Aligned. Score:  41
Sequences (25:26) Aligned. Score:  67
Sequences (25:27) Aligned. Score:  61
Sequences (25:28) Aligned. Score:  68
Sequences (25:29) Aligned. Score:  44
Sequences (25:30) Aligned. Score:  95
Sequences (25:31) Aligned. Score:  41
Sequences (25:32) Aligned. Score:  56
Sequences (25:33) Aligned. Score:  31
Sequences (25:34) Aligned. Score:  48
Sequences (25:35) Aligned. Score:  44
Sequences (25:36) Aligned. Score:  58
Sequences (25:37) Aligned. Score:  69
Sequences (25:38) Aligned. Score:  65
Sequences (25:39) Aligned. Score:  66
Sequences (25:40) Aligned. Score:  51
Sequences (25:41) Aligned. Score:  42
Sequences (25:42) Aligned. Score:  41
Sequences (26:27) Aligned. Score:  66
Sequences (26:28) Aligned. Score:  78
Sequences (26:29) Aligned. Score:  46
Sequences (26:30) Aligned. Score:  64
Sequences (26:31) Aligned. Score:  38
Sequences (26:32) Aligned. Score:  56
Sequences (26:33) Aligned. Score:  32
Sequences (26:34) Aligned. Score:  50
Sequences (26:35) Aligned. Score:  41
Sequences (26:36) Aligned. Score:  71
Sequences (26:37) Aligned. Score:  83
Sequences (26:38) Aligned. Score:  94
Sequences (26:39) Aligned. Score:  98
Sequences (26:40) Aligned. Score:  50
Sequences (26:41) Aligned. Score:  41
Sequences (26:42) Aligned. Score:  41
Sequences (27:28) Aligned. Score:  65
Sequences (27:29) Aligned. Score:  42
Sequences (27:30) Aligned. Score:  59
Sequences (27:31) Aligned. Score:  34
Sequences (27:32) Aligned. Score:  65
Sequences (27:33) Aligned. Score:  29
Sequences (27:34) Aligned. Score:  48
Sequences (27:35) Aligned. Score:  42
Sequences (27:36) Aligned. Score:  55
Sequences (27:37) Aligned. Score:  67
Sequences (27:38) Aligned. Score:  67
Sequences (27:39) Aligned. Score:  65
Sequences (27:40) Aligned. Score:  48
Sequences (27:41) Aligned. Score:  39
Sequences (27:42) Aligned. Score:  39
Sequences (28:29) Aligned. Score:  47
Sequences (28:30) Aligned. Score:  67
Sequences (28:31) Aligned. Score:  35
Sequences (28:32) Aligned. Score:  60
Sequences (28:33) Aligned. Score:  31
Sequences (28:34) Aligned. Score:  46
Sequences (28:35) Aligned. Score:  41
Sequences (28:36) Aligned. Score:  67
Sequences (28:37) Aligned. Score:  85
Sequences (28:38) Aligned. Score:  81
Sequences (28:39) Aligned. Score:  78
Sequences (28:40) Aligned. Score:  45
Sequences (28:41) Aligned. Score:  39
Sequences (28:42) Aligned. Score:  38
Sequences (29:30) Aligned. Score:  44
Sequences (29:31) Aligned. Score:  38
Sequences (29:32) Aligned. Score:  40
Sequences (29:33) Aligned. Score:  35
Sequences (29:34) Aligned. Score:  50
Sequences (29:35) Aligned. Score:  45
Sequences (29:36) Aligned. Score:  42
Sequences (29:37) Aligned. Score:  46
Sequences (29:38) Aligned. Score:  46
Sequences (29:39) Aligned. Score:  45
Sequences (29:40) Aligned. Score:  48
Sequences (29:41) Aligned. Score:  40
Sequences (29:42) Aligned. Score:  41
Sequences (30:31) Aligned. Score:  40
Sequences (30:32) Aligned. Score:  55
Sequences (30:33) Aligned. Score:  29
Sequences (30:34) Aligned. Score:  50
Sequences (30:35) Aligned. Score:  43
Sequences (30:36) Aligned. Score:  57
Sequences (30:37) Aligned. Score:  66
Sequences (30:38) Aligned. Score:  65
Sequences (30:39) Aligned. Score:  63
Sequences (30:40) Aligned. Score:  50
Sequences (30:41) Aligned. Score:  42
Sequences (30:42) Aligned. Score:  42
Sequences (31:32) Aligned. Score:  34
Sequences (31:33) Aligned. Score:  35
Sequences (31:34) Aligned. Score:  56
Sequences (31:35) Aligned. Score:  50
Sequences (31:36) Aligned. Score:  35
Sequences (31:37) Aligned. Score:  34
Sequences (31:38) Aligned. Score:  37
Sequences (31:39) Aligned. Score:  37
Sequences (31:40) Aligned. Score:  57
Sequences (31:41) Aligned. Score:  52
Sequences (31:42) Aligned. Score:  50
Sequences (32:33) Aligned. Score:  35
Sequences (32:34) Aligned. Score:  42
Sequences (32:35) Aligned. Score:  36
Sequences (32:36) Aligned. Score:  51
Sequences (32:37) Aligned. Score:  59
Sequences (32:38) Aligned. Score:  58
Sequences (32:39) Aligned. Score:  56
Sequences (32:40) Aligned. Score:  42
Sequences (32:41) Aligned. Score:  34
Sequences (32:42) Aligned. Score:  39
Sequences (33:34) Aligned. Score:  36
Sequences (33:35) Aligned. Score:  30
Sequences (33:36) Aligned. Score:  29
Sequences (33:37) Aligned. Score:  30
Sequences (33:38) Aligned. Score:  30
Sequences (33:39) Aligned. Score:  32
Sequences (33:40) Aligned. Score:  35
Sequences (33:41) Aligned. Score:  32
Sequences (33:42) Aligned. Score:  35
Sequences (34:35) Aligned. Score:  54
Sequences (34:36) Aligned. Score:  46
Sequences (34:37) Aligned. Score:  47
Sequences (34:38) Aligned. Score:  50
Sequences (34:39) Aligned. Score:  48
Sequences (34:40) Aligned. Score:  92
Sequences (34:41) Aligned. Score:  63
Sequences (34:42) Aligned. Score:  56
Sequences (35:36) Aligned. Score:  42
Sequences (35:37) Aligned. Score:  41
Sequences (35:38) Aligned. Score:  40
Sequences (35:39) Aligned. Score:  41
Sequences (35:40) Aligned. Score:  56
Sequences (35:41) Aligned. Score:  53
Sequences (35:42) Aligned. Score:  51
Sequences (36:37) Aligned. Score:  69
Sequences (36:38) Aligned. Score:  70
Sequences (36:39) Aligned. Score:  70
Sequences (36:40) Aligned. Score:  46
Sequences (36:41) Aligned. Score:  38
Sequences (36:42) Aligned. Score:  36
Sequences (37:38) Aligned. Score:  84
Sequences (37:39) Aligned. Score:  83
Sequences (37:40) Aligned. Score:  47
Sequences (37:41) Aligned. Score:  40
Sequences (37:42) Aligned. Score:  39
Sequences (38:39) Aligned. Score:  93
Sequences (38:40) Aligned. Score:  50
Sequences (38:41) Aligned. Score:  41
Sequences (38:42) Aligned. Score:  40
Sequences (39:40) Aligned. Score:  48
Sequences (39:41) Aligned. Score:  40
Sequences (39:42) Aligned. Score:  41
Sequences (40:41) Aligned. Score:  60
Sequences (40:42) Aligned. Score:  54
Sequences (41:42) Aligned. Score:  51


Guide tree file created:   [./seqalign-1234567890.1234.dnd]

Start of Multiple Alignment

Sequence:39     Score:1453
Sequence:26     Score:1426
Sequence:38     Score:1399
Sequence:15     Score:1411
Sequence:14     Score:1310
Sequence:37     Score:1348
Sequence:28     Score:1320
Sequence:20     Score:1368
Sequence:36     Score:1411
Sequence:5     Score:1309
Sequence:25     Score:1351
Sequence:21     Score:1366
Sequence:30     Score:1390
Sequence:22     Score:1287
Sequence:27     Score:1284
Sequence:32     Score:753
Sequence:6     Score:725
Sequence:7     Score:754
Sequence:12     Score:671
Sequence:4     Score:667
Sequence:35     Score:714
Sequence:13     Score:709
Sequence:40     Score:720
Sequence:16     Score:745
Sequence:34     Score:756
Sequence:41     Score:689
Sequence:17     Score:683
Sequence:18     Score:677
Sequence:19     Score:689
Sequence:9     Score:684
Sequence:31     Score:669
Sequence:42     Score:683
Sequence:11     Score:690
Sequence:8     Score:708
Sequence:3     Score:668
Sequence:29     Score:667
Sequence:23     Score:676
Sequence:24     Score:615
Sequence:10     Score:608
Sequence:33     Score:587
Alignment Score 209199

CLUSTAL-Alignment file created  [./seqalign-1234567890.1234.out]




 CLUSTAL 2.1 Multiple Sequence Alignments


Sequence type explicitly set to Protein
Sequence format is Pearson
No. of seqs = 2
Sequences assumed to be PROTEIN
Sequence 1: d1cs4a__0    252 aa
Sequence 2: d1fx2a__1    252 aa
before profileInput
Sequence format is Pearson
No. of seqs in profile=100
Total no. of seqs     =102
Sequences assumed to be PROTEIN
Sequence 3: Q9WVI4_1_149     149 aa
Sequence 4: Q9ERL9_1_152     152 aa
Sequence 5: Q9DGG6_1_181     181 aa
Sequence 6: Q99396_1_212     212 aa
Sequence 7: Q99280_6_216     211 aa
Sequence 8: Q99279_1_218     218 aa
Sequence 9: Q91WF3_1_165     165 aa
Sequence 10: Q91WF3_1_158     158 aa
Sequence 11: Q8VHH7_1_186     186 aa
Sequence 12: Q8NFM4_1_161     161 aa
Sequence 13: Q8NFM4_1_158     158 aa
Sequence 14: Q29450_1_186     186 aa
Sequence 15: Q29450_1_58       58 aa
Sequence 16: Q27675_1_217     217 aa
Sequence 17: Q26896_6_216     211 aa
Sequence 18: Q26721_1_206     206 aa
Sequence 19: Q25263_1_217     217 aa
Sequence 20: Q09435_1_161     161 aa
Sequence 21: Q08828_1_186     186 aa
Sequence 22: Q08828_1_51       51 aa
Sequence 23: Q08462_1_186     186 aa
Sequence 24: Q08462_1_167     167 aa
Sequence 25: Q07553_1_152     152 aa
Sequence 26: Q07093_1_158     158 aa
Sequence 27: Q04400_1_189     189 aa
Sequence 28: Q04400_1_159     159 aa
Sequence 29: Q03343_1_189     189 aa
Sequence 30: Q03343_1_159     159 aa
Sequence 31: Q03101_1_149     149 aa
Sequence 32: Q02846_1_152     152 aa
Sequence 33: Q02153_1_165     165 aa
Sequence 34: Q02108_1_160     160 aa
Sequence 35: Q01341_1_188     188 aa
Sequence 36: Q01341_1_159     159 aa
Sequence 37: P98999_1_150     150 aa
Sequence 38: P97490_1_186     186 aa
Sequence 39: P97490_1_162     162 aa
Sequence 40: P70106_1_150     150 aa
Sequence 41: P55205_1_154     154 aa
Sequence 42: P55204_1_150     150 aa
Sequence 43: P55203_1_151     151 aa
Sequence 44: P55202_1_154     154 aa
Sequence 45: P52785_1_150     150 aa
Sequence 46: P51842_1_152     152 aa
Sequence 47: P51841_1_152     152 aa
Sequence 48: P51840_1_150     150 aa
Sequence 49: P51839_1_163     163 aa
Sequence 50: P51830_1_179     179 aa
Sequence 51: P51829_109_166    58 aa
Sequence 52: P51829_1_186     186 aa
Sequence 53: P51828_1_186     186 aa
Sequence 54: P51828_1_58       58 aa
Sequence 55: P46197_1_168     168 aa
Sequence 56: P40146_1_186     186 aa
Sequence 57: P40146_1_162     162 aa
Sequence 58: P40145_1_186     186 aa
Sequence 59: P40145_1_162     162 aa
Sequence 60: P40144_1_189     189 aa
Sequence 61: P40144_1_159     159 aa
Sequence 62: P40137_1_139     139 aa
Sequence 63: P33402_1_149     149 aa
Sequence 64: P32870_1_186     186 aa
Sequence 65: P32870_1_58       58 aa
Sequence 66: P30804_1_188     188 aa
Sequence 67: P30804_1_159     159 aa
Sequence 68: P30803_1_189     189 aa
Sequence 69: P30803_1_159     159 aa
Sequence 70: P26770_1_165     165 aa
Sequence 71: P26770_1_158     158 aa
Sequence 72: P26769_1_186     186 aa
Sequence 73: P26769_1_163     163 aa
Sequence 74: P26338_1_216     216 aa
Sequence 75: P25092_1_150     150 aa
Sequence 76: P23897_1_150     150 aa
Sequence 77: P23466_1_154     154 aa
Sequence 78: P22717_1_147     147 aa
Sequence 79: P21932_1_186     186 aa
Sequence 80: P20595_1_165     165 aa
Sequence 81: P20594_1_168     168 aa
Sequence 82: P19754_1_186     186 aa
Sequence 83: P19754_1_51       51 aa
Sequence 84: P19687_1_161     161 aa
Sequence 85: P19686_1_160     160 aa
Sequence 86: P18910_1_168     168 aa
Sequence 87: P18293_1_168     168 aa
Sequence 88: P16068_1_165     165 aa
Sequence 89: P16067_1_168     168 aa
Sequence 90: P16066_1_168     168 aa
Sequence 91: P16065_1_143     143 aa
Sequence 92: O95622_1_189     189 aa
Sequence 93: O95622_1_159     159 aa
Sequence 94: O75343_1_147     147 aa
Sequence 95: O60503_1_179     179 aa
Sequence 96: O60266_1_186     186 aa
Sequence 97: O60266_1_54       54 aa
Sequence 98: O43306_1_189     189 aa
Sequence 99: O43306_1_159     159 aa
Sequence 100: O30820_1_149     149 aa
Sequence 101: O19179_1_150     150 aa
Sequence 102: O02740_1_162     162 aa
after profileInput
Start of Pairwise alignments
Aligning...

Sequences (1:3) Aligned. Score:  36
Sequences (1:4) Aligned. Score:  32
Sequences (1:5) Aligned. Score:  46
Sequences (1:6) Aligned. Score:  15
Sequences (1:7) Aligned. Score:  15
Sequences (1:8) Aligned. Score:  16
Sequences (1:9) Aligned. Score:  29
Sequences (1:10) Aligned. Score:  63
Sequences (1:11) Aligned. Score:  61
Sequences (1:12) Aligned. Score:  30
Sequences (1:13) Aligned. Score:  63
Sequences (1:14) Aligned. Score:  62
Sequences (1:15) Aligned. Score:  43
Sequences (1:16) Aligned. Score:  14
Sequences (1:17) Aligned. Score:  15
Sequences (1:18) Aligned. Score:  15
Sequences (1:19) Aligned. Score:  14
Sequences (1:20) Aligned. Score:  29
Sequences (1:21) Aligned. Score:  74
Sequences (1:22) Aligned. Score:  43
Sequences (1:23) Aligned. Score:  58
Sequences (1:24) Aligned. Score:  27
Sequences (1:25) Aligned. Score:  32
Sequences (1:26) Aligned. Score:  30
Sequences (1:27) Aligned. Score:  96
Sequences (1:28) Aligned. Score:  29
Sequences (1:29) Aligned. Score:  93
Sequences (1:30) Aligned. Score:  29
Sequences (1:31) Aligned. Score:  29
Sequences (1:32) Aligned. Score:  31
Sequences (1:33) Aligned. Score:  33
Sequences (1:34) Aligned. Score:  31
Sequences (1:35) Aligned. Score:  93
Sequences (1:36) Aligned. Score:  29
Sequences (1:37) Aligned. Score:  56
Sequences (1:38) Aligned. Score:  68
Sequences (1:39) Aligned. Score:  30
Sequences (1:40) Aligned. Score:  27
Sequences (1:41) Aligned. Score:  26
Sequences (1:42) Aligned. Score:  27
Sequences (1:43) Aligned. Score:  31
Sequences (1:44) Aligned. Score:  27
Sequences (1:45) Aligned. Score:  32
Sequences (1:46) Aligned. Score:  30
Sequences (1:47) Aligned. Score:  31
Sequences (1:48) Aligned. Score:  32
Sequences (1:49) Aligned. Score:  26
Sequences (1:50) Aligned. Score:  47
Sequences (1:51) Aligned. Score:  43
Sequences (1:52) Aligned. Score:  61
Sequences (1:53) Aligned. Score:  62
Sequences (1:54) Aligned. Score:  43
Sequences (1:55) Aligned. Score:  30
Sequences (1:56) Aligned. Score:  68
Sequences (1:57) Aligned. Score:  30
Sequences (1:58) Aligned. Score:  68
Sequences (1:59) Aligned. Score:  30
Sequences (1:60) Aligned. Score:  96
Sequences (1:61) Aligned. Score:  29
Sequences (1:62) Aligned. Score:  25
Sequences (1:63) Aligned. Score:  34
Sequences (1:64) Aligned. Score:  72
Sequences (1:65) Aligned. Score:  39
Sequences (1:66) Aligned. Score:  93
Sequences (1:67) Aligned. Score:  27
Sequences (1:68) Aligned. Score:  97
Sequences (1:69) Aligned. Score:  29
Sequences (1:70) Aligned. Score:  30
Sequences (1:71) Aligned. Score:  63
Sequences (1:72) Aligned. Score:  59
Sequences (1:73) Aligned. Score:  28
Sequences (1:74) Aligned. Score:  15
Sequences (1:75) Aligned. Score:  26
Sequences (1:76) Aligned. Score:  27
Sequences (1:77) Aligned. Score:  4
Sequences (1:78) Aligned. Score:  25
Sequences (1:79) Aligned. Score:  61
Sequences (1:80) Aligned. Score:  33
Sequences (1:81) Aligned. Score:  30
Sequences (1:82) Aligned. Score:  74
Sequences (1:83) Aligned. Score:  43
Sequences (1:84) Aligned. Score:  31
Sequences (1:85) Aligned. Score:  31
Sequences (1:86) Aligned. Score:  31
Sequences (1:87) Aligned. Score:  32
Sequences (1:88) Aligned. Score:  33
Sequences (1:89) Aligned. Score:  30
Sequences (1:90) Aligned. Score:  29
Sequences (1:91) Aligned. Score:  32
Sequences (1:92) Aligned. Score:  96
Sequences (1:93) Aligned. Score:  29
Sequences (1:94) Aligned. Score:  25
Sequences (1:95) Aligned. Score:  48
Sequences (1:96) Aligned. Score:  61
Sequences (1:97) Aligned. Score:  38
Sequences (1:98) Aligned. Score:  93
Sequences (1:99) Aligned. Score:  29
Sequences (1:100) Aligned. Score:  35
Sequences (1:101) Aligned. Score:  32
Sequences (1:102) Aligned. Score:  32
Sequences (2:3) Aligned. Score:  22
Sequences (2:4) Aligned. Score:  17
Sequences (2:5) Aligned. Score:  11
Sequences (2:6) Aligned. Score:  73
Sequences (2:7) Aligned. Score:  85
Sequences (2:8) Aligned. Score:  92
Sequences (2:9) Aligned. Score:  17
Sequences (2:10) Aligned. Score:  16
Sequences (2:11) Aligned. Score:  14
Sequences (2:12) Aligned. Score:  18
Sequences (2:13) Aligned. Score:  15
Sequences (2:14) Aligned. Score:  16
Sequences (2:15) Aligned. Score:  34
Sequences (2:16) Aligned. Score:  58
Sequences (2:17) Aligned. Score:  69
Sequences (2:18) Aligned. Score:  81
Sequences (2:19) Aligned. Score:  58
Sequences (2:20) Aligned. Score:  18
Sequences (2:21) Aligned. Score:  15
Sequences (2:22) Aligned. Score:  31
Sequences (2:23) Aligned. Score:  9
Sequences (2:24) Aligned. Score:  14
Sequences (2:25) Aligned. Score:  22
Sequences (2:26) Aligned. Score:  17
Sequences (2:27) Aligned. Score:  14
Sequences (2:28) Aligned. Score:  13
Sequences (2:29) Aligned. Score:  12
Sequences (2:30) Aligned. Score:  12
Sequences (2:31) Aligned. Score:  23
Sequences (2:32) Aligned. Score:  23
Sequences (2:33) Aligned. Score:  15
Sequences (2:34) Aligned. Score:  16
Sequences (2:35) Aligned. Score:  10
Sequences (2:36) Aligned. Score:  12
Sequences (2:37) Aligned. Score:  13
Sequences (2:38) Aligned. Score:  13
Sequences (2:39) Aligned. Score:  12
Sequences (2:40) Aligned. Score:  20
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Sequences (2:74) Aligned. Score:  80
Sequences (2:75) Aligned. Score:  20
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Sequences (3:21) Aligned. Score:  36
Sequences (3:22) Aligned. Score:  39
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Sequences (3:24) Aligned. Score:  27
Sequences (3:25) Aligned. Score:  52
Sequences (3:26) Aligned. Score:  61
Sequences (3:27) Aligned. Score:  37
Sequences (3:28) Aligned. Score:  33
Sequences (3:29) Aligned. Score:  38
Sequences (3:30) Aligned. Score:  32
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Sequences (3:32) Aligned. Score:  50
Sequences (3:33) Aligned. Score:  48
Sequences (3:34) Aligned. Score:  78
Sequences (3:35) Aligned. Score:  38
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Sequences (3:63) Aligned. Score:  98
Sequences (3:64) Aligned. Score:  36
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Sequences (3:84) Aligned. Score:  78
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Sequences (3:101) Aligned. Score:  51
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Sequences (4:25) Aligned. Score:  48
Sequences (4:26) Aligned. Score:  61
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Sequences (4:32) Aligned. Score:  49
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Sequences (4:34) Aligned. Score:  98
Sequences (4:35) Aligned. Score:  30
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Sequences (4:63) Aligned. Score:  79
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Sequences (4:84) Aligned. Score:  97
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Sequences (4:96) Aligned. Score:  35
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Sequences (4:98) Aligned. Score:  32
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Sequences (4:100) Aligned. Score:  33
Sequences (4:101) Aligned. Score:  51
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Sequences (5:6) Aligned. Score:  13
Sequences (5:7) Aligned. Score:  11
Sequences (5:8) Aligned. Score:  17
Sequences (5:9) Aligned. Score:  27
Sequences (5:10) Aligned. Score:  47
Sequences (5:11) Aligned. Score:  51
Sequences (5:12) Aligned. Score:  27
Sequences (5:13) Aligned. Score:  47
Sequences (5:14) Aligned. Score:  46
Sequences (5:15) Aligned. Score:  37
Sequences (5:16) Aligned. Score:  17
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Sequences (5:18) Aligned. Score:  12
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Sequences (5:20) Aligned. Score:  27
Sequences (5:21) Aligned. Score:  49
Sequences (5:22) Aligned. Score:  37
Sequences (5:23) Aligned. Score:  43
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Sequences (5:25) Aligned. Score:  30
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Sequences (5:37) Aligned. Score:  96
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Sequences (5:50) Aligned. Score:  97
Sequences (5:51) Aligned. Score:  37
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Sequences (5:56) Aligned. Score:  49
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Sequences (5:75) Aligned. Score:  30
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Sequences (5:77) Aligned. Score:  3
Sequences (5:78) Aligned. Score:  36
Sequences (5:79) Aligned. Score:  51
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Sequences (5:81) Aligned. Score:  32
Sequences (5:82) Aligned. Score:  49
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Sequences (5:84) Aligned. Score:  31
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Sequences (5:88) Aligned. Score:  35
Sequences (5:89) Aligned. Score:  32
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Sequences (5:92) Aligned. Score:  50
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Sequences (5:94) Aligned. Score:  35
Sequences (5:95) Aligned. Score:  97
Sequences (5:96) Aligned. Score:  51
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Sequences (5:100) Aligned. Score:  36
Sequences (5:101) Aligned. Score:  31
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Sequences (6:7) Aligned. Score:  76
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Sequences (6:15) Aligned. Score:  37
Sequences (6:16) Aligned. Score:  59
Sequences (6:17) Aligned. Score:  71
Sequences (6:18) Aligned. Score:  75
Sequences (6:19) Aligned. Score:  59
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Sequences (6:24) Aligned. Score:  10
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Sequences (6:27) Aligned. Score:  12
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Sequences (6:51) Aligned. Score:  37
Sequences (6:52) Aligned. Score:  11
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Sequences (6:55) Aligned. Score:  26
Sequences (6:56) Aligned. Score:  13
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Sequences (6:66) Aligned. Score:  7
Sequences (6:67) Aligned. Score:  13
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Sequences (6:74) Aligned. Score:  77
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Sequences (6:77) Aligned. Score:  33
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Sequences (6:82) Aligned. Score:  13
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Sequences (6:84) Aligned. Score:  15
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Sequences (7:8) Aligned. Score:  89
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Sequences (7:16) Aligned. Score:  63
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Sequences (7:63) Aligned. Score:  22
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Sequences (7:65) Aligned. Score:  31
Sequences (7:66) Aligned. Score:  17
Sequences (7:67) Aligned. Score:  13
Sequences (7:68) Aligned. Score:  17
Sequences (7:69) Aligned. Score:  13
Sequences (7:70) Aligned. Score:  18
Sequences (7:71) Aligned. Score:  15
Sequences (7:72) Aligned. Score:  12
Sequences (7:73) Aligned. Score:  15
Sequences (7:74) Aligned. Score:  82
Sequences (7:75) Aligned. Score:  22
Sequences (7:76) Aligned. Score:  21
Sequences (7:77) Aligned. Score:  38
Sequences (7:78) Aligned. Score:  24
Sequences (7:79) Aligned. Score:  13
Sequences (7:80) Aligned. Score:  19
Sequences (7:81) Aligned. Score:  25
Sequences (7:82) Aligned. Score:  13
Sequences (7:83) Aligned. Score:  19
Sequences (7:84) Aligned. Score:  20
Sequences (7:85) Aligned. Score:  20
Sequences (7:86) Aligned. Score:  26
Sequences (7:87) Aligned. Score:  26
Sequences (7:88) Aligned. Score:  19
Sequences (7:89) Aligned. Score:  25
Sequences (7:90) Aligned. Score:  25
Sequences (7:91) Aligned. Score:  27
Sequences (7:92) Aligned. Score:  17
Sequences (7:93) Aligned. Score:  13
Sequences (7:94) Aligned. Score:  24
Sequences (7:95) Aligned. Score:  14
Sequences (7:96) Aligned. Score:  13
Sequences (7:97) Aligned. Score:  18
Sequences (7:98) Aligned. Score:  17
Sequences (7:99) Aligned. Score:  13
Sequences (7:100) Aligned. Score:  19
Sequences (7:101) Aligned. Score:  26
Sequences (7:102) Aligned. Score:  24
Sequences (8:9) Aligned. Score:  17
Sequences (8:10) Aligned. Score:  13
Sequences (8:11) Aligned. Score:  16
Sequences (8:12) Aligned. Score:  18
Sequences (8:13) Aligned. Score:  13
Sequences (8:14) Aligned. Score:  12
Sequences (8:15) Aligned. Score:  32
Sequences (8:16) Aligned. Score:  64
Sequences (8:17) Aligned. Score:  72
Sequences (8:18) Aligned. Score:  85
Sequences (8:19) Aligned. Score:  63
Sequences (8:20) Aligned. Score:  20
Sequences (8:21) Aligned. Score:  11
Sequences (8:22) Aligned. Score:  31
Sequences (8:23) Aligned. Score:  11
Sequences (8:24) Aligned. Score:  9
Sequences (8:25) Aligned. Score:  24
Sequences (8:26) Aligned. Score:  18
Sequences (8:27) Aligned. Score:  17
Sequences (8:28) Aligned. Score:  13
Sequences (8:29) Aligned. Score:  17
Sequences (8:30) Aligned. Score:  13
Sequences (8:31) Aligned. Score:  20
Sequences (8:32) Aligned. Score:  25
Sequences (8:33) Aligned. Score:  22
Sequences (8:34) Aligned. Score:  20
Sequences (8:35) Aligned. Score:  15
Sequences (8:36) Aligned. Score:  13
Sequences (8:37) Aligned. Score:  20
Sequences (8:38) Aligned. Score:  16
Sequences (8:39) Aligned. Score:  12
Sequences (8:40) Aligned. Score:  16
Sequences (8:41) Aligned. Score:  22
Sequences (8:42) Aligned. Score:  22
Sequences (8:43) Aligned. Score:  25
Sequences (8:44) Aligned. Score:  25
Sequences (8:45) Aligned. Score:  25
Sequences (8:46) Aligned. Score:  25
Sequences (8:47) Aligned. Score:  25
Sequences (8:48) Aligned. Score:  25
Sequences (8:49) Aligned. Score:  25
Sequences (8:50) Aligned. Score:  13
Sequences (8:51) Aligned. Score:  32
Sequences (8:52) Aligned. Score:  12
Sequences (8:53) Aligned. Score:  12
Sequences (8:54) Aligned. Score:  32
Sequences (8:55) Aligned. Score:  25
Sequences (8:56) Aligned. Score:  16
Sequences (8:57) Aligned. Score:  12
Sequences (8:58) Aligned. Score:  16
Sequences (8:59) Aligned. Score:  12
Sequences (8:60) Aligned. Score:  17
Sequences (8:61) Aligned. Score:  13
Sequences (8:62) Aligned. Score:  25
Sequences (8:63) Aligned. Score:  22
Sequences (8:64) Aligned. Score:  21
Sequences (8:65) Aligned. Score:  31
Sequences (8:66) Aligned. Score:  15
Sequences (8:67) Aligned. Score:  13
Sequences (8:68) Aligned. Score:  17
Sequences (8:69) Aligned. Score:  13
Sequences (8:70) Aligned. Score:  18
Sequences (8:71) Aligned. Score:  13
Sequences (8:72) Aligned. Score:  11
Sequences (8:73) Aligned. Score:  9
Sequences (8:74) Aligned. Score:  85
Sequences (8:75) Aligned. Score:  22
Sequences (8:76) Aligned. Score:  21
Sequences (8:77) Aligned. Score:  37
Sequences (8:78) Aligned. Score:  24
Sequences (8:79) Aligned. Score:  16
Sequences (8:80) Aligned. Score:  22
Sequences (8:81) Aligned. Score:  25
Sequences (8:82) Aligned. Score:  11
Sequences (8:83) Aligned. Score:  31
Sequences (8:84) Aligned. Score:  20
Sequences (8:85) Aligned. Score:  20
Sequences (8:86) Aligned. Score:  26
Sequences (8:87) Aligned. Score:  26
Sequences (8:88) Aligned. Score:  22
Sequences (8:89) Aligned. Score:  25
Sequences (8:90) Aligned. Score:  24
Sequences (8:91) Aligned. Score:  25
Sequences (8:92) Aligned. Score:  17
Sequences (8:93) Aligned. Score:  13
Sequences (8:94) Aligned. Score:  24
Sequences (8:95) Aligned. Score:  10
Sequences (8:96) Aligned. Score:  16
Sequences (8:97) Aligned. Score:  25
Sequences (8:98) Aligned. Score:  17
Sequences (8:99) Aligned. Score:  13
Sequences (8:100) Aligned. Score:  19
Sequences (8:101) Aligned. Score:  25
Sequences (8:102) Aligned. Score:  24
Sequences (9:10) Aligned. Score:  29
Sequences (9:11) Aligned. Score:  27
Sequences (9:12) Aligned. Score:  98
Sequences (9:13) Aligned. Score:  29
Sequences (9:14) Aligned. Score:  27
Sequences (9:15) Aligned. Score:  86
Sequences (9:16) Aligned. Score:  20
Sequences (9:17) Aligned. Score:  19
Sequences (9:18) Aligned. Score:  19
Sequences (9:19) Aligned. Score:  20
Sequences (9:20) Aligned. Score:  31
Sequences (9:21) Aligned. Score:  29
Sequences (9:22) Aligned. Score:  82
Sequences (9:23) Aligned. Score:  26
Sequences (9:24) Aligned. Score:  79
Sequences (9:25) Aligned. Score:  35
Sequences (9:26) Aligned. Score:  27
Sequences (9:27) Aligned. Score:  29
Sequences (9:28) Aligned. Score:  61
Sequences (9:29) Aligned. Score:  29
Sequences (9:30) Aligned. Score:  61
Sequences (9:31) Aligned. Score:  34
Sequences (9:32) Aligned. Score:  33
Sequences (9:33) Aligned. Score:  32
Sequences (9:34) Aligned. Score:  29
Sequences (9:35) Aligned. Score:  26
Sequences (9:36) Aligned. Score:  61
Sequences (9:37) Aligned. Score:  31
Sequences (9:38) Aligned. Score:  27
Sequences (9:39) Aligned. Score:  61
Sequences (9:40) Aligned. Score:  29
Sequences (9:41) Aligned. Score:  36
Sequences (9:42) Aligned. Score:  32
Sequences (9:43) Aligned. Score:  33
Sequences (9:44) Aligned. Score:  28
Sequences (9:45) Aligned. Score:  34
Sequences (9:46) Aligned. Score:  33
Sequences (9:47) Aligned. Score:  33
Sequences (9:48) Aligned. Score:  34
Sequences (9:49) Aligned. Score:  31
Sequences (9:50) Aligned. Score:  27
Sequences (9:51) Aligned. Score:  86
Sequences (9:52) Aligned. Score:  27
Sequences (9:53) Aligned. Score:  27
Sequences (9:54) Aligned. Score:  86
Sequences (9:55) Aligned. Score:  32
Sequences (9:56) Aligned. Score:  27
Sequences (9:57) Aligned. Score:  61
Sequences (9:58) Aligned. Score:  27
Sequences (9:59) Aligned. Score:  61
Sequences (9:60) Aligned. Score:  29
Sequences (9:61) Aligned. Score:  61
Sequences (9:62) Aligned. Score:  20
Sequences (9:63) Aligned. Score:  28
Sequences (9:64) Aligned. Score:  29
Sequences (9:65) Aligned. Score:  77
Sequences (9:66) Aligned. Score:  26
Sequences (9:67) Aligned. Score:  61
Sequences (9:68) Aligned. Score:  29
Sequences (9:69) Aligned. Score:  60
Sequences (9:70) Aligned. Score:  98
Sequences (9:71) Aligned. Score:  29
Sequences (9:72) Aligned. Score:  26
Sequences (9:73) Aligned. Score:  79
Sequences (9:74) Aligned. Score:  18
Sequences (9:75) Aligned. Score:  31
Sequences (9:76) Aligned. Score:  30
Sequences (9:77) Aligned. Score:  14
Sequences (9:78) Aligned. Score:  35
Sequences (9:79) Aligned. Score:  27
Sequences (9:80) Aligned. Score:  32
Sequences (9:81) Aligned. Score:  32
Sequences (9:82) Aligned. Score:  29
Sequences (9:83) Aligned. Score:  82
Sequences (9:84) Aligned. Score:  29
Sequences (9:85) Aligned. Score:  29
Sequences (9:86) Aligned. Score:  32
Sequences (9:87) Aligned. Score:  31
Sequences (9:88) Aligned. Score:  32
Sequences (9:89) Aligned. Score:  32
Sequences (9:90) Aligned. Score:  31
Sequences (9:91) Aligned. Score:  36
Sequences (9:92) Aligned. Score:  29
Sequences (9:93) Aligned. Score:  61
Sequences (9:94) Aligned. Score:  36
Sequences (9:95) Aligned. Score:  27
Sequences (9:96) Aligned. Score:  27
Sequences (9:97) Aligned. Score:  79
Sequences (9:98) Aligned. Score:  29
Sequences (9:99) Aligned. Score:  61
Sequences (9:100) Aligned. Score:  36
Sequences (9:101) Aligned. Score:  35
Sequences (9:102) Aligned. Score:  31
Sequences (10:11) Aligned. Score:  57
Sequences (10:12) Aligned. Score:  29
Sequences (10:13) Aligned. Score:  99
Sequences (10:14) Aligned. Score:  82
Sequences (10:15) Aligned. Score:  39
Sequences (10:16) Aligned. Score:  13
Sequences (10:17) Aligned. Score:  10
Sequences (10:18) Aligned. Score:  4
Sequences (10:19) Aligned. Score:  13
Sequences (10:20) Aligned. Score:  32
Sequences (10:21) Aligned. Score:  67
Sequences (10:22) Aligned. Score:  43
Sequences (10:23) Aligned. Score:  86
Sequences (10:24) Aligned. Score:  27
Sequences (10:25) Aligned. Score:  34
Sequences (10:26) Aligned. Score:  31
Sequences (10:27) Aligned. Score:  65
Sequences (10:28) Aligned. Score:  29
Sequences (10:29) Aligned. Score:  65
Sequences (10:30) Aligned. Score:  28
Sequences (10:31) Aligned. Score:  29
Sequences (10:32) Aligned. Score:  34
Sequences (10:33) Aligned. Score:  29
Sequences (10:34) Aligned. Score:  35
Sequences (10:35) Aligned. Score:  64
Sequences (10:36) Aligned. Score:  28
Sequences (10:37) Aligned. Score:  50
Sequences (10:38) Aligned. Score:  60
Sequences (10:39) Aligned. Score:  31
Sequences (10:40) Aligned. Score:  37
Sequences (10:41) Aligned. Score:  29
Sequences (10:42) Aligned. Score:  35
Sequences (10:43) Aligned. Score:  34
Sequences (10:44) Aligned. Score:  28
Sequences (10:45) Aligned. Score:  34
Sequences (10:46) Aligned. Score:  34
Sequences (10:47) Aligned. Score:  34
Sequences (10:48) Aligned. Score:  34
Sequences (10:49) Aligned. Score:  30
Sequences (10:50) Aligned. Score:  47
Sequences (10:51) Aligned. Score:  39
Sequences (10:52) Aligned. Score:  82
Sequences (10:53) Aligned. Score:  83
Sequences (10:54) Aligned. Score:  39
Sequences (10:55) Aligned. Score:  32
Sequences (10:56) Aligned. Score:  60
Sequences (10:57) Aligned. Score:  31
Sequences (10:58) Aligned. Score:  60
Sequences (10:59) Aligned. Score:  31
Sequences (10:60) Aligned. Score:  65
Sequences (10:61) Aligned. Score:  29
Sequences (10:62) Aligned. Score:  28
Sequences (10:63) Aligned. Score:  35
Sequences (10:64) Aligned. Score:  65
Sequences (10:65) Aligned. Score:  39
Sequences (10:66) Aligned. Score:  63
Sequences (10:67) Aligned. Score:  28
Sequences (10:68) Aligned. Score:  65
Sequences (10:69) Aligned. Score:  29
Sequences (10:70) Aligned. Score:  30
Sequences (10:71) Aligned. Score:  100
Sequences (10:72) Aligned. Score:  86
Sequences (10:73) Aligned. Score:  27
Sequences (10:74) Aligned. Score:  18
Sequences (10:75) Aligned. Score:  35
Sequences (10:76) Aligned. Score:  34
Sequences (10:77) Aligned. Score:  4
Sequences (10:78) Aligned. Score:  31
Sequences (10:79) Aligned. Score:  57
Sequences (10:80) Aligned. Score:  29
Sequences (10:81) Aligned. Score:  32
Sequences (10:82) Aligned. Score:  67
Sequences (10:83) Aligned. Score:  43
Sequences (10:84) Aligned. Score:  35
Sequences (10:85) Aligned. Score:  35
Sequences (10:86) Aligned. Score:  32
Sequences (10:87) Aligned. Score:  32
Sequences (10:88) Aligned. Score:  29
Sequences (10:89) Aligned. Score:  32
Sequences (10:90) Aligned. Score:  32
Sequences (10:91) Aligned. Score:  33
Sequences (10:92) Aligned. Score:  65
Sequences (10:93) Aligned. Score:  29
Sequences (10:94) Aligned. Score:  31
Sequences (10:95) Aligned. Score:  48
Sequences (10:96) Aligned. Score:  57
Sequences (10:97) Aligned. Score:  38
Sequences (10:98) Aligned. Score:  65
Sequences (10:99) Aligned. Score:  28
Sequences (10:100) Aligned. Score:  36
Sequences (10:101) Aligned. Score:  34
Sequences (10:102) Aligned. Score:  33
Sequences (11:12) Aligned. Score:  27
Sequences (11:13) Aligned. Score:  57
Sequences (11:14) Aligned. Score:  55
Sequences (11:15) Aligned. Score:  36
Sequences (11:16) Aligned. Score:  16
Sequences (11:17) Aligned. Score:  18
Sequences (11:18) Aligned. Score:  16
Sequences (11:19) Aligned. Score:  16
Sequences (11:20) Aligned. Score:  26
Sequences (11:21) Aligned. Score:  59
Sequences (11:22) Aligned. Score:  39
Sequences (11:23) Aligned. Score:  56
Sequences (11:24) Aligned. Score:  25
Sequences (11:25) Aligned. Score:  33
Sequences (11:26) Aligned. Score:  32
Sequences (11:27) Aligned. Score:  63
Sequences (11:28) Aligned. Score:  28
Sequences (11:29) Aligned. Score:  63
Sequences (11:30) Aligned. Score:  27
Sequences (11:31) Aligned. Score:  32
Sequences (11:32) Aligned. Score:  30
Sequences (11:33) Aligned. Score:  31
Sequences (11:34) Aligned. Score:  34
Sequences (11:35) Aligned. Score:  62
Sequences (11:36) Aligned. Score:  27
Sequences (11:37) Aligned. Score:  56
Sequences (11:38) Aligned. Score:  61
Sequences (11:39) Aligned. Score:  28
Sequences (11:40) Aligned. Score:  32
Sequences (11:41) Aligned. Score:  33
Sequences (11:42) Aligned. Score:  28
Sequences (11:43) Aligned. Score:  29
Sequences (11:44) Aligned. Score:  26
Sequences (11:45) Aligned. Score:  30
Sequences (11:46) Aligned. Score:  31
Sequences (11:47) Aligned. Score:  30
Sequences (11:48) Aligned. Score:  30
Sequences (11:49) Aligned. Score:  26
Sequences (11:50) Aligned. Score:  47
Sequences (11:51) Aligned. Score:  36
Sequences (11:52) Aligned. Score:  55
Sequences (11:53) Aligned. Score:  55
Sequences (11:54) Aligned. Score:  36
Sequences (11:55) Aligned. Score:  29
Sequences (11:56) Aligned. Score:  61
Sequences (11:57) Aligned. Score:  28
Sequences (11:58) Aligned. Score:  62
Sequences (11:59) Aligned. Score:  28
Sequences (11:60) Aligned. Score:  63
Sequences (11:61) Aligned. Score:  28
Sequences (11:62) Aligned. Score:  28
Sequences (11:63) Aligned. Score:  34
Sequences (11:64) Aligned. Score:  62
Sequences (11:65) Aligned. Score:  37
Sequences (11:66) Aligned. Score:  62
Sequences (11:67) Aligned. Score:  28
Sequences (11:68) Aligned. Score:  63
Sequences (11:69) Aligned. Score:  27
Sequences (11:70) Aligned. Score:  27
Sequences (11:71) Aligned. Score:  57
Sequences (11:72) Aligned. Score:  56
Sequences (11:73) Aligned. Score:  26
Sequences (11:74) Aligned. Score:  16
Sequences (11:75) Aligned. Score:  32
Sequences (11:76) Aligned. Score:  30
Sequences (11:77) Aligned. Score:  9
Sequences (11:78) Aligned. Score:  34
Sequences (11:79) Aligned. Score:  100
Sequences (11:80) Aligned. Score:  31
Sequences (11:81) Aligned. Score:  29
Sequences (11:82) Aligned. Score:  59
Sequences (11:83) Aligned. Score:  39
Sequences (11:84) Aligned. Score:  34
Sequences (11:85) Aligned. Score:  33
Sequences (11:86) Aligned. Score:  27
Sequences (11:87) Aligned. Score:  28
Sequences (11:88) Aligned. Score:  31
Sequences (11:89) Aligned. Score:  29
Sequences (11:90) Aligned. Score:  29
Sequences (11:91) Aligned. Score:  33
Sequences (11:92) Aligned. Score:  63
Sequences (11:93) Aligned. Score:  28
Sequences (11:94) Aligned. Score:  32
Sequences (11:95) Aligned. Score:  47
Sequences (11:96) Aligned. Score:  99
Sequences (11:97) Aligned. Score:  35
Sequences (11:98) Aligned. Score:  63
Sequences (11:99) Aligned. Score:  27
Sequences (11:100) Aligned. Score:  34
Sequences (11:101) Aligned. Score:  30
Sequences (11:102) Aligned. Score:  29
Sequences (12:13) Aligned. Score:  29
Sequences (12:14) Aligned. Score:  27
Sequences (12:15) Aligned. Score:  84
Sequences (12:16) Aligned. Score:  19
Sequences (12:17) Aligned. Score:  19
Sequences (12:18) Aligned. Score:  19
Sequences (12:19) Aligned. Score:  19
Sequences (12:20) Aligned. Score:  31
Sequences (12:21) Aligned. Score:  29
Sequences (12:22) Aligned. Score:  82
Sequences (12:23) Aligned. Score:  26
Sequences (12:24) Aligned. Score:  81
Sequences (12:25) Aligned. Score:  33
Sequences (12:26) Aligned. Score:  27
Sequences (12:27) Aligned. Score:  29
Sequences (12:28) Aligned. Score:  61
Sequences (12:29) Aligned. Score:  29
Sequences (12:30) Aligned. Score:  60
Sequences (12:31) Aligned. Score:  34
Sequences (12:32) Aligned. Score:  31
Sequences (12:33) Aligned. Score:  29
Sequences (12:34) Aligned. Score:  28
Sequences (12:35) Aligned. Score:  27
Sequences (12:36) Aligned. Score:  60
Sequences (12:37) Aligned. Score:  30
Sequences (12:38) Aligned. Score:  27
Sequences (12:39) Aligned. Score:  61
Sequences (12:40) Aligned. Score:  28
Sequences (12:41) Aligned. Score:  33
Sequences (12:42) Aligned. Score:  30
Sequences (12:43) Aligned. Score:  31
Sequences (12:44) Aligned. Score:  28
Sequences (12:45) Aligned. Score:  32
Sequences (12:46) Aligned. Score:  31
Sequences (12:47) Aligned. Score:  31
Sequences (12:48) Aligned. Score:  32
Sequences (12:49) Aligned. Score:  29
Sequences (12:50) Aligned. Score:  27
Sequences (12:51) Aligned. Score:  84
Sequences (12:52) Aligned. Score:  27
Sequences (12:53) Aligned. Score:  27
Sequences (12:54) Aligned. Score:  84
Sequences (12:55) Aligned. Score:  32
Sequences (12:56) Aligned. Score:  27
Sequences (12:57) Aligned. Score:  61
Sequences (12:58) Aligned. Score:  27
Sequences (12:59) Aligned. Score:  61
Sequences (12:60) Aligned. Score:  29
Sequences (12:61) Aligned. Score:  60
Sequences (12:62) Aligned. Score:  23
Sequences (12:63) Aligned. Score:  27
Sequences (12:64) Aligned. Score:  29
Sequences (12:65) Aligned. Score:  75
Sequences (12:66) Aligned. Score:  26
Sequences (12:67) Aligned. Score:  61
Sequences (12:68) Aligned. Score:  29
Sequences (12:69) Aligned. Score:  59
Sequences (12:70) Aligned. Score:  97
Sequences (12:71) Aligned. Score:  29
Sequences (12:72) Aligned. Score:  26
Sequences (12:73) Aligned. Score:  81
Sequences (12:74) Aligned. Score:  19
Sequences (12:75) Aligned. Score:  29
Sequences (12:76) Aligned. Score:  28
Sequences (12:77) Aligned. Score:  14
Sequences (12:78) Aligned. Score:  34
Sequences (12:79) Aligned. Score:  27
Sequences (12:80) Aligned. Score:  29
Sequences (12:81) Aligned. Score:  32
Sequences (12:82) Aligned. Score:  29
Sequences (12:83) Aligned. Score:  82
Sequences (12:84) Aligned. Score:  29
Sequences (12:85) Aligned. Score:  29
Sequences (12:86) Aligned. Score:  32
Sequences (12:87) Aligned. Score:  31
Sequences (12:88) Aligned. Score:  29
Sequences (12:89) Aligned. Score:  32
Sequences (12:90) Aligned. Score:  31
Sequences (12:91) Aligned. Score:  33
Sequences (12:92) Aligned. Score:  29
Sequences (12:93) Aligned. Score:  60
Sequences (12:94) Aligned. Score:  35
Sequences (12:95) Aligned. Score:  27
Sequences (12:96) Aligned. Score:  27
Sequences (12:97) Aligned. Score:  79
Sequences (12:98) Aligned. Score:  29
Sequences (12:99) Aligned. Score:  60
Sequences (12:100) Aligned. Score:  34
Sequences (12:101) Aligned. Score:  33
Sequences (12:102) Aligned. Score:  30
Sequences (13:14) Aligned. Score:  82
Sequences (13:15) Aligned. Score:  39
Sequences (13:16) Aligned. Score:  9
Sequences (13:17) Aligned. Score:  11
Sequences (13:18) Aligned. Score:  15
Sequences (13:19) Aligned. Score:  9
Sequences (13:20) Aligned. Score:  31
Sequences (13:21) Aligned. Score:  67
Sequences (13:22) Aligned. Score:  43
Sequences (13:23) Aligned. Score:  86
Sequences (13:24) Aligned. Score:  27
Sequences (13:25) Aligned. Score:  34
Sequences (13:26) Aligned. Score:  31
Sequences (13:27) Aligned. Score:  65
Sequences (13:28) Aligned. Score:  29
Sequences (13:29) Aligned. Score:  65
Sequences (13:30) Aligned. Score:  28
Sequences (13:31) Aligned. Score:  29
Sequences (13:32) Aligned. Score:  34
Sequences (13:33) Aligned. Score:  29
Sequences (13:34) Aligned. Score:  35
Sequences (13:35) Aligned. Score:  64
Sequences (13:36) Aligned. Score:  28
Sequences (13:37) Aligned. Score:  50
Sequences (13:38) Aligned. Score:  60
Sequences (13:39) Aligned. Score:  31
Sequences (13:40) Aligned. Score:  38
Sequences (13:41) Aligned. Score:  29
Sequences (13:42) Aligned. Score:  36
Sequences (13:43) Aligned. Score:  34
Sequences (13:44) Aligned. Score:  28
Sequences (13:45) Aligned. Score:  34
Sequences (13:46) Aligned. Score:  34
Sequences (13:47) Aligned. Score:  34
Sequences (13:48) Aligned. Score:  34
Sequences (13:49) Aligned. Score:  30
Sequences (13:50) Aligned. Score:  47
Sequences (13:51) Aligned. Score:  39
Sequences (13:52) Aligned. Score:  82
Sequences (13:53) Aligned. Score:  83
Sequences (13:54) Aligned. Score:  39
Sequences (13:55) Aligned. Score:  32
Sequences (13:56) Aligned. Score:  60
Sequences (13:57) Aligned. Score:  31
Sequences (13:58) Aligned. Score:  60
Sequences (13:59) Aligned. Score:  31
Sequences (13:60) Aligned. Score:  65
Sequences (13:61) Aligned. Score:  29
Sequences (13:62) Aligned. Score:  29
Sequences (13:63) Aligned. Score:  35
Sequences (13:64) Aligned. Score:  65
Sequences (13:65) Aligned. Score:  39
Sequences (13:66) Aligned. Score:  63
Sequences (13:67) Aligned. Score:  28
Sequences (13:68) Aligned. Score:  65
Sequences (13:69) Aligned. Score:  29
Sequences (13:70) Aligned. Score:  29
Sequences (13:71) Aligned. Score:  99
Sequences (13:72) Aligned. Score:  86
Sequences (13:73) Aligned. Score:  27
Sequences (13:74) Aligned. Score:  18
Sequences (13:75) Aligned. Score:  36
Sequences (13:76) Aligned. Score:  35
Sequences (13:77) Aligned. Score:  4
Sequences (13:78) Aligned. Score:  31
Sequences (13:79) Aligned. Score:  57
Sequences (13:80) Aligned. Score:  29
Sequences (13:81) Aligned. Score:  32
Sequences (13:82) Aligned. Score:  67
Sequences (13:83) Aligned. Score:  43
Sequences (13:84) Aligned. Score:  35
Sequences (13:85) Aligned. Score:  35
Sequences (13:86) Aligned. Score:  32
Sequences (13:87) Aligned. Score:  32
Sequences (13:88) Aligned. Score:  29
Sequences (13:89) Aligned. Score:  32
Sequences (13:90) Aligned. Score:  32
Sequences (13:91) Aligned. Score:  32
Sequences (13:92) Aligned. Score:  65
Sequences (13:93) Aligned. Score:  29
Sequences (13:94) Aligned. Score:  31
Sequences (13:95) Aligned. Score:  48
Sequences (13:96) Aligned. Score:  57
Sequences (13:97) Aligned. Score:  38
Sequences (13:98) Aligned. Score:  65
Sequences (13:99) Aligned. Score:  28
Sequences (13:100) Aligned. Score:  36
Sequences (13:101) Aligned. Score:  34
Sequences (13:102) Aligned. Score:  33
Sequences (14:15) Aligned. Score:  46
Sequences (14:16) Aligned. Score:  12
Sequences (14:17) Aligned. Score:  7
Sequences (14:18) Aligned. Score:  12
Sequences (14:19) Aligned. Score:  12
Sequences (14:20) Aligned. Score:  32
Sequences (14:21) Aligned. Score:  64
Sequences (14:22) Aligned. Score:  49
Sequences (14:23) Aligned. Score:  82
Sequences (14:24) Aligned. Score:  26
Sequences (14:25) Aligned. Score:  34
Sequences (14:26) Aligned. Score:  30
Sequences (14:27) Aligned. Score:  63
Sequences (14:28) Aligned. Score:  29
Sequences (14:29) Aligned. Score:  63
Sequences (14:30) Aligned. Score:  29
Sequences (14:31) Aligned. Score:  30
Sequences (14:32) Aligned. Score:  34
Sequences (14:33) Aligned. Score:  33
Sequences (14:34) Aligned. Score:  33
Sequences (14:35) Aligned. Score:  63
Sequences (14:36) Aligned. Score:  29
Sequences (14:37) Aligned. Score:  52
Sequences (14:38) Aligned. Score:  57
Sequences (14:39) Aligned. Score:  30
Sequences (14:40) Aligned. Score:  35
Sequences (14:41) Aligned. Score:  29
Sequences (14:42) Aligned. Score:  35
Sequences (14:43) Aligned. Score:  33
Sequences (14:44) Aligned. Score:  31
Sequences (14:45) Aligned. Score:  35
Sequences (14:46) Aligned. Score:  33
Sequences (14:47) Aligned. Score:  34
Sequences (14:48) Aligned. Score:  34
Sequences (14:49) Aligned. Score:  32
Sequences (14:50) Aligned. Score:  46
Sequences (14:51) Aligned. Score:  46
Sequences (14:52) Aligned. Score:  97
Sequences (14:53) Aligned. Score:  97
Sequences (14:54) Aligned. Score:  46
Sequences (14:55) Aligned. Score:  30
Sequences (14:56) Aligned. Score:  57
Sequences (14:57) Aligned. Score:  30
Sequences (14:58) Aligned. Score:  57
Sequences (14:59) Aligned. Score:  30
Sequences (14:60) Aligned. Score:  63
Sequences (14:61) Aligned. Score:  29
Sequences (14:62) Aligned. Score:  30
Sequences (14:63) Aligned. Score:  34
Sequences (14:64) Aligned. Score:  62
Sequences (14:65) Aligned. Score:  44
Sequences (14:66) Aligned. Score:  63
Sequences (14:67) Aligned. Score:  29
Sequences (14:68) Aligned. Score:  63
Sequences (14:69) Aligned. Score:  30
Sequences (14:70) Aligned. Score:  28
Sequences (14:71) Aligned. Score:  82
Sequences (14:72) Aligned. Score:  82
Sequences (14:73) Aligned. Score:  27
Sequences (14:74) Aligned. Score:  14
Sequences (14:75) Aligned. Score:  34
Sequences (14:76) Aligned. Score:  34
Sequences (14:77) Aligned. Score:  6
Sequences (14:78) Aligned. Score:  35
Sequences (14:79) Aligned. Score:  55
Sequences (14:80) Aligned. Score:  33
Sequences (14:81) Aligned. Score:  30
Sequences (14:82) Aligned. Score:  65
Sequences (14:83) Aligned. Score:  49
Sequences (14:84) Aligned. Score:  33
Sequences (14:85) Aligned. Score:  33
Sequences (14:86) Aligned. Score:  30
Sequences (14:87) Aligned. Score:  31
Sequences (14:88) Aligned. Score:  33
Sequences (14:89) Aligned. Score:  30
Sequences (14:90) Aligned. Score:  30
Sequences (14:91) Aligned. Score:  35
Sequences (14:92) Aligned. Score:  63
Sequences (14:93) Aligned. Score:  29
Sequences (14:94) Aligned. Score:  36
Sequences (14:95) Aligned. Score:  46
Sequences (14:96) Aligned. Score:  55
Sequences (14:97) Aligned. Score:  44
Sequences (14:98) Aligned. Score:  63
Sequences (14:99) Aligned. Score:  29
Sequences (14:100) Aligned. Score:  36
Sequences (14:101) Aligned. Score:  34
Sequences (14:102) Aligned. Score:  35
Sequences (15:16) Aligned. Score:  29
Sequences (15:17) Aligned. Score:  32
Sequences (15:18) Aligned. Score:  32
Sequences (15:19) Aligned. Score:  29
Sequences (15:20) Aligned. Score:  44
Sequences (15:21) Aligned. Score:  43
Sequences (15:22) Aligned. Score:  82
Sequences (15:23) Aligned. Score:  37
Sequences (15:24) Aligned. Score:  84
Sequences (15:25) Aligned. Score:  46
Sequences (15:26) Aligned. Score:  34
Sequences (15:27) Aligned. Score:  43
Sequences (15:28) Aligned. Score:  67
Sequences (15:29) Aligned. Score:  43
Sequences (15:30) Aligned. Score:  65
Sequences (15:31) Aligned. Score:  55
Sequences (15:32) Aligned. Score:  48
Sequences (15:33) Aligned. Score:  51
Sequences (15:34) Aligned. Score:  36
Sequences (15:35) Aligned. Score:  34
Sequences (15:36) Aligned. Score:  65
Sequences (15:37) Aligned. Score:  37
Sequences (15:38) Aligned. Score:  37
Sequences (15:39) Aligned. Score:  72
Sequences (15:40) Aligned. Score:  44
Sequences (15:41) Aligned. Score:  44
Sequences (15:42) Aligned. Score:  48
Sequences (15:43) Aligned. Score:  46
Sequences (15:44) Aligned. Score:  50
Sequences (15:45) Aligned. Score:  48
Sequences (15:46) Aligned. Score:  51
Sequences (15:47) Aligned. Score:  51
Sequences (15:48) Aligned. Score:  48
Sequences (15:49) Aligned. Score:  46
Sequences (15:50) Aligned. Score:  37
Sequences (15:51) Aligned. Score:  100
Sequences (15:52) Aligned. Score:  46
Sequences (15:53) Aligned. Score:  46
Sequences (15:54) Aligned. Score:  100
Sequences (15:55) Aligned. Score:  50
Sequences (15:56) Aligned. Score:  37
Sequences (15:57) Aligned. Score:  72
Sequences (15:58) Aligned. Score:  37
Sequences (15:59) Aligned. Score:  72
Sequences (15:60) Aligned. Score:  43
Sequences (15:61) Aligned. Score:  67
Sequences (15:62) Aligned. Score:  32
Sequences (15:63) Aligned. Score:  39
Sequences (15:64) Aligned. Score:  46
Sequences (15:65) Aligned. Score:  75
Sequences (15:66) Aligned. Score:  41
Sequences (15:67) Aligned. Score:  65
Sequences (15:68) Aligned. Score:  43
Sequences (15:69) Aligned. Score:  67
Sequences (15:70) Aligned. Score:  86
Sequences (15:71) Aligned. Score:  39
Sequences (15:72) Aligned. Score:  37
Sequences (15:73) Aligned. Score:  82
Sequences (15:74) Aligned. Score:  34
Sequences (15:75) Aligned. Score:  46
Sequences (15:76) Aligned. Score:  44
Sequences (15:77) Aligned. Score:  20
Sequences (15:78) Aligned. Score:  44
Sequences (15:79) Aligned. Score:  36
Sequences (15:80) Aligned. Score:  51
Sequences (15:81) Aligned. Score:  50
Sequences (15:82) Aligned. Score:  43
Sequences (15:83) Aligned. Score:  82
Sequences (15:84) Aligned. Score:  36
Sequences (15:85) Aligned. Score:  36
Sequences (15:86) Aligned. Score:  53
Sequences (15:87) Aligned. Score:  51
Sequences (15:88) Aligned. Score:  51
Sequences (15:89) Aligned. Score:  50
Sequences (15:90) Aligned. Score:  53
Sequences (15:91) Aligned. Score:  41
Sequences (15:92) Aligned. Score:  43
Sequences (15:93) Aligned. Score:  67
Sequences (15:94) Aligned. Score:  44
Sequences (15:95) Aligned. Score:  37
Sequences (15:96) Aligned. Score:  36
Sequences (15:97) Aligned. Score:  77
Sequences (15:98) Aligned. Score:  43
Sequences (15:99) Aligned. Score:  65
Sequences (15:100) Aligned. Score:  56
Sequences (15:101) Aligned. Score:  48
Sequences (15:102) Aligned. Score:  51
Sequences (16:17) Aligned. Score:  63
Sequences (16:18) Aligned. Score:  66
Sequences (16:19) Aligned. Score:  99
Sequences (16:20) Aligned. Score:  18
Sequences (16:21) Aligned. Score:  19
Sequences (16:22) Aligned. Score:  17
Sequences (16:23) Aligned. Score:  6
Sequences (16:24) Aligned. Score:  16
Sequences (16:25) Aligned. Score:  24
Sequences (16:26) Aligned. Score:  15
Sequences (16:27) Aligned. Score:  14
Sequences (16:28) Aligned. Score:  13
Sequences (16:29) Aligned. Score:  17
Sequences (16:30) Aligned. Score:  13
Sequences (16:31) Aligned. Score:  21
Sequences (16:32) Aligned. Score:  23
Sequences (16:33) Aligned. Score:  18
Sequences (16:34) Aligned. Score:  21
Sequences (16:35) Aligned. Score:  10
Sequences (16:36) Aligned. Score:  13
Sequences (16:37) Aligned. Score:  20
Sequences (16:38) Aligned. Score:  10
Sequences (16:39) Aligned. Score:  11
Sequences (16:40) Aligned. Score:  16
Sequences (16:41) Aligned. Score:  23
Sequences (16:42) Aligned. Score:  16
Sequences (16:43) Aligned. Score:  17
Sequences (16:44) Aligned. Score:  23
Sequences (16:45) Aligned. Score:  24
Sequences (16:46) Aligned. Score:  23
Sequences (16:47) Aligned. Score:  22
Sequences (16:48) Aligned. Score:  24
Sequences (16:49) Aligned. Score:  17
Sequences (16:50) Aligned. Score:  16
Sequences (16:51) Aligned. Score:  29
Sequences (16:52) Aligned. Score:  14
Sequences (16:53) Aligned. Score:  17
Sequences (16:54) Aligned. Score:  29
Sequences (16:55) Aligned. Score:  21
Sequences (16:56) Aligned. Score:  10
Sequences (16:57) Aligned. Score:  11
Sequences (16:58) Aligned. Score:  10
Sequences (16:59) Aligned. Score:  11
Sequences (16:60) Aligned. Score:  17
Sequences (16:61) Aligned. Score:  13
Sequences (16:62) Aligned. Score:  27
Sequences (16:63) Aligned. Score:  20
Sequences (16:64) Aligned. Score:  21
Sequences (16:65) Aligned. Score:  15
Sequences (16:66) Aligned. Score:  10
Sequences (16:67) Aligned. Score:  13
Sequences (16:68) Aligned. Score:  17
Sequences (16:69) Aligned. Score:  13
Sequences (16:70) Aligned. Score:  20
Sequences (16:71) Aligned. Score:  13
Sequences (16:72) Aligned. Score:  6
Sequences (16:73) Aligned. Score:  15
Sequences (16:74) Aligned. Score:  63
Sequences (16:75) Aligned. Score:  17
Sequences (16:76) Aligned. Score:  17
Sequences (16:77) Aligned. Score:  37
Sequences (16:78) Aligned. Score:  25
Sequences (16:79) Aligned. Score:  16
Sequences (16:80) Aligned. Score:  18
Sequences (16:81) Aligned. Score:  21
Sequences (16:82) Aligned. Score:  20
Sequences (16:83) Aligned. Score:  17
Sequences (16:84) Aligned. Score:  21
Sequences (16:85) Aligned. Score:  21
Sequences (16:86) Aligned. Score:  22
Sequences (16:87) Aligned. Score:  22
Sequences (16:88) Aligned. Score:  18
Sequences (16:89) Aligned. Score:  21
Sequences (16:90) Aligned. Score:  23
Sequences (16:91) Aligned. Score:  18
Sequences (16:92) Aligned. Score:  17
Sequences (16:93) Aligned. Score:  13
Sequences (16:94) Aligned. Score:  24
Sequences (16:95) Aligned. Score:  17
Sequences (16:96) Aligned. Score:  16
Sequences (16:97) Aligned. Score:  18
Sequences (16:98) Aligned. Score:  17
Sequences (16:99) Aligned. Score:  13
Sequences (16:100) Aligned. Score:  19
Sequences (16:101) Aligned. Score:  24
Sequences (16:102) Aligned. Score:  20
Sequences (17:18) Aligned. Score:  75
Sequences (17:19) Aligned. Score:  63
Sequences (17:20) Aligned. Score:  22
Sequences (17:21) Aligned. Score:  15
Sequences (17:22) Aligned. Score:  21
Sequences (17:23) Aligned. Score:  10
Sequences (17:24) Aligned. Score:  15
Sequences (17:25) Aligned. Score:  26
Sequences (17:26) Aligned. Score:  15
Sequences (17:27) Aligned. Score:  19
Sequences (17:28) Aligned. Score:  13
Sequences (17:29) Aligned. Score:  19
Sequences (17:30) Aligned. Score:  13
Sequences (17:31) Aligned. Score:  22
Sequences (17:32) Aligned. Score:  23
Sequences (17:33) Aligned. Score:  18
Sequences (17:34) Aligned. Score:  21
Sequences (17:35) Aligned. Score:  10
Sequences (17:36) Aligned. Score:  13
Sequences (17:37) Aligned. Score:  11
Sequences (17:38) Aligned. Score:  16
Sequences (17:39) Aligned. Score:  17
Sequences (17:40) Aligned. Score:  12
Sequences (17:41) Aligned. Score:  23
Sequences (17:42) Aligned. Score:  18
Sequences (17:43) Aligned. Score:  16
Sequences (17:44) Aligned. Score:  25
Sequences (17:45) Aligned. Score:  24
Sequences (17:46) Aligned. Score:  13
Sequences (17:47) Aligned. Score:  13
Sequences (17:48) Aligned. Score:  24
Sequences (17:49) Aligned. Score:  23
Sequences (17:50) Aligned. Score:  20
Sequences (17:51) Aligned. Score:  32
Sequences (17:52) Aligned. Score:  7
Sequences (17:53) Aligned. Score:  7
Sequences (17:54) Aligned. Score:  32
Sequences (17:55) Aligned. Score:  25
Sequences (17:56) Aligned. Score:  17
Sequences (17:57) Aligned. Score:  17
Sequences (17:58) Aligned. Score:  16
Sequences (17:59) Aligned. Score:  17
Sequences (17:60) Aligned. Score:  19
Sequences (17:61) Aligned. Score:  14
Sequences (17:62) Aligned. Score:  27
Sequences (17:63) Aligned. Score:  24
Sequences (17:64) Aligned. Score:  18
Sequences (17:65) Aligned. Score:  22
Sequences (17:66) Aligned. Score:  10
Sequences (17:67) Aligned. Score:  13
Sequences (17:68) Aligned. Score:  19
Sequences (17:69) Aligned. Score:  14
Sequences (17:70) Aligned. Score:  19
Sequences (17:71) Aligned. Score:  10
Sequences (17:72) Aligned. Score:  10
Sequences (17:73) Aligned. Score:  15
Sequences (17:74) Aligned. Score:  75
Sequences (17:75) Aligned. Score:  18
Sequences (17:76) Aligned. Score:  16
Sequences (17:77) Aligned. Score:  36
Sequences (17:78) Aligned. Score:  21
Sequences (17:79) Aligned. Score:  18
Sequences (17:80) Aligned. Score:  18
Sequences (17:81) Aligned. Score:  25
Sequences (17:82) Aligned. Score:  15
Sequences (17:83) Aligned. Score:  21
Sequences (17:84) Aligned. Score:  21
Sequences (17:85) Aligned. Score:  21
Sequences (17:86) Aligned. Score:  25
Sequences (17:87) Aligned. Score:  25
Sequences (17:88) Aligned. Score:  18
Sequences (17:89) Aligned. Score:  25
Sequences (17:90) Aligned. Score:  25
Sequences (17:91) Aligned. Score:  28
Sequences (17:92) Aligned. Score:  19
Sequences (17:93) Aligned. Score:  14
Sequences (17:94) Aligned. Score:  23
Sequences (17:95) Aligned. Score:  20
Sequences (17:96) Aligned. Score:  18
Sequences (17:97) Aligned. Score:  22
Sequences (17:98) Aligned. Score:  19
Sequences (17:99) Aligned. Score:  13
Sequences (17:100) Aligned. Score:  18
Sequences (17:101) Aligned. Score:  24
Sequences (17:102) Aligned. Score:  12
Sequences (18:19) Aligned. Score:  65
Sequences (18:20) Aligned. Score:  16
Sequences (18:21) Aligned. Score:  13
Sequences (18:22) Aligned. Score:  19
Sequences (18:23) Aligned. Score:  13
Sequences (18:24) Aligned. Score:  9
Sequences (18:25) Aligned. Score:  25
Sequences (18:26) Aligned. Score:  15
Sequences (18:27) Aligned. Score:  15
Sequences (18:28) Aligned. Score:  14
Sequences (18:29) Aligned. Score:  16
Sequences (18:30) Aligned. Score:  14
Sequences (18:31) Aligned. Score:  21
Sequences (18:32) Aligned. Score:  25
Sequences (18:33) Aligned. Score:  18
Sequences (18:34) Aligned. Score:  20
Sequences (18:35) Aligned. Score:  8
Sequences (18:36) Aligned. Score:  14
Sequences (18:37) Aligned. Score:  14
Sequences (18:38) Aligned. Score:  15
Sequences (18:39) Aligned. Score:  10
Sequences (18:40) Aligned. Score:  16
Sequences (18:41) Aligned. Score:  24
Sequences (18:42) Aligned. Score:  22
Sequences (18:43) Aligned. Score:  19
Sequences (18:44) Aligned. Score:  25
Sequences (18:45) Aligned. Score:  25
Sequences (18:46) Aligned. Score:  19
Sequences (18:47) Aligned. Score:  19
Sequences (18:48) Aligned. Score:  25
Sequences (18:49) Aligned. Score:  22
Sequences (18:50) Aligned. Score:  12
Sequences (18:51) Aligned. Score:  32
Sequences (18:52) Aligned. Score:  11
Sequences (18:53) Aligned. Score:  15
Sequences (18:54) Aligned. Score:  32
Sequences (18:55) Aligned. Score:  24
Sequences (18:56) Aligned. Score:  16
Sequences (18:57) Aligned. Score:  10
Sequences (18:58) Aligned. Score:  16
Sequences (18:59) Aligned. Score:  10
Sequences (18:60) Aligned. Score:  16
Sequences (18:61) Aligned. Score:  14
Sequences (18:62) Aligned. Score:  27
Sequences (18:63) Aligned. Score:  22
Sequences (18:64) Aligned. Score:  11
Sequences (18:65) Aligned. Score:  20
Sequences (18:66) Aligned. Score:  8
Sequences (18:67) Aligned. Score:  14
Sequences (18:68) Aligned. Score:  16
Sequences (18:69) Aligned. Score:  14
Sequences (18:70) Aligned. Score:  20
Sequences (18:71) Aligned. Score:  4
Sequences (18:72) Aligned. Score:  13
Sequences (18:73) Aligned. Score:  9
Sequences (18:74) Aligned. Score:  92
Sequences (18:75) Aligned. Score:  21
Sequences (18:76) Aligned. Score:  22
Sequences (18:77) Aligned. Score:  35
Sequences (18:78) Aligned. Score:  25
Sequences (18:79) Aligned. Score:  16
Sequences (18:80) Aligned. Score:  18
Sequences (18:81) Aligned. Score:  24
Sequences (18:82) Aligned. Score:  13
Sequences (18:83) Aligned. Score:  19
Sequences (18:84) Aligned. Score:  19
Sequences (18:85) Aligned. Score:  20
Sequences (18:86) Aligned. Score:  25
Sequences (18:87) Aligned. Score:  25
Sequences (18:88) Aligned. Score:  18
Sequences (18:89) Aligned. Score:  24
Sequences (18:90) Aligned. Score:  23
Sequences (18:91) Aligned. Score:  28
Sequences (18:92) Aligned. Score:  16
Sequences (18:93) Aligned. Score:  14
Sequences (18:94) Aligned. Score:  27
Sequences (18:95) Aligned. Score:  12
Sequences (18:96) Aligned. Score:  16
Sequences (18:97) Aligned. Score:  18
Sequences (18:98) Aligned. Score:  16
Sequences (18:99) Aligned. Score:  14
Sequences (18:100) Aligned. Score:  20
Sequences (18:101) Aligned. Score:  25
Sequences (18:102) Aligned. Score:  24
Sequences (19:20) Aligned. Score:  18
Sequences (19:21) Aligned. Score:  19
Sequences (19:22) Aligned. Score:  17
Sequences (19:23) Aligned. Score:  6
Sequences (19:24) Aligned. Score:  16
Sequences (19:25) Aligned. Score:  24
Sequences (19:26) Aligned. Score:  15
Sequences (19:27) Aligned. Score:  14
Sequences (19:28) Aligned. Score:  12
Sequences (19:29) Aligned. Score:  15
Sequences (19:30) Aligned. Score:  13
Sequences (19:31) Aligned. Score:  21
Sequences (19:32) Aligned. Score:  23
Sequences (19:33) Aligned. Score:  18
Sequences (19:34) Aligned. Score:  21
Sequences (19:35) Aligned. Score:  10
Sequences (19:36) Aligned. Score:  13
Sequences (19:37) Aligned. Score:  20
Sequences (19:38) Aligned. Score:  10
Sequences (19:39) Aligned. Score:  11
Sequences (19:40) Aligned. Score:  16
Sequences (19:41) Aligned. Score:  23
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Sequences (19:49) Aligned. Score:  17
Sequences (19:50) Aligned. Score:  16
Sequences (19:51) Aligned. Score:  29
Sequences (19:52) Aligned. Score:  13
Sequences (19:53) Aligned. Score:  17
Sequences (19:54) Aligned. Score:  29
Sequences (19:55) Aligned. Score:  21
Sequences (19:56) Aligned. Score:  10
Sequences (19:57) Aligned. Score:  11
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Sequences (19:60) Aligned. Score:  17
Sequences (19:61) Aligned. Score:  13
Sequences (19:62) Aligned. Score:  27
Sequences (19:63) Aligned. Score:  20
Sequences (19:64) Aligned. Score:  20
Sequences (19:65) Aligned. Score:  15
Sequences (19:66) Aligned. Score:  10
Sequences (19:67) Aligned. Score:  13
Sequences (19:68) Aligned. Score:  17
Sequences (19:69) Aligned. Score:  13
Sequences (19:70) Aligned. Score:  20
Sequences (19:71) Aligned. Score:  13
Sequences (19:72) Aligned. Score:  6
Sequences (19:73) Aligned. Score:  15
Sequences (19:74) Aligned. Score:  63
Sequences (19:75) Aligned. Score:  17
Sequences (19:76) Aligned. Score:  17
Sequences (19:77) Aligned. Score:  37
Sequences (19:78) Aligned. Score:  25
Sequences (19:79) Aligned. Score:  16
Sequences (19:80) Aligned. Score:  18
Sequences (19:81) Aligned. Score:  21
Sequences (19:82) Aligned. Score:  19
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Sequences (19:84) Aligned. Score:  21
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Sequences (19:89) Aligned. Score:  21
Sequences (19:90) Aligned. Score:  23
Sequences (19:91) Aligned. Score:  18
Sequences (19:92) Aligned. Score:  17
Sequences (19:93) Aligned. Score:  13
Sequences (19:94) Aligned. Score:  27
Sequences (19:95) Aligned. Score:  17
Sequences (19:96) Aligned. Score:  16
Sequences (19:97) Aligned. Score:  18
Sequences (19:98) Aligned. Score:  15
Sequences (19:99) Aligned. Score:  13
Sequences (19:100) Aligned. Score:  20
Sequences (19:101) Aligned. Score:  24
Sequences (19:102) Aligned. Score:  20
Sequences (20:21) Aligned. Score:  31
Sequences (20:22) Aligned. Score:  49
Sequences (20:23) Aligned. Score:  32
Sequences (20:24) Aligned. Score:  29
Sequences (20:25) Aligned. Score:  54
Sequences (20:26) Aligned. Score:  37
Sequences (20:27) Aligned. Score:  31
Sequences (20:28) Aligned. Score:  35
Sequences (20:29) Aligned. Score:  30
Sequences (20:30) Aligned. Score:  33
Sequences (20:31) Aligned. Score:  31
Sequences (20:32) Aligned. Score:  55
Sequences (20:33) Aligned. Score:  39
Sequences (20:34) Aligned. Score:  42
Sequences (20:35) Aligned. Score:  27
Sequences (20:36) Aligned. Score:  33
Sequences (20:37) Aligned. Score:  29
Sequences (20:38) Aligned. Score:  29
Sequences (20:39) Aligned. Score:  31
Sequences (20:40) Aligned. Score:  54
Sequences (20:41) Aligned. Score:  56
Sequences (20:42) Aligned. Score:  52
Sequences (20:43) Aligned. Score:  54
Sequences (20:44) Aligned. Score:  54
Sequences (20:45) Aligned. Score:  56
Sequences (20:46) Aligned. Score:  54
Sequences (20:47) Aligned. Score:  55
Sequences (20:48) Aligned. Score:  56
Sequences (20:49) Aligned. Score:  49
Sequences (20:50) Aligned. Score:  28
Sequences (20:51) Aligned. Score:  44
Sequences (20:52) Aligned. Score:  32
Sequences (20:53) Aligned. Score:  32
Sequences (20:54) Aligned. Score:  44
Sequences (20:55) Aligned. Score:  54
Sequences (20:56) Aligned. Score:  29
Sequences (20:57) Aligned. Score:  31
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Sequences (20:59) Aligned. Score:  31
Sequences (20:60) Aligned. Score:  31
Sequences (20:61) Aligned. Score:  35
Sequences (20:62) Aligned. Score:  35
Sequences (20:63) Aligned. Score:  43
Sequences (20:64) Aligned. Score:  30
Sequences (20:65) Aligned. Score:  46
Sequences (20:66) Aligned. Score:  29
Sequences (20:67) Aligned. Score:  33
Sequences (20:68) Aligned. Score:  31
Sequences (20:69) Aligned. Score:  34
Sequences (20:70) Aligned. Score:  31
Sequences (20:71) Aligned. Score:  32
Sequences (20:72) Aligned. Score:  32
Sequences (20:73) Aligned. Score:  29
Sequences (20:74) Aligned. Score:  21
Sequences (20:75) Aligned. Score:  52
Sequences (20:76) Aligned. Score:  53
Sequences (20:77) Aligned. Score:  14
Sequences (20:78) Aligned. Score:  49
Sequences (20:79) Aligned. Score:  26
Sequences (20:80) Aligned. Score:  39
Sequences (20:81) Aligned. Score:  54
Sequences (20:82) Aligned. Score:  31
Sequences (20:83) Aligned. Score:  49
Sequences (20:84) Aligned. Score:  42
Sequences (20:85) Aligned. Score:  43
Sequences (20:86) Aligned. Score:  53
Sequences (20:87) Aligned. Score:  53
Sequences (20:88) Aligned. Score:  39
Sequences (20:89) Aligned. Score:  54
Sequences (20:90) Aligned. Score:  53
Sequences (20:91) Aligned. Score:  60
Sequences (20:92) Aligned. Score:  31
Sequences (20:93) Aligned. Score:  35
Sequences (20:94) Aligned. Score:  48
Sequences (20:95) Aligned. Score:  27
Sequences (20:96) Aligned. Score:  26
Sequences (20:97) Aligned. Score:  46
Sequences (20:98) Aligned. Score:  30
Sequences (20:99) Aligned. Score:  33
Sequences (20:100) Aligned. Score:  38
Sequences (20:101) Aligned. Score:  56
Sequences (20:102) Aligned. Score:  52
Sequences (21:22) Aligned. Score:  41
Sequences (21:23) Aligned. Score:  64
Sequences (21:24) Aligned. Score:  27
Sequences (21:25) Aligned. Score:  30
Sequences (21:26) Aligned. Score:  33
Sequences (21:27) Aligned. Score:  76
Sequences (21:28) Aligned. Score:  30
Sequences (21:29) Aligned. Score:  74
Sequences (21:30) Aligned. Score:  29
Sequences (21:31) Aligned. Score:  28
Sequences (21:32) Aligned. Score:  32
Sequences (21:33) Aligned. Score:  33
Sequences (21:34) Aligned. Score:  33
Sequences (21:35) Aligned. Score:  74
Sequences (21:36) Aligned. Score:  29
Sequences (21:37) Aligned. Score:  56
Sequences (21:38) Aligned. Score:  66
Sequences (21:39) Aligned. Score:  31
Sequences (21:40) Aligned. Score:  32
Sequences (21:41) Aligned. Score:  31
Sequences (21:42) Aligned. Score:  30
Sequences (21:43) Aligned. Score:  33
Sequences (21:44) Aligned. Score:  30
Sequences (21:45) Aligned. Score:  34
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Sequences (21:47) Aligned. Score:  33
Sequences (21:48) Aligned. Score:  34
Sequences (21:49) Aligned. Score:  30
Sequences (21:50) Aligned. Score:  49
Sequences (21:51) Aligned. Score:  43
Sequences (21:52) Aligned. Score:  63
Sequences (21:53) Aligned. Score:  65
Sequences (21:54) Aligned. Score:  43
Sequences (21:55) Aligned. Score:  32
Sequences (21:56) Aligned. Score:  66
Sequences (21:57) Aligned. Score:  31
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Sequences (21:59) Aligned. Score:  31
Sequences (21:60) Aligned. Score:  75
Sequences (21:61) Aligned. Score:  30
Sequences (21:62) Aligned. Score:  29
Sequences (21:63) Aligned. Score:  34
Sequences (21:64) Aligned. Score:  74
Sequences (21:65) Aligned. Score:  39
Sequences (21:66) Aligned. Score:  74
Sequences (21:67) Aligned. Score:  29
Sequences (21:68) Aligned. Score:  75
Sequences (21:69) Aligned. Score:  30
Sequences (21:70) Aligned. Score:  30
Sequences (21:71) Aligned. Score:  67
Sequences (21:72) Aligned. Score:  64
Sequences (21:73) Aligned. Score:  27
Sequences (21:74) Aligned. Score:  17
Sequences (21:75) Aligned. Score:  30
Sequences (21:76) Aligned. Score:  30
Sequences (21:77) Aligned. Score:  3
Sequences (21:78) Aligned. Score:  34
Sequences (21:79) Aligned. Score:  59
Sequences (21:80) Aligned. Score:  33
Sequences (21:81) Aligned. Score:  32
Sequences (21:82) Aligned. Score:  99
Sequences (21:83) Aligned. Score:  41
Sequences (21:84) Aligned. Score:  33
Sequences (21:85) Aligned. Score:  32
Sequences (21:86) Aligned. Score:  32
Sequences (21:87) Aligned. Score:  31
Sequences (21:88) Aligned. Score:  33
Sequences (21:89) Aligned. Score:  32
Sequences (21:90) Aligned. Score:  32
Sequences (21:91) Aligned. Score:  34
Sequences (21:92) Aligned. Score:  75
Sequences (21:93) Aligned. Score:  30
Sequences (21:94) Aligned. Score:  34
Sequences (21:95) Aligned. Score:  50
Sequences (21:96) Aligned. Score:  59
Sequences (21:97) Aligned. Score:  38
Sequences (21:98) Aligned. Score:  74
Sequences (21:99) Aligned. Score:  29
Sequences (21:100) Aligned. Score:  37
Sequences (21:101) Aligned. Score:  34
Sequences (21:102) Aligned. Score:  31
Sequences (22:23) Aligned. Score:  41
Sequences (22:24) Aligned. Score:  84
Sequences (22:25) Aligned. Score:  47
Sequences (22:26) Aligned. Score:  31
Sequences (22:27) Aligned. Score:  43
Sequences (22:28) Aligned. Score:  80
Sequences (22:29) Aligned. Score:  43
Sequences (22:30) Aligned. Score:  78
Sequences (22:31) Aligned. Score:  56
Sequences (22:32) Aligned. Score:  49
Sequences (22:33) Aligned. Score:  47
Sequences (22:34) Aligned. Score:  35
Sequences (22:35) Aligned. Score:  35
Sequences (22:36) Aligned. Score:  78
Sequences (22:37) Aligned. Score:  37
Sequences (22:38) Aligned. Score:  39
Sequences (22:39) Aligned. Score:  76
Sequences (22:40) Aligned. Score:  45
Sequences (22:41) Aligned. Score:  49
Sequences (22:42) Aligned. Score:  49
Sequences (22:43) Aligned. Score:  47
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Sequences (22:45) Aligned. Score:  49
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Sequences (22:48) Aligned. Score:  49
Sequences (22:49) Aligned. Score:  49
Sequences (22:50) Aligned. Score:  37
Sequences (22:51) Aligned. Score:  82
Sequences (22:52) Aligned. Score:  49
Sequences (22:53) Aligned. Score:  49
Sequences (22:54) Aligned. Score:  82
Sequences (22:55) Aligned. Score:  47
Sequences (22:56) Aligned. Score:  39
Sequences (22:57) Aligned. Score:  76
Sequences (22:58) Aligned. Score:  39
Sequences (22:59) Aligned. Score:  76
Sequences (22:60) Aligned. Score:  43
Sequences (22:61) Aligned. Score:  80
Sequences (22:62) Aligned. Score:  37
Sequences (22:63) Aligned. Score:  41
Sequences (22:64) Aligned. Score:  45
Sequences (22:65) Aligned. Score:  86
Sequences (22:66) Aligned. Score:  33
Sequences (22:67) Aligned. Score:  78
Sequences (22:68) Aligned. Score:  43
Sequences (22:69) Aligned. Score:  80
Sequences (22:70) Aligned. Score:  82
Sequences (22:71) Aligned. Score:  43
Sequences (22:72) Aligned. Score:  41
Sequences (22:73) Aligned. Score:  84
Sequences (22:74) Aligned. Score:  21
Sequences (22:75) Aligned. Score:  47
Sequences (22:76) Aligned. Score:  45
Sequences (22:77) Aligned. Score:  17
Sequences (22:78) Aligned. Score:  45
Sequences (22:79) Aligned. Score:  39
Sequences (22:80) Aligned. Score:  47
Sequences (22:81) Aligned. Score:  47
Sequences (22:82) Aligned. Score:  41
Sequences (22:83) Aligned. Score:  100
Sequences (22:84) Aligned. Score:  35
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Sequences (22:86) Aligned. Score:  47
Sequences (22:87) Aligned. Score:  49
Sequences (22:88) Aligned. Score:  47
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Sequences (22:91) Aligned. Score:  49
Sequences (22:92) Aligned. Score:  43
Sequences (22:93) Aligned. Score:  80
Sequences (22:94) Aligned. Score:  45
Sequences (22:95) Aligned. Score:  37
Sequences (22:96) Aligned. Score:  39
Sequences (22:97) Aligned. Score:  74
Sequences (22:98) Aligned. Score:  43
Sequences (22:99) Aligned. Score:  78
Sequences (22:100) Aligned. Score:  62
Sequences (22:101) Aligned. Score:  49
Sequences (22:102) Aligned. Score:  50
Sequences (23:24) Aligned. Score:  24
Sequences (23:25) Aligned. Score:  34
Sequences (23:26) Aligned. Score:  32
Sequences (23:27) Aligned. Score:  63
Sequences (23:28) Aligned. Score:  27
Sequences (23:29) Aligned. Score:  62
Sequences (23:30) Aligned. Score:  26
Sequences (23:31) Aligned. Score:  29
Sequences (23:32) Aligned. Score:  33
Sequences (23:33) Aligned. Score:  31
Sequences (23:34) Aligned. Score:  36
Sequences (23:35) Aligned. Score:  62
Sequences (23:36) Aligned. Score:  26
Sequences (23:37) Aligned. Score:  52
Sequences (23:38) Aligned. Score:  58
Sequences (23:39) Aligned. Score:  29
Sequences (23:40) Aligned. Score:  37
Sequences (23:41) Aligned. Score:  29
Sequences (23:42) Aligned. Score:  35
Sequences (23:43) Aligned. Score:  33
Sequences (23:44) Aligned. Score:  31
Sequences (23:45) Aligned. Score:  34
Sequences (23:46) Aligned. Score:  34
Sequences (23:47) Aligned. Score:  34
Sequences (23:48) Aligned. Score:  34
Sequences (23:49) Aligned. Score:  32
Sequences (23:50) Aligned. Score:  43
Sequences (23:51) Aligned. Score:  37
Sequences (23:52) Aligned. Score:  81
Sequences (23:53) Aligned. Score:  81
Sequences (23:54) Aligned. Score:  37
Sequences (23:55) Aligned. Score:  30
Sequences (23:56) Aligned. Score:  57
Sequences (23:57) Aligned. Score:  29
Sequences (23:58) Aligned. Score:  58
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Sequences (23:60) Aligned. Score:  63
Sequences (23:61) Aligned. Score:  27
Sequences (23:62) Aligned. Score:  29
Sequences (23:63) Aligned. Score:  36
Sequences (23:64) Aligned. Score:  64
Sequences (23:65) Aligned. Score:  37
Sequences (23:66) Aligned. Score:  61
Sequences (23:67) Aligned. Score:  26
Sequences (23:68) Aligned. Score:  63
Sequences (23:69) Aligned. Score:  27
Sequences (23:70) Aligned. Score:  26
Sequences (23:71) Aligned. Score:  86
Sequences (23:72) Aligned. Score:  99
Sequences (23:73) Aligned. Score:  25
Sequences (23:74) Aligned. Score:  14
Sequences (23:75) Aligned. Score:  35
Sequences (23:76) Aligned. Score:  36
Sequences (23:77) Aligned. Score:  6
Sequences (23:78) Aligned. Score:  34
Sequences (23:79) Aligned. Score:  56
Sequences (23:80) Aligned. Score:  31
Sequences (23:81) Aligned. Score:  30
Sequences (23:82) Aligned. Score:  64
Sequences (23:83) Aligned. Score:  41
Sequences (23:84) Aligned. Score:  36
Sequences (23:85) Aligned. Score:  35
Sequences (23:86) Aligned. Score:  29
Sequences (23:87) Aligned. Score:  30
Sequences (23:88) Aligned. Score:  31
Sequences (23:89) Aligned. Score:  30
Sequences (23:90) Aligned. Score:  29
Sequences (23:91) Aligned. Score:  34
Sequences (23:92) Aligned. Score:  63
Sequences (23:93) Aligned. Score:  27
Sequences (23:94) Aligned. Score:  34
Sequences (23:95) Aligned. Score:  44
Sequences (23:96) Aligned. Score:  56
Sequences (23:97) Aligned. Score:  37
Sequences (23:98) Aligned. Score:  62
Sequences (23:99) Aligned. Score:  26
Sequences (23:100) Aligned. Score:  35
Sequences (23:101) Aligned. Score:  34
Sequences (23:102) Aligned. Score:  32
Sequences (24:25) Aligned. Score:  35
Sequences (24:26) Aligned. Score:  24
Sequences (24:27) Aligned. Score:  27
Sequences (24:28) Aligned. Score:  61
Sequences (24:29) Aligned. Score:  27
Sequences (24:30) Aligned. Score:  61
Sequences (24:31) Aligned. Score:  35
Sequences (24:32) Aligned. Score:  30
Sequences (24:33) Aligned. Score:  29
Sequences (24:34) Aligned. Score:  26
Sequences (24:35) Aligned. Score:  25
Sequences (24:36) Aligned. Score:  61
Sequences (24:37) Aligned. Score:  28
Sequences (24:38) Aligned. Score:  26
Sequences (24:39) Aligned. Score:  62
Sequences (24:40) Aligned. Score:  27
Sequences (24:41) Aligned. Score:  33
Sequences (24:42) Aligned. Score:  30
Sequences (24:43) Aligned. Score:  29
Sequences (24:44) Aligned. Score:  33
Sequences (24:45) Aligned. Score:  30
Sequences (24:46) Aligned. Score:  30
Sequences (24:47) Aligned. Score:  30
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Sequences (24:50) Aligned. Score:  24
Sequences (24:51) Aligned. Score:  84
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Sequences (24:55) Aligned. Score:  32
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Sequences (24:57) Aligned. Score:  62
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Sequences (24:59) Aligned. Score:  62
Sequences (24:60) Aligned. Score:  27
Sequences (24:61) Aligned. Score:  61
Sequences (24:62) Aligned. Score:  22
Sequences (24:63) Aligned. Score:  28
Sequences (24:64) Aligned. Score:  28
Sequences (24:65) Aligned. Score:  74
Sequences (24:66) Aligned. Score:  25
Sequences (24:67) Aligned. Score:  61
Sequences (24:68) Aligned. Score:  27
Sequences (24:69) Aligned. Score:  61
Sequences (24:70) Aligned. Score:  80
Sequences (24:71) Aligned. Score:  27
Sequences (24:72) Aligned. Score:  24
Sequences (24:73) Aligned. Score:  98
Sequences (24:74) Aligned. Score:  16
Sequences (24:75) Aligned. Score:  29
Sequences (24:76) Aligned. Score:  28
Sequences (24:77) Aligned. Score:  7
Sequences (24:78) Aligned. Score:  31
Sequences (24:79) Aligned. Score:  25
Sequences (24:80) Aligned. Score:  29
Sequences (24:81) Aligned. Score:  32
Sequences (24:82) Aligned. Score:  27
Sequences (24:83) Aligned. Score:  84
Sequences (24:84) Aligned. Score:  26
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Sequences (24:86) Aligned. Score:  33
Sequences (24:87) Aligned. Score:  32
Sequences (24:88) Aligned. Score:  29
Sequences (24:89) Aligned. Score:  32
Sequences (24:90) Aligned. Score:  32
Sequences (24:91) Aligned. Score:  30
Sequences (24:92) Aligned. Score:  27
Sequences (24:93) Aligned. Score:  61
Sequences (24:94) Aligned. Score:  31
Sequences (24:95) Aligned. Score:  24
Sequences (24:96) Aligned. Score:  25
Sequences (24:97) Aligned. Score:  74
Sequences (24:98) Aligned. Score:  27
Sequences (24:99) Aligned. Score:  61
Sequences (24:100) Aligned. Score:  32
Sequences (24:101) Aligned. Score:  31
Sequences (24:102) Aligned. Score:  28
Sequences (25:26) Aligned. Score:  44
Sequences (25:27) Aligned. Score:  32
Sequences (25:28) Aligned. Score:  35
Sequences (25:29) Aligned. Score:  33
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Sequences (25:32) Aligned. Score:  63
Sequences (25:33) Aligned. Score:  49
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Sequences (25:35) Aligned. Score:  33
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Sequences (25:37) Aligned. Score:  30
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Sequences (25:39) Aligned. Score:  37
Sequences (25:40) Aligned. Score:  63
Sequences (25:41) Aligned. Score:  61
Sequences (25:42) Aligned. Score:  65
Sequences (25:43) Aligned. Score:  64
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Sequences (25:49) Aligned. Score:  63
Sequences (25:50) Aligned. Score:  30
Sequences (25:51) Aligned. Score:  46
Sequences (25:52) Aligned. Score:  34
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Sequences (25:55) Aligned. Score:  67
Sequences (25:56) Aligned. Score:  34
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Sequences (25:63) Aligned. Score:  51
Sequences (25:64) Aligned. Score:  29
Sequences (25:65) Aligned. Score:  37
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Sequences (25:68) Aligned. Score:  32
Sequences (25:69) Aligned. Score:  35
Sequences (25:70) Aligned. Score:  36
Sequences (25:71) Aligned. Score:  34
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Sequences (25:75) Aligned. Score:  66
Sequences (25:76) Aligned. Score:  65
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Sequences (25:78) Aligned. Score:  52
Sequences (25:79) Aligned. Score:  33
Sequences (25:80) Aligned. Score:  49
Sequences (25:81) Aligned. Score:  67
Sequences (25:82) Aligned. Score:  30
Sequences (25:83) Aligned. Score:  47
Sequences (25:84) Aligned. Score:  48
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Sequences (25:86) Aligned. Score:  65
Sequences (25:87) Aligned. Score:  66
Sequences (25:88) Aligned. Score:  49
Sequences (25:89) Aligned. Score:  67
Sequences (25:90) Aligned. Score:  65
Sequences (25:91) Aligned. Score:  70
Sequences (25:92) Aligned. Score:  32
Sequences (25:93) Aligned. Score:  35
Sequences (25:94) Aligned. Score:  52
Sequences (25:95) Aligned. Score:  30
Sequences (25:96) Aligned. Score:  33
Sequences (25:97) Aligned. Score:  48
Sequences (25:98) Aligned. Score:  33
Sequences (25:99) Aligned. Score:  35
Sequences (25:100) Aligned. Score:  38
Sequences (25:101) Aligned. Score:  64
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Sequences (26:27) Aligned. Score:  32
Sequences (26:28) Aligned. Score:  25
Sequences (26:29) Aligned. Score:  32
Sequences (26:30) Aligned. Score:  24
Sequences (26:31) Aligned. Score:  28
Sequences (26:32) Aligned. Score:  40
Sequences (26:33) Aligned. Score:  39
Sequences (26:34) Aligned. Score:  58
Sequences (26:35) Aligned. Score:  29
Sequences (26:36) Aligned. Score:  24
Sequences (26:37) Aligned. Score:  32
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Sequences (26:39) Aligned. Score:  27
Sequences (26:40) Aligned. Score:  48
Sequences (26:41) Aligned. Score:  47
Sequences (26:42) Aligned. Score:  50
Sequences (26:43) Aligned. Score:  41
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Sequences (26:50) Aligned. Score:  31
Sequences (26:51) Aligned. Score:  34
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Sequences (26:55) Aligned. Score:  51
Sequences (26:56) Aligned. Score:  32
Sequences (26:57) Aligned. Score:  27
Sequences (26:58) Aligned. Score:  32
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Sequences (26:60) Aligned. Score:  32
Sequences (26:61) Aligned. Score:  25
Sequences (26:62) Aligned. Score:  29
Sequences (26:63) Aligned. Score:  61
Sequences (26:64) Aligned. Score:  32
Sequences (26:65) Aligned. Score:  24
Sequences (26:66) Aligned. Score:  29
Sequences (26:67) Aligned. Score:  24
Sequences (26:68) Aligned. Score:  32
Sequences (26:69) Aligned. Score:  25
Sequences (26:70) Aligned. Score:  27
Sequences (26:71) Aligned. Score:  31
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Sequences (26:73) Aligned. Score:  24
Sequences (26:74) Aligned. Score:  14
Sequences (26:75) Aligned. Score:  47
Sequences (26:76) Aligned. Score:  48
Sequences (26:77) Aligned. Score:  5
Sequences (26:78) Aligned. Score:  45
Sequences (26:79) Aligned. Score:  32
Sequences (26:80) Aligned. Score:  39
Sequences (26:81) Aligned. Score:  51
Sequences (26:82) Aligned. Score:  33
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Sequences (26:84) Aligned. Score:  58
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Sequences (26:86) Aligned. Score:  51
Sequences (26:87) Aligned. Score:  50
Sequences (26:88) Aligned. Score:  39
Sequences (26:89) Aligned. Score:  51
Sequences (26:90) Aligned. Score:  51
Sequences (26:91) Aligned. Score:  43
Sequences (26:92) Aligned. Score:  32
Sequences (26:93) Aligned. Score:  25
Sequences (26:94) Aligned. Score:  43
Sequences (26:95) Aligned. Score:  31
Sequences (26:96) Aligned. Score:  32
Sequences (26:97) Aligned. Score:  37
Sequences (26:98) Aligned. Score:  32
Sequences (26:99) Aligned. Score:  24
Sequences (26:100) Aligned. Score:  32
Sequences (26:101) Aligned. Score:  41
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Sequences (27:28) Aligned. Score:  29
Sequences (27:29) Aligned. Score:  95
Sequences (27:30) Aligned. Score:  29
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Sequences (27:35) Aligned. Score:  95
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Sequences (27:37) Aligned. Score:  56
Sequences (27:38) Aligned. Score:  69
Sequences (27:39) Aligned. Score:  32
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Sequences (27:42) Aligned. Score:  30
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Sequences (27:56) Aligned. Score:  69
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Sequences (27:60) Aligned. Score:  99
Sequences (27:61) Aligned. Score:  29
Sequences (27:62) Aligned. Score:  27
Sequences (27:63) Aligned. Score:  36
Sequences (27:64) Aligned. Score:  74
Sequences (27:65) Aligned. Score:  39
Sequences (27:66) Aligned. Score:  95
Sequences (27:67) Aligned. Score:  29
Sequences (27:68) Aligned. Score:  98
Sequences (27:69) Aligned. Score:  29
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Sequences (27:71) Aligned. Score:  65
Sequences (27:72) Aligned. Score:  63
Sequences (27:73) Aligned. Score:  28
Sequences (27:74) Aligned. Score:  16
Sequences (27:75) Aligned. Score:  29
Sequences (27:76) Aligned. Score:  30
Sequences (27:77) Aligned. Score:  5
Sequences (27:78) Aligned. Score:  29
Sequences (27:79) Aligned. Score:  63
Sequences (27:80) Aligned. Score:  33
Sequences (27:81) Aligned. Score:  30
Sequences (27:82) Aligned. Score:  76
Sequences (27:83) Aligned. Score:  43
Sequences (27:84) Aligned. Score:  31
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Sequences (27:86) Aligned. Score:  30
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Sequences (27:88) Aligned. Score:  33
Sequences (27:89) Aligned. Score:  30
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Sequences (27:91) Aligned. Score:  34
Sequences (27:92) Aligned. Score:  99
Sequences (27:93) Aligned. Score:  29
Sequences (27:94) Aligned. Score:  29
Sequences (27:95) Aligned. Score:  50
Sequences (27:96) Aligned. Score:  63
Sequences (27:97) Aligned. Score:  38
Sequences (27:98) Aligned. Score:  95
Sequences (27:99) Aligned. Score:  29
Sequences (27:100) Aligned. Score:  36
Sequences (27:101) Aligned. Score:  32
Sequences (27:102) Aligned. Score:  30
Sequences (28:29) Aligned. Score:  29
Sequences (28:30) Aligned. Score:  91
Sequences (28:31) Aligned. Score:  34
Sequences (28:32) Aligned. Score:  33
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Sequences (28:36) Aligned. Score:  91
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Sequences (28:39) Aligned. Score:  64
Sequences (28:40) Aligned. Score:  28
Sequences (28:41) Aligned. Score:  33
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Sequences (28:51) Aligned. Score:  67
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Sequences (28:54) Aligned. Score:  67
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Sequences (28:57) Aligned. Score:  64
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Sequences (28:60) Aligned. Score:  29
Sequences (28:61) Aligned. Score:  99
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Sequences (28:63) Aligned. Score:  33
Sequences (28:64) Aligned. Score:  30
Sequences (28:65) Aligned. Score:  75
Sequences (28:66) Aligned. Score:  25
Sequences (28:67) Aligned. Score:  91
Sequences (28:68) Aligned. Score:  29
Sequences (28:69) Aligned. Score:  98
Sequences (28:70) Aligned. Score:  61
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Sequences (28:73) Aligned. Score:  60
Sequences (28:74) Aligned. Score:  15
Sequences (28:75) Aligned. Score:  32
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Sequences (28:77) Aligned. Score:  5
Sequences (28:78) Aligned. Score:  28
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Sequences (28:80) Aligned. Score:  29
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Sequences (28:83) Aligned. Score:  80
Sequences (28:84) Aligned. Score:  29
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Sequences (28:86) Aligned. Score:  30
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Sequences (28:89) Aligned. Score:  30
Sequences (28:90) Aligned. Score:  30
Sequences (28:91) Aligned. Score:  36
Sequences (28:92) Aligned. Score:  29
Sequences (28:93) Aligned. Score:  99
Sequences (28:94) Aligned. Score:  29
Sequences (28:95) Aligned. Score:  24
Sequences (28:96) Aligned. Score:  28
Sequences (28:97) Aligned. Score:  70
Sequences (28:98) Aligned. Score:  29
Sequences (28:99) Aligned. Score:  91
Sequences (28:100) Aligned. Score:  38
Sequences (28:101) Aligned. Score:  34
Sequences (28:102) Aligned. Score:  32
Sequences (29:30) Aligned. Score:  29
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Sequences (29:32) Aligned. Score:  31
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Sequences (29:35) Aligned. Score:  98
Sequences (29:36) Aligned. Score:  29
Sequences (29:37) Aligned. Score:  56
Sequences (29:38) Aligned. Score:  68
Sequences (29:39) Aligned. Score:  32
Sequences (29:40) Aligned. Score:  31
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Sequences (29:42) Aligned. Score:  30
Sequences (29:43) Aligned. Score:  33
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Sequences (29:49) Aligned. Score:  28
Sequences (29:50) Aligned. Score:  51
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Sequences (29:52) Aligned. Score:  63
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Sequences (29:56) Aligned. Score:  68
Sequences (29:57) Aligned. Score:  32
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Sequences (29:60) Aligned. Score:  95
Sequences (29:61) Aligned. Score:  29
Sequences (29:62) Aligned. Score:  27
Sequences (29:63) Aligned. Score:  36
Sequences (29:64) Aligned. Score:  74
Sequences (29:65) Aligned. Score:  39
Sequences (29:66) Aligned. Score:  98
Sequences (29:67) Aligned. Score:  29
Sequences (29:68) Aligned. Score:  95
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Sequences (29:70) Aligned. Score:  30
Sequences (29:71) Aligned. Score:  65
Sequences (29:72) Aligned. Score:  62
Sequences (29:73) Aligned. Score:  28
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Sequences (29:76) Aligned. Score:  30
Sequences (29:77) Aligned. Score:  7
Sequences (29:78) Aligned. Score:  29
Sequences (29:79) Aligned. Score:  63
Sequences (29:80) Aligned. Score:  33
Sequences (29:81) Aligned. Score:  29
Sequences (29:82) Aligned. Score:  74
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Sequences (29:84) Aligned. Score:  31
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Sequences (29:88) Aligned. Score:  33
Sequences (29:89) Aligned. Score:  29
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Sequences (29:92) Aligned. Score:  95
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Sequences (29:95) Aligned. Score:  51
Sequences (29:96) Aligned. Score:  63
Sequences (29:97) Aligned. Score:  38
Sequences (29:98) Aligned. Score:  98
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Sequences (29:100) Aligned. Score:  36
Sequences (29:101) Aligned. Score:  32
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Sequences (30:32) Aligned. Score:  32
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Sequences (30:36) Aligned. Score:  100
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Sequences (30:38) Aligned. Score:  27
Sequences (30:39) Aligned. Score:  62
Sequences (30:40) Aligned. Score:  28
Sequences (30:41) Aligned. Score:  33
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Sequences (30:45) Aligned. Score:  33
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Sequences (30:51) Aligned. Score:  65
Sequences (30:52) Aligned. Score:  29
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Sequences (30:54) Aligned. Score:  65
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Sequences (30:57) Aligned. Score:  62
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Sequences (30:60) Aligned. Score:  29
Sequences (30:61) Aligned. Score:  91
Sequences (30:62) Aligned. Score:  18
Sequences (30:63) Aligned. Score:  32
Sequences (30:64) Aligned. Score:  28
Sequences (30:65) Aligned. Score:  72
Sequences (30:66) Aligned. Score:  25
Sequences (30:67) Aligned. Score:  99
Sequences (30:68) Aligned. Score:  29
Sequences (30:69) Aligned. Score:  91
Sequences (30:70) Aligned. Score:  61
Sequences (30:71) Aligned. Score:  28
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Sequences (30:73) Aligned. Score:  59
Sequences (30:74) Aligned. Score:  15
Sequences (30:75) Aligned. Score:  31
Sequences (30:76) Aligned. Score:  29
Sequences (30:77) Aligned. Score:  9
Sequences (30:78) Aligned. Score:  27
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Sequences (30:80) Aligned. Score:  30
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Sequences (30:83) Aligned. Score:  78
Sequences (30:84) Aligned. Score:  27
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Sequences (30:86) Aligned. Score:  28
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Sequences (30:91) Aligned. Score:  36
Sequences (30:92) Aligned. Score:  29
Sequences (30:93) Aligned. Score:  91
Sequences (30:94) Aligned. Score:  27
Sequences (30:95) Aligned. Score:  23
Sequences (30:96) Aligned. Score:  27
Sequences (30:97) Aligned. Score:  68
Sequences (30:98) Aligned. Score:  29
Sequences (30:99) Aligned. Score:  100
Sequences (30:100) Aligned. Score:  38
Sequences (30:101) Aligned. Score:  34
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Sequences (31:83) Aligned. Score:  56
Sequences (31:84) Aligned. Score:  31
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Sequences (32:49) Aligned. Score:  82
Sequences (32:50) Aligned. Score:  30
Sequences (32:51) Aligned. Score:  48
Sequences (32:52) Aligned. Score:  34
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Sequences (32:55) Aligned. Score:  69
Sequences (32:56) Aligned. Score:  34
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Sequences (32:60) Aligned. Score:  31
Sequences (32:61) Aligned. Score:  33
Sequences (32:62) Aligned. Score:  37
Sequences (32:63) Aligned. Score:  50
Sequences (32:64) Aligned. Score:  34
Sequences (32:65) Aligned. Score:  44
Sequences (32:66) Aligned. Score:  27
Sequences (32:67) Aligned. Score:  32
Sequences (32:68) Aligned. Score:  31
Sequences (32:69) Aligned. Score:  32
Sequences (32:70) Aligned. Score:  33
Sequences (32:71) Aligned. Score:  34
Sequences (32:72) Aligned. Score:  33
Sequences (32:73) Aligned. Score:  29
Sequences (32:74) Aligned. Score:  26
Sequences (32:75) Aligned. Score:  73
Sequences (32:76) Aligned. Score:  72
Sequences (32:77) Aligned. Score:  14
Sequences (32:78) Aligned. Score:  51
Sequences (32:79) Aligned. Score:  30
Sequences (32:80) Aligned. Score:  44
Sequences (32:81) Aligned. Score:  69
Sequences (32:82) Aligned. Score:  32
Sequences (32:83) Aligned. Score:  49
Sequences (32:84) Aligned. Score:  48
Sequences (32:85) Aligned. Score:  49
Sequences (32:86) Aligned. Score:  66
Sequences (32:87) Aligned. Score:  67
Sequences (32:88) Aligned. Score:  44
Sequences (32:89) Aligned. Score:  69
Sequences (32:90) Aligned. Score:  65
Sequences (32:91) Aligned. Score:  70
Sequences (32:92) Aligned. Score:  31
Sequences (32:93) Aligned. Score:  33
Sequences (32:94) Aligned. Score:  49
Sequences (32:95) Aligned. Score:  30
Sequences (32:96) Aligned. Score:  30
Sequences (32:97) Aligned. Score:  44
Sequences (32:98) Aligned. Score:  31
Sequences (32:99) Aligned. Score:  32
Sequences (32:100) Aligned. Score:  37
Sequences (32:101) Aligned. Score:  97
Sequences (32:102) Aligned. Score:  93
Sequences (33:34) Aligned. Score:  46
Sequences (33:35) Aligned. Score:  30
Sequences (33:36) Aligned. Score:  30
Sequences (33:37) Aligned. Score:  40
Sequences (33:38) Aligned. Score:  32
Sequences (33:39) Aligned. Score:  34
Sequences (33:40) Aligned. Score:  44
Sequences (33:41) Aligned. Score:  45
Sequences (33:42) Aligned. Score:  47
Sequences (33:43) Aligned. Score:  46
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Sequences (33:47) Aligned. Score:  46
Sequences (33:48) Aligned. Score:  46
Sequences (33:49) Aligned. Score:  42
Sequences (33:50) Aligned. Score:  35
Sequences (33:51) Aligned. Score:  51
Sequences (33:52) Aligned. Score:  33
Sequences (33:53) Aligned. Score:  33
Sequences (33:54) Aligned. Score:  51
Sequences (33:55) Aligned. Score:  45
Sequences (33:56) Aligned. Score:  32
Sequences (33:57) Aligned. Score:  34
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Sequences (33:59) Aligned. Score:  34
Sequences (33:60) Aligned. Score:  33
Sequences (33:61) Aligned. Score:  29
Sequences (33:62) Aligned. Score:  31
Sequences (33:63) Aligned. Score:  48
Sequences (33:64) Aligned. Score:  35
Sequences (33:65) Aligned. Score:  39
Sequences (33:66) Aligned. Score:  32
Sequences (33:67) Aligned. Score:  30
Sequences (33:68) Aligned. Score:  33
Sequences (33:69) Aligned. Score:  28
Sequences (33:70) Aligned. Score:  32
Sequences (33:71) Aligned. Score:  29
Sequences (33:72) Aligned. Score:  31
Sequences (33:73) Aligned. Score:  29
Sequences (33:74) Aligned. Score:  20
Sequences (33:75) Aligned. Score:  46
Sequences (33:76) Aligned. Score:  46
Sequences (33:77) Aligned. Score:  14
Sequences (33:78) Aligned. Score:  48
Sequences (33:79) Aligned. Score:  31
Sequences (33:80) Aligned. Score:  100
Sequences (33:81) Aligned. Score:  45
Sequences (33:82) Aligned. Score:  33
Sequences (33:83) Aligned. Score:  47
Sequences (33:84) Aligned. Score:  47
Sequences (33:85) Aligned. Score:  46
Sequences (33:86) Aligned. Score:  46
Sequences (33:87) Aligned. Score:  46
Sequences (33:88) Aligned. Score:  100
Sequences (33:89) Aligned. Score:  45
Sequences (33:90) Aligned. Score:  46
Sequences (33:91) Aligned. Score:  45
Sequences (33:92) Aligned. Score:  33
Sequences (33:93) Aligned. Score:  29
Sequences (33:94) Aligned. Score:  48
Sequences (33:95) Aligned. Score:  35
Sequences (33:96) Aligned. Score:  31
Sequences (33:97) Aligned. Score:  46
Sequences (33:98) Aligned. Score:  33
Sequences (33:99) Aligned. Score:  30
Sequences (33:100) Aligned. Score:  38
Sequences (33:101) Aligned. Score:  47
Sequences (33:102) Aligned. Score:  44
Sequences (34:35) Aligned. Score:  30
Sequences (34:36) Aligned. Score:  27
Sequences (34:37) Aligned. Score:  34
Sequences (34:38) Aligned. Score:  32
Sequences (34:39) Aligned. Score:  31
Sequences (34:40) Aligned. Score:  49
Sequences (34:41) Aligned. Score:  52
Sequences (34:42) Aligned. Score:  51
Sequences (34:43) Aligned. Score:  49
Sequences (34:44) Aligned. Score:  48
Sequences (34:45) Aligned. Score:  50
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Sequences (34:49) Aligned. Score:  46
Sequences (34:50) Aligned. Score:  30
Sequences (34:51) Aligned. Score:  36
Sequences (34:52) Aligned. Score:  33
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Sequences (34:55) Aligned. Score:  50
Sequences (34:56) Aligned. Score:  32
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Sequences (34:62) Aligned. Score:  33
Sequences (34:63) Aligned. Score:  79
Sequences (34:64) Aligned. Score:  33
Sequences (34:65) Aligned. Score:  32
Sequences (34:66) Aligned. Score:  31
Sequences (34:67) Aligned. Score:  27
Sequences (34:68) Aligned. Score:  32
Sequences (34:69) Aligned. Score:  28
Sequences (34:70) Aligned. Score:  30
Sequences (34:71) Aligned. Score:  35
Sequences (34:72) Aligned. Score:  36
Sequences (34:73) Aligned. Score:  26
Sequences (34:74) Aligned. Score:  20
Sequences (34:75) Aligned. Score:  51
Sequences (34:76) Aligned. Score:  50
Sequences (34:77) Aligned. Score:  5
Sequences (34:78) Aligned. Score:  53
Sequences (34:79) Aligned. Score:  34
Sequences (34:80) Aligned. Score:  46
Sequences (34:81) Aligned. Score:  50
Sequences (34:82) Aligned. Score:  33
Sequences (34:83) Aligned. Score:  35
Sequences (34:84) Aligned. Score:  96
Sequences (34:85) Aligned. Score:  97
Sequences (34:86) Aligned. Score:  49
Sequences (34:87) Aligned. Score:  48
Sequences (34:88) Aligned. Score:  46
Sequences (34:89) Aligned. Score:  50
Sequences (34:90) Aligned. Score:  49
Sequences (34:91) Aligned. Score:  50
Sequences (34:92) Aligned. Score:  32
Sequences (34:93) Aligned. Score:  28
Sequences (34:94) Aligned. Score:  51
Sequences (34:95) Aligned. Score:  31
Sequences (34:96) Aligned. Score:  34
Sequences (34:97) Aligned. Score:  38
Sequences (34:98) Aligned. Score:  32
Sequences (34:99) Aligned. Score:  27
Sequences (34:100) Aligned. Score:  32
Sequences (34:101) Aligned. Score:  50
Sequences (34:102) Aligned. Score:  48
Sequences (35:36) Aligned. Score:  26
Sequences (35:37) Aligned. Score:  55
Sequences (35:38) Aligned. Score:  68
Sequences (35:39) Aligned. Score:  29
Sequences (35:40) Aligned. Score:  28
Sequences (35:41) Aligned. Score:  23
Sequences (35:42) Aligned. Score:  27
Sequences (35:43) Aligned. Score:  33
Sequences (35:44) Aligned. Score:  27
Sequences (35:45) Aligned. Score:  28
Sequences (35:46) Aligned. Score:  28
Sequences (35:47) Aligned. Score:  28
Sequences (35:48) Aligned. Score:  28
Sequences (35:49) Aligned. Score:  28
Sequences (35:50) Aligned. Score:  50
Sequences (35:51) Aligned. Score:  34
Sequences (35:52) Aligned. Score:  62
Sequences (35:53) Aligned. Score:  63
Sequences (35:54) Aligned. Score:  34
Sequences (35:55) Aligned. Score:  26
Sequences (35:56) Aligned. Score:  67
Sequences (35:57) Aligned. Score:  29
Sequences (35:58) Aligned. Score:  68
Sequences (35:59) Aligned. Score:  29
Sequences (35:60) Aligned. Score:  95
Sequences (35:61) Aligned. Score:  26
Sequences (35:62) Aligned. Score:  27
Sequences (35:63) Aligned. Score:  34
Sequences (35:64) Aligned. Score:  73
Sequences (35:65) Aligned. Score:  34
Sequences (35:66) Aligned. Score:  97
Sequences (35:67) Aligned. Score:  26
Sequences (35:68) Aligned. Score:  95
Sequences (35:69) Aligned. Score:  26
Sequences (35:70) Aligned. Score:  27
Sequences (35:71) Aligned. Score:  64
Sequences (35:72) Aligned. Score:  62
Sequences (35:73) Aligned. Score:  26
Sequences (35:74) Aligned. Score:  16
Sequences (35:75) Aligned. Score:  26
Sequences (35:76) Aligned. Score:  27
Sequences (35:77) Aligned. Score:  3
Sequences (35:78) Aligned. Score:  28
Sequences (35:79) Aligned. Score:  62
Sequences (35:80) Aligned. Score:  30
Sequences (35:81) Aligned. Score:  26
Sequences (35:82) Aligned. Score:  74
Sequences (35:83) Aligned. Score:  35
Sequences (35:84) Aligned. Score:  29
Sequences (35:85) Aligned. Score:  30
Sequences (35:86) Aligned. Score:  26
Sequences (35:87) Aligned. Score:  26
Sequences (35:88) Aligned. Score:  30
Sequences (35:89) Aligned. Score:  26
Sequences (35:90) Aligned. Score:  26
Sequences (35:91) Aligned. Score:  30
Sequences (35:92) Aligned. Score:  95
Sequences (35:93) Aligned. Score:  26
Sequences (35:94) Aligned. Score:  27
Sequences (35:95) Aligned. Score:  50
Sequences (35:96) Aligned. Score:  62
Sequences (35:97) Aligned. Score:  33
Sequences (35:98) Aligned. Score:  98
Sequences (35:99) Aligned. Score:  26
Sequences (35:100) Aligned. Score:  34
Sequences (35:101) Aligned. Score:  28
Sequences (35:102) Aligned. Score:  30
Sequences (36:37) Aligned. Score:  26
Sequences (36:38) Aligned. Score:  27
Sequences (36:39) Aligned. Score:  62
Sequences (36:40) Aligned. Score:  28
Sequences (36:41) Aligned. Score:  33
Sequences (36:42) Aligned. Score:  31
Sequences (36:43) Aligned. Score:  33
Sequences (36:44) Aligned. Score:  28
Sequences (36:45) Aligned. Score:  33
Sequences (36:46) Aligned. Score:  33
Sequences (36:47) Aligned. Score:  33
Sequences (36:48) Aligned. Score:  33
Sequences (36:49) Aligned. Score:  30
Sequences (36:50) Aligned. Score:  23
Sequences (36:51) Aligned. Score:  65
Sequences (36:52) Aligned. Score:  29
Sequences (36:53) Aligned. Score:  28
Sequences (36:54) Aligned. Score:  65
Sequences (36:55) Aligned. Score:  29
Sequences (36:56) Aligned. Score:  27
Sequences (36:57) Aligned. Score:  62
Sequences (36:58) Aligned. Score:  27
Sequences (36:59) Aligned. Score:  62
Sequences (36:60) Aligned. Score:  29
Sequences (36:61) Aligned. Score:  91
Sequences (36:62) Aligned. Score:  18
Sequences (36:63) Aligned. Score:  32
Sequences (36:64) Aligned. Score:  28
Sequences (36:65) Aligned. Score:  72
Sequences (36:66) Aligned. Score:  25
Sequences (36:67) Aligned. Score:  99
Sequences (36:68) Aligned. Score:  29
Sequences (36:69) Aligned. Score:  91
Sequences (36:70) Aligned. Score:  61
Sequences (36:71) Aligned. Score:  28
Sequences (36:72) Aligned. Score:  26
Sequences (36:73) Aligned. Score:  59
Sequences (36:74) Aligned. Score:  15
Sequences (36:75) Aligned. Score:  31
Sequences (36:76) Aligned. Score:  29
Sequences (36:77) Aligned. Score:  9
Sequences (36:78) Aligned. Score:  27
Sequences (36:79) Aligned. Score:  27
Sequences (36:80) Aligned. Score:  30
Sequences (36:81) Aligned. Score:  29
Sequences (36:82) Aligned. Score:  29
Sequences (36:83) Aligned. Score:  78
Sequences (36:84) Aligned. Score:  27
Sequences (36:85) Aligned. Score:  27
Sequences (36:86) Aligned. Score:  28
Sequences (36:87) Aligned. Score:  29
Sequences (36:88) Aligned. Score:  30
Sequences (36:89) Aligned. Score:  29
Sequences (36:90) Aligned. Score:  29
Sequences (36:91) Aligned. Score:  36
Sequences (36:92) Aligned. Score:  29
Sequences (36:93) Aligned. Score:  91
Sequences (36:94) Aligned. Score:  27
Sequences (36:95) Aligned. Score:  23
Sequences (36:96) Aligned. Score:  27
Sequences (36:97) Aligned. Score:  68
Sequences (36:98) Aligned. Score:  29
Sequences (36:99) Aligned. Score:  100
Sequences (36:100) Aligned. Score:  38
Sequences (36:101) Aligned. Score:  34
Sequences (36:102) Aligned. Score:  32
Sequences (37:38) Aligned. Score:  56
Sequences (37:39) Aligned. Score:  29
Sequences (37:40) Aligned. Score:  30
Sequences (37:41) Aligned. Score:  32
Sequences (37:42) Aligned. Score:  29
Sequences (37:43) Aligned. Score:  31
Sequences (37:44) Aligned. Score:  34
Sequences (37:45) Aligned. Score:  32
Sequences (37:46) Aligned. Score:  32
Sequences (37:47) Aligned. Score:  32
Sequences (37:48) Aligned. Score:  32
Sequences (37:49) Aligned. Score:  33
Sequences (37:50) Aligned. Score:  94
Sequences (37:51) Aligned. Score:  37
Sequences (37:52) Aligned. Score:  51
Sequences (37:53) Aligned. Score:  52
Sequences (37:54) Aligned. Score:  37
Sequences (37:55) Aligned. Score:  36
Sequences (37:56) Aligned. Score:  56
Sequences (37:57) Aligned. Score:  29
Sequences (37:58) Aligned. Score:  56
Sequences (37:59) Aligned. Score:  29
Sequences (37:60) Aligned. Score:  56
Sequences (37:61) Aligned. Score:  26
Sequences (37:62) Aligned. Score:  28
Sequences (37:63) Aligned. Score:  32
Sequences (37:64) Aligned. Score:  59
Sequences (37:65) Aligned. Score:  32
Sequences (37:66) Aligned. Score:  56
Sequences (37:67) Aligned. Score:  26
Sequences (37:68) Aligned. Score:  56
Sequences (37:69) Aligned. Score:  25
Sequences (37:70) Aligned. Score:  32
Sequences (37:71) Aligned. Score:  50
Sequences (37:72) Aligned. Score:  52
Sequences (37:73) Aligned. Score:  27
Sequences (37:74) Aligned. Score:  20
Sequences (37:75) Aligned. Score:  30
Sequences (37:76) Aligned. Score:  30
Sequences (37:77) Aligned. Score:  3
Sequences (37:78) Aligned. Score:  36
Sequences (37:79) Aligned. Score:  56
Sequences (37:80) Aligned. Score:  40
Sequences (37:81) Aligned. Score:  36
Sequences (37:82) Aligned. Score:  56
Sequences (37:83) Aligned. Score:  37
Sequences (37:84) Aligned. Score:  34
Sequences (37:85) Aligned. Score:  34
Sequences (37:86) Aligned. Score:  36
Sequences (37:87) Aligned. Score:  35
Sequences (37:88) Aligned. Score:  40
Sequences (37:89) Aligned. Score:  36
Sequences (37:90) Aligned. Score:  35
Sequences (37:91) Aligned. Score:  34
Sequences (37:92) Aligned. Score:  56
Sequences (37:93) Aligned. Score:  26
Sequences (37:94) Aligned. Score:  35
Sequences (37:95) Aligned. Score:  95
Sequences (37:96) Aligned. Score:  56
Sequences (37:97) Aligned. Score:  38
Sequences (37:98) Aligned. Score:  56
Sequences (37:99) Aligned. Score:  26
Sequences (37:100) Aligned. Score:  37
Sequences (37:101) Aligned. Score:  32
Sequences (37:102) Aligned. Score:  32
Sequences (38:39) Aligned. Score:  29
Sequences (38:40) Aligned. Score:  30
Sequences (38:41) Aligned. Score:  29
Sequences (38:42) Aligned. Score:  30
Sequences (38:43) Aligned. Score:  33
Sequences (38:44) Aligned. Score:  29
Sequences (38:45) Aligned. Score:  33
Sequences (38:46) Aligned. Score:  32
Sequences (38:47) Aligned. Score:  33
Sequences (38:48) Aligned. Score:  33
Sequences (38:49) Aligned. Score:  31
Sequences (38:50) Aligned. Score:  49
Sequences (38:51) Aligned. Score:  37
Sequences (38:52) Aligned. Score:  56
Sequences (38:53) Aligned. Score:  57
Sequences (38:54) Aligned. Score:  37
Sequences (38:55) Aligned. Score:  29
Sequences (38:56) Aligned. Score:  98
Sequences (38:57) Aligned. Score:  29
Sequences (38:58) Aligned. Score:  98
Sequences (38:59) Aligned. Score:  29
Sequences (38:60) Aligned. Score:  69
Sequences (38:61) Aligned. Score:  28
Sequences (38:62) Aligned. Score:  27
Sequences (38:63) Aligned. Score:  35
Sequences (38:64) Aligned. Score:  68
Sequences (38:65) Aligned. Score:  36
Sequences (38:66) Aligned. Score:  67
Sequences (38:67) Aligned. Score:  27
Sequences (38:68) Aligned. Score:  69
Sequences (38:69) Aligned. Score:  28
Sequences (38:70) Aligned. Score:  26
Sequences (38:71) Aligned. Score:  60
Sequences (38:72) Aligned. Score:  58
Sequences (38:73) Aligned. Score:  26
Sequences (38:74) Aligned. Score:  16
Sequences (38:75) Aligned. Score:  30
Sequences (38:76) Aligned. Score:  31
Sequences (38:77) Aligned. Score:  5
Sequences (38:78) Aligned. Score:  33
Sequences (38:79) Aligned. Score:  61
Sequences (38:80) Aligned. Score:  32
Sequences (38:81) Aligned. Score:  29
Sequences (38:82) Aligned. Score:  67
Sequences (38:83) Aligned. Score:  39
Sequences (38:84) Aligned. Score:  33
Sequences (38:85) Aligned. Score:  31
Sequences (38:86) Aligned. Score:  30
Sequences (38:87) Aligned. Score:  30
Sequences (38:88) Aligned. Score:  32
Sequences (38:89) Aligned. Score:  29
Sequences (38:90) Aligned. Score:  30
Sequences (38:91) Aligned. Score:  34
Sequences (38:92) Aligned. Score:  69
Sequences (38:93) Aligned. Score:  28
Sequences (38:94) Aligned. Score:  32
Sequences (38:95) Aligned. Score:  50
Sequences (38:96) Aligned. Score:  61
Sequences (38:97) Aligned. Score:  38
Sequences (38:98) Aligned. Score:  68
Sequences (38:99) Aligned. Score:  27
Sequences (38:100) Aligned. Score:  34
Sequences (38:101) Aligned. Score:  33
Sequences (38:102) Aligned. Score:  31
Sequences (39:40) Aligned. Score:  33
Sequences (39:41) Aligned. Score:  32
Sequences (39:42) Aligned. Score:  36
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Sequences (39:45) Aligned. Score:  37
Sequences (39:46) Aligned. Score:  38
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Sequences (39:49) Aligned. Score:  32
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Sequences (39:51) Aligned. Score:  72
Sequences (39:52) Aligned. Score:  30
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Sequences (39:54) Aligned. Score:  72
Sequences (39:55) Aligned. Score:  33
Sequences (39:56) Aligned. Score:  30
Sequences (39:57) Aligned. Score:  100
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Sequences (39:60) Aligned. Score:  32
Sequences (39:61) Aligned. Score:  64
Sequences (39:62) Aligned. Score:  22
Sequences (39:63) Aligned. Score:  35
Sequences (39:64) Aligned. Score:  30
Sequences (39:65) Aligned. Score:  68
Sequences (39:66) Aligned. Score:  28
Sequences (39:67) Aligned. Score:  62
Sequences (39:68) Aligned. Score:  32
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Sequences (39:70) Aligned. Score:  61
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Sequences (39:73) Aligned. Score:  61
Sequences (39:74) Aligned. Score:  10
Sequences (39:75) Aligned. Score:  34
Sequences (39:76) Aligned. Score:  32
Sequences (39:77) Aligned. Score:  8
Sequences (39:78) Aligned. Score:  31
Sequences (39:79) Aligned. Score:  28
Sequences (39:80) Aligned. Score:  34
Sequences (39:81) Aligned. Score:  33
Sequences (39:82) Aligned. Score:  31
Sequences (39:83) Aligned. Score:  76
Sequences (39:84) Aligned. Score:  31
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Sequences (39:86) Aligned. Score:  34
Sequences (39:87) Aligned. Score:  35
Sequences (39:88) Aligned. Score:  34
Sequences (39:89) Aligned. Score:  33
Sequences (39:90) Aligned. Score:  35
Sequences (39:91) Aligned. Score:  35
Sequences (39:92) Aligned. Score:  32
Sequences (39:93) Aligned. Score:  64
Sequences (39:94) Aligned. Score:  30
Sequences (39:95) Aligned. Score:  26
Sequences (39:96) Aligned. Score:  28
Sequences (39:97) Aligned. Score:  74
Sequences (39:98) Aligned. Score:  32
Sequences (39:99) Aligned. Score:  62
Sequences (39:100) Aligned. Score:  40
Sequences (39:101) Aligned. Score:  36
Sequences (39:102) Aligned. Score:  35
Sequences (40:41) Aligned. Score:  61
Sequences (40:42) Aligned. Score:  90
Sequences (40:43) Aligned. Score:  72
Sequences (40:44) Aligned. Score:  58
Sequences (40:45) Aligned. Score:  71
Sequences (40:46) Aligned. Score:  71
Sequences (40:47) Aligned. Score:  72
Sequences (40:48) Aligned. Score:  71
Sequences (40:49) Aligned. Score:  68
Sequences (40:50) Aligned. Score:  31
Sequences (40:51) Aligned. Score:  44
Sequences (40:52) Aligned. Score:  35
Sequences (40:53) Aligned. Score:  34
Sequences (40:54) Aligned. Score:  44
Sequences (40:55) Aligned. Score:  63
Sequences (40:56) Aligned. Score:  30
Sequences (40:57) Aligned. Score:  33
Sequences (40:58) Aligned. Score:  30
Sequences (40:59) Aligned. Score:  33
Sequences (40:60) Aligned. Score:  31
Sequences (40:61) Aligned. Score:  28
Sequences (40:62) Aligned. Score:  32
Sequences (40:63) Aligned. Score:  51
Sequences (40:64) Aligned. Score:  32
Sequences (40:65) Aligned. Score:  39
Sequences (40:66) Aligned. Score:  27
Sequences (40:67) Aligned. Score:  28
Sequences (40:68) Aligned. Score:  31
Sequences (40:69) Aligned. Score:  28
Sequences (40:70) Aligned. Score:  29
Sequences (40:71) Aligned. Score:  37
Sequences (40:72) Aligned. Score:  37
Sequences (40:73) Aligned. Score:  27
Sequences (40:74) Aligned. Score:  18
Sequences (40:75) Aligned. Score:  91
Sequences (40:76) Aligned. Score:  95
Sequences (40:77) Aligned. Score:  16
Sequences (40:78) Aligned. Score:  50
Sequences (40:79) Aligned. Score:  32
Sequences (40:80) Aligned. Score:  44
Sequences (40:81) Aligned. Score:  63
Sequences (40:82) Aligned. Score:  32
Sequences (40:83) Aligned. Score:  45
Sequences (40:84) Aligned. Score:  48
Sequences (40:85) Aligned. Score:  50
Sequences (40:86) Aligned. Score:  61
Sequences (40:87) Aligned. Score:  62
Sequences (40:88) Aligned. Score:  44
Sequences (40:89) Aligned. Score:  63
Sequences (40:90) Aligned. Score:  61
Sequences (40:91) Aligned. Score:  60
Sequences (40:92) Aligned. Score:  31
Sequences (40:93) Aligned. Score:  28
Sequences (40:94) Aligned. Score:  48
Sequences (40:95) Aligned. Score:  31
Sequences (40:96) Aligned. Score:  32
Sequences (40:97) Aligned. Score:  44
Sequences (40:98) Aligned. Score:  31
Sequences (40:99) Aligned. Score:  28
Sequences (40:100) Aligned. Score:  38
Sequences (40:101) Aligned. Score:  72
Sequences (40:102) Aligned. Score:  72
Sequences (41:42) Aligned. Score:  65
Sequences (41:43) Aligned. Score:  66
Sequences (41:44) Aligned. Score:  63
Sequences (41:45) Aligned. Score:  69
Sequences (41:46) Aligned. Score:  69
Sequences (41:47) Aligned. Score:  69
Sequences (41:48) Aligned. Score:  69
Sequences (41:49) Aligned. Score:  64
Sequences (41:50) Aligned. Score:  30
Sequences (41:51) Aligned. Score:  44
Sequences (41:52) Aligned. Score:  29
Sequences (41:53) Aligned. Score:  29
Sequences (41:54) Aligned. Score:  44
Sequences (41:55) Aligned. Score:  66
Sequences (41:56) Aligned. Score:  29
Sequences (41:57) Aligned. Score:  32
Sequences (41:58) Aligned. Score:  29
Sequences (41:59) Aligned. Score:  32
Sequences (41:60) Aligned. Score:  26
Sequences (41:61) Aligned. Score:  33
Sequences (41:62) Aligned. Score:  36
Sequences (41:63) Aligned. Score:  50
Sequences (41:64) Aligned. Score:  31
Sequences (41:65) Aligned. Score:  44
Sequences (41:66) Aligned. Score:  23
Sequences (41:67) Aligned. Score:  33
Sequences (41:68) Aligned. Score:  26
Sequences (41:69) Aligned. Score:  33
Sequences (41:70) Aligned. Score:  37
Sequences (41:71) Aligned. Score:  29
Sequences (41:72) Aligned. Score:  29
Sequences (41:73) Aligned. Score:  33
Sequences (41:74) Aligned. Score:  25
Sequences (41:75) Aligned. Score:  65
Sequences (41:76) Aligned. Score:  62
Sequences (41:77) Aligned. Score:  24
Sequences (41:78) Aligned. Score:  52
Sequences (41:79) Aligned. Score:  33
Sequences (41:80) Aligned. Score:  45
Sequences (41:81) Aligned. Score:  66
Sequences (41:82) Aligned. Score:  31
Sequences (41:83) Aligned. Score:  49
Sequences (41:84) Aligned. Score:  52
Sequences (41:85) Aligned. Score:  53
Sequences (41:86) Aligned. Score:  65
Sequences (41:87) Aligned. Score:  66
Sequences (41:88) Aligned. Score:  45
Sequences (41:89) Aligned. Score:  66
Sequences (41:90) Aligned. Score:  65
Sequences (41:91) Aligned. Score:  68
Sequences (41:92) Aligned. Score:  26
Sequences (41:93) Aligned. Score:  33
Sequences (41:94) Aligned. Score:  52
Sequences (41:95) Aligned. Score:  30
Sequences (41:96) Aligned. Score:  33
Sequences (41:97) Aligned. Score:  46
Sequences (41:98) Aligned. Score:  26
Sequences (41:99) Aligned. Score:  33
Sequences (41:100) Aligned. Score:  40
Sequences (41:101) Aligned. Score:  68
Sequences (41:102) Aligned. Score:  68
Sequences (42:43) Aligned. Score:  74
Sequences (42:44) Aligned. Score:  61
Sequences (42:45) Aligned. Score:  73
Sequences (42:46) Aligned. Score:  74
Sequences (42:47) Aligned. Score:  74
Sequences (42:48) Aligned. Score:  73
Sequences (42:49) Aligned. Score:  73
Sequences (42:50) Aligned. Score:  29
Sequences (42:51) Aligned. Score:  48
Sequences (42:52) Aligned. Score:  35
Sequences (42:53) Aligned. Score:  34
Sequences (42:54) Aligned. Score:  48
Sequences (42:55) Aligned. Score:  65
Sequences (42:56) Aligned. Score:  31
Sequences (42:57) Aligned. Score:  36
Sequences (42:58) Aligned. Score:  31
Sequences (42:59) Aligned. Score:  36
Sequences (42:60) Aligned. Score:  30
Sequences (42:61) Aligned. Score:  32
Sequences (42:62) Aligned. Score:  31
Sequences (42:63) Aligned. Score:  55
Sequences (42:64) Aligned. Score:  32
Sequences (42:65) Aligned. Score:  43
Sequences (42:66) Aligned. Score:  26
Sequences (42:67) Aligned. Score:  31
Sequences (42:68) Aligned. Score:  30
Sequences (42:69) Aligned. Score:  32
Sequences (42:70) Aligned. Score:  32
Sequences (42:71) Aligned. Score:  35
Sequences (42:72) Aligned. Score:  35
Sequences (42:73) Aligned. Score:  30
Sequences (42:74) Aligned. Score:  23
Sequences (42:75) Aligned. Score:  98
Sequences (42:76) Aligned. Score:  93
Sequences (42:77) Aligned. Score:  16
Sequences (42:78) Aligned. Score:  55
Sequences (42:79) Aligned. Score:  28
Sequences (42:80) Aligned. Score:  47
Sequences (42:81) Aligned. Score:  65
Sequences (42:82) Aligned. Score:  30
Sequences (42:83) Aligned. Score:  49
Sequences (42:84) Aligned. Score:  51
Sequences (42:85) Aligned. Score:  52
Sequences (42:86) Aligned. Score:  64
Sequences (42:87) Aligned. Score:  64
Sequences (42:88) Aligned. Score:  47
Sequences (42:89) Aligned. Score:  65
Sequences (42:90) Aligned. Score:  64
Sequences (42:91) Aligned. Score:  64
Sequences (42:92) Aligned. Score:  30
Sequences (42:93) Aligned. Score:  32
Sequences (42:94) Aligned. Score:  53
Sequences (42:95) Aligned. Score:  29
Sequences (42:96) Aligned. Score:  28
Sequences (42:97) Aligned. Score:  46
Sequences (42:98) Aligned. Score:  30
Sequences (42:99) Aligned. Score:  31
Sequences (42:100) Aligned. Score:  37
Sequences (42:101) Aligned. Score:  74
Sequences (42:102) Aligned. Score:  74
Sequences (43:44) Aligned. Score:  63
Sequences (43:45) Aligned. Score:  95
Sequences (43:46) Aligned. Score:  92
Sequences (43:47) Aligned. Score:  92
Sequences (43:48) Aligned. Score:  96
Sequences (43:49) Aligned. Score:  84
Sequences (43:50) Aligned. Score:  31
Sequences (43:51) Aligned. Score:  46
Sequences (43:52) Aligned. Score:  34
Sequences (43:53) Aligned. Score:  33
Sequences (43:54) Aligned. Score:  46
Sequences (43:55) Aligned. Score:  68
Sequences (43:56) Aligned. Score:  33
Sequences (43:57) Aligned. Score:  35
Sequences (43:58) Aligned. Score:  33
Sequences (43:59) Aligned. Score:  35
Sequences (43:60) Aligned. Score:  31
Sequences (43:61) Aligned. Score:  34
Sequences (43:62) Aligned. Score:  37
Sequences (43:63) Aligned. Score:  51
Sequences (43:64) Aligned. Score:  35
Sequences (43:65) Aligned. Score:  43
Sequences (43:66) Aligned. Score:  32
Sequences (43:67) Aligned. Score:  33
Sequences (43:68) Aligned. Score:  31
Sequences (43:69) Aligned. Score:  33
Sequences (43:70) Aligned. Score:  33
Sequences (43:71) Aligned. Score:  34
Sequences (43:72) Aligned. Score:  33
Sequences (43:73) Aligned. Score:  29
Sequences (43:74) Aligned. Score:  26
Sequences (43:75) Aligned. Score:  73
Sequences (43:76) Aligned. Score:  72
Sequences (43:77) Aligned. Score:  7
Sequences (43:78) Aligned. Score:  52
Sequences (43:79) Aligned. Score:  29
Sequences (43:80) Aligned. Score:  46
Sequences (43:81) Aligned. Score:  68
Sequences (43:82) Aligned. Score:  33
Sequences (43:83) Aligned. Score:  47
Sequences (43:84) Aligned. Score:  49
Sequences (43:85) Aligned. Score:  50
Sequences (43:86) Aligned. Score:  66
Sequences (43:87) Aligned. Score:  66
Sequences (43:88) Aligned. Score:  46
Sequences (43:89) Aligned. Score:  68
Sequences (43:90) Aligned. Score:  66
Sequences (43:91) Aligned. Score:  70
Sequences (43:92) Aligned. Score:  31
Sequences (43:93) Aligned. Score:  34
Sequences (43:94) Aligned. Score:  49
Sequences (43:95) Aligned. Score:  31
Sequences (43:96) Aligned. Score:  29
Sequences (43:97) Aligned. Score:  44
Sequences (43:98) Aligned. Score:  33
Sequences (43:99) Aligned. Score:  33
Sequences (43:100) Aligned. Score:  38
Sequences (43:101) Aligned. Score:  96
Sequences (43:102) Aligned. Score:  92
Sequences (44:45) Aligned. Score:  64
Sequences (44:46) Aligned. Score:  67
Sequences (44:47) Aligned. Score:  67
Sequences (44:48) Aligned. Score:  64
Sequences (44:49) Aligned. Score:  61
Sequences (44:50) Aligned. Score:  33
Sequences (44:51) Aligned. Score:  50
Sequences (44:52) Aligned. Score:  31
Sequences (44:53) Aligned. Score:  31
Sequences (44:54) Aligned. Score:  50
Sequences (44:55) Aligned. Score:  85
Sequences (44:56) Aligned. Score:  29
Sequences (44:57) Aligned. Score:  34
Sequences (44:58) Aligned. Score:  29
Sequences (44:59) Aligned. Score:  34
Sequences (44:60) Aligned. Score:  30
Sequences (44:61) Aligned. Score:  29
Sequences (44:62) Aligned. Score:  35
Sequences (44:63) Aligned. Score:  47
Sequences (44:64) Aligned. Score:  32
Sequences (44:65) Aligned. Score:  39
Sequences (44:66) Aligned. Score:  26
Sequences (44:67) Aligned. Score:  28
Sequences (44:68) Aligned. Score:  30
Sequences (44:69) Aligned. Score:  28
Sequences (44:70) Aligned. Score:  32
Sequences (44:71) Aligned. Score:  28
Sequences (44:72) Aligned. Score:  31
Sequences (44:73) Aligned. Score:  33
Sequences (44:74) Aligned. Score:  27
Sequences (44:75) Aligned. Score:  60
Sequences (44:76) Aligned. Score:  60
Sequences (44:77) Aligned. Score:  16
Sequences (44:78) Aligned. Score:  51
Sequences (44:79) Aligned. Score:  26
Sequences (44:80) Aligned. Score:  46
Sequences (44:81) Aligned. Score:  85
Sequences (44:82) Aligned. Score:  30
Sequences (44:83) Aligned. Score:  47
Sequences (44:84) Aligned. Score:  48
Sequences (44:85) Aligned. Score:  49
Sequences (44:86) Aligned. Score:  87
Sequences (44:87) Aligned. Score:  86
Sequences (44:88) Aligned. Score:  46
Sequences (44:89) Aligned. Score:  85
Sequences (44:90) Aligned. Score:  86
Sequences (44:91) Aligned. Score:  70
Sequences (44:92) Aligned. Score:  30
Sequences (44:93) Aligned. Score:  29
Sequences (44:94) Aligned. Score:  50
Sequences (44:95) Aligned. Score:  33
Sequences (44:96) Aligned. Score:  26
Sequences (44:97) Aligned. Score:  46
Sequences (44:98) Aligned. Score:  30
Sequences (44:99) Aligned. Score:  28
Sequences (44:100) Aligned. Score:  34
Sequences (44:101) Aligned. Score:  64
Sequences (44:102) Aligned. Score:  66
Sequences (45:46) Aligned. Score:  92
Sequences (45:47) Aligned. Score:  93
Sequences (45:48) Aligned. Score:  99
Sequences (45:49) Aligned. Score:  82
Sequences (45:50) Aligned. Score:  31
Sequences (45:51) Aligned. Score:  48
Sequences (45:52) Aligned. Score:  36
Sequences (45:53) Aligned. Score:  35
Sequences (45:54) Aligned. Score:  48
Sequences (45:55) Aligned. Score:  70
Sequences (45:56) Aligned. Score:  34
Sequences (45:57) Aligned. Score:  37
Sequences (45:58) Aligned. Score:  34
Sequences (45:59) Aligned. Score:  37
Sequences (45:60) Aligned. Score:  32
Sequences (45:61) Aligned. Score:  34
Sequences (45:62) Aligned. Score:  36
Sequences (45:63) Aligned. Score:  50
Sequences (45:64) Aligned. Score:  34
Sequences (45:65) Aligned. Score:  44
Sequences (45:66) Aligned. Score:  28
Sequences (45:67) Aligned. Score:  33
Sequences (45:68) Aligned. Score:  32
Sequences (45:69) Aligned. Score:  33
Sequences (45:70) Aligned. Score:  34
Sequences (45:71) Aligned. Score:  34
Sequences (45:72) Aligned. Score:  34
Sequences (45:73) Aligned. Score:  30
Sequences (45:74) Aligned. Score:  27
Sequences (45:75) Aligned. Score:  72
Sequences (45:76) Aligned. Score:  72
Sequences (45:77) Aligned. Score:  14
Sequences (45:78) Aligned. Score:  53
Sequences (45:79) Aligned. Score:  30
Sequences (45:80) Aligned. Score:  46
Sequences (45:81) Aligned. Score:  70
Sequences (45:82) Aligned. Score:  34
Sequences (45:83) Aligned. Score:  49
Sequences (45:84) Aligned. Score:  50
Sequences (45:85) Aligned. Score:  50
Sequences (45:86) Aligned. Score:  68
Sequences (45:87) Aligned. Score:  68
Sequences (45:88) Aligned. Score:  46
Sequences (45:89) Aligned. Score:  70
Sequences (45:90) Aligned. Score:  67
Sequences (45:91) Aligned. Score:  70
Sequences (45:92) Aligned. Score:  32
Sequences (45:93) Aligned. Score:  34
Sequences (45:94) Aligned. Score:  50
Sequences (45:95) Aligned. Score:  31
Sequences (45:96) Aligned. Score:  30
Sequences (45:97) Aligned. Score:  44
Sequences (45:98) Aligned. Score:  32
Sequences (45:99) Aligned. Score:  33
Sequences (45:100) Aligned. Score:  37
Sequences (45:101) Aligned. Score:  98
Sequences (45:102) Aligned. Score:  93
Sequences (46:47) Aligned. Score:  99
Sequences (46:48) Aligned. Score:  93
Sequences (46:49) Aligned. Score:  81
Sequences (46:50) Aligned. Score:  32
Sequences (46:51) Aligned. Score:  51
Sequences (46:52) Aligned. Score:  34
Sequences (46:53) Aligned. Score:  33
Sequences (46:54) Aligned. Score:  51
Sequences (46:55) Aligned. Score:  69
Sequences (46:56) Aligned. Score:  32
Sequences (46:57) Aligned. Score:  38
Sequences (46:58) Aligned. Score:  32
Sequences (46:59) Aligned. Score:  38
Sequences (46:60) Aligned. Score:  31
Sequences (46:61) Aligned. Score:  34
Sequences (46:62) Aligned. Score:  38
Sequences (46:63) Aligned. Score:  49
Sequences (46:64) Aligned. Score:  34
Sequences (46:65) Aligned. Score:  46
Sequences (46:66) Aligned. Score:  27
Sequences (46:67) Aligned. Score:  33
Sequences (46:68) Aligned. Score:  31
Sequences (46:69) Aligned. Score:  33
Sequences (46:70) Aligned. Score:  33
Sequences (46:71) Aligned. Score:  34
Sequences (46:72) Aligned. Score:  34
Sequences (46:73) Aligned. Score:  29
Sequences (46:74) Aligned. Score:  27
Sequences (46:75) Aligned. Score:  73
Sequences (46:76) Aligned. Score:  72
Sequences (46:77) Aligned. Score:  13
Sequences (46:78) Aligned. Score:  55
Sequences (46:79) Aligned. Score:  31
Sequences (46:80) Aligned. Score:  46
Sequences (46:81) Aligned. Score:  69
Sequences (46:82) Aligned. Score:  34
Sequences (46:83) Aligned. Score:  50
Sequences (46:84) Aligned. Score:  50
Sequences (46:85) Aligned. Score:  50
Sequences (46:86) Aligned. Score:  67
Sequences (46:87) Aligned. Score:  67
Sequences (46:88) Aligned. Score:  46
Sequences (46:89) Aligned. Score:  69
Sequences (46:90) Aligned. Score:  67
Sequences (46:91) Aligned. Score:  70
Sequences (46:92) Aligned. Score:  31
Sequences (46:93) Aligned. Score:  34
Sequences (46:94) Aligned. Score:  52
Sequences (46:95) Aligned. Score:  32
Sequences (46:96) Aligned. Score:  31
Sequences (46:97) Aligned. Score:  46
Sequences (46:98) Aligned. Score:  31
Sequences (46:99) Aligned. Score:  33
Sequences (46:100) Aligned. Score:  39
Sequences (46:101) Aligned. Score:  92
Sequences (46:102) Aligned. Score:  98
Sequences (47:48) Aligned. Score:  94
Sequences (47:49) Aligned. Score:  82
Sequences (47:50) Aligned. Score:  31
Sequences (47:51) Aligned. Score:  51
Sequences (47:52) Aligned. Score:  34
Sequences (47:53) Aligned. Score:  34
Sequences (47:54) Aligned. Score:  51
Sequences (47:55) Aligned. Score:  69
Sequences (47:56) Aligned. Score:  33
Sequences (47:57) Aligned. Score:  38
Sequences (47:58) Aligned. Score:  33
Sequences (47:59) Aligned. Score:  38
Sequences (47:60) Aligned. Score:  32
Sequences (47:61) Aligned. Score:  34
Sequences (47:62) Aligned. Score:  37
Sequences (47:63) Aligned. Score:  50
Sequences (47:64) Aligned. Score:  34
Sequences (47:65) Aligned. Score:  46
Sequences (47:66) Aligned. Score:  28
Sequences (47:67) Aligned. Score:  33
Sequences (47:68) Aligned. Score:  32
Sequences (47:69) Aligned. Score:  33
Sequences (47:70) Aligned. Score:  33
Sequences (47:71) Aligned. Score:  34
Sequences (47:72) Aligned. Score:  34
Sequences (47:73) Aligned. Score:  29
Sequences (47:74) Aligned. Score:  26
Sequences (47:75) Aligned. Score:  74
Sequences (47:76) Aligned. Score:  72
Sequences (47:77) Aligned. Score:  13
Sequences (47:78) Aligned. Score:  55
Sequences (47:79) Aligned. Score:  30
Sequences (47:80) Aligned. Score:  46
Sequences (47:81) Aligned. Score:  69
Sequences (47:82) Aligned. Score:  33
Sequences (47:83) Aligned. Score:  50
Sequences (47:84) Aligned. Score:  50
Sequences (47:85) Aligned. Score:  50
Sequences (47:86) Aligned. Score:  66
Sequences (47:87) Aligned. Score:  67
Sequences (47:88) Aligned. Score:  46
Sequences (47:89) Aligned. Score:  69
Sequences (47:90) Aligned. Score:  66
Sequences (47:91) Aligned. Score:  71
Sequences (47:92) Aligned. Score:  32
Sequences (47:93) Aligned. Score:  34
Sequences (47:94) Aligned. Score:  51
Sequences (47:95) Aligned. Score:  31
Sequences (47:96) Aligned. Score:  30
Sequences (47:97) Aligned. Score:  46
Sequences (47:98) Aligned. Score:  32
Sequences (47:99) Aligned. Score:  33
Sequences (47:100) Aligned. Score:  38
Sequences (47:101) Aligned. Score:  93
Sequences (47:102) Aligned. Score:  98
Sequences (48:49) Aligned. Score:  83
Sequences (48:50) Aligned. Score:  31
Sequences (48:51) Aligned. Score:  48
Sequences (48:52) Aligned. Score:  35
Sequences (48:53) Aligned. Score:  34
Sequences (48:54) Aligned. Score:  48
Sequences (48:55) Aligned. Score:  70
Sequences (48:56) Aligned. Score:  34
Sequences (48:57) Aligned. Score:  37
Sequences (48:58) Aligned. Score:  34
Sequences (48:59) Aligned. Score:  37
Sequences (48:60) Aligned. Score:  32
Sequences (48:61) Aligned. Score:  34
Sequences (48:62) Aligned. Score:  36
Sequences (48:63) Aligned. Score:  50
Sequences (48:64) Aligned. Score:  34
Sequences (48:65) Aligned. Score:  44
Sequences (48:66) Aligned. Score:  28
Sequences (48:67) Aligned. Score:  33
Sequences (48:68) Aligned. Score:  32
Sequences (48:69) Aligned. Score:  33
Sequences (48:70) Aligned. Score:  34
Sequences (48:71) Aligned. Score:  34
Sequences (48:72) Aligned. Score:  34
Sequences (48:73) Aligned. Score:  30
Sequences (48:74) Aligned. Score:  27
Sequences (48:75) Aligned. Score:  72
Sequences (48:76) Aligned. Score:  72
Sequences (48:77) Aligned. Score:  14
Sequences (48:78) Aligned. Score:  53
Sequences (48:79) Aligned. Score:  30
Sequences (48:80) Aligned. Score:  46
Sequences (48:81) Aligned. Score:  70
Sequences (48:82) Aligned. Score:  34
Sequences (48:83) Aligned. Score:  49
Sequences (48:84) Aligned. Score:  50
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Sequences (48:86) Aligned. Score:  68
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Sequences (48:88) Aligned. Score:  46
Sequences (48:89) Aligned. Score:  70
Sequences (48:90) Aligned. Score:  67
Sequences (48:91) Aligned. Score:  70
Sequences (48:92) Aligned. Score:  32
Sequences (48:93) Aligned. Score:  34
Sequences (48:94) Aligned. Score:  50
Sequences (48:95) Aligned. Score:  31
Sequences (48:96) Aligned. Score:  30
Sequences (48:97) Aligned. Score:  44
Sequences (48:98) Aligned. Score:  32
Sequences (48:99) Aligned. Score:  33
Sequences (48:100) Aligned. Score:  37
Sequences (48:101) Aligned. Score:  99
Sequences (48:102) Aligned. Score:  94
Sequences (49:50) Aligned. Score:  30
Sequences (49:51) Aligned. Score:  46
Sequences (49:52) Aligned. Score:  32
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Sequences (49:55) Aligned. Score:  64
Sequences (49:56) Aligned. Score:  31
Sequences (49:57) Aligned. Score:  32
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Sequences (49:60) Aligned. Score:  28
Sequences (49:61) Aligned. Score:  30
Sequences (49:62) Aligned. Score:  33
Sequences (49:63) Aligned. Score:  52
Sequences (49:64) Aligned. Score:  29
Sequences (49:65) Aligned. Score:  44
Sequences (49:66) Aligned. Score:  27
Sequences (49:67) Aligned. Score:  30
Sequences (49:68) Aligned. Score:  28
Sequences (49:69) Aligned. Score:  30
Sequences (49:70) Aligned. Score:  31
Sequences (49:71) Aligned. Score:  30
Sequences (49:72) Aligned. Score:  32
Sequences (49:73) Aligned. Score:  28
Sequences (49:74) Aligned. Score:  24
Sequences (49:75) Aligned. Score:  73
Sequences (49:76) Aligned. Score:  70
Sequences (49:77) Aligned. Score:  14
Sequences (49:78) Aligned. Score:  55
Sequences (49:79) Aligned. Score:  26
Sequences (49:80) Aligned. Score:  42
Sequences (49:81) Aligned. Score:  64
Sequences (49:82) Aligned. Score:  30
Sequences (49:83) Aligned. Score:  49
Sequences (49:84) Aligned. Score:  46
Sequences (49:85) Aligned. Score:  47
Sequences (49:86) Aligned. Score:  62
Sequences (49:87) Aligned. Score:  63
Sequences (49:88) Aligned. Score:  42
Sequences (49:89) Aligned. Score:  64
Sequences (49:90) Aligned. Score:  61
Sequences (49:91) Aligned. Score:  67
Sequences (49:92) Aligned. Score:  28
Sequences (49:93) Aligned. Score:  30
Sequences (49:94) Aligned. Score:  54
Sequences (49:95) Aligned. Score:  30
Sequences (49:96) Aligned. Score:  26
Sequences (49:97) Aligned. Score:  44
Sequences (49:98) Aligned. Score:  28
Sequences (49:99) Aligned. Score:  30
Sequences (49:100) Aligned. Score:  41
Sequences (49:101) Aligned. Score:  84
Sequences (49:102) Aligned. Score:  79
Sequences (50:51) Aligned. Score:  37
Sequences (50:52) Aligned. Score:  45
Sequences (50:53) Aligned. Score:  47
Sequences (50:54) Aligned. Score:  37
Sequences (50:55) Aligned. Score:  32
Sequences (50:56) Aligned. Score:  49
Sequences (50:57) Aligned. Score:  25
Sequences (50:58) Aligned. Score:  49
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Sequences (50:60) Aligned. Score:  49
Sequences (50:61) Aligned. Score:  23
Sequences (50:62) Aligned. Score:  28
Sequences (50:63) Aligned. Score:  32
Sequences (50:64) Aligned. Score:  53
Sequences (50:65) Aligned. Score:  32
Sequences (50:66) Aligned. Score:  50
Sequences (50:67) Aligned. Score:  23
Sequences (50:68) Aligned. Score:  49
Sequences (50:69) Aligned. Score:  23
Sequences (50:70) Aligned. Score:  28
Sequences (50:71) Aligned. Score:  47
Sequences (50:72) Aligned. Score:  43
Sequences (50:73) Aligned. Score:  24
Sequences (50:74) Aligned. Score:  18
Sequences (50:75) Aligned. Score:  30
Sequences (50:76) Aligned. Score:  30
Sequences (50:77) Aligned. Score:  3
Sequences (50:78) Aligned. Score:  36
Sequences (50:79) Aligned. Score:  47
Sequences (50:80) Aligned. Score:  35
Sequences (50:81) Aligned. Score:  32
Sequences (50:82) Aligned. Score:  49
Sequences (50:83) Aligned. Score:  37
Sequences (50:84) Aligned. Score:  31
Sequences (50:85) Aligned. Score:  30
Sequences (50:86) Aligned. Score:  32
Sequences (50:87) Aligned. Score:  31
Sequences (50:88) Aligned. Score:  35
Sequences (50:89) Aligned. Score:  32
Sequences (50:90) Aligned. Score:  31
Sequences (50:91) Aligned. Score:  33
Sequences (50:92) Aligned. Score:  49
Sequences (50:93) Aligned. Score:  23
Sequences (50:94) Aligned. Score:  35
Sequences (50:95) Aligned. Score:  98
Sequences (50:96) Aligned. Score:  47
Sequences (50:97) Aligned. Score:  38
Sequences (50:98) Aligned. Score:  51
Sequences (50:99) Aligned. Score:  23
Sequences (50:100) Aligned. Score:  37
Sequences (50:101) Aligned. Score:  31
Sequences (50:102) Aligned. Score:  29
Sequences (51:52) Aligned. Score:  46
Sequences (51:53) Aligned. Score:  46
Sequences (51:54) Aligned. Score:  100
Sequences (51:55) Aligned. Score:  50
Sequences (51:56) Aligned. Score:  37
Sequences (51:57) Aligned. Score:  72
Sequences (51:58) Aligned. Score:  37
Sequences (51:59) Aligned. Score:  72
Sequences (51:60) Aligned. Score:  43
Sequences (51:61) Aligned. Score:  67
Sequences (51:62) Aligned. Score:  32
Sequences (51:63) Aligned. Score:  39
Sequences (51:64) Aligned. Score:  46
Sequences (51:65) Aligned. Score:  75
Sequences (51:66) Aligned. Score:  41
Sequences (51:67) Aligned. Score:  65
Sequences (51:68) Aligned. Score:  43
Sequences (51:69) Aligned. Score:  67
Sequences (51:70) Aligned. Score:  86
Sequences (51:71) Aligned. Score:  39
Sequences (51:72) Aligned. Score:  37
Sequences (51:73) Aligned. Score:  82
Sequences (51:74) Aligned. Score:  34
Sequences (51:75) Aligned. Score:  46
Sequences (51:76) Aligned. Score:  44
Sequences (51:77) Aligned. Score:  20
Sequences (51:78) Aligned. Score:  44
Sequences (51:79) Aligned. Score:  36
Sequences (51:80) Aligned. Score:  51
Sequences (51:81) Aligned. Score:  50
Sequences (51:82) Aligned. Score:  43
Sequences (51:83) Aligned. Score:  82
Sequences (51:84) Aligned. Score:  36
Sequences (51:85) Aligned. Score:  36
Sequences (51:86) Aligned. Score:  53
Sequences (51:87) Aligned. Score:  51
Sequences (51:88) Aligned. Score:  51
Sequences (51:89) Aligned. Score:  50
Sequences (51:90) Aligned. Score:  53
Sequences (51:91) Aligned. Score:  41
Sequences (51:92) Aligned. Score:  43
Sequences (51:93) Aligned. Score:  67
Sequences (51:94) Aligned. Score:  44
Sequences (51:95) Aligned. Score:  37
Sequences (51:96) Aligned. Score:  36
Sequences (51:97) Aligned. Score:  77
Sequences (51:98) Aligned. Score:  43
Sequences (51:99) Aligned. Score:  65
Sequences (51:100) Aligned. Score:  56
Sequences (51:101) Aligned. Score:  48
Sequences (51:102) Aligned. Score:  51
Sequences (52:53) Aligned. Score:  96
Sequences (52:54) Aligned. Score:  46
Sequences (52:55) Aligned. Score:  30
Sequences (52:56) Aligned. Score:  56
Sequences (52:57) Aligned. Score:  30
Sequences (52:58) Aligned. Score:  56
Sequences (52:59) Aligned. Score:  30
Sequences (52:60) Aligned. Score:  63
Sequences (52:61) Aligned. Score:  30
Sequences (52:62) Aligned. Score:  29
Sequences (52:63) Aligned. Score:  34
Sequences (52:64) Aligned. Score:  62
Sequences (52:65) Aligned. Score:  44
Sequences (52:66) Aligned. Score:  63
Sequences (52:67) Aligned. Score:  29
Sequences (52:68) Aligned. Score:  63
Sequences (52:69) Aligned. Score:  30
Sequences (52:70) Aligned. Score:  28
Sequences (52:71) Aligned. Score:  82
Sequences (52:72) Aligned. Score:  81
Sequences (52:73) Aligned. Score:  27
Sequences (52:74) Aligned. Score:  13
Sequences (52:75) Aligned. Score:  34
Sequences (52:76) Aligned. Score:  34
Sequences (52:77) Aligned. Score:  6
Sequences (52:78) Aligned. Score:  34
Sequences (52:79) Aligned. Score:  55
Sequences (52:80) Aligned. Score:  33
Sequences (52:81) Aligned. Score:  30
Sequences (52:82) Aligned. Score:  64
Sequences (52:83) Aligned. Score:  49
Sequences (52:84) Aligned. Score:  33
Sequences (52:85) Aligned. Score:  33
Sequences (52:86) Aligned. Score:  30
Sequences (52:87) Aligned. Score:  31
Sequences (52:88) Aligned. Score:  33
Sequences (52:89) Aligned. Score:  30
Sequences (52:90) Aligned. Score:  30
Sequences (52:91) Aligned. Score:  35
Sequences (52:92) Aligned. Score:  63
Sequences (52:93) Aligned. Score:  30
Sequences (52:94) Aligned. Score:  34
Sequences (52:95) Aligned. Score:  45
Sequences (52:96) Aligned. Score:  55
Sequences (52:97) Aligned. Score:  44
Sequences (52:98) Aligned. Score:  63
Sequences (52:99) Aligned. Score:  29
Sequences (52:100) Aligned. Score:  35
Sequences (52:101) Aligned. Score:  35
Sequences (52:102) Aligned. Score:  32
Sequences (53:54) Aligned. Score:  46
Sequences (53:55) Aligned. Score:  30
Sequences (53:56) Aligned. Score:  57
Sequences (53:57) Aligned. Score:  29
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Sequences (53:60) Aligned. Score:  63
Sequences (53:61) Aligned. Score:  30
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Sequences (53:63) Aligned. Score:  34
Sequences (53:64) Aligned. Score:  63
Sequences (53:65) Aligned. Score:  44
Sequences (53:66) Aligned. Score:  63
Sequences (53:67) Aligned. Score:  28
Sequences (53:68) Aligned. Score:  63
Sequences (53:69) Aligned. Score:  30
Sequences (53:70) Aligned. Score:  28
Sequences (53:71) Aligned. Score:  83
Sequences (53:72) Aligned. Score:  81
Sequences (53:73) Aligned. Score:  27
Sequences (53:74) Aligned. Score:  17
Sequences (53:75) Aligned. Score:  33
Sequences (53:76) Aligned. Score:  34
Sequences (53:77) Aligned. Score:  5
Sequences (53:78) Aligned. Score:  35
Sequences (53:79) Aligned. Score:  55
Sequences (53:80) Aligned. Score:  33
Sequences (53:81) Aligned. Score:  30
Sequences (53:82) Aligned. Score:  65
Sequences (53:83) Aligned. Score:  49
Sequences (53:84) Aligned. Score:  33
Sequences (53:85) Aligned. Score:  33
Sequences (53:86) Aligned. Score:  30
Sequences (53:87) Aligned. Score:  31
Sequences (53:88) Aligned. Score:  33
Sequences (53:89) Aligned. Score:  30
Sequences (53:90) Aligned. Score:  30
Sequences (53:91) Aligned. Score:  34
Sequences (53:92) Aligned. Score:  63
Sequences (53:93) Aligned. Score:  30
Sequences (53:94) Aligned. Score:  35
Sequences (53:95) Aligned. Score:  47
Sequences (53:96) Aligned. Score:  55
Sequences (53:97) Aligned. Score:  44
Sequences (53:98) Aligned. Score:  63
Sequences (53:99) Aligned. Score:  28
Sequences (53:100) Aligned. Score:  36
Sequences (53:101) Aligned. Score:  34
Sequences (53:102) Aligned. Score:  35
Sequences (54:55) Aligned. Score:  50
Sequences (54:56) Aligned. Score:  37
Sequences (54:57) Aligned. Score:  72
Sequences (54:58) Aligned. Score:  37
Sequences (54:59) Aligned. Score:  72
Sequences (54:60) Aligned. Score:  43
Sequences (54:61) Aligned. Score:  67
Sequences (54:62) Aligned. Score:  32
Sequences (54:63) Aligned. Score:  39
Sequences (54:64) Aligned. Score:  46
Sequences (54:65) Aligned. Score:  75
Sequences (54:66) Aligned. Score:  41
Sequences (54:67) Aligned. Score:  65
Sequences (54:68) Aligned. Score:  43
Sequences (54:69) Aligned. Score:  67
Sequences (54:70) Aligned. Score:  86
Sequences (54:71) Aligned. Score:  39
Sequences (54:72) Aligned. Score:  37
Sequences (54:73) Aligned. Score:  82
Sequences (54:74) Aligned. Score:  34
Sequences (54:75) Aligned. Score:  46
Sequences (54:76) Aligned. Score:  44
Sequences (54:77) Aligned. Score:  20
Sequences (54:78) Aligned. Score:  44
Sequences (54:79) Aligned. Score:  36
Sequences (54:80) Aligned. Score:  51
Sequences (54:81) Aligned. Score:  50
Sequences (54:82) Aligned. Score:  43
Sequences (54:83) Aligned. Score:  82
Sequences (54:84) Aligned. Score:  36
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Sequences (54:86) Aligned. Score:  53
Sequences (54:87) Aligned. Score:  51
Sequences (54:88) Aligned. Score:  51
Sequences (54:89) Aligned. Score:  50
Sequences (54:90) Aligned. Score:  53
Sequences (54:91) Aligned. Score:  41
Sequences (54:92) Aligned. Score:  43
Sequences (54:93) Aligned. Score:  67
Sequences (54:94) Aligned. Score:  44
Sequences (54:95) Aligned. Score:  37
Sequences (54:96) Aligned. Score:  36
Sequences (54:97) Aligned. Score:  77
Sequences (54:98) Aligned. Score:  43
Sequences (54:99) Aligned. Score:  65
Sequences (54:100) Aligned. Score:  56
Sequences (54:101) Aligned. Score:  48
Sequences (54:102) Aligned. Score:  51
Sequences (55:56) Aligned. Score:  30
Sequences (55:57) Aligned. Score:  33
Sequences (55:58) Aligned. Score:  30
Sequences (55:59) Aligned. Score:  33
Sequences (55:60) Aligned. Score:  29
Sequences (55:61) Aligned. Score:  30
Sequences (55:62) Aligned. Score:  37
Sequences (55:63) Aligned. Score:  51
Sequences (55:64) Aligned. Score:  32
Sequences (55:65) Aligned. Score:  43
Sequences (55:66) Aligned. Score:  26
Sequences (55:67) Aligned. Score:  29
Sequences (55:68) Aligned. Score:  29
Sequences (55:69) Aligned. Score:  30
Sequences (55:70) Aligned. Score:  33
Sequences (55:71) Aligned. Score:  32
Sequences (55:72) Aligned. Score:  30
Sequences (55:73) Aligned. Score:  33
Sequences (55:74) Aligned. Score:  26
Sequences (55:75) Aligned. Score:  66
Sequences (55:76) Aligned. Score:  64
Sequences (55:77) Aligned. Score:  6
Sequences (55:78) Aligned. Score:  53
Sequences (55:79) Aligned. Score:  29
Sequences (55:80) Aligned. Score:  45
Sequences (55:81) Aligned. Score:  100
Sequences (55:82) Aligned. Score:  32
Sequences (55:83) Aligned. Score:  47
Sequences (55:84) Aligned. Score:  49
Sequences (55:85) Aligned. Score:  50
Sequences (55:86) Aligned. Score:  88
Sequences (55:87) Aligned. Score:  88
Sequences (55:88) Aligned. Score:  45
Sequences (55:89) Aligned. Score:  100
Sequences (55:90) Aligned. Score:  88
Sequences (55:91) Aligned. Score:  74
Sequences (55:92) Aligned. Score:  29
Sequences (55:93) Aligned. Score:  30
Sequences (55:94) Aligned. Score:  52
Sequences (55:95) Aligned. Score:  32
Sequences (55:96) Aligned. Score:  29
Sequences (55:97) Aligned. Score:  48
Sequences (55:98) Aligned. Score:  29
Sequences (55:99) Aligned. Score:  29
Sequences (55:100) Aligned. Score:  38
Sequences (55:101) Aligned. Score:  71
Sequences (55:102) Aligned. Score:  66
Sequences (56:57) Aligned. Score:  30
Sequences (56:58) Aligned. Score:  98
Sequences (56:59) Aligned. Score:  30
Sequences (56:60) Aligned. Score:  69
Sequences (56:61) Aligned. Score:  28
Sequences (56:62) Aligned. Score:  27
Sequences (56:63) Aligned. Score:  35
Sequences (56:64) Aligned. Score:  69
Sequences (56:65) Aligned. Score:  36
Sequences (56:66) Aligned. Score:  67
Sequences (56:67) Aligned. Score:  27
Sequences (56:68) Aligned. Score:  69
Sequences (56:69) Aligned. Score:  28
Sequences (56:70) Aligned. Score:  26
Sequences (56:71) Aligned. Score:  60
Sequences (56:72) Aligned. Score:  57
Sequences (56:73) Aligned. Score:  26
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Sequences (56:75) Aligned. Score:  30
Sequences (56:76) Aligned. Score:  31
Sequences (56:77) Aligned. Score:  5
Sequences (56:78) Aligned. Score:  33
Sequences (56:79) Aligned. Score:  61
Sequences (56:80) Aligned. Score:  32
Sequences (56:81) Aligned. Score:  30
Sequences (56:82) Aligned. Score:  66
Sequences (56:83) Aligned. Score:  39
Sequences (56:84) Aligned. Score:  33
Sequences (56:85) Aligned. Score:  31
Sequences (56:86) Aligned. Score:  30
Sequences (56:87) Aligned. Score:  30
Sequences (56:88) Aligned. Score:  32
Sequences (56:89) Aligned. Score:  30
Sequences (56:90) Aligned. Score:  30
Sequences (56:91) Aligned. Score:  34
Sequences (56:92) Aligned. Score:  69
Sequences (56:93) Aligned. Score:  28
Sequences (56:94) Aligned. Score:  32
Sequences (56:95) Aligned. Score:  50
Sequences (56:96) Aligned. Score:  61
Sequences (56:97) Aligned. Score:  38
Sequences (56:98) Aligned. Score:  68
Sequences (56:99) Aligned. Score:  27
Sequences (56:100) Aligned. Score:  34
Sequences (56:101) Aligned. Score:  34
Sequences (56:102) Aligned. Score:  31
Sequences (57:58) Aligned. Score:  30
Sequences (57:59) Aligned. Score:  100
Sequences (57:60) Aligned. Score:  32
Sequences (57:61) Aligned. Score:  64
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Sequences (57:63) Aligned. Score:  35
Sequences (57:64) Aligned. Score:  30
Sequences (57:65) Aligned. Score:  68
Sequences (57:66) Aligned. Score:  28
Sequences (57:67) Aligned. Score:  62
Sequences (57:68) Aligned. Score:  32
Sequences (57:69) Aligned. Score:  63
Sequences (57:70) Aligned. Score:  61
Sequences (57:71) Aligned. Score:  31
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Sequences (57:73) Aligned. Score:  61
Sequences (57:74) Aligned. Score:  10
Sequences (57:75) Aligned. Score:  34
Sequences (57:76) Aligned. Score:  32
Sequences (57:77) Aligned. Score:  8
Sequences (57:78) Aligned. Score:  31
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Sequences (57:80) Aligned. Score:  34
Sequences (57:81) Aligned. Score:  33
Sequences (57:82) Aligned. Score:  31
Sequences (57:83) Aligned. Score:  76
Sequences (57:84) Aligned. Score:  31
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Sequences (57:86) Aligned. Score:  34
Sequences (57:87) Aligned. Score:  35
Sequences (57:88) Aligned. Score:  34
Sequences (57:89) Aligned. Score:  33
Sequences (57:90) Aligned. Score:  35
Sequences (57:91) Aligned. Score:  35
Sequences (57:92) Aligned. Score:  32
Sequences (57:93) Aligned. Score:  64
Sequences (57:94) Aligned. Score:  30
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Sequences (57:96) Aligned. Score:  28
Sequences (57:97) Aligned. Score:  74
Sequences (57:98) Aligned. Score:  32
Sequences (57:99) Aligned. Score:  62
Sequences (57:100) Aligned. Score:  40
Sequences (57:101) Aligned. Score:  36
Sequences (57:102) Aligned. Score:  35
Sequences (58:59) Aligned. Score:  30
Sequences (58:60) Aligned. Score:  69
Sequences (58:61) Aligned. Score:  28
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Sequences (58:63) Aligned. Score:  35
Sequences (58:64) Aligned. Score:  68
Sequences (58:65) Aligned. Score:  36
Sequences (58:66) Aligned. Score:  67
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Sequences (58:68) Aligned. Score:  69
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Sequences (58:71) Aligned. Score:  60
Sequences (58:72) Aligned. Score:  58
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Sequences (58:75) Aligned. Score:  30
Sequences (58:76) Aligned. Score:  31
Sequences (58:77) Aligned. Score:  5
Sequences (58:78) Aligned. Score:  33
Sequences (58:79) Aligned. Score:  62
Sequences (58:80) Aligned. Score:  32
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Sequences (58:82) Aligned. Score:  67
Sequences (58:83) Aligned. Score:  39
Sequences (58:84) Aligned. Score:  33
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Sequences (58:89) Aligned. Score:  30
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Sequences (58:91) Aligned. Score:  34
Sequences (58:92) Aligned. Score:  69
Sequences (58:93) Aligned. Score:  28
Sequences (58:94) Aligned. Score:  32
Sequences (58:95) Aligned. Score:  50
Sequences (58:96) Aligned. Score:  62
Sequences (58:97) Aligned. Score:  38
Sequences (58:98) Aligned. Score:  68
Sequences (58:99) Aligned. Score:  27
Sequences (58:100) Aligned. Score:  34
Sequences (58:101) Aligned. Score:  34
Sequences (58:102) Aligned. Score:  31
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Sequences (59:61) Aligned. Score:  64
Sequences (59:62) Aligned. Score:  22
Sequences (59:63) Aligned. Score:  35
Sequences (59:64) Aligned. Score:  30
Sequences (59:65) Aligned. Score:  68
Sequences (59:66) Aligned. Score:  28
Sequences (59:67) Aligned. Score:  62
Sequences (59:68) Aligned. Score:  32
Sequences (59:69) Aligned. Score:  63
Sequences (59:70) Aligned. Score:  61
Sequences (59:71) Aligned. Score:  31
Sequences (59:72) Aligned. Score:  29
Sequences (59:73) Aligned. Score:  61
Sequences (59:74) Aligned. Score:  10
Sequences (59:75) Aligned. Score:  34
Sequences (59:76) Aligned. Score:  32
Sequences (59:77) Aligned. Score:  8
Sequences (59:78) Aligned. Score:  31
Sequences (59:79) Aligned. Score:  28
Sequences (59:80) Aligned. Score:  34
Sequences (59:81) Aligned. Score:  33
Sequences (59:82) Aligned. Score:  31
Sequences (59:83) Aligned. Score:  76
Sequences (59:84) Aligned. Score:  31
Sequences (59:85) Aligned. Score:  31
Sequences (59:86) Aligned. Score:  34
Sequences (59:87) Aligned. Score:  35
Sequences (59:88) Aligned. Score:  34
Sequences (59:89) Aligned. Score:  33
Sequences (59:90) Aligned. Score:  35
Sequences (59:91) Aligned. Score:  35
Sequences (59:92) Aligned. Score:  32
Sequences (59:93) Aligned. Score:  64
Sequences (59:94) Aligned. Score:  30
Sequences (59:95) Aligned. Score:  26
Sequences (59:96) Aligned. Score:  28
Sequences (59:97) Aligned. Score:  74
Sequences (59:98) Aligned. Score:  32
Sequences (59:99) Aligned. Score:  62
Sequences (59:100) Aligned. Score:  40
Sequences (59:101) Aligned. Score:  36
Sequences (59:102) Aligned. Score:  35
Sequences (60:61) Aligned. Score:  29
Sequences (60:62) Aligned. Score:  27
Sequences (60:63) Aligned. Score:  36
Sequences (60:64) Aligned. Score:  74
Sequences (60:65) Aligned. Score:  39
Sequences (60:66) Aligned. Score:  95
Sequences (60:67) Aligned. Score:  29
Sequences (60:68) Aligned. Score:  99
Sequences (60:69) Aligned. Score:  29
Sequences (60:70) Aligned. Score:  29
Sequences (60:71) Aligned. Score:  65
Sequences (60:72) Aligned. Score:  63
Sequences (60:73) Aligned. Score:  28
Sequences (60:74) Aligned. Score:  17
Sequences (60:75) Aligned. Score:  29
Sequences (60:76) Aligned. Score:  30
Sequences (60:77) Aligned. Score:  6
Sequences (60:78) Aligned. Score:  29
Sequences (60:79) Aligned. Score:  63
Sequences (60:80) Aligned. Score:  33
Sequences (60:81) Aligned. Score:  29
Sequences (60:82) Aligned. Score:  75
Sequences (60:83) Aligned. Score:  43
Sequences (60:84) Aligned. Score:  31
Sequences (60:85) Aligned. Score:  31
Sequences (60:86) Aligned. Score:  29
Sequences (60:87) Aligned. Score:  30
Sequences (60:88) Aligned. Score:  33
Sequences (60:89) Aligned. Score:  29
Sequences (60:90) Aligned. Score:  29
Sequences (60:91) Aligned. Score:  34
Sequences (60:92) Aligned. Score:  100
Sequences (60:93) Aligned. Score:  29
Sequences (60:94) Aligned. Score:  29
Sequences (60:95) Aligned. Score:  50
Sequences (60:96) Aligned. Score:  63
Sequences (60:97) Aligned. Score:  38
Sequences (60:98) Aligned. Score:  96
Sequences (60:99) Aligned. Score:  29
Sequences (60:100) Aligned. Score:  36
Sequences (60:101) Aligned. Score:  32
Sequences (60:102) Aligned. Score:  30
Sequences (61:62) Aligned. Score:  20
Sequences (61:63) Aligned. Score:  33
Sequences (61:64) Aligned. Score:  30
Sequences (61:65) Aligned. Score:  75
Sequences (61:66) Aligned. Score:  25
Sequences (61:67) Aligned. Score:  91
Sequences (61:68) Aligned. Score:  29
Sequences (61:69) Aligned. Score:  99
Sequences (61:70) Aligned. Score:  61
Sequences (61:71) Aligned. Score:  29
Sequences (61:72) Aligned. Score:  27
Sequences (61:73) Aligned. Score:  60
Sequences (61:74) Aligned. Score:  15
Sequences (61:75) Aligned. Score:  32
Sequences (61:76) Aligned. Score:  30
Sequences (61:77) Aligned. Score:  9
Sequences (61:78) Aligned. Score:  28
Sequences (61:79) Aligned. Score:  28
Sequences (61:80) Aligned. Score:  29
Sequences (61:81) Aligned. Score:  30
Sequences (61:82) Aligned. Score:  30
Sequences (61:83) Aligned. Score:  80
Sequences (61:84) Aligned. Score:  28
Sequences (61:85) Aligned. Score:  28
Sequences (61:86) Aligned. Score:  30
Sequences (61:87) Aligned. Score:  30
Sequences (61:88) Aligned. Score:  29
Sequences (61:89) Aligned. Score:  30
Sequences (61:90) Aligned. Score:  30
Sequences (61:91) Aligned. Score:  36
Sequences (61:92) Aligned. Score:  29
Sequences (61:93) Aligned. Score:  100
Sequences (61:94) Aligned. Score:  29
Sequences (61:95) Aligned. Score:  24
Sequences (61:96) Aligned. Score:  28
Sequences (61:97) Aligned. Score:  70
Sequences (61:98) Aligned. Score:  29
Sequences (61:99) Aligned. Score:  91
Sequences (61:100) Aligned. Score:  39
Sequences (61:101) Aligned. Score:  34
Sequences (61:102) Aligned. Score:  32
Sequences (62:63) Aligned. Score:  30
Sequences (62:64) Aligned. Score:  31
Sequences (62:65) Aligned. Score:  31
Sequences (62:66) Aligned. Score:  27
Sequences (62:67) Aligned. Score:  20
Sequences (62:68) Aligned. Score:  27
Sequences (62:69) Aligned. Score:  20
Sequences (62:70) Aligned. Score:  20
Sequences (62:71) Aligned. Score:  28
Sequences (62:72) Aligned. Score:  29
Sequences (62:73) Aligned. Score:  21
Sequences (62:74) Aligned. Score:  31
Sequences (62:75) Aligned. Score:  33
Sequences (62:76) Aligned. Score:  32
Sequences (62:77) Aligned. Score:  14
Sequences (62:78) Aligned. Score:  36
Sequences (62:79) Aligned. Score:  28
Sequences (62:80) Aligned. Score:  31
Sequences (62:81) Aligned. Score:  37
Sequences (62:82) Aligned. Score:  29
Sequences (62:83) Aligned. Score:  37
Sequences (62:84) Aligned. Score:  33
Sequences (62:85) Aligned. Score:  33
Sequences (62:86) Aligned. Score:  38
Sequences (62:87) Aligned. Score:  38
Sequences (62:88) Aligned. Score:  31
Sequences (62:89) Aligned. Score:  37
Sequences (62:90) Aligned. Score:  37
Sequences (62:91) Aligned. Score:  31
Sequences (62:92) Aligned. Score:  27
Sequences (62:93) Aligned. Score:  20
Sequences (62:94) Aligned. Score:  33
Sequences (62:95) Aligned. Score:  28
Sequences (62:96) Aligned. Score:  28
Sequences (62:97) Aligned. Score:  29
Sequences (62:98) Aligned. Score:  27
Sequences (62:99) Aligned. Score:  18
Sequences (62:100) Aligned. Score:  38
Sequences (62:101) Aligned. Score:  37
Sequences (62:102) Aligned. Score:  37
Sequences (63:64) Aligned. Score:  36
Sequences (63:65) Aligned. Score:  36
Sequences (63:66) Aligned. Score:  33
Sequences (63:67) Aligned. Score:  32
Sequences (63:68) Aligned. Score:  36
Sequences (63:69) Aligned. Score:  33
Sequences (63:70) Aligned. Score:  28
Sequences (63:71) Aligned. Score:  35
Sequences (63:72) Aligned. Score:  36
Sequences (63:73) Aligned. Score:  27
Sequences (63:74) Aligned. Score:  23
Sequences (63:75) Aligned. Score:  54
Sequences (63:76) Aligned. Score:  51
Sequences (63:77) Aligned. Score:  14
Sequences (63:78) Aligned. Score:  51
Sequences (63:79) Aligned. Score:  34
Sequences (63:80) Aligned. Score:  48
Sequences (63:81) Aligned. Score:  51
Sequences (63:82) Aligned. Score:  34
Sequences (63:83) Aligned. Score:  41
Sequences (63:84) Aligned. Score:  79
Sequences (63:85) Aligned. Score:  79
Sequences (63:86) Aligned. Score:  50
Sequences (63:87) Aligned. Score:  51
Sequences (63:88) Aligned. Score:  48
Sequences (63:89) Aligned. Score:  51
Sequences (63:90) Aligned. Score:  50
Sequences (63:91) Aligned. Score:  51
Sequences (63:92) Aligned. Score:  36
Sequences (63:93) Aligned. Score:  33
Sequences (63:94) Aligned. Score:  49
Sequences (63:95) Aligned. Score:  32
Sequences (63:96) Aligned. Score:  34
Sequences (63:97) Aligned. Score:  42
Sequences (63:98) Aligned. Score:  36
Sequences (63:99) Aligned. Score:  32
Sequences (63:100) Aligned. Score:  34
Sequences (63:101) Aligned. Score:  51
Sequences (63:102) Aligned. Score:  52
Sequences (64:65) Aligned. Score:  46
Sequences (64:66) Aligned. Score:  73
Sequences (64:67) Aligned. Score:  28
Sequences (64:68) Aligned. Score:  74
Sequences (64:69) Aligned. Score:  30
Sequences (64:70) Aligned. Score:  30
Sequences (64:71) Aligned. Score:  65
Sequences (64:72) Aligned. Score:  63
Sequences (64:73) Aligned. Score:  28
Sequences (64:74) Aligned. Score:  14
Sequences (64:75) Aligned. Score:  30
Sequences (64:76) Aligned. Score:  30
Sequences (64:77) Aligned. Score:  8
Sequences (64:78) Aligned. Score:  34
Sequences (64:79) Aligned. Score:  62
Sequences (64:80) Aligned. Score:  35
Sequences (64:81) Aligned. Score:  32
Sequences (64:82) Aligned. Score:  74
Sequences (64:83) Aligned. Score:  45
Sequences (64:84) Aligned. Score:  32
Sequences (64:85) Aligned. Score:  33
Sequences (64:86) Aligned. Score:  32
Sequences (64:87) Aligned. Score:  32
Sequences (64:88) Aligned. Score:  35
Sequences (64:89) Aligned. Score:  32
Sequences (64:90) Aligned. Score:  32
Sequences (64:91) Aligned. Score:  34
Sequences (64:92) Aligned. Score:  74
Sequences (64:93) Aligned. Score:  30
Sequences (64:94) Aligned. Score:  33
Sequences (64:95) Aligned. Score:  53
Sequences (64:96) Aligned. Score:  62
Sequences (64:97) Aligned. Score:  40
Sequences (64:98) Aligned. Score:  74
Sequences (64:99) Aligned. Score:  28
Sequences (64:100) Aligned. Score:  38
Sequences (64:101) Aligned. Score:  34
Sequences (64:102) Aligned. Score:  32
Sequences (65:66) Aligned. Score:  32
Sequences (65:67) Aligned. Score:  72
Sequences (65:68) Aligned. Score:  39
Sequences (65:69) Aligned. Score:  75
Sequences (65:70) Aligned. Score:  77
Sequences (65:71) Aligned. Score:  39
Sequences (65:72) Aligned. Score:  37
Sequences (65:73) Aligned. Score:  74
Sequences (65:74) Aligned. Score:  22
Sequences (65:75) Aligned. Score:  41
Sequences (65:76) Aligned. Score:  39
Sequences (65:77) Aligned. Score:  13
Sequences (65:78) Aligned. Score:  43
Sequences (65:79) Aligned. Score:  37
Sequences (65:80) Aligned. Score:  39
Sequences (65:81) Aligned. Score:  43
Sequences (65:82) Aligned. Score:  39
Sequences (65:83) Aligned. Score:  86
Sequences (65:84) Aligned. Score:  32
Sequences (65:85) Aligned. Score:  32
Sequences (65:86) Aligned. Score:  39
Sequences (65:87) Aligned. Score:  39
Sequences (65:88) Aligned. Score:  39
Sequences (65:89) Aligned. Score:  43
Sequences (65:90) Aligned. Score:  39
Sequences (65:91) Aligned. Score:  37
Sequences (65:92) Aligned. Score:  39
Sequences (65:93) Aligned. Score:  75
Sequences (65:94) Aligned. Score:  43
Sequences (65:95) Aligned. Score:  32
Sequences (65:96) Aligned. Score:  37
Sequences (65:97) Aligned. Score:  75
Sequences (65:98) Aligned. Score:  39
Sequences (65:99) Aligned. Score:  72
Sequences (65:100) Aligned. Score:  56
Sequences (65:101) Aligned. Score:  44
Sequences (65:102) Aligned. Score:  46
Sequences (66:67) Aligned. Score:  25
Sequences (66:68) Aligned. Score:  95
Sequences (66:69) Aligned. Score:  25
Sequences (66:70) Aligned. Score:  26
Sequences (66:71) Aligned. Score:  63
Sequences (66:72) Aligned. Score:  61
Sequences (66:73) Aligned. Score:  25
Sequences (66:74) Aligned. Score:  9
Sequences (66:75) Aligned. Score:  25
Sequences (66:76) Aligned. Score:  26
Sequences (66:77) Aligned. Score:  3
Sequences (66:78) Aligned. Score:  27
Sequences (66:79) Aligned. Score:  62
Sequences (66:80) Aligned. Score:  32
Sequences (66:81) Aligned. Score:  26
Sequences (66:82) Aligned. Score:  74
Sequences (66:83) Aligned. Score:  33
Sequences (66:84) Aligned. Score:  30
Sequences (66:85) Aligned. Score:  30
Sequences (66:86) Aligned. Score:  26
Sequences (66:87) Aligned. Score:  26
Sequences (66:88) Aligned. Score:  32
Sequences (66:89) Aligned. Score:  26
Sequences (66:90) Aligned. Score:  26
Sequences (66:91) Aligned. Score:  29
Sequences (66:92) Aligned. Score:  95
Sequences (66:93) Aligned. Score:  25
Sequences (66:94) Aligned. Score:  27
Sequences (66:95) Aligned. Score:  50
Sequences (66:96) Aligned. Score:  62
Sequences (66:97) Aligned. Score:  31
Sequences (66:98) Aligned. Score:  99
Sequences (66:99) Aligned. Score:  25
Sequences (66:100) Aligned. Score:  34
Sequences (66:101) Aligned. Score:  28
Sequences (66:102) Aligned. Score:  32
Sequences (67:68) Aligned. Score:  29
Sequences (67:69) Aligned. Score:  90
Sequences (67:70) Aligned. Score:  61
Sequences (67:71) Aligned. Score:  28
Sequences (67:72) Aligned. Score:  26
Sequences (67:73) Aligned. Score:  59
Sequences (67:74) Aligned. Score:  15
Sequences (67:75) Aligned. Score:  31
Sequences (67:76) Aligned. Score:  29
Sequences (67:77) Aligned. Score:  9
Sequences (67:78) Aligned. Score:  27
Sequences (67:79) Aligned. Score:  28
Sequences (67:80) Aligned. Score:  30
Sequences (67:81) Aligned. Score:  29
Sequences (67:82) Aligned. Score:  29
Sequences (67:83) Aligned. Score:  78
Sequences (67:84) Aligned. Score:  27
Sequences (67:85) Aligned. Score:  27
Sequences (67:86) Aligned. Score:  28
Sequences (67:87) Aligned. Score:  29
Sequences (67:88) Aligned. Score:  30
Sequences (67:89) Aligned. Score:  29
Sequences (67:90) Aligned. Score:  29
Sequences (67:91) Aligned. Score:  36
Sequences (67:92) Aligned. Score:  29
Sequences (67:93) Aligned. Score:  91
Sequences (67:94) Aligned. Score:  28
Sequences (67:95) Aligned. Score:  23
Sequences (67:96) Aligned. Score:  28
Sequences (67:97) Aligned. Score:  68
Sequences (67:98) Aligned. Score:  29
Sequences (67:99) Aligned. Score:  99
Sequences (67:100) Aligned. Score:  38
Sequences (67:101) Aligned. Score:  34
Sequences (67:102) Aligned. Score:  32
Sequences (68:69) Aligned. Score:  29
Sequences (68:70) Aligned. Score:  29
Sequences (68:71) Aligned. Score:  65
Sequences (68:72) Aligned. Score:  63
Sequences (68:73) Aligned. Score:  28
Sequences (68:74) Aligned. Score:  17
Sequences (68:75) Aligned. Score:  29
Sequences (68:76) Aligned. Score:  30
Sequences (68:77) Aligned. Score:  3
Sequences (68:78) Aligned. Score:  29
Sequences (68:79) Aligned. Score:  63
Sequences (68:80) Aligned. Score:  33
Sequences (68:81) Aligned. Score:  29
Sequences (68:82) Aligned. Score:  75
Sequences (68:83) Aligned. Score:  43
Sequences (68:84) Aligned. Score:  31
Sequences (68:85) Aligned. Score:  31
Sequences (68:86) Aligned. Score:  29
Sequences (68:87) Aligned. Score:  30
Sequences (68:88) Aligned. Score:  33
Sequences (68:89) Aligned. Score:  29
Sequences (68:90) Aligned. Score:  29
Sequences (68:91) Aligned. Score:  34
Sequences (68:92) Aligned. Score:  99
Sequences (68:93) Aligned. Score:  29
Sequences (68:94) Aligned. Score:  29
Sequences (68:95) Aligned. Score:  50
Sequences (68:96) Aligned. Score:  63
Sequences (68:97) Aligned. Score:  38
Sequences (68:98) Aligned. Score:  96
Sequences (68:99) Aligned. Score:  29
Sequences (68:100) Aligned. Score:  36
Sequences (68:101) Aligned. Score:  32
Sequences (68:102) Aligned. Score:  30
Sequences (69:70) Aligned. Score:  61
Sequences (69:71) Aligned. Score:  29
Sequences (69:72) Aligned. Score:  27
Sequences (69:73) Aligned. Score:  59
Sequences (69:74) Aligned. Score:  15
Sequences (69:75) Aligned. Score:  32
Sequences (69:76) Aligned. Score:  30
Sequences (69:77) Aligned. Score:  9
Sequences (69:78) Aligned. Score:  28
Sequences (69:79) Aligned. Score:  27
Sequences (69:80) Aligned. Score:  28
Sequences (69:81) Aligned. Score:  30
Sequences (69:82) Aligned. Score:  30
Sequences (69:83) Aligned. Score:  80
Sequences (69:84) Aligned. Score:  28
Sequences (69:85) Aligned. Score:  28
Sequences (69:86) Aligned. Score:  29
Sequences (69:87) Aligned. Score:  30
Sequences (69:88) Aligned. Score:  28
Sequences (69:89) Aligned. Score:  30
Sequences (69:90) Aligned. Score:  29
Sequences (69:91) Aligned. Score:  35
Sequences (69:92) Aligned. Score:  29
Sequences (69:93) Aligned. Score:  99
Sequences (69:94) Aligned. Score:  29
Sequences (69:95) Aligned. Score:  23
Sequences (69:96) Aligned. Score:  27
Sequences (69:97) Aligned. Score:  70
Sequences (69:98) Aligned. Score:  29
Sequences (69:99) Aligned. Score:  91
Sequences (69:100) Aligned. Score:  39
Sequences (69:101) Aligned. Score:  34
Sequences (69:102) Aligned. Score:  32
Sequences (70:71) Aligned. Score:  30
Sequences (70:72) Aligned. Score:  26
Sequences (70:73) Aligned. Score:  80
Sequences (70:74) Aligned. Score:  19
Sequences (70:75) Aligned. Score:  31
Sequences (70:76) Aligned. Score:  30
Sequences (70:77) Aligned. Score:  14
Sequences (70:78) Aligned. Score:  35
Sequences (70:79) Aligned. Score:  27
Sequences (70:80) Aligned. Score:  32
Sequences (70:81) Aligned. Score:  33
Sequences (70:82) Aligned. Score:  30
Sequences (70:83) Aligned. Score:  82
Sequences (70:84) Aligned. Score:  29
Sequences (70:85) Aligned. Score:  30
Sequences (70:86) Aligned. Score:  32
Sequences (70:87) Aligned. Score:  32
Sequences (70:88) Aligned. Score:  32
Sequences (70:89) Aligned. Score:  33
Sequences (70:90) Aligned. Score:  32
Sequences (70:91) Aligned. Score:  37
Sequences (70:92) Aligned. Score:  29
Sequences (70:93) Aligned. Score:  61
Sequences (70:94) Aligned. Score:  36
Sequences (70:95) Aligned. Score:  28
Sequences (70:96) Aligned. Score:  27
Sequences (70:97) Aligned. Score:  79
Sequences (70:98) Aligned. Score:  30
Sequences (70:99) Aligned. Score:  61
Sequences (70:100) Aligned. Score:  36
Sequences (70:101) Aligned. Score:  35
Sequences (70:102) Aligned. Score:  31
Sequences (71:72) Aligned. Score:  86
Sequences (71:73) Aligned. Score:  27
Sequences (71:74) Aligned. Score:  18
Sequences (71:75) Aligned. Score:  35
Sequences (71:76) Aligned. Score:  34
Sequences (71:77) Aligned. Score:  4
Sequences (71:78) Aligned. Score:  31
Sequences (71:79) Aligned. Score:  57
Sequences (71:80) Aligned. Score:  29
Sequences (71:81) Aligned. Score:  32
Sequences (71:82) Aligned. Score:  67
Sequences (71:83) Aligned. Score:  43
Sequences (71:84) Aligned. Score:  35
Sequences (71:85) Aligned. Score:  35
Sequences (71:86) Aligned. Score:  32
Sequences (71:87) Aligned. Score:  32
Sequences (71:88) Aligned. Score:  29
Sequences (71:89) Aligned. Score:  32
Sequences (71:90) Aligned. Score:  32
Sequences (71:91) Aligned. Score:  33
Sequences (71:92) Aligned. Score:  65
Sequences (71:93) Aligned. Score:  29
Sequences (71:94) Aligned. Score:  31
Sequences (71:95) Aligned. Score:  48
Sequences (71:96) Aligned. Score:  57
Sequences (71:97) Aligned. Score:  38
Sequences (71:98) Aligned. Score:  65
Sequences (71:99) Aligned. Score:  28
Sequences (71:100) Aligned. Score:  36
Sequences (71:101) Aligned. Score:  34
Sequences (71:102) Aligned. Score:  33
Sequences (72:73) Aligned. Score:  25
Sequences (72:74) Aligned. Score:  14
Sequences (72:75) Aligned. Score:  35
Sequences (72:76) Aligned. Score:  36
Sequences (72:77) Aligned. Score:  6
Sequences (72:78) Aligned. Score:  34
Sequences (72:79) Aligned. Score:  56
Sequences (72:80) Aligned. Score:  31
Sequences (72:81) Aligned. Score:  30
Sequences (72:82) Aligned. Score:  64
Sequences (72:83) Aligned. Score:  41
Sequences (72:84) Aligned. Score:  36
Sequences (72:85) Aligned. Score:  35
Sequences (72:86) Aligned. Score:  29
Sequences (72:87) Aligned. Score:  30
Sequences (72:88) Aligned. Score:  31
Sequences (72:89) Aligned. Score:  30
Sequences (72:90) Aligned. Score:  29
Sequences (72:91) Aligned. Score:  34
Sequences (72:92) Aligned. Score:  63
Sequences (72:93) Aligned. Score:  27
Sequences (72:94) Aligned. Score:  34
Sequences (72:95) Aligned. Score:  44
Sequences (72:96) Aligned. Score:  56
Sequences (72:97) Aligned. Score:  37
Sequences (72:98) Aligned. Score:  62
Sequences (72:99) Aligned. Score:  26
Sequences (72:100) Aligned. Score:  35
Sequences (72:101) Aligned. Score:  34
Sequences (72:102) Aligned. Score:  32
Sequences (73:74) Aligned. Score:  12
Sequences (73:75) Aligned. Score:  29
Sequences (73:76) Aligned. Score:  28
Sequences (73:77) Aligned. Score:  7
Sequences (73:78) Aligned. Score:  30
Sequences (73:79) Aligned. Score:  26
Sequences (73:80) Aligned. Score:  29
Sequences (73:81) Aligned. Score:  33
Sequences (73:82) Aligned. Score:  27
Sequences (73:83) Aligned. Score:  84
Sequences (73:84) Aligned. Score:  25
Sequences (73:85) Aligned. Score:  25
Sequences (73:86) Aligned. Score:  33
Sequences (73:87) Aligned. Score:  33
Sequences (73:88) Aligned. Score:  29
Sequences (73:89) Aligned. Score:  33
Sequences (73:90) Aligned. Score:  33
Sequences (73:91) Aligned. Score:  30
Sequences (73:92) Aligned. Score:  28
Sequences (73:93) Aligned. Score:  60
Sequences (73:94) Aligned. Score:  31
Sequences (73:95) Aligned. Score:  24
Sequences (73:96) Aligned. Score:  26
Sequences (73:97) Aligned. Score:  74
Sequences (73:98) Aligned. Score:  28
Sequences (73:99) Aligned. Score:  59
Sequences (73:100) Aligned. Score:  32
Sequences (73:101) Aligned. Score:  31
Sequences (73:102) Aligned. Score:  28
Sequences (74:75) Aligned. Score:  22
Sequences (74:76) Aligned. Score:  22
Sequences (74:77) Aligned. Score:  36
Sequences (74:78) Aligned. Score:  25
Sequences (74:79) Aligned. Score:  16
Sequences (74:80) Aligned. Score:  20
Sequences (74:81) Aligned. Score:  26
Sequences (74:82) Aligned. Score:  17
Sequences (74:83) Aligned. Score:  21
Sequences (74:84) Aligned. Score:  20
Sequences (74:85) Aligned. Score:  20
Sequences (74:86) Aligned. Score:  26
Sequences (74:87) Aligned. Score:  26
Sequences (74:88) Aligned. Score:  20
Sequences (74:89) Aligned. Score:  26
Sequences (74:90) Aligned. Score:  25
Sequences (74:91) Aligned. Score:  28
Sequences (74:92) Aligned. Score:  17
Sequences (74:93) Aligned. Score:  15
Sequences (74:94) Aligned. Score:  27
Sequences (74:95) Aligned. Score:  18
Sequences (74:96) Aligned. Score:  16
Sequences (74:97) Aligned. Score:  20
Sequences (74:98) Aligned. Score:  17
Sequences (74:99) Aligned. Score:  15
Sequences (74:100) Aligned. Score:  20
Sequences (74:101) Aligned. Score:  27
Sequences (74:102) Aligned. Score:  25
Sequences (75:76) Aligned. Score:  94
Sequences (75:77) Aligned. Score:  16
Sequences (75:78) Aligned. Score:  54
Sequences (75:79) Aligned. Score:  32
Sequences (75:80) Aligned. Score:  46
Sequences (75:81) Aligned. Score:  66
Sequences (75:82) Aligned. Score:  30
Sequences (75:83) Aligned. Score:  47
Sequences (75:84) Aligned. Score:  51
Sequences (75:85) Aligned. Score:  52
Sequences (75:86) Aligned. Score:  63
Sequences (75:87) Aligned. Score:  64
Sequences (75:88) Aligned. Score:  46
Sequences (75:89) Aligned. Score:  66
Sequences (75:90) Aligned. Score:  63
Sequences (75:91) Aligned. Score:  63
Sequences (75:92) Aligned. Score:  29
Sequences (75:93) Aligned. Score:  32
Sequences (75:94) Aligned. Score:  53
Sequences (75:95) Aligned. Score:  30
Sequences (75:96) Aligned. Score:  32
Sequences (75:97) Aligned. Score:  46
Sequences (75:98) Aligned. Score:  29
Sequences (75:99) Aligned. Score:  31
Sequences (75:100) Aligned. Score:  37
Sequences (75:101) Aligned. Score:  73
Sequences (75:102) Aligned. Score:  74
Sequences (76:77) Aligned. Score:  15
Sequences (76:78) Aligned. Score:  52
Sequences (76:79) Aligned. Score:  30
Sequences (76:80) Aligned. Score:  46
Sequences (76:81) Aligned. Score:  64
Sequences (76:82) Aligned. Score:  30
Sequences (76:83) Aligned. Score:  45
Sequences (76:84) Aligned. Score:  50
Sequences (76:85) Aligned. Score:  51
Sequences (76:86) Aligned. Score:  62
Sequences (76:87) Aligned. Score:  63
Sequences (76:88) Aligned. Score:  46
Sequences (76:89) Aligned. Score:  64
Sequences (76:90) Aligned. Score:  62
Sequences (76:91) Aligned. Score:  61
Sequences (76:92) Aligned. Score:  30
Sequences (76:93) Aligned. Score:  30
Sequences (76:94) Aligned. Score:  51
Sequences (76:95) Aligned. Score:  30
Sequences (76:96) Aligned. Score:  30
Sequences (76:97) Aligned. Score:  44
Sequences (76:98) Aligned. Score:  30
Sequences (76:99) Aligned. Score:  29
Sequences (76:100) Aligned. Score:  37
Sequences (76:101) Aligned. Score:  72
Sequences (76:102) Aligned. Score:  72
Sequences (77:78) Aligned. Score:  12
Sequences (77:79) Aligned. Score:  9
Sequences (77:80) Aligned. Score:  14
Sequences (77:81) Aligned. Score:  6
Sequences (77:82) Aligned. Score:  3
Sequences (77:83) Aligned. Score:  17
Sequences (77:84) Aligned. Score:  11
Sequences (77:85) Aligned. Score:  5
Sequences (77:86) Aligned. Score:  16
Sequences (77:87) Aligned. Score:  16
Sequences (77:88) Aligned. Score:  14
Sequences (77:89) Aligned. Score:  6
Sequences (77:90) Aligned. Score:  16
Sequences (77:91) Aligned. Score:  17
Sequences (77:92) Aligned. Score:  6
Sequences (77:93) Aligned. Score:  9
Sequences (77:94) Aligned. Score:  12
Sequences (77:95) Aligned. Score:  3
Sequences (77:96) Aligned. Score:  3
Sequences (77:97) Aligned. Score:  18
Sequences (77:98) Aligned. Score:  3
Sequences (77:99) Aligned. Score:  9
Sequences (77:100) Aligned. Score:  16
Sequences (77:101) Aligned. Score:  14
Sequences (77:102) Aligned. Score:  13
Sequences (78:79) Aligned. Score:  34
Sequences (78:80) Aligned. Score:  48
Sequences (78:81) Aligned. Score:  53
Sequences (78:82) Aligned. Score:  34
Sequences (78:83) Aligned. Score:  45
Sequences (78:84) Aligned. Score:  53
Sequences (78:85) Aligned. Score:  53
Sequences (78:86) Aligned. Score:  55
Sequences (78:87) Aligned. Score:  54
Sequences (78:88) Aligned. Score:  48
Sequences (78:89) Aligned. Score:  53
Sequences (78:90) Aligned. Score:  55
Sequences (78:91) Aligned. Score:  53
Sequences (78:92) Aligned. Score:  29
Sequences (78:93) Aligned. Score:  28
Sequences (78:94) Aligned. Score:  92
Sequences (78:95) Aligned. Score:  36
Sequences (78:96) Aligned. Score:  34
Sequences (78:97) Aligned. Score:  40
Sequences (78:98) Aligned. Score:  29
Sequences (78:99) Aligned. Score:  27
Sequences (78:100) Aligned. Score:  41
Sequences (78:101) Aligned. Score:  53
Sequences (78:102) Aligned. Score:  54
Sequences (79:80) Aligned. Score:  31
Sequences (79:81) Aligned. Score:  29
Sequences (79:82) Aligned. Score:  59
Sequences (79:83) Aligned. Score:  39
Sequences (79:84) Aligned. Score:  34
Sequences (79:85) Aligned. Score:  33
Sequences (79:86) Aligned. Score:  27
Sequences (79:87) Aligned. Score:  28
Sequences (79:88) Aligned. Score:  31
Sequences (79:89) Aligned. Score:  29
Sequences (79:90) Aligned. Score:  29
Sequences (79:91) Aligned. Score:  33
Sequences (79:92) Aligned. Score:  63
Sequences (79:93) Aligned. Score:  28
Sequences (79:94) Aligned. Score:  32
Sequences (79:95) Aligned. Score:  47
Sequences (79:96) Aligned. Score:  99
Sequences (79:97) Aligned. Score:  35
Sequences (79:98) Aligned. Score:  63
Sequences (79:99) Aligned. Score:  27
Sequences (79:100) Aligned. Score:  34
Sequences (79:101) Aligned. Score:  30
Sequences (79:102) Aligned. Score:  29
Sequences (80:81) Aligned. Score:  45
Sequences (80:82) Aligned. Score:  33
Sequences (80:83) Aligned. Score:  47
Sequences (80:84) Aligned. Score:  47
Sequences (80:85) Aligned. Score:  46
Sequences (80:86) Aligned. Score:  46
Sequences (80:87) Aligned. Score:  46
Sequences (80:88) Aligned. Score:  100
Sequences (80:89) Aligned. Score:  45
Sequences (80:90) Aligned. Score:  46
Sequences (80:91) Aligned. Score:  45
Sequences (80:92) Aligned. Score:  33
Sequences (80:93) Aligned. Score:  29
Sequences (80:94) Aligned. Score:  48
Sequences (80:95) Aligned. Score:  35
Sequences (80:96) Aligned. Score:  31
Sequences (80:97) Aligned. Score:  46
Sequences (80:98) Aligned. Score:  33
Sequences (80:99) Aligned. Score:  30
Sequences (80:100) Aligned. Score:  38
Sequences (80:101) Aligned. Score:  47
Sequences (80:102) Aligned. Score:  44
Sequences (81:82) Aligned. Score:  32
Sequences (81:83) Aligned. Score:  47
Sequences (81:84) Aligned. Score:  49
Sequences (81:85) Aligned. Score:  50
Sequences (81:86) Aligned. Score:  88
Sequences (81:87) Aligned. Score:  88
Sequences (81:88) Aligned. Score:  45
Sequences (81:89) Aligned. Score:  100
Sequences (81:90) Aligned. Score:  88
Sequences (81:91) Aligned. Score:  74
Sequences (81:92) Aligned. Score:  29
Sequences (81:93) Aligned. Score:  30
Sequences (81:94) Aligned. Score:  52
Sequences (81:95) Aligned. Score:  32
Sequences (81:96) Aligned. Score:  29
Sequences (81:97) Aligned. Score:  48
Sequences (81:98) Aligned. Score:  29
Sequences (81:99) Aligned. Score:  29
Sequences (81:100) Aligned. Score:  38
Sequences (81:101) Aligned. Score:  71
Sequences (81:102) Aligned. Score:  66
Sequences (82:83) Aligned. Score:  41
Sequences (82:84) Aligned. Score:  33
Sequences (82:85) Aligned. Score:  32
Sequences (82:86) Aligned. Score:  32
Sequences (82:87) Aligned. Score:  31
Sequences (82:88) Aligned. Score:  33
Sequences (82:89) Aligned. Score:  32
Sequences (82:90) Aligned. Score:  32
Sequences (82:91) Aligned. Score:  34
Sequences (82:92) Aligned. Score:  75
Sequences (82:93) Aligned. Score:  30
Sequences (82:94) Aligned. Score:  34
Sequences (82:95) Aligned. Score:  50
Sequences (82:96) Aligned. Score:  59
Sequences (82:97) Aligned. Score:  38
Sequences (82:98) Aligned. Score:  74
Sequences (82:99) Aligned. Score:  29
Sequences (82:100) Aligned. Score:  37
Sequences (82:101) Aligned. Score:  34
Sequences (82:102) Aligned. Score:  31
Sequences (83:84) Aligned. Score:  35
Sequences (83:85) Aligned. Score:  35
Sequences (83:86) Aligned. Score:  47
Sequences (83:87) Aligned. Score:  49
Sequences (83:88) Aligned. Score:  47
Sequences (83:89) Aligned. Score:  47
Sequences (83:90) Aligned. Score:  47
Sequences (83:91) Aligned. Score:  49
Sequences (83:92) Aligned. Score:  43
Sequences (83:93) Aligned. Score:  80
Sequences (83:94) Aligned. Score:  45
Sequences (83:95) Aligned. Score:  37
Sequences (83:96) Aligned. Score:  39
Sequences (83:97) Aligned. Score:  74
Sequences (83:98) Aligned. Score:  43
Sequences (83:99) Aligned. Score:  78
Sequences (83:100) Aligned. Score:  62
Sequences (83:101) Aligned. Score:  49
Sequences (83:102) Aligned. Score:  50
Sequences (84:85) Aligned. Score:  95
Sequences (84:86) Aligned. Score:  49
Sequences (84:87) Aligned. Score:  48
Sequences (84:88) Aligned. Score:  47
Sequences (84:89) Aligned. Score:  49
Sequences (84:90) Aligned. Score:  49
Sequences (84:91) Aligned. Score:  50
Sequences (84:92) Aligned. Score:  31
Sequences (84:93) Aligned. Score:  28
Sequences (84:94) Aligned. Score:  51
Sequences (84:95) Aligned. Score:  31
Sequences (84:96) Aligned. Score:  34
Sequences (84:97) Aligned. Score:  38
Sequences (84:98) Aligned. Score:  31
Sequences (84:99) Aligned. Score:  27
Sequences (84:100) Aligned. Score:  32
Sequences (84:101) Aligned. Score:  50
Sequences (84:102) Aligned. Score:  47
Sequences (85:86) Aligned. Score:  50
Sequences (85:87) Aligned. Score:  49
Sequences (85:88) Aligned. Score:  46
Sequences (85:89) Aligned. Score:  50
Sequences (85:90) Aligned. Score:  50
Sequences (85:91) Aligned. Score:  51
Sequences (85:92) Aligned. Score:  31
Sequences (85:93) Aligned. Score:  28
Sequences (85:94) Aligned. Score:  51
Sequences (85:95) Aligned. Score:  31
Sequences (85:96) Aligned. Score:  33
Sequences (85:97) Aligned. Score:  38
Sequences (85:98) Aligned. Score:  31
Sequences (85:99) Aligned. Score:  27
Sequences (85:100) Aligned. Score:  34
Sequences (85:101) Aligned. Score:  51
Sequences (85:102) Aligned. Score:  48
Sequences (86:87) Aligned. Score:  99
Sequences (86:88) Aligned. Score:  46
Sequences (86:89) Aligned. Score:  88
Sequences (86:90) Aligned. Score:  98
Sequences (86:91) Aligned. Score:  72
Sequences (86:92) Aligned. Score:  29
Sequences (86:93) Aligned. Score:  30
Sequences (86:94) Aligned. Score:  54
Sequences (86:95) Aligned. Score:  32
Sequences (86:96) Aligned. Score:  27
Sequences (86:97) Aligned. Score:  48
Sequences (86:98) Aligned. Score:  29
Sequences (86:99) Aligned. Score:  28
Sequences (86:100) Aligned. Score:  37
Sequences (86:101) Aligned. Score:  68
Sequences (86:102) Aligned. Score:  62
Sequences (87:88) Aligned. Score:  46
Sequences (87:89) Aligned. Score:  88
Sequences (87:90) Aligned. Score:  97
Sequences (87:91) Aligned. Score:  72
Sequences (87:92) Aligned. Score:  30
Sequences (87:93) Aligned. Score:  30
Sequences (87:94) Aligned. Score:  53
Sequences (87:95) Aligned. Score:  31
Sequences (87:96) Aligned. Score:  28
Sequences (87:97) Aligned. Score:  48
Sequences (87:98) Aligned. Score:  30
Sequences (87:99) Aligned. Score:  29
Sequences (87:100) Aligned. Score:  37
Sequences (87:101) Aligned. Score:  69
Sequences (87:102) Aligned. Score:  62
Sequences (88:89) Aligned. Score:  45
Sequences (88:90) Aligned. Score:  46
Sequences (88:91) Aligned. Score:  45
Sequences (88:92) Aligned. Score:  33
Sequences (88:93) Aligned. Score:  29
Sequences (88:94) Aligned. Score:  48
Sequences (88:95) Aligned. Score:  35
Sequences (88:96) Aligned. Score:  31
Sequences (88:97) Aligned. Score:  46
Sequences (88:98) Aligned. Score:  33
Sequences (88:99) Aligned. Score:  30
Sequences (88:100) Aligned. Score:  38
Sequences (88:101) Aligned. Score:  47
Sequences (88:102) Aligned. Score:  44
Sequences (89:90) Aligned. Score:  88
Sequences (89:91) Aligned. Score:  74
Sequences (89:92) Aligned. Score:  29
Sequences (89:93) Aligned. Score:  30
Sequences (89:94) Aligned. Score:  52
Sequences (89:95) Aligned. Score:  32
Sequences (89:96) Aligned. Score:  29
Sequences (89:97) Aligned. Score:  48
Sequences (89:98) Aligned. Score:  29
Sequences (89:99) Aligned. Score:  29
Sequences (89:100) Aligned. Score:  38
Sequences (89:101) Aligned. Score:  71
Sequences (89:102) Aligned. Score:  66
Sequences (90:91) Aligned. Score:  72
Sequences (90:92) Aligned. Score:  29
Sequences (90:93) Aligned. Score:  30
Sequences (90:94) Aligned. Score:  54
Sequences (90:95) Aligned. Score:  31
Sequences (90:96) Aligned. Score:  29
Sequences (90:97) Aligned. Score:  48
Sequences (90:98) Aligned. Score:  29
Sequences (90:99) Aligned. Score:  29
Sequences (90:100) Aligned. Score:  37
Sequences (90:101) Aligned. Score:  68
Sequences (90:102) Aligned. Score:  62
Sequences (91:92) Aligned. Score:  34
Sequences (91:93) Aligned. Score:  36
Sequences (91:94) Aligned. Score:  53
Sequences (91:95) Aligned. Score:  33
Sequences (91:96) Aligned. Score:  33
Sequences (91:97) Aligned. Score:  44
Sequences (91:98) Aligned. Score:  32
Sequences (91:99) Aligned. Score:  36
Sequences (91:100) Aligned. Score:  37
Sequences (91:101) Aligned. Score:  71
Sequences (91:102) Aligned. Score:  71
Sequences (92:93) Aligned. Score:  29
Sequences (92:94) Aligned. Score:  29
Sequences (92:95) Aligned. Score:  50
Sequences (92:96) Aligned. Score:  63
Sequences (92:97) Aligned. Score:  38
Sequences (92:98) Aligned. Score:  96
Sequences (92:99) Aligned. Score:  29
Sequences (92:100) Aligned. Score:  36
Sequences (92:101) Aligned. Score:  32
Sequences (92:102) Aligned. Score:  30
Sequences (93:94) Aligned. Score:  29
Sequences (93:95) Aligned. Score:  24
Sequences (93:96) Aligned. Score:  28
Sequences (93:97) Aligned. Score:  70
Sequences (93:98) Aligned. Score:  29
Sequences (93:99) Aligned. Score:  91
Sequences (93:100) Aligned. Score:  39
Sequences (93:101) Aligned. Score:  34
Sequences (93:102) Aligned. Score:  32
Sequences (94:95) Aligned. Score:  35
Sequences (94:96) Aligned. Score:  32
Sequences (94:97) Aligned. Score:  40
Sequences (94:98) Aligned. Score:  29
Sequences (94:99) Aligned. Score:  27
Sequences (94:100) Aligned. Score:  42
Sequences (94:101) Aligned. Score:  51
Sequences (94:102) Aligned. Score:  51
Sequences (95:96) Aligned. Score:  51
Sequences (95:97) Aligned. Score:  38
Sequences (95:98) Aligned. Score:  51
Sequences (95:99) Aligned. Score:  23
Sequences (95:100) Aligned. Score:  36
Sequences (95:101) Aligned. Score:  31
Sequences (95:102) Aligned. Score:  29
Sequences (96:97) Aligned. Score:  35
Sequences (96:98) Aligned. Score:  63
Sequences (96:99) Aligned. Score:  27
Sequences (96:100) Aligned. Score:  34
Sequences (96:101) Aligned. Score:  30
Sequences (96:102) Aligned. Score:  29
Sequences (97:98) Aligned. Score:  38
Sequences (97:99) Aligned. Score:  68
Sequences (97:100) Aligned. Score:  55
Sequences (97:101) Aligned. Score:  44
Sequences (97:102) Aligned. Score:  48
Sequences (98:99) Aligned. Score:  29
Sequences (98:100) Aligned. Score:  36
Sequences (98:101) Aligned. Score:  32
Sequences (98:102) Aligned. Score:  30
Sequences (99:100) Aligned. Score:  38
Sequences (99:101) Aligned. Score:  34
Sequences (99:102) Aligned. Score:  32
Sequences (100:101) Aligned. Score:  38
Sequences (100:102) Aligned. Score:  38
Sequences (101:102) Aligned. Score:  93


Guide tree file created:   [./seqalign-1234567890.1234.dnd]

Start of Multiple Alignment

Sequence:27     Score:1663
Sequence:60     Score:2788
Sequence:68     Score:2903
Sequence:92     Score:2636
Sequence:29     Score:2617
Sequence:98     Score:2663
Sequence:35     Score:2635
Sequence:66     Score:2648
Sequence:8     Score:1579
Sequence:7     Score:1584
Sequence:74     Score:1690
Sequence:18     Score:1729
Sequence:6     Score:1649
Sequence:21     Score:1370
Sequence:82     Score:1493
Sequence:64     Score:1460
Sequence:17     Score:1546
Sequence:38     Score:1437
Sequence:56     Score:1497
Sequence:58     Score:1547
Sequence:11     Score:1410
Sequence:79     Score:1476
Sequence:96     Score:1530
Sequence:16     Score:1390
Sequence:19     Score:1511
Sequence:10     Score:1216
Sequence:13     Score:1245
Sequence:71     Score:1269
Sequence:23     Score:1410
Sequence:72     Score:1449
Sequence:14     Score:1444
Sequence:52     Score:1466
Sequence:53     Score:1494
Sequence:37     Score:1132
Sequence:5     Score:1275
Sequence:50     Score:1316
Sequence:95     Score:1361
Sequence:22     Score:360
Sequence:83     Score:363
Sequence:15     Score:402
Sequence:51     Score:404
Sequence:54     Score:405
Sequence:65     Score:403
Sequence:9     Score:812
Sequence:12     Score:878
Sequence:70     Score:942
Sequence:97     Score:397
Sequence:24     Score:903
Sequence:73     Score:948
Sequence:28     Score:887
Sequence:61     Score:915
Sequence:69     Score:930
Sequence:93     Score:956
Sequence:30     Score:962
Sequence:36     Score:977
Sequence:67     Score:980
Sequence:99     Score:1001
Sequence:39     Score:942
Sequence:57     Score:973
Sequence:59     Score:1011
Sequence:100     Score:888
Sequence:31     Score:861
Sequence:91     Score:823
Sequence:55     Score:930
Sequence:81     Score:958
Sequence:89     Score:970
Sequence:87     Score:976
Sequence:86     Score:995
Sequence:90     Score:1015
Sequence:44     Score:960
Sequence:25     Score:960
Sequence:32     Score:979
Sequence:45     Score:973
Sequence:48     Score:987
Sequence:101     Score:967
Sequence:43     Score:969
Sequence:46     Score:1018
Sequence:47     Score:997
Sequence:102     Score:1018
Sequence:49     Score:1036
Sequence:42     Score:1016
Sequence:75     Score:1032
Sequence:40     Score:1041
Sequence:76     Score:1064
Sequence:41     Score:1013
Sequence:20     Score:1007
Sequence:78     Score:942
Sequence:94     Score:969
Sequence:3     Score:934
Sequence:63     Score:951
Sequence:4     Score:956
Sequence:85     Score:989
Sequence:34     Score:1002
Sequence:84     Score:1014
Sequence:26     Score:946
Sequence:33     Score:983
Sequence:80     Score:1012
Sequence:88     Score:1038
Sequence:62     Score:749
Sequence:77     Score:1070
Alignment Score 1454950

CLUSTAL-Alignment file created  [./seqalign-1234567890.1234.out]

Processing /homes/user/test/qa/domainalign-keep/daf/54894.daf

/shared/software/bin/clustalw -type=protein -profile1=./seqalign-1234567890.1234.aln -sequences -profile2=./seqalign-1234567890.1234.seqs -MATRIX=BLOSUM -GAPOPEN=10 -GAPEXT=0.5 -outfile=./seqalign-1234567890.1234.out

Processing /homes/user/test/qa/domainalign-keep/daf/55074.daf

/shared/software/bin/clustalw -type=protein -profile1=./seqalign-1234567890.1234.aln -sequences -profile2=./seqalign-1234567890.1234.seqs -MATRIX=BLOSUM -GAPOPEN=10 -GAPEXT=0.5 -outfile=./seqalign-1234567890.1234.out


Go to the output files for this example




7.0 KNOWN BUGS & WARNINGS

None.


8.0 NOTES

1. Use of CLUSTAL
clustalw must be installed on the system that is running SEQSEARCH.

2. Empty domain hits file (input)
If no sequences are given in the domain hits file then no extended alignment will be generated.

8.1 GLOSSARY OF FILE TYPES

FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
Domain hits file DHF format (FASTA-like). Database hits (sequences) with domain classification information. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a discriminating element (e.g. a protein signature, hidden Markov model, simple frequency matrix, Gribskov profile or Hennikoff profile) against a sequence database. SEQSEARCH (hits retrieved by PSIBLAST). SIGSCAN (hits retrieved by sparse protein signature). LIBSCAN (hits retrieved by various types of HMM and profile). N.A.
Domain alignment file DAF format (CLUSTAL-like format with domain classification information). Contains a sequence alignment of domains belonging to the same SCOP or CATH family. The file is annotated with domain family classification information. DOMAINALIGN (structure-based sequence alignment of domains of known structure). DOMAINALIGN alignments can be extended with sequence relatives (of unknown structure) to the family in question by using SEQALIGN.
None


9.0 DESCRIPTION

The generation of sequence alignments for large datasets such as SCOP or CATH potentially requires a lot of time for preparation of datasets, running jobs and so on, in addition to the compute time required for the alignments themselves. SEQALIGN will generate an extended alignment for each seed alignment in a directory for which a file of sequences is available, by using CLUSTALW. Sequences are added one by one to the appropriate seed alignment.


10.0 ALGORITHM

None.


11.0 RELATED APPLICATIONS

See also

Program name Description
cathparse Generate DCF file from raw CATH files
domainalign Generate alignments (DAF file) for nodes in a DCF file
domainnr Remove redundant domains from a DCF file
domainrep Reorder DCF file to identify representative structures
domainseqs Add sequence records to a DCF file
domainsse Add secondary structure records to a DCF file
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
libgen Generate discriminating elements from alignments
matcher Waterman-Eggert local alignment of two sequences
matgen3d Generate a 3D-1D scoring matrix from CCF files
oalistat Statistics for multiple alignment files
pepcoil Predict coiled coil regions in protein sequences
rocon Generate a hits file from comparing two DHF files
rocplot Perform ROC analysis on hits files
scopparse Generate DCF file from raw SCOP files
seqfraggle Remove fragment sequences from DHF files
seqmatchall All-against-all word comparison of a sequence set
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generate DHF files from keyword search of UniProt
ssematch Search a DCF file for secondary structure matches
supermatcher Calculate approximate local pair-wise alignments of larger sequences
water Smith-Waterman local alignment of sequences
wordfinder Match large sequences against one or more other sequences
wordmatch Find regions of identity (exact matches) of two sequences



12.0 DIAGNOSTIC ERROR MESSAGES

The log file might contain the following messages:

Could not open seed sequence file my.file (file read error on input sequence alignment or sequence file)
Empty alignment in my.file (input alignment was empty.)
Empty singlet sequence for my.file (singlet sequence file was empty.)
Could not open domain hits file my.file (file read error on input sequence file.)
Not enough sequences found in domain hits file (insufficient sequences (i.e. < 2) in input sequence file.)


13.0 AUTHORS

Ranjeeva Ranasinghe

Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK


14.0 REFERENCES

Please cite the authors and EMBOSS.

Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

14.1 Other useful references


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ALLVERSUSALL documentation


 


CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES



1.0 SUMMARY

Sequence similarity data from all-versus-all comparison


2.0 INPUTS & OUTPUTS

ALLVERSUSALL reads a directory of files each containing a set of 2 or more sequences, performs an all-versus-all global alignment on each set and writes a file of sequence similarity values for each input file. The output files have the same base name as the input files. The path and extension of the input and output files are specified by the user in the ACD file.


3.0 INPUT FILE FORMAT

All common sequence format are supported.


4.0 OUTPUT FILE FORMAT

The output file contains 7 columns as follows:
  • (1) Sequence number (sequential order in input file) of first sequence of a pair.
  • (2) Accesion number of first sequence of a pair.
  • (3) A ':' is always given.
  • (4) Sequence number of second sequence.
  • (5) Accesion number of second sequence.
  • (6) A ':' is always given.
  • (7) Sequence similarity value (2dp).

Output files for usage example

File: swtiny1.out

1 Q9WVI4 : 2 Q9ERL9 : 90.48
1 Q9WVI4 : 3 Q9DGG6 : 55.70
1 Q9WVI4 : 4 Q99396 : 54.74
1 Q9WVI4 : 5 Q99280 : 57.66
2 Q9ERL9 : 3 Q9DGG6 : 58.28
2 Q9ERL9 : 4 Q99396 : 56.39
2 Q9ERL9 : 5 Q99280 : 62.31
3 Q9DGG6 : 4 Q99396 : 52.26
3 Q9DGG6 : 5 Q99280 : 53.99
4 Q99396 : 5 Q99280 : 83.41

File: swtiny2.out

1 O58452 : 2 O30129 : 82.42
1 O58452 : 3 O26938 : 75.56
2 O30129 : 3 O26938 : 71.43

File: allversusall.log

//
/homes/user/test/data/structure/allversusall/swtiny1.fasta
//
/homes/user/test/data/structure/allversusall/swtiny2.fasta




5.0 DATA FILES

ALLVERSUSALL uses a residue substitution matrix.


6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Sequence similarity data from all-versus-all comparison.
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-seqinpath]         dirlist    [./] Sequence directories
  [-datoutdir]         outdir     [./] This option specifies the location of
                                  sequence similarity data files (output).
   -logfile            outfile    [allversusall.log] This option specifies the
                                  name of ALLVERSUSALL log file (output). The
                                  log file contains messages about any errors
                                  arising while ALLVERSUSALL ran.

   Additional (Optional) qualifiers:
   -matrix             matrixf    [EBLOSUM62] This option specifies the
                                  residue substitution matrix that is used for
                                  sequence comparison.
   -gapopen            float      [10.0 for any sequence] This option
                                  specifies the gap insertion penalty. The gap
                                  insertion penalty is the score taken away
                                  when a gap is created. The best value
                                  depends on the choice of comparison matrix.
                                  The default value assumes you are using the
                                  EBLOSUM62 matrix for protein sequences, and
                                  the EDNAFULL matrix for nucleotide
                                  sequences. (Floating point number from 1.0
                                  to 100.0)
   -gapextend          float      [0.5 for any sequence] This option specifies
                                  the gap extension penalty. The gap
                                  extension, penalty is added to the standard
                                  gap penalty for each base or residue in the
                                  gap. This is how long gaps are penalized.
                                  Usually you will expect a few long gaps
                                  rather than many short gaps, so the gap
                                  extension penalty should be lower than the
                                  gap penalty. An exception is where one or
                                  both sequences are single reads with
                                  possible sequencing errors in which case you
                                  would expect many single base gaps. You can
                                  get this result by setting the gap open
                                  penalty to zero (or very low) and using the
                                  gap extension penalty to control gap
                                  scoring. (Floating point number from 0.0 to
                                  10.0)

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-seqinpath" associated qualifiers
   -extension1         string     Default file extension

   "-datoutdir" associated qualifiers
   -extension2         string     Default file extension

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-seqinpath]
(Parameter 1)
dirlist Sequence directories Directory with files ./
[-datoutdir]
(Parameter 2)
outdir This option specifies the location of sequence similarity data files (output). Output directory ./
-logfile outfile This option specifies the name of ALLVERSUSALL log file (output). The log file contains messages about any errors arising while ALLVERSUSALL ran. Output file allversusall.log
Additional (Optional) qualifiers
-matrix matrixf This option specifies the residue substitution matrix that is used for sequence comparison. Comparison matrix file in EMBOSS data path EBLOSUM62
-gapopen float This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Floating point number from 1.0 to 100.0 10.0 for any sequence
-gapextend float This option specifies the gap extension penalty. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Floating point number from 0.0 to 10.0 0.5 for any sequence
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-seqinpath" associated dirlist qualifiers
-extension1
-extension_seqinpath
string Default file extension Any string fasta
"-datoutdir" associated outdir qualifiers
-extension2
-extension_datoutdir
string Default file extension Any string out
"-logfile" associated outfile qualifiers
-odirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

6.2 EXAMPLE SESSION

An example of interactive use of ALLVERSUSALL is shown below. Here is a sample session with allversusall


% allversusall 
Sequence similarity data from all-versus-all comparison.
Sequence directories [./]: allversusall/
Location of sequence similarity data files (output) [./]: 
Domainatrix log output file [allversusall.log]: 

Processing /homes/user/test/data/structure/allversusall/swtiny1.fasta
Processing /homes/user/test/data/structure/allversusall/swtiny2.fasta

Go to the output files for this example




7.0 KNOWN BUGS & WARNINGS

None.


8.0 NOTES

8.1 GLOSSARY OF FILE TYPES

FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
Domain hits file DHF format (FASTA-like). Database hits (sequences) with domain classification information. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a discriminating element (e.g. a protein signature, hidden Markov model, simple frequency matrix, Gribskov profile or Hennikoff profile) against a sequence database. SEQSEARCH (hits retrieved by PSIBLAST). SIGSCAN (hits retrieved by sparse protein signature). LIBSCAN (hits retrieved by various types of HMM and profile). N.A.



9.0 DESCRIPTION

All-versus-all sequence comparisons are commonly required. ALLVERSUSALL performs a full global pair-wise alignment for every permutation of pair of sequence in each input set of sequences. It writes a file of sequence similarity values for each input set of sequences.


10.0 ALGORITHM

Standard N&W type alignment.


11.0 RELATED APPLICATIONS

See also

Program name Description
aaindexextract Extract amino acid property data from AAINDEX
cathparse Generate DCF file from raw CATH files
cutgextract Extract codon usage tables from CUTG database
domainer Generate domain CCF files from protein CCF files
domainnr Remove redundant domains from a DCF file
domainseqs Add sequence records to a DCF file
domainsse Add secondary structure records to a DCF file
hetparse Convert heterogen group dictionary to EMBL-like format
jaspextract Extract data from JASPAR
pdbparse Parse PDB files and writes protein CCF files
pdbplus Add accessibility and secondary structure to a CCF file
pdbtosp Convert swissprot:PDB codes file to EMBL-like format
printsextract Extract data from PRINTS database for use by pscan
prosextract Process the PROSITE motif database for use by patmatmotifs
rebaseextract Process the REBASE database for use by restriction enzyme applications
scopparse Generate DCF file from raw SCOP files
seqnr Remove redundancy from DHF files
sites Generate residue-ligand CON files from CCF files
ssematch Search a DCF file for secondary structure matches
tfextract Process TRANSFAC transcription factor database for use by tfscan



12.0 DIAGNOSTIC ERROR MESSAGES

None.


13.0 AUTHORS

Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK


14.0 REFERENCES

Please cite the authors and EMBOSS. Please cite the authors and EMBOSS.

Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

14.1 Other useful references


DOMALIGN-0.1.650/emboss_doc/html/index.html0000664000175000017500000000364610455215124015066 00000000000000 DOMALIGN Applications

DOMALIGN Applications


The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

Applications in the current domalign release

Program name Description
allversusall Sequence similarity data from all-versus-all comparison
domainalign Generate alignments (DAF file) for nodes in a DCF file
domainrep Reorder DCF file to identify representative structures
seqalign Extend alignments (DAF file) with sequences (DHF file)

DOMALIGN-0.1.650/emboss_doc/html/domainrep.html0000664000175000017500000007007312171064326015736 00000000000000 EMBASSY: DOMAINREP documentation.

DOMAINREP documentation


 


CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES



1.0 SUMMARY

Reorder DCF file to identify representative structures


2.0 INPUTS & OUTPUTS

DOMAINREP reads a DCF file (domain classification file) and writes a DCF file containing the same data except that the order of domains within each user-specified node (e.g. family) in the hierarchy may be changed so that the representative structure of each node is given first. The representative structure is found by using stamp and this application must be installed on the system that is running DOMAINREP and correctly configured (see 'Notes' below). A 'domain PDB file' for each domain in the DCF file must exist in a directory specified in the stamp "pdb.directories" file (see 'Notes' below). The domain PDB file contains coordinate data for a single domain from SCOP or CATH, in PDB format. The input and output files are specified by the user.


3.0 INPUT FILE FORMAT

The format of the DCF file is described in the SCOPPARSE documentation.

Input files for usage example

File: all.scop2

ID   D1CS4A_
XX
EN   1CS4
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Adenylyl cyclase VC1, domain C1a
XX
OS   Dog (Canis familiaris)
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1FX2A_
XX
EN   1FX2
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Receptor-type monomeric adenylyl cyclase
XX
OS   Trypanosome (Trypanosoma brucei), different isoform
XX
NC   1
XX
CN   [1]
XX


  [Part of this file has been deleted for brevity]

XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   B CHAIN; 8 START; 100 END;
//
ID   D4AT1D1
XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   D CHAIN; 8 START; 100 END;
//




4.0 OUTPUT FILE FORMAT

The format of the DCF file is described in the SCOPPARSE documentation.

Output files for usage example

File: all_rep1st.scop

ID   D4AT1B1
XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   B CHAIN; 8 START; 100 END;
//
ID   D1CS4A_
XX
EN   1CS4
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Adenylyl cyclase VC1, domain C1a
XX
OS   Dog (Canis familiaris)
XX
NC   1
XX
CN   [1]
XX


  [Part of this file has been deleted for brevity]

XX
EN   1FX2
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
DO   Receptor-type monomeric adenylyl cyclase
XX
OS   Trypanosome (Trypanosoma brucei), different isoform
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D4AT1D1
XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   D CHAIN; 8 START; 100 END;
//




5.0 DATA FILES

DOMAINREP does not use any data files but does make use of the stamp "pdb.directories" file (see 'Notes').


6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Reorder DCF file to identify representative structures.
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-dcfinfile]         infile     This option specifies the name of DCF file
                                  (domain classification file) (input). A
                                  'domain classification file' contains
                                  classification and other data for domains
                                  from SCOP or CATH, in DCF format
                                  (EMBL-like). The files are generated by
                                  using SCOPPARSE and CATHPARSE. Domain
                                  sequence information can be added to the
                                  file by using DOMAINSEQS.
   -node               menu       [1] This option specifies the node fore
                                  reordering the file. Reordering can be done
                                  for any specified node in the SCOP or CATH
                                  hierarchies. For example by selecting
                                  'Class' entries belonging to the same Class
                                  will be reordered in turn. (Values: 1 (Class
                                  (SCOP)); 2 (Fold (SCOP)); 3 (Superfamily
                                  (SCOP)); 4 (Family (SCOP)); 5 (Class
                                  (CATH)); 6 (Architecture (CATH)); 7
                                  (Topology (CATH)); 8 (Homologous Superfamily
                                  (CATH)); 9 (Family (CATH)))
  [-dcfoutfile]        outfile    [test.scop] This option specifies the name
                                  of DCF file (domain classification file)
                                  (output). A 'domain classification file'
                                  contains classification and other data for
                                  domains from SCOP or CATH, in DCF format
                                  (EMBL-like). The files are generated by
                                  using SCOPPARSE and CATHPARSE. Domain
                                  sequence information can be added to the
                                  file by using DOMAINSEQS.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-dcfoutfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-dcfinfile]
(Parameter 1)
infile This option specifies the name of DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. Input file Required
-node list This option specifies the node fore reordering the file. Reordering can be done for any specified node in the SCOP or CATH hierarchies. For example by selecting 'Class' entries belonging to the same Class will be reordered in turn.
1 (Class (SCOP))
2 (Fold (SCOP))
3 (Superfamily (SCOP))
4 (Family (SCOP))
5 (Class (CATH))
6 (Architecture (CATH))
7 (Topology (CATH))
8 (Homologous Superfamily (CATH))
9 (Family (CATH))
1
[-dcfoutfile]
(Parameter 2)
outfile This option specifies the name of DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. Output file test.scop
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-dcfoutfile" associated outfile qualifiers
-odirectory2
-odirectory_dcfoutfile
string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

6.2 EXAMPLE SESSION

An example of interactive use of DOMAINREP is shown below. Here is a sample session with domainrep


% domainrep 
Reorder DCF file to identify representative structures.
Domain classification file: all.scop2
Node at which to reorder
         1 : Class (SCOP)
         2 : Fold (SCOP)
         3 : Superfamily (SCOP)
         4 : Family (SCOP)
         5 : Class (CATH)
         6 : Architecture (CATH)
         7 : Topology (CATH)
         8 : Homologous Superfamily (CATH)
         9 : Family (CATH)
Select number. [1]: 2
Domain classification output file [test.scop]: all_rep1st.scop

/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set
/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set
/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set
/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set
/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set
/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set

Go to the input files for this example
Go to the output files for this example



The following command line would achieve the same result.
 
domainrep test_data/all.scop test_data/domainrep/all_rep1st.scop -node 4



7.0 KNOWN BUGS & WARNINGS

None.


8.0 NOTES

stamp modification
DOMAINREP will only run with with a version of stamp which has been modified so that PDB id codes of length greater than 4 characters are acceptable. This involves a trivial change to the stamp module getdomain.c (around line number 155), a 4 must be changed to a 7 as follows:

temp=getfile(domain[0].id,dirfile,4,OUTPUT); 
< change to ... >
temp=getfile(domain[0].id,dirfile,7,OUTPUT); 

stamp configuration
stamp searches for pdb files with a certain prefix, extension and path as specified in the stamp "pdb.directories" file, which should look like something like this (change the text according to your system setup):

/data/pdb - -
/data/pdb _ .ent
/data/pdb _ .pdb
/data/pdb pdb .ent
/data/pdbscop _ _
/data/pdbscop _ .ent
/data/pdbscop _ .pdb
/data/pdbscop pdb .ent
./ _ _
./ _ .ent
./ _ .ent.z
./ _ .ent.gz
./ _ .pdb
./ _ .pdb.Z
./ _ .pdb.gz
./ pdb .ent
./ pdb .ent.Z
./ pdb .ent.gz
/data/CASS1/pdb/coords/ _ .pdb
/data/CASS1/pdb/coords/ _ .pdb.Z
/data/CASS1/pdb/coords/ _ .pdb.gz

None

8.1 GLOSSARY OF FILE TYPES

FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
Domain classification file (for SCOP) DCF format (EMBL-like format for domain classification data). Classification and other data for domains from SCOP. SCOPPARSE Domain sequence information can be added to the file by using DOMAINSEQS.
Domain classification file (for CATH) DCF format (EMBL-like format for domain classification data). Classification and other data for domains from CATH. CATHPARSE Domain sequence information can be added to the file by using DOMAINSEQS.
Domain PDB file PDB format for domain coordinate data. Coordinate data for a single domain from SCOP or CATH. DOMAINER N.A.



9.0 DESCRIPTION

The protein structural alignment program stamp aligns multiple structures to a seed structure. The best alignments will result when the seed is the best available representative of the entire set, i.e. in structural terms, is more similar to the other structures than any other structure.
DOMAINALIGN calls stamp to generate alignments of domains belonging to the same node (e.g. family) in a DCF file. DOMAINALIGN will produce better alignments if the DCF file is reordered so that the representative structure of each node is given first, because the first strucutres are used as the seeds. The reordering of the DCF file is done by using DOMAINREP.


10.0 ALGORITHM

More information on stamp can be found at http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/


11.0 RELATED APPLICATIONS

See also

Program name Description
cathparse Generate DCF file from raw CATH files
contacts Generate intra-chain CON files from CCF files
domainalign Generate alignments (DAF file) for nodes in a DCF file
domainnr Remove redundant domains from a DCF file
domainreso Remove low resolution domains from a DCF file
domainseqs Add sequence records to a DCF file
domainsse Add secondary structure records to a DCF file
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
interface Generate inter-chain CON files from CCF files
libgen Generate discriminating elements from alignments
matcher Waterman-Eggert local alignment of two sequences
matgen3d Generate a 3D-1D scoring matrix from CCF files
oalistat Statistics for multiple alignment files
pepcoil Predict coiled coil regions in protein sequences
psiphi Calculates phi and psi torsion angles from protein coordinates
rocon Generate a hits file from comparing two DHF files
rocplot Perform ROC analysis on hits files
scopparse Generate DCF file from raw SCOP files
seqalign Extend alignments (DAF file) with sequences (DHF file)
seqfraggle Remove fragment sequences from DHF files
seqmatchall All-against-all word comparison of a sequence set
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generate DHF files from keyword search of UniProt
ssematch Search a DCF file for secondary structure matches
supermatcher Calculate approximate local pair-wise alignments of larger sequences
water Smith-Waterman local alignment of sequences
wordfinder Match large sequences against one or more other sequences
wordmatch Find regions of identity (exact matches) of two sequences



12.0 DIAGNOSTIC ERROR MESSAGES

None.


13.0 AUTHORS

Mat Blades (Matthew.Blades@astrazeneca.com)

Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK


14.0 REFERENCES

Please cite the authors and EMBOSS.

Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

14.1 Other useful references


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" >&6; } if ${lt_cv_sys_max_cmd_len+:} false; then : $as_echo_n "(cached) " >&6 else i=0 teststring="ABCD" case $build_os in msdosdjgpp*) # On DJGPP, this test can blow up pretty badly due to problems in libc # (any single argument exceeding 2000 bytes causes a buffer overrun # during glob expansion). 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Likely further. if test -x /sbin/sysctl; then lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax` elif test -x /usr/sbin/sysctl; then lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax` else lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs fi # And add a safety zone lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` ;; interix*) # We know the value 262144 and hardcode it with a safety zone (like BSD) lt_cv_sys_max_cmd_len=196608 ;; os2*) # The test takes a long time on OS/2. lt_cv_sys_max_cmd_len=8192 ;; osf*) # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not # nice to cause kernel panics so lets avoid the loop below. # First set a reasonable default. lt_cv_sys_max_cmd_len=16384 # if test -x /sbin/sysconfig; then case `/sbin/sysconfig -q proc exec_disable_arg_limit` in *1*) lt_cv_sys_max_cmd_len=-1 ;; esac fi ;; sco3.2v5*) lt_cv_sys_max_cmd_len=102400 ;; sysv5* | sco5v6* | sysv4.2uw2*) kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null` if test -n "$kargmax"; then lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'` else lt_cv_sys_max_cmd_len=32768 fi ;; *) lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null` if test -n "$lt_cv_sys_max_cmd_len"; then lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` else # Make teststring a little bigger before we do anything with it. # a 1K string should be a reasonable start. for i in 1 2 3 4 5 6 7 8 ; do teststring=$teststring$teststring done SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}} # If test is not a shell built-in, we'll probably end up computing a # maximum length that is only half of the actual maximum length, but # we can't tell. while { test "X"`env echo "$teststring$teststring" 2>/dev/null` \ = "X$teststring$teststring"; } >/dev/null 2>&1 && test $i != 17 # 1/2 MB should be enough do i=`expr $i + 1` teststring=$teststring$teststring done # Only check the string length outside the loop. lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1` teststring= # Add a significant safety factor because C++ compilers can tack on # massive amounts of additional arguments before passing them to the # linker. It appears as though 1/2 is a usable value. lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2` fi ;; esac fi if test -n $lt_cv_sys_max_cmd_len ; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_sys_max_cmd_len" >&5 $as_echo "$lt_cv_sys_max_cmd_len" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: none" >&5 $as_echo "none" >&6; } fi max_cmd_len=$lt_cv_sys_max_cmd_len : ${CP="cp -f"} : ${MV="mv -f"} : ${RM="rm -f"} { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands some XSI constructs" >&5 $as_echo_n "checking whether the shell understands some XSI constructs... " >&6; } # Try some XSI features xsi_shell=no ( _lt_dummy="a/b/c" test "${_lt_dummy##*/},${_lt_dummy%/*},${_lt_dummy#??}"${_lt_dummy%"$_lt_dummy"}, \ = c,a/b,b/c, \ && eval 'test $(( 1 + 1 )) -eq 2 \ && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \ && xsi_shell=yes { $as_echo "$as_me:${as_lineno-$LINENO}: result: $xsi_shell" >&5 $as_echo "$xsi_shell" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands \"+=\"" >&5 $as_echo_n "checking whether the shell understands \"+=\"... " >&6; } lt_shell_append=no ( foo=bar; set foo baz; eval "$1+=\$2" && test "$foo" = barbaz ) \ >/dev/null 2>&1 \ && lt_shell_append=yes { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_shell_append" >&5 $as_echo "$lt_shell_append" >&6; } if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then lt_unset=unset else lt_unset=false fi # test EBCDIC or ASCII case `echo X|tr X '\101'` in A) # ASCII based system # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr lt_SP2NL='tr \040 \012' lt_NL2SP='tr \015\012 \040\040' ;; *) # EBCDIC based system lt_SP2NL='tr \100 \n' lt_NL2SP='tr \r\n \100\100' ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to convert $build file names to $host format" >&5 $as_echo_n "checking how to convert $build file names to $host format... " >&6; } if ${lt_cv_to_host_file_cmd+:} false; then : $as_echo_n "(cached) " >&6 else case $host in *-*-mingw* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_host_file_cmd=func_convert_file_msys_to_w32 ;; *-*-cygwin* ) lt_cv_to_host_file_cmd=func_convert_file_cygwin_to_w32 ;; * ) # otherwise, assume *nix lt_cv_to_host_file_cmd=func_convert_file_nix_to_w32 ;; esac ;; *-*-cygwin* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_host_file_cmd=func_convert_file_msys_to_cygwin ;; *-*-cygwin* ) lt_cv_to_host_file_cmd=func_convert_file_noop ;; * ) # otherwise, assume *nix lt_cv_to_host_file_cmd=func_convert_file_nix_to_cygwin ;; esac ;; * ) # unhandled hosts (and "normal" native builds) lt_cv_to_host_file_cmd=func_convert_file_noop ;; esac fi to_host_file_cmd=$lt_cv_to_host_file_cmd { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_to_host_file_cmd" >&5 $as_echo "$lt_cv_to_host_file_cmd" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to convert $build file names to toolchain format" >&5 $as_echo_n "checking how to convert $build file names to toolchain format... " >&6; } if ${lt_cv_to_tool_file_cmd+:} false; then : $as_echo_n "(cached) " >&6 else #assume ordinary cross tools, or native build. lt_cv_to_tool_file_cmd=func_convert_file_noop case $host in *-*-mingw* ) case $build in *-*-mingw* ) # actually msys lt_cv_to_tool_file_cmd=func_convert_file_msys_to_w32 ;; esac ;; esac fi to_tool_file_cmd=$lt_cv_to_tool_file_cmd { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_to_tool_file_cmd" >&5 $as_echo "$lt_cv_to_tool_file_cmd" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $LD option to reload object files" >&5 $as_echo_n "checking for $LD option to reload object files... " >&6; } if ${lt_cv_ld_reload_flag+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_ld_reload_flag='-r' fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_reload_flag" >&5 $as_echo "$lt_cv_ld_reload_flag" >&6; } reload_flag=$lt_cv_ld_reload_flag case $reload_flag in "" | " "*) ;; *) reload_flag=" $reload_flag" ;; esac reload_cmds='$LD$reload_flag -o $output$reload_objs' case $host_os in cygwin* | mingw* | pw32* | cegcc*) if test "$GCC" != yes; then reload_cmds=false fi ;; darwin*) if test "$GCC" = yes; then reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs' else reload_cmds='$LD$reload_flag -o $output$reload_objs' fi ;; esac if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}objdump", so it can be a program name with args. set dummy ${ac_tool_prefix}objdump; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_OBJDUMP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$OBJDUMP"; then ac_cv_prog_OBJDUMP="$OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OBJDUMP=$ac_cv_prog_OBJDUMP if test -n "$OBJDUMP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OBJDUMP" >&5 $as_echo "$OBJDUMP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OBJDUMP"; then ac_ct_OBJDUMP=$OBJDUMP # Extract the first word of "objdump", so it can be a program name with args. set dummy objdump; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_OBJDUMP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OBJDUMP"; then ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_OBJDUMP="objdump" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP if test -n "$ac_ct_OBJDUMP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OBJDUMP" >&5 $as_echo "$ac_ct_OBJDUMP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OBJDUMP" = x; then OBJDUMP="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OBJDUMP=$ac_ct_OBJDUMP fi else OBJDUMP="$ac_cv_prog_OBJDUMP" fi test -z "$OBJDUMP" && OBJDUMP=objdump { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to recognize dependent libraries" >&5 $as_echo_n "checking how to recognize dependent libraries... " >&6; } if ${lt_cv_deplibs_check_method+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_file_magic_cmd='$MAGIC_CMD' lt_cv_file_magic_test_file= lt_cv_deplibs_check_method='unknown' # Need to set the preceding variable on all platforms that support # interlibrary dependencies. # 'none' -- dependencies not supported. # `unknown' -- same as none, but documents that we really don't know. # 'pass_all' -- all dependencies passed with no checks. # 'test_compile' -- check by making test program. # 'file_magic [[regex]]' -- check by looking for files in library path # which responds to the $file_magic_cmd with a given extended regex. # If you have `file' or equivalent on your system and you're not sure # whether `pass_all' will *always* work, you probably want this one. case $host_os in aix[4-9]*) lt_cv_deplibs_check_method=pass_all ;; beos*) lt_cv_deplibs_check_method=pass_all ;; bsdi[45]*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)' lt_cv_file_magic_cmd='/usr/bin/file -L' lt_cv_file_magic_test_file=/shlib/libc.so ;; cygwin*) # func_win32_libid is a shell function defined in ltmain.sh lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' ;; mingw* | pw32*) # Base MSYS/MinGW do not provide the 'file' command needed by # func_win32_libid shell function, so use a weaker test based on 'objdump', # unless we find 'file', for example because we are cross-compiling. # func_win32_libid assumes BSD nm, so disallow it if using MS dumpbin. if ( test "$lt_cv_nm_interface" = "BSD nm" && file / ) >/dev/null 2>&1; then lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' else # Keep this pattern in sync with the one in func_win32_libid. lt_cv_deplibs_check_method='file_magic file format (pei*-i386(.*architecture: i386)?|pe-arm-wince|pe-x86-64)' lt_cv_file_magic_cmd='$OBJDUMP -f' fi ;; cegcc*) # use the weaker test based on 'objdump'. See mingw*. lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' lt_cv_file_magic_cmd='$OBJDUMP -f' ;; darwin* | rhapsody*) lt_cv_deplibs_check_method=pass_all ;; freebsd* | dragonfly*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then case $host_cpu in i*86 ) # Not sure whether the presence of OpenBSD here was a mistake. # Let's accept both of them until this is cleared up. lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` ;; esac else lt_cv_deplibs_check_method=pass_all fi ;; gnu*) lt_cv_deplibs_check_method=pass_all ;; haiku*) lt_cv_deplibs_check_method=pass_all ;; hpux10.20* | hpux11*) lt_cv_file_magic_cmd=/usr/bin/file case $host_cpu in ia64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64' lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so ;; hppa*64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF[ -][0-9][0-9])(-bit)?( [LM]SB)? shared object( file)?[, -]* PA-RISC [0-9]\.[0-9]' lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9]\.[0-9]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[3-9]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be glibc/ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) lt_cv_deplibs_check_method=pass_all ;; netbsd*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$' fi ;; newos6*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=/usr/lib/libnls.so ;; *nto* | *qnx*) lt_cv_deplibs_check_method=pass_all ;; openbsd*) if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' fi ;; osf3* | osf4* | osf5*) lt_cv_deplibs_check_method=pass_all ;; rdos*) lt_cv_deplibs_check_method=pass_all ;; solaris*) lt_cv_deplibs_check_method=pass_all ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) lt_cv_deplibs_check_method=pass_all ;; sysv4 | sysv4.3*) case $host_vendor in motorola) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]' lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` ;; ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_deplibs_check_method" >&5 $as_echo "$lt_cv_deplibs_check_method" >&6; } file_magic_glob= want_nocaseglob=no if test "$build" = "$host"; then case $host_os in mingw* | pw32*) if ( shopt | grep nocaseglob ) >/dev/null 2>&1; then want_nocaseglob=yes else file_magic_glob=`echo aAbBcCdDeEfFgGhHiIjJkKlLmMnNoOpPqQrRsStTuUvVwWxXyYzZ | $SED -e "s/\(..\)/s\/[\1]\/[\1]\/g;/g"` fi ;; esac fi file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dlltool", so it can be a program name with args. set dummy ${ac_tool_prefix}dlltool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_DLLTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$DLLTOOL"; then ac_cv_prog_DLLTOOL="$DLLTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_DLLTOOL="${ac_tool_prefix}dlltool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DLLTOOL=$ac_cv_prog_DLLTOOL if test -n "$DLLTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DLLTOOL" >&5 $as_echo "$DLLTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_DLLTOOL"; then ac_ct_DLLTOOL=$DLLTOOL # Extract the first word of "dlltool", so it can be a program name with args. set dummy dlltool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_DLLTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DLLTOOL"; then ac_cv_prog_ac_ct_DLLTOOL="$ac_ct_DLLTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_DLLTOOL="dlltool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DLLTOOL=$ac_cv_prog_ac_ct_DLLTOOL if test -n "$ac_ct_DLLTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DLLTOOL" >&5 $as_echo "$ac_ct_DLLTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_DLLTOOL" = x; then DLLTOOL="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DLLTOOL=$ac_ct_DLLTOOL fi else DLLTOOL="$ac_cv_prog_DLLTOOL" fi test -z "$DLLTOOL" && DLLTOOL=dlltool { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to associate runtime and link libraries" >&5 $as_echo_n "checking how to associate runtime and link libraries... " >&6; } if ${lt_cv_sharedlib_from_linklib_cmd+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_sharedlib_from_linklib_cmd='unknown' case $host_os in cygwin* | mingw* | pw32* | cegcc*) # two different shell functions defined in ltmain.sh # decide which to use based on capabilities of $DLLTOOL case `$DLLTOOL --help 2>&1` in *--identify-strict*) lt_cv_sharedlib_from_linklib_cmd=func_cygming_dll_for_implib ;; *) lt_cv_sharedlib_from_linklib_cmd=func_cygming_dll_for_implib_fallback ;; esac ;; *) # fallback: assume linklib IS sharedlib lt_cv_sharedlib_from_linklib_cmd="$ECHO" ;; esac fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_sharedlib_from_linklib_cmd" >&5 $as_echo "$lt_cv_sharedlib_from_linklib_cmd" >&6; } sharedlib_from_linklib_cmd=$lt_cv_sharedlib_from_linklib_cmd test -z "$sharedlib_from_linklib_cmd" && sharedlib_from_linklib_cmd=$ECHO if test -n "$ac_tool_prefix"; then for ac_prog in ar do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_AR+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$AR"; then ac_cv_prog_AR="$AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_AR="$ac_tool_prefix$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi AR=$ac_cv_prog_AR if test -n "$AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5 $as_echo "$AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$AR" && break done fi if test -z "$AR"; then ac_ct_AR=$AR for ac_prog in ar do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_AR+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_AR"; then ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_AR="$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_AR=$ac_cv_prog_ac_ct_AR if test -n "$ac_ct_AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_AR" >&5 $as_echo "$ac_ct_AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$ac_ct_AR" && break done if test "x$ac_ct_AR" = x; then AR="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac AR=$ac_ct_AR fi fi : ${AR=ar} : ${AR_FLAGS=cru} { $as_echo "$as_me:${as_lineno-$LINENO}: checking for archiver @FILE support" >&5 $as_echo_n "checking for archiver @FILE support... " >&6; } if ${lt_cv_ar_at_file+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_ar_at_file=no cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO"; then : echo conftest.$ac_objext > conftest.lst lt_ar_try='$AR $AR_FLAGS libconftest.a @conftest.lst >&5' { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$lt_ar_try\""; } >&5 (eval $lt_ar_try) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } if test "$ac_status" -eq 0; then # Ensure the archiver fails upon bogus file names. rm -f conftest.$ac_objext libconftest.a { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$lt_ar_try\""; } >&5 (eval $lt_ar_try) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } if test "$ac_status" -ne 0; then lt_cv_ar_at_file=@ fi fi rm -f conftest.* libconftest.a fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ar_at_file" >&5 $as_echo "$lt_cv_ar_at_file" >&6; } if test "x$lt_cv_ar_at_file" = xno; then archiver_list_spec= else archiver_list_spec=$lt_cv_ar_at_file fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_STRIP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then ac_cv_prog_STRIP="$STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5 $as_echo "$STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_STRIP+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_STRIP="strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 $as_echo "$ac_ct_STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_STRIP" = x; then STRIP=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac STRIP=$ac_ct_STRIP fi else STRIP="$ac_cv_prog_STRIP" fi test -z "$STRIP" && STRIP=: if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. set dummy ${ac_tool_prefix}ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_RANLIB+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$RANLIB"; then ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi RANLIB=$ac_cv_prog_RANLIB if test -n "$RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5 $as_echo "$RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_RANLIB"; then ac_ct_RANLIB=$RANLIB # Extract the first word of "ranlib", so it can be a program name with args. set dummy ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_RANLIB+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_RANLIB"; then ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_RANLIB="ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB if test -n "$ac_ct_RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5 $as_echo "$ac_ct_RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_RANLIB" = x; then RANLIB=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac RANLIB=$ac_ct_RANLIB fi else RANLIB="$ac_cv_prog_RANLIB" fi test -z "$RANLIB" && RANLIB=: # Determine commands to create old-style static archives. old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs' old_postinstall_cmds='chmod 644 $oldlib' old_postuninstall_cmds= if test -n "$RANLIB"; then case $host_os in openbsd*) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$tool_oldlib" ;; *) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$tool_oldlib" ;; esac old_archive_cmds="$old_archive_cmds~\$RANLIB \$tool_oldlib" fi case $host_os in darwin*) lock_old_archive_extraction=yes ;; *) lock_old_archive_extraction=no ;; esac # If no C compiler was specified, use CC. LTCC=${LTCC-"$CC"} # If no C compiler flags were specified, use CFLAGS. LTCFLAGS=${LTCFLAGS-"$CFLAGS"} # Allow CC to be a program name with arguments. compiler=$CC # Check for command to grab the raw symbol name followed by C symbol from nm. { $as_echo "$as_me:${as_lineno-$LINENO}: checking command to parse $NM output from $compiler object" >&5 $as_echo_n "checking command to parse $NM output from $compiler object... " >&6; } if ${lt_cv_sys_global_symbol_pipe+:} false; then : $as_echo_n "(cached) " >&6 else # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[BCDEGRST]' # Regexp to match symbols that can be accessed directly from C. sympat='\([_A-Za-z][_A-Za-z0-9]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[BCDT]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[ABCDGISTW]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[ABCDEGRST]' fi ;; irix* | nonstopux*) symcode='[BCDEGRST]' ;; osf*) symcode='[BCDEGQRST]' ;; solaris*) symcode='[BDRT]' ;; sco3.2v5*) symcode='[DT]' ;; sysv4.2uw2*) symcode='[DT]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[ABDT]' ;; sysv4) symcode='[DFNSTU]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[ABCDGIRSTW]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\)[ ]*$/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\)[ ]*$/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK '"\ " {last_section=section; section=\$ 3};"\ " /^COFF SYMBOL TABLE/{for(i in hide) delete hide[i]};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi lt_cv_sys_global_symbol_pipe="$lt_cv_sys_global_symbol_pipe | sed '/ __gnu_lto/d'" # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then # Now try to grab the symbols. nlist=conftest.nm if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$NM conftest.$ac_objext \| "$lt_cv_sys_global_symbol_pipe" \> $nlist\""; } >&5 (eval $NM conftest.$ac_objext \| "$lt_cv_sys_global_symbol_pipe" \> $nlist) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext /* Keep this code in sync between libtool.m4, ltmain, lt_system.h, and tests. */ #if defined(_WIN32) || defined(__CYGWIN__) || defined(_WIN32_WCE) /* DATA imports from DLLs on WIN32 con't be const, because runtime relocations are performed -- see ld's documentation on pseudo-relocs. */ # define LT_DLSYM_CONST #elif defined(__osf__) /* This system does not cope well with relocations in const data. */ # define LT_DLSYM_CONST #else # define LT_DLSYM_CONST const #endif #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ LT_DLSYM_CONST struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_globsym_save_LIBS=$LIBS lt_globsym_save_CFLAGS=$CFLAGS LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag" if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5 (eval $ac_link) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS=$lt_globsym_save_LIBS CFLAGS=$lt_globsym_save_CFLAGS else echo "cannot find nm_test_func in $nlist" >&5 fi else echo "cannot find nm_test_var in $nlist" >&5 fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5 fi else echo "$progname: failed program was:" >&5 cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done fi if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: failed" >&5 $as_echo "failed" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: ok" >&5 $as_echo "ok" >&6; } fi # Response file support. if test "$lt_cv_nm_interface" = "MS dumpbin"; then nm_file_list_spec='@' elif $NM --help 2>/dev/null | grep '[@]FILE' >/dev/null; then nm_file_list_spec='@' fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for sysroot" >&5 $as_echo_n "checking for sysroot... " >&6; } # Check whether --with-sysroot was given. if test "${with_sysroot+set}" = set; then : withval=$with_sysroot; else with_sysroot=no fi lt_sysroot= case ${with_sysroot} in #( yes) if test "$GCC" = yes; then lt_sysroot=`$CC --print-sysroot 2>/dev/null` fi ;; #( /*) lt_sysroot=`echo "$with_sysroot" | sed -e "$sed_quote_subst"` ;; #( no|'') ;; #( *) { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${with_sysroot}" >&5 $as_echo "${with_sysroot}" >&6; } as_fn_error $? "The sysroot must be an absolute path." "$LINENO" 5 ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${lt_sysroot:-no}" >&5 $as_echo "${lt_sysroot:-no}" >&6; } # Check whether --enable-libtool-lock was given. if test "${enable_libtool_lock+set}" = set; then : enableval=$enable_libtool_lock; fi test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes # Some flags need to be propagated to the compiler or linker for good # libtool support. case $host in ia64-*-hpux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.$ac_objext` in *ELF-32*) HPUX_IA64_MODE="32" ;; *ELF-64*) HPUX_IA64_MODE="64" ;; esac fi rm -rf conftest* ;; *-*-irix6*) # Find out which ABI we are using. echo '#line '$LINENO' "configure"' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then if test "$lt_cv_prog_gnu_ld" = yes; then case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -melf32bsmip" ;; *N32*) LD="${LD-ld} -melf32bmipn32" ;; *64-bit*) LD="${LD-ld} -melf64bmip" ;; esac else case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -32" ;; *N32*) LD="${LD-ld} -n32" ;; *64-bit*) LD="${LD-ld} -64" ;; esac fi fi rm -rf conftest* ;; x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \ s390*-*linux*|s390*-*tpf*|sparc*-*linux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *32-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_i386_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_i386" ;; ppc64-*linux*|powerpc64-*linux*) LD="${LD-ld} -m elf32ppclinux" ;; s390x-*linux*) LD="${LD-ld} -m elf_s390" ;; sparc64-*linux*) LD="${LD-ld} -m elf32_sparc" ;; esac ;; *64-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_x86_64_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_x86_64" ;; ppc*-*linux*|powerpc*-*linux*) LD="${LD-ld} -m elf64ppc" ;; s390*-*linux*|s390*-*tpf*) LD="${LD-ld} -m elf64_s390" ;; sparc*-*linux*) LD="${LD-ld} -m elf64_sparc" ;; esac ;; esac fi rm -rf conftest* ;; *-*-sco3.2v5*) # On SCO OpenServer 5, we need -belf to get full-featured binaries. SAVE_CFLAGS="$CFLAGS" CFLAGS="$CFLAGS -belf" { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler needs -belf" >&5 $as_echo_n "checking whether the C compiler needs -belf... " >&6; } if ${lt_cv_cc_needs_belf+:} false; then : $as_echo_n "(cached) " >&6 else ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_cv_cc_needs_belf=yes else lt_cv_cc_needs_belf=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_cc_needs_belf" >&5 $as_echo "$lt_cv_cc_needs_belf" >&6; } if test x"$lt_cv_cc_needs_belf" != x"yes"; then # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf CFLAGS="$SAVE_CFLAGS" fi ;; *-*solaris*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *64-bit*) case $lt_cv_prog_gnu_ld in yes*) case $host in i?86-*-solaris*) LD="${LD-ld} -m elf_x86_64" ;; sparc*-*-solaris*) LD="${LD-ld} -m elf64_sparc" ;; esac # GNU ld 2.21 introduced _sol2 emulations. Use them if available. if ${LD-ld} -V | grep _sol2 >/dev/null 2>&1; then LD="${LD-ld}_sol2" fi ;; *) if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then LD="${LD-ld} -64" fi ;; esac ;; esac fi rm -rf conftest* ;; esac need_locks="$enable_libtool_lock" if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}mt", so it can be a program name with args. set dummy ${ac_tool_prefix}mt; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_MANIFEST_TOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$MANIFEST_TOOL"; then ac_cv_prog_MANIFEST_TOOL="$MANIFEST_TOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_MANIFEST_TOOL="${ac_tool_prefix}mt" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi MANIFEST_TOOL=$ac_cv_prog_MANIFEST_TOOL if test -n "$MANIFEST_TOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MANIFEST_TOOL" >&5 $as_echo "$MANIFEST_TOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_MANIFEST_TOOL"; then ac_ct_MANIFEST_TOOL=$MANIFEST_TOOL # Extract the first word of "mt", so it can be a program name with args. set dummy mt; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_MANIFEST_TOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_MANIFEST_TOOL"; then ac_cv_prog_ac_ct_MANIFEST_TOOL="$ac_ct_MANIFEST_TOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_MANIFEST_TOOL="mt" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_MANIFEST_TOOL=$ac_cv_prog_ac_ct_MANIFEST_TOOL if test -n "$ac_ct_MANIFEST_TOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_MANIFEST_TOOL" >&5 $as_echo "$ac_ct_MANIFEST_TOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_MANIFEST_TOOL" = x; then MANIFEST_TOOL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac MANIFEST_TOOL=$ac_ct_MANIFEST_TOOL fi else MANIFEST_TOOL="$ac_cv_prog_MANIFEST_TOOL" fi test -z "$MANIFEST_TOOL" && MANIFEST_TOOL=mt { $as_echo "$as_me:${as_lineno-$LINENO}: checking if $MANIFEST_TOOL is a manifest tool" >&5 $as_echo_n "checking if $MANIFEST_TOOL is a manifest tool... " >&6; } if ${lt_cv_path_mainfest_tool+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_path_mainfest_tool=no echo "$as_me:$LINENO: $MANIFEST_TOOL '-?'" >&5 $MANIFEST_TOOL '-?' 2>conftest.err > conftest.out cat conftest.err >&5 if $GREP 'Manifest Tool' conftest.out > /dev/null; then lt_cv_path_mainfest_tool=yes fi rm -f conftest* fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_path_mainfest_tool" >&5 $as_echo "$lt_cv_path_mainfest_tool" >&6; } if test "x$lt_cv_path_mainfest_tool" != xyes; then MANIFEST_TOOL=: fi case $host_os in rhapsody* | darwin*) if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args. set dummy ${ac_tool_prefix}dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_DSYMUTIL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$DSYMUTIL"; then ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DSYMUTIL=$ac_cv_prog_DSYMUTIL if test -n "$DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DSYMUTIL" >&5 $as_echo "$DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_DSYMUTIL"; then ac_ct_DSYMUTIL=$DSYMUTIL # Extract the first word of "dsymutil", so it can be a program name with args. set dummy dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_DSYMUTIL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DSYMUTIL"; then ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_DSYMUTIL="dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL if test -n "$ac_ct_DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DSYMUTIL" >&5 $as_echo "$ac_ct_DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_DSYMUTIL" = x; then DSYMUTIL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DSYMUTIL=$ac_ct_DSYMUTIL fi else DSYMUTIL="$ac_cv_prog_DSYMUTIL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args. set dummy ${ac_tool_prefix}nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_NMEDIT+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$NMEDIT"; then ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi NMEDIT=$ac_cv_prog_NMEDIT if test -n "$NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $NMEDIT" >&5 $as_echo "$NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_NMEDIT"; then ac_ct_NMEDIT=$NMEDIT # Extract the first word of "nmedit", so it can be a program name with args. set dummy nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_NMEDIT+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_NMEDIT"; then ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_NMEDIT="nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT if test -n "$ac_ct_NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_NMEDIT" >&5 $as_echo "$ac_ct_NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_NMEDIT" = x; then NMEDIT=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac NMEDIT=$ac_ct_NMEDIT fi else NMEDIT="$ac_cv_prog_NMEDIT" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args. set dummy ${ac_tool_prefix}lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_LIPO+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$LIPO"; then ac_cv_prog_LIPO="$LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_LIPO="${ac_tool_prefix}lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi LIPO=$ac_cv_prog_LIPO if test -n "$LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LIPO" >&5 $as_echo "$LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_LIPO"; then ac_ct_LIPO=$LIPO # Extract the first word of "lipo", so it can be a program name with args. set dummy lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_LIPO+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_LIPO"; then ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_LIPO="lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO if test -n "$ac_ct_LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_LIPO" >&5 $as_echo "$ac_ct_LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_LIPO" = x; then LIPO=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac LIPO=$ac_ct_LIPO fi else LIPO="$ac_cv_prog_LIPO" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args. set dummy ${ac_tool_prefix}otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_OTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$OTOOL"; then ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_OTOOL="${ac_tool_prefix}otool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL=$ac_cv_prog_OTOOL if test -n "$OTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL" >&5 $as_echo "$OTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL"; then ac_ct_OTOOL=$OTOOL # Extract the first word of "otool", so it can be a program name with args. set dummy otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_OTOOL+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL"; then ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_OTOOL="otool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL if test -n "$ac_ct_OTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL" >&5 $as_echo "$ac_ct_OTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL" = x; then OTOOL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL=$ac_ct_OTOOL fi else OTOOL="$ac_cv_prog_OTOOL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args. set dummy ${ac_tool_prefix}otool64; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_OTOOL64+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$OTOOL64"; then ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL64=$ac_cv_prog_OTOOL64 if test -n "$OTOOL64"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL64" >&5 $as_echo "$OTOOL64" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL64"; then ac_ct_OTOOL64=$OTOOL64 # Extract the first word of "otool64", so it can be a program name with args. set dummy otool64; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_prog_ac_ct_OTOOL64+:} false; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL64"; then ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_OTOOL64="otool64" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64 if test -n "$ac_ct_OTOOL64"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL64" >&5 $as_echo "$ac_ct_OTOOL64" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL64" = x; then OTOOL64=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL64=$ac_ct_OTOOL64 fi else OTOOL64="$ac_cv_prog_OTOOL64" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -single_module linker flag" >&5 $as_echo_n "checking for -single_module linker flag... " >&6; } if ${lt_cv_apple_cc_single_mod+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_apple_cc_single_mod=no if test -z "${LT_MULTI_MODULE}"; then # By default we will add the -single_module flag. You can override # by either setting the environment variable LT_MULTI_MODULE # non-empty at configure time, or by adding -multi_module to the # link flags. rm -rf libconftest.dylib* echo "int foo(void){return 1;}" > conftest.c echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c" >&5 $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err _lt_result=$? # If there is a non-empty error log, and "single_module" # appears in it, assume the flag caused a linker warning if test -s conftest.err && $GREP single_module conftest.err; then cat conftest.err >&5 # Otherwise, if the output was created with a 0 exit code from # the compiler, it worked. elif test -f libconftest.dylib && test $_lt_result -eq 0; then lt_cv_apple_cc_single_mod=yes else cat conftest.err >&5 fi rm -rf libconftest.dylib* rm -f conftest.* fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_apple_cc_single_mod" >&5 $as_echo "$lt_cv_apple_cc_single_mod" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -exported_symbols_list linker flag" >&5 $as_echo_n "checking for -exported_symbols_list linker flag... " >&6; } if ${lt_cv_ld_exported_symbols_list+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_ld_exported_symbols_list=no save_LDFLAGS=$LDFLAGS echo "_main" > conftest.sym LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_cv_ld_exported_symbols_list=yes else lt_cv_ld_exported_symbols_list=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS="$save_LDFLAGS" fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_exported_symbols_list" >&5 $as_echo "$lt_cv_ld_exported_symbols_list" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -force_load linker flag" >&5 $as_echo_n "checking for -force_load linker flag... " >&6; } if ${lt_cv_ld_force_load+:} false; then : $as_echo_n "(cached) " >&6 else lt_cv_ld_force_load=no cat > conftest.c << _LT_EOF int forced_loaded() { return 2;} _LT_EOF echo "$LTCC $LTCFLAGS -c -o conftest.o conftest.c" >&5 $LTCC $LTCFLAGS -c -o conftest.o conftest.c 2>&5 echo "$AR cru libconftest.a conftest.o" >&5 $AR cru libconftest.a conftest.o 2>&5 echo "$RANLIB libconftest.a" >&5 $RANLIB libconftest.a 2>&5 cat > conftest.c << _LT_EOF int main() { return 0;} _LT_EOF echo "$LTCC $LTCFLAGS $LDFLAGS -o conftest conftest.c -Wl,-force_load,./libconftest.a" >&5 $LTCC $LTCFLAGS $LDFLAGS -o conftest conftest.c -Wl,-force_load,./libconftest.a 2>conftest.err _lt_result=$? if test -s conftest.err && $GREP force_load conftest.err; then cat conftest.err >&5 elif test -f conftest && test $_lt_result -eq 0 && $GREP forced_load conftest >/dev/null 2>&1 ; then lt_cv_ld_force_load=yes else cat conftest.err >&5 fi rm -f conftest.err libconftest.a conftest conftest.c rm -rf conftest.dSYM fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_force_load" >&5 $as_echo "$lt_cv_ld_force_load" >&6; } case $host_os in rhapsody* | darwin1.[012]) _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;; darwin1.*) _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; darwin*) # darwin 5.x on # if running on 10.5 or later, the deployment target defaults # to the OS version, if on x86, and 10.4, the deployment # target defaults to 10.4. Don't you love it? case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in 10.0,*86*-darwin8*|10.0,*-darwin[91]*) _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; 10.[012]*) _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; 10.*) _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; esac ;; esac if test "$lt_cv_apple_cc_single_mod" = "yes"; then _lt_dar_single_mod='$single_module' fi if test "$lt_cv_ld_exported_symbols_list" = "yes"; then _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym' else _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}' fi if test "$DSYMUTIL" != ":" && test "$lt_cv_ld_force_load" = "no"; then _lt_dsymutil='~$DSYMUTIL $lib || :' else _lt_dsymutil= fi ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5 $as_echo_n "checking for ANSI C header files... " >&6; } if ${ac_cv_header_stdc+:} false; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include #include #include int main () { ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO"; then : ac_cv_header_stdc=yes else ac_cv_header_stdc=no fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext if test $ac_cv_header_stdc = yes; then # SunOS 4.x string.h does not declare mem*, contrary to ANSI. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | $EGREP "memchr" >/dev/null 2>&1; then : else ac_cv_header_stdc=no fi rm -f conftest* fi if test $ac_cv_header_stdc = yes; then # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | $EGREP "free" >/dev/null 2>&1; then : else ac_cv_header_stdc=no fi rm -f conftest* fi if test $ac_cv_header_stdc = yes; then # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. if test "$cross_compiling" = yes; then : : else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include #if ((' ' & 0x0FF) == 0x020) # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) #else # define ISLOWER(c) \ (('a' <= (c) && (c) <= 'i') \ || ('j' <= (c) && (c) <= 'r') \ || ('s' <= (c) && (c) <= 'z')) # define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) #endif #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main () { int i; for (i = 0; i < 256; i++) if (XOR (islower (i), ISLOWER (i)) || toupper (i) != TOUPPER (i)) return 2; return 0; } _ACEOF if ac_fn_c_try_run "$LINENO"; then : else ac_cv_header_stdc=no fi rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ conftest.$ac_objext conftest.beam conftest.$ac_ext fi fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 $as_echo "$ac_cv_header_stdc" >&6; } if test $ac_cv_header_stdc = yes; then $as_echo "#define STDC_HEADERS 1" >>confdefs.h fi # On IRIX 5.3, sys/types and inttypes.h are conflicting. for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ inttypes.h stdint.h unistd.h do : as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default " if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi done for ac_header in dlfcn.h do : ac_fn_c_check_header_compile "$LINENO" "dlfcn.h" "ac_cv_header_dlfcn_h" "$ac_includes_default " if test "x$ac_cv_header_dlfcn_h" = xyes; then : cat >>confdefs.h <<_ACEOF #define HAVE_DLFCN_H 1 _ACEOF fi done func_stripname_cnf () { case ${2} in .*) func_stripname_result=`$ECHO "${3}" | $SED "s%^${1}%%; s%\\\\${2}\$%%"`;; *) func_stripname_result=`$ECHO "${3}" | $SED "s%^${1}%%; s%${2}\$%%"`;; esac } # func_stripname_cnf # Set options enable_dlopen=no enable_win32_dll=no # Check whether --enable-shared was given. if test "${enable_shared+set}" = set; then : enableval=$enable_shared; p=${PACKAGE-default} case $enableval in yes) enable_shared=yes ;; no) enable_shared=no ;; *) enable_shared=no # Look at the argument we got. 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We use all the common list separators. lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," for lt_pkg in $withval; do IFS="$lt_save_ifs" if test "X$lt_pkg" = "X$lt_p"; then pic_mode=yes fi done IFS="$lt_save_ifs" ;; esac else pic_mode=default fi test -z "$pic_mode" && pic_mode=default # Check whether --enable-fast-install was given. if test "${enable_fast_install+set}" = set; then : enableval=$enable_fast_install; p=${PACKAGE-default} case $enableval in yes) enable_fast_install=yes ;; no) enable_fast_install=no ;; *) enable_fast_install=no # Look at the argument we got. We use all the common list separators. lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," for pkg in $enableval; do IFS="$lt_save_ifs" if test "X$pkg" = "X$p"; then enable_fast_install=yes fi done IFS="$lt_save_ifs" ;; esac else enable_fast_install=yes fi # This can be used to rebuild libtool when needed LIBTOOL_DEPS="$ltmain" # Always use our own libtool. LIBTOOL='$(SHELL) $(top_builddir)/libtool' test -z "$LN_S" && LN_S="ln -s" if test -n "${ZSH_VERSION+set}" ; then setopt NO_GLOB_SUBST fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for objdir" >&5 $as_echo_n "checking for objdir... " >&6; } if ${lt_cv_objdir+:} false; then : $as_echo_n "(cached) " >&6 else rm -f .libs 2>/dev/null mkdir .libs 2>/dev/null if test -d .libs; then lt_cv_objdir=.libs else # MS-DOS does not allow filenames that begin with a dot. lt_cv_objdir=_libs fi rmdir .libs 2>/dev/null fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_objdir" >&5 $as_echo "$lt_cv_objdir" >&6; } objdir=$lt_cv_objdir cat >>confdefs.h <<_ACEOF #define LT_OBJDIR "$lt_cv_objdir/" _ACEOF case $host_os in aix3*) # AIX sometimes has problems with the GCC collect2 program. 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The following line is correct: shared_flag='-G' else if test "$aix_use_runtimelinking" = yes; then shared_flag='${wl}-G' else shared_flag='${wl}-bM:SRE' fi fi fi export_dynamic_flag_spec='${wl}-bexpall' # It seems that -bexpall does not export symbols beginning with # underscore (_), so it is better to generate a list of symbols to export. always_export_symbols=yes if test "$aix_use_runtimelinking" = yes; then # Warning - without using the other runtime loading flags (-brtl), # -berok will link without error, but may produce a broken library. allow_undefined_flag='-berok' # Determine the default libpath from the value encoded in an # empty executable. if test "${lt_cv_aix_libpath+set}" = set; then aix_libpath=$lt_cv_aix_libpath else if ${lt_cv_aix_libpath_+:} false; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_aix_libpath_sed=' /Import File Strings/,/^$/ { /^0/ { s/^0 *\([^ ]*\) *$/\1/ p } }' lt_cv_aix_libpath_=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` # Check for a 64-bit object if we didn't find anything. if test -z "$lt_cv_aix_libpath_"; then lt_cv_aix_libpath_=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$lt_cv_aix_libpath_"; then lt_cv_aix_libpath_="/usr/lib:/lib" fi fi aix_libpath=$lt_cv_aix_libpath_ fi hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then func_echo_all "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib' allow_undefined_flag="-z nodefs" archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an # empty executable. if test "${lt_cv_aix_libpath+set}" = set; then aix_libpath=$lt_cv_aix_libpath else if ${lt_cv_aix_libpath_+:} false; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_aix_libpath_sed=' /Import File Strings/,/^$/ { /^0/ { s/^0 *\([^ ]*\) *$/\1/ p } }' lt_cv_aix_libpath_=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` # Check for a 64-bit object if we didn't find anything. if test -z "$lt_cv_aix_libpath_"; then lt_cv_aix_libpath_=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$lt_cv_aix_libpath_"; then lt_cv_aix_libpath_="/usr/lib:/lib" fi fi aix_libpath=$lt_cv_aix_libpath_ fi hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" # Warning - without using the other run time loading flags, # -berok will link without error, but may produce a broken library. no_undefined_flag=' ${wl}-bernotok' allow_undefined_flag=' ${wl}-berok' if test "$with_gnu_ld" = yes; then # We only use this code for GNU lds that support --whole-archive. whole_archive_flag_spec='${wl}--whole-archive$convenience ${wl}--no-whole-archive' else # Exported symbols can be pulled into shared objects from archives whole_archive_flag_spec='$convenience' fi archive_cmds_need_lc=yes # This is similar to how AIX traditionally builds its shared libraries. archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='' ;; m68k) archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes ;; esac ;; bsdi[45]*) export_dynamic_flag_spec=-rdynamic ;; cygwin* | mingw* | pw32* | cegcc*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. case $cc_basename in cl*) # Native MSVC hardcode_libdir_flag_spec=' ' allow_undefined_flag=unsupported always_export_symbols=yes file_list_spec='@' # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds='$CC -o $output_objdir/$soname $libobjs $compiler_flags $deplibs -Wl,-dll~linknames=' archive_expsym_cmds='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then sed -n -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' -e '1\\\!p' < $export_symbols > $output_objdir/$soname.exp; else sed -e 's/\\\\\\\(.*\\\\\\\)/-link\\\ -EXPORT:\\\\\\\1/' < $export_symbols > $output_objdir/$soname.exp; fi~ $CC -o $tool_output_objdir$soname $libobjs $compiler_flags $deplibs "@$tool_output_objdir$soname.exp" -Wl,-DLL,-IMPLIB:"$tool_output_objdir$libname.dll.lib"~ linknames=' # The linker will not automatically build a static lib if we build a DLL. # _LT_TAGVAR(old_archive_from_new_cmds, )='true' enable_shared_with_static_runtimes=yes exclude_expsyms='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*' export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1,DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols' # Don't use ranlib old_postinstall_cmds='chmod 644 $oldlib' postlink_cmds='lt_outputfile="@OUTPUT@"~ lt_tool_outputfile="@TOOL_OUTPUT@"~ case $lt_outputfile in *.exe|*.EXE) ;; *) lt_outputfile="$lt_outputfile.exe" lt_tool_outputfile="$lt_tool_outputfile.exe" ;; esac~ if test "$MANIFEST_TOOL" != ":" && test -f "$lt_outputfile.manifest"; then $MANIFEST_TOOL -manifest "$lt_tool_outputfile.manifest" -outputresource:"$lt_tool_outputfile" || exit 1; $RM "$lt_outputfile.manifest"; fi' ;; *) # Assume MSVC wrapper hardcode_libdir_flag_spec=' ' allow_undefined_flag=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds='$CC -o $lib $libobjs $compiler_flags `func_echo_all "$deplibs" | $SED '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. old_archive_from_new_cmds='true' # FIXME: Should let the user specify the lib program. old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs' enable_shared_with_static_runtimes=yes ;; esac ;; darwin* | rhapsody*) archive_cmds_need_lc=no hardcode_direct=no hardcode_automatic=yes hardcode_shlibpath_var=unsupported if test "$lt_cv_ld_force_load" = "yes"; then whole_archive_flag_spec='`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience ${wl}-force_load,$conv\"; done; func_echo_all \"$new_convenience\"`' else whole_archive_flag_spec='' fi link_all_deplibs=yes allow_undefined_flag="$_lt_dar_allow_undefined" case $cc_basename in ifort*) _lt_dar_can_shared=yes ;; *) _lt_dar_can_shared=$GCC ;; esac if test "$_lt_dar_can_shared" = "yes"; then output_verbose_link_cmd=func_echo_all archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}" module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}" archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}" module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}" else ld_shlibs=no fi ;; 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*) archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' ;; esac fi else ld_shlibs=no fi ;; os2*) hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes allow_undefined_flag=unsupported archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~echo DATA >> $output_objdir/$libname.def~echo " SINGLE NONSHARED" >> $output_objdir/$libname.def~echo EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: ;; osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $pic_flag $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && func_echo_all "${wl}-set_version ${wl}$verstring"` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && func_echo_all "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "-set_version $verstring"` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' # Both c and cxx compiler support -rpath directly hardcode_libdir_flag_spec='-rpath $libdir' fi archive_cmds_need_lc='no' hardcode_libdir_separator=: ;; solaris*) no_undefined_flag=' -z defs' if test "$GCC" = yes; then wlarc='${wl}' archive_cmds='$CC -shared $pic_flag ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -shared $pic_flag ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' else case `$CC -V 2>&1` in *"Compilers 5.0"*) wlarc='' archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp' ;; *) wlarc='${wl}' archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' ;; esac fi hardcode_libdir_flag_spec='-R$libdir' hardcode_shlibpath_var=no case $host_os in solaris2.[0-5] | solaris2.[0-5].*) ;; *) # The compiler driver will combine and reorder linker options, # but understands `-z linker_flag'. GCC discards it without `$wl', # but is careful enough not to reorder. # Supported since Solaris 2.6 (maybe 2.5.1?) if test "$GCC" = yes; then whole_archive_flag_spec='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract' else whole_archive_flag_spec='-z allextract$convenience -z defaultextract' fi ;; esac link_all_deplibs=yes ;; sunos4*) if test "x$host_vendor" = xsequent; then # Use $CC to link under sequent, because it throws in some extra .o # files that make .init and .fini sections work. archive_cmds='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags' fi hardcode_libdir_flag_spec='-L$libdir' hardcode_direct=yes hardcode_minus_L=yes hardcode_shlibpath_var=no ;; sysv4) case $host_vendor in sni) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes # is this really true??? ;; siemens) ## LD is ld it makes a PLAMLIB ## CC just makes a GrossModule. archive_cmds='$LD -G -o $lib $libobjs $deplibs $linker_flags' reload_cmds='$CC -r -o $output$reload_objs' hardcode_direct=no ;; motorola) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=no #Motorola manual says yes, but my tests say they lie ;; esac runpath_var='LD_RUN_PATH' hardcode_shlibpath_var=no ;; sysv4.3*) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var=no export_dynamic_flag_spec='-Bexport' ;; sysv4*MP*) if test -d /usr/nec; then archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var=no runpath_var=LD_RUN_PATH hardcode_runpath_var=yes ld_shlibs=yes fi ;; sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*) no_undefined_flag='${wl}-z,text' archive_cmds_need_lc=no hardcode_shlibpath_var=no runpath_var='LD_RUN_PATH' if test "$GCC" = yes; then archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' fi ;; sysv5* | sco3.2v5* | sco5v6*) # Note: We can NOT use -z defs as we might desire, because we do not # link with -lc, and that would cause any symbols used from libc to # always be unresolved, which means just about no library would # ever link correctly. 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The import file would start with # the line `#! .'. This would cause the generated library to # depend on `.', always an invalid library. This was fixed in # development snapshots of GCC prior to 3.0. case $host_os in aix4 | aix4.[01] | aix4.[01].*) if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)' echo ' yes ' echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then : else can_build_shared=no fi ;; esac # AIX (on Power*) has no versioning support, so currently we can not hardcode correct # soname into executable. Probably we can add versioning support to # collect2, so additional links can be useful in future. if test "$aix_use_runtimelinking" = yes; then # If using run time linking (on AIX 4.2 or later) use lib.so # instead of lib.a to let people know that these are not # typical AIX shared libraries. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' else # We preserve .a as extension for shared libraries through AIX4.2 # and later when we are not doing run time linking. library_names_spec='${libname}${release}.a $libname.a' soname_spec='${libname}${release}${shared_ext}$major' fi shlibpath_var=LIBPATH fi ;; amigaos*) case $host_cpu in powerpc) # Since July 2007 AmigaOS4 officially supports .so libraries. # When compiling the executable, add -use-dynld -Lsobjs: to the compileline. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' ;; m68k) library_names_spec='$libname.ixlibrary $libname.a' # Create ${libname}_ixlibrary.a entries in /sys/libs. finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`func_echo_all "$lib" | $SED '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done' ;; esac ;; beos*) library_names_spec='${libname}${shared_ext}' dynamic_linker="$host_os ld.so" shlibpath_var=LIBRARY_PATH ;; bsdi[45]*) version_type=linux # correct to gnu/linux during the next big refactor need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib" sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib" # the default ld.so.conf also contains /usr/contrib/lib and # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow # libtool to hard-code these into programs ;; 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" >&6; } ac_xsave_LIBS=$LIBS; LIBS="$LIBS -R$x_libraries" ac_xsave_c_werror_flag=$ac_c_werror_flag ac_c_werror_flag=yes cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } X_LIBS="$X_LIBS -R$x_libraries" else LIBS="$ac_xsave_LIBS -R $x_libraries" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } X_LIBS="$X_LIBS -R $x_libraries" else { $as_echo "$as_me:${as_lineno-$LINENO}: result: neither works" >&5 $as_echo "neither works" >&6; } fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext ac_c_werror_flag=$ac_xsave_c_werror_flag LIBS=$ac_xsave_LIBS fi # Check for system-dependent libraries X programs must link with. # Do this before checking for the system-independent R6 libraries # (-lICE), since we may need -lsocket or whatever for X linking. if test "$ISC" = yes; then X_EXTRA_LIBS="$X_EXTRA_LIBS -lnsl_s -linet" else # Martyn Johnson says this is needed for Ultrix, if the X # libraries were built with DECnet support. And Karl Berry says # the Alpha needs dnet_stub (dnet does not exist). ac_xsave_LIBS="$LIBS"; LIBS="$LIBS $X_LIBS -lX11" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char XOpenDisplay (); int main () { return XOpenDisplay (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dnet_ntoa in -ldnet" >&5 $as_echo_n "checking for dnet_ntoa in -ldnet... " >&6; } if ${ac_cv_lib_dnet_dnet_ntoa+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldnet $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dnet_ntoa (); int main () { return dnet_ntoa (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dnet_dnet_ntoa=yes else ac_cv_lib_dnet_dnet_ntoa=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dnet_dnet_ntoa" >&5 $as_echo "$ac_cv_lib_dnet_dnet_ntoa" >&6; } if test "x$ac_cv_lib_dnet_dnet_ntoa" = xyes; then : X_EXTRA_LIBS="$X_EXTRA_LIBS -ldnet" fi if test $ac_cv_lib_dnet_dnet_ntoa = no; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dnet_ntoa in -ldnet_stub" >&5 $as_echo_n "checking for dnet_ntoa in -ldnet_stub... " >&6; } if ${ac_cv_lib_dnet_stub_dnet_ntoa+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldnet_stub $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dnet_ntoa (); int main () { return dnet_ntoa (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dnet_stub_dnet_ntoa=yes else ac_cv_lib_dnet_stub_dnet_ntoa=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dnet_stub_dnet_ntoa" >&5 $as_echo "$ac_cv_lib_dnet_stub_dnet_ntoa" >&6; } if test "x$ac_cv_lib_dnet_stub_dnet_ntoa" = xyes; then : X_EXTRA_LIBS="$X_EXTRA_LIBS -ldnet_stub" fi fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS="$ac_xsave_LIBS" # msh@cis.ufl.edu says -lnsl (and -lsocket) are needed for his 386/AT, # to get the SysV transport functions. # Chad R. Larson says the Pyramis MIS-ES running DC/OSx (SVR4) # needs -lnsl. # The nsl library prevents programs from opening the X display # on Irix 5.2, according to T.E. Dickey. # The functions gethostbyname, getservbyname, and inet_addr are # in -lbsd on LynxOS 3.0.1/i386, according to Lars Hecking. ac_fn_c_check_func "$LINENO" "gethostbyname" "ac_cv_func_gethostbyname" if test "x$ac_cv_func_gethostbyname" = xyes; then : fi if test $ac_cv_func_gethostbyname = no; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for gethostbyname in -lnsl" >&5 $as_echo_n "checking for gethostbyname in -lnsl... " >&6; } if ${ac_cv_lib_nsl_gethostbyname+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lnsl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char gethostbyname (); int main () { return gethostbyname (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_nsl_gethostbyname=yes else ac_cv_lib_nsl_gethostbyname=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_nsl_gethostbyname" >&5 $as_echo "$ac_cv_lib_nsl_gethostbyname" >&6; } if test "x$ac_cv_lib_nsl_gethostbyname" = xyes; then : X_EXTRA_LIBS="$X_EXTRA_LIBS -lnsl" fi if test $ac_cv_lib_nsl_gethostbyname = no; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for gethostbyname in -lbsd" >&5 $as_echo_n "checking for gethostbyname in -lbsd... " >&6; } if ${ac_cv_lib_bsd_gethostbyname+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lbsd $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char gethostbyname (); int main () { return gethostbyname (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_bsd_gethostbyname=yes else ac_cv_lib_bsd_gethostbyname=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_bsd_gethostbyname" >&5 $as_echo "$ac_cv_lib_bsd_gethostbyname" >&6; } if test "x$ac_cv_lib_bsd_gethostbyname" = xyes; then : X_EXTRA_LIBS="$X_EXTRA_LIBS -lbsd" fi fi fi # lieder@skyler.mavd.honeywell.com says without -lsocket, # socket/setsockopt and other routines are undefined under SCO ODT # 2.0. But -lsocket is broken on IRIX 5.2 (and is not necessary # on later versions), says Simon Leinen: it contains gethostby* # variants that don't use the name server (or something). -lsocket # must be given before -lnsl if both are needed. We assume that # if connect needs -lnsl, so does gethostbyname. ac_fn_c_check_func "$LINENO" "connect" "ac_cv_func_connect" if test "x$ac_cv_func_connect" = xyes; then : fi if test $ac_cv_func_connect = no; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for connect in -lsocket" >&5 $as_echo_n "checking for connect in -lsocket... " >&6; } if ${ac_cv_lib_socket_connect+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lsocket $X_EXTRA_LIBS $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char connect (); int main () { return connect (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_socket_connect=yes else ac_cv_lib_socket_connect=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_socket_connect" >&5 $as_echo "$ac_cv_lib_socket_connect" >&6; } if test "x$ac_cv_lib_socket_connect" = xyes; then : X_EXTRA_LIBS="-lsocket $X_EXTRA_LIBS" fi fi # Guillermo Gomez says -lposix is necessary on A/UX. ac_fn_c_check_func "$LINENO" "remove" "ac_cv_func_remove" if test "x$ac_cv_func_remove" = xyes; then : fi if test $ac_cv_func_remove = no; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for remove in -lposix" >&5 $as_echo_n "checking for remove in -lposix... " >&6; } if ${ac_cv_lib_posix_remove+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lposix $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char remove (); int main () { return remove (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_posix_remove=yes else ac_cv_lib_posix_remove=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_posix_remove" >&5 $as_echo "$ac_cv_lib_posix_remove" >&6; } if test "x$ac_cv_lib_posix_remove" = xyes; then : X_EXTRA_LIBS="$X_EXTRA_LIBS -lposix" fi fi # BSDI BSD/OS 2.1 needs -lipc for XOpenDisplay. ac_fn_c_check_func "$LINENO" "shmat" "ac_cv_func_shmat" if test "x$ac_cv_func_shmat" = xyes; then : fi if test $ac_cv_func_shmat = no; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for shmat in -lipc" >&5 $as_echo_n "checking for shmat in -lipc... " >&6; } if ${ac_cv_lib_ipc_shmat+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lipc $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char shmat (); int main () { return shmat (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_ipc_shmat=yes else ac_cv_lib_ipc_shmat=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_ipc_shmat" >&5 $as_echo "$ac_cv_lib_ipc_shmat" >&6; } if test "x$ac_cv_lib_ipc_shmat" = xyes; then : X_EXTRA_LIBS="$X_EXTRA_LIBS -lipc" fi fi fi # Check for libraries that X11R6 Xt/Xaw programs need. ac_save_LDFLAGS=$LDFLAGS test -n "$x_libraries" && LDFLAGS="$LDFLAGS -L$x_libraries" # SM needs ICE to (dynamically) link under SunOS 4.x (so we have to # check for ICE first), but we must link in the order -lSM -lICE or # we get undefined symbols. So assume we have SM if we have ICE. # These have to be linked with before -lX11, unlike the other # libraries we check for below, so use a different variable. # John Interrante, Karl Berry { $as_echo "$as_me:${as_lineno-$LINENO}: checking for IceConnectionNumber in -lICE" >&5 $as_echo_n "checking for IceConnectionNumber in -lICE... " >&6; } if ${ac_cv_lib_ICE_IceConnectionNumber+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lICE $X_EXTRA_LIBS $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char IceConnectionNumber (); int main () { return IceConnectionNumber (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_ICE_IceConnectionNumber=yes else ac_cv_lib_ICE_IceConnectionNumber=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_ICE_IceConnectionNumber" >&5 $as_echo "$ac_cv_lib_ICE_IceConnectionNumber" >&6; } if test "x$ac_cv_lib_ICE_IceConnectionNumber" = xyes; then : X_PRE_LIBS="$X_PRE_LIBS -lSM -lICE" fi LDFLAGS=$ac_save_LDFLAGS fi ac_header_dirent=no for ac_hdr in dirent.h sys/ndir.h sys/dir.h ndir.h; do as_ac_Header=`$as_echo "ac_cv_header_dirent_$ac_hdr" | $as_tr_sh` { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_hdr that defines DIR" >&5 $as_echo_n "checking for $ac_hdr that defines DIR... " >&6; } if eval \${$as_ac_Header+:} false; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include <$ac_hdr> int main () { if ((DIR *) 0) return 0; ; return 0; } _ACEOF if ac_fn_c_try_compile "$LINENO"; then : eval "$as_ac_Header=yes" else eval "$as_ac_Header=no" fi rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi eval ac_res=\$$as_ac_Header { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 $as_echo "$ac_res" >&6; } if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_hdr" | $as_tr_cpp` 1 _ACEOF ac_header_dirent=$ac_hdr; break fi done # Two versions of opendir et al. are in -ldir and -lx on SCO Xenix. if test $ac_header_dirent = dirent.h; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing opendir" >&5 $as_echo_n "checking for library containing opendir... " >&6; } if ${ac_cv_search_opendir+:} false; then : $as_echo_n "(cached) " >&6 else ac_func_search_save_LIBS=$LIBS cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char opendir (); int main () { return opendir (); ; return 0; } _ACEOF for ac_lib in '' dir; do if test -z "$ac_lib"; then ac_res="none required" else ac_res=-l$ac_lib LIBS="-l$ac_lib $ac_func_search_save_LIBS" fi if ac_fn_c_try_link "$LINENO"; then : ac_cv_search_opendir=$ac_res fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext if ${ac_cv_search_opendir+:} false; then : break fi done if ${ac_cv_search_opendir+:} false; then : else ac_cv_search_opendir=no fi rm conftest.$ac_ext LIBS=$ac_func_search_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_opendir" >&5 $as_echo "$ac_cv_search_opendir" >&6; } ac_res=$ac_cv_search_opendir if test "$ac_res" != no; then : test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" fi else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing opendir" >&5 $as_echo_n "checking for library containing opendir... 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Test for this by using a static variable whose address is put into a register that is clobbered by the vfork. */ static void #ifdef __cplusplus sparc_address_test (int arg) # else sparc_address_test (arg) int arg; #endif { static pid_t child; if (!child) { child = vfork (); if (child < 0) { perror ("vfork"); _exit(2); } if (!child) { arg = getpid(); write(-1, "", 0); _exit (arg); } } } int main () { pid_t parent = getpid (); pid_t child; sparc_address_test (0); child = vfork (); if (child == 0) { /* Here is another test for sparc vfork register problems. This test uses lots of local variables, at least as many local variables as main has allocated so far including compiler temporaries. 4 locals are enough for gcc 1.40.3 on a Solaris 4.1.3 sparc, but we use 8 to be safe. A buggy compiler should reuse the register of parent for one of the local variables, since it will think that parent can't possibly be used any more in this routine. 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(This shouldn't happen.) */ || status /* Did the vfork/compiler bug occur? */ || parent != getpid() /* Did the file descriptor bug occur? */ || fstat(fileno(stdout), &st) != 0 ); } } _ACEOF if ac_fn_c_try_run "$LINENO"; then : ac_cv_func_vfork_works=yes else ac_cv_func_vfork_works=no fi rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ conftest.$ac_objext conftest.beam conftest.$ac_ext fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_vfork_works" >&5 $as_echo "$ac_cv_func_vfork_works" >&6; } fi; if test "x$ac_cv_func_fork_works" = xcross; then ac_cv_func_vfork_works=$ac_cv_func_vfork { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: result $ac_cv_func_vfork_works guessed because of cross compilation" >&5 $as_echo "$as_me: WARNING: result $ac_cv_func_vfork_works guessed because of cross compilation" >&2;} fi if test "x$ac_cv_func_vfork_works" = xyes; then $as_echo "#define HAVE_WORKING_VFORK 1" >>confdefs.h else $as_echo "#define vfork fork" >>confdefs.h fi if test "x$ac_cv_func_fork_works" = xyes; then $as_echo "#define HAVE_WORKING_FORK 1" >>confdefs.h fi for ac_func in vprintf do : ac_fn_c_check_func "$LINENO" "vprintf" "ac_cv_func_vprintf" if test "x$ac_cv_func_vprintf" = xyes; then : cat >>confdefs.h <<_ACEOF #define HAVE_VPRINTF 1 _ACEOF ac_fn_c_check_func "$LINENO" "_doprnt" "ac_cv_func__doprnt" if test "x$ac_cv_func__doprnt" = xyes; then : $as_echo "#define HAVE_DOPRNT 1" >>confdefs.h fi fi done for ac_func in strdup strstr strchr erand48 memmove do : as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var" if eval test \"x\$"$as_ac_var"\" = x"yes"; then : cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 _ACEOF fi done if test "x${with_x}" != "xno"; then : CFLAGS="$CFLAGS $X_CFLAGS" case $host_os in irix*) XLIB="-lX11 $X_EXTRA_LIBS" ;; *) XLIB="$X_LIBS -lX11 $X_EXTRA_LIBS" ;; esac ac_fn_c_check_header_mongrel "$LINENO" "X11/Xlib.h" "ac_cv_header_X11_Xlib_h" "$ac_includes_default" if test "x$ac_cv_header_X11_Xlib_h" = xyes; then : $as_echo "#define PLD_xwin 1" >>confdefs.h else echo "" echo "X11 graphics have been selected but no X11 header files" echo "have been found." echo "" echo "This error usually happens on Linux/MacOSX distributions" echo "where the optional X11 development files have not been installed." echo "On Linux RPM systems this package is usually called something" echo "like xorg-x11-proto-devel whereas on Debian/Ubuntu it may" echo "be called x-dev. On MacOSX installation DVDs the X11 files" echo "can usually be found as an explicitly named optional" echo "installation." echo "" echo "After installing the X11 development files you should do a" echo "'make clean' and perform the configure stage again." echo "" echo "Alternatively, to install EMBOSS without X11 support, you can add" echo "the --without-x switch to the configure command." echo "" exit $? fi fi # Library checks. { $as_echo "$as_me:${as_lineno-$LINENO}: checking for socket in -lc" >&5 $as_echo_n "checking for socket in -lc... " >&6; } if ${ac_cv_lib_c_socket+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lc $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char socket (); int main () { return socket (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_c_socket=yes else ac_cv_lib_c_socket=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_c_socket" >&5 $as_echo "$ac_cv_lib_c_socket" >&6; } if test "x$ac_cv_lib_c_socket" = xyes; then : LIBS="${LIBS}" else LIBS="${LIBS} -lsocket" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lm" >&5 $as_echo_n "checking for main in -lm... " >&6; } if ${ac_cv_lib_m_main+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lm $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { return main (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_m_main=yes else ac_cv_lib_m_main=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_main" >&5 $as_echo "$ac_cv_lib_m_main" >&6; } if test "x$ac_cv_lib_m_main" = xyes; then : cat >>confdefs.h <<_ACEOF #define HAVE_LIBM 1 _ACEOF LIBS="-lm $LIBS" fi # GD for FreeBSD requires libiconv case ${host_os} in #( freebsd*) : if test "x${with_pngdriver}" != "xno"; then : { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -liconv" >&5 $as_echo_n "checking for main in -liconv... " >&6; } if ${ac_cv_lib_iconv_main+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-liconv $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { return main (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_iconv_main=yes else ac_cv_lib_iconv_main=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_iconv_main" >&5 $as_echo "$ac_cv_lib_iconv_main" >&6; } if test "x$ac_cv_lib_iconv_main" = xyes; then : LIBS="${LIBS}" else LIBS="-liconv ${LIBS}" fi fi ;; #( *) : ;; esac if false; then AMPNG_TRUE= AMPNG_FALSE='#' else AMPNG_TRUE='#' AMPNG_FALSE= fi if false; then AMPDF_TRUE= AMPDF_FALSE='#' else AMPDF_TRUE='#' AMPDF_FALSE= fi # # Handle general setup e.g. documentation directory # { $as_echo "$as_me:${as_lineno-$LINENO}: checking if docroot is given" >&5 $as_echo_n "checking if docroot is given... 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" >&6; } # Check whether --with-gccprofile was given. if test "${with_gccprofile+set}" = set; then : withval=$with_gccprofile; if test "$withval" != no ; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } CFLAGS="$CFLAGS -g -pg" LDFLAGS="$LDFLAGS -pg" fi else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi JAVA_CFLAGS="" JAVA_CPPFLAGS="" JAVA_LDFLAGS="" have_java="yes" auth_java="" { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Java JNI" >&5 $as_echo_n "checking for Java JNI... 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" >&6; } # Check whether --with-javaos was given. if test "${with_javaos+set}" = set; then : withval=$with_javaos; { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${withval}" >&5 $as_echo "${withval}" >&6; } if test "x${withval}" != "xno"; then : # If specified, the Java JNI OS include directory has to exist. if test "x${have_java}" = "xyes" && test -d ${withval}; then : as_fn_append JAVA_CPPFLAGS " -I${withval}" else have_java="no" as_fn_error $? "Java OS include directory ${withval} does not exist" "$LINENO" 5 fi fi else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi # Authorisation type { $as_echo "$as_me:${as_lineno-$LINENO}: checking for authorisation type" >&5 $as_echo_n "checking for authorisation type... " >&6; } # Check whether --with-auth was given. if test "${with_auth+set}" = set; then : withval=$with_auth; if test "x${withval}" != "xno"; then : { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } case ${withval} in #( yes) : auth_java="PAM" { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lpam" >&5 $as_echo_n "checking for main in -lpam... " >&6; } if ${ac_cv_lib_pam_main+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lpam $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { return main (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_pam_main=yes else ac_cv_lib_pam_main=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_pam_main" >&5 $as_echo "$ac_cv_lib_pam_main" >&6; } if test "x$ac_cv_lib_pam_main" = xyes; then : as_fn_append JAVA_LDFLAGS " -lpam" fi ;; #( pam) : auth_java="PAM" { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lpam" >&5 $as_echo_n "checking for main in -lpam... " >&6; } if ${ac_cv_lib_pam_main+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lpam $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { return main (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_pam_main=yes else ac_cv_lib_pam_main=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_pam_main" >&5 $as_echo "$ac_cv_lib_pam_main" >&6; } if test "x$ac_cv_lib_pam_main" = xyes; then : as_fn_append JAVA_LDFLAGS " -lpam" fi ;; #( shadow) : auth_java="N_SHADOW" { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lcrypy" >&5 $as_echo_n "checking for main in -lcrypy... " >&6; } if ${ac_cv_lib_crypy_main+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lcrypy $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { return main (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_crypy_main=yes else ac_cv_lib_crypy_main=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_crypy_main" >&5 $as_echo "$ac_cv_lib_crypy_main" >&6; } if test "x$ac_cv_lib_crypy_main" = xyes; then : as_fn_append JAVA_LDFLAGS " -lcrypt" fi ;; #( rshadow) : auth_java="R_SHADOW" { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lcrypy" >&5 $as_echo_n "checking for main in -lcrypy... " >&6; } if ${ac_cv_lib_crypy_main+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lcrypy $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { return main (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_crypy_main=yes else ac_cv_lib_crypy_main=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_crypy_main" >&5 $as_echo "$ac_cv_lib_crypy_main" >&6; } if test "x$ac_cv_lib_crypy_main" = xyes; then : as_fn_append JAVA_LDFLAGS " -lcrypt" fi ;; #( noshadow) : auth_java="NO_SHADOW" ;; #( rnoshadow) : auth_java="RNO_SHADOW" ;; #( aixshadow) : auth_java="AIX_SHADOW" ;; #( hpuxshadow) : auth_java="HPUX_SHADOW" ;; #( *) : ;; esac else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test -n "${auth_java}"; then : as_fn_append JAVA_CPPFLAGS " -D${auth_java}" else as_fn_append JAVA_CPPFLAGS " -DNO_AUTH" fi # Threading type { $as_echo "$as_me:${as_lineno-$LINENO}: checking for threading type" >&5 $as_echo_n "checking for threading type... 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" >&6; } if ${ac_cv_path_ANT+:} false; then : $as_echo_n "(cached) " >&6 else case $ANT in [\\/]* | ?:[\\/]*) ac_cv_path_ANT="$ANT" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ANT="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS test -z "$ac_cv_path_ANT" && ac_cv_path_ANT="no" ;; esac fi ANT=$ac_cv_path_ANT if test -n "$ANT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ANT" >&5 $as_echo "$ANT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x${ANT}" = "xno"; then : have_java="no" fi # Extract the first word of "jar", so it can be a program name with args. set dummy jar; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_path_JAR+:} false; then : $as_echo_n "(cached) " >&6 else case $JAR in [\\/]* | ?:[\\/]*) ac_cv_path_JAR="$JAR" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_JAR="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS test -z "$ac_cv_path_JAR" && ac_cv_path_JAR="no" ;; esac fi JAR=$ac_cv_path_JAR if test -n "$JAR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $JAR" >&5 $as_echo "$JAR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x${JAR}" = "xno"; then : have_java="no" fi # Extract the first word of "java", so it can be a program name with args. set dummy java; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_path_JAVA+:} false; then : $as_echo_n "(cached) " >&6 else case $JAVA in [\\/]* | ?:[\\/]*) ac_cv_path_JAVA="$JAVA" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_JAVA="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS test -z "$ac_cv_path_JAVA" && ac_cv_path_JAVA="no" ;; esac fi JAVA=$ac_cv_path_JAVA if test -n "$JAVA"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $JAVA" >&5 $as_echo "$JAVA" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x${JAVA}" = "xno"; then : have_java="no" fi # Extract the first word of "javac", so it can be a program name with args. set dummy javac; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_path_JAVAC+:} false; then : $as_echo_n "(cached) " >&6 else case $JAVAC in [\\/]* | ?:[\\/]*) ac_cv_path_JAVAC="$JAVAC" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_JAVAC="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS test -z "$ac_cv_path_JAVAC" && ac_cv_path_JAVAC="no" ;; esac fi JAVAC=$ac_cv_path_JAVAC if test -n "$JAVAC"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $JAVAC" >&5 $as_echo "$JAVAC" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x${JAVAC}" = "xno"; then : have_java="no" fi fi if test "x${have_java}" = "xyes"; then : $as_echo "#define HAVE_JAVA 1" >>confdefs.h ### FIXME: Append -DDEBIAN for the moment. # Debian uses PAM service "ssh" instead of "login", see ajjava.c # This could use AC_DEFINE() if no better option was avialable. # Ultimately, this should be configurable via server configuration # files. if test -f "/etc/debian_release" || test -f /etc/debian_version; then : as_fn_append JAVA_CPPFLAGS " -DDEBIAN" fi fi if test "x${have_java}" = "xyes"; then JAVA_BUILD_TRUE= JAVA_BUILD_FALSE='#' else JAVA_BUILD_TRUE='#' JAVA_BUILD_FALSE= fi # # Handle user hints # { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to look for pdf support" >&5 $as_echo_n "checking whether to look for pdf support... 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" >&6; } if ${ac_cv_lib_hpdf_HPDF_New+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lhpdf -L${ALT_HOME}/lib $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char HPDF_New (); int main () { return HPDF_New (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_hpdf_HPDF_New=yes else ac_cv_lib_hpdf_HPDF_New=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_hpdf_HPDF_New" >&5 $as_echo "$ac_cv_lib_hpdf_HPDF_New" >&6; } if test "x$ac_cv_lib_hpdf_HPDF_New" = xyes; then : CHECK=1 else CHECK=0 fi # # # If everything found okay then proceed to include png driver in config. # if test $CHECK = "1" ; then LIBS="$LIBS -lhpdf" case $host_os in solaris*) LDFLAGS="$LDFLAGS -R$ALT_HOME/lib" ;; esac $as_echo "#define PLD_pdf 1" >>confdefs.h if true; then AMPDF_TRUE= AMPDF_FALSE='#' else AMPDF_TRUE='#' AMPDF_FALSE= fi echo PDF support found if test $ALT_HOME = "/usr" ; then LDFLAGS="$ALT_LDFLAGS" CPPFLAGS="$ALT_CPPFLAGS" fi else # # If not okay then reset FLAGS. # if false; then AMPDF_TRUE= AMPDF_FALSE='#' else AMPDF_TRUE='#' AMPDF_FALSE= fi LDFLAGS="$ALT_LDFLAGS" CPPFLAGS="$ALT_CPPFLAGS" echo "No pdf support (libhpdf) found." fi else if test $withval != "no"; then echo "Directory $ALT_HOME does not exist" exit 0 fi fi # # Handle user hints # { $as_echo "$as_me:${as_lineno-$LINENO}: checking if png driver is wanted" >&5 $as_echo_n "checking if png driver is wanted... " >&6; } # Check whether --with-pngdriver was given. if test "${with_pngdriver+set}" = set; then : withval=$with_pngdriver; if test "$withval" != no ; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } ALT_HOME="$withval" else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi else { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } ALT_HOME=/usr fi # # Locate png/gd/zlib, if wanted # if test -d "${ALT_HOME}" then # # Keep a copy if it fails # ALT_LDFLAGS="$LDFLAGS" ALT_CPPFLAGS="$CPPFLAGS" # # Set # LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib" CPPFLAGS="$CPPFLAGS -I$ALT_HOME/include" ICCHECK=0 case $host_os in solaris*) { $as_echo "$as_me:${as_lineno-$LINENO}: checking for libiconv_close in -liconv" >&5 $as_echo_n "checking for libiconv_close in -liconv... " >&6; } if ${ac_cv_lib_iconv_libiconv_close+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-liconv -L${ALT_HOME}/lib -liconv $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char libiconv_close (); int main () { return libiconv_close (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_iconv_libiconv_close=yes else ac_cv_lib_iconv_libiconv_close=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_iconv_libiconv_close" >&5 $as_echo "$ac_cv_lib_iconv_libiconv_close" >&6; } if test "x$ac_cv_lib_iconv_libiconv_close" = xyes; then : ICCHECK=1 else ICCHECK=0 fi if test $ICCHECK = "1" ; then LDFLAGS="${LDFLAGS} -L${ALT_HOME}/lib -liconv" fi LDFLAGS="$LDFLAGS -R$ALT_HOME/lib" ;; esac # # Check for zlib in ALT_HOME # { $as_echo "$as_me:${as_lineno-$LINENO}: checking for inflateEnd in -lz" >&5 $as_echo_n "checking for inflateEnd in -lz... " >&6; } if ${ac_cv_lib_z_inflateEnd+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lz -L${ALT_HOME}/lib -lz $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char inflateEnd (); int main () { return inflateEnd (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_z_inflateEnd=yes else ac_cv_lib_z_inflateEnd=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_z_inflateEnd" >&5 $as_echo "$ac_cv_lib_z_inflateEnd" >&6; } if test "x$ac_cv_lib_z_inflateEnd" = xyes; then : CHECK=1 else CHECK=0 fi # # # Check for png # if test $CHECK = "1" ; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for png_destroy_read_struct in -lpng" >&5 $as_echo_n "checking for png_destroy_read_struct in -lpng... " >&6; } if ${ac_cv_lib_png_png_destroy_read_struct+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lpng -L${ALT_HOME}/lib -lz $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char png_destroy_read_struct (); int main () { return png_destroy_read_struct (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_png_png_destroy_read_struct=yes else ac_cv_lib_png_png_destroy_read_struct=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_png_png_destroy_read_struct" >&5 $as_echo "$ac_cv_lib_png_png_destroy_read_struct" >&6; } if test "x$ac_cv_lib_png_png_destroy_read_struct" = xyes; then : CHECK=1 else CHECK=0 fi fi # # Check for gd # if test $CHECK = "1"; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for gdImageCreateFromPng in -lgd" >&5 $as_echo_n "checking for gdImageCreateFromPng in -lgd... " >&6; } if ${ac_cv_lib_gd_gdImageCreateFromPng+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lgd -L${ALT_HOME}/lib -lgd -lpng -lz -lm $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char gdImageCreateFromPng (); int main () { return gdImageCreateFromPng (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_gd_gdImageCreateFromPng=yes else ac_cv_lib_gd_gdImageCreateFromPng=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_gd_gdImageCreateFromPng" >&5 $as_echo "$ac_cv_lib_gd_gdImageCreateFromPng" >&6; } if test "x$ac_cv_lib_gd_gdImageCreateFromPng" = xyes; then : CHECK=1 else CHECK=0 fi if test $CHECK = "0"; then echo need to upgrade gd for png driver for plplot fi fi # # If everything found okay then proceed to include png driver in config. # if test $CHECK = "1" ; then LIBS="$LIBS -lgd -lpng -lz -lm" if test $ICCHECK = "1" ; then LIBS="$LIBS -liconv" fi case $host_os in solaris*) LDFLAGS="$LDFLAGS -R$ALT_HOME/lib" ;; esac $as_echo "#define PLD_png 1" >>confdefs.h if true; then AMPNG_TRUE= AMPNG_FALSE='#' else AMPNG_TRUE='#' AMPNG_FALSE= fi echo PNG libraries found if test $ALT_HOME = "/usr" ; then LDFLAGS="$ALT_LDFLAGS" CPPFLAGS="$ALT_CPPFLAGS" fi else # # If not okay then reset FLAGS. # if false; then AMPNG_TRUE= AMPNG_FALSE='#' else AMPNG_TRUE='#' AMPNG_FALSE= fi LDFLAGS="$ALT_LDFLAGS" CPPFLAGS="$ALT_CPPFLAGS" echo No png driver will be made due to librarys missing/old. fi # echo PNG STUFF FOLLOWS!!! # echo CHECK = $CHECK # echo LIBS = $LIBS # echo LDFLAGS = $LDFLAGS # echo CPPFLAGS = $CPPFLAGS else if test $withval != "no"; then echo "Directory $ALT_HOME does not exist" exit 0 fi fi MYSQL_CFLAGS="" MYSQL_CPPFLAGS="" MYSQL_LDFLAGS="" MYSQL_CONFIG="" MYSQL_VERSION="" # Check whether --with-mysql was given. if test "${with_mysql+set}" = set; then : withval=$with_mysql; if test "x${withval}" = "xno"; then : want_mysql="no" elif test "x${withval}" = "xyes"; then : want_mysql="yes" else want_mysql="yes" MYSQL_CONFIG="${withval}" fi else want_mysql="yes" fi if test "x${want_mysql}" = "xyes"; then : if test -z "${MYSQL_CONFIG}" -o test; then : # Extract the first word of "mysql_config", so it can be a program name with args. set dummy mysql_config; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if ${ac_cv_path_MYSQL_CONFIG+:} false; then : $as_echo_n "(cached) " >&6 else case $MYSQL_CONFIG in [\\/]* | ?:[\\/]*) ac_cv_path_MYSQL_CONFIG="$MYSQL_CONFIG" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_MYSQL_CONFIG="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS test -z "$ac_cv_path_MYSQL_CONFIG" && ac_cv_path_MYSQL_CONFIG="no" ;; esac fi MYSQL_CONFIG=$ac_cv_path_MYSQL_CONFIG if test -n "$MYSQL_CONFIG"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MYSQL_CONFIG" >&5 $as_echo "$MYSQL_CONFIG" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test "x${MYSQL_CONFIG}" != "xno"; then : { $as_echo "$as_me:${as_lineno-$LINENO}: checking for MySQL libraries" >&5 $as_echo_n "checking for MySQL libraries... " >&6; } MYSQL_CFLAGS="`${MYSQL_CONFIG} --cflags`" MYSQL_CPPFLAGS="`${MYSQL_CONFIG} --include`" MYSQL_LDFLAGS="`${MYSQL_CONFIG} --libs`" MYSQL_VERSION=`${MYSQL_CONFIG} --version` EMBCPPFLAGS="${CPPFLAGS}" EMBLDFLAGS="${LDFLAGS}" CPPFLAGS="${MYSQL_CPPFLAGS} ${EMBCPPFLAGS}" LDFLAGS="${MYSQL_LDFLAGS} ${EMBLDFLAGS}" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include "mysql.h" int main () { mysql_info(NULL) ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : havemysql="yes" else havemysql="no" fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext CPPFLAGS="${EMBCPPFLAGS}" LDFLAGS="${EMBLDFLAGS}" if test "x${havemysql}" = "xyes"; then : $as_echo "#define HAVE_MYSQL 1" >>confdefs.h found_mysql="yes" { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } else MYSQL_CFLAGS="" MYSQL_CPPFLAGS="" MYSQL_LDFLAGS="" found_mysql="no" { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi else found_mysql="no" fi fi mysql_version_req= if test "x${found_mysql}" = "xyes" -a -n "${mysql_version_req}"; then : { $as_echo "$as_me:${as_lineno-$LINENO}: checking if MySQL version is >= ${mysql_version_req}" >&5 $as_echo_n "checking if MySQL version is >= ${mysql_version_req}... 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