DOMAINATRIX-0.1.650/0002775000175000017500000000000012171070632010446 500000000000000DOMAINATRIX-0.1.650/config.sub0000755000175000017500000010532712171070614012355 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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-qnx*) case $basic_machine in x86-* | i*86-*) ;; *) os=-nto$os ;; esac ;; -nto-qnx*) ;; -nto*) os=`echo $os | sed -e 's|nto|nto-qnx|'` ;; -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \ | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \ | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*) ;; -mac*) os=`echo $os | sed -e 's|mac|macos|'` ;; -linux-dietlibc) os=-linux-dietlibc ;; -linux*) os=`echo $os | sed -e 's|linux|linux-gnu|'` ;; -sunos5*) os=`echo $os | sed -e 's|sunos5|solaris2|'` ;; -sunos6*) os=`echo $os | sed -e 's|sunos6|solaris3|'` ;; -opened*) os=-openedition ;; -os400*) os=-os400 ;; -wince*) os=-wince ;; -osfrose*) os=-osfrose ;; -osf*) os=-osf ;; -utek*) os=-bsd ;; -dynix*) os=-bsd ;; -acis*) os=-aos ;; -atheos*) os=-atheos ;; -syllable*) os=-syllable ;; -386bsd) os=-bsd ;; -ctix* | -uts*) os=-sysv ;; -nova*) os=-rtmk-nova ;; -ns2 ) os=-nextstep2 ;; -nsk*) os=-nsk ;; # Preserve the version number of sinix5. -sinix5.*) os=`echo $os | sed -e 's|sinix|sysv|'` ;; -sinix*) os=-sysv4 ;; -tpf*) os=-tpf ;; -triton*) os=-sysv3 ;; -oss*) os=-sysv3 ;; -svr4) os=-sysv4 ;; -svr3) os=-sysv3 ;; -sysvr4) os=-sysv4 ;; # This must come after -sysvr4. -sysv*) ;; -ose*) os=-ose ;; -es1800*) os=-ose ;; -xenix) os=-xenix ;; -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*) os=-mint ;; -aros*) os=-aros ;; -kaos*) os=-kaos ;; -zvmoe) os=-zvmoe ;; -dicos*) os=-dicos ;; -nacl*) ;; -none) ;; *) # Get rid of the `-' at the beginning of $os. os=`echo $os | sed 's/[^-]*-//'` echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2 exit 1 ;; esac else # Here we handle the default operating systems that come with various machines. # The value should be what the vendor currently ships out the door with their # machine or put another way, the most popular os provided with the machine. # Note that if you're going to try to match "-MANUFACTURER" here (say, # "-sun"), then you have to tell the case statement up towards the top # that MANUFACTURER isn't an operating system. Otherwise, code above # will signal an error saying that MANUFACTURER isn't an operating # system, and we'll never get to this point. case $basic_machine in score-*) os=-elf ;; spu-*) os=-elf ;; *-acorn) os=-riscix1.2 ;; arm*-rebel) os=-linux ;; arm*-semi) os=-aout ;; c4x-* | tic4x-*) os=-coff ;; hexagon-*) os=-elf ;; tic54x-*) os=-coff ;; tic55x-*) os=-coff ;; tic6x-*) os=-coff ;; # This must come before the *-dec entry. pdp10-*) os=-tops20 ;; pdp11-*) os=-none ;; *-dec | vax-*) os=-ultrix4.2 ;; m68*-apollo) os=-domain ;; i386-sun) os=-sunos4.0.2 ;; m68000-sun) os=-sunos3 ;; m68*-cisco) os=-aout ;; mep-*) os=-elf ;; mips*-cisco) os=-elf ;; mips*-*) os=-elf ;; or32-*) os=-coff ;; *-tti) # must be before sparc entry or we get the wrong os. os=-sysv3 ;; sparc-* | *-sun) os=-sunos4.1.1 ;; *-be) os=-beos ;; *-haiku) os=-haiku ;; *-ibm) os=-aix ;; *-knuth) os=-mmixware ;; *-wec) os=-proelf ;; *-winbond) os=-proelf ;; *-oki) os=-proelf ;; *-hp) os=-hpux ;; *-hitachi) os=-hiux ;; i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent) os=-sysv ;; *-cbm) os=-amigaos ;; *-dg) os=-dgux ;; *-dolphin) os=-sysv3 ;; m68k-ccur) os=-rtu ;; m88k-omron*) os=-luna ;; *-next ) os=-nextstep ;; *-sequent) os=-ptx ;; *-crds) os=-unos ;; *-ns) os=-genix ;; i370-*) os=-mvs ;; *-next) os=-nextstep3 ;; *-gould) os=-sysv ;; *-highlevel) os=-bsd ;; *-encore) os=-bsd ;; *-sgi) os=-irix ;; *-siemens) os=-sysv4 ;; *-masscomp) os=-rtu ;; f30[01]-fujitsu | f700-fujitsu) os=-uxpv ;; *-rom68k) os=-coff ;; *-*bug) os=-coff ;; *-apple) os=-macos ;; *-atari*) os=-mint ;; *) os=-none ;; esac fi # Here we handle the case where we know the os, and the CPU type, but not the # manufacturer. 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: DOMAINATRIX-0.1.650/src/0002775000175000017500000000000012171070631011234 500000000000000DOMAINATRIX-0.1.650/src/scopparse.c0000664000175000017500000000630511741637063013333 00000000000000/* @source scopparse application ** ** Reads raw SCOP classification files and writes a DCF file (domain ** classification file). ** ** @author: Copyright (C) Jon Ison (jison@ebi.ac.uk) ** @author: Copyright (C) Alan Bleasby (ableasby@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. ** ** ******************************************************************************* ** ** SCOPPARSE 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 ** na. ******************************************************************************/ #include #include "emboss.h" /* @prog scopparse ************************************************************ ** ** Converts raw scop classification files to a file in embl-like format. ** ******************************************************************************/ int main(int argc, char **argv) { AjPFile inf1 = NULL; AjPFile inf2 = NULL; AjPFile outf = NULL; AjPList list = NULL; AjPScop tmp = NULL; AjBool nosegments = ajFalse; AjBool nomultichain = ajFalse; AjBool nominor = ajFalse; embInitPV("scopparse", argc, argv, "DOMAINATRIX",VERSION); /* Read data from acd. */ inf1 = ajAcdGetInfile("classfile"); inf2 = ajAcdGetInfile("desinfile"); outf = ajAcdGetOutfile("dcffile"); nosegments = ajAcdGetBoolean("nosegments"); nomultichain = ajAcdGetBoolean("nomultichain"); nominor = ajAcdGetBoolean("nominor"); /* ajFmtPrint("nosegments: %B\n", nosegments); ajFmtPrint("nomultichain: %B\n", nomultichain); ajFmtPrint("nominor: %B\n", nominor); */ /* Main body of code. */ list = ajScopReadAllRawNew(inf1, inf2, nomultichain); while(ajListPop(list, (void**) &tmp)) { if(((!nosegments) || (tmp->Number == 1)) && ((!nominor) || ((tmp->Sunid_Class == 46456) || /* All alpha*/ (tmp->Sunid_Class == 48724) || /* All beta */ (tmp->Sunid_Class == 51349) || /* a/b */ (tmp->Sunid_Class == 53931)))) /* a+b */ ajScopWrite(outf, tmp); ajScopDel(&tmp); } /* Memory management. */ ajFileClose(&outf); ajFileClose(&inf1); ajFileClose(&inf2); ajListFree(&list); ajExit(); return 0; } DOMAINATRIX-0.1.650/src/domainsse.c0000664000175000017500000001751611741637020013315 00000000000000/* @source domainsse application ** ** Adds secondary structure records to a DCF file (domain classification file). ** ** @author: Copyright (C) Amanda O'Reilly ** @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.ac.uk. ** ** NOTES ** SS: ** Secondary structure string - string of secondary structure assignments ** for all residues, calculated by the Stride programme. ** STRIDE-assigned secondary structure: 'H' (Alpha helix), ** 'G' (3-10 helix), 'I' (PI-helix), ** 'E' (Extended conformation), 'B' or 'b' (Isolated bridge), ** 'T' (Turn), 'C' (Coil, none of the above) ** SE: ** Secondary structure element map- string of element assignments ** derived from Stridewrap output. Element length is set when running ** Stridewrap (default is set to 4). Elements are made of residues with ** H, G, I, E structure only. ** ******************************************************************************/ #include #include "emboss.h" /* @prog domainsse ************************************************************ ** ** Adds secondary structure records to a DCF file (domain classification file). ** ******************************************************************************/ int main(int argc, char **argv) { ajint num = 0; AjPStr msg = NULL; /* Pointer to String used for messages. */ AjPDir dccf = NULL; /* Pointer to Path of dccf (clean domain) files*/ AjPStr dccf_name = NULL; /* Pointer to Name of dccf (clean domain) file */ AjPStr sse = NULL; /* Pointer to Secondary structure element map. */ AjPStr sss = NULL; /* Pointer to Secondary structure string. */ char ss; AjPFile dccf_inf = NULL; /* File pointer for input domain files. */ AjPFile dcf_inf = NULL; /* File pointer to input scop file. */ AjPFile dcf_outf = NULL; /* File pointer for scop output file. */ AjPFile errf = NULL; /* File pointer for output log */ AjPScop scop = NULL; /* Pointer to scopstride object. */ AjPPdb pdb = NULL; /* Pointer to pdb object. */ AjPResidue temp_res= NULL; /* Pointer to Residue object. */ AjIList iter = NULL; /* Initialise strings, lists, etc */ msg = ajStrNew(); dccf_name = ajStrNew(); /* Read data from acd */ embInitPV("domainsse",argc,argv,"DOMAINATRIX",VERSION); dcf_inf = ajAcdGetInfile("dcfinfile"); dcf_outf = ajAcdGetOutfile("dcfoutfile"); dccf = ajAcdGetDirectory("dccfdir"); errf = ajAcdGetOutfile("logfile"); /* Start of main application loop. ajScopReadC creates a Scop object from a scop file in embl-like format. */ while((scop = (ajScopReadCNew(dcf_inf, "*")))) { /* construct name of domain coordinate file*/ ajStrAssignS(&dccf_name,scop->Entry); ajStrFmtLower(&dccf_name); ajFmtPrint("Processing %S\n", scop->Entry); fflush(stdout); /*ajFileNewDF opens domain files dir, looks for named domain file, returns new file object */ if(!(dccf_inf = ajFileNewListinDirPre(dccf, dccf_name))) { ajFmtPrintF(errf, "%-15s\n", "FILE_OPEN"); ajFmtPrintF(errf, "Could not open dccf file %S\n", dccf_name); ajFmtPrintS(&msg, "Could not open dccf file %S\n", dccf_name); ajWarn(ajStrGetPtr(msg)); ajScopDel(&scop); continue; /* move on to next item in scopfile*/ } /* Read the coordinate file for the domain. */ if(!(pdb = ajPdbReadFirstModelNew(dccf_inf))) { ajFmtPrintF(errf, "%-15s\n", "FILE_READ"); ajFmtPrintF(errf, "Could not read dccf file %S", dccf_name); ajFmtPrintS(&msg, "Could not read dccf file %S", dccf_name); ajWarn(ajStrGetPtr(msg)); ajFileClose(&dccf_inf); ajScopDel(&scop); ajPdbDel(&pdb); continue; /* Move on to next item in scopfile*/ } /* Construct SSE string from data in pdb object. */ /* Initialise an sse string object. */ sse = ajStrNew(); /* Initialise the iterator. */ /* iter=ajListIterNew(pdb->Chains[0]->Atoms); */ iter = ajListIterNew(pdb->Chains[0]->Residues); /* Iiterate through the list of residues in the Pdb object, temp_res is an AjPResidue used to point to the current residue. */ num = 0; while((temp_res = (AjPResidue) ajListIterGet(iter))) { /* If this residue is part of a new element. eNum is the Serial number of the STRIDE-assigned element. */ if(temp_res->eNum > num) { /* Append one instance of eType for each new element to make sse map. */ ajStrAppendK(&sse, temp_res->eType); num++; } } /* Add the completed sse to the scop structure. */ ajStrAssignS(&scop->Sse, sse); ajListIterDel(&iter); /* Construct SSS string from data in pdb object. */ /* Initialise an sss string object. */ sss = ajStrNew(); /* Initialise the iterator. */ /* iter = ajListIterNew(pdb->Chains[0]->Atoms); */ iter = ajListIterNew(pdb->Chains[0]->Residues); /* Iiterate through the list of residues in the Pdb object. */ while((temp_res = (AjPResidue) ajListIterGet(iter))) { /* Idx is the Residue number - index into sequence. */ /* Append one instance of eType for each new residue to make ss string. */ ss = temp_res->eType; if (ss == '.') ss = 'L'; ajStrAppendK(&sss, ss); } /* Add the completed sss to the scop structure. */ ajStrAssignS(&scop->Sss, sss); ajListIterDel(&iter); /* Write out the scop structure to the scop output file. */ if(!ajScopWrite(dcf_outf, scop)) { ajFmtPrintF(errf, "%-15s\n", "FILE_WRITE"); ajFmtPrintF(errf, "Could not write scop structure for %S to scop " "output file\n ", dccf_name); ajFmtPrintS(&msg, "Could not write scop structure for %S to scop " "output file ", dccf_name); ajWarn(ajStrGetPtr(msg)); ajFileClose(&dccf_inf); ajScopDel(&scop); ajPdbDel(&pdb); ajStrDel(&sse); ajStrDel(&sss); continue; /* Move on to next item in scopfile. */ } ajFileClose(&dccf_inf); ajPdbDel(&pdb); ajScopDel(&scop); ajStrDel(&sse); ajStrDel(&sss); } /* Print message that DOMAINSSE has finished, giving name of output & error files. */ ajFmtPrint("\nDone!\n output file name: %S\n log file name: %S\n", dcf_outf->Name, errf->Name); /* Memory management. */ ajStrDel(&msg); ajStrDel(&dccf_name); ajFileClose(&errf); ajFileClose(&dcf_inf); ajFileClose(&dcf_outf); ajDirDel(&dccf); embExit(); return 0; } DOMAINATRIX-0.1.650/src/domainnr.c0000664000175000017500000004146411741636734013154 00000000000000/* @source domainnr application ** ** Removes redundant domains from a DCF file (domain classification file). ** The file must contain domain sequence information, which can be added by ** using DOMAINSEQS. ** ** @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. ** ******************************************************************************* ** ** DOMAINNR 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 ** ******************************************************************************/ #include #include "emboss.h" /****************************************************************************** ** ** PROTOTYPES ** ******************************************************************************/ static void domainnr_diagnostic(AjPFile errf, AjPDomain domain, ajint noden); static void domainnr_writelast(AjPDomain domain, ajint noden, AjPStr *last_node, ajint *last_nodeid); /* @prog domainnr ************************************************************* ** ** Removes redundant domains from a DCF file (domain classification file). ** The file must contain domain sequence information, which can be added by ** using DOMAINSEQS. ** ******************************************************************************/ int main(int argc, char **argv) { ajint x = 0; ajint nset = 0; /* No. proteins in our set. */ ajint nsetnr = 0; /* No. proteins in the non-redundant set. */ ajint nfam = 0; /* Counter of domain families. */ float gapopen = 0.0; /* Gap insertion penalty. */ float gapextend = 0.0; /* Gap extension penalty. */ float thresh = 0.0; /* Threshold for non-redundancy (single value)*/ float threshlow = 0.0; /* Threshold for non-redundancy (lower limit)*/ float threshup = 0.0; /* Threshold for non-redundancy (upper limit)*/ ajint last_nodeid = 0; /* Domain id (e.g. SCOP Sunid) of last node that was processed. */ AjPStr last_node = NULL; /* Last node that was processed. */ AjPStr msg = NULL; /* String used for messages. */ AjPFile domain_inf= NULL; /* File pointer for original domain file. */ AjPFile domain_outf= NULL;/* File pointer for domain output file. */ AjPFile red_outf = NULL; /* File pointer for redundant sequences file.*/ AjPFile errf = NULL; AjPList list_seqs = NULL; /* List of sequences for a family. */ AjPList list_domain = NULL;/* List of domain structures for a family. */ AjIList iter = NULL; /* Iterator for domain list. */ AjPUint keep = NULL; /*1: This sequence was kept after. */ /* redundancy removal, 0: it was discarded. */ EmbPDmxNrseq nrseq = NULL; /* A temporary pointer. */ AjPMatrixf matrix = NULL; /* Substitution matrix. */ AjPDomain domain = NULL; /* Pointer to domain structure. */ AjPDomain domain_tmp= NULL; /* Pointer to domain structure. */ AjPStr *mode = NULL; /* Mode of operation from acd. */ ajint moden = 0; /* Program mode as int 1: use single threshold value to remove redundancy, 2: use lower and upper limit to remove redundancy */ AjPStr *node = NULL; /* Node of redundancy removal. */ ajint noden =0; /*1: Class (SCOP), 2: Fold (SCOP) etc, see ACD file */ const char* const nodes[]= { "Classes", "Folds", "Superfamilies", "Families", "Classes", "Architectures", "Topologies", "Homologous Superfamilies", "Families" }; AjBool ret = ajFalse; AjBool retain = ajFalse; /*Whether to retain redundant sequences and write them to an output file. */ AjEDomainType type = ajEDomainTypeNULL; /* AJAX Domain Type enumeration ** of domain (ajEDomainTypeSCOP or ** ajEDomainTypeCATH) in the ** DCF file */ /* Initialise strings etc & last_node with a value that is not in a DCF file */ msg = ajStrNew(); last_node = ajStrNew(); keep = ajUintNew(); ajStrAssignC(&last_node,"!!!!!"); embInitPV("domainnr", argc, argv, "DOMAINATRIX", VERSION); /* Read data from acd */ domain_inf = ajAcdGetInfile("dcfinfile"); domain_outf = ajAcdGetOutfile("dcfoutfile"); matrix = ajAcdGetMatrixf("datafile"); gapopen = ajAcdGetFloat("gapopen"); gapextend = ajAcdGetFloat("gapextend"); errf = ajAcdGetOutfile("logfile"); mode = ajAcdGetList("mode"); node = ajAcdGetList("node"); retain = ajAcdGetToggle("retain"); if(ajStrGetCharFirst(*mode) == '1') { moden = 1; thresh = ajAcdGetFloat("threshold"); } else if(ajStrGetCharFirst(*mode) == '2') { moden = 2; threshlow = ajAcdGetFloat("threshlow"); threshup = ajAcdGetFloat("threshup"); } if(retain) red_outf = ajAcdGetOutfile("redoutfile"); /* Convert the selected node to an integer. */ if(!(ajStrToInt(node[0], &noden))) ajFatal("Could not parse ACD node option"); /* ** Write header of log file. ** Replace hard-coded 'FAMILIES' with appropriate string when. ** redundancy removal is implemented for any node in DCF file. */ ajFmtPrintF(errf, "%s are non-redundant\n" "%.0f%% redundancy threshold\n", nodes[noden - 1], thresh); type = ajDomainDCFType(domain_inf); /* Start of main application loop. */ while((domain=(ajDomainReadCNew(domain_inf, "*", type)))) { /* If we are on to 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) { /* If the family does not have any members*/ if(!nset) { /* Write diagnostic. */ ajWarn("Empty node - should never happen\n"); } /* Last family had members, so remove redundancy. */ else { /* Remove redundancy from list_seqs. */ if(moden == 1) ret = embDmxSeqNR(list_seqs, &keep, &nsetnr, matrix, gapopen, gapextend, thresh, ajFalse); else ret = embDmxSeqNRRange(list_seqs, &keep, &nsetnr, matrix, gapopen, gapextend,threshlow, threshup, ajFalse); if(!ret) { ajStrDel(&last_node); ajStrDel(&msg); ajUintDel(&keep); ajMatrixfDel(&matrix); ajFileClose(&errf); ajFileClose(&domain_outf); if(retain) ajFileClose(&red_outf); ajStrDel(&mode[0]); AJFREE(mode); ajStrDel(&node[0]); AJFREE(node); ajFatal("Unexpected embDmxSeqNR error"); } /* Write file with domain entries that are retained. */ for(iter = ajListIterNewread(list_domain), x = 0; (domain_tmp=(AjPDomain) ajListIterGet(iter)); x++) if(ajUintGet(keep, x)) ajDomainWrite(domain_outf, domain_tmp); else ajDomainWrite(red_outf, domain_tmp); ajListIterDel(&iter); /* Write diagnostic. */ ajFmtPrintF(errf, "Retained\n"); for(iter = ajListIterNewread(list_domain), x = 0; (domain_tmp = (AjPDomain) ajListIterGet(iter)); x++) if(ajUintGet(keep,x)) ajFmtPrintF(errf, "%S\n", ajDomainGetId(domain_tmp)); ajListIterDel(&iter); ajFmtPrintF(errf, "Rejected\n"); for(iter = ajListIterNewread(list_domain), x = 0; (domain_tmp = (AjPDomain) ajListIterGet(iter)); x++) if(!(ajUintGet(keep,x))) ajFmtPrintF(errf, "%S\n", ajDomainGetId(domain_tmp)); ajListIterDel(&iter); /* Write diagnostic. */ domainnr_diagnostic(errf, domain, noden); } /* Intitiliase counter for number in family. */ nset = 0; /* Free up the domain list and create a new one. */ iter = ajListIterNewread(list_domain); while((domain_tmp = (AjPDomain) ajListIterGet(iter))) ajDomainDel(&domain_tmp); ajListIterDel(&iter); ajListFree(&list_domain); /* Free up the seqs list and create a new one. */ iter = ajListIterNewread(list_seqs); while((nrseq = (EmbPDmxNrseq) ajListIterGet(iter))) { ajSeqDel(&nrseq->Seq); AJFREE(nrseq); } ajListIterDel(&iter); ajListFree(&list_seqs); } else { /* We have not done the first family. Write diagnostic. */ domainnr_diagnostic(errf, domain, noden); } /* Write the current family to last_node. */ domainnr_writelast(domain, noden, &last_node, &last_nodeid); /* Create new list for domain and seqs. */ list_seqs = ajListNew(); list_domain = ajListNew(); /* Increment counter for number of families. */ nfam++; } /* Write diagnostic. */ ajFmtPrint("%S\n", ajDomainGetId(domain)); /* Add a new sequence to the list - only ever one chain (chain 0) for domain files. */ nset++; AJNEW0(nrseq); nrseq->Seq = ajSeqNew(); /* pdb sequence has priority. */ if((ajStrGetLen(ajDomainGetSeqPdb(domain))) == 0) ajStrAssignS(&nrseq->Seq->Seq, ajDomainGetSeqSpr(domain)); else ajStrAssignS(&nrseq->Seq->Seq, ajDomainGetSeqPdb(domain)); ajStrAssignS(&nrseq->Seq->Name, ajDomainGetPdb(domain)); ajListPushAppend(list_seqs, nrseq); /* Add the current domain structure to the list. */ ajListPushAppend(list_domain, domain); } /* End of main application loop. */ /* Close the domain input file. */ ajFileClose(&domain_inf); /* Process the last family. If the family does not have any members */ if(!nset) { /* Write diagnostic. */ ajFmtPrint("WARN Empty node\n"); ajFmtPrintF(errf, "WARN Empty node\n"); } /* Last family had members, so remove redundancy. */ else { /* Remove redundancy from list_seqs. */ if(moden == 1) embDmxSeqNR(list_seqs, &keep, &nsetnr, matrix, gapopen, gapextend, thresh, ajFalse); else embDmxSeqNRRange(list_seqs, &keep, &nsetnr, matrix, gapopen, gapextend, threshlow, threshup, ajFalse); /* Write file with domain entries that are retained. */ for(iter = ajListIterNewread(list_domain), x = 0; (domain_tmp = (AjPDomain) ajListIterGet(iter)); x++) if(ajUintGet(keep, x)) ajDomainWrite(domain_outf, domain_tmp); else ajDomainWrite(red_outf, domain_tmp); ajListIterDel(&iter); /* Write diagnostic. */ ajFmtPrintF(errf, "Retained\n"); for(iter = ajListIterNewread(list_domain), x = 0; (domain_tmp = (AjPDomain) ajListIterGet(iter)); x++) if(ajUintGet(keep, x)) ajFmtPrintF(errf, "%S\n", ajDomainGetId(domain_tmp)); ajListIterDel(&iter); ajFmtPrintF(errf, "Rejected\n"); for(iter = ajListIterNewread(list_domain), x = 0; (domain_tmp = (AjPDomain) ajListIterGet(iter)); x++) if(!(ajUintGet(keep, x))) ajFmtPrintF(errf, "%S\n", ajDomainGetId(domain_tmp)); ajListIterDel(&iter); } /* Free up the domain list. */ iter = ajListIterNewread(list_domain); while((domain_tmp = (AjPDomain) ajListIterGet(iter))) ajDomainDel(&domain_tmp); ajListIterDel(&iter); ajListFree(&list_domain); /* Free up the seqs list. */ iter = ajListIterNewread(list_seqs); while((nrseq = (EmbPDmxNrseq) ajListIterGet(iter))) { ajSeqDel(&nrseq->Seq); AJFREE(nrseq); } ajListIterDel(&iter); ajListFree(&list_seqs); /* Tidy up. */ ajMatrixfDel(&matrix); ajUintDel(&keep); ajStrDel(&last_node); ajStrDel(&msg); ajFileClose(&errf); ajFileClose(&domain_outf); if(retain) ajFileClose(&red_outf); ajStrDel(&mode[0]); AJFREE(mode); ajStrDel(&node[0]); AJFREE(node); /* Bye Bye. */ ajExit(); return 0; } /* @funcstatic domainnr_diagnostic ******************************************** ** ** Writes diagnostics messages to file. ** ** @@ ******************************************************************************/ static void domainnr_diagnostic(AjPFile errf, AjPDomain domain, ajint noden) { if(noden == 1) { ajFmtPrintF(errf, "// %S\n", domain->Scop->Class); ajFmtPrint("// %S\n", domain->Scop->Class); } else if(noden == 2) { ajFmtPrintF(errf, "// %S\n", domain->Scop->Fold); ajFmtPrint("// %S\n",domain->Scop->Fold); } else if(noden == 3) { ajFmtPrintF(errf, "// %S\n", domain->Scop->Superfamily); ajFmtPrint("// %S\n", domain->Scop->Superfamily); } else if(noden == 4) { ajFmtPrintF(errf, "// %S\n", domain->Scop->Family); ajFmtPrint("// %S\n",domain->Scop->Family); } else if(noden == 5) { ajFmtPrintF(errf, "// %S\n", domain->Cath->Class); ajFmtPrint("// %S\n",domain->Cath->Class); } else if(noden == 6) { ajFmtPrintF(errf, "// %S\n", domain->Cath->Architecture); ajFmtPrint("// %S\n",domain->Cath->Architecture); } else if(noden == 7) { ajFmtPrintF(errf, "// %S\n", domain->Cath->Topology); ajFmtPrint("// %S\n",domain->Cath->Topology); } else if(noden == 8) { ajFmtPrintF(errf, "// %S\n", domain->Cath->Superfamily); ajFmtPrint("// %S\n",domain->Cath->Superfamily); } else if(noden == 9) { /* There is no text describing the CATH families. */ ajFmtPrintF(errf, "// %d\n", domain->Cath->Family_Id); ajFmtPrint("// %d\n", domain->Cath->Family_Id); } return; } /* @funcstatic domainnr_writelast ********************************************* ** ** House-keeping function. ** ** @@ ******************************************************************************/ static void domainnr_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; } return; } DOMAINATRIX-0.1.650/src/domainseqs.c0000664000175000017500000004772211741636776013521 00000000000000/* @source domainseqs application ** ** Adds sequence records to 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. ** ******************************************************************************* ** ** DOMAINSEQS 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 ** ******************************************************************************/ #include #include "emboss.h" /****************************************************************************** ** ** PROTOTYPES ** ******************************************************************************/ static AjBool domainseqs_AlignDomain(AjPSeq sp_seq, AjPSeq pdb_seq, AjPMatrixf matrix, float gapopen, float gapextend, ajint* start, ajint* end); static AjBool domainseqs_FindDomainLimits(AjPSeq sp_seq, AjPSeq pdb_seq, AjPStr m, AjPStr n, ajint start1, ajint start2, float gapopen, float gapextend, float score, AjPMatrixf matrix, ajint begina, ajint beginb, ajint* start, ajint* end); /* @prog domainseqs *********************************************************** ** ** Adds sequence records to a DCF file (domain classification file). ** ******************************************************************************/ int main(int argc, char **argv) { ajint start = 0; /* Start of the domain in the swissprot sequence. */ ajint end = 0; /* End of the domain inthe swissprot sequence. */ float gapopen = 0.0F; /* Gap insertion penalty. */ float gapextend = 0.0F; /* Gap extension penalty. */ AjPStr msg = NULL; /* String used for messages. */ AjPDir dpdb_path = NULL; /* Path of dpdb (clean domain) files. */ AjPStr dpdb_name = NULL; /* Name of dpdb (clean domain) file. */ AjPStr dpdb_seq = NULL; /* Holds the clean pdb sequence. */ AjPStr acc = NULL; /* A string to hold an accession number. */ AjPStr db = NULL; /* The name of the sequence database to retrieve the sequences. */ AjPStr sp_dom_seq = NULL; /* The swissprot domain sequence. */ AjPFile dpdb_inf = NULL; /* File pointer for clean domain files. */ AjPFile domain_inf = NULL; /* File pointer to DCF file. */ AjPFile pdbtosp_inf= NULL; /* File pointer to Epdbtosp.dat. */ AjPFile domain_outf= NULL; /* File pointer for DCF output file. */ AjPFile errf = NULL; /* Output log file. */ AjPList list = NULL; /* A list to hold pdbtosp structures. */ AjPSeq sp_seq = NULL; /* Sequence object to hold the retrieved swissprot sequence. */ AjPSeq pdb_seq = NULL; /* Sequence object to hold the retrieved dpdb sequence. */ AjPMatrixf matrix; /* Substitution matrix. */ AjPDomain domain = NULL; /* Pointer to domain structure. */ AjPPdb pdb = NULL; /* Pointer to pdb structure. */ AjBool getswiss = ajFalse; /* Whether to retrieve swissprot sequences for the domains. */ AjEDomainType type = ajEDomainTypeNULL; /* Type of domain ** (ajEDomainTypeSCOP or ** ajEDomainTypeCATH) in the ** DCF file. */ AjPPdbtosp pdbtosp = NULL; /* Initialise strings, lists, etc */ msg = ajStrNew(); dpdb_name = ajStrNew(); dpdb_seq = ajStrNew(); acc = ajStrNew(); db = ajStrNew(); sp_dom_seq = ajStrNew(); embInitPV("domainseqs",argc,argv,"DOMAINATRIX",VERSION); /* Read data from acd */ domain_inf = ajAcdGetInfile("dcfinfile"); getswiss = ajAcdGetToggle("getswiss"); if(getswiss) { pdbtosp_inf = ajAcdGetInfile("pdbtospfile"); matrix = ajAcdGetMatrixf("datafile"); gapopen = ajAcdGetFloat("gapopen"); gapextend = ajAcdGetFloat("gapextend"); } domain_outf = ajAcdGetOutfile("dcfoutfile"); dpdb_path = ajAcdGetDirectory("dpdbdir"); errf = ajAcdGetOutfile("logfile"); /* Set up the pdbtosp object list. */ if(getswiss) list = ajPdbtospReadAllNew(pdbtosp_inf); type = ajDomainDCFType(domain_inf); /* Start of main application loop. */ while((domain=(ajDomainReadCNew(domain_inf, "*", type)))) { ajStrAssignS(&dpdb_name,ajDomainGetId(domain)); ajStrFmtLower(&dpdb_name); ajFmtPrintF(errf, "//\n%-15S\n", ajDomainGetId(domain)); ajFmtPrint("//\n%-15S\n", ajDomainGetId(domain)); if(!(dpdb_inf=ajFileNewListinDirPre(dpdb_path, dpdb_name))) { ajStrAssignS(&msg, dpdb_name); ajStrAppendC(&msg, "."); ajStrAppendS(&msg,ajDirGetExt(dpdb_path)); ajFmtPrintF(errf, "%-15s\n", "FILE_OPEN"); ajWarn("Could not open ccf file %S", msg); ajDomainDel(&domain); continue; } /* Read the coordinate file for the domain. */ if((!(pdb=ajPdbReadFirstModelNew(dpdb_inf)))) { ajFmtPrintF(errf, "%-15s\n", "FILE_READ"); ajFmtPrintS(&msg, "Error reading ccf file %S", dpdb_name); ajWarn(ajStrGetPtr(msg)); ajFileClose(&dpdb_inf); ajDomainDel(&domain); ajPdbDel(&pdb); continue; } /* Get and assign the pdb sequence. */ ajStrAssignS(&dpdb_seq, pdb->Chains[0]->Seq); /* Create a pdb sequence object. */ pdb_seq = ajSeqNew(); ajStrAssignS(&pdb_seq->Name,dpdb_name); ajStrAssignS(&pdb_seq->Seq,dpdb_seq); /* Add pdb sequence to the domain structure. */ if((domain->Type == ajEDomainTypeSCOP)) ajStrAssignS(&domain->Scop->SeqPdb, dpdb_seq); else ajStrAssignS(&domain->Cath->SeqPdb, dpdb_seq); /* If we do not need the swissprot sequence. */ if(!getswiss) { ajDomainWrite(domain_outf,domain); ajFileClose(&dpdb_inf); ajSeqDel(&pdb_seq); ajPdbDel(&pdb); ajDomainDel(&domain); continue; } /* We only want to retrieve a swissprot sequence if the domain is not comprised of segments. */ if(ajDomainGetN(domain) != 1) { ajWarn("Will not retrieve swissprot sequence for " "segmented domain %S\n", dpdb_name); ajFmtPrintF(errf, "%-15s\n", "SEGMENTED_DOMAIN_NO_SP_SEQ"); ajDomainWrite(domain_outf,domain); ajFileClose(&dpdb_inf); ajDomainDel(&domain); ajPdbDel(&pdb); ajSeqDel(&pdb_seq); continue; } /* Given a pdb code get the accession number and list of pdbtoscop structures. */ if(!embPdbidToAcc(ajDomainGetPdb(domain),&acc,list)) { ajFmtPrintF(errf, "%-15s\n", "NO_ACCESSION_NUMBER"); ajDomainWrite(domain_outf,domain); ajFileClose(&dpdb_inf); ajDomainDel(&domain); ajPdbDel(&pdb); ajSeqDel(&pdb_seq); continue; } /* Add the accession number to the domain structure. */ if((domain->Type == ajEDomainTypeSCOP)) ajStrAssignS(&domain->Scop->Acc,acc); else ajStrAssignS(&domain->Cath->Acc,acc); /* Get the swissprot sequence. */ sp_seq = ajSeqNew(); ajStrAssignC(&db, "swissprot-acc:"); ajStrAppendS(&db, acc); if(!(ajSeqGetFromUsa(db,ajTrue,sp_seq))) { ajFmtPrintF(errf, "%-15s\n", "ENTRY_NOT_FOUND_IN_SW"); ajDomainWrite(domain_outf,domain); ajFileClose(&dpdb_inf); ajDomainDel(&domain); ajPdbDel(&pdb); ajSeqDel(&pdb_seq); ajSeqDel(&sp_seq); continue; } else { if((domain->Type == ajEDomainTypeSCOP)) ajStrAssignS(&domain->Scop->Spr,sp_seq->Name); else ajStrAssignS(&domain->Cath->Spr,sp_seq->Name); } if((domain->Type == ajEDomainTypeSCOP)) ajStrAssignS(&domain->Scop->Spr,sp_seq->Name); else ajStrAssignS(&domain->Cath->Spr,sp_seq->Name); /* Find swissprot sequence segment corresponding to pdb sequence. */ /* First look for identical match. */ if((ajStrFindS(sp_seq->Seq,dpdb_seq))>=0) { start = ajStrFindS(sp_seq->Seq,dpdb_seq); end = start + dpdb_seq->Len - 1; if((domain->Type == ajEDomainTypeSCOP)) { domain->Scop->Startd = start+1; domain->Scop->Endd = end+1; } else { domain->Cath->Startd = start+1; domain->Cath->Endd = end+1; } } /* Carry out Needle_Wunch pairwise alignment to find the location of domain. */ else if (domainseqs_AlignDomain(sp_seq, pdb_seq, matrix, gapopen, gapextend, &start, &end)) { ajFmtPrintF(errf, "%-15s\n", "ALIGNMENT_NECESSARY"); if((domain->Type == ajEDomainTypeSCOP)) { domain->Scop->Startd = (start+1); domain->Scop->Endd = end; } else { domain->Cath->Startd = (start+1); domain->Cath->Endd = end; } } else ajFatal("Fatal failure in domainseqs_AlignDomain\n"); /* Get the domain sequence from the swissprot sequence trim it and write to domain structure. */ ajStrAssignSubS(&sp_dom_seq, sp_seq->Seq, start, end); if((domain->Type == ajEDomainTypeSCOP)) ajStrAssignS(&domain->Scop->SeqSpr,sp_dom_seq); else ajStrAssignS(&domain->Cath->SeqSpr,sp_dom_seq); /* write out the domain structure. */ ajDomainWrite(domain_outf,domain); /* Memory management. */ start = 0; end = 0; ajFileClose(&dpdb_inf); ajSeqDel(&sp_seq); ajSeqDel(&pdb_seq); ajPdbDel(&pdb); ajDomainDel(&domain); } /* Memory management. */ while(ajListPop(list, (void**) &pdbtosp)) ajPdbtospDel(&pdbtosp); ajListFree(&list); ajDirDel(&dpdb_path); ajMatrixfDel(&matrix); ajStrDel(&msg); ajStrDel(&dpdb_name); ajStrDel(&dpdb_seq); ajStrDel(&acc); ajFileClose(&errf); ajFileClose(&domain_inf); if(getswiss) ajFileClose(&pdbtosp_inf); ajFileClose(&domain_outf); embExit(); return 0; } /* @funcstatic domainseqs_AlignDomain ***************************************** ** ** Align the pdb sequence to the full length swissprot sequence using Needleman ** and Wunsch (adapted to find location (start & end) of pdb sequence in ** swissprot sequence). ** ** @param [r] sp_seq [AjPSeq] Swissprot sequence object ** @param [r] pdb_seq [AjPSeq] Pdb sequence object ** @param [r] matrix [AjPMatrixf] Residue substitution matrix ** @param [r] gapopen [float] Gap insertion penalty ** @param [r] gapextend [float] Gap extension penalty ** @param [w] start [int *] Start of domain in swissprot sequence ** @param [w] end [int *] End of domain in swissprot sequence ** ** @return [AjBool] ajTrue on success ** @@ ******************************************************************************/ static AjBool domainseqs_AlignDomain(AjPSeq sp_seq, AjPSeq pdb_seq, AjPMatrixf matrix, float gapopen, float gapextend, ajint* start, ajint* end) { ajint start1 = 0; /* Start of seq 1, passed but not used. */ ajint start2 = 0; /* Start of seq 2, passed but not used. */ ajint maxarr = 300; /* Initial size for matrix. */ ajint len; ajint lena; ajint lenb; ajint *compass; ajint begina; ajint beginb; const char *p; const char *q; float **sub; float id = 0.; /* Passed as arg but not used here. */ float sim = 0.; float idx = 0.; /* Passed as arg but not used here. */ float simx = 0.; /* Passed as arg but not used here. */ float *path; float score; AjPStr m = NULL; /* Passed as arg but not used here. */ AjPStr n = NULL; /* Passed as arg but not used here. */ AjPSeqCvt cvt = 0; AjBool show = ajFalse; /* Passed as arg but not used here. */ /* Check args. */ if(!sp_seq || !pdb_seq || !matrix || !start || !end) { ajWarn("Bad args passed to domainseqs_AlignDomain"); return ajFalse; } /*Intitialise some variables*/ AJCNEW(path, maxarr); AJCNEW(compass, maxarr); m = ajStrNew(); n = ajStrNew(); gapopen = ajRoundFloat(gapopen,8); gapextend = ajRoundFloat(gapextend,8); sub = ajMatrixfGetMatrix(matrix); cvt = ajMatrixfGetCvt(matrix); begina = ajSeqGetBegin(sp_seq)+ajSeqGetOffset(sp_seq); lena = ajSeqGetLen(sp_seq); ajSeqTrim(pdb_seq); lenb = ajSeqGetLen(pdb_seq); len = ajSeqGetLen(sp_seq)*ajSeqGetLen(pdb_seq); if(len>maxarr) { AJCRESIZE(path,len); AJCRESIZE(compass,len); maxarr=len; } beginb = ajSeqGetBegin(pdb_seq)+ajSeqGetOffset(pdb_seq); p = ajSeqGetSeqC(sp_seq); q = ajSeqGetSeqC(pdb_seq); ajStrAssignC(&m,""); ajStrAssignC(&n,""); /* Call alignment functions. */ score = embAlignPathCalc(p,q,lena,lenb, gapopen,gapextend,path,sub,cvt, compass,show); /*score = embAlignScoreNWMatrix(path,compass,gapopen,gapextend, sp_seq,pdb_seq,lena,lenb, sub,cvt,&start1,&start2);*/ embAlignWalkNWMatrix(path,sp_seq,pdb_seq,&m,&n,lena,lenb,&start1, &start2,gapopen,gapextend,compass); embAlignCalcSimilarity(m,n,sub,cvt,lena,lenb,&id,&sim,&idx, &simx); /* Calculate the start and end of the alignment relative to the swissprot numbering. */ domainseqs_FindDomainLimits(sp_seq, pdb_seq, m, n, start1, start2, gapopen, gapextend, score, matrix, begina, beginb, start, end); AJFREE(compass); AJFREE(path); ajStrDel(&m); ajStrDel(&n); return ajTrue; } /* @funcstatic domainseqs_FindDomainLimits ************************************ ** ** Calculates the start and end of the alignment relative to the swissprot ** numbering. ** ** @param [r] sp_seq [AjPSeq] Completefirst sequence ** @param [r] pdb_seq [AjPSeq] Complete second sequence ** @param [r] m [AjPStr] Walk alignment for first sequence ** @param [r] n [AjPStr] Walk alignment for second sequence ** @param [r] start1 [ajint] Start of alignment in first sequence ** @param [r] start2 [ajint] Start of alignment in second sequence ** @param [r] gapopen [float] Gap open penalty to report ** @param [r] gapextend [float] Gap extend penalty to report ** @param [r] score [float] Alignment score from AlignScoreX ** @param [r] matrix [AjPMatrixf] Floating point matrix ** @param [r] begina [ajint] first sequence offset ** @param [r] beginb [ajint] Second sequence offset ** @param [w] start [ajint*] The start of the alignment (domain) in the ** swissprot sequence. ** @param [w] end [ajint*] The end of the alignment (domain) in the ** swissprot sequence. ** @return [AjBool] ******************************************************************************/ static AjBool domainseqs_FindDomainLimits(AjPSeq sp_seq, AjPSeq pdb_seq, AjPStr m, AjPStr n, ajint start1, ajint start2, float gapopen, float gapextend, float score, AjPMatrixf matrix, ajint begina, ajint beginb, ajint* start, ajint* end) { AjPSeq res1 = NULL; AjPSeq res2 = NULL; ajint end1 = 0; ajint end2 = 0; AjPStr fa = NULL; AjPStr fb = NULL; AjPSeqset seqset = NULL; ajint maxlen = 0; ajint i = 0; ajint alen = 0; ajint blen = 0; ajint apos = 0; ajint bpos = 0; ajint nc = 0; const char* a = NULL; const char* b = NULL; ajint no_gaps_sp = 0; /* The number of gaps in the swissprot sequence. */ /* ajint no_gaps_pdb = 0; *//* The number of gaps in the pdb sequence. */ /* TODO: The following parameters are unused. */ (void) gapopen; (void) gapextend; (void) score; (void) matrix; (void) begina; (void) beginb; ajDebug("embAlignReportGlobal %d %d\n", start1, start2); ajDebug(" sp_seq: '%S' \n", ajSeqGetSeqS(sp_seq)); ajDebug(" pdb_seq: '%S' \n", ajSeqGetSeqS(pdb_seq)); ajDebug(" alim: '%S' \n", m); ajDebug(" alin: '%S' \n", n); maxlen = AJMAX(ajSeqGetLen(sp_seq), ajSeqGetLen(pdb_seq)); seqset = ajSeqsetNew(); res1 = ajSeqNew(); res2 = ajSeqNew(); ajSeqAssignNameS(res1, ajSeqGetNameS(sp_seq)); ajSeqAssignNameS(res2, ajSeqGetNameS(pdb_seq)); ajSeqAssignUsaS(res1, ajSeqGetUsaS(sp_seq)); ajSeqAssignUsaS(res2, ajSeqGetUsaS(pdb_seq)); a = ajSeqGetSeqC(sp_seq); b = ajSeqGetSeqC(pdb_seq); /* Generate the full aligned sequences. */ ajStrSetRes(&fa, maxlen); ajStrSetRes(&fb, maxlen); /* Pad the start of either sequence. */ if(start1>start2) { for(i=0;istart1) { for(i=0;iblen) { (void) ajStrAppendC(&fa,&a[apos]); for(i=0;ialen) { (void) ajStrAppendC(&fb,&b[bpos]); for(i=0;iSeq))); /*no_gaps_pdb = (blen + (end2 - ajStrGetLen(pdb_seq->Seq)));*/ *end = (((*start + (end2-start2)) - no_gaps_sp)); ajStrDel(&fa); ajStrDel(&fb); ajSeqsetDel(&seqset); ajSeqDel(&res1); ajSeqDel(&res2); return ajTrue; } DOMAINATRIX-0.1.650/src/cathparse.c0000664000175000017500000000573611741636701013313 00000000000000/* @source cathparse application ** ** Reads raw CATH classification files and writes DCF file (domain ** classification file). ** ** ** @author: Copyright (C) Mike Hurley ** @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. ** ** ******************************************************************************* ** ** CATHPARSE 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 ** na. ****************************************************************************/ #include #include "emboss.h" /* @prog cathparse ********************************************************** ** ** Reads raw CATH classification files and writes DCF file (domain ** classification file). ** *****************************************************************************/ int main(int argc, char **argv) { AjPFile listf = NULL; /* File to be read - caths.list.v2.4. */ AjPFile domf = NULL; /* File to be read - domlist.v2.4. */ AjPFile namesf = NULL; /* File to be read - CAT.names.all.v2.4. */ AjPFile outf = NULL; /* Output file. */ AjPFile logf = NULL; /* Log file. */ AjPList list = NULL; /* List of CATH objects. */ AjPCath cath = NULL; /* Temp. pointer. */ embInitPV("cathparse", argc, argv, "DOMAINATRIX", VERSION); listf = ajAcdGetInfile("listfile"); domf = ajAcdGetInfile("domfile"); namesf = ajAcdGetInfile("namesfile"); outf = ajAcdGetOutfile("outfile"); logf = ajAcdGetOutfile("logfile"); list = ajCathReadAllRawNew(listf, domf, namesf, logf); while(ajListPop(list, (void **) &cath)) { ajCathWrite(outf, cath); ajCathDel(&cath); } /* Close CATH parsable files and output file */ ajFileClose(&listf); ajFileClose(&domf); ajFileClose(&namesf); ajFileClose(&outf); ajFileClose(&logf); ajListFree(&list); ajExit(); return 0; } DOMAINATRIX-0.1.650/src/domainreso.c0000664000175000017500000002037411741636755013505 00000000000000/* @source domainreso application ** ** Removes low resolution domains from a DCF file (domain ** classification file). ** ** @author: Copyright (C) Matt 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. ** ******************************************************************************* ** ** DOMAINRESO 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 ** ******************************************************************************/ #include #include #include "emboss.h" /****************************************************************************** ** ** PROTOTYPES ** ******************************************************************************/ static ajint domainreso_StrBinSearchDomain(AjPStr identifier, AjPStr *array, ajint size); static ajint domainreso_StrComp(const void *item1, const void *item2); /* @prog domainreso *********************************************************** ** ** Removes low resolution domains from a DCF file (domain ** classification file). ** ******************************************************************************/ int main(ajint argc, char **argv) { AjPList cpdb_path = NULL; /* Location of coordinate files for input */ AjPStr cpdb_name = NULL; /* Name of coordinate file */ AjPStr temp = NULL; /* temp string */ AjPStr temp2 = NULL; /* temp string */ AjPList entry = NULL; /* List of pdb codes with resolution */ /* ABOVE the threshold */ AjPStr *entryarr = NULL; /* entry as an array */ AjPFile fptr_cpdb = NULL; /* Pointer to current coordinate file */ AjPFile dcfin = NULL; /* DCF input file */ AjPFile dcfout = NULL; /* DCF output file */ AjPPdb pdb = NULL; /* Pdb object pointer */ AjPDomain domain = NULL; /* Domain structure */ float threshold = 0.0F; /* Resolution threshold */ ajint num = 0; /* number of nodes in list */ AjEDomainType type = ajEDomainTypeNULL; /* Type of domain ** (ajEDomainTypeSCOP or ** ajEDomainTypeCATH) in ** the DCF file */ embInitPV("domainreso",argc,argv,"DOMAINATRIX",VERSION); /* Read data from acd */ cpdb_path = ajAcdGetDirlist("cpdbpath"); threshold = ajAcdGetFloat("threshold"); dcfin = ajAcdGetInfile("dcfinfile"); dcfout = ajAcdGetOutfile("dcfoutfile"); /* Allocate strings etc. */ cpdb_name = ajStrNew(); temp = ajStrNew(); /* Create list . */ entry = ajListNew(); /* Create list of files in CPDB directory. */ /* Determine number of nodes on list */ num = ajListGetLength(cpdb_path); /* domainreso reads a directory of clean coordinate files file, creates a list of the files, then reads every list entry and extracts the resolution of the structure. If the value is less than a threshold (user defined) then the domain identifier is pushed onto a list. The DCF file (domain classification file) is then read and domain identifiers compared to those on the list, if found then the domain structure data is written the new DCF file. */ type = ajDomainDCFType(dcfin); /* Start of main application loop */ /* Produce list of pdb codes with resolution */ /* ABOVE the threshold. */ while(ajListPop(cpdb_path, (void**) &temp)) { /* Open coordinate file. */ if((fptr_cpdb = ajFileNewInNameS(temp)) == NULL) { ajWarn("Could not open cpdb file"); ajStrDel(&temp); continue; } ajFmtPrint("%S\n", temp); fflush(stdout); /* Read coordinate data file. */ pdb = ajPdbReadFirstModelNew(fptr_cpdb); /* Check if resolution is above threshold. */ if(pdb->Reso > threshold) { /* assign ID to list. */ temp2 = ajStrNew(); ajStrAssignS(&temp2, pdb->Pdb); ajListPush(entry, (AjPStr) temp2); } /* Close coordinate file and tidy up*/ ajPdbDel(&pdb); ajFileClose(&fptr_cpdb); ajStrDel(&temp); } num = ajListGetLength(entry); /* Sort the list of pdb codes & convert to an array. */ ajListSort(entry, &domainreso_StrComp); ajListToarray(entry, (void ***)&entryarr); /* Read DCF file and compare IDs to those in list if not present then write domain structure data to output. . */ while((domain=(ajDomainReadCNew(dcfin, "*", type)))) { /* DOMAIN id not found in the list of domains with resolution above the threshold, so include it in the output file. */ if((domainreso_StrBinSearchDomain(ajDomainGetId(domain), entryarr, num)) == -1) ajDomainWrite(dcfout, domain); /* Delete domain structure. */ ajDomainDel(&domain); } /* Tidy up. */ ajStrDel(&temp2); ajStrDel(&cpdb_name); ajFileClose(&dcfout); ajFileClose(&dcfin); ajListFree(&cpdb_path); ajListFree(&entry); AJFREE(entryarr); /* Return. */ ajExit(); return 0; } /* @funcstatic domainreso_StrBinSearchDomain ********************************** ** ** Performs a binary search for a DOMAIN domain code over an array of AjPStr ** (which of course must first have been sorted, e.g. by domainreso_StrComp). ** This is a case-insensitive search. ** ** @param [r] identifier [AjPStr] Search term ** @param [r] array [AjPStr*] Array of AjPStr objects ** @param [r] size [ajint] Size of array ** ** @return [ajint] Index of first AjPStr object found with an PDB code ** matching id, or -1 if id is not found. ** @@ ******************************************************************************/ static ajint domainreso_StrBinSearchDomain(AjPStr identifier, AjPStr* array, ajint size) { ajint l = 0; ajint m = 0; ajint h = size - 1; ajint c; while(l <= h) { m = (l + h) >> 1; if((c = ajStrCmpCaseS(identifier, array[m])) < 0) h = m - 1; else if(c > 0) l = m + 1; else return m; } return -1; } /* @funcstatic domainreso_StrComp ********************************************* ** ** Function to compare AJAX String objects. ** ** @param [r] item1 [const void*] AJAX String address 1 ** @param [r] item2 [const void*] AJAX String address 2 ** ** @return [ajint] -1 if str1 should sort before str2, +1 if the str2 should ** sort first. 0 if they are identical in length and content. ** @@ ******************************************************************************/ static ajint domainreso_StrComp(const void* item1, const void* item2) { AjPStr str1 = *(AjOStr* const*) item1; AjPStr str2 = *(AjOStr* const*) item2; return ajStrCmpS(str1, str2); } DOMAINATRIX-0.1.650/src/config.h.in0000664000175000017500000001213112171070613013173 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 DOMAINATRIX-0.1.650/src/ssematch.c0000664000175000017500000003546511741637110013145 00000000000000/* @source ssematch application ** ** Searches a DCF file (domain classification file) for secondary structure ** matches. ** ** @author: Copyright (C) Amanda O'Reilly ** @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. ******************************************************************************* ** ** SSEMATCH 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 ** ** ****************************************************************************/ #include #include "emboss.h" /****************************************************************************** ** ** PROTOTYPES ** ******************************************************************************/ static ajint ssematch_CompScoreInv(const void *item1, const void *item2); static AjBool ssematch_NWScore(AjPScop temp_scop, AjPSeq pseq, ajint mode, AjPMatrixf matrix, float gapopen, float gapextend); static AjPSeq ssematch_convertbases(AjPStr qse); /* @prog ssematch *********************************************************** ** ** Searches a DCF file (domain classification file) for secondary structure ** matches. ** ****************************************************************************/ int main(int argc, char **argv) { /* Variables declarations */ AjPFile dcfin = NULL; /* Domain classification file */ AjPFile ssin = NULL; /* Secondary structure input file*/ AjPMatrixf matrix = NULL; /* Substitution matrix */ AjPFile out_ss = NULL; /* For ss top matches*/ AjPFile out_se = NULL; /* For se top matches*/ AjPFile outfile = NULL; /* Output file*/ AjPFile logf = NULL; /* Log file */ float gapopen_sss = 0.0F; /* Gap insertion penalty */ float gapopen_sse = 0.0F; float gapopen = 0.0F; float gapextend_sss = 0.0F; /* Gap extension penalty */ float gapextend_sse = 0.0F; float gapextend = 0.0F; ajint max_hits = 0; /* number of top alignments to display*/ ajint mode = 0; ajint x = 0; AjPScop temp_scop = NULL; /* scop object pointer*/ AjPList scop_list = NULL; /* list of scop objects for entire domain classification file */ AjIList iter = NULL; AjPStr msg = NULL; /* Pointer to String used for messages */ AjPStr line = NULL; AjPStr qse = NULL; /* query secondary structure elements*/ AjPStr qss = NULL; /* query secondary structure (by residue)*/ AjPSeq q3se = NULL; /* query secondary structure elements, 3-letter code*/ AjPSeq q3ss = NULL; /* query secondary structure (by residue), 3-letter code*/ AjPSeq query = NULL; embInitPV("ssematch", argc, argv, "DOMAINATRIX", VERSION); /* Read data from acd */ dcfin = ajAcdGetInfile("dcfinfile"); ssin = ajAcdGetInfile("ssinfile"); max_hits = ajAcdGetInt("maxhits"); matrix = ajAcdGetMatrixf("datafile"); gapopen_sss = ajAcdGetFloat("rgapopen"); gapextend_sss = ajAcdGetFloat("rgapextend"); gapopen_sse = ajAcdGetFloat("egapopen"); gapextend_sse = ajAcdGetFloat("egapextend"); out_ss = ajAcdGetOutfile("outssfile"); out_se = ajAcdGetOutfile("outsefile"); logf = ajAcdGetOutfile("logfile"); /* Create list of scop objects for entire input domain classification file. */ scop_list = ajListNew(); while((temp_scop = ajScopReadCNew(dcfin, "*"))) ajListPushAppend(scop_list, temp_scop); /* Error handing if domain classification file was empty. */ if(!ajListGetLength(scop_list)) { ajWarn("Empty list from scop input file\n"); ajFileClose(&dcfin); ajFileClose(&ssin); ajMatrixfDel(&matrix); ajFileClose(&out_ss); ajFileClose(&out_se); ajFileClose(&logf); while(ajListPop(scop_list, (void *) &temp_scop)) ajScopDel(&temp_scop); ajListFree(&scop_list); ajListIterDel(&iter); ajExit(); return 1; } /* Error handling in case of empty query file. */ if(ssin == NULL) { ajWarn("Empty secondary structure query file\n"); ajFileClose(&dcfin); ajFileClose(&ssin); ajMatrixfDel(&matrix); ajFileClose(&out_ss); ajFileClose(&out_se); ajFileClose(&logf); while(ajListPop(scop_list, (void *) &temp_scop)) ajScopDel(&temp_scop); ajListFree(&scop_list); ajListIterDel(&iter); ajExit(); return 1; } /* Assign sequences in query file to sequence objects. */ qse = ajStrNew(); qss = ajStrNew(); while(ajReadlineTrim(ssin,&line)) { /* SE string */ if(ajStrPrefixC(line,"SE")) { ajFmtScanS(line, "%*s %S", &qse); /* Convert this string to 3-letter code & then convert to AjPSeq object. */ q3se = ssematch_convertbases(qse); } /* SS string */ else if(ajStrPrefixC(line,"SS")) { while((ajReadlineTrim(ssin,&line)) && !ajStrPrefixC(line,"XX")) ajStrAppendS(&qss,line); ajStrRemoveWhite(&qss); /* Convert this string to 3-letter code & then to AjPSeq object. */ q3ss = ssematch_convertbases(qss); } } /* For se & then for ss, modes 0 & 1. */ for(mode = 0; mode <= 1; mode++) { /* Assign arguments for alignment function. */ if (mode == 0) { query = q3se; gapopen = gapopen_sse; gapextend = gapextend_sse; outfile = out_se; } else if(mode == 1) { query = q3ss; gapopen = gapopen_sss; gapextend = gapextend_sss; outfile = out_ss; } /* Iterate through list of scop objects & calculate alignment scores. */ iter=ajListIterNew(scop_list); while((temp_scop = (AjPScop) ajListIterGet(iter))) { /* The function extracts the se (mode 0) or ss (mode 1) subject sequences from the scop object, performs a Needleman-Wunsch global alignment with the query sequence & allocates the score to the Score element of the scop object*/ if(!(ssematch_NWScore(temp_scop , query, mode, matrix, gapopen, gapextend))) { ajFmtPrintF(logf, "%-15s\n", "ALIGNMENT"); ajFmtPrintF(logf, "Could not align sequence in scop domain %S\n ", temp_scop->Entry); ajFmtPrintS(&msg, "Could not align sequence in scop domain %S\n ", temp_scop->Entry); ajWarn(ajStrGetPtr(msg)); continue; } } ajListIterDel(&iter); temp_scop = NULL; /* Sort list of Scop objects by Score */ ajListSort(scop_list, &ssematch_CompScoreInv); iter=ajListIterNew(scop_list); /* Write top-scoring hits to outfile. */ for(x=0; x < max_hits; x++ ) { temp_scop=(AjPScop)ajListIterGet(iter); /* Print score to output file. */ ajFmtPrintF(outfile, "XX ALIGNMENT SCORE %.3f\nXX\n", temp_scop->Score); /* Could also write alignment - later modification. */ if(!ajScopWrite(outfile, temp_scop)) ajFatal("Could not write output file %S\n", outfile); } ajListIterDel(&iter); temp_scop = NULL; } /* Memoryt management. */ ajFileClose(&dcfin); ajFileClose(&ssin); ajMatrixfDel(&matrix); ajFileClose(&out_ss); ajFileClose(&out_se); ajFileClose(&logf); while(ajListPop(scop_list, (void *) &temp_scop)) ajScopDel(&temp_scop); ajListFree(&scop_list); ajStrDel(&msg); ajStrDel(&line); ajStrDel(&qse); ajStrDel(&qss); ajSeqDel(&q3se); ajSeqDel(&q3ss); ajExit(); return 0; } /* @funcstatic ssematch_CompScoreInv ****************************************** ** ** Function to sort AjOScop objects by Score element. ** ** @param [r] item1 [const void*] AJAX SCOP address 1 ** @param [r] item2 [const void*] AJAX SCOP address 2 ** @see ajListSort ** ** @return [ajint] +1 if Score1 should sort before Score2, -1 if the Score2 ** should sort first. 0 if they are identical in value. ** @@ ******************************************************************************/ static ajint ssematch_CompScoreInv(const void* item1, const void* item2) { AjPScop scop1 = *(AjOScop* const*) item1; AjPScop scop2 = *(AjOScop* const*) item2; if(scop1->Score < scop2->Score) return 1; else if(scop1->Score == scop2->Score) return 0; else return -1; } /* @funcstatic ssematch_NWScore *********************************************** ** ** Calculate the similarity between query sequence and subject sequence. ** ** @param [r] temp_scop [AjPScop] Scop object ** @param [r] pseq [AjPSeq] Query sequence ** @param [r] mode [int] Mode ** @param [r] matrix [AjPMatrixf] Substitution matrix ** @param [r] gapopen [float] Gap insertion penalty ** @param [r] gapextend [float] Gap extension penalty ** ** @return [AjBool] True on success ** @@ ******************************************************************************/ static AjBool ssematch_NWScore(AjPScop temp_scop, AjPSeq pseq, ajint mode, AjPMatrixf matrix, float gapopen, float gapextend) { ajint start1 =0; /* Start of seq 1, passed as arg but not used.*/ ajint start2 =0; /* Start of seq 2, passed as arg but not used.*/ ajint maxarr =300; /* Initial size for matrix. */ ajint len; ajint *compass; const char *p; /* Query sequence. */ const char *q; /* Subject sequence from scop object. */ float **sub; float id = 0.0F; /* Passed as arg but not used here. */ float sim = 0.0F; float idx = 0.0F; /* Passed as arg but not used here. */ float simx = 0.0F; /* Passed as arg but not used here. */ float *path; AjPStr pstr = NULL; /* m walk alignment for first sequence Passed as arg but not used here. */ AjPStr qstr = NULL; /* n walk alignment for second sequence Passed as arg but not used here. */ AjPSeq qseq = NULL; /* Subject sequence. */ ajint lenp; /* Length of query sequence. */ ajint lenq; /* Length of subject sequence. */ AjPSeqCvt cvt = 0; AjBool show = ajFalse; /*Passed as arg but not used here. */ AJCNEW(path, maxarr); AJCNEW(compass, maxarr); pstr = ajStrNew(); qstr = ajStrNew(); gapopen = ajRoundFloat(gapopen,8); gapextend = ajRoundFloat(gapextend,8); sub = ajMatrixfGetMatrix(matrix); cvt = ajMatrixfGetCvt(matrix); /* Extract subject sequence from scop object, convert to 3 letter code. */ if (mode == 0) qseq = ssematch_convertbases(temp_scop->Sse); else if (mode == 1) qseq = ssematch_convertbases(temp_scop->Sss); lenp = ajSeqGetLen(pseq); /* Length of query sequence. */ lenq = ajSeqGetLen(qseq); /* Length of subject sequence. */ /* Start of main application loop */ /* Intitialise variables for use by alignment functions*/ len = (lenp * lenq); if(len>maxarr) { AJCRESIZE(path,len); AJCRESIZE(compass,len); maxarr=len; } p = ajSeqGetSeqC(pseq); q = ajSeqGetSeqC(qseq); ajStrAssignC(&pstr, ""); ajStrAssignC(&qstr, ""); /* Check that no sequence length is 0. */ if((lenp == 0)||(lenq == 0)) { AJFREE(compass); AJFREE(path); ajStrDel(&pstr); ajStrDel(&qstr); } /* Call alignment functions. */ embAlignPathCalc(p,q,lenp,lenq, gapopen, gapextend,path,sub,cvt,compass,show); /*embAlignScoreNWMatrix(path,compass,gapopen,gapextend, pseq, qseq, lenp,lenq,sub,cvt, &start1,&start2);*/ embAlignWalkNWMatrix(path,pseq,qseq,&pstr,&qstr, lenp,lenq,&start1,&start2, gapopen,gapextend,compass); embAlignCalcSimilarity(pstr,qstr,sub,cvt,lenp, lenq,&id,&sim,&idx, &simx); /* Assign score. */ temp_scop->Score = sim; /* Tidy up */ AJFREE(compass); AJFREE(path); ajStrDel(&pstr); ajStrDel(&qstr); ajSeqDel(&qseq); /* Bye Bye */ return ajTrue; } /* @funcstatic ssematch_convertbases ****************************************** ** ** Convert AjPStr of stride-assigned secondary structures to AjPSeq of ** secondary structures in 3-state assignment. ** ** @param [r] qs [AjPstr] String ** ** @return [w] q3s [AjPSeq] Sequence ** ** @@ ******************************************************************************/ static AjPSeq ssematch_convertbases(AjPStr qs) { AjIStr iter = NULL; char base; AjPSeq tmp_seq = NULL; AjPStr tmp_str = NULL; AjPStr name_str = NULL; /* Iterate through letters of string*/ /* StrIterGetK:returns Current text string within iterator, char* */ /* helices H, G, I -> G & I are changed to H extended conformation -> E stays as E bridge B/b, turn T, coil C -> all changed to L 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If bindir is libdir, return empty string, # else relative path ending with a slash; either way, target # file name can be directly appended. if test ! -z "$func_relative_path_result"; then func_stripname './' '' "$func_relative_path_result/" func_relative_path_result=$func_stripname_result fi } # The name of this program: func_dirname_and_basename "$progpath" progname=$func_basename_result # Make sure we have an absolute path for reexecution: case $progpath in [\\/]*|[A-Za-z]:\\*) ;; *[\\/]*) progdir=$func_dirname_result progdir=`cd "$progdir" && pwd` progpath="$progdir/$progname" ;; *) save_IFS="$IFS" IFS=${PATH_SEPARATOR-:} for progdir in $PATH; do IFS="$save_IFS" test -x "$progdir/$progname" && break done IFS="$save_IFS" test -n "$progdir" || progdir=`pwd` progpath="$progdir/$progname" ;; esac # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. 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If an odd number of `\' preceded a '$' # in input to double_quote_subst, that '$' was protected from expansion. # Since each input `\' is now two `\'s, look for any number of runs of # four `\'s followed by two `\'s and then a '$'. `\' that '$'. bs='\\' bs2='\\\\' bs4='\\\\\\\\' dollar='\$' sed_double_backslash="\ s/$bs4/&\\ /g s/^$bs2$dollar/$bs&/ s/\\([^$bs]\\)$bs2$dollar/\\1$bs2$bs$dollar/g s/\n//g" # Standard options: opt_dry_run=false opt_help=false opt_quiet=false opt_verbose=false opt_warning=: # func_echo arg... # Echo program name prefixed message, along with the current mode # name if it has been set yet. func_echo () { $ECHO "$progname: ${opt_mode+$opt_mode: }$*" } # func_verbose arg... # Echo program name prefixed message in verbose mode only. func_verbose () { $opt_verbose && func_echo ${1+"$@"} # A bug in bash halts the script if the last line of a function # fails when set -e is in force, so we need another command to # work around that: : } # func_echo_all arg... # Invoke $ECHO with all args, space-separated. func_echo_all () { $ECHO "$*" } # func_error arg... # Echo program name prefixed message to standard error. func_error () { $ECHO "$progname: ${opt_mode+$opt_mode: }"${1+"$@"} 1>&2 } # func_warning arg... # Echo program name prefixed warning message to standard error. func_warning () { $opt_warning && $ECHO "$progname: ${opt_mode+$opt_mode: }warning: "${1+"$@"} 1>&2 # bash bug again: : } # func_fatal_error arg... # Echo program name prefixed message to standard error, and exit. func_fatal_error () { func_error ${1+"$@"} exit $EXIT_FAILURE } # func_fatal_help arg... # Echo program name prefixed message to standard error, followed by # a help hint, and exit. func_fatal_help () { func_error ${1+"$@"} func_fatal_error "$help" } help="Try \`$progname --help' for more information." ## default # func_grep expression filename # Check whether EXPRESSION matches any line of FILENAME, without output. func_grep () { $GREP "$1" "$2" >/dev/null 2>&1 } # func_mkdir_p directory-path # Make sure the entire path to DIRECTORY-PATH is available. func_mkdir_p () { my_directory_path="$1" my_dir_list= if test -n "$my_directory_path" && test "$opt_dry_run" != ":"; then # Protect directory names starting with `-' case $my_directory_path in -*) my_directory_path="./$my_directory_path" ;; esac # While some portion of DIR does not yet exist... while test ! -d "$my_directory_path"; do # ...make a list in topmost first order. Use a colon delimited # list incase some portion of path contains whitespace. my_dir_list="$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" $ECHO "*** using a file magic. 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But I can only do this if you have a" echo "*** shared version of the library, which you do not appear to have" echo "*** because I did check the linker path looking for a file starting" if test -z "$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. 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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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Create the # directory the slow way, step by step, checking for races as we go. case $dstdir in /*) prefix='/';; [-=\(\)!]*) prefix='./';; *) prefix='';; esac eval "$initialize_posix_glob" oIFS=$IFS IFS=/ $posix_glob set -f set fnord $dstdir shift $posix_glob set +f IFS=$oIFS prefixes= for d do test X"$d" = X && continue prefix=$prefix$d if test -d "$prefix"; then prefixes= else if $posix_mkdir; then (umask=$mkdir_umask && $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break # Don't fail if two instances are running concurrently. test -d "$prefix" || exit 1 else case $prefix in *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;; *) qprefix=$prefix;; esac prefixes="$prefixes '$qprefix'" fi fi prefix=$prefix/ done if test -n "$prefixes"; then # Don't fail if two instances are running concurrently. (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: DOMAINATRIX-0.1.650/INSTALL0000644000175000017500000003660512171070614011425 00000000000000Installation Instructions ************************* Copyright (C) 1994-1996, 1999-2002, 2004-2012 Free Software Foundation, Inc. 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DOMAINATRIX-0.1.650/emboss_acd/0002775000175000017500000000000012171070632012545 500000000000000DOMAINATRIX-0.1.650/emboss_acd/domainnr.acd0000664000175000017500000002076511727433152014763 00000000000000application: domainnr [ documentation: "Remove redundant domains from a DCF file." groups: "Utils:Database creation, Protein:Domains" gui: "yes" batch: "yes" cpu: "medium" embassy: "domainatrix" relations: "EDAM_topic:0091 Data handling" relations: "EDAM_topic:0736 Protein domains and folds" relations: "EDAM_topic:0182 Sequence alignment" relations: "EDAM_operation:0290 Sequence redundancy removal" ] section: input [ information: "Input section" type: "page" ] infile: dcfinfile [ parameter: "Y" information: "Domain classification file" help: "This option specifies 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" ] matrixf: datafile [ additional: "Y" information: "Residue substitution matrix." help: "This option specifies the residue substitution matrix. This is used for sequence comparison." default: "EBLOSUM62" relations: "EDAM_data:1449 Comparison matrix (amino acid)" ] toggle: retain [ standard: "Y" information: "Write redundant domains to separate file." help: "This option specifies whether to write redundant domains to a separate file. If this option is selected, redundant domains are written to a separate output file." default: "N" relations: "EDAM_data:2527 Parameter" ] 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: Remove redundancy at a single threshold % sequence similarity,2: Remove redundancy outside a range of acceptable threshold % similarity" help: "This option specifies whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity. All permutations of pair-wise sequence alignments are calculated for each domain family in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded." delimiter: "," codedelimiter: ":" header: "Redundancy removal options" information: "Select number." relations: "EDAM_data:2527 Parameter" ] float: threshold [ standard: "@($(mode)==1)" information: "The % sequence identity redundancy threshold." help: "This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded." default: "95.0" relations: "EDAM_data:2146 Threshold" ] float: threshlow [ standard: "@($(mode)==2)" information: "The % sequence identity redundancy threshold (lower limit)" help: "This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded." default: "30.0" relations: "EDAM_data:2146 Threshold" ] float: threshup [ standard: "@($(mode)==2)" information: "The % sequence identity redundancy threshold (upper limit)." help: "This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded." default: "90.0" relations: "EDAM_data:2146 Threshold" ] endsection: required section: additional [ information: "Additional section" type: "page" ] float: gapopen [ additional: "Y" information: "Gap insertion penalty" minimum: "1." maximum: "100." 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. This 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." 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. This 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." relations: "EDAM_data:1398 Gap extension penalty" ] endsection: additional section: advanced [ information: "Advanced section" type: "page" ] endsection: advanced section: output [ information: "Output section" type: "page" ] outfile: dcfoutfile [ parameter: "Y" information: "Domain classification output file" help: "This option specifies the name of non-redundant 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" ] outfile: redoutfile [ standard: "$(retain)" information: "Domain classification redundant output file (optional)" help: "This option specifies the name of DCF file (domain classification file) for redundant sequences (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." nullok: "Y" nulldefault: "Y" extension: "scop" knowntype: "Domain classification" relations: "EDAM_data:0900 Protein domain classification" ] outfile: logfile [ standard: "Y" information: "Domainatrix log output file" help: "This option specifies the name of log file for the build. The log file contains messages about any errors arising while domainnr ran." default: "domainnr.log" knowntype: "domainatrix log" relations: "EDAM_data:1678 Tool log" ] endsection: output DOMAINATRIX-0.1.650/emboss_acd/domainsse.acd0000664000175000017500000000624611727433152015134 00000000000000application: domainsse [ documentation: "Add secondary structure records to a DCF file." groups: "Utils:Database creation, Protein:Domains" gui: "yes" batch: "yes" cpu: "medium" embassy: "domainatrix" relations: "EDAM_topic:0091 Data handling" relations: "EDAM_topic:0736 Protein domains and folds" relations: "EDAM_operation:2234 Structure file processing" ] section: input [ information: "Input section" type: "page" ] infile: dcfinfile [ parameter: "Y" information: "Domain classification file" help: "This option specifies the name of the 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: dccfdir [ parameter: "Y" information: "Clean domain coordinates directory" help: "This option specifies the location of the domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS." default: "./" extension: "ccf" knowntype: "domain clean coordinates" relations: "EDAM_identifier:1049 Directory name" relations: "EDAM_data:1468 Protein domain" ] endsection: input section: required [ information: "Required section" type: "page" ] endsection: required section: advanced [ information: "Advanced section" type: "page" ] endsection: advanced section: output [ information: "Output section" type: "page" ] outfile: dcfoutfile [ parameter: "Y" help: "This option specifies the name of the DCF file (domain classification file) with secondary structure records (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." knowntype: "domain classification" information: "Domain classification output file" relations: "EDAM_data:0900 Protein domain classification" ] outfile: logfile [ parameter: "Y" help: "This option specifies the name of the DOMAINSSE log file." default: "domainsse.log" knowntype: "domainatrix log" information: "Domainatrix log output file" relations: "EDAM_data:1678 Tool log" ] endsection: output DOMAINATRIX-0.1.650/emboss_acd/ssematch.acd0000664000175000017500000001473611727433152014764 00000000000000application: ssematch [ documentation: "Search a DCF file for secondary structure matches." groups: "Utils:Database creation, Protein:Domains" gui: "yes" batch: "yes" cpu: "medium" embassy: "domainatrix" relations: "EDAM_topic:0091 Data handling" relations: "EDAM_topic:0736 Protein domains and folds" relations: "EDAM_operation:0500 Secondary structure alignment construction" ] section: input [ information: "Input section" type: "page" ] infile: ssinfile [ parameter: "Y" information: "Secondary structure file" help: "This option specifies the name of the file of secondary structure (input)." knowntype: "Secondary structure" relations: "EDAM_data:0876 Protein features (secondary structure)" ] infile: dcfinfile [ parameter: "Y" information: "Domain classification file" help: "This option specifies the name of the 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" ] matrixf: datafile [ additional: "Y" information: "Residue substitution matrix" help: "This option specifies the secondary structure substitution matrix." default: "SSSUB" relations: "EDAM_data:1449 Comparison matrix (amino acid)" ] endsection: input section: required [ information: "Required section" type: "page" ] integer: maxhits [ standard: "Y" information: "Number of top-scoring matches to report." help: "This option specifies the number of top-scoring matches to report." default: "5" relations: "EDAM_data:1694 Number of output entities" ] endsection: required section: additional [ information: "Additional section" type: "page" ] float: rgapopen [ additional: "Y" information: "Gap insertion penalty for reside-based alignment" minimum: "1." maximum: "100." default: "10" valid: "Floating point number from 1.0 to 100.0" expected: "10.0 for any sequence" help: "This options specifies the gap insertion penalty for reside-based alignment. 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: rgapextend [ additional: "Y" information: "Gap extension penalty for residue-based alignment" minimum: "0.0" maximum: "10." default: "0.5" valid: "Floating point number from 0.0 to 10.0" expected: "0.5 for any sequence" help: "This options specifies the gap extension penalty for residue-based alignment. 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." relations: "EDAM_data:1398 Gap extension penalty" ] float: egapopen [ additional: "Y" information: "Gap insertion penalty for secondary structure element-based alignment." minimum: "1." maximum: "100." default: "10" valid: "Floating point number from 1.0 to 100.0" expected: "10.0 for any sequence" help: "This options specifies the gap insertion penalty for element-based alignment. 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: egapextend [ additional: "Y" information: "Gap extension penalty for secondary structure element-based alignment" minimum: "0.0" maximum: "10." default: "0.5" valid: "Floating point number from 0.0 to 10.0" expected: "0.5 for any sequence" help: "This options specifies the gap extension penalty for secondary structure element-based alignment. 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." relations: "EDAM_data:1398 Gap extension penalty" ] endsection: additional section: output [ information: "Output section" type: "page" ] outfile: outssfile [ parameter: "Y" information: "Domain classification residue-based output file" help: "This option specifies the name of the file containing top-scoring domains for residue-based alignment (output).A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like)." knowntype: "domain classification" relations: "EDAM_data:0900 Protein domain classification" ] outfile: outsefile [ parameter: "Y" information: "Domain classification structure-based output file" help: "This option specifies the name of the file containing top-scoring domains for secondary structure element-based alignment (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like)." knowntype: "domain classification" relations: "EDAM_data:0900 Protein domain classification" ] outfile: logfile [ standard: "Y" information: "Domainatrix log output file" help: "This option specifies the name of the ssematch log file (output)." default: "ssematch.log" knowntype: "domainatrix log" relations: "EDAM_data:1678 Tool log" ] endsection: output DOMAINATRIX-0.1.650/emboss_acd/domainreso.acd0000664000175000017500000000574711727433152015317 00000000000000application: domainreso [ documentation: "Remove low resolution domains from a DCF file." groups: "PROTEIN:3D STRUCTURE" gui: "yes" batch: "yes" cpu: "low" embassy: "domainatrix" relations: "EDAM_topic:0736 Protein domains and folds" relations: "EDAM_operation:2234 Structure file processing" ] section: input [ information: "Input section" type: "page" ] dirlist: cpdbpath [ parameter: "Y" information: "Clean domain coordinates directories" help: "This option specifies the location of domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL-like). The files, generated by using PDBPARSE (pdb files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS." default: "./" extension: "ccf" knowntype: "domain clean coordinates" relations: "EDAM_identifier:1049 Directory name" relations: "EDAM_data:1468 Protein domain" ] 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" ] float: threshold [ standard: "Y" information: "Threshold for inclusion (Angstroms)." help: "This option specifies the threshold for inclusion (Angstroms). Domains exceeding the threshold for inclusion (Angstroms) will not be given in the output file." default: "2.8" relations: "EDAM_data:2146 Threshold" ] 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 DOMAINATRIX-0.1.650/emboss_acd/Makefile0000664000175000017500000003441112171070631014125 00000000000000# Makefile.in generated by automake 1.12.2 from Makefile.am. # emboss_acd/Makefile. 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The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4)." default: "caths.list.v2.4" knowntype: "Raw cath list" relations: "EDAM_data:0900 Protein domain classification" ] infile: domfile [ parameter: "Y" information: "Raw cath domlist file" help: "This option specifies the name of raw CATH classification file (domlist.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4)." default: "domlist.v2.4" knowntype: "Raw cath domlist" relations: "EDAM_data:0900 Protein domain classification" ] infile: namesfile [ parameter: "Y" information: "Raw cath names file" help: "This option specifies the name of raw CATH classification file (CAT.names.all.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4)." default: "CAT.names.all.v2.4" knowntype: "Raw cath names" relations: "EDAM_data:0900 Protein domain classification" ] endsection: input section: output [ information: "Output section" type: "page" ] outfile: outfile [ parameter: "Y" information: "Domain classification output file" help: "This option specifies the name of CATH 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: "Ecath.dat" knowntype: "domain classification" relations: "EDAM_data:0900 Protein domain classification" ] outfile: logfile [ standard: "Y" information: "Domainatrix log output file" help: "This option specifies the name of the CATHPARSE log file." default: "cathparse.log" knowntype: "domainatrix log" relations: "EDAM_data:1678 Tool log" ] endsection: output DOMAINATRIX-0.1.650/emboss_acd/libscan.acd0000664000175000017500000002474611727433152014572 00000000000000application: libscan [ documentation: "Diagnostic searches for protein families." groups: "Protein:3D Structure" external: "hmmsearch HMMER 2.3.2 available from http://hmmer.wustl.edu/" external: "formatdb NCBI toolkit and blast executables" external: "blastpgp NCBI toolkit and blast executables" external: "rpsblast NCBI toolkit and blast executables" external: "hmmscore SAM Hidden Markov Model package" external: "prophet EMBOSS" relations: "EDAM_topic:0736 Protein domains" relations: "EDAM_topic:0180 Protein fold recognition" relations: "EDAM_operation:0303 Protein fold recognition" ] list: mode [ standard: "Y" default: "2" minimum: "1" maximum: "1" delimiter: "," codedelimiter: ":" values: "1: Database search mode, 2: Library screen mode" header: "The scanning modes" information: "Select mode of operation " button: "Y" help: "libscan runs in one of two modes either (i) database search mode or (ii) library screen mode. In database search mode libscan reads one or more directories each containing a single type of discriminating element, the permitted types are sparse sequence signature, Gribskov profile, Henikoff profile or hidden Markov model. In library screen mode, libscan reads a sequence set, screens each sequence against the library (directories of discriminating elements) and writes a library scan file (of top-scoring families) for each one." relations: "EDAM: Generic string array" ] boolean: grib [ standard: "Y" information: "Use Gribskov profile " default: "N" relations: "EDAM_data:2527 Parameter" ] boolean: henik [ standard: "Y" information: "Use Henikoff profile " default: "N" relations: "EDAM_data:2527 Parameter" ] boolean: hmm [ standard: "Y" information: "Use HMM profile " default: "N" relations: "EDAM_data:2527 Parameter" ] boolean: sam [ standard: "Y" information: "Use SAM HMM profile " default: "N" relations: "EDAM_data:2527 Parameter" ] boolean: pssm [ standard: "Y" information: "Use PSSM profile " default: "Y" relations: "EDAM_data:2527 Parameter" ] boolean: sig [ standard: "Y" information: "Use signature " default: "N" relations: "EDAM_data:2527 Parameter" ] # Hmm parameters string: hmmpath [ standard: "$(hmm)" information: "Location of HMM profile files (input)" default: "./lib/" relations: "EDAM_data:1049 Directory name" relations: "EDAM_data:1364 Hidden Markov model" ] string: hmmextn [ standard: "$(hmm)" information: "Extension of HMM profile files (input)" default: ".hmm" relations: "EDAM_data:1059 File name extension" ] string: hmmoutpath [ standard: "$(hmm)" information: "Location of signature hits/library scan files for hmm searches (output)" default: "./" relations: "EDAM_data:1049 Directory name" relations: "EDAM_data:0849 Sequence record" relations: "EDAM_data:1219 Pure protein sequence" ] string: hmmoutextn [ standard: "$(hmm)" information: "Extension of signature hits/library scan files for hmm searches (output)" default: ".hmmout" relations: "EDAM_data:1059 File name extension" ] # Sam parameters string: sampath [ standard: "$(sam)" information: "Location of SAM HMM profile files (input)" default: "./" relations: "EDAM_data:1049 Directory name" relations: "EDAM_data:1364 Hidden Markov model" ] string: samextn [ standard: "$(sam)" information: "Extension of SAM HMM profile files (input)" default: ".mod" relations: "EDAM_data:1059 File name extension" ] string: samoutpath [ standard: "$(sam)" information: "Location of signature hits/library scan files for sam hmm searches (output)" default: "./" relations: "EDAM_data:1049 Directory name" relations: "EDAM_data:0849 Sequence record" relations: "EDAM_data:1219 Pure protein sequence" ] string: samoutextn [ standard: "$(sam)" information: "Extension of signature hits/library scan files for sam hmm searches (output)" default: ".samout" relations: "EDAM_data:1059 File name extension" ] # pssm parameters string: pssmpath [ standard: "$(pssm)" information: "Location of PSSM profile files (input)" default: "/data/structure/lib/pssm/" relations: "EDAM_data:1049 Directory name" ] string: pssmextn [ standard: "$(pssm)" information: "Extension of PSSM profile files (input)" default: ".chk" relations: "EDAM_data:1059 File name extension" ] integer: niter [ standard: "$(pssm)" information: "No. of iterations (input)" default: "1" relations: "EDAM_data:1693 Number of iterations" ] float: thresh [ standard: "$(pssm)" information: "E-value threshold (input)" default: "100" relations: "EDAM_data:2146 Threshold" ] integer: maxhit [ standard: "$(pssm)" information: "Maximum No. of hits to database (input)" default: "1000" relations: "EDAM_data:1694 Number of output entities" ] string: pssmoutpath [ standard: "$(pssm)" information: "Location of signature hits/library scan files for pssm searches (output)" default: "./" relations: "EDAM_data:1049 Directory name" relations: "EDAM_data:0849 Sequence record" relations: "EDAM_data:1219 Pure protein sequence" ] string: pssmoutextn [ standard: "$(pssm)" information: "Extension of signature hits/library scan files for pssm searches (output)" default: ".pssmout" relations: "EDAM_data:1059 File name extension" ] # Gribskov parameters string: gbvpath [ standard: "$(grib)" information: "Location of Gribskov profile files (input)" default: "./" relations: "EDAM_data:1049 Directory name" ] string: gbvextn [ standard: "$(grib)" information: "Extension of Gribskov profile files (input)" default: ".grib" relations: "EDAM_data:1059 File name extension" ] float: gbvgapo [ standard: "$(grib)" default: "10.0" information: "Gap insertion penalty " relations: "EDAM_data:1397 Gap opening penalty" ] float: gbvgape [ standard: "$(grib)" default: "0.5" information: "Gap extension penalty " relations: "EDAM_data:1398 Gap extension penalty" ] string: gbvoutpath [ standard: "$(grib)" information: "Location of signature hits/library scan files for Gribskov profile searches (output)" default: "./" relations: "EDAM_data:1049 Directory name" relations: "EDAM_data:0849 Sequence record" relations: "EDAM_data:1219 Pure protein sequence" ] string: gbvoutextn [ standard: "$(grib)" information: "Extension of signature hits/library scan files for Gribskov profile searches (output)" default: ".gribout" relations: "EDAM_data:1059 File name extension" ] # Hennikoff parameters string: hnfpath [ standard: "$(henik)" information: "Location of Hennikoff profile files (input)" default: "./" relations: "EDAM_data:1049 Directory name" ] string: hnfextn [ standard: "$(henik)" information: "Extension of Hennikoff profile files (input)" default: ".henik" relations: "EDAM_data:1059 File name extension" ] float: hnfgapo [ standard: "$(henik)" default: "10.0" information: "Gap insertion penalty " relations: "EDAM_data:1397 Gap opening penalty" ] float: hnfgape [ standard: "$(henik)" default: "0.5" information: "Gap extension penalty " relations: "EDAM_data:1398 Gap extension penalty" ] string: hnfoutpath [ standard: "$(henik)" information: "Location of signature hits/library scan files for Henikoff profile searches (output)" default: "./" relations: "EDAM_data:1049 Directory name" relations: "EDAM_data:0849 Sequence record" relations: "EDAM_data:1219 Pure protein sequence" ] string: hnfoutextn [ standard: "$(henik)" information: "Extension of signature hits/library scan files for Henikoff profile searches (output)" default: ".henikout" relations: "EDAM_data:1059 File name extension" ] # Signature parameters string: sigpath [ standard: "$(sig)" information: "Location of signature files (input)" default: "./" relations: "EDAM_data:1049 Directory name" ] string: sigextn [ standard: "$(sig)" information: "Extension of signature files (input)" default: ".sig" relations: "EDAM_data:1059 File name extension" ] list: nterm [ standard: "$(sig)" default: "1" minimum: "1" maximum: "3" values: "1: Align anywhere and allow only complete signature-sequence fit,2: Align anywhere and allow partial signature-sequence fit,3: Use empirical gaps only" delimiter: "," codedelimiter: ":" header: "N-terminal matching options" information: "Select number" relations: "EDAM_data:2527 Parameter" ] matrixf: sub [ standard: "$(sig)" information: "Residue substitution matrix" default: "EBLOSUM62" relations: "EDAM_data:1449 Comparison matrix (amino acid)" ] float: siggapo [ standard: "$(sig)" default: "10.0" information: "Gap insertion penalty " relations: "EDAM_data:1397 Gap opening penalty" ] float: siggape [ standard: "$(sig)" default: "0.5" information: "Gap extension penalty " relations: "EDAM_data:1398 Gap extension penalty" ] string: sigoutpath [ standard: "$(sig)" information: "Location of signature hits/library scan files for signature searches (output)" default: "./" relations: "EDAM_data:1049 Directory name" relations: "EDAM_data:0849 Sequence record" relations: "EDAM_data:1219 Pure protein sequence" ] string: sigoutextn [ standard: "$(sig)" information: "Extension for signature hits/library scan files for signature searches (output)" default: ".sigout" relations: "EDAM_data:1059 File name extension" ] # Database parameters seqset: db [ standard: "Y" information: "File containing sequences to search or screen" help: "In database search mode libscan scans each discriminating element against a sequence set. In library screen mode, libscan reads a sequence set and screens each sequence against the library (directories of disciminating elements)" default: "49142.vdhf" relations: "EDAM_data:0849 Sequence record" relations: "EDAM_data:1219 Pure protein sequence" ] # other parameters infile: scopf [ standard: "Y" information: "SCOP classification file (input)" help: "In either mode, a 'scop classification file' is required as a source of family classification data. A scop classification file contains classification and other data for domains from the scop database. The file is in embl-like format and is generated by scopparse. Domain sequence information can be added to the file by using scopseqs." default: "/data/structure/dcf/scop_raw.dcf" relations: "EDAM_data:0900 Protein domain classification" ] DOMAINATRIX-0.1.650/emboss_acd/scopparse.acd0000664000175000017500000000727611727433152015155 00000000000000application: scopparse [ documentation: "Generate DCF file from raw SCOP files." groups: "Utils:Database creation, Protein:Domains" gui: "yes" batch: "yes" cpu: "low" embassy: "domainatrix" relations: "EDAM_topic:0091 Data handling" relations: "EDAM_topic:0736 Protein domains and folds" relations: "EDAM_operation:0335 File reformatting" relations: "EDAM_operation:2234 Structure file processing" ] section: input [ information: "Input section" type: "page" ] infile: classfile [ information: "Raw scop classification file" help: "This option specifies the name of raw SCOP classification file dir.cla.scop.txt_X.XX (input). This is the raw SCOP classification file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57." knowntype: "Raw scop classification" parameter: "Y" relations: "EDAM_data:0900 Protein domain classification" ] infile: desinfile [ information: "Raw scop description file" help: "This option specifies the name of raw SCOP description file dir.des.scop.txt_X.XX (input). This is the raw SCOP description file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57." knowntype: "raw scop description" parameter: "Y" relations: "EDAM_data:0900 Protein domain classification" ] endsection: input section: required [ information: "Required section" type: "page" ] boolean: nosegments [ standard: "Y" information: "Omit domains comprising of more than one segment." help: "This option specifies whether to omit domains comprising of more than one segment. This is necessary if a continuous residue sequence is required." default: "N" relations: "EDAM_data:2527 Parameter" ] boolean: nomultichain [ standard: "Y" information: "Omit domains comprising segments from more than one chain." help: "This option specifies whether to omit domains comprising segments from more than one chain. This is necessary if a continuous residue sequence is required." default: "N" relations: "EDAM_data:2527 Parameter" ] endsection: required section: additional [ information: "Additional section" type: "page" ] boolean: nominor [ additional: "Y" information: "Omit domains from minor classes. This is defined as anything not in class 'All alpha proteins', 'All beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta proteins (a+b)'." help: "This option specifies whether to omit domains from minor classes (defined as anything not in class 'All alpha proteins', 'All beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta proteins (a+b)'). This is necessary or appropriate for many analyses." default: "N" relations: "EDAM_data:2527 Parameter" ] endsection: additional section: output [ information: "Output section" type: "page" ] outfile: dcffile [ information: "Domain classification output file" help: "This option specifies the name of SCOP DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from the SCOP or CATH databases. The file is generated by using DOMAINER and is in DCF format (EMBL-like). Domain sequence information can be added to the file by using DOMAINSEQS." default: "test.scop" knowntype: "domain classification" parameter: "Y" relations: "EDAM_data:0900 Protein domain classification" ] endsection: output DOMAINATRIX-0.1.650/emboss_acd/domainseqs.acd0000664000175000017500000001242111727433152015305 00000000000000application: domainseqs [ documentation: "Add sequence records to a DCF file." groups: "Utils:Database creation, Protein:Domains" gui: "yes" batch: "yes" cpu: "medium" embassy: "domainatrix" relations: "EDAM_topic:0091 Data handling" relations: "EDAM_topic:0736 Protein domains and folds" relations: "EDAM_operation:2234 Structure file processing" ] 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: dpdbdir [ parameter: "Y" information: "Clean domain coordinates directory" help: "This option specifies the location of domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS." default: "./" extension: "ccf" knowntype: "domain clean coordinates" relations: "EDAM_identifier:1049 Directory name" relations: "EDAM_data:1468 Protein domain" ] toggle: getswiss [ standard: "Y" information: "Retrieve swissprot sequence." default: "N" relations: "EDAM_data:2527 Parameter" ] infile: pdbtospfile [ standard: "$(getswiss)" information: "Swissprot:pdb equivalence table file (optional)" help: "This option specifies the name of the pdbcodes to swissprot indexing file. The swissprot:PDB equivalence file is generated by PDBTOSP" knowntype: "swissprot pdb equivalence table" nullok: "Y" relations: "EDAM_data:0954 Database cross-mapping" ] matrixf: datafile [ additional: "$(getswiss)" information: "Residue substitution matrix." help: "This option specifies the residue substitution matrix, which 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: "$(getswiss)" information: "Gap insertion penalty." minimum: "1." maximum: "100." default: "10" valid: "Floating point number from 1.0 to 100.0" expected: "10.0 for any sequence" help: "This option specifies the gap insertion penalty. This is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences." relations: "EDAM_data:1397 Gap opening penalty" ] float: gapextend [ additional: "$(getswiss)" information: "Gap extension penalty." minimum: "0.0" maximum: "10." 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. This 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." relations: "EDAM_data:1398 Gap extension penalty" ] endsection: additional 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: "domainseqs.out" knowntype: "domain classification" relations: "EDAM_data:0900 Protein domain classification" ] outfile: logfile [ standard: "Y" information: "Domainatrix log output file" help: "This option specifies the name of log file for the build. The log file contains messages about any errors arising while domainseqs ran." default: "domainseqs.log" knowntype: "domainatrix log" relations: "EDAM_data:1678 Tool log" ] endsection: output DOMAINATRIX-0.1.650/emboss_acd/Makefile.am0000664000175000017500000000025210231745270014520 00000000000000 pkgdata_DATA = cathparse.acd domainnr.acd domainreso.acd domainseqs.acd \ domainsse.acd scopparse.acd ssematch.acd pkgdatadir=$(prefix)/share/EMBOSS/acd DOMAINATRIX-0.1.650/emboss_acd/Makefile.in0000664000175000017500000003314512171070614014536 00000000000000# Makefile.in generated by automake 1.12.2 from Makefile.am. # @configure_input@ # Copyright (C) 1994-2012 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; 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A 'domain hits file' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats. 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." knowntype: "domain hits" relations: "EDAM_data:0849 Sequence record" relations: "EDAM_data:1219 Pure protein sequence" relations: "EDAM_data:0857 Sequence database hits" ] endsection: input section: required [ information: "Required section" type: "page" ] endsection: required section: output [ information: "Output section" type: "page" ] outfile: outfile [ parameter: "Y" information: "Name of summary file (output)." help: "This option specifies the location of the summary file (output). 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AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wall"]) # This option tells the compiler to display a shorter form of # diagnostic output. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wbrief"]) # This option warns if cast is used to override pointer type # qualifier AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wcast-qual"]) # This option tells the compiler to perform compile-time code # checking for certain code. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wcheck"]) # This option determines whether a warning is issued when /* # appears in the middle of a /* */ comment. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wcomment"]) # Set maximum number of template instantiation contexts shown in # diagnostic. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wcontext-limit=n"]) # This option enables warnings for implicit conversions that may # alter a value. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wconversion"]) # This option determines whether warnings are issued for deprecated # features. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wdeprecated"]) # This option enables warnings based on certain C++ programming # guidelines. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Weffc++"]) # This option changes all warnings to errors. # Alternate: -diag-error warn # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Werror"]) # This option changes all warnings and remarks to errors. # Alternate: -diag-error warn, remark # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Werror-all"]) # This option determines whether warnings are issued about extra # tokens at the end of preprocessor directives. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wextra-tokens"]) # This option determines whether argument checking is enabled for # calls to printf, scanf, and so forth. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wformat"]) # This option determines whether the compiler issues a warning when # the use of format functions may cause security problems. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wformat-security"]) # This option enables diagnostics about what is inlined and what is # not inlined. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Winline"]) # This option determines whether a warning is issued if the return # type of main is not expected. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wmain"]) # This option determines whether warnings are issued for global # functions and variables without prior declaration. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wmissing-declarations"]) # Determines whether warnings are issued for missing prototypes. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wmissing-prototypes"]) # This option enables warnings if a multicharacter constant # ('ABC') is used. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wmultichar"]) # Issue a warning when a class appears to be polymorphic, # yet it declares a non-virtual one. # This option is supported in C++ only. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wnon-virtual-dtor"]) # This option warns about operations that could result in # integer overflow. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Woverflow"]) # This option tells the compiler to display diagnostics for 64-bit # porting. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wp64"]) # Determines whether warnings are issued for questionable pointer # arithmetic. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wpointer-arith"]) # his option determines whether a warning is issued about the # use of #pragma once. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wpragma-once"]) # Issue a warning when the order of member initializers does not # match the order in which they must be executed. # This option is supported with C++ only. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wreorder"]) # This option determines whether warnings are issued when a function # uses the default int return type or when a return statement is # used in a void function. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wreturn-type"]) # This option determines whether a warning is issued when a variable # declaration hides a previous declaration. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wshadow"]) # This option warns for code that might violate the optimizer's # strict aliasing rules. Warnings are issued only when using # -fstrict-aliasing or -ansi-alias. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wstrict-aliasing"]) # This option determines whether warnings are issued for functions # declared or defined without specified argument types. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wstrict-prototypes"]) # This option determines whether warnings are issued if any trigraphs # are encountered that might change the meaning of the program. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wtrigraphs"]) # This option determines whether a warning is issued if a variable # is used before being initialized. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wuninitialized"]) # This option determines whether a warning is issued if an unknown # #pragma directive is used. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wunknown-pragmas"]) # This option determines whether a warning is issued if a declared # function is not used. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wunused-function"]) # This option determines whether a warning is issued if a local or # non-constant static variable is unused after being declared. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wunused-variable"]) # This option issues a diagnostic message if const char* is # converted to (non-const) char *. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wwrite-strings"]) # Disable warning #981 operands are evaluated in unspecified order # http://software.intel.com/en-us/articles/cdiag981/ AS_VAR_APPEND([DEVWARN_CFLAGS], [" -diag-disable 981"]) ]) ]) AC_SUBST([DEVWARN_CFLAGS]) # Compiler extra developer warning settings: --enable-devextrawarnings, # appends DEVWARN_CFLAGS # Will only have an effect if --enable-devwarnings also given AC_ARG_ENABLE([devextrawarnings], [AS_HELP_STRING([--enable-devextrawarnings], [add extra warnings to devwarnings])]) AS_IF([test "x${enable_devwarnings}" = "xyes" && test "x${enable_devextrawarnings}" = "xyes"], [ AS_CASE([${CC}], [gcc], [ # flags used by Ubuntu 8.10 to check open has 2/3 arguments etc. AC_DEFINE([_FORTIFY_SOURCE], [2], [Set to 2 for open args]) # compiler flags CPPFLAGS="-fstack-protector ${CPPFLAGS}" # warnings used by Ubuntu 8.10 # -Wall already includes: # -Wformat AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wformat-security -Wl,-z,relro"]) # -Wpadded means moving char to end of structs - but also flags # end of struct so need to add padding at end AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wpadded"]) ]) ]) # Compile deprecated functions still used in the book text for 6.2.0 AC_ARG_ENABLE([buildbookdeprecated], [AS_HELP_STRING([--enable-buildbookdeprecated], [build deprecated functions used in books for 6.2.0])]) # Compile all deprecated functions AC_ARG_ENABLE([buildalldeprecated], [AS_HELP_STRING([--enable-buildalldeprecated], [build all deprecated functions])]) AS_IF([test "x${enable_buildbookdeprecated}" = "xyes" || test "x${enable_buildalldeprecated}" = "xyes"], [ AC_DEFINE([AJ_COMPILE_DEPRECATED_BOOK], [1], [Define to 1 to compile deprecated functions used in book texts for 6.2.0]) ]) AS_IF([test "x${enable_buildalldeprecated}" = "xyes"], [ AC_DEFINE([AJ_COMPILE_DEPRECATED], [1], [Define to 1 to compile all deprecated functions]) ]) # Add extensions to Solaris for some reentrant functions AS_CASE([${host_os}], [solaris*], [AS_VAR_APPEND([CFLAGS], [" -D__EXTENSIONS__"])]) # Test whether --with-sgiabi given for IRIX (n32m3 n32m4 64m3 64m4) AS_CASE([${host_os}], [irix*], [ AS_CASE([${CC}], [gcc], [], [cc], [CHECK_SGI]) ]) dnl PCRE library definitions - see the MAJOR and MINOR values dnl to see which version's configure.in these lines come from dnl Provide the current PCRE version information. Do not use numbers dnl with leading zeros for the minor version, as they end up in a C dnl macro, and may be treated as octal constants. Stick to single dnl digits for minor numbers less than 10. There are unlikely to be dnl that many releases anyway. PCRE_MAJOR="7" PCRE_MINOR="9" PCRE_DATE="11-Apr-2009" PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" dnl Default values for miscellaneous macros POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" dnl Provide versioning information for libtool shared libraries that dnl are built by default on Unix systems. PCRE_LIB_VERSION="0:1:0" PCRE_POSIXLIB_VERSION="0:0:0" dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], dnl [ dnl AS_CASE([${host_os}], dnl [darwin*], dnl [ dnl OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` dnl AS_IF([test ${OSXX} '>' '10.4'], dnl [AS_VAR_APPEND([CFLAGS], [" -I/usr/X11/include -L/usr/X11/lib"])]) dnl ]) dnl ]) # Checks for header files. AC_PATH_XTRA AC_HEADER_DIRENT AC_HEADER_STDC AC_CHECK_HEADERS([unistd.h TargetConfig.h]) # Checks for typedefs, structures, and compiler characteristics. AC_C_BIGENDIAN AC_C_CONST AC_C_INLINE AC_TYPE_PID_T AC_TYPE_SIZE_T AC_STRUCT_TM # Checks for library functions. AC_FUNC_GETPGRP AC_FUNC_STRFTIME AC_FUNC_FORK AC_FUNC_VPRINTF AC_CHECK_FUNCS([strdup strstr strchr erand48 memmove]) AS_IF([test "x${with_x}" != "xno"], [LF_EMBOSS_PATH_XLIB]) # Library checks. AC_CHECK_LIB([c], [socket], [LIBS="${LIBS}"], [LIBS="${LIBS} -lsocket"]) AC_CHECK_LIB([m], [main]) # GD for FreeBSD requires libiconv AS_CASE([${host_os}], [freebsd*], [ AS_IF([test "x${with_pngdriver}" != "xno"], [AC_CHECK_LIB([iconv], [main], [LIBS="${LIBS}"], [LIBS="-liconv ${LIBS}"])]) ]) AM_CONDITIONAL([AMPNG], [false]) AM_CONDITIONAL([AMPDF], [false]) CHECK_GENERAL CHECK_JAVA CHECK_HPDF CHECK_PNGDRIVER AX_LIB_MYSQL AX_LIB_POSTGRESQL dnl "Export" these variables for PCRE AC_SUBST([HAVE_MEMMOVE]) AC_SUBST([HAVE_STRERROR]) AC_SUBST([PCRE_MAJOR]) AC_SUBST([PCRE_MINOR]) AC_SUBST([PCRE_DATE]) AC_SUBST([PCRE_VERSION]) AC_SUBST([PCRE_LIB_VERSION]) AC_SUBST([PCRE_POSIXLIB_VERSION]) AC_SUBST([POSIX_MALLOC_THRESHOLD]) dnl Test if --enable-localforce given locallink="no" embprefix="/usr/local" AC_ARG_ENABLE([localforce], [AS_HELP_STRING([--enable-localforce], [force compile/link against /usr/local])]) AS_IF([test "x${enable_localforce}" = "xyes"], [embprefix="/usr/local"]) AS_IF([test "x${prefix}" = "xNONE"], [ AS_IF([test "x${enable_localforce}" != "xyes"], [locallink="yes"], [ locallink="no" embprefix="/usr/local" ]) ], [ embprefix="${prefix}" ]) AM_CONDITIONAL([LOCALLINK], [test "x${locallink}" = "xyes"]) AC_SUBST([embprefix]) # Enable debugging: --enable-debug, sets CFLAGS AC_ARG_ENABLE([debug], [AS_HELP_STRING([--enable-debug], [debug (-g option on compiler)])]) AS_IF([test "x${enable_debug}" = "xyes"], [AS_VAR_APPEND([CFLAGS], [" -g"])]) # Turn off irritating linker warnings in IRIX AS_CASE([${host_os}], [irix*], [ CFLAGS="-Wl,-LD_MSG:off=85:off=84:off=16:off=134 ${CFLAGS}" ]) # Enable the large file interface: --enable-large, appends CPPFLAGS AC_ARG_ENABLE([large], [AS_HELP_STRING([--enable-large], [over 2Gb file support @<:@default=yes@:>@])]) AC_MSG_CHECKING([for large file support]) AS_IF([test "x${enable_large}" = "xno"], [ AC_MSG_RESULT([no]) ], [ AS_CASE([${host_os}], [linux*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_LinuxLF"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE_SOURCE"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE64_SOURCE"]) AS_VAR_APPEND([CPPFLAGS], [" -D_FILE_OFFSET_BITS=64"]) ], [freebsd*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_FreeBSDLF"]) ], [solaris*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_SolarisLF"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE_SOURCE"]) AS_VAR_APPEND([CPPFLAGS], [" -D_FILE_OFFSET_BITS=64"]) ], [osf*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_OSF1LF"]) ], [irix*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_IRIXLF"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE64_SOURCE"]) ], [aix*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_AIXLF"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGE_FILES"]) ], [hpux*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_HPUXLF"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE_SOURCE"]) AS_VAR_APPEND([CPPFLAGS], [" -D_FILE_OFFSET_BITS=64"]) ], [darwin*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_MACOSXLF"]) ]) AC_MSG_RESULT([yes]) ]) # Enable libraries provided by the system rather than EMBOSS: # --enable-systemlibs, sets ESYSTEMLIBS AC_ARG_ENABLE([systemlibs], [AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])]) AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) # Enable the purify tool: --enable-purify, sets CC and LIBTOOL AC_ARG_ENABLE([purify], [AS_HELP_STRING([--enable-purify], [purify])]) AC_MSG_CHECKING([for purify]) AS_IF([test "x${enable_purify}" = "xyes"], [ dnl if(purify -version) < /dev/null > /dev/null 2>&1; then CC="purify --chain-length=20 -best-effort -windows=yes gcc -g" LIBTOOL="${LIBTOOL} --tag=CC" AC_MSG_RESULT([yes]) dnl fi ], [ AC_MSG_RESULT([no]) ]) dnl Set extra needed compiler flags if test "x${CC}" = "xcc"; then case "${host}" in alpha*-dec-osf*) CFLAGS="${CFLAGS} -ieee";; esac fi AM_CONDITIONAL([PURIFY], [test "x${enable_purify}" = "xyes"]) dnl Test for cygwin to set AM_LDFLAGS in library & apps Makefile.ams dnl Replaces original version which used 'expr' and so wasn't entirely dnl portable. platform_cygwin="no" AC_MSG_CHECKING([for cygwin]) case "${host}" in *-*-mingw*|*-*-cygwin*) platform_cygwin="yes" ;; *) platform_cygwin="no" ;; esac AC_MSG_RESULT([${platform_cygwin}]) AM_CONDITIONAL([ISCYGWIN], [test "x${platform_cygwin}" = "xyes"]) dnl Tests for AIX dnl If shared needs -Wl,-G in plplot,ajax,nucleus, -lX11 in plplot, dnl and -Wl,brtl -Wl,-bdynamic in emboss dnl We therefore need a static test as well needajax="no" AS_CASE([${host_os}], [aix*], [AM_CONDITIONAL([ISAIXIA64], [true])], [AM_CONDITIONAL([ISAIXIA64], [false])]) AM_CONDITIONAL([ISSHARED], [test "x${enable_shared}" = "xyes"]) AS_CASE([${host_os}], [aix*], [ AS_IF([test -d ajax/.libs], [AS_ECHO(["AIX ajax/.libs exists"])], [mkdir ajax/.libs]) AS_CASE([${host_os}], [aix5*], [needajax="no"], [aix4.3.3*], [needajax="yes"], [needajax="no"]) ]) AM_CONDITIONAL([NEEDAJAX], [test "x${needajax}" = "xyes"]) # HP-UX needs -lsec for shadow passwords AS_CASE([${host_os}], [hpux*], [AS_VAR_APPEND([LDFLAGS], [" -lsec"])]) # GNU mcheck functions: --enable-mcheck, defines HAVE_MCHECK AC_ARG_ENABLE([mcheck], [AS_HELP_STRING([--enable-mcheck], [mcheck and mprobe memory allocation test])]) AS_IF([test "x${enable_mcheck}" = "xyes"], [AC_CHECK_FUNCS([mcheck])]) # Collect AJAX statistics: --enable-savestats, defines AJ_SAVESTATS AC_ARG_ENABLE([savestats], [AS_HELP_STRING([--enable-savestats], [save AJAX statistics and print with debug output])]) AC_MSG_CHECKING([for savestats]) AS_IF([test "x${enable_savestats}" = "xyes"], [ AC_DEFINE([AJ_SAVESTATS], [1], [Define to 1 to collect AJAX library usage statistics.]) AC_MSG_RESULT([yes]) ], [ AC_MSG_RESULT([no]) ]) AC_CONFIG_FILES([Makefile src/Makefile emboss_acd/Makefile emboss_doc/Makefile emboss_doc/html/Makefile emboss_doc/text/Makefile ]) AC_OUTPUT DOMAINATRIX-0.1.650/config.guess0000755000175000017500000012743212171070614012713 00000000000000#! /bin/sh # Attempt to guess a canonical system name. # 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='2012-06-10' # 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. # 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. Otherwise, it exits with 1. # # You can get the latest version of this script from: # http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] Output the configuration name of the system \`$me' is run on. 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.guess ($timestamp) Originally written by Per Bothner. Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012 Free Software Foundation, Inc. This is free software; see the source for copying conditions. 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) HP_ARCH=m68000 ;; 9000/[34]?? ) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) if [ -x /usr/bin/getconf ]; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` case "${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. 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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: DOMAINATRIX-0.1.650/README0000664000175000017500000000000010231745270011234 00000000000000DOMAINATRIX-0.1.650/ChangeLog0000664000175000017500000000026011137347346012146 00000000000000Version 7.0.0 Renamed ssematch qualifiers to make non-ambiguous names shorter. gapopenr => rgapopen gapextendr => rgapextend gapopene => egapopen gapextende => egapextend DOMAINATRIX-0.1.650/COPYING0000664000175000017500000004311010231745270011420 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. DOMAINATRIX-0.1.650/depcomp0000755000175000017500000005055212171070615011747 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 : \\" > "$depfile" # Clip off the initial element (the dependent). Don't try to be # clever and replace this with sed code, as IRIX sed won't handle # lines with more than a fixed number of characters (4096 in # IRIX 6.2 sed, 8192 in IRIX 6.5). 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This case will never be run, # since it is checked for above. exit 1 ;; none) exec "$@" ;; *) echo "Unknown depmode $depmode" 1>&2 exit 1 ;; esac exit 0 # Local Variables: # mode: shell-script # sh-indentation: 2 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-time-zone: "UTC" # time-stamp-end: "; # UTC" # End: DOMAINATRIX-0.1.650/m4/0002775000175000017500000000000012171070631010765 500000000000000DOMAINATRIX-0.1.650/m4/ltsugar.m40000644000175000017500000001042412171070610012622 00000000000000# ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*- # # Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc. # Written by Gary V. Vaughan, 2004 # # This file is free software; the Free Software Foundation gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # serial 6 ltsugar.m4 # This is to help aclocal find these macros, as it can't see m4_define. AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])]) # lt_join(SEP, ARG1, [ARG2...]) # ----------------------------- # Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their # associated separator. # Needed until we can rely on m4_join from Autoconf 2.62, since all earlier # versions in m4sugar had bugs. m4_define([lt_join], [m4_if([$#], [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 ]) DOMAINATRIX-0.1.650/m4/lf_x11.m40000664000175000017500000000547311546377050012262 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 $? ]) ]) DOMAINATRIX-0.1.650/m4/pngdriver.m40000664000175000017500000000641211430325236013151 00000000000000dnl @synopsis CHECK_PNGDRIVER() dnl dnl This macro searches for an installed png/gd/zlib library. If nothing dnl was specified when calling configure, it searches first in /usr/local dnl and then in /usr. If the --with-pngdriver=DIR is specified, it will try dnl to find it in DIR/include/zlib.h and DIR/lib/libz.a. If --without-pngdriver dnl is specified, the library is not searched at all. dnl dnl It defines the symbol PLD_png if the librarys are found. You should dnl use autoheader to include a definition for this symbol in a config.h dnl file. dnl dnl Sources files should then use something like dnl dnl #ifdef PLD_png dnl #include dnl #endif /* PLD_png */ dnl dnl @author Ian Longden dnl Modified: Alan Bleasby. Corrected library order dnl AC_DEFUN([CHECK_PNGDRIVER], # # Handle user hints # [AC_MSG_CHECKING([if png driver is wanted]) AC_ARG_WITH([pngdriver], [AS_HELP_STRING([--with-pngdriver=@<:@DIR@:>@], [root directory path of png/gd/zlib installation (defaults to /usr)])], [if test "$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 $ALT_HOME does not exist" exit 0 fi fi ]) DOMAINATRIX-0.1.650/m4/postgresql.m40000664000175000017500000001334311732713445013365 00000000000000dnl -*- Autoconf -*- ##### http://autoconf-archive.cryp.to/ax_lib_postgresql.html # # SYNOPSIS # # AX_LIB_POSTGRESQL([MINIMUM-VERSION]) # # DESCRIPTION # # This macro provides tests of availability of PostgreSQL 'libpq' # library of particular version or newer. # # AX_LIB_POSTGRESQL macro takes only one argument which is optional. # If there is no required version passed, then macro does not run # version test. # # The --with-postgresql option takes one of three possible values: # # no - do not check for PostgreSQL client library # # yes - do check for PostgreSQL library in standard locations # (pg_config should be in the PATH) # # path - complete path to pg_config utility, use this option if # pg_config can't be found in the PATH # # This macro calls: # # AC_SUBST([POSTGRESQL_CFLAGS]) # AC_SUBST([POSTGRESQL_CPPFLAGS]) # AC_SUBST([POSTGRESQL_LDFLAGS]) # AC_SUBST([POSTGRESQL_VERSION]) # # And sets: # # HAVE_POSTGRESQL # # LAST MODIFICATION # # 2006-07-16 # 2010-05-14 MKS: Added POSTGRESQL_CPPFLAGS # 2011-06-21 AJB: Added workaround for Fedora pg_config oddity # 2011-08-01 MKS: Changed PG_CONFIG to POSTGRESQL_CONFIG # Made test constructs more portable # # COPYLEFT # # Copyright (c) 2006 Mateusz Loskot # # Copying and distribution of this file, with or without # modification, are permitted in any medium without royalty provided # the copyright notice and this notice are preserved. AC_DEFUN([AX_LIB_POSTGRESQL], [ POSTGRESQL_CFLAGS="" POSTGRESQL_CPPFLAGS="" POSTGRESQL_LDFLAGS="" POSTGRESQL_CONFIG="" POSTGRESQL_VERSION="" AC_ARG_WITH([postgresql], [AS_HELP_STRING([--with-postgresql@<:=@ARG@:>@], [use PostgreSQL library @<:@default=yes@:>@, optionally specify path to pg_config])], [ AS_IF([test "x${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]) ]) DOMAINATRIX-0.1.650/m4/libtool.m40000644000175000017500000105743212171070610012620 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 $build files to toolchain format])dnl ])# _LT_PATH_CONVERSION_FUNCTIONS DOMAINATRIX-0.1.650/m4/java.m40000664000175000017500000001505511732713220012074 00000000000000dnl -*- Autoconf -*- dnl @synopsis CHECK_JAVA() dnl dnl Need to specify --with-java and --with-javaos dnl @author Alan Bleasby dnl dnl This macro calls: dnl dnl AC_SUBST([JAVA_CFLAGS]) dnl AC_SUBST([JAVA_CPPFLAGS]) dnl AC_SUBST([JAVA_LDFLAGS]) dnl dnl AM_CONDITIONAL([JAVA_BUILD], ...) dnl dnl And sets: dnl dnl AC_DEFINE([HAVE_JAVA], ...) dnl dnl AC_PATH_PROG([ANT], ...) dnl AC_PATH_PROG([JAR], ...) dnl AC_PATH_PROG([JAVA], ...) dnl AC_PATH_PROG([JAVAC], ...) AC_DEFUN([CHECK_JAVA], [ JAVA_CFLAGS="" JAVA_CPPFLAGS="" JAVA_LDFLAGS="" have_java="yes" auth_java="" AC_MSG_CHECKING([for Java JNI]) AC_ARG_WITH([java], [AS_HELP_STRING([--with-java@<:@=ARG@:>@], [root directory path of Java installation])], [ AC_MSG_RESULT([${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"]) ]) DOMAINATRIX-0.1.650/m4/ltversion.m40000644000175000017500000000126212171070610013166 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) ]) DOMAINATRIX-0.1.650/m4/general.m40000664000175000017500000000125311374607600012571 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) ]) ] ) DOMAINATRIX-0.1.650/m4/mysql.m40000664000175000017500000001266311732713347012334 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]) ]) DOMAINATRIX-0.1.650/m4/hpdf.m40000664000175000017500000000353011430325236012070 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 ]) DOMAINATRIX-0.1.650/m4/lt~obsolete.m40000644000175000017500000001375612171070610013526 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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5817 MW; D8CCAE0E1FC0849A CRC64;\n/ FI 1ii7.ccf FC = 462 FZ = 44223 FP /^SQ SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64;\n/ FI 2hhb.ccf FC = 5398 FZ = 533177 FP /^SQ SEQUENCE 141 AA; 15126 MW; 34D13618E62A33C1 CRC64;\n/ // ID domainer-domainatrix AY structure DL keep AX domainer IN ../scopparse-keep/all.scop IN ../pdbplus-domainatrix/ IN IN IN 1 IN domainer_embl.log IN domainer_pdb.log FI stderr FC = 5 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 2 FP /^D1CS4A_\n/ FP /^D1II7A_\n/ FI domainer_embl.log FZ = 0 FI domainer_pdb.log FZ = 0 FI d1cs4a_.ent FZ = 29889 FC = 369 FP /^ATOM\s+31\s+CA\s+PHE\s+A\s\d+\s+60\.914 -11\.143 59\.200 1\.00 58\.07\s+C\s+\n/ FI d1cs4a_.ccf FZ = 40517 FC = 418 FP /SQ SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64;\n/ FI d1ii7a_.ent FZ = 29727 FC = 367 FP /ATOM 1 N ASP A 8 7\.977 32\.254 19\.055 1\.00 26\.65 N / FI d1ii7a_.ccf FZ = 39756 FC = 413 FP /SQ SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64;/ // ID cathparse-ex AB domainatrix AA cathparse IN ../../data/structure/caths.list.small IN ../../data/structure/domlist.small IN ../../data/structure/CAT.names.all.small IN IN FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI Ecath.dat FC = 48 FZ = 606 FP 2 /^ID/ FP /CH 0 CHAIN; 156 START; 203 END;\n/ FP /CH 0 CHAIN; 159 START; 202 END;\n/ FP /NR 48\n/ FP /NR 44\n/ FP 2 /SF DNA helicase RuvA subunit, C-terminal domain\n/ FI cathparse.log FC = 8 FZ = 64 FP 4 /^1\.10\.8/ // ID domainseqs-keep AB domainatrix DL keep AA domainseqs IN ../scopparse-keep/all.scop IN ../domainer-domainatrix IN Y IN ../pdbtosp-domainatrix/Epdbtosp.dat IN all_s.scop IN FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI stdout FC = 4 FZ = 38 FP 2 /^\/\/\n/ FI all_s.scop FC = 59 FZ = 1080 FP 2 /^ID / FI domainseqs.log FC = 6 FZ = 78 FP 2 /^NO_ACCESSION_NUMBER\n/ FP 2 /\/\/\n/ FP /^D1CS4A_ +\n/ FP /^D1II7A_ +\n/ // ID domainnr-ex AB domainatrix AA domainnr IN ../domainseqs-keep/all_s.scop IN IN 1 IN 1 IN 5 IN all_nr.scop IN FI stdout FC = 3 FP 1 /^\/\/ / FP 2 /^D1/ FI stderr FC = 15 FP 0 /Error: / FP 0 /Died: / FI all_nr.scop FC = 30 FZ = 535 FP 1 /^ID/ FI domainnr.log FC = 7 FZ = 117 FP 1 /^Retained/ FP 1 /^Rejected/ FP 1 /^\/\/ / // ID domainreso-ex AB domainatrix AA domainreso IN ../domainer-domainatrix/ IN ../scopparse-keep/all.scop IN 2.3 IN all_2.3.scop FI stdout FC = 2 FP 2 /\.ccf\n/ FI stderr FC = 2 FP 0 /Warning: / FP 0 /Error: / FP 0 /Died: / FI all_2.3.scop FC = 26 FZ = 390 FP 1 /^ID/ FP /SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;\n/ // ID domainsse-keep AB domainatrix DL keep AA domainsse IN ../scopparse-keep/all.scop IN ../domainer-domainatrix IN domainsse.out IN domainsse.log FI stdout FC = 6 FP 2 /^Processing/ FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI domainsse.out FC = 62 FZ = 1068 FP 2 /^ID / FI domainsse.log FZ = 0 // ID ssematch-ex AB domainatrix AA ssematch IN ../../data/structure/sse.in IN ../domainsse-keep/domainsse.out IN 1 IN res.dcf IN elm.dcf IN FI stderr FC = 2 FP 0 /^Warning:/ FP 0 /^Error:/ FP 0 /^Died:/ FI res.dcf FC = 33 FZ = 551 FP 1 /^ID / FI elm.dcf FC = 33 FZ = 581 FP 1 /^ID / FP /^SE HH\n/ FI ssematch.log FC = 0 FZ = 0 // DOMAINATRIX-0.1.650/aclocal.m40000664000175000017500000010504512171070612012227 00000000000000# generated automatically by aclocal 1.12.2 -*- Autoconf -*- # Copyright (C) 1996-2012 Free Software Foundation, Inc. # 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. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; 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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: DOMAINATRIX-0.1.650/Makefile.am0000664000175000017500000000062011614226107012417 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) DOMAINATRIX-0.1.650/emboss_doc/0002775000175000017500000000000012171070632012563 500000000000000DOMAINATRIX-0.1.650/emboss_doc/text/0002775000175000017500000000000012171070631013546 500000000000000DOMAINATRIX-0.1.650/emboss_doc/text/CVS/0002775000175000017500000000000012171064326014205 500000000000000DOMAINATRIX-0.1.650/emboss_doc/text/CVS/Entries0000664000175000017500000000064512171064326015464 00000000000000/.cvsignore/1.1/Thu Jan 21 17:58:52 2010/-kk/ /Makefile.am/1.1/Tue Mar 7 12:47:19 2006// /cathparse.txt/1.15/Mon Jul 15 21:25:42 2013// /domainnr.txt/1.17/Mon Jul 15 21:25:42 2013// /domainreso.txt/1.15/Mon Jul 15 21:25:42 2013// /domainseqs.txt/1.19/Mon Jul 15 21:25:42 2013// /domainsse.txt/1.16/Mon Jul 15 21:25:42 2013// /scopparse.txt/1.14/Mon Jul 15 21:25:42 2013// /ssematch.txt/1.18/Mon Jul 15 21:25:42 2013// D DOMAINATRIX-0.1.650/emboss_doc/text/CVS/Root0000664000175000017500000000005612000651452014763 00000000000000rice@dev.open-bio.org:/home/repository/emboss DOMAINATRIX-0.1.650/emboss_doc/text/CVS/Repository0000664000175000017500000000006212000651452016214 00000000000000emboss/emboss/embassy/domainatrix/emboss_doc/text DOMAINATRIX-0.1.650/emboss_doc/text/domainnr.txt0000664000175000017500000003255312171064326016050 00000000000000 DOMAINNR 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 Input files for usage example File: ../domainseqs-keep/all_s.scop 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 DS SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64; ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // ID D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX DS SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64; MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT LKKAI XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // 2.0 INPUTS & OUTPUTS DOMAINNR reads a DCF file (domain classification file) containing domain sequence information and writes a DCF file in which the redundant domains are removed from each node (e.g. family, superfamily etc). Optionally, the redundant domains are written to a second DCF output file. The node of operation and input and output files are specified by the user. A log file is also written. 3.0 INPUT FILE FORMAT The format of the DCF file is described in the SCOPPARSE documentation. Input files for usage example File: ../domainseqs-keep/all_s.scop 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 DS SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64; ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // ID D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX DS SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64; MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT LKKAI XX NC 1 XX CN [1] XX CH A CHAIN; . START; . 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_nr.scop ID D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX DS SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64; MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT LKKAI XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // File: domainnr.log Classes are non-redundant 5% redundancy threshold // Alpha and beta proteins (a+b) Retained D1II7A_ Rejected D1CS4A_ 5.0 DATA FILES DOMAINNR requires a residue substitution matrix. 6.0 USAGE 6.1 COMMAND LINE ARGUMENTS Remove redundant domains from a DCF file. Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers (* if not always prompted): [-dcfinfile] infile This option specifies 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. -retain toggle [N] This option specifies whether to write redundant domains to a separate file. If this option is selected, redundant domains are written to a separate output file. -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 whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity. All permutations of pair-wise sequence alignments are calculated for each domain family in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded. (Values: 1 (Remove redundancy at a single threshold % sequence similarity); 2 (Remove redundancy outside a range of acceptable threshold % similarity)) * -threshold float [95.0] This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded. (Any numeric value) * -threshlow float [30.0] This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded. (Any numeric value) * -threshup float [90.0] This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded. (Any numeric value) [-dcfoutfile] outfile [test.scop] This option specifies the name of non-redundant 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. * -redoutfile outfile [*.domainnr] This option specifies the name of DCF file (domain classification file) for redundant sequences (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. -logfile outfile [domainnr.log] This option specifies the name of log file for the build. The log file contains messages about any errors arising while domainnr ran. Additional (Optional) qualifiers: -datafile matrixf [EBLOSUM62] This option specifies the residue substitution matrix. This is used for sequence comparison. -gapopen float [10.0 for any sequence] This option specifies the gap insertion penalty. This 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. This 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. (Floating point number from 0.0 to 10.0) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-dcfoutfile" associated qualifiers -odirectory2 string Output directory "-redoutfile" associated qualifiers -odirectory string Output directory "-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 DOMAINATRIX-0.1.650/emboss_doc/text/scopparse.txt0000664000175000017500000002624412171064326016240 00000000000000 SCOPPARSE 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 DCF file from raw SCOP files 2.0 INPUTS & OUTPUTS SCOPPARSE parses the dir.cla.scop.txt and dir.des.scop.txt SCOP classification files, e.g. available at URLs: http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57 http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57 The format of these files is explained at URL: http://scop.mrc-lmb.cam.ac.uk/scop/release-notes-1.55.html SCOPPARSE writes the classification to a DCF file (EMBL-like format). No changes are made to the data other than changing the format in which it is held. The file does not include domain sequence information. The input and output files are specified by the user. 3.0 INPUT FILE FORMAT An excerpt from the dir.cla.scop.txt (Figure 1) and dir.des.scop.txt (Figure 2) SCOP input files is shown below. The format of these files is explained on the SCOP website: http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57 Input files for usage example File: scop.cla.raw # dir.cla.scop.txt # SCOP release 1.57 (January 2002) [File format version 1.00] # http://scop.mrc-lmb.cam.ac.uk/scop/ # Copyright (c) 1994-2002 the scop authors; see http://scop.mrc-lmb.cam.ac.uk/sc op/lic/copy.html d1cs4a_ 1cs4 A: d.58.29.1 39418 cl=53931,cf=54861,sf=55073,fa=55 074,dm=55077,sp=55078,px=39418 d1ii7a_ 1ii7 A: d.159.1.4 62415 cl=53931,cf=56299,sf=56300,fa=64 427,dm=64428,sp=64429,px=62415 File: scop.des.raw # dir.des.scop.txt # SCOP release 1.57 (January 2002) [File format version 1.00] # http://scop.mrc-lmb.cam.ac.uk/scop/ # Copyright (c) 1994-2002 the scop authors; see http://scop.mrc-lmb.cam.ac.uk/sc op/lic/copy.html 53931 cl d - Alpha and beta proteins (a+b) 54861 cf d.58 - Ferredoxin-like 55073 sf d.58.29 - Adenylyl and guanylyl cyclase catalytic domain 55074 fa d.58.29.1 - Adenylyl and guanylyl cyclase catalytic domain 55077 dm d.58.29.1 - Adenylyl cyclase VC1, domain C1a 55078 sp d.58.29.1 - Dog (Canis familiaris) 39418 px d.58.29.1 d1cs4a_ 1cs4 A: 56299 cf d.159 - Metallo-dependent phosphatases 56300 sf d.159.1 - Metallo-dependent phosphatases 64427 fa d.159.1.4 - DNA double-strand break repair nuclease 64428 dm d.159.1.4 - Mre11 64429 sp d.159.1.4 - Archaeon Pyrococcus furiosus 62415 px d.159.1.4 d1ii7a_ 1ii7 A: 4.0 OUTPUT FILE FORMAT An example of the DCF output file is shown in Figure 3. The records used to describe an entry are as follows. Records (4) to (9) are used to describe the position of the domain in the SCOP hierarchy. Various other ADDITIONAL RECORDS may be present if the file is processed by other programs, e.g. DOMAINSEQS or DOMAINSSE. * (1) ID - Domain identifier code. This is a 7-character code that uniquely identifies the domain in SCOP. It is identical to the first 7 characters of a line in the SCOP classification file. The first character is always 'D', the next four characters are the PDB identifier code, the fifth character is the PDB chain identifier to which the domain belongs (a '.' is given in cases where the domain is composed of multiple chains, a '_' is given where a chain identifier was not specified in the PDB file) and the final character is the number of the domain in the chain (for chains comprising more than one domain) or '_' (the chain comprises a single domain only). * (2) EN - PDB identifier code. This is the 4-character PDB identifier code of the PDB entry containing the domain. * (3) TY - domain type. "CATH" or "SCOP" is given ("SCOP" for DCF files generated by using SCOPPARSE). * (4) SI - SCOP Sunid's. The integers preceeding the codes CL, FO, SF, FA, DO, SO and DD are the SCOP sunids for Class, Fold, Superfamily, Family, Domain, Source and domain data respectively. These numbers uniquely identify the appropriate node in the SCOP parsable files. * (5) CL - Domain class. It is identical to the text given after 'Class' in the SCOP classification file. * (6) FO - Domain fold. It is identical to the text given after 'Fold' in the SCOP classification file. * (7) SF - Domain superfamily. It is identical to the text given after 'Superfamily' in the SCOP classification file. * (8) FA - Domain family. It is identical to the text given after 'Family' in the SCOP classification file. * (9) DO - Domain name. It is identical to the text given after 'Protein' in the SCOP classification file. * (10) OS - Source of the protein. It is identical to the text given after 'Species' in the SCOP classification file. * (11) DS - Sequence of the domain according to the PDB file. This sequence is taken from the domain clean coordinate file generated by DOMAINER. The DS record will only be present if the DCF file has been processed using DOMAINSEQS. * (12) NC - Number of chains comprising the domain, or number of segments from the same chain that the domain is comprised of. NC is usually 1. If the number of chains is greater than 1, then the domain entry will have a section containing a CN and a CH record (see below) for each chain. * (13) CN - Chain number. The number given in brackets after this record indicates the start of the data for the relevent chain. * (14) CH - Domain definition. The character given before CHAIN is the PDB chain identifier (a '.' is given in cases where a chain identifier was not specified in the DCF file), the strings before START and END give the start and end positions respectively of the domain in the PDB file (a '.' is given in cases where a position was not specified). Note that the start and end positions refer to residue numbering given in the original PDB file and therefore must be treated as strings. * (15) XX - used for spacing. * (16) // - used to delimit records for a domain. Output files for usage example File: all.scop 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 D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // 5.0 DATA FILES No data files are used. 6.0 USAGE Generate DCF file from raw SCOP files. Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-classfile] infile This option specifies the name of raw SCOP classification file dir.cla.scop.txt_X.XX (input). This is the raw SCOP classification file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.c la.scop.txt_1.57. [-desinfile] infile This option specifies the name of raw SCOP description file dir.des.scop.txt_X.XX (input). This is the raw SCOP description file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.d es.scop.txt_1.57. -nosegments boolean [N] This option specifies whether to omit domains comprising of more than one segment. This is necessary if a continuous residue sequence is required. -nomultichain boolean [N] This option specifies whether to omit domains comprising segments from more than one chain. This is necessary if a continuous residue sequence is required. [-dcffile] outfile [test.scop] This option specifies the name of SCOP DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from the SCOP or CATH databases. The file is generated by using DOMAINER and is in DCF format (EMBL-like). Domain sequence information can be added to the file by using DOMAINSEQS. Additional (Optional) qualifiers: -nominor boolean [N] This option specifies whether to omit domains from minor classes (defined as anything not in class 'All alpha proteins', 'All beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta proteins (a+b)'). This is necessary or appropriate for many analyses. Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-dcffile" associated qualifiers -odirectory3 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 6.1 COMMAND LINE ARGUMENTS DOMAINATRIX-0.1.650/emboss_doc/text/domainsse.txt0000664000175000017500000001734012171064326016220 00000000000000 DOMAINSSE 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 Add secondary structure records to a DCF file 2.0 INPUTS & OUTPUTS DOMAINSSE parses a DCF file (domain classification file) and writes a file containing the same data, except that domain secondary structure information derived from structural are added. Domain sequences are taken from domain CCF files (clean coordinate files). The CCF files must contain secondary structure information, which can be added by using PDBPLUS. The path for the CCF files (input) and names of DCF files (input and output) are specified by the user. The extension of CCF files is specified in the ACD file. A log file is also written. 3.0 INPUT FILE FORMAT The format of the DCF file is described in the SCOPPARSE documentation. An example of the input file is shown in Figure 1. Input files for usage example File: ../scopparse-keep/all.scop 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 D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // 4.0 OUTPUT FILE FORMAT The format of the DCF file is described in the SCOPPARSE documentation. DOMAINRESO adds the following records: * (1) SS - Secondary structure assignment (per residue). A simplified 3-state assignment: H (helix), E (extended, beta strand) and L (loop, open coil) is used. * (2) SE - Secondary structure element assignment (per secondary structure element). The same 3-state assignment as for the SS record is used: H (helix), E (extended, beta strand) and L (loop, open coil). Output files for usage example File: domainsse.out 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 SE HH XX SS SEQUENCE 46 AA; 6039 MW; 32D7FC5C51294C12 CRC64; LLLHHHHHHH LLHHHHHHHH HHHHHHHHHH HHHHHLLEEE EEELLL XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // ID D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX SE HEEE XX SS SEQUENCE 43 AA; 5411 MW; F2A5FA03304F5F35 CRC64; LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // File: domainsse.log 5.0 DATA FILES None. 6.0 USAGE 6.1 COMMAND LINE ARGUMENTS Add secondary structure records to a DCF file. Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-dcfinfile] infile This option specifies the name of the 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. [-dccfdir] directory [./] This option specifies the location of the domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. [-dcfoutfile] outfile [*.domainsse] This option specifies the name of the DCF file (domain classification file) with secondary structure records (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). 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The resolution data are taken from CCF (clean coordinate files) whose path and file extension (via the ACD file) are specified by the user. The names of the input and output files are also 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: ../scopparse-keep/all.scop 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 D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX NC 1 XX CN [1] XX CH A CHAIN; . START; . 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_2.3.scop ID D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // 5.0 DATA FILES DOMAINRESO does not use any data files. 6.0 USAGE 6.1 COMMAND LINE ARGUMENTS Remove low resolution domains from a DCF file. Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-cpdbpath] dirlist [./] This option specifies the location of domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL-like). The files, generated by using PDBPARSE (pdb files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. [-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. -threshold float [2.8] This option specifies the threshold for inclusion (Angstroms). Domains exceeding the threshold for inclusion (Angstroms) will not be given in the output file. (Any numeric value) [-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: "-cpdbpath" associated qualifiers -extension1 string Default file extension "-dcfoutfile" associated qualifiers -odirectory3 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 DOMAINATRIX-0.1.650/emboss_doc/text/cathparse.txt0000664000175000017500000002202612171064326016205 00000000000000 CATHPARSE 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 DCF file from raw CATH files 2.0 INPUTS & OUTPUTS CATHPARSE parses the CATH classification files, e.g. caths.list.v2.4, domlist.v2.4 and CAT.names.all.v2.4. These files are available by anonymous ftp from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4) The format of these files is explained in the README file available there. CATHPARSE writes the CATH classification to a DCF file (EMBL-like format). No changes are made to the data other than changing the format in which it is held. The input and output files are specified by the user. 3.0 INPUT FILE FORMAT An excerpt from the raw CATH classification files, of the type caths.list.vX.X (Figure 1), domlist.vX.X (Figure 2) and CAT.names.all.vX.X (Figure 3) is shown below. The format of these files is explained in the CATH README file available by anonymous ftp from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4). Input files for usage example File: caths.list.small 1cuk03 1 10 8 10 1 1 1 48 1.900 1hjp03 1 10 8 10 1 1 2 44 2.500 File: domlist.small 1cuk00 D03 F00 1 0 1 - 0 66 - 1 0 67 - 0 142 - 1 0 156 - 0 20 3 - 1hjp00 D03 F01 1 0 1 - 0 66 - 1 0 67 - 0 158 - 1 0 159 - 0 202 - 0 203 - 0 203 - (1) File: CAT.names.all.small 1.10.8 1cuk03 :Helicase, Ruva Protein, domain 3 1.10.8.10 1cuk03 :DNA helicase RuvA subunit, C-terminal domain 0001 2ccyA0 :Mainly Alpha 0001.0010 1eca00 :Orthogonal Bundle 4.0 OUTPUT FILE FORMAT An example of the DCF output file is shown in Figure 4. The records used to describe an entry are as follows. Records (5) to (8) are used to describe the position of the domain in the CATH hierarchy. * (1) ID - Domain identifier code. This is a 6-character code that uniquely identifies the domain in CATH. The first four characters are the PDB identifier code, the fifth character is the PDB chain identifier to which the domain belongs and the final character is the number of the domain in the chain (for chains comprising more than one domain). This character is '0' if the chain comprises a single domain only. * (2) EN - PDB identifier code. This is the 4-character PDB identifier code of the PDB entry containing the domain. * (3) TY - domain type. "CATH" or "SCOP" is given ("CATH" for DCF files generated by using CATHPARSE). * (4) CI - CATH Classification Numbers. The integers preceeding the codes CL, AR, TP, SF, FA, NI, IF are the CATH classification numbers for CLass, ARchitecture, ToPology, Homologous SuPerfamily, FAmily, Near Identical family and Identical Family respectively. These numbers uniquely identify the appropriate node in the CATH parsable files. * (5) CL - Class. It is the identical text taken from CAT.names.all.vX.X. * (6) AR - Architecture. It is the identical text taken from CAT.names.all.vX.X. * (7) TP - Topology. It is the identical text taken from CAT.names.all.vX.X. * (8) SF - Homologous Superfamily. It is the identical text taken from CAT.names.all.vX.X. * (9) DS - Sequence of the domain according to the PDB file. This sequence is taken from the domain CCF file (clean coordinate file) generated by DOMAINER. The DS record will only be present if the DCF file has been processed using DOMAINSEQS. * (10) NR - Number of residues in domain * (11) NC - Number of segments comprising the domain. All domains in CATH are from single chains. If the number of segments is greater than 1, then the domain entry will have a section containing a CN and a CH record (see below) for each segment. * (12) CN - Segment number. The number given in brackets after this record indicates the start of the data for the relevent segment. * (13) CH - Domain definition. The character given before CHAIN is the PDB chain identifier, the strings before START and END give the start and end positions respectively of the domain in the PDB file (a '.' is given in cases where a position was not specified). Note that the start and end positions refer to residue numbering given in the original pdb file and therefore must be treated as strings. (14) XX - used for spacing. (15) // - used to delimit records for a domain. Output files for usage example File: Ecath.dat ID 1CUK03 XX EN 1CUK XX TY CATH XX CI 1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;1 IF; XX CL Mainly Alpha XX AR Orthogonal Bundle XX TP Helicase, Ruva Protein, domain 3 XX SF DNA helicase RuvA subunit, C-terminal domain XX NR 48 XX NC 1 XX CN [1] XX CH 0 CHAIN; 156 START; 203 END; // ID 1HJP03 XX EN 1HJP XX TY CATH XX CI 1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;2 IF; XX CL Mainly Alpha XX AR Orthogonal Bundle XX TP Helicase, Ruva Protein, domain 3 XX SF DNA helicase RuvA subunit, C-terminal domain XX NR 44 XX NC 1 XX CN [1] XX CH 0 CHAIN; 159 START; 202 END; // File: cathparse.log 1.10.8.10 1.10.8 0001.0010 0001 1.10.8.10 1.10.8 0001.0010 0001 5.0 DATA FILES None. 6.0 USAGE 6.1 COMMAND LINE ARGUMENTS Generate DCF file from raw CATH files. Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-listfile] infile [caths.list.v2.4] This option specifies the name of raw CATH classification file (caths.list.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). [-domfile] infile [domlist.v2.4] This option specifies the name of raw CATH classification file (domlist.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). [-namesfile] infile [CAT.names.all.v2.4] This option specifies the name of raw CATH classification file (CAT.names.all.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). [-outfile] outfile [Ecath.dat] This option specifies the name of CATH 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. -logfile outfile [cathparse.log] This option specifies the name of the CATHPARSE log file. Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outfile" associated qualifiers -odirectory4 string Output directory "-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 DOMAINATRIX-0.1.650/emboss_doc/text/domainseqs.txt0000664000175000017500000002625512171064326016406 00000000000000 DOMAINSEQS 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 Add sequence records to a DCF file 2.0 INPUTS & OUTPUTS DOMAINSEQS parses a DCF file (domain classification file) and writes a file containing the same data, except that domain sequence information derived from structural and, optionally, sequence databases are added. Domain sequences are taken from domain CCF files (clean coordinate files) and (optionally) the swissprot database. If the swissprot sequence is used, DOMAINSEQS requires a swissprot:PDB equivalence file that gives the accession number of each PDB file corresponding to the domains in the DCF file. The path for the CCF files (input) and names of DCF files (input and output) are specified by the user. A log file is also written. 3.0 INPUT FILE FORMAT The format of the DCF file is described in the SCOPPARSE documentation. Input files for usage example File: ../scopparse-keep/all.scop 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 D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // File: ../pdbtosp-domainatrix/Epdbtosp.dat EN 101M XX NE 1 XX IN MYG_PHYCA ID; P02185 ACC; XX // EN 102L XX NE 1 XX IN LYCV_BPT4 ID; P00720 ACC; XX // EN 102M XX NE 1 XX IN MYG_PHYCA ID; P02185 ACC; XX // EN 103L XX NE 1 XX IN LYCV_BPT4 ID; P00720 ACC; XX // EN 103M XX NE 1 XX IN MYG_PHYCA ID; P02185 ACC; XX // EN 9XIA XX NE 1 XX IN XYLA_STRRU ID; P24300 ACC; XX // EN 9XIM XX NE 1 XX IN XYLA_ACTMI ID; P12851 ACC; XX // 4.0 OUTPUT FILE FORMAT The format of the DCF file is described in the SCOPPARSE documentation. DOMAINSEQS may add the following records: * (1) AC - Accession number of the domain sequence. This record will only be present if the DCF file has been processed using DOMAINSEQS and if an accession number for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of. * (2) SP - Swissprot code of the domain sequence. This record will only be present if the domain classification file has been processed using DOMAINSEQS and if an swissprot code for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of. * (3) RA - Position of domain in swissprot sequence. The integers preceeding START and END give the start and end points respectively of the domain sequence relative to the full-length swissprot sequence. * (4) SQ - Sequence of the domain according to swissprot. This sequence is taken from the swissprot database. The SQ record will only be present if the SCOP classification file has been processed using DOMAINSEQS and if an accession number for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of. Output files for usage example File: all_s.scop 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 DS SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64; ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // ID D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX DS SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64; MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT LKKAI XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // File: domainseqs.log // D1CS4A_ NO_ACCESSION_NUMBER // D1II7A_ NO_ACCESSION_NUMBER 5.0 DATA FILES If the user specified retrieval of sequences from a sequence database, DOMAINSEQS uses a swissprot:PDB equivalence file is generated by using PDBTOSP. 6.0 USAGE 6.1 COMMAND LINE ARGUMENTS Add sequence records to 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. [-dpdbdir] directory [./] This option specifies the location of domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. -getswiss toggle [N] Retrieve swissprot sequence. * -pdbtospfile infile This option specifies the name of the pdbcodes to swissprot indexing file. The swissprot:PDB equivalence file is generated by PDBTOSP [-dcfoutfile] outfile [domainseqs.out] 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. -logfile outfile [domainseqs.log] This option specifies the name of log file for the build. The log file contains messages about any errors arising while domainseqs ran. Additional (Optional) qualifiers (* if not always prompted): * -datafile matrixf [EBLOSUM62] This option specifies the residue substitution matrix, which is used for sequence comparison. * -gapopen float [10.0 for any sequence] This option specifies the gap insertion penalty. This 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. This 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. (Floating point number from 0.0 to 10.0) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-dpdbdir" associated qualifiers -extension2 string Default file extension "-dcfoutfile" associated qualifiers -odirectory3 string Output directory "-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. 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The secondary strructure file contains a (1) secondary structure element map (a string where each character represents a secondary structure element) and (2) a secondary structure string (each character represents an amino acid residue) for a given query. Matches are found by global alignment of (1) element maps and (2) strings (individual residues) to generate the two DCF (output) files. The DCF input file must contain domain secondary structure information, which can be added by using DOMAINSSE. The names of the secondary structure file, DCF files (input and output) and number of top-scoring matches to report are specified by the user. A log file is also written. 3.0 INPUT FILE FORMAT Domain classification file The format of the DCF file is described in the SCOPPARSE documentation. The DCF input file must contain domain secondary structure information, which can be added by using DOMAINSSE. Secondary structure file The format of the secondary structure file (Figure 1) is identical to the SS and SE records from a DCF file (see DOMAINSSE documentation.). The records are as follows: * (1) SS - Secondary structure assignment (per residue). A simplified 3-state assignment: H (helix), E (extended, beta strand) and L (loop, open coil) should be used. * (2) SE - Secondary structure element assignment (per secondary structure element). The same 3-state assignment as for the SS record should be used. Note that if the file contains secondary structure characters other than H, E and L they will be converted before they are used by SSEMATCH (see NOTES below). Input files for usage example File: sse.in SE HEEE SS SEQUENCE 43 AA; 5411 MW; 61C5458D CRC32; LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL File: ../domainsse-keep/domainsse.out 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 SE HH XX SS SEQUENCE 46 AA; 6039 MW; 32D7FC5C51294C12 CRC64; LLLHHHHHHH LLHHHHHHHH HHHHHHHHHH HHHHHLLEEE EEELLL XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // ID D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX SE HEEE XX SS SEQUENCE 43 AA; 5411 MW; F2A5FA03304F5F35 CRC64; LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // 4.0 OUTPUT FILE FORMAT The format of the DCF file is described in the SCOPPARSE documentation. SSEMATCH adds an extra comment line at the top containing the score for the appropriate alignment (residue or element). Output files for usage example File: res.dcf XX ALIGNMENT SCORE 100.000 XX ID D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX SE HEEE XX SS SEQUENCE 43 AA; 5411 MW; F2A5FA03304F5F35 CRC64; LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // File: elm.dcf XX ALIGNMENT SCORE 100.000 XX 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 SE HH XX SS SEQUENCE 46 AA; 6039 MW; 32D7FC5C51294C12 CRC64; LLLHHHHHHH LLHHHHHHHH HHHHHHHHHH HHHHHLLEEE EEELLL XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // File: ssematch.log 5.0 DATA FILES SSEMATCH requires a secondary structure substitution table such as SSSUB distributed with EMBOSS. An example (taken from Wallqvist et al) is shown in Figure 3. Figure 3 Excerpt from a DCF (output) file H E C * H 2 -15 -4 -7 E -15 4 -4 -7 C -4 -4 2 -7 * -7 -7 -7 1 6.0 USAGE 6.1 COMMAND LINE ARGUMENTS Search a DCF file for secondary structure matches. Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-ssinfile] infile This option specifies the name of the file of secondary structure (input). [-dcfinfile] infile This option specifies the name of the 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. -maxhits integer [5] This option specifies the number of top-scoring matches to report. (Any integer value) [-outssfile] outfile [*.ssematch] This option specifies the name of the file containing top-scoring domains for residue-based alignment (output).A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). [-outsefile] outfile [*.ssematch] This option specifies the name of the file containing top-scoring domains for secondary structure element-based alignment (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). -logfile outfile [ssematch.log] This option specifies the name of the ssematch log file (output). Additional (Optional) qualifiers: -datafile matrixf [SSSUB] This option specifies the secondary structure substitution matrix. -rgapopen float [10.0 for any sequence] This options specifies the gap insertion penalty for reside-based alignment. 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) -rgapextend float [0.5 for any sequence] This options specifies the gap extension penalty for residue-based alignment. 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. (Floating point number from 0.0 to 10.0) -egapopen float [10.0 for any sequence] This options specifies the gap insertion penalty for element-based alignment. 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) -egapextend float [0.5 for any sequence] This options specifies the gap extension penalty for secondary structure element-based alignment. 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. (Floating point number from 0.0 to 10.0) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outssfile" associated qualifiers -odirectory3 string Output directory "-outsefile" associated qualifiers -odirectory4 string Output directory "-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 DOMAINATRIX-0.1.650/emboss_doc/text/.cvsignore0000664000175000017500000000002511326112734015463 00000000000000Makefile Makefile.in DOMAINATRIX-0.1.650/emboss_doc/html/0002775000175000017500000000000012171070631013526 500000000000000DOMAINATRIX-0.1.650/emboss_doc/html/CVS/0002775000175000017500000000000012171064326014165 500000000000000DOMAINATRIX-0.1.650/emboss_doc/html/CVS/Entries0000664000175000017500000000072712171064326015445 00000000000000/.cvsignore/1.1/Thu Jan 21 17:58:52 2010/-kk/ /Makefile.am/1.1/Tue Mar 7 12:47:18 2006// /index.html/1.3/Wed Aug 3 11:37:08 2011// /cathparse.html/1.22/Mon Jul 15 21:25:42 2013// /domainnr.html/1.25/Mon Jul 15 21:25:42 2013// /domainreso.html/1.28/Mon Jul 15 21:25:42 2013// /domainseqs.html/1.26/Mon Jul 15 21:25:42 2013// /domainsse.html/1.26/Mon Jul 15 21:25:42 2013// /scopparse.html/1.22/Mon Jul 15 21:25:42 2013// /ssematch.html/1.26/Mon Jul 15 21:25:42 2013// D DOMAINATRIX-0.1.650/emboss_doc/html/CVS/Root0000664000175000017500000000005612000651451014742 00000000000000rice@dev.open-bio.org:/home/repository/emboss DOMAINATRIX-0.1.650/emboss_doc/html/CVS/Repository0000664000175000017500000000006212000651451016173 00000000000000emboss/emboss/embassy/domainatrix/emboss_doc/html DOMAINATRIX-0.1.650/emboss_doc/html/domainnr.html0000664000175000017500000011450612171064326016154 00000000000000 EMBASSY: DOMAINNR documentation.

DOMAINNR 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

Input files for usage example

File: ../domainseqs-keep/all_s.scop

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
DS   SEQUENCE    52 AA;   5817 MW;  D8CCAE0E1FC0849A CRC64;
     ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
DS   SEQUENCE    65 AA;   7395 MW;  75FBE75B22FD3678 CRC64;
     MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
     LKKAI
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//




2.0 INPUTS & OUTPUTS

DOMAINNR reads a DCF file (domain classification file) containing domain sequence information and writes a DCF file in which the redundant domains are removed from each node (e.g. family, superfamily etc). Optionally, the redundant domains are written to a second DCF output file. The node of operation and input and output files are specified by the user. A log file is also written.


3.0 INPUT FILE FORMAT

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

Input files for usage example

File: ../domainseqs-keep/all_s.scop

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
DS   SEQUENCE    52 AA;   5817 MW;  D8CCAE0E1FC0849A CRC64;
     ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
DS   SEQUENCE    65 AA;   7395 MW;  75FBE75B22FD3678 CRC64;
     MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
     LKKAI
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . 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_nr.scop

ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
DS   SEQUENCE    65 AA;   7395 MW;  75FBE75B22FD3678 CRC64;
     MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
     LKKAI
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

File: domainnr.log

Classes are non-redundant
5% redundancy threshold
// Alpha and beta proteins (a+b)
Retained
D1II7A_
Rejected
D1CS4A_




5.0 DATA FILES

DOMAINNR requires a residue substitution matrix.


6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Remove redundant domains from a DCF file.
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-dcfinfile]         infile     This option specifies 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.
   -retain             toggle     [N] This option specifies whether to write
                                  redundant domains to a separate file. If
                                  this option is selected, redundant domains
                                  are written to a separate output file.
   -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 whether to remove
                                  redundancy at a single threshold % sequence
                                  similarity or remove redundancy outside a
                                  range of acceptable threshold % similarity.
                                  All permutations of pair-wise sequence
                                  alignments are calculated for each domain
                                  family in turn using the EMBOSS
                                  implementation of the Needleman and Wunsch
                                  global alignment algorithm. Redundant
                                  sequences are removed in one of two modes as
                                  follows: (i) If a pair of proteins achieve
                                  greater than a threshold percentage sequence
                                  similarity (specified by the user) the
                                  shortest sequence is discarded. (ii) If a
                                  pair of proteins have a percentage sequence
                                  similarity that lies outside an acceptable
                                  range (specified by the user) the shortest
                                  sequence is discarded. (Values: 1 (Remove
                                  redundancy at a single threshold % sequence
                                  similarity); 2 (Remove redundancy outside a
                                  range of acceptable threshold % similarity))
*  -threshold          float      [95.0] This option specifies the % sequence
                                  identity redundancy threshold, which
                                  determines the redundancy calculation. If a
                                  pair of proteins achieve greater than this
                                  threshold the shortest sequence is
                                  discarded. (Any numeric value)
*  -threshlow          float      [30.0] This option specifies the % sequence
                                  identity redundancy threshold, which
                                  determines the redundancy calculation. If a
                                  pair of proteins have a percentage sequence
                                  similarity that lies outside an acceptable
                                  range the shortest sequence is discarded.
                                  (Any numeric value)
*  -threshup           float      [90.0] This option specifies the % sequence
                                  identity redundancy threshold, which
                                  determines the redundancy calculation. If a
                                  pair of proteins have a percentage sequence
                                  similarity that lies outside an acceptable
                                  range the shortest sequence is discarded.
                                  (Any numeric value)
  [-dcfoutfile]        outfile    [test.scop] This option specifies the name
                                  of non-redundant 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.
*  -redoutfile         outfile    [*.domainnr] This option specifies the name
                                  of DCF file (domain classification file) for
                                  redundant sequences (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.
   -logfile            outfile    [domainnr.log] This option specifies the
                                  name of log file for the build. The log file
                                  contains messages about any errors arising
                                  while domainnr ran.

   Additional (Optional) qualifiers:
   -datafile           matrixf    [EBLOSUM62] This option specifies the
                                  residue substitution matrix. This is used
                                  for sequence comparison.
   -gapopen            float      [10.0 for any sequence] This option
                                  specifies the gap insertion penalty. This 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. This 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. (Floating point number
                                  from 0.0 to 10.0)

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

   "-dcfoutfile" associated qualifiers
   -odirectory2        string     Output directory

   "-redoutfile" associated qualifiers
   -odirectory         string     Output directory

   "-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 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
-retain toggle This option specifies whether to write redundant domains to a separate file. If this option is selected, redundant domains are written to a separate output file. Toggle value Yes/No No
-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 whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity. All permutations of pair-wise sequence alignments are calculated for each domain family in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded.
1 (Remove redundancy at a single threshold % sequence similarity)
2 (Remove redundancy outside a range of acceptable threshold % similarity)
1
-threshold float This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded. Any numeric value 95.0
-threshlow float This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded. Any numeric value 30.0
-threshup float This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded. Any numeric value 90.0
[-dcfoutfile]
(Parameter 2)
outfile This option specifies the name of non-redundant 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
-redoutfile outfile This option specifies the name of DCF file (domain classification file) for redundant sequences (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 <*>.domainnr
-logfile outfile This option specifies the name of log file for the build. The log file contains messages about any errors arising while domainnr ran. Output file domainnr.log
Additional (Optional) qualifiers
-datafile matrixf This option specifies the residue substitution matrix. This is used for sequence comparison. Comparison matrix file in EMBOSS data path EBLOSUM62
-gapopen float This option specifies the gap insertion penalty. This 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. This 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. Floating point number from 0.0 to 10.0 0.5 for any sequence
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-dcfoutfile" associated outfile qualifiers
-odirectory2
-odirectory_dcfoutfile
string Output directory Any string  
"-redoutfile" associated outfile qualifiers
-odirectory string Output directory Any string  
"-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 DOMAINNR is shown below. Here is a sample session with domainnr


% domainnr 
Remove redundant domains from a DCF file.
Domain classification file: ../domainseqs-keep/all_s.scop
Write redundant domains to separate file. [N]: 
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]: 1
Redundancy removal options
         1 : Remove redundancy at a single threshold % sequence similarity
         2 : Remove redundancy outside a range of acceptable threshold % similarity
Select number. [1]: 1
The % sequence identity redundancy threshold. [95.0]: 5
Domain classification output file [test.scop]: all_nr.scop
Domainatrix log output file [domainnr.log]: 
Warning: Bad args passed to ajDomainWrite

// Alpha and beta proteins (a+b)
D1CS4A_
D1II7A_

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






7.0 KNOWN BUGS & WARNINGS

None.


8.0 NOTES

If for example the user selected the node to be "Family (SCOP)" then DOMAINNR removes redundancy at the level of the SCOP family, i.e. entries belonging to the same family will be non-redundant.

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.
None


9.0 DESCRIPTION

The inclusion of very similar sequences in certain analyses will introduce undesirable bias. For example, a family may possess 100 sequences in the sequence database, but 90 of these might be essentially the same sequence, e.g. very close relatives or mutations of a single sequence. Although 100 sequences are known, the family only contains 11 sequences that are essentially unique. For many methods it is desirable to use sets of sequences that are truly representative of the larger family. DOMAINNR reads a DCF file (domain classification file) and writes a DCF file with redundant domains removed from each node in the domain classification hierarchy, e.g. family, superfamily or class.


10.0 ALGORITHM

All permutations of pair-wise sequence alignments are calculated for each node (family etc) in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded. The user must specify gap insertion and extension penalties and a residue substitution matrix for use in the alignments. % sequence similarity is calculated by using the EMBOSS function embAlignCalcSimilarity.


11.0 RELATED APPLICATIONS

See also

Program name Description
aaindexextract Extract amino acid property data from AAINDEX
allversusall Sequence similarity data from all-versus-all comparison
cathparse Generate DCF file from raw CATH files
cutgextract Extract codon usage tables from CUTG database
domainalign Generate alignments (DAF file) for nodes in a DCF file
domainer Generate domain CCF files from protein CCF files
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
hetparse Convert heterogen group dictionary to EMBL-like format
jaspextract Extract data from JASPAR
libgen Generate discriminating elements from alignments
matgen3d Generate a 3D-1D scoring matrix from CCF files
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
pepcoil Predict coiled coil regions in protein sequences
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
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
seqnr Remove redundancy from DHF files
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generate DHF files from keyword search of UniProt
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

DOMAINNR generates a log file an excerpt of which is shown in Figure 1. The first two lines give the level in the SCOP or CATH hierarchy at which redundancy was removed (e.g. 'Families') and the value of the redundancy threshold. The file then contains a section for each node, e.g. each family. Each section contains a line with the record '//' immediately followed by the name of the node (family in this case), and two lines containing 'Retained' and 'Rejected' respectively. Domain identifier codes of domains that appear in output file are listed under 'Retained', while redundant domains are listed under 'Rejected'. Tthese will be saved in a second output file if the user has specified redundant domains to be retained. The text 'ERROR filename file read error' will be given when an error was encountered during a file read.

Figure 1 Summary of ROCPLOT output
Excerpt from DOMAINNR log file
Families are non-redundant
95% redundancy threshold
// Homeodomain
Retained
D2HDDA_
D1AKHA_
D1MNMC_
Rejected
D2HDDB_
D1ENH__
D3HDDA_
WARN  d3hdda_.pxyz not found
// Di-haem cytohrome c peroxidase
WARN  ds005__.pxyz not found
WARN  Empty family
// Nuclear receptor coactivator Src-1
Retained
D2PRGC_
Rejected



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


DOMAINATRIX-0.1.650/emboss_doc/html/domainreso.html0000664000175000017500000005163112171064326016504 00000000000000 EMBASSY: DOMAINRESO documentation.

DOMAINRESO 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

Remove low resolution domains from a DCF file


2.0 INPUTS & OUTPUTS

DOMAINRESO reads a DCF file and writes a DCF file containing the same domains excluding those whose resolution (Angstrom) of structure determination exceeds a user-defined threshold. The resolution data are taken from CCF (clean coordinate files) whose path and file extension (via the ACD file) are specified by the user. The names of the input and output files are also 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: ../scopparse-keep/all.scop

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   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . 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_2.3.scop

ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//




5.0 DATA FILES

DOMAINRESO does not use any data files.


6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Remove low resolution domains from a DCF file.
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-cpdbpath]          dirlist    [./] This option specifies the location of
                                  domain CCF file (clean coordinate files)
                                  (input). A 'clean cordinate file' contains
                                  coordinate and other data for a single PDB
                                  file or a single domain from SCOP or CATH,
                                  in CCF format (EMBL-like). The files,
                                  generated by using PDBPARSE (pdb files) or
                                  DOMAINER (domains), contain 'cleaned-up'
                                  data that is self-consistent and
                                  error-corrected. Records for residue solvent
                                  accessibility and secondary structure are
                                  added to the file by using PDBPLUS.
  [-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.
   -threshold          float      [2.8] This option specifies the threshold
                                  for inclusion (Angstroms). Domains exceeding
                                  the threshold for inclusion (Angstroms)
                                  will not be given in the output file. (Any
                                  numeric value)
  [-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:

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

   "-dcfoutfile" associated qualifiers
   -odirectory3        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
[-cpdbpath]
(Parameter 1)
dirlist This option specifies the location of domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL-like). The files, generated by using PDBPARSE (pdb files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. Directory with files ./
[-dcfinfile]
(Parameter 2)
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
-threshold float This option specifies the threshold for inclusion (Angstroms). Domains exceeding the threshold for inclusion (Angstroms) will not be given in the output file. Any numeric value 2.8
[-dcfoutfile]
(Parameter 3)
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
"-cpdbpath" associated dirlist qualifiers
-extension1
-extension_cpdbpath
string Default file extension Any string ccf
"-dcfoutfile" associated outfile qualifiers
-odirectory3
-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 DOMAINRESO is shown below. Here is a sample session with domainreso


% domainreso 
Remove low resolution domains from a DCF file.
Clean domain coordinates directories [./]: ../domainer-domainatrix/
Domain classification file: ../scopparse-keep/all.scop
Threshold for inclusion (Angstroms). [2.8]: 2.3
Domain classification output file [test.scop]: all_2.3.scop

/homes/user/test/qa/domainer-domainatrix/d1cs4a_.ccf
/homes/user/test/qa/domainer-domainatrix/d1ii7a_.ccf

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.
 
domainreso /test_data /test_data/all.scop /test_data/domainreso/all_2.3.scop -threshold 2.3



7.0 KNOWN BUGS & WARNINGS

No known bugs.


8.0 NOTES

Domains that lack a value for resolution in the CCF file (e.g. theoretical models and NMR structures) are included in the output file.

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.
Clean coordinate file (for domain) CCF format (EMBL-like format for protein coordinate and derived data). Coordinate and other data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. DOMAINER Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS.
None


9.0 DESCRIPTION

It is desirable to omit poor resolution protein structures when performing certain analyses of protein domains. DOMAINRESO reads a DCF file (domain classification file) and writes one containing the same domains excluding those whose resolution (Angstrom) of structure determination exceeds a user-defined threshold.


10.0 ALGORITHM

None.


11.0 RELATED APPLICATIONS

See also

Program name Description
contacts Generate intra-chain CON files from CCF files
domainrep Reorder DCF file to identify representative structures
interface Generate inter-chain CON files from CCF files
psiphi Calculates phi and psi torsion angles from protein coordinates



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


DOMAINATRIX-0.1.650/emboss_doc/html/cathparse.html0000664000175000017500000007626112171064326016324 00000000000000 EMBASSY: CATHPARSE documentation.

CATHPARSE 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 DCF file from raw CATH files


2.0 INPUTS & OUTPUTS

CATHPARSE parses the CATH classification files, e.g. caths.list.v2.4, domlist.v2.4 and CAT.names.all.v2.4. These files are available by anonymous ftp from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4) The format of these files is explained in the README file available there. CATHPARSE writes the CATH classification to a DCF file (EMBL-like format). No changes are made to the data other than changing the format in which it is held. The input and output files are specified by the user.


3.0 INPUT FILE FORMAT

An excerpt from the raw CATH classification files, of the type caths.list.vX.X (Figure 1), domlist.vX.X (Figure 2) and CAT.names.all.vX.X (Figure 3) is shown below. The format of these files is explained in the CATH README file available by anonymous ftp from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4).

Input files for usage example

File: caths.list.small

1cuk03    1  10   8  10   1   1   1  48 1.900
1hjp03    1  10   8  10   1   1   2  44 2.500

File: domlist.small

1cuk00  D03   F00    1  0   1 - 0  66 -    1  0  67 - 0 142 -    1  0 156 - 0 203 - 
1hjp00 D03 F01  1  0    1 - 0   66 -  1  0   67 - 0  158 -  1  0  159 - 0  202 -  0  203 - 0  203 - (1) 

File: CAT.names.all.small

1.10.8           1cuk03            :Helicase, Ruva Protein, domain 3	
1.10.8.10         1cuk03    :DNA helicase RuvA subunit, C-terminal domain 
0001             2ccyA0        :Mainly Alpha
0001.0010        1eca00          :Orthogonal Bundle




4.0 OUTPUT FILE FORMAT

An example of the DCF output file is shown in Figure 4. The records used to describe an entry are as follows. Records (5) to (8) are used to describe the position of the domain in the CATH hierarchy.
  • (1) ID - Domain identifier code. This is a 6-character code that uniquely identifies the domain in CATH. The first four characters are the PDB identifier code, the fifth character is the PDB chain identifier to which the domain belongs and the final character is the number of the domain in the chain (for chains comprising more than one domain). This character is '0' if the chain comprises a single domain only.
  • (2) EN - PDB identifier code. This is the 4-character PDB identifier code of the PDB entry containing the domain.
  • (3) TY - domain type. "CATH" or "SCOP" is given ("CATH" for DCF files generated by using CATHPARSE).
  • (4) CI - CATH Classification Numbers. The integers preceeding the codes CL, AR, TP, SF, FA, NI, IF are the CATH classification numbers for CLass, ARchitecture, ToPology, Homologous SuPerfamily, FAmily, Near Identical family and Identical Family respectively. These numbers uniquely identify the appropriate node in the CATH parsable files.
  • (5) CL - Class. It is the identical text taken from CAT.names.all.vX.X.
  • (6) AR - Architecture. It is the identical text taken from CAT.names.all.vX.X.
  • (7) TP - Topology. It is the identical text taken from CAT.names.all.vX.X.
  • (8) SF - Homologous Superfamily. It is the identical text taken from CAT.names.all.vX.X.
  • (9) DS - Sequence of the domain according to the PDB file. This sequence is taken from the domain CCF file (clean coordinate file) generated by DOMAINER. The DS record will only be present if the DCF file has been processed using DOMAINSEQS.
  • (10) NR - Number of residues in domain
  • (11) NC - Number of segments comprising the domain. All domains in CATH are from single chains. If the number of segments is greater than 1, then the domain entry will have a section containing a CN and a CH record (see below) for each segment.
  • (12) CN - Segment number. The number given in brackets after this record indicates the start of the data for the relevent segment.
  • (13) CH - Domain definition. The character given before CHAIN is the PDB chain identifier, the strings before START and END give the start and end positions respectively of the domain in the PDB file (a '.' is given in cases where a position was not specified). Note that the start and end positions refer to residue numbering given in the original pdb file and therefore must be treated as strings. (14) XX - used for spacing. (15) // - used to delimit records for a domain.

Output files for usage example

File: Ecath.dat

ID   1CUK03
XX
EN   1CUK
XX
TY   CATH
XX
CI   1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;1 IF;
XX
CL   Mainly Alpha
XX
AR   Orthogonal Bundle
XX
TP   Helicase, Ruva Protein, domain 3
XX
SF   DNA helicase RuvA subunit, C-terminal domain
XX
NR   48
XX
NC   1
XX
CN   [1]
XX
CH   0 CHAIN; 156 START; 203 END;
//
ID   1HJP03
XX
EN   1HJP
XX
TY   CATH
XX
CI   1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;2 IF;
XX
CL   Mainly Alpha
XX
AR   Orthogonal Bundle
XX
TP   Helicase, Ruva Protein, domain 3
XX
SF   DNA helicase RuvA subunit, C-terminal domain
XX
NR   44
XX
NC   1
XX
CN   [1]
XX
CH   0 CHAIN; 159 START; 202 END;
//

File: cathparse.log

1.10.8.10
1.10.8
0001.0010
0001
1.10.8.10
1.10.8
0001.0010
0001




5.0 DATA FILES

None.


6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Generate DCF file from raw CATH files.
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-listfile]          infile     [caths.list.v2.4] This option specifies the
                                  name of raw CATH classification file
                                  (caths.list.vX.X) (input). The raw CATH
                                  parsable files (classification and
                                  description files) available from
                                  ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).
  [-domfile]           infile     [domlist.v2.4] This option specifies the
                                  name of raw CATH classification file
                                  (domlist.vX.X) (input). The raw CATH
                                  parsable files (classification and
                                  description files) available from
                                  ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).
  [-namesfile]         infile     [CAT.names.all.v2.4] This option specifies
                                  the name of raw CATH classification file
                                  (CAT.names.all.vX.X) (input). The raw CATH
                                  parsable files (classification and
                                  description files) available from
                                  ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).
  [-outfile]           outfile    [Ecath.dat] This option specifies the name
                                  of CATH 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.
   -logfile            outfile    [cathparse.log] This option specifies the
                                  name of the CATHPARSE log file.

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

   "-outfile" associated qualifiers
   -odirectory4        string     Output directory

   "-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
[-listfile]
(Parameter 1)
infile This option specifies the name of raw CATH classification file (caths.list.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). Input file caths.list.v2.4
[-domfile]
(Parameter 2)
infile This option specifies the name of raw CATH classification file (domlist.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). Input file domlist.v2.4
[-namesfile]
(Parameter 3)
infile This option specifies the name of raw CATH classification file (CAT.names.all.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). Input file CAT.names.all.v2.4
[-outfile]
(Parameter 4)
outfile This option specifies the name of CATH 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 Ecath.dat
-logfile outfile This option specifies the name of the CATHPARSE log file. Output file cathparse.log
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory4
-odirectory_outfile
string Output directory Any string  
"-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 CATHPARSE is shown below. Here is a sample session with cathparse


% cathparse 
Generate DCF file from raw CATH files.
Raw cath list file [caths.list.v2.4]: caths.list.small
Raw cath domlist file [domlist.v2.4]: domlist.small
Raw cath names file [CAT.names.all.v2.4]: CAT.names.all.small
Domain classification output file [Ecath.dat]: 
Domainatrix log output file [cathparse.log]: 

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




7.0 KNOWN BUGS & WARNINGS




8.0 NOTES

A future implementation will give the option of omitting from the output file domains that consist of more than one segment.

CATH includes several minor classes which are not appropriate for some anaylses. A future implementation will give the option to omit domains from minor classes.

8.1 GLOSSARY OF FILE TYPES

FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
SCOP parsable files CATH format. Raw CATH classification data. Available from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4) N.A.
Domain classification file (for CATH) DCF format (EMBL-like). Classification and other data for domains from CATH. CATHPARSE Domain sequence information can be added to the file by using DOMAINSEQS.



9.0 DESCRIPTION

The raw CATH classification files are inconvenient for some uses because the text describing the domain classification is given in a different file to the classification itself, the file formats are not easily extended and differ from other related classifications such as SCOP. CATHPARSE reads the raw CATH classification files and writes a single file in DCF (EMBL-like) format, which is an easier format to work with, is more human-readable and is more extensible than the native CATH database format.


10.0 ALGORITHM

None.


11.0 RELATED APPLICATIONS

See also

Program name Description
aaindexextract Extract amino acid property data from AAINDEX
allversusall Sequence similarity data from all-versus-all comparison
cutgextract Extract codon usage tables from CUTG database
domainalign Generate alignments (DAF file) for nodes in a DCF file
domainer Generate domain CCF files from protein CCF 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
hetparse Convert heterogen group dictionary to EMBL-like format
jaspextract Extract data from JASPAR
libgen Generate discriminating elements from alignments
matgen3d Generate a 3D-1D scoring matrix from CCF files
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
pepcoil Predict coiled coil regions in protein sequences
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
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
seqnr Remove redundancy from DHF files
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generate DHF files from keyword search of UniProt
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

Mike Hurley
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

1. Conte, L.L., Ailey, B., Hubbard, T.J. Brenner, S.E., Murzin, A.G. and Chothia, C. (2000) SCOP: a structural classification of proteins database. Nucleic Acids Res. 28, 257-259. DOMAINATRIX-0.1.650/emboss_doc/html/domainseqs.html0000664000175000017500000010333512171064326016506 00000000000000 EMBASSY: DOMAINSEQS documentation.

DOMAINSEQS 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

Add sequence records to a DCF file


2.0 INPUTS & OUTPUTS

DOMAINSEQS parses a DCF file (domain classification file) and writes a file containing the same data, except that domain sequence information derived from structural and, optionally, sequence databases are added. Domain sequences are taken from domain CCF files (clean coordinate files) and (optionally) the swissprot database. If the swissprot sequence is used, DOMAINSEQS requires a swissprot:PDB equivalence file that gives the accession number of each PDB file corresponding to the domains in the DCF file. The path for the CCF files (input) and names of DCF files (input and output) are specified by the user. A log file is also written.


3.0 INPUT FILE FORMAT

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

Input files for usage example

File: ../scopparse-keep/all.scop

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   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

File: ../pdbtosp-domainatrix/Epdbtosp.dat

EN   101M
XX
NE   1
XX
IN   MYG_PHYCA ID; P02185 ACC;
XX
//
EN   102L
XX
NE   1
XX
IN   LYCV_BPT4 ID; P00720 ACC;
XX
//
EN   102M
XX
NE   1
XX
IN   MYG_PHYCA ID; P02185 ACC;
XX
//
EN   103L
XX
NE   1
XX
IN   LYCV_BPT4 ID; P00720 ACC;
XX
//
EN   103M
XX
NE   1
XX
IN   MYG_PHYCA ID; P02185 ACC;
XX
//
EN   9XIA
XX
NE   1
XX
IN   XYLA_STRRU ID; P24300 ACC;
XX
//
EN   9XIM
XX
NE   1
XX
IN   XYLA_ACTMI ID; P12851 ACC;
XX
//




4.0 OUTPUT FILE FORMAT

The format of the DCF file is described in the SCOPPARSE documentation.
DOMAINSEQS may add the following records:
  • (1) AC - Accession number of the domain sequence. This record will only be present if the DCF file has been processed using DOMAINSEQS and if an accession number for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of.
  • (2) SP - Swissprot code of the domain sequence. This record will only be present if the domain classification file has been processed using DOMAINSEQS and if an swissprot code for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of.
  • (3) RA - Position of domain in swissprot sequence. The integers preceeding START and END give the start and end points respectively of the domain sequence relative to the full-length swissprot sequence.
  • (4) SQ - Sequence of the domain according to swissprot. This sequence is taken from the swissprot database. The SQ record will only be present if the SCOP classification file has been processed using DOMAINSEQS and if an accession number for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of.

Output files for usage example

File: all_s.scop

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
DS   SEQUENCE    52 AA;   5817 MW;  D8CCAE0E1FC0849A CRC64;
     ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
DS   SEQUENCE    65 AA;   7395 MW;  75FBE75B22FD3678 CRC64;
     MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
     LKKAI
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

File: domainseqs.log

//
D1CS4A_        
NO_ACCESSION_NUMBER
//
D1II7A_        
NO_ACCESSION_NUMBER




5.0 DATA FILES

If the user specified retrieval of sequences from a sequence database, DOMAINSEQS uses a swissprot:PDB equivalence file is generated by using PDBTOSP.


6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Add sequence records to 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.
  [-dpdbdir]           directory  [./] This option specifies the location of
                                  domain CCF file (clean coordinate files)
                                  (input). A 'clean cordinate file' contains
                                  coordinate and other data for a single PDB
                                  file or a single domain from SCOP or CATH,
                                  in CCF format (EMBL-like). The files,
                                  generated by using PDBPARSE (PDB files) or
                                  DOMAINER (domains), contain 'cleaned-up'
                                  data that is self-consistent and
                                  error-corrected. Records for residue solvent
                                  accessibility and secondary structure are
                                  added to the file by using PDBPLUS.
   -getswiss           toggle     [N] Retrieve swissprot sequence.
*  -pdbtospfile        infile     This option specifies the name of the
                                  pdbcodes to swissprot indexing file. The
                                  swissprot:PDB equivalence file is generated
                                  by PDBTOSP
  [-dcfoutfile]        outfile    [domainseqs.out] 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.
   -logfile            outfile    [domainseqs.log] This option specifies the
                                  name of log file for the build. The log file
                                  contains messages about any errors arising
                                  while domainseqs ran.

   Additional (Optional) qualifiers (* if not always prompted):
*  -datafile           matrixf    [EBLOSUM62] This option specifies the
                                  residue substitution matrix, which is used
                                  for sequence comparison.
*  -gapopen            float      [10.0 for any sequence] This option
                                  specifies the gap insertion penalty. This 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. This 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. (Floating point number
                                  from 0.0 to 10.0)

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

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

   "-dcfoutfile" associated qualifiers
   -odirectory3        string     Output directory

   "-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
[-dpdbdir]
(Parameter 2)
directory This option specifies the location of domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. Directory ./
-getswiss toggle Retrieve swissprot sequence. Toggle value Yes/No No
-pdbtospfile infile This option specifies the name of the pdbcodes to swissprot indexing file. The swissprot:PDB equivalence file is generated by PDBTOSP Input file Required
[-dcfoutfile]
(Parameter 3)
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 domainseqs.out
-logfile outfile This option specifies the name of log file for the build. The log file contains messages about any errors arising while domainseqs ran. Output file domainseqs.log
Additional (Optional) qualifiers
-datafile matrixf This option specifies the residue substitution matrix, which is used for sequence comparison. Comparison matrix file in EMBOSS data path EBLOSUM62
-gapopen float This option specifies the gap insertion penalty. This 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. This 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. Floating point number from 0.0 to 10.0 0.5 for any sequence
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-dpdbdir" associated directory qualifiers
-extension2
-extension_dpdbdir
string Default file extension Any string ccf
"-dcfoutfile" associated outfile qualifiers
-odirectory3
-odirectory_dcfoutfile
string Output directory Any string  
"-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 DOMAINSEQS is shown below. Here is a sample session with domainseqs


% domainseqs 
Add sequence records to a DCF file.
Domain classification file: ../scopparse-keep/all.scop
Clean domain coordinates directory [./]: ../domainer-domainatrix
Retrieve swissprot sequence. [N]: Y
Swissprot:pdb equivalence table file (optional): ../pdbtosp-domainatrix/Epdbtosp.dat
Domain classification output file [domainseqs.out]: all_s.scop
Domainatrix log output file [domainseqs.log]: 

//
D1CS4A_        
//
D1II7A_        

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






7.0 KNOWN BUGS & WARNINGS

The swissprot:PDB equivalence file available as part of the EMBOSS distribution does not contain accession numbers for all PDB files and covers only a relatively small proportion of domains in SCOP.


8.0 NOTES

DOMAINSEQS will not attempt to retrieve a swissprot sequence for any domains comprised of more than a single segment, i.e. for domains whose NC record in the DCF file has a value other than 1 (see SCOPPARSE documentation).
The region of sequence to retrieve is identified by alignment of the sequence from the CCF file (structural database) to the full length sequences in swissprot. If this were to be done for segmented domains, the start and end point for the retrieved sequence (relative to the full length sequence) might actually include a completely different domain.

Consider :
(A) represents a sequence from the coordinate file for a segmented domain D1
(B) represents the full-length swissprot sequence, it includes D1, but D1 is split by a second domain D2
 
                 D1
  (A)  XXXXXXXXXXXXXXXXXXXXX
  
          D1         D2        D1
  (B) XXXXXXXXXX-----------XXXXXXXXXXX
It should be clear that for an alignment retrieving B, the start and end points for the retrieved sequence would be misleading.

The user should be aware that sequences from the domain CCF file for domains comprised of more than a single segment are not biologically significant, as the sequences are derived from different segments of one or more chains. However, such sequences might be acceptable for redundancy calculations (e.g. by using DOMAINNR) because two redundant domains made of similar fragments will have similar sequences, so the redundancy should be detectable.

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.
Clean coordinate file (for protein) CCF format (EMBL-like format for protein coordinate and derived data). Coordinate and other data for a single PDB file. The data are 'cleaned-up': self-consistent and error-corrected. PDBPARSE Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS.
Clean coordinate file (for domain) CCF format (EMBL-like format for protein coordinate and derived data). Coordinate and other data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. DOMAINER Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS.
swissprot:PDB equivalence file EMBL-like format. A file containing swissprot identifiers for PDB codes. Included in the EMBOSS distribution N.A.
None


9.0 DESCRIPTION

Domain sequences are not given in the raw SCOP or CATH parsable files, but are required for many analyses and for convenience should, ideally, be provided along with the classification itself. DOMAINSEQS reads a DCF file (domain classificaiton file) that lacks sequence information and writes one containing sequence information.


10.0 ALGORITHM

In order to find the start and end of a domain in a sequence from swissprot, the domain sequence from the domain CCF file is aligned to the full length protein sequence from swissprot. Alignment is performed first by string handling and if that fails, by using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm. Gap insertion and extension penalties used in the alignments are user-specified.


11.0 RELATED APPLICATIONS

See also

Program name Description
aaindexextract Extract amino acid property data from AAINDEX
allversusall Sequence similarity data from all-versus-all comparison
cathparse Generate DCF file from raw CATH files
cutgextract Extract codon usage tables from CUTG database
domainalign Generate alignments (DAF file) for nodes in a DCF file
domainer Generate domain CCF files from protein CCF files
domainnr Remove redundant domains from a DCF file
domainrep Reorder DCF file to identify representative structures
domainsse Add secondary structure records to a DCF file
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
hetparse Convert heterogen group dictionary to EMBL-like format
jaspextract Extract data from JASPAR
libgen Generate discriminating elements from alignments
matgen3d Generate a 3D-1D scoring matrix from CCF files
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
pepcoil Predict coiled coil regions in protein sequences
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
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
seqnr Remove redundancy from DHF files
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generate DHF files from keyword search of UniProt
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

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


DOMAINATRIX-0.1.650/emboss_doc/html/ssematch.html0000664000175000017500000010332312171064326016147 00000000000000 EMBASSY: SSEMATCH documentation.

SSEMATCH 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

Search a DCF file for secondary structure matches


2.0 INPUTS & OUTPUTS

Reads a DCF file (domain classification file) and a file of secondary structure (query) and writes DCF files containing the top-scoring matches (domains) between the query and domains from the DCF file. The secondary strructure file contains a (1) secondary structure element map (a string where each character represents a secondary structure element) and (2) a secondary structure string (each character represents an amino acid residue) for a given query. Matches are found by global alignment of (1) element maps and (2) strings (individual residues) to generate the two DCF (output) files.
The DCF input file must contain domain secondary structure information, which can be added by using DOMAINSSE.
The names of the secondary structure file, DCF files (input and output) and number of top-scoring matches to report are specified by the user. A log file is also written.


3.0 INPUT FILE FORMAT

Domain classification file
The format of the DCF file is described in the SCOPPARSE documentation.
The DCF input file must contain domain secondary structure information, which can be added by using DOMAINSSE.


Secondary structure file
The format of the secondary structure file (Figure 1) is identical to the SS and SE records from a DCF file (see DOMAINSSE documentation.).
The records are as follows:
  • (1) SS - Secondary structure assignment (per residue). A simplified 3-state assignment: H (helix), E (extended, beta strand) and L (loop, open coil) should be used.
  • (2) SE - Secondary structure element assignment (per secondary structure element). The same 3-state assignment as for the SS record should be used.
Note that if the file contains secondary structure characters other than H, E and L they will be converted before they are used by SSEMATCH (see NOTES below).

Input files for usage example

File: sse.in

SE   HEEE
SS   SEQUENCE    43 AA;   5411 MW;  61C5458D CRC32;
     LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL

File: ../domainsse-keep/domainsse.out

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
SE   HH
XX
SS   SEQUENCE    46 AA;   6039 MW;  32D7FC5C51294C12 CRC64;
     LLLHHHHHHH LLHHHHHHHH HHHHHHHHHH HHHHHLLEEE EEELLL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
SE   HEEE
XX
SS   SEQUENCE    43 AA;   5411 MW;  F2A5FA03304F5F35 CRC64;
     LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//




4.0 OUTPUT FILE FORMAT


The format of the DCF file is described in the SCOPPARSE documentation. SSEMATCH adds an extra comment line at the top containing the score for the appropriate alignment (residue or element).

Output files for usage example

File: res.dcf

XX   ALIGNMENT SCORE 100.000
XX
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
SE   HEEE
XX
SS   SEQUENCE    43 AA;   5411 MW;  F2A5FA03304F5F35 CRC64;
     LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

File: elm.dcf

XX   ALIGNMENT SCORE 100.000
XX
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
SE   HH
XX
SS   SEQUENCE    46 AA;   6039 MW;  32D7FC5C51294C12 CRC64;
     LLLHHHHHHH LLHHHHHHHH HHHHHHHHHH HHHHHLLEEE EEELLL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

File: ssematch.log





5.0 DATA FILES

SSEMATCH requires a secondary structure substitution table such as SSSUB distributed with EMBOSS. An example (taken from Wallqvist et al) is shown in Figure 3.

Figure 3 Excerpt from a DCF (output) file
    H   E   C   *
H   2 -15  -4  -7
E -15   4  -4  -7
C  -4  -4   2  -7
*  -7  -7  -7   1



6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Search a DCF file for secondary structure matches.
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-ssinfile]          infile     This option specifies the name of the file
                                  of secondary structure (input).
  [-dcfinfile]         infile     This option specifies the name of the 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.
   -maxhits            integer    [5] This option specifies the number of
                                  top-scoring matches to report. (Any integer
                                  value)
  [-outssfile]         outfile    [*.ssematch] This option specifies the name
                                  of the file containing top-scoring domains
                                  for residue-based alignment (output).A
                                  'domain classification file' contains
                                  classification and other data for domains
                                  from SCOP or CATH, in DCF format
                                  (EMBL-like).
  [-outsefile]         outfile    [*.ssematch] This option specifies the name
                                  of the file containing top-scoring domains
                                  for secondary structure element-based
                                  alignment (output). A 'domain classification
                                  file' contains classification and other
                                  data for domains from SCOP or CATH, in DCF
                                  format (EMBL-like).
   -logfile            outfile    [ssematch.log] This option specifies the
                                  name of the ssematch log file (output).

   Additional (Optional) qualifiers:
   -datafile           matrixf    [SSSUB] This option specifies the secondary
                                  structure substitution matrix.
   -rgapopen           float      [10.0 for any sequence] This options
                                  specifies the gap insertion penalty for
                                  reside-based alignment. 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)
   -rgapextend         float      [0.5 for any sequence] This options
                                  specifies the gap extension penalty for
                                  residue-based alignment. 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.
                                  (Floating point number from 0.0 to 10.0)
   -egapopen           float      [10.0 for any sequence] This options
                                  specifies the gap insertion penalty for
                                  element-based alignment. 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)
   -egapextend         float      [0.5 for any sequence] This options
                                  specifies the gap extension penalty for
                                  secondary structure element-based alignment.
                                  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. (Floating point number
                                  from 0.0 to 10.0)

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

   "-outssfile" associated qualifiers
   -odirectory3        string     Output directory

   "-outsefile" associated qualifiers
   -odirectory4        string     Output directory

   "-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
[-ssinfile]
(Parameter 1)
infile This option specifies the name of the file of secondary structure (input). Input file Required
[-dcfinfile]
(Parameter 2)
infile This option specifies the name of the 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
-maxhits integer This option specifies the number of top-scoring matches to report. Any integer value 5
[-outssfile]
(Parameter 3)
outfile This option specifies the name of the file containing top-scoring domains for residue-based alignment (output).A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). Output file <*>.ssematch
[-outsefile]
(Parameter 4)
outfile This option specifies the name of the file containing top-scoring domains for secondary structure element-based alignment (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). Output file <*>.ssematch
-logfile outfile This option specifies the name of the ssematch log file (output). Output file ssematch.log
Additional (Optional) qualifiers
-datafile matrixf This option specifies the secondary structure substitution matrix. Comparison matrix file in EMBOSS data path SSSUB
-rgapopen float This options specifies the gap insertion penalty for reside-based alignment. 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
-rgapextend float This options specifies the gap extension penalty for residue-based alignment. 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. Floating point number from 0.0 to 10.0 0.5 for any sequence
-egapopen float This options specifies the gap insertion penalty for element-based alignment. 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
-egapextend float This options specifies the gap extension penalty for secondary structure element-based alignment. 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. Floating point number from 0.0 to 10.0 0.5 for any sequence
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outssfile" associated outfile qualifiers
-odirectory3
-odirectory_outssfile
string Output directory Any string  
"-outsefile" associated outfile qualifiers
-odirectory4
-odirectory_outsefile
string Output directory Any string  
"-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 SSEMATCH is shown below. Here is a sample session with ssematch


% ssematch 
Search a DCF file for secondary structure matches.
Secondary structure file: sse.in
Domain classification file: ../domainsse-keep/domainsse.out
Number of top-scoring matches to report. [5]: 1
Domain classification residue-based output file [sse.ssematch]: res.dcf
Domain classification structure-based output file [sse.out2]: elm.dcf
Domainatrix log output file [ssematch.log]: 

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




7.0 KNOWN BUGS & WARNINGS

The SSEMATCH implementation of secondary structure mapping is the most basic and more powerful algorithms are available. Input file
The DCF input file must contain domain secondary structure information, which can be added by using DOMAINSSE.


8.0 NOTES

Conversion of secondary structure file
SSEMATCH currently only works with 3-state secondary structure assignments. The following conversions are applied to the characters in the secondary structure input file:
  • Bridge B/b, turn T, coil C are changed to 'L'.
  • Helices 'H', 'G', 'I' are changed to / remain 'H'.
  • Extended conformation ('E') remains 'E'.

8.1 GLOSSARY OF FILE TYPES

FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
Domain classification file (for SCOP) DCF format (EMBL-like). 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). Classification and other data for domains from CATH. CATHPARSE Domain sequence information can be added to the file by using DOMAINSEQS.
None


9.0 DESCRIPTION

Secondary structure element mapping is a coarse but powerful approach for identifying similarities between protein sequences. SSEMATCH implements a very basic approach whereby a query sequence of secondary structure (of elements or residues) is scanned against a library of known secondary structures for domains in SCOP or CATH, as held in a DCF file (domain classification file).


10.0 ALGORITHM

Standard N&W-type global alignment.


11.0 RELATED APPLICATIONS

See also

Program name Description
aaindexextract Extract amino acid property data from AAINDEX
allversusall Sequence similarity data from all-versus-all comparison
cathparse Generate DCF file from raw CATH files
cutgextract Extract codon usage tables from CUTG database
domainalign Generate alignments (DAF file) for nodes in a DCF file
domainer Generate domain CCF files from protein CCF 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
hetparse Convert heterogen group dictionary to EMBL-like format
jaspextract Extract data from JASPAR
libgen Generate discriminating elements from alignments
matgen3d Generate a 3D-1D scoring matrix from CCF files
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
pepcoil Predict coiled coil regions in protein sequences
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
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
seqnr Remove redundancy from DHF files
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generate DHF files from keyword search of UniProt
sites Generate residue-ligand CON files from CCF files
tfextract Process TRANSFAC transcription factor database for use by tfscan



12.0 DIAGNOSTIC ERROR MESSAGES

None.


13.0 AUTHORS

Amanda O'Reilly
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, 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

14.1 Other useful references

Wallqvist A, Fukunishi Y, Murphy LR, Fadel A, Levy RM.
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases.
Bioinformatics. 2000 Nov;16(11):988-1002.
DOMAINATRIX-0.1.650/emboss_doc/html/domainsse.html0000664000175000017500000007114612171064326016331 00000000000000 EMBASSY: DOMAINSSE documentation.

DOMAINSSE 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

Add secondary structure records to a DCF file


2.0 INPUTS & OUTPUTS

DOMAINSSE parses a DCF file (domain classification file) and writes a file containing the same data, except that domain secondary structure information derived from structural are added. Domain sequences are taken from domain CCF files (clean coordinate files). The CCF files must contain secondary structure information, which can be added by using PDBPLUS. The path for the CCF files (input) and names of DCF files (input and output) are specified by the user. The extension of CCF files is specified in the ACD file. A log file is also written.


3.0 INPUT FILE FORMAT

The format of the DCF file is described in the SCOPPARSE documentation. An example of the input file is shown in Figure 1.

Input files for usage example

File: ../scopparse-keep/all.scop

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   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//




4.0 OUTPUT FILE FORMAT

The format of the DCF file is described in the SCOPPARSE documentation. DOMAINRESO adds the following records:
  • (1) SS - Secondary structure assignment (per residue). A simplified 3-state assignment: H (helix), E (extended, beta strand) and L (loop, open coil) is used.
  • (2) SE - Secondary structure element assignment (per secondary structure element). The same 3-state assignment as for the SS record is used: H (helix), E (extended, beta strand) and L (loop, open coil).

Output files for usage example

File: domainsse.out

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
SE   HH
XX
SS   SEQUENCE    46 AA;   6039 MW;  32D7FC5C51294C12 CRC64;
     LLLHHHHHHH LLHHHHHHHH HHHHHHHHHH HHHHHLLEEE EEELLL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
SE   HEEE
XX
SS   SEQUENCE    43 AA;   5411 MW;  F2A5FA03304F5F35 CRC64;
     LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

File: domainsse.log





5.0 DATA FILES

None.


6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Add secondary structure records to a DCF file.
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-dcfinfile]         infile     This option specifies the name of the 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.
  [-dccfdir]           directory  [./] This option specifies the location of
                                  the domain CCF file (clean coordinate files)
                                  (input). A 'clean cordinate file' contains
                                  protein coordinate and derived data for a
                                  single PDB file ('protein clean coordinate
                                  file') or a single domain from SCOP or CATH
                                  ('domain clean coordinate file'), in CCF
                                  format (EMBL-like). The files, generated by
                                  using PDBPARSE (PDB files) or DOMAINER
                                  (domains), contain 'cleaned-up' data that is
                                  self-consistent and error-corrected.
                                  Records for residue solvent accessibility
                                  and secondary structure are added to the
                                  file by using PDBPLUS.
  [-dcfoutfile]        outfile    [*.domainsse] This option specifies the name
                                  of the DCF file (domain classification
                                  file) with secondary structure records
                                  (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.
  [-logfile]           outfile    [domainsse.log] This option specifies the
                                  name of the DOMAINSSE log file.

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

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

   "-dcfoutfile" associated qualifiers
   -odirectory3        string     Output directory

   "-logfile" associated qualifiers
   -odirectory4        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 the 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
[-dccfdir]
(Parameter 2)
directory This option specifies the location of the domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. Directory ./
[-dcfoutfile]
(Parameter 3)
outfile This option specifies the name of the DCF file (domain classification file) with secondary structure records (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 <*>.domainsse
[-logfile]
(Parameter 4)
outfile This option specifies the name of the DOMAINSSE log file. Output file domainsse.log
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-dccfdir" associated directory qualifiers
-extension2
-extension_dccfdir
string Default file extension Any string ccf
"-dcfoutfile" associated outfile qualifiers
-odirectory3
-odirectory_dcfoutfile
string Output directory Any string  
"-logfile" associated outfile qualifiers
-odirectory4
-odirectory_logfile
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 DOMAINSSE is shown below. Here is a sample session with domainsse


% domainsse 
Add secondary structure records to a DCF file.
Domain classification file: ../scopparse-keep/all.scop
Clean domain coordinates directory [./]: ../domainer-domainatrix
Domain classification output file [all.domainsse]: domainsse.out
Domainatrix log output file [domainsse.log]: domainsse.log

Processing D1CS4A_
Processing D1II7A_

Done!
 output file name: domainsse.out
 log file name: domainsse.log

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






7.0 KNOWN BUGS & WARNINGS

None.


8.0 NOTES

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.
Clean coordinate file (for protein) CCF format (EMBL-like format for protein coordinate and derived data). Coordinate and other data for a single PDB file. The data are 'cleaned-up': self-consistent and error-corrected. PDBPARSE Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS.
Clean coordinate file (for domain) CCF format (EMBL-like format for protein coordinate and derived data). Coordinate and other data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. DOMAINER Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS.
None


9.0 DESCRIPTION

Domain secondary structure information is not given in the raw SCOP or CATH parsable files, but is required for many analyses and for convenience should, ideally, be provided along with the classification itself. DOMAINSSE reads a DCF file (domain classificaiton file) that lacks secondary structure information and writes one containing such information.


10.0 ALGORITHM

None.


11.0 RELATED APPLICATIONS

See also

Program name Description
aaindexextract Extract amino acid property data from AAINDEX
allversusall Sequence similarity data from all-versus-all comparison
cathparse Generate DCF file from raw CATH files
cutgextract Extract codon usage tables from CUTG database
domainalign Generate alignments (DAF file) for nodes in a DCF file
domainer Generate domain CCF files from protein CCF 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
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
hetparse Convert heterogen group dictionary to EMBL-like format
jaspextract Extract data from JASPAR
libgen Generate discriminating elements from alignments
matgen3d Generate a 3D-1D scoring matrix from CCF files
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
pepcoil Predict coiled coil regions in protein sequences
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
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
seqnr Remove redundancy from DHF files
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generate DHF files from keyword search of UniProt
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


DOMAINATRIX-0.1.650/emboss_doc/html/scopparse.html0000664000175000017500000010375612171064326016351 00000000000000 EMBASSY: SCOPPARSE documentation.

SCOPPARSE 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 DCF file from raw SCOP files


2.0 INPUTS & OUTPUTS

SCOPPARSE parses the dir.cla.scop.txt and dir.des.scop.txt SCOP classification files, e.g. available at URLs:
http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57
http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57

The format of these files is explained at URL:
http://scop.mrc-lmb.cam.ac.uk/scop/release-notes-1.55.html

SCOPPARSE writes the classification to a DCF file (EMBL-like format). No changes are made to the data other than changing the format in which it is held. The file does not include domain sequence information. The input and output files are specified by the user.


3.0 INPUT FILE FORMAT

An excerpt from the dir.cla.scop.txt (Figure 1) and dir.des.scop.txt (Figure 2) SCOP input files is shown below. The format of these files is explained on the SCOP website:
http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57

Input files for usage example

File: scop.cla.raw

# dir.cla.scop.txt 
# SCOP release 1.57 (January 2002)  [File format version 1.00]
# http://scop.mrc-lmb.cam.ac.uk/scop/
# Copyright (c) 1994-2002 the scop authors; see http://scop.mrc-lmb.cam.ac.uk/scop/lic/copy.html
d1cs4a_	1cs4	A:	d.58.29.1	39418	cl=53931,cf=54861,sf=55073,fa=55074,dm=55077,sp=55078,px=39418
d1ii7a_	1ii7	A:	d.159.1.4	62415	cl=53931,cf=56299,sf=56300,fa=64427,dm=64428,sp=64429,px=62415

File: scop.des.raw

# dir.des.scop.txt 
# SCOP release 1.57 (January 2002)  [File format version 1.00]
# http://scop.mrc-lmb.cam.ac.uk/scop/
# Copyright (c) 1994-2002 the scop authors; see http://scop.mrc-lmb.cam.ac.uk/scop/lic/copy.html
53931	cl	d	-	Alpha and beta proteins (a+b)
54861	cf	d.58	-	Ferredoxin-like
55073	sf	d.58.29	-	Adenylyl and guanylyl cyclase catalytic domain
55074	fa	d.58.29.1	-	Adenylyl and guanylyl cyclase catalytic domain
55077	dm	d.58.29.1	-	Adenylyl cyclase VC1, domain C1a
55078	sp	d.58.29.1	-	Dog (Canis familiaris)
39418	px	d.58.29.1	d1cs4a_	1cs4 A:
56299	cf	d.159	-	Metallo-dependent phosphatases
56300	sf	d.159.1	-	Metallo-dependent phosphatases
64427	fa	d.159.1.4	-	DNA double-strand break repair nuclease
64428	dm	d.159.1.4	-	Mre11
64429	sp	d.159.1.4	-	Archaeon Pyrococcus furiosus
62415	px	d.159.1.4	d1ii7a_	1ii7 A:




4.0 OUTPUT FILE FORMAT

An example of the DCF output file is shown in Figure 3. The records used to describe an entry are as follows. Records (4) to (9) are used to describe the position of the domain in the SCOP hierarchy. Various other ADDITIONAL RECORDS may be present if the file is processed by other programs, e.g. DOMAINSEQS or DOMAINSSE.
  • (1) ID - Domain identifier code. This is a 7-character code that uniquely identifies the domain in SCOP. It is identical to the first 7 characters of a line in the SCOP classification file. The first character is always 'D', the next four characters are the PDB identifier code, the fifth character is the PDB chain identifier to which the domain belongs (a '.' is given in cases where the domain is composed of multiple chains, a '_' is given where a chain identifier was not specified in the PDB file) and the final character is the number of the domain in the chain (for chains comprising more than one domain) or '_' (the chain comprises a single domain only).
  • (2) EN - PDB identifier code. This is the 4-character PDB identifier code of the PDB entry containing the domain.
  • (3) TY - domain type. "CATH" or "SCOP" is given ("SCOP" for DCF files generated by using SCOPPARSE).
  • (4) SI - SCOP Sunid's. The integers preceeding the codes CL, FO, SF, FA, DO, SO and DD are the SCOP sunids for Class, Fold, Superfamily, Family, Domain, Source and domain data respectively. These numbers uniquely identify the appropriate node in the SCOP parsable files.
  • (5) CL - Domain class. It is identical to the text given after 'Class' in the SCOP classification file.
  • (6) FO - Domain fold. It is identical to the text given after 'Fold' in the SCOP classification file.
  • (7) SF - Domain superfamily. It is identical to the text given after 'Superfamily' in the SCOP classification file.
  • (8) FA - Domain family. It is identical to the text given after 'Family' in the SCOP classification file.
  • (9) DO - Domain name. It is identical to the text given after 'Protein' in the SCOP classification file.
  • (10) OS - Source of the protein. It is identical to the text given after 'Species' in the SCOP classification file.
  • (11) DS - Sequence of the domain according to the PDB file. This sequence is taken from the domain clean coordinate file generated by DOMAINER. The DS record will only be present if the DCF file has been processed using DOMAINSEQS.
  • (12) NC - Number of chains comprising the domain, or number of segments from the same chain that the domain is comprised of. NC is usually 1. If the number of chains is greater than 1, then the domain entry will have a section containing a CN and a CH record (see below) for each chain.
  • (13) CN - Chain number. The number given in brackets after this record indicates the start of the data for the relevent chain.
  • (14) CH - Domain definition. The character given before CHAIN is the PDB chain identifier (a '.' is given in cases where a chain identifier was not specified in the DCF file), the strings before START and END give the start and end positions respectively of the domain in the PDB file (a '.' is given in cases where a position was not specified). Note that the start and end positions refer to residue numbering given in the original PDB file and therefore must be treated as strings.
  • (15) XX - used for spacing.
  • (16) // - used to delimit records for a domain.

Output files for usage example

File: all.scop

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   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//




5.0 DATA FILES

No data files are used.


6.0 USAGE

Generate DCF file from raw SCOP files.
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-classfile]         infile     This option specifies the name of raw SCOP
                                  classification file dir.cla.scop.txt_X.XX
                                  (input). This is the raw SCOP classification
                                  file available at
                                  http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57.
  [-desinfile]         infile     This option specifies the name of raw SCOP
                                  description file dir.des.scop.txt_X.XX
                                  (input). This is the raw SCOP description
                                  file available at
                                  http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57.
   -nosegments         boolean    [N] This option specifies whether to omit
                                  domains comprising of more than one segment.
                                  This is necessary if a continuous residue
                                  sequence is required.
   -nomultichain       boolean    [N] This option specifies whether to omit
                                  domains comprising segments from more than
                                  one chain. This is necessary if a continuous
                                  residue sequence is required.
  [-dcffile]           outfile    [test.scop] This option specifies the name
                                  of SCOP DCF file (domain classification
                                  file) (output). A 'domain classification
                                  file' contains classification and other data
                                  for domains from the SCOP or CATH
                                  databases. The file is generated by using
                                  DOMAINER and is in DCF format (EMBL-like).
                                  Domain sequence information can be added to
                                  the file by using DOMAINSEQS.

   Additional (Optional) qualifiers:
   -nominor            boolean    [N] This option specifies whether to omit
                                  domains from minor classes (defined as
                                  anything not in class 'All alpha proteins',
                                  'All beta proteins', 'Alpha and beta
                                  proteins (a/b)' or 'Alpha and beta proteins
                                  (a+b)'). This is necessary or appropriate
                                  for many analyses.

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

   "-dcffile" associated qualifiers
   -odirectory3        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

6.1 COMMAND LINE ARGUMENTS

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-classfile]
(Parameter 1)
infile This option specifies the name of raw SCOP classification file dir.cla.scop.txt_X.XX (input). This is the raw SCOP classification file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57. Input file Required
[-desinfile]
(Parameter 2)
infile This option specifies the name of raw SCOP description file dir.des.scop.txt_X.XX (input). This is the raw SCOP description file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57. Input file Required
-nosegments boolean This option specifies whether to omit domains comprising of more than one segment. This is necessary if a continuous residue sequence is required. Boolean value Yes/No No
-nomultichain boolean This option specifies whether to omit domains comprising segments from more than one chain. This is necessary if a continuous residue sequence is required. Boolean value Yes/No No
[-dcffile]
(Parameter 3)
outfile This option specifies the name of SCOP DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from the SCOP or CATH databases. The file is generated by using DOMAINER and is in DCF format (EMBL-like). Domain sequence information can be added to the file by using DOMAINSEQS. Output file test.scop
Additional (Optional) qualifiers
-nominor boolean This option specifies whether to omit domains from minor classes (defined as anything not in class 'All alpha proteins', 'All beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta proteins (a+b)'). This is necessary or appropriate for many analyses. Boolean value Yes/No No
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-dcffile" associated outfile qualifiers
-odirectory3
-odirectory_dcffile
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 SCOPPARSE is shown below. Here is a sample session with scopparse


% scopparse 
Generate DCF file from raw SCOP files.
Raw scop classification file: scop.cla.raw
Raw scop description file: scop.des.raw
Omit domains comprising of more than one segment. [N]: Y
Omit domains comprising segments from more than one chain. [N]: N
Domain classification output file [test.scop]: all.scop

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





7.0 KNOWN BUGS & WARNINGS

None.


8.0 NOTES

Some SCOP domains are comprised of more than one segments of polypeptide chain, these segments belonging to a single or more than one polypeptide chains. It is debatable whether a domain (using the widely accepted definition) can truly consist of regions from more than polypeptide. Accordingly, SCOPPARSE gives the option of omitting from the output file domains that consist of more than one segment and domains that consist of more than one segment where the segments are from different chains.

SCOP includes several minor classes which are not appropriate for some anaylses. Accordingly, SCOPPARSE gives the option to omit domains from minor classes. This is defined as anything not in class 'All alpha proteins', 'All beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta proteins (a+b)'

8.1 GLOSSARY OF FILE TYPES

FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
SCOP parsable files SCOP format. Raw SCOP classification data. Available from http://scop.mrc-lmb.cam.ac.uk/scop/parse/ N.A.
Domain classification file (for SCOP) DCF format (EMBL-like format for domain classification data). Classification and other data for domains from SCOP. The file is in DCF format (EMBL-like). SCOPPARSE Domain sequence information can be added to the file by using DOMAINSEQS.



8.3 ADDITIONAL RECORDS

The following records for database sequence and secondary structure may be present in a DCF file that has been processed by using DOMAINSEQS or DOMAINSSE.
  • (1) AC - Accession number of the domain sequence. This record will only be present if the DCF file has been processed using DOMAINSEQS and if an accession number for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of.
  • (2) SP - Swissprot code of the domain sequence. This record will only be present if the domain classification file has been processed using DOMAINSEQS and if an swissprot code for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of.
  • (3) RA - Position of domain in swissprot sequence. The integers preceeding START and END give the start and end points respectively of the domain sequence relative to the full-length swissprot sequence.
  • (4) SQ - Sequence of the domain according to swissprot. This sequence is taken from the swissprot database. The SQ record will only be present if the SCOP classification file has been processed using DOMAINSEQS and if an accession number for the PDB file corresponding to the domain is given in the swissprot:PDB equivalence file (generated by PDBTOSP) that DOMAINSEQS makes use of.
  • (5) SS - Secondary structure assignment (per residue). A simplified 3-state assignment: H (helix), E (extended, beta strand) and L (loop, open coil) is used.
  • (6) SE - Secondary structure element assignment (per secondary structure element). The same 3-state assignment as for the SS record is used: H (helix), E (extended, beta strand) and L (loop, open coil).
XX
AC   P02213
XX
SP   GLB1_SCAIN
XX
RA   1 START; 146 END;
XX
SQ   SEQUENCE   146 AA;  15947 MW;  5868B4E5 CRC32;
     PSVYDAAAQL TADVKKDLRD SWKVIGSDKK GNGVALMTTL FADNQETIGY FKRLGDVSQG
     MANDKLRGHS ITLMYALQNF IDQLDNPDDL VCVVEKFAVN HITRKISAAE FGKINGPIKK
     VLASKNFGDK YANAWAKLVA VVQAAL
XX
AC   P02213
XX
SP   GLB1_SCAIN
XX
RA   1 START; 146 END; 
XX
SQ   SEQUENCE   146 AA;  15947 MW;  5868B4E5 CRC32;
     PSVYDAAAQL TADVKKDLRD SWKVIGSDKK GNGVALMTTL FADNQETIGY FKRLGDVSQG
     MANDKLRGHS ITLMYALQNF IDQLDNPDDL VCVVEKFAVN HITRKISAAE FGKINGPIKK
     VLASKNFGDK YANAWAKLVA VVQAAL
None


9.0 DESCRIPTION

The raw SCOP classification files are inconvenient for some uses because the text describing the domain classification is given in a different file to the classification itself, the file formats are not easily extended and differ from other related classifications such as CATH. SCOPPARSE reads the raw SCOP classification files and writes a single file in DCF (EMBL-like) format, which is an easier format to work with, is more human-readable and is more extensible than the native SCOP database format.


10.0 ALGORITHM

None.


11.0 RELATED APPLICATIONS

See also

Program name Description
aaindexextract Extract amino acid property data from AAINDEX
allversusall Sequence similarity data from all-versus-all comparison
cathparse Generate DCF file from raw CATH files
cutgextract Extract codon usage tables from CUTG database
domainalign Generate alignments (DAF file) for nodes in a DCF file
domainer Generate domain CCF files from protein CCF 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
hetparse Convert heterogen group dictionary to EMBL-like format
jaspextract Extract data from JASPAR
libgen Generate discriminating elements from alignments
matgen3d Generate a 3D-1D scoring matrix from CCF files
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
pepcoil Predict coiled coil regions in protein sequences
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
rocon Generate a hits file from comparing two DHF files
rocplot Perform ROC analysis on hits files
seqalign Extend alignments (DAF file) with sequences (DHF file)
seqfraggle Remove fragment sequences from DHF files
seqnr Remove redundancy from DHF files
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generate DHF files from keyword search of UniProt
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

Alan Bleasby (ableasby@ebi.ac.uk)

Jon Ison (jison@ebi.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, 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

1. Conte, L.L., Ailey, B., Hubbard, T.J. Brenner, S.E., Murzin, A.G. and Chothia, C. (2000) SCOP: a structural classification of proteins database. Nucleic Acids Res. 28, 257-259. DOMAINATRIX-0.1.650/emboss_doc/html/Makefile0000664000175000017500000003452312171070631015113 00000000000000# Makefile.in generated by automake 1.12.2 from Makefile.am. # emboss_doc/html/Makefile. 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DOMAINATRIX Applications


The DOMAINATRIX 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 domainatrix release

Program name Description
cathparse Generate DCF file from raw CATH files
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
scopparse Generate DCF file from raw SCOP files
ssematch Search a DCF file for secondary structure matches

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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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