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+ GNU GENERAL PUBLIC LICENSE
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+
+ 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
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
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+ This program is free software: you can redistribute it and/or modify
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+
+Also add information on how to contact you by electronic and paper mail.
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+ If the program does terminal interaction, make it output a short
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+
+ <program> Copyright (C) <year> <name of author>
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+ This is free software, and you are welcome to redistribute it
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+For more information on this, and how to apply and follow the GNU GPL, see
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+
+ The GNU General Public License does not permit incorporating your program
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+may consider it more useful to permit linking proprietary applications with
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+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
--- /dev/null
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
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+
+ This version of the GNU Lesser General Public License incorporates
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+Library.
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# Tell versions [3.59,3.63) of GNU make to not export all variables.
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# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
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Clustal W is a general purpose multiple alignment program for DNA or proteins.
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#! /bin/sh
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echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
exit ;;
+ padre:Linux:*:*)
+ echo sparc-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
elf32-i386)
TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu"
;;
- a.out-i386-linux)
- echo "${UNAME_MACHINE}-pc-linux-gnuaout"
- exit ;;
- coff-i386)
- echo "${UNAME_MACHINE}-pc-linux-gnucoff"
- exit ;;
- "")
- # Either a pre-BFD a.out linker (linux-gnuoldld) or
- # one that does not give us useful --help.
- echo "${UNAME_MACHINE}-pc-linux-gnuoldld"
- exit ;;
esac
# Determine whether the default compiler is a.out or elf
eval $set_cc_for_build
i*86:syllable:*:*)
echo ${UNAME_MACHINE}-pc-syllable
exit ;;
- i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*)
+ i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
echo i386-unknown-lynxos${UNAME_RELEASE}
exit ;;
i*86:*DOS:*:*)
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 i386.
- echo i386-pc-msdosdjgpp
+ # 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
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 ;;
rs6000:LynxOS:2.*:*)
echo rs6000-unknown-lynxos${UNAME_RELEASE}
exit ;;
- PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*)
+ PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
echo powerpc-unknown-lynxos${UNAME_RELEASE}
exit ;;
SM[BE]S:UNIX_SV:*:*)
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 ;;
i*86:rdos:*:*)
echo ${UNAME_MACHINE}-pc-rdos
exit ;;
+ i*86:AROS:*:*)
+ echo ${UNAME_MACHINE}-pc-aros
+ exit ;;
esac
#echo '(No uname command or uname output not recognized.)' 1>&2
--- /dev/null
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by clustalw configure 2.1, which was
+generated by GNU Autoconf 2.65. Invocation command line was
+
+ $ ./configure
+
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = ningal.cluster.lifesci.dundee.ac.uk
+uname -m = x86_64
+uname -r = 2.6.32-642.6.1.el6.x86_64
+uname -s = Linux
+uname -v = #1 SMP Wed Oct 5 00:36:12 UTC 2016
+
+/usr/bin/uname -p = unknown
+/bin/uname -X = unknown
+
+/bin/arch = x86_64
+/usr/bin/arch -k = unknown
+/usr/convex/getsysinfo = unknown
+/usr/bin/hostinfo = unknown
+/bin/machine = unknown
+/usr/bin/oslevel = unknown
+/bin/universe = unknown
+
+PATH: /gridware/sge/bin/lx-amd64
+PATH: /homes/fmmarquesmadeira/.local/anaconda/envs/python3/bin
+PATH: /gridware/sge/bin/lx-amd64
+PATH: /usr/lib64/qt-3.3/bin
+PATH: /usr/local/bin
+PATH: /bin
+PATH: /usr/bin
+PATH: /usr/local/sbin
+PATH: /usr/sbin
+PATH: /sbin
+PATH: /opt/dell/srvadmin/bin
+PATH: /homes/fmmarquesmadeira/.local/anaconda/bin
+PATH: /homes/fmmarquesmadeira/.local/bin/stamp4.4.2/bin/linux
+PATH: /homes/fmmarquesmadeira/.local/bin/mustang3.2.2/bin
+PATH: /homes/fmmarquesmadeira/.local/bin/mafft7.273/bin
+PATH: /homes/fmmarquesmadeira/.local/bin/foldx_Linux/bin
+PATH: /homes/fmmarquesmadeira/NOBACK/lib/oxbench_1_3//bin
+PATH: /homes/fmmarquesmadeira/.local/bin/Intellij/bin
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+configure:2211: checking build system type
+configure:2225: result: x86_64-unknown-linux-gnu
+configure:2245: checking host system type
+configure:2258: result: x86_64-unknown-linux-gnu
+configure:2278: checking target system type
+configure:2291: result: x86_64-unknown-linux-gnu
+configure:2377: checking for a BSD-compatible install
+configure:2445: result: /usr/bin/install -c
+configure:2456: checking whether build environment is sane
+configure:2506: result: yes
+configure:2647: checking for a thread-safe mkdir -p
+configure:2686: result: /bin/mkdir -p
+configure:2699: checking for gawk
+configure:2715: found /bin/gawk
+configure:2726: result: gawk
+configure:2737: checking whether make sets $(MAKE)
+configure:2759: result: yes
+configure:2840: checking whether make sets $(MAKE)
+configure:2862: result: yes
+configure:2922: checking for gcc
+configure:2938: found /usr/bin/gcc
+configure:2949: result: gcc
+configure:3178: checking for C compiler version
+configure:3187: gcc --version >&5
+gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)
+Copyright (C) 2010 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.
+
+configure:3198: $? = 0
+configure:3187: gcc -v >&5
+Using built-in specs.
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
+Thread model: posix
+gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
+configure:3198: $? = 0
+configure:3187: gcc -V >&5
+gcc: '-V' option must have argument
+configure:3198: $? = 1
+configure:3187: gcc -qversion >&5
+gcc: unrecognized option '-qversion'
+gcc: no input files
+configure:3198: $? = 1
+configure:3218: checking whether the C compiler works
+configure:3240: gcc conftest.c >&5
+configure:3244: $? = 0
+configure:3293: result: yes
+configure:3296: checking for C compiler default output file name
+configure:3298: result: a.out
+configure:3304: checking for suffix of executables
+configure:3311: gcc -o conftest conftest.c >&5
+configure:3315: $? = 0
+configure:3337: result:
+configure:3359: checking whether we are cross compiling
+configure:3367: gcc -o conftest conftest.c >&5
+configure:3371: $? = 0
+configure:3378: ./conftest
+configure:3382: $? = 0
+configure:3397: result: no
+configure:3402: checking for suffix of object files
+configure:3424: gcc -c conftest.c >&5
+configure:3428: $? = 0
+configure:3449: result: o
+configure:3453: checking whether we are using the GNU C compiler
+configure:3472: gcc -c conftest.c >&5
+configure:3472: $? = 0
+configure:3481: result: yes
+configure:3490: checking whether gcc accepts -g
+configure:3510: gcc -c -g conftest.c >&5
+configure:3510: $? = 0
+configure:3551: result: yes
+configure:3568: checking for gcc option to accept ISO C89
+configure:3632: gcc -c -g -O2 conftest.c >&5
+configure:3632: $? = 0
+configure:3645: result: none needed
+configure:3676: checking for style of include used by make
+configure:3704: result: GNU
+configure:3729: checking dependency style of gcc
+configure:3839: result: gcc3
+configure:3912: checking for g++
+configure:3928: found /usr/bin/g++
+configure:3939: result: g++
+configure:3966: checking for C++ compiler version
+configure:3975: g++ --version >&5
+g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)
+Copyright (C) 2010 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.
+
+configure:3986: $? = 0
+configure:3975: g++ -v >&5
+Using built-in specs.
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
+Thread model: posix
+gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
+configure:3986: $? = 0
+configure:3975: g++ -V >&5
+g++: '-V' option must have argument
+configure:3986: $? = 1
+configure:3975: g++ -qversion >&5
+g++: unrecognized option '-qversion'
+g++: no input files
+configure:3986: $? = 1
+configure:3990: checking whether we are using the GNU C++ compiler
+configure:4009: g++ -c conftest.cpp >&5
+configure:4009: $? = 0
+configure:4018: result: yes
+configure:4027: checking whether g++ accepts -g
+configure:4047: g++ -c -g conftest.cpp >&5
+configure:4047: $? = 0
+configure:4088: result: yes
+configure:4113: checking dependency style of g++
+configure:4223: result: gcc3
+configure:4284: checking for ranlib
+configure:4300: found /usr/bin/ranlib
+configure:4311: result: ranlib
+configure:4353: checking how to run the C++ preprocessor
+configure:4380: g++ -E conftest.cpp
+configure:4380: $? = 0
+configure:4394: g++ -E conftest.cpp
+conftest.cpp:12:28: error: ac_nonexistent.h: No such file or directory
+configure:4394: $? = 1
+configure: failed program was:
+| /* confdefs.h */
+| #define PACKAGE_NAME "clustalw"
+| #define PACKAGE_TARNAME "clustalw"
+| #define PACKAGE_VERSION "2.1"
+| #define PACKAGE_STRING "clustalw 2.1"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE_URL ""
+| #define OS_UNIX 1
+| #define PACKAGE "clustalw"
+| #define VERSION "2.1"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:4419: result: g++ -E
+configure:4439: g++ -E conftest.cpp
+configure:4439: $? = 0
+configure:4453: g++ -E conftest.cpp
+conftest.cpp:12:28: error: ac_nonexistent.h: No such file or directory
+configure:4453: $? = 1
+configure: failed program was:
+| /* confdefs.h */
+| #define PACKAGE_NAME "clustalw"
+| #define PACKAGE_TARNAME "clustalw"
+| #define PACKAGE_VERSION "2.1"
+| #define PACKAGE_STRING "clustalw 2.1"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE_URL ""
+| #define OS_UNIX 1
+| #define PACKAGE "clustalw"
+| #define VERSION "2.1"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:4482: checking for grep that handles long lines and -e
+configure:4540: result: /bin/grep
+configure:4545: checking for egrep
+configure:4607: result: /bin/grep -E
+configure:4612: checking for ANSI C header files
+configure:4632: g++ -c -g -O2 conftest.cpp >&5
+configure:4632: $? = 0
+configure:4705: g++ -o conftest -g -O2 conftest.cpp >&5
+configure:4705: $? = 0
+configure:4705: ./conftest
+configure:4705: $? = 0
+configure:4716: result: yes
+configure:4732: checking for sys/types.h
+configure:4732: g++ -c -g -O2 conftest.cpp >&5
+configure:4732: $? = 0
+configure:4732: result: yes
+configure:4732: checking for sys/stat.h
+configure:4732: g++ -c -g -O2 conftest.cpp >&5
+configure:4732: $? = 0
+configure:4732: result: yes
+configure:4732: checking for stdlib.h
+configure:4732: g++ -c -g -O2 conftest.cpp >&5
+configure:4732: $? = 0
+configure:4732: result: yes
+configure:4732: checking for string.h
+configure:4732: g++ -c -g -O2 conftest.cpp >&5
+configure:4732: $? = 0
+configure:4732: result: yes
+configure:4732: checking for memory.h
+configure:4732: g++ -c -g -O2 conftest.cpp >&5
+configure:4732: $? = 0
+configure:4732: result: yes
+configure:4732: checking for strings.h
+configure:4732: g++ -c -g -O2 conftest.cpp >&5
+configure:4732: $? = 0
+configure:4732: result: yes
+configure:4732: checking for inttypes.h
+configure:4732: g++ -c -g -O2 conftest.cpp >&5
+configure:4732: $? = 0
+configure:4732: result: yes
+configure:4732: checking for stdint.h
+configure:4732: g++ -c -g -O2 conftest.cpp >&5
+configure:4732: $? = 0
+configure:4732: result: yes
+configure:4732: checking for unistd.h
+configure:4732: g++ -c -g -O2 conftest.cpp >&5
+configure:4732: $? = 0
+configure:4732: result: yes
+configure:4745: checking for stdbool.h that conforms to C99
+configure:4830: g++ -c -g -O2 conftest.cpp >&5
+configure:4830: $? = 0
+configure:4837: result: yes
+configure:4839: checking for _Bool
+configure:4839: g++ -c -g -O2 conftest.cpp >&5
+conftest.cpp: In function 'int main()':
+conftest.cpp:58: error: '_Bool' was not declared in this scope
+configure:4839: $? = 1
+configure: failed program was:
+| /* confdefs.h */
+| #define PACKAGE_NAME "clustalw"
+| #define PACKAGE_TARNAME "clustalw"
+| #define PACKAGE_VERSION "2.1"
+| #define PACKAGE_STRING "clustalw 2.1"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE_URL ""
+| #define OS_UNIX 1
+| #define PACKAGE "clustalw"
+| #define VERSION "2.1"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| /* end confdefs.h. */
+| #include <stdio.h>
+| #ifdef HAVE_SYS_TYPES_H
+| # include <sys/types.h>
+| #endif
+| #ifdef HAVE_SYS_STAT_H
+| # include <sys/stat.h>
+| #endif
+| #ifdef STDC_HEADERS
+| # include <stdlib.h>
+| # include <stddef.h>
+| #else
+| # ifdef HAVE_STDLIB_H
+| # include <stdlib.h>
+| # endif
+| #endif
+| #ifdef HAVE_STRING_H
+| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
+| # include <memory.h>
+| # endif
+| # include <string.h>
+| #endif
+| #ifdef HAVE_STRINGS_H
+| # include <strings.h>
+| #endif
+| #ifdef HAVE_INTTYPES_H
+| # include <inttypes.h>
+| #endif
+| #ifdef HAVE_STDINT_H
+| # include <stdint.h>
+| #endif
+| #ifdef HAVE_UNISTD_H
+| # include <unistd.h>
+| #endif
+| int
+| main ()
+| {
+| if (sizeof (_Bool))
+| return 0;
+| ;
+| return 0;
+| }
+configure:4839: result: no
+configure:4855: checking for an ANSI C-conforming const
+configure:4920: g++ -c -g -O2 conftest.cpp >&5
+configure:4920: $? = 0
+configure:4927: result: yes
+configure:4935: checking for size_t
+configure:4935: g++ -c -g -O2 conftest.cpp >&5
+configure:4935: $? = 0
+configure:4935: g++ -c -g -O2 conftest.cpp >&5
+conftest.cpp: In function 'int main()':
+conftest.cpp:59: error: expected primary-expression before ')' token
+configure:4935: $? = 1
+configure: failed program was:
+| /* confdefs.h */
+| #define PACKAGE_NAME "clustalw"
+| #define PACKAGE_TARNAME "clustalw"
+| #define PACKAGE_VERSION "2.1"
+| #define PACKAGE_STRING "clustalw 2.1"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE_URL ""
+| #define OS_UNIX 1
+| #define PACKAGE "clustalw"
+| #define VERSION "2.1"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_STDBOOL_H 1
+| /* end confdefs.h. */
+| #include <stdio.h>
+| #ifdef HAVE_SYS_TYPES_H
+| # include <sys/types.h>
+| #endif
+| #ifdef HAVE_SYS_STAT_H
+| # include <sys/stat.h>
+| #endif
+| #ifdef STDC_HEADERS
+| # include <stdlib.h>
+| # include <stddef.h>
+| #else
+| # ifdef HAVE_STDLIB_H
+| # include <stdlib.h>
+| # endif
+| #endif
+| #ifdef HAVE_STRING_H
+| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
+| # include <memory.h>
+| # endif
+| # include <string.h>
+| #endif
+| #ifdef HAVE_STRINGS_H
+| # include <strings.h>
+| #endif
+| #ifdef HAVE_INTTYPES_H
+| # include <inttypes.h>
+| #endif
+| #ifdef HAVE_STDINT_H
+| # include <stdint.h>
+| #endif
+| #ifdef HAVE_UNISTD_H
+| # include <unistd.h>
+| #endif
+| int
+| main ()
+| {
+| if (sizeof ((size_t)))
+| return 0;
+| ;
+| return 0;
+| }
+configure:4935: result: yes
+configure:4961: checking for stdlib.h
+configure:4961: result: yes
+configure:4971: checking for GNU libc compatible malloc
+configure:4995: g++ -o conftest -g -O2 conftest.cpp >&5
+configure:4995: $? = 0
+configure:4995: ./conftest
+configure:4995: $? = 0
+configure:5005: result: yes
+configure:5229: creating ./config.status
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by clustalw config.status 2.1, which was
+generated by GNU Autoconf 2.65. Invocation command line was
+
+ CONFIG_FILES =
+ CONFIG_HEADERS =
+ CONFIG_LINKS =
+ CONFIG_COMMANDS =
+ $ ./config.status
+
+on ningal.cluster.lifesci.dundee.ac.uk
+
+config.status:878: creating Makefile
+config.status:878: creating m4/Makefile
+config.status:878: creating src/Makefile
+config.status:878: creating src/clustalw_version.h
+config.status:878: creating src/config.h
+config.status:1098: executing depfiles commands
+
+## ---------------- ##
+## Cache variables. ##
+## ---------------- ##
+
+ac_cv_build=x86_64-unknown-linux-gnu
+ac_cv_c_compiler_gnu=yes
+ac_cv_c_const=yes
+ac_cv_cxx_compiler_gnu=yes
+ac_cv_env_CCC_set=
+ac_cv_env_CCC_value=
+ac_cv_env_CC_set=
+ac_cv_env_CC_value=
+ac_cv_env_CFLAGS_set=
+ac_cv_env_CFLAGS_value=
+ac_cv_env_CPPFLAGS_set=
+ac_cv_env_CPPFLAGS_value=
+ac_cv_env_CXXCPP_set=
+ac_cv_env_CXXCPP_value=
+ac_cv_env_CXXFLAGS_set=
+ac_cv_env_CXXFLAGS_value=
+ac_cv_env_CXX_set=
+ac_cv_env_CXX_value=
+ac_cv_env_LDFLAGS_set=
+ac_cv_env_LDFLAGS_value=
+ac_cv_env_LIBS_set=
+ac_cv_env_LIBS_value=
+ac_cv_env_build_alias_set=
+ac_cv_env_build_alias_value=
+ac_cv_env_host_alias_set=
+ac_cv_env_host_alias_value=
+ac_cv_env_target_alias_set=
+ac_cv_env_target_alias_value=
+ac_cv_func_malloc_0_nonnull=yes
+ac_cv_header_inttypes_h=yes
+ac_cv_header_memory_h=yes
+ac_cv_header_stdbool_h=yes
+ac_cv_header_stdc=yes
+ac_cv_header_stdint_h=yes
+ac_cv_header_stdlib_h=yes
+ac_cv_header_string_h=yes
+ac_cv_header_strings_h=yes
+ac_cv_header_sys_stat_h=yes
+ac_cv_header_sys_types_h=yes
+ac_cv_header_unistd_h=yes
+ac_cv_host=x86_64-unknown-linux-gnu
+ac_cv_objext=o
+ac_cv_path_EGREP='/bin/grep -E'
+ac_cv_path_GREP=/bin/grep
+ac_cv_path_install='/usr/bin/install -c'
+ac_cv_path_mkdir=/bin/mkdir
+ac_cv_prog_AWK=gawk
+ac_cv_prog_CXXCPP='g++ -E'
+ac_cv_prog_ac_ct_CC=gcc
+ac_cv_prog_ac_ct_CXX=g++
+ac_cv_prog_ac_ct_RANLIB=ranlib
+ac_cv_prog_cc_c89=
+ac_cv_prog_cc_g=yes
+ac_cv_prog_cxx_g=yes
+ac_cv_prog_make_make_set=yes
+ac_cv_target=x86_64-unknown-linux-gnu
+ac_cv_type__Bool=no
+ac_cv_type_size_t=yes
+am_cv_CC_dependencies_compiler_type=gcc3
+am_cv_CXX_dependencies_compiler_type=gcc3
+
+## ----------------- ##
+## Output variables. ##
+## ----------------- ##
+
+ACLOCAL='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run aclocal-1.11'
+AMDEPBACKSLASH='\'
+AMDEP_FALSE='#'
+AMDEP_TRUE=''
+AMTAR='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run tar'
+AUTOCONF='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoconf'
+AUTOHEADER='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoheader'
+AUTOMAKE='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run automake-1.11'
+AWK='gawk'
+CC='gcc'
+CCDEPMODE='depmode=gcc3'
+CFLAGS='-g -O2'
+CLUSTALW_NAME='ClustalW'
+CLUSTALW_VERSION='2.1'
+CPPFLAGS=''
+CXX='g++'
+CXXCPP='g++ -E'
+CXXDEPMODE='depmode=gcc3'
+CXXFLAGS='-g -O2'
+CYGPATH_W='echo'
+DEFS='-DHAVE_CONFIG_H'
+DEPDIR='.deps'
+ECHO_C=''
+ECHO_N='-n'
+ECHO_T=''
+EGREP='/bin/grep -E'
+EXEEXT=''
+GREP='/bin/grep'
+INSTALL_DATA='${INSTALL} -m 644'
+INSTALL_PROGRAM='${INSTALL}'
+INSTALL_SCRIPT='${INSTALL}'
+INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
+LDFLAGS=''
+LIBOBJS=''
+LIBS=''
+LTLIBOBJS=''
+MAKEINFO='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run makeinfo'
+MKDIR_P='/bin/mkdir -p'
+OBJEXT='o'
+PACKAGE='clustalw'
+PACKAGE_BUGREPORT='clustalw@ucd.ie'
+PACKAGE_NAME='clustalw'
+PACKAGE_STRING='clustalw 2.1'
+PACKAGE_TARNAME='clustalw'
+PACKAGE_URL=''
+PACKAGE_VERSION='2.1'
+PATH_SEPARATOR=':'
+RANLIB='ranlib'
+SET_MAKE=''
+SHELL='/bin/sh'
+STRIP=''
+VERSION='2.1'
+ac_ct_CC='gcc'
+ac_ct_CXX='g++'
+am__EXEEXT_FALSE=''
+am__EXEEXT_TRUE='#'
+am__fastdepCC_FALSE='#'
+am__fastdepCC_TRUE=''
+am__fastdepCXX_FALSE='#'
+am__fastdepCXX_TRUE=''
+am__include='include'
+am__isrc=''
+am__leading_dot='.'
+am__quote=''
+am__tar='${AMTAR} chof - "$$tardir"'
+am__untar='${AMTAR} xf -'
+bindir='${exec_prefix}/bin'
+build='x86_64-unknown-linux-gnu'
+build_alias=''
+build_cpu='x86_64'
+build_os='linux-gnu'
+build_vendor='unknown'
+datadir='${datarootdir}'
+datarootdir='${prefix}/share'
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
+dvidir='${docdir}'
+exec_prefix='${prefix}'
+host='x86_64-unknown-linux-gnu'
+host_alias=''
+host_cpu='x86_64'
+host_os='linux-gnu'
+host_vendor='unknown'
+htmldir='${docdir}'
+includedir='${prefix}/include'
+infodir='${datarootdir}/info'
+install_sh='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/install-sh'
+libdir='${exec_prefix}/lib'
+libexecdir='${exec_prefix}/libexec'
+localedir='${datarootdir}/locale'
+localstatedir='${prefix}/var'
+mandir='${datarootdir}/man'
+mkdir_p='/bin/mkdir -p'
+oldincludedir='/usr/include'
+pdfdir='${docdir}'
+prefix='/usr/local'
+program_transform_name='s,x,x,'
+psdir='${docdir}'
+sbindir='${exec_prefix}/sbin'
+sharedstatedir='${prefix}/com'
+sysconfdir='${prefix}/etc'
+target='x86_64-unknown-linux-gnu'
+target_alias=''
+target_cpu='x86_64'
+target_os='linux-gnu'
+target_vendor='unknown'
+
+## ----------- ##
+## confdefs.h. ##
+## ----------- ##
+
+/* confdefs.h */
+#define PACKAGE_NAME "clustalw"
+#define PACKAGE_TARNAME "clustalw"
+#define PACKAGE_VERSION "2.1"
+#define PACKAGE_STRING "clustalw 2.1"
+#define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+#define PACKAGE_URL ""
+#define OS_UNIX 1
+#define PACKAGE "clustalw"
+#define VERSION "2.1"
+#define STDC_HEADERS 1
+#define HAVE_SYS_TYPES_H 1
+#define HAVE_SYS_STAT_H 1
+#define HAVE_STDLIB_H 1
+#define HAVE_STRING_H 1
+#define HAVE_MEMORY_H 1
+#define HAVE_STRINGS_H 1
+#define HAVE_INTTYPES_H 1
+#define HAVE_STDINT_H 1
+#define HAVE_UNISTD_H 1
+#define HAVE_STDBOOL_H 1
+#define HAVE_STDLIB_H 1
+#define HAVE_MALLOC 1
+
+configure: exit 0
debug=false
ac_cs_recheck=false
ac_cs_silent=false
+
SHELL=${CONFIG_SHELL-/bin/sh}
-## --------------------- ##
-## M4sh Initialization. ##
-## --------------------- ##
+export SHELL
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
# Be more Bourne compatible
DUALCASE=1; export DUALCASE # for MKS sh
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
emulate sh
NULLCMD=:
# Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
alias -g '${1+"$@"}'='"$@"'
setopt NO_GLOB_SUBST
else
- case `(set -o) 2>/dev/null` in
- *posix*) set -o posix ;;
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
esac
-
fi
-
-
-# PATH needs CR
-# Avoid depending upon Character Ranges.
-as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-as_cr_digits='0123456789'
-as_cr_alnum=$as_cr_Letters$as_cr_digits
-
as_nl='
'
export as_nl
as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
as_echo='printf %s\n'
as_echo_n='printf %s'
else
as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
as_echo_n_body='eval
arg=$1;
- case $arg in
+ case $arg in #(
*"$as_nl"*)
expr "X$arg" : "X\\(.*\\)$as_nl";
arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
}
fi
-# Support unset when possible.
-if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
- as_unset=unset
-else
- as_unset=false
-fi
-
# IFS
# We need space, tab and new line, in precisely that order. Quoting is
IFS=" "" $as_nl"
# Find who we are. Look in the path if we contain no directory separator.
-case $0 in
+case $0 in #((
*[\\/]* ) as_myself=$0 ;;
*) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
-done
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
IFS=$as_save_IFS
;;
fi
if test ! -f "$as_myself"; then
$as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
- { (exit 1); exit 1; }
+ exit 1
fi
-# Work around bugs in pre-3.0 UWIN ksh.
-for as_var in ENV MAIL MAILPATH
-do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
done
PS1='$ '
PS2='> '
LANGUAGE=C
export LANGUAGE
-# Required to use basename.
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+
+# as_fn_error ERROR [LINENO LOG_FD]
+# ---------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with status $?, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$?; test $as_status -eq 0 && as_status=1
+ if test "$3"; then
+ as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3
+ fi
+ $as_echo "$as_me: error: $1" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
if expr a : '\(a\)' >/dev/null 2>&1 &&
test "X`expr 00001 : '.*\(...\)'`" = X001; then
as_expr=expr
as_basename=false
fi
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
-# Name of the executable.
as_me=`$as_basename -- "$0" ||
$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
X"$0" : 'X\(//\)$' \| \
}
s/.*/./; q'`
-# CDPATH.
-$as_unset CDPATH
-
-
-
- as_lineno_1=$LINENO
- as_lineno_2=$LINENO
- test "x$as_lineno_1" != "x$as_lineno_2" &&
- test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
-
- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
- # uniformly replaced by the line number. The first 'sed' inserts a
- # line-number line after each line using $LINENO; the second 'sed'
- # does the real work. The second script uses 'N' to pair each
- # line-number line with the line containing $LINENO, and appends
- # trailing '-' during substitution so that $LINENO is not a special
- # case at line end.
- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
- # scripts with optimization help from Paolo Bonzini. Blame Lee
- # E. McMahon (1931-1989) for sed's syntax. :-)
- sed -n '
- p
- /[$]LINENO/=
- ' <$as_myself |
- sed '
- s/[$]LINENO.*/&-/
- t lineno
- b
- :lineno
- N
- :loop
- s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
- t loop
- s/-\n.*//
- ' >$as_me.lineno &&
- chmod +x "$as_me.lineno" ||
- { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
- { (exit 1); exit 1; }; }
-
- # Don't try to exec as it changes $[0], causing all sort of problems
- # (the dirname of $[0] is not the place where we might find the
- # original and so on. Autoconf is especially sensitive to this).
- . "./$as_me.lineno"
- # Exit status is that of the last command.
- exit
-}
-
-
-if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
- as_dirname=dirname
-else
- as_dirname=false
-fi
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
ECHO_C= ECHO_N= ECHO_T=
-case `echo -n x` in
+case `echo -n x` in #(((((
-n*)
- case `echo 'x\c'` in
+ case `echo 'xy\c'` in
*c*) ECHO_T=' ';; # ECHO_T is single tab character.
- *) ECHO_C='\c';;
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
esac;;
*)
ECHO_N='-n';;
esac
-if expr a : '\(a\)' >/dev/null 2>&1 &&
- test "X`expr 00001 : '.*\(...\)'`" = X001; then
- as_expr=expr
-else
- as_expr=false
-fi
rm -f conf$$ conf$$.exe conf$$.file
if test -d conf$$.dir; then
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
if mkdir -p . 2>/dev/null; then
- as_mkdir_p=:
+ as_mkdir_p='mkdir -p "$as_dir"'
else
test -d ./-p && rmdir ./-p
as_mkdir_p=false
if test -d "$1"; then
test -d "$1/.";
else
- case $1 in
+ case $1 in #(
-*)set "./$1";;
esac;
- case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
???[sx]*):;;*)false;;esac;fi
'\'' sh
'
exec 6>&1
-
-# Save the log message, to keep $[0] and so on meaningful, and to
+## ----------------------------------- ##
+## Main body of $CONFIG_STATUS script. ##
+## ----------------------------------- ##
+# Save the log message, to keep $0 and so on meaningful, and to
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by clustalw $as_me 2.0.12, which was
-generated by GNU Autoconf 2.63. Invocation command line was
+This file was extended by clustalw $as_me 2.1, which was
+generated by GNU Autoconf 2.65. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
CONFIG_HEADERS = $CONFIG_HEADERS
config_commands=" depfiles"
ac_cs_usage="\
-\`$as_me' instantiates files from templates according to the
-current configuration.
+\`$as_me' instantiates files and other configuration actions
+from templates according to the current configuration. Unless the files
+and actions are specified as TAGs, all are instantiated by default.
-Usage: $0 [OPTION]... [FILE]...
+Usage: $0 [OPTION]... [TAG]...
-h, --help print this help, then exit
-V, --version print version number and configuration settings, then exit
+ --config print configuration, then exit
-q, --quiet, --silent
do not print progress messages
-d, --debug don't remove temporary files
Configuration commands:
$config_commands
-Report bugs to <bug-autoconf@gnu.org>."
+Report bugs to <clustalw@ucd.ie>."
+ac_cs_config=""
ac_cs_version="\
-clustalw config.status 2.0.12
-configured by ./configure, generated by GNU Autoconf 2.63,
- with options \"\"
+clustalw config.status 2.1
+configured by ./configure, generated by GNU Autoconf 2.65,
+ with options \"$ac_cs_config\"
-Copyright (C) 2008 Free Software Foundation, Inc.
+Copyright (C) 2009 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it."
-ac_pwd='/homes/pvtroshin/workspace/clustengine/binaries/src/clustalw'
+ac_pwd='/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw'
srcdir='.'
INSTALL='/usr/bin/install -c'
MKDIR_P='/bin/mkdir -p'
ac_cs_recheck=: ;;
--version | --versio | --versi | --vers | --ver | --ve | --v | -V )
$as_echo "$ac_cs_version"; exit ;;
+ --config | --confi | --conf | --con | --co | --c )
+ $as_echo "$ac_cs_config"; exit ;;
--debug | --debu | --deb | --de | --d | -d )
debug=: ;;
--file | --fil | --fi | --f )
case $ac_optarg in
*\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
esac
- CONFIG_FILES="$CONFIG_FILES '$ac_optarg'"
+ as_fn_append CONFIG_FILES " '$ac_optarg'"
ac_need_defaults=false;;
--header | --heade | --head | --hea )
$ac_shift
case $ac_optarg in
*\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
esac
- CONFIG_HEADERS="$CONFIG_HEADERS '$ac_optarg'"
+ as_fn_append CONFIG_HEADERS " '$ac_optarg'"
ac_need_defaults=false;;
--he | --h)
# Conflict between --help and --header
- { $as_echo "$as_me: error: ambiguous option: $1
-Try \`$0 --help' for more information." >&2
- { (exit 1); exit 1; }; };;
+ as_fn_error "ambiguous option: \`$1'
+Try \`$0 --help' for more information.";;
--help | --hel | -h )
$as_echo "$ac_cs_usage"; exit ;;
-q | -quiet | --quiet | --quie | --qui | --qu | --q \
ac_cs_silent=: ;;
# This is an error.
- -*) { $as_echo "$as_me: error: unrecognized option: $1
-Try \`$0 --help' for more information." >&2
- { (exit 1); exit 1; }; } ;;
+ -*) as_fn_error "unrecognized option: \`$1'
+Try \`$0 --help' for more information." ;;
- *) ac_config_targets="$ac_config_targets $1"
+ *) as_fn_append ac_config_targets " $1"
ac_need_defaults=false ;;
esac
"src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
"src/clustalw_version.h") CONFIG_FILES="$CONFIG_FILES src/clustalw_version.h" ;;
- *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
-$as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
- { (exit 1); exit 1; }; };;
+ *) as_fn_error "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
esac
done
trap 'exit_status=$?
{ test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
' 0
- trap '{ (exit 1); exit 1; }' 1 2 13 15
+ trap 'as_fn_exit 1' 1 2 13 15
}
# Create a (secure) tmp directory for tmp files.
{
tmp=./conf$$-$RANDOM
(umask 077 && mkdir "$tmp")
-} ||
-{
- $as_echo "$as_me: cannot create a temporary directory in ." >&2
- { (exit 1); exit 1; }
-}
+} || as_fn_error "cannot create a temporary directory in ." "$LINENO" 5
# Set up the scripts for CONFIG_FILES section.
# No need to generate them if there are no CONFIG_FILES.
if test -n "$CONFIG_FILES"; then
-ac_cr='\r'
+ac_cr=`echo X | tr X '\015'`
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
+# But we know of no other shell where ac_cr would be empty at this
+# point, so we can use a bashism as a fallback.
+if test "x$ac_cr" = x; then
+ eval ac_cr=\$\'\\r\'
+fi
ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
- ac_cs_awk_cr='\\r'
+ ac_cs_awk_cr='\r'
else
ac_cs_awk_cr=$ac_cr
fi
echo 'BEGIN {' >"$tmp/subs1.awk" &&
cat >>"$tmp/subs1.awk" <<\_ACAWK &&
+S["am__EXEEXT_FALSE"]=""
+S["am__EXEEXT_TRUE"]="#"
S["LTLIBOBJS"]=""
S["LIBOBJS"]=""
S["EGREP"]="/bin/grep -E"
S["CC"]="gcc"
S["am__untar"]="${AMTAR} xf -"
S["am__tar"]="${AMTAR} chof - \"$$tardir\""
-S["AMTAR"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run tar"
+S["AMTAR"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run tar"
S["am__leading_dot"]="."
S["SET_MAKE"]=""
S["AWK"]="gawk"
S["MKDIR_P"]="/bin/mkdir -p"
S["INSTALL_STRIP_PROGRAM"]="$(install_sh) -c -s"
S["STRIP"]=""
-S["install_sh"]="$(SHELL) /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/install-sh"
-S["MAKEINFO"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run makeinfo"
-S["AUTOHEADER"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoheader"
-S["AUTOMAKE"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run automake-1.10"
-S["AUTOCONF"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoconf"
-S["ACLOCAL"]="${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run aclocal-1.10"
-S["VERSION"]="2.0.12"
+S["install_sh"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/install-sh"
+S["MAKEINFO"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run makeinfo"
+S["AUTOHEADER"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoheader"
+S["AUTOMAKE"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run automake-1.11"
+S["AUTOCONF"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoconf"
+S["ACLOCAL"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run aclocal-1.11"
+S["VERSION"]="2.1"
S["PACKAGE"]="clustalw"
S["CYGPATH_W"]="echo"
S["am__isrc"]=""
S["INSTALL_SCRIPT"]="${INSTALL}"
S["INSTALL_PROGRAM"]="${INSTALL}"
S["CLUSTALW_NAME"]="ClustalW"
-S["CLUSTALW_VERSION"]="2.0.12"
+S["CLUSTALW_VERSION"]="2.1"
S["target_os"]="linux-gnu"
S["target_vendor"]="unknown"
S["target_cpu"]="x86_64"
S["program_transform_name"]="s,x,x,"
S["prefix"]="/usr/local"
S["exec_prefix"]="${prefix}"
+S["PACKAGE_URL"]=""
S["PACKAGE_BUGREPORT"]="clustalw@ucd.ie"
-S["PACKAGE_STRING"]="clustalw 2.0.12"
-S["PACKAGE_VERSION"]="2.0.12"
+S["PACKAGE_STRING"]="clustalw 2.1"
+S["PACKAGE_VERSION"]="2.1"
S["PACKAGE_TARNAME"]="clustalw"
S["PACKAGE_NAME"]="clustalw"
S["PATH_SEPARATOR"]=":"
else
cat
fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
- || { { $as_echo "$as_me:$LINENO: error: could not setup config files machinery" >&5
-$as_echo "$as_me: error: could not setup config files machinery" >&2;}
- { (exit 1); exit 1; }; }
+ || as_fn_error "could not setup config files machinery" "$LINENO" 5
fi # test -n "$CONFIG_FILES"
# Set up the scripts for CONFIG_HEADERS section.
BEGIN {
D["PACKAGE_NAME"]=" \"clustalw\""
D["PACKAGE_TARNAME"]=" \"clustalw\""
-D["PACKAGE_VERSION"]=" \"2.0.12\""
-D["PACKAGE_STRING"]=" \"clustalw 2.0.12\""
+D["PACKAGE_VERSION"]=" \"2.1\""
+D["PACKAGE_STRING"]=" \"clustalw 2.1\""
D["PACKAGE_BUGREPORT"]=" \"clustalw@ucd.ie\""
+D["PACKAGE_URL"]=" \"\""
D["OS_UNIX"]=" 1"
D["PACKAGE"]=" \"clustalw\""
-D["VERSION"]=" \"2.0.12\""
+D["VERSION"]=" \"2.1\""
D["STDC_HEADERS"]=" 1"
D["HAVE_SYS_TYPES_H"]=" 1"
D["HAVE_SYS_STAT_H"]=" 1"
}
{ print }
_ACAWK
- { { $as_echo "$as_me:$LINENO: error: could not setup config headers machinery" >&5
-$as_echo "$as_me: error: could not setup config headers machinery" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "could not setup config headers machinery" "$LINENO" 5
fi # test -n "$CONFIG_HEADERS"
esac
case $ac_mode$ac_tag in
:[FHL]*:*);;
- :L* | :C*:*) { { $as_echo "$as_me:$LINENO: error: invalid tag $ac_tag" >&5
-$as_echo "$as_me: error: invalid tag $ac_tag" >&2;}
- { (exit 1); exit 1; }; };;
+ :L* | :C*:*) as_fn_error "invalid tag \`$ac_tag'" "$LINENO" 5;;
:[FH]-) ac_tag=-:-;;
:[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
esac
[\\/$]*) false;;
*) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
esac ||
- { { $as_echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5
-$as_echo "$as_me: error: cannot find input file: $ac_f" >&2;}
- { (exit 1); exit 1; }; };;
+ as_fn_error "cannot find input file: \`$ac_f'" "$LINENO" 5;;
esac
case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
- ac_file_inputs="$ac_file_inputs '$ac_f'"
+ as_fn_append ac_file_inputs " '$ac_f'"
done
# Let's still pretend it is `configure' which instantiates (i.e., don't
`' by configure.'
if test x"$ac_file" != x-; then
configure_input="$ac_file. $configure_input"
- { $as_echo "$as_me:$LINENO: creating $ac_file" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5
$as_echo "$as_me: creating $ac_file" >&6;}
fi
# Neutralize special characters interpreted by sed in replacement strings.
case $ac_tag in
*:-:* | *:-) cat >"$tmp/stdin" \
- || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
-$as_echo "$as_me: error: could not create $ac_file" >&2;}
- { (exit 1); exit 1; }; } ;;
+ || as_fn_error "could not create $ac_file" "$LINENO" 5 ;;
esac
;;
esac
q
}
s/.*/./; q'`
- { as_dir="$ac_dir"
- case $as_dir in #(
- -*) as_dir=./$as_dir;;
- esac
- test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
- as_dirs=
- while :; do
- case $as_dir in #(
- *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
- *) as_qdir=$as_dir;;
- esac
- as_dirs="'$as_qdir' $as_dirs"
- as_dir=`$as_dirname -- "$as_dir" ||
-$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$as_dir" : 'X\(//\)[^/]' \| \
- X"$as_dir" : 'X\(//\)$' \| \
- X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$as_dir" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
- }
- /^X\(\/\/\)[^/].*/{
- s//\1/
- q
- }
- /^X\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'`
- test -d "$as_dir" && break
- done
- test -z "$as_dirs" || eval "mkdir $as_dirs"
- } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
-$as_echo "$as_me: error: cannot create directory $as_dir" >&2;}
- { (exit 1); exit 1; }; }; }
+ as_dir="$ac_dir"; as_fn_mkdir_p
ac_builddir=.
case "$ac_dir" in
# If the template does not know about datarootdir, expand it.
# FIXME: This hack should be removed a few years after 2.60.
ac_datarootdir_hack=; ac_datarootdir_seen=
-
ac_sed_dataroot='
/datarootdir/ {
p
/@docdir@/p
/@infodir@/p
/@localedir@/p
-/@mandir@/p
-'
+/@mandir@/p'
case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
*datarootdir*) ac_datarootdir_seen=yes;;
*@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*)
- { $as_echo "$as_me:$LINENO: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5
$as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;}
ac_datarootdir_hack='
s&@datadir@&${datarootdir}&g
s&@infodir@&${datarootdir}/info&g
s&@localedir@&${datarootdir}/locale&g
s&@mandir@&${datarootdir}/man&g
- s&\${datarootdir}&${prefix}/share&g' ;;
+ s&\${datarootdir}&${prefix}/share&g' ;;
esac
ac_sed_extra="/^[ ]*VPATH[ ]*=/{
s/:*\$(srcdir):*/:/
$ac_datarootdir_hack
"
eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \
- || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
-$as_echo "$as_me: error: could not create $ac_file" >&2;}
- { (exit 1); exit 1; }; }
+ || as_fn_error "could not create $ac_file" "$LINENO" 5
test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
{ ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } &&
{ ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } &&
- { $as_echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir'
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir'
which seems to be undefined. Please make sure it is defined." >&5
$as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir'
which seems to be undefined. Please make sure it is defined." >&2;}
-) cat "$tmp/out" && rm -f "$tmp/out";;
*) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";;
esac \
- || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
-$as_echo "$as_me: error: could not create $ac_file" >&2;}
- { (exit 1); exit 1; }; }
+ || as_fn_error "could not create $ac_file" "$LINENO" 5
;;
:H)
#
$as_echo "/* $configure_input */" \
&& eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs"
} >"$tmp/config.h" \
- || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
-$as_echo "$as_me: error: could not create $ac_file" >&2;}
- { (exit 1); exit 1; }; }
+ || as_fn_error "could not create $ac_file" "$LINENO" 5
if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then
- { $as_echo "$as_me:$LINENO: $ac_file is unchanged" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5
$as_echo "$as_me: $ac_file is unchanged" >&6;}
else
rm -f "$ac_file"
mv "$tmp/config.h" "$ac_file" \
- || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
-$as_echo "$as_me: error: could not create $ac_file" >&2;}
- { (exit 1); exit 1; }; }
+ || as_fn_error "could not create $ac_file" "$LINENO" 5
fi
else
$as_echo "/* $configure_input */" \
&& eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \
- || { { $as_echo "$as_me:$LINENO: error: could not create -" >&5
-$as_echo "$as_me: error: could not create -" >&2;}
- { (exit 1); exit 1; }; }
+ || as_fn_error "could not create -" "$LINENO" 5
fi
# Compute "$ac_file"'s index in $config_headers.
_am_arg="$ac_file"
s/.*/./; q'`/stamp-h$_am_stamp_count
;;
- :C) { $as_echo "$as_me:$LINENO: executing $ac_file commands" >&5
+ :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
$as_echo "$as_me: executing $ac_file commands" >&6;}
;;
esac
q
}
s/.*/./; q'`
- { as_dir=$dirpart/$fdir
- case $as_dir in #(
- -*) as_dir=./$as_dir;;
- esac
- test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
- as_dirs=
- while :; do
- case $as_dir in #(
- *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
- *) as_qdir=$as_dir;;
- esac
- as_dirs="'$as_qdir' $as_dirs"
- as_dir=`$as_dirname -- "$as_dir" ||
-$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$as_dir" : 'X\(//\)[^/]' \| \
- X"$as_dir" : 'X\(//\)$' \| \
- X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$as_dir" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
- }
- /^X\(\/\/\)[^/].*/{
- s//\1/
- q
- }
- /^X\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'`
- test -d "$as_dir" && break
- done
- test -z "$as_dirs" || eval "mkdir $as_dirs"
- } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5
-$as_echo "$as_me: error: cannot create directory $as_dir" >&2;}
- { (exit 1); exit 1; }; }; }
+ as_dir=$dirpart/$fdir; as_fn_mkdir_p
# echo "creating $dirpart/$file"
echo '# dummy' > "$dirpart/$file"
done
done # for ac_tag
-{ (exit 0); exit 0; }
+as_fn_exit 0
#! /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
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009
# Free Software Foundation, Inc.
-timestamp='2008-01-16'
+timestamp='2009-06-11'
# This file is (in principle) common to ALL GNU software.
# The presence of a machine in this file suggests that SOME GNU software
case $maybe_os in
nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \
uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \
+ kopensolaris*-gnu* | \
storm-chaos* | os2-emx* | rtmk-nova*)
os=-$maybe_os
basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
os=
basic_machine=$1
;;
+ -bluegene*)
+ os=-cnk
+ ;;
-sim | -cisco | -oki | -wec | -winbond)
os=
basic_machine=$1
| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
| i370 | i860 | i960 | ia64 \
| ip2k | iq2000 \
+ | lm32 \
| m32c | m32r | m32rle | m68000 | m68k | m88k \
- | maxq | mb | microblaze | mcore | mep \
+ | maxq | mb | microblaze | mcore | mep | metag \
| mips | mipsbe | mipseb | mipsel | mipsle \
| mips16 \
| mips64 | mips64el \
- | mips64vr | mips64vrel \
+ | mips64octeon | mips64octeonel \
| mips64orion | mips64orionel \
+ | mips64r5900 | mips64r5900el \
+ | mips64vr | mips64vrel \
| mips64vr4100 | mips64vr4100el \
| mips64vr4300 | mips64vr4300el \
| mips64vr5000 | mips64vr5000el \
| mipsisa64sr71k | mipsisa64sr71kel \
| mipstx39 | mipstx39el \
| mn10200 | mn10300 \
+ | moxie \
| mt \
| msp430 \
| nios | nios2 \
| powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
| pyramid \
| score \
- | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
+ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
| sh64 | sh64le \
| sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
| sparcv8 | sparcv9 | sparcv9b | sparcv9v \
| v850 | v850e \
| we32k \
| x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \
- | z8k)
+ | z8k | z80)
basic_machine=$basic_machine-unknown
;;
m6811 | m68hc11 | m6812 | m68hc12)
| hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
| i*86-* | i860-* | i960-* | ia64-* \
| ip2k-* | iq2000-* \
+ | lm32-* \
| m32c-* | m32r-* | m32rle-* \
| m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
- | m88110-* | m88k-* | maxq-* | mcore-* \
+ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* \
| mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
| mips16-* \
| mips64-* | mips64el-* \
- | mips64vr-* | mips64vrel-* \
+ | mips64octeon-* | mips64octeonel-* \
| mips64orion-* | mips64orionel-* \
+ | mips64r5900-* | mips64r5900el-* \
+ | mips64vr-* | mips64vrel-* \
| mips64vr4100-* | mips64vr4100el-* \
| mips64vr4300-* | mips64vr4300el-* \
| mips64vr5000-* | mips64vr5000el-* \
| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
| pyramid-* \
| romp-* | rs6000-* \
- | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
+ | 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-* | strongarm-* | sv1-* | sx?-* \
| tahoe-* | thumb-* \
- | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* | tile-* \
| tron-* \
| v850-* | v850e-* | vax-* \
| we32k-* \
| x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \
| xstormy16-* | xtensa*-* \
| ymp-* \
- | z8k-*)
+ | z8k-* | z80-*)
;;
# Recognize the basic CPU types without company name, with glob match.
xtensa*)
basic_machine=m68k-apollo
os=-bsd
;;
+ aros)
+ basic_machine=i386-pc
+ os=-aros
+ ;;
aux)
basic_machine=m68k-apple
os=-aux
basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'`
os=-linux
;;
+ bluegene*)
+ basic_machine=powerpc-ibm
+ os=-cnk
+ ;;
c90)
basic_machine=c90-cray
os=-unicos
;;
+ cegcc)
+ basic_machine=arm-unknown
+ os=-cegcc
+ ;;
convex-c1)
basic_machine=c1-convex
os=-bsd
basic_machine=m88k-motorola
os=-sysv3
;;
+ dicos)
+ basic_machine=i686-pc
+ os=-dicos
+ ;;
djgpp)
basic_machine=i586-pc
os=-msdosdjgpp
basic_machine=z8k-unknown
os=-sim
;;
+ z80-*-coff)
+ basic_machine=z80-unknown
+ os=-sim
+ ;;
none)
basic_machine=none-none
os=-none
we32k)
basic_machine=we32k-att
;;
- sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele)
+ sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele)
basic_machine=sh-unknown
;;
sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
# Each alternative MUST END IN A *, to match a version number.
# -sysv* is not here because it comes later, after sysvr4.
-gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
- | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\
+ | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\
| -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \
+ | -kopensolaris* \
| -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
- | -aos* \
+ | -aos* | -aros* \
| -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
| -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
| -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
| -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
| -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
| -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
- | -chorusos* | -chorusrdb* \
+ | -chorusos* | -chorusrdb* | -cegcc* \
| -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
| -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \
| -uxpv* | -beos* | -mpeix* | -udk* \
-zvmoe)
os=-zvmoe
;;
+ -dicos*)
+ os=-dicos
+ ;;
-none)
;;
*)
-sunos*)
vendor=sun
;;
- -aix*)
+ -cnk*|-aix*)
vendor=ibm
;;
-beos*)
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.63 for clustalw 2.0.12.
+# Generated by GNU Autoconf 2.65 for clustalw 2.1.
#
# Report bugs to <clustalw@ucd.ie>.
#
+#
# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
-# 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
+# Inc.
+#
+#
# This configure script is free software; the Free Software Foundation
# gives unlimited permission to copy, distribute and modify it.
-## --------------------- ##
-## M4sh Initialization. ##
-## --------------------- ##
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
# Be more Bourne compatible
DUALCASE=1; export DUALCASE # for MKS sh
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
emulate sh
NULLCMD=:
# Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
alias -g '${1+"$@"}'='"$@"'
setopt NO_GLOB_SUBST
else
- case `(set -o) 2>/dev/null` in
- *posix*) set -o posix ;;
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
esac
-
fi
-
-
-# PATH needs CR
-# Avoid depending upon Character Ranges.
-as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-as_cr_digits='0123456789'
-as_cr_alnum=$as_cr_Letters$as_cr_digits
-
as_nl='
'
export as_nl
as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
as_echo='printf %s\n'
as_echo_n='printf %s'
else
as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
as_echo_n_body='eval
arg=$1;
- case $arg in
+ case $arg in #(
*"$as_nl"*)
expr "X$arg" : "X\\(.*\\)$as_nl";
arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
}
fi
-# Support unset when possible.
-if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
- as_unset=unset
-else
- as_unset=false
-fi
-
# IFS
# We need space, tab and new line, in precisely that order. Quoting is
IFS=" "" $as_nl"
# Find who we are. Look in the path if we contain no directory separator.
-case $0 in
+case $0 in #((
*[\\/]* ) as_myself=$0 ;;
*) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
-done
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
IFS=$as_save_IFS
;;
fi
if test ! -f "$as_myself"; then
$as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
- { (exit 1); exit 1; }
+ exit 1
fi
-# Work around bugs in pre-3.0 UWIN ksh.
-for as_var in ENV MAIL MAILPATH
-do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
done
PS1='$ '
PS2='> '
LANGUAGE=C
export LANGUAGE
-# Required to use basename.
-if expr a : '\(a\)' >/dev/null 2>&1 &&
- test "X`expr 00001 : '.*\(...\)'`" = X001; then
- as_expr=expr
-else
- as_expr=false
-fi
-
-if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
- as_basename=basename
-else
- as_basename=false
-fi
-
-
-# Name of the executable.
-as_me=`$as_basename -- "$0" ||
-$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
- X"$0" : 'X\(//\)$' \| \
- X"$0" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X/"$0" |
- sed '/^.*\/\([^/][^/]*\)\/*$/{
- s//\1/
- q
- }
- /^X\/\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\/\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'`
-
# CDPATH.
-$as_unset CDPATH
-
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
if test "x$CONFIG_SHELL" = x; then
- if (eval ":") 2>/dev/null; then
- as_have_required=yes
+ as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
else
- as_have_required=no
+ case \`(set -o) 2>/dev/null\` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
fi
-
- if test $as_have_required = yes && (eval ":
-(as_func_return () {
- (exit \$1)
-}
-as_func_success () {
- as_func_return 0
-}
-as_func_failure () {
- as_func_return 1
-}
-as_func_ret_success () {
- return 0
-}
-as_func_ret_failure () {
- return 1
-}
+"
+ as_required="as_fn_return () { (exit \$1); }
+as_fn_success () { as_fn_return 0; }
+as_fn_failure () { as_fn_return 1; }
+as_fn_ret_success () { return 0; }
+as_fn_ret_failure () { return 1; }
exitcode=0
-if as_func_success; then
- :
-else
- exitcode=1
- echo as_func_success failed.
-fi
-
-if as_func_failure; then
- exitcode=1
- echo as_func_failure succeeded.
-fi
-
-if as_func_ret_success; then
- :
+as_fn_success || { exitcode=1; echo as_fn_success failed.; }
+as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
+as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
+as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
+if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
+
+else
+ exitcode=1; echo positional parameters were not saved.
+fi
+test x\$exitcode = x0 || exit 1"
+ as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
+ as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
+ eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
+ test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1
+test \$(( 1 + 1 )) = 2 || exit 1"
+ if (eval "$as_required") 2>/dev/null; then :
+ as_have_required=yes
else
- exitcode=1
- echo as_func_ret_success failed.
-fi
-
-if as_func_ret_failure; then
- exitcode=1
- echo as_func_ret_failure succeeded.
+ as_have_required=no
fi
+ if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
-if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
- :
else
- exitcode=1
- echo positional parameters were not saved.
-fi
-
-test \$exitcode = 0) || { (exit 1); exit 1; }
-
-(
- as_lineno_1=\$LINENO
- as_lineno_2=\$LINENO
- test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" &&
- test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; }
-") 2> /dev/null; then
- :
-else
- as_candidate_shells=
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+as_found=false
for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- case $as_dir in
+ as_found=:
+ case $as_dir in #(
/*)
for as_base in sh bash ksh sh5; do
- as_candidate_shells="$as_candidate_shells $as_dir/$as_base"
+ # Try only shells that exist, to save several forks.
+ as_shell=$as_dir/$as_base
+ if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ CONFIG_SHELL=$as_shell as_have_required=yes
+ if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ break 2
+fi
+fi
done;;
esac
+ as_found=false
done
+$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
+ CONFIG_SHELL=$SHELL as_have_required=yes
+fi; }
IFS=$as_save_IFS
- for as_shell in $as_candidate_shells $SHELL; do
- # Try only shells that exist, to save several forks.
- if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
- { ("$as_shell") 2> /dev/null <<\_ASEOF
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
- emulate sh
- NULLCMD=:
- # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
- # is contrary to our usage. Disable this feature.
- alias -g '${1+"$@"}'='"$@"'
- setopt NO_GLOB_SUBST
-else
- case `(set -o) 2>/dev/null` in
- *posix*) set -o posix ;;
-esac
-
-fi
-
-
-:
-_ASEOF
-}; then
- CONFIG_SHELL=$as_shell
- as_have_required=yes
- if { "$as_shell" 2> /dev/null <<\_ASEOF
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
- emulate sh
- NULLCMD=:
- # Pre-4.2 versions of Zsh do 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
-
-
-:
-(as_func_return () {
- (exit $1)
-}
-as_func_success () {
- as_func_return 0
-}
-as_func_failure () {
- as_func_return 1
-}
-as_func_ret_success () {
- return 0
-}
-as_func_ret_failure () {
- return 1
-}
-
-exitcode=0
-if as_func_success; then
- :
-else
- exitcode=1
- echo as_func_success failed.
-fi
-
-if as_func_failure; then
- exitcode=1
- echo as_func_failure succeeded.
-fi
-
-if as_func_ret_success; then
- :
-else
- exitcode=1
- echo as_func_ret_success failed.
-fi
-
-if as_func_ret_failure; then
- exitcode=1
- echo as_func_ret_failure succeeded.
-fi
-
-if ( set x; as_func_ret_success y && test x = "$1" ); then
- :
-else
- exitcode=1
- echo positional parameters were not saved.
-fi
-
-test $exitcode = 0) || { (exit 1); exit 1; }
-
-(
- as_lineno_1=$LINENO
- as_lineno_2=$LINENO
- test "x$as_lineno_1" != "x$as_lineno_2" &&
- test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; }
-
-_ASEOF
-}; then
- break
-fi
-
-fi
-
- done
-
- if test "x$CONFIG_SHELL" != x; then
- for as_var in BASH_ENV ENV
- do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
- done
+ if test "x$CONFIG_SHELL" != x; then :
+ # We cannot yet assume a decent shell, so we have to provide a
+ # neutralization value for shells without unset; and this also
+ # works around shells that cannot unset nonexistent variables.
+ BASH_ENV=/dev/null
+ ENV=/dev/null
+ (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
export CONFIG_SHELL
exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
fi
-
- if test $as_have_required = no; then
- echo This script requires a shell more modern than all the
- echo shells that I found on your system. Please install a
- echo modern shell, or manually run the script under such a
- echo shell if you do have one.
- { (exit 1); exit 1; }
+ if test x$as_have_required = xno; then :
+ $as_echo "$0: This script requires a shell more modern than all"
+ $as_echo "$0: the shells that I found on your system."
+ if test x${ZSH_VERSION+set} = xset ; then
+ $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
+ $as_echo "$0: be upgraded to zsh 4.3.4 or later."
+ else
+ $as_echo "$0: Please tell bug-autoconf@gnu.org and clustalw@ucd.ie
+$0: about your system, including any error possibly output
+$0: before this message. Then install a modern shell, or
+$0: manually run the script under such a shell if you do
+$0: have one."
+ fi
+ exit 1
fi
-
-
fi
-
fi
+SHELL=${CONFIG_SHELL-/bin/sh}
+export SHELL
+# Unset more variables known to interfere with behavior of common tools.
+CLICOLOR_FORCE= GREP_OPTIONS=
+unset CLICOLOR_FORCE GREP_OPTIONS
+## --------------------- ##
+## M4sh Shell Functions. ##
+## --------------------- ##
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
-(eval "as_func_return () {
- (exit \$1)
-}
-as_func_success () {
- as_func_return 0
-}
-as_func_failure () {
- as_func_return 1
-}
-as_func_ret_success () {
- return 0
-}
-as_func_ret_failure () {
- return 1
-}
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
-exitcode=0
-if as_func_success; then
- :
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
else
- exitcode=1
- echo as_func_success failed.
-fi
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
-if as_func_failure; then
- exitcode=1
- echo as_func_failure succeeded.
-fi
-if as_func_ret_success; then
- :
+# as_fn_error ERROR [LINENO LOG_FD]
+# ---------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with status $?, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$?; test $as_status -eq 0 && as_status=1
+ if test "$3"; then
+ as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3
+ fi
+ $as_echo "$as_me: error: $1" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
else
- exitcode=1
- echo as_func_ret_success failed.
+ as_expr=false
fi
-if as_func_ret_failure; then
- exitcode=1
- echo as_func_ret_failure succeeded.
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
fi
-if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
- :
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
else
- exitcode=1
- echo positional parameters were not saved.
+ as_dirname=false
fi
-test \$exitcode = 0") || {
- echo No shell found that supports shell functions.
- echo Please tell bug-autoconf@gnu.org about your system,
- echo including any error possibly output before this message.
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# Name of the host.
# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
subdirs=
MFLAGS=
MAKEFLAGS=
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if test "$ac_abs_confdir" = "$ac_pwd"; then
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# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures clustalw 2.0.12 to adapt to many kinds of systems.
+\`configure' configures clustalw 2.1 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of clustalw 2.0.12:";;
+ short | recursive ) echo "Configuration of clustalw 2.1:";;
esac
cat <<\_ACEOF
LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
nonstandard directory <lib dir>
LIBS libraries to pass to the linker, e.g. -l<library>
- CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
+ CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
you have headers in a nonstandard directory <include dir>
CXX C++ compiler command
CXXFLAGS C++ compiler flags
Use these variables to override the choices made by `configure' or to help
it to find libraries and programs with nonstandard names/locations.
-Report bugs to <clustalw@ucd.ie>.
+Report bugs to <clustalw@ucd.ie>.
+_ACEOF
+ac_status=$?
+fi
+
+if test "$ac_init_help" = "recursive"; then
+ # If there are subdirs, report their specific --help.
+ for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
+ test -d "$ac_dir" ||
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+ ac_builddir=.
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+ac_abs_builddir=$ac_pwd$ac_dir_suffix
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+ ac_srcdir=.
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+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
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+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
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+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+ cd "$ac_dir" || { ac_status=$?; continue; }
+ # Check for guested configure.
+ if test -f "$ac_srcdir/configure.gnu"; then
+ echo &&
+ $SHELL "$ac_srcdir/configure.gnu" --help=recursive
+ elif test -f "$ac_srcdir/configure"; then
+ echo &&
+ $SHELL "$ac_srcdir/configure" --help=recursive
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+ $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
+ fi || ac_status=$?
+ cd "$ac_pwd" || { ac_status=$?; break; }
+ done
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+
+test -n "$ac_init_help" && exit $ac_status
+if $ac_init_version; then
+ cat <<\_ACEOF
+clustalw configure 2.1
+generated by GNU Autoconf 2.65
+
+Copyright (C) 2009 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
+_ACEOF
+ exit
+fi
+
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+ if { { ac_try="$ac_compile"
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+ ac_status=$?
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+ as_fn_set_status $ac_retval
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+
+# ac_fn_cxx_check_type LINENO TYPE VAR INCLUDES
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+if (sizeof ($2))
+ return 0;
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+_ACEOF
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+/* end confdefs.h. */
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+ return 0;
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+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+
+else
+ eval "$3=yes"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_cxx_check_type
+
+# ac_fn_cxx_check_header_compile LINENO HEADER VAR INCLUDES
+# ---------------------------------------------------------
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+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_cxx_check_header_compile
+
+# ac_fn_cxx_check_header_mongrel LINENO HEADER VAR INCLUDES
+# ---------------------------------------------------------
+# Tests whether HEADER exists, giving a warning if it cannot be compiled using
+# the include files in INCLUDES and setting the cache variable VAR
+# accordingly.
+ac_fn_cxx_check_header_mongrel ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
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+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
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+ # Is the header compilable?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5
+$as_echo_n "checking $2 usability... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
_ACEOF
-ac_status=$?
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_header_compiler=yes
+else
+ ac_header_compiler=no
fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5
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- { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } ||
- continue
- ac_builddir=.
+# Is the header present?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 presence" >&5
+$as_echo_n "checking $2 presence... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <$2>
+_ACEOF
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+ ac_header_preproc=yes
+else
+ ac_header_preproc=no
+fi
+rm -f conftest.err conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
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- *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
- esac ;;
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in #((
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+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
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+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $2: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
+( cat <<\_ASBOX
+## ------------------------------ ##
+## Report this to clustalw@ucd.ie ##
+## ------------------------------ ##
+_ASBOX
+ ) | sed "s/^/$as_me: WARNING: /" >&2
+ ;;
esac
-ac_abs_top_builddir=$ac_pwd
-ac_abs_builddir=$ac_pwd$ac_dir_suffix
-# for backward compatibility:
-ac_top_builddir=$ac_top_build_prefix
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=\$ac_header_compiler"
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+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
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+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
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- ac_srcdir=.
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- ac_top_srcdir=$ac_top_build_prefix$srcdir
- ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+} # ac_fn_cxx_check_header_mongrel
+
+# ac_fn_cxx_try_link LINENO
+# -------------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_link ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext conftest$ac_exeext
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
esac
-ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>conftest.err
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+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
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+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
- cd "$ac_dir" || { ac_status=$?; continue; }
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- $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
- fi || ac_status=$?
- cd "$ac_pwd" || { ac_status=$?; break; }
- done
+ ac_retval=1
fi
+ # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
+ # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
+ # interfere with the next link command; also delete a directory that is
+ # left behind by Apple's compiler. We do this before executing the actions.
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
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-if $ac_init_version; then
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+} # ac_fn_cxx_try_link
cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by clustalw $as_me 2.0.12, which was
-generated by GNU Autoconf 2.63. Invocation command line was
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do
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- $as_echo "PATH: $as_dir"
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+ $as_echo "PATH: $as_dir"
+ done
IFS=$as_save_IFS
} >&5
ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
esac
case $ac_pass in
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+ 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;;
2)
- ac_configure_args1="$ac_configure_args1 '$ac_arg'"
+ as_fn_append ac_configure_args1 " '$ac_arg'"
if test $ac_must_keep_next = true; then
ac_must_keep_next=false # Got value, back to normal.
else
-* ) ac_must_keep_next=true ;;
esac
fi
- ac_configure_args="$ac_configure_args '$ac_arg'"
+ as_fn_append ac_configure_args " '$ac_arg'"
;;
esac
done
done
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+{ ac_configure_args0=; unset ac_configure_args0;}
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# When interrupted or exit'd, cleanup temporary files, and complete
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*${as_nl}*)
case $ac_var in #(
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case $ac_var in #(
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esac
done
exit $exit_status
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for ac_signal in 1 2 13 15; do
- trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal
+ trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal
done
ac_signal=0
# confdefs.h avoids OS command line length limits that DEFS can exceed.
rm -f -r conftest* confdefs.h
+$as_echo "/* confdefs.h */" > confdefs.h
+
# Predefined preprocessor variables.
cat >>confdefs.h <<_ACEOF
#define PACKAGE_NAME "$PACKAGE_NAME"
_ACEOF
-
cat >>confdefs.h <<_ACEOF
#define PACKAGE_TARNAME "$PACKAGE_TARNAME"
_ACEOF
-
cat >>confdefs.h <<_ACEOF
#define PACKAGE_VERSION "$PACKAGE_VERSION"
_ACEOF
-
cat >>confdefs.h <<_ACEOF
#define PACKAGE_STRING "$PACKAGE_STRING"
_ACEOF
-
cat >>confdefs.h <<_ACEOF
#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
_ACEOF
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_URL "$PACKAGE_URL"
+_ACEOF
+
# Let the site file select an alternate cache file if it wants to.
# Prefer an explicitly selected file to automatically selected ones.
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do
test "x$ac_site_file" = xNONE && continue
- if test -r "$ac_site_file"; then
- { $as_echo "$as_me:$LINENO: loading site script $ac_site_file" >&5
+ if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5
$as_echo "$as_me: loading site script $ac_site_file" >&6;}
sed 's/^/| /' "$ac_site_file" >&5
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- if test -f "$cache_file"; then
- { $as_echo "$as_me:$LINENO: loading cache $cache_file" >&5
+ # Some versions of bash will fail to source /dev/null (special files
+ # actually), so we avoid doing that. DJGPP emulates it as a regular file.
+ if test /dev/null != "$cache_file" && test -f "$cache_file"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5
$as_echo "$as_me: loading cache $cache_file" >&6;}
case $cache_file in
[\\/]* | ?:[\\/]* ) . "$cache_file";;
esac
fi
else
- { $as_echo "$as_me:$LINENO: creating cache $cache_file" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5
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>$cache_file
fi
eval ac_new_val=\$ac_env_${ac_var}_value
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set,)
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ac_cache_corrupted=: ;;
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+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5
$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
ac_cache_corrupted=:
else
- { $as_echo "$as_me:$LINENO: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
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eval $ac_var=\$ac_old_val
fi
- { $as_echo "$as_me:$LINENO: former value: \`$ac_old_val'" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5
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- { $as_echo "$as_me:$LINENO: current value: \`$ac_new_val'" >&5
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esac
esac
case " $ac_configure_args " in
*" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
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esac
fi
done
if $ac_cache_corrupted; then
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$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
- { $as_echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5
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- { { $as_echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5
-$as_echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;}
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fi
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
-
-
-
-
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ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
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- break
- elif test -f "$ac_dir/shtool"; then
- ac_aux_dir=$ac_dir
- ac_install_sh="$ac_aux_dir/shtool install -c"
- break
- fi
+ for ac_t in install-sh install.sh shtool; do
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+ ac_install_sh="$ac_aux_dir/$ac_t -c"
+ break 2
+ fi
+ done
done
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fi
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-$as_echo "$as_me: error: cannot run $SHELL $ac_aux_dir/config.sub" >&2;}
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+ as_fn_error "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5
-{ $as_echo "$as_me:$LINENO: checking build system type" >&5
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$as_echo_n "checking build system type... " >&6; }
-if test "${ac_cv_build+set}" = set; then
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ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
- { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&5
-$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_build" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5
$as_echo "$ac_cv_build" >&6; }
case $ac_cv_build in
*-*-*) ;;
-*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical build" >&5
-$as_echo "$as_me: error: invalid value of canonical build" >&2;}
- { (exit 1); exit 1; }; };;
+*) as_fn_error "invalid value of canonical build" "$LINENO" 5;;
esac
build=$ac_cv_build
ac_save_IFS=$IFS; IFS='-'
case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
-{ $as_echo "$as_me:$LINENO: checking host system type" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5
$as_echo_n "checking host system type... " >&6; }
-if test "${ac_cv_host+set}" = set; then
+if test "${ac_cv_host+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if test "x$host_alias" = x; then
ac_cv_host=$ac_cv_build
else
ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
- { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&5
-$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_host" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5
$as_echo "$ac_cv_host" >&6; }
case $ac_cv_host in
*-*-*) ;;
-*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical host" >&5
-$as_echo "$as_me: error: invalid value of canonical host" >&2;}
- { (exit 1); exit 1; }; };;
+*) as_fn_error "invalid value of canonical host" "$LINENO" 5;;
esac
host=$ac_cv_host
ac_save_IFS=$IFS; IFS='-'
case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
-{ $as_echo "$as_me:$LINENO: checking target system type" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking target system type" >&5
$as_echo_n "checking target system type... " >&6; }
-if test "${ac_cv_target+set}" = set; then
+if test "${ac_cv_target+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if test "x$target_alias" = x; then
ac_cv_target=$ac_cv_host
else
ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` ||
- { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&5
-$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_target" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_target" >&5
$as_echo "$ac_cv_target" >&6; }
case $ac_cv_target in
*-*-*) ;;
-*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical target" >&5
-$as_echo "$as_me: error: invalid value of canonical target" >&2;}
- { (exit 1); exit 1; }; };;
+*) as_fn_error "invalid value of canonical target" "$LINENO" 5;;
esac
target=$ac_cv_target
ac_save_IFS=$IFS; IFS='-'
test "$program_prefix$program_suffix$program_transform_name" = \
NONENONEs,x,x, &&
program_prefix=${target_alias}-
+
# DEFINES here are going to config.h and have to be the same as in clustalx.pro
#echo "host_os $host_os"
case $target_os in
*linux*|*solaris*|*bsd*)
-cat >>confdefs.h <<\_ACEOF
-#define OS_UNIX 1
-_ACEOF
+$as_echo "#define OS_UNIX 1" >>confdefs.h
;;
*darwin*)
-cat >>confdefs.h <<\_ACEOF
-#define OS_MAC 1
-_ACEOF
+$as_echo "#define OS_MAC 1" >>confdefs.h
-cat >>confdefs.h <<\_ACEOF
-#define OS_UNIX 1
-_ACEOF
+$as_echo "#define OS_UNIX 1" >>confdefs.h
;;
*cygwin*|*mingw*)
-cat >>confdefs.h <<\_ACEOF
-#define OS_WINDOWS 1
-_ACEOF
+$as_echo "#define OS_WINDOWS 1" >>confdefs.h
;;
*)
- { $as_echo "$as_me:$LINENO: WARNING: \"Couldn't determine target operating system. Using Unix\"" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \"Couldn't determine target operating system. Using Unix\"" >&5
$as_echo "$as_me: WARNING: \"Couldn't determine target operating system. Using Unix\"" >&2;};
-cat >>confdefs.h <<\_ACEOF
-#define OS_UNIX 1
-_ACEOF
+$as_echo "#define OS_UNIX 1" >>confdefs.h
;;
esac
# The AM_INIT_AUTOMAKE line adds several standard checks.
# This macro is always needed for automake
# Obsolete: It takes the program name and version number as arguments.
-am__api_version='1.10'
+am__api_version='1.11'
# Find a good install program. We prefer a C program (faster),
# so one script is as good as another. But avoid the broken or
# OS/2's system install, which has a completely different semantic
# ./install, which can be erroneously created by make from ./install.sh.
# Reject install programs that cannot install multiple files.
-{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5
$as_echo_n "checking for a BSD-compatible install... " >&6; }
if test -z "$INSTALL"; then
-if test "${ac_cv_path_install+set}" = set; then
+if test "${ac_cv_path_install+set}" = set; then :
$as_echo_n "(cached) " >&6
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- # Account for people who put trailing slashes in PATH elements.
-case $as_dir/ in
- ./ | .// | /cC/* | \
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in #((
+ ./ | .// | /[cC]/* | \
/etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
- ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
+ ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \
/usr/ucb/* ) ;;
*)
# OSF1 and SCO ODT 3.0 have their own names for install.
;;
esac
-done
+ done
IFS=$as_save_IFS
rm -rf conftest.one conftest.two conftest.dir
INSTALL=$ac_install_sh
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5
$as_echo "$INSTALL" >&6; }
# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
-{ $as_echo "$as_me:$LINENO: checking whether build environment is sane" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5
$as_echo_n "checking whether build environment is sane... " >&6; }
# Just in case
sleep 1
echo timestamp > conftest.file
+# Reject unsafe characters in $srcdir or the absolute working directory
+# name. Accept space and tab only in the latter.
+am_lf='
+'
+case `pwd` in
+ *[\\\"\#\$\&\'\`$am_lf]*)
+ as_fn_error "unsafe absolute working directory name" "$LINENO" 5;;
+esac
+case $srcdir in
+ *[\\\"\#\$\&\'\`$am_lf\ \ ]*)
+ as_fn_error "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;;
+esac
+
# Do `set' in a subshell so we don't clobber the current shell's
# arguments. Must try -L first in case configure is actually a
# symlink; some systems play weird games with the mod time of symlinks
# (eg FreeBSD returns the mod time of the symlink's containing
# directory).
if (
- set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null`
+ set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
if test "$*" = "X"; then
# -L didn't work.
- set X `ls -t $srcdir/configure conftest.file`
+ set X `ls -t "$srcdir/configure" conftest.file`
fi
rm -f conftest.file
if test "$*" != "X $srcdir/configure conftest.file" \
# if, for instance, CONFIG_SHELL is bash and it inherits a
# broken ls alias from the environment. This has actually
# happened. Such a system could not be considered "sane".
- { { $as_echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken
-alias in your environment" >&5
-$as_echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken
-alias in your environment" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "ls -t appears to fail. Make sure there is not a broken
+alias in your environment" "$LINENO" 5
fi
test "$2" = conftest.file
# Ok.
:
else
- { { $as_echo "$as_me:$LINENO: error: newly created file is older than distributed files!
-Check your system clock" >&5
-$as_echo "$as_me: error: newly created file is older than distributed files!
-Check your system clock" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "newly created file is older than distributed files!
+Check your system clock" "$LINENO" 5
fi
-{ $as_echo "$as_me:$LINENO: result: yes" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
$as_echo "yes" >&6; }
test "$program_prefix" != NONE &&
program_transform_name="s&^&$program_prefix&;$program_transform_name"
# expand $ac_aux_dir to an absolute path
am_aux_dir=`cd $ac_aux_dir && pwd`
-test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing"
+if test x"${MISSING+set}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ MISSING="\${SHELL} \"$am_aux_dir/missing\"" ;;
+ *)
+ MISSING="\${SHELL} $am_aux_dir/missing" ;;
+ esac
+fi
# Use eval to expand $SHELL
if eval "$MISSING --run true"; then
am_missing_run="$MISSING --run "
else
am_missing_run=
- { $as_echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5
$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
fi
-{ $as_echo "$as_me:$LINENO: checking for a thread-safe mkdir -p" >&5
+if test x"${install_sh}" != xset; then
+ case $am_aux_dir in
+ *\ * | *\ *)
+ install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
+ *)
+ install_sh="\${SHELL} $am_aux_dir/install-sh"
+ esac
+fi
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+ 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 $ac_word... " >&6; }
+if test "${ac_cv_prog_STRIP+set}" = set; 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 '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$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 $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; 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 '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$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
+
+fi
+INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
+
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5
$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
if test -z "$MKDIR_P"; then
- if test "${ac_cv_path_mkdir+set}" = set; then
+ if test "${ac_cv_path_mkdir+set}" = set; then :
$as_echo_n "(cached) " >&6
else
as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_prog in mkdir gmkdir; do
+ for ac_prog in mkdir gmkdir; do
for ac_exec_ext in '' $ac_executable_extensions; do
{ test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue
case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #(
esac
done
done
-done
+ done
IFS=$as_save_IFS
fi
+ test -d ./--version && rmdir ./--version
if test "${ac_cv_path_mkdir+set}" = set; then
MKDIR_P="$ac_cv_path_mkdir -p"
else
# value for MKDIR_P within a source directory, because that will
# break other packages using the cache if that directory is
# removed, or if the value is a relative name.
- test -d ./--version && rmdir ./--version
MKDIR_P="$ac_install_sh -d"
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $MKDIR_P" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
$as_echo "$MKDIR_P" >&6; }
mkdir_p="$MKDIR_P"
do
# Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
-{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_AWK+set}" = set; then
+if test "${ac_cv_prog_AWK+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if test -n "$AWK"; then
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_AWK="$ac_prog"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
-done
+ done
IFS=$as_save_IFS
fi
fi
AWK=$ac_cv_prog_AWK
if test -n "$AWK"; then
- { $as_echo "$as_me:$LINENO: result: $AWK" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5
$as_echo "$AWK" >&6; }
else
- { $as_echo "$as_me:$LINENO: result: no" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
fi
test -n "$AWK" && break
done
-{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
set x ${MAKE-make}
ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
-if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then
+if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then :
$as_echo_n "(cached) " >&6
else
cat >conftest.make <<\_ACEOF
rm -f conftest.make
fi
if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
$as_echo "yes" >&6; }
SET_MAKE=
else
- { $as_echo "$as_me:$LINENO: result: no" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
SET_MAKE="MAKE=${MAKE-make}"
fi
am__isrc=' -I$(srcdir)'
# test to see if srcdir already configured
if test -f $srcdir/config.status; then
- { { $as_echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5
-$as_echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "source directory already configured; run \"make distclean\" there first" "$LINENO" 5
fi
fi
# Define the identity of the package.
PACKAGE='clustalw'
- VERSION='2.0.12'
+ VERSION='2.1'
cat >>confdefs.h <<_ACEOF
MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
-install_sh=${install_sh-"\$(SHELL) $am_aux_dir/install-sh"}
-
-# Installed binaries are usually stripped using `strip' when the user
-# run `make install-strip'. However `strip' might not be the right
-# tool to use in cross-compilation environments, therefore Automake
-# will honor the `STRIP' environment variable to overrule this program.
-if test "$cross_compiling" != no; then
- 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:$LINENO: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_STRIP+set}" = set; 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 '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_prog_STRIP="${ac_tool_prefix}strip"
- $as_echo "$as_me:$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:$LINENO: result: $STRIP" >&5
-$as_echo "$STRIP" >&6; }
-else
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$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:$LINENO: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; 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 '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
- ac_cv_prog_ac_ct_STRIP="strip"
- $as_echo "$as_me:$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:$LINENO: result: $ac_ct_STRIP" >&5
-$as_echo "$ac_ct_STRIP" >&6; }
-else
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$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:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
-$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
-
-fi
-INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
-
# We need awk for the "check" target. The system "awk" is bad on
# some platforms.
# Always define AMTAR for backward compatibility.
-{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5
$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
set x ${MAKE-make}
ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
-if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then
+if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then :
$as_echo_n "(cached) " >&6
else
cat >conftest.make <<\_ACEOF
rm -f conftest.make
fi
if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
$as_echo "yes" >&6; }
SET_MAKE=
else
- { $as_echo "$as_me:$LINENO: result: no" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
SET_MAKE="MAKE=${MAKE-make}"
fi
if test -n "$ac_tool_prefix"; then
# Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
set dummy ${ac_tool_prefix}gcc; ac_word=$2
-{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_CC+set}" = set; then
+if test "${ac_cv_prog_CC+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_CC="${ac_tool_prefix}gcc"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
-done
+ done
IFS=$as_save_IFS
fi
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
- { $as_echo "$as_me:$LINENO: result: $CC" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
$as_echo "$CC" >&6; }
else
- { $as_echo "$as_me:$LINENO: result: no" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
fi
ac_ct_CC=$CC
# Extract the first word of "gcc", so it can be a program name with args.
set dummy gcc; ac_word=$2
-{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if test -n "$ac_ct_CC"; then
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_ac_ct_CC="gcc"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
-done
+ done
IFS=$as_save_IFS
fi
fi
ac_ct_CC=$ac_cv_prog_ac_ct_CC
if test -n "$ac_ct_CC"; then
- { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
$as_echo "$ac_ct_CC" >&6; }
else
- { $as_echo "$as_me:$LINENO: result: no" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
fi
else
case $cross_compiling:$ac_tool_warned in
yes:)
-{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+{ $as_echo "$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
if test -n "$ac_tool_prefix"; then
# Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
set dummy ${ac_tool_prefix}cc; ac_word=$2
-{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_CC+set}" = set; then
+if test "${ac_cv_prog_CC+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_CC="${ac_tool_prefix}cc"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
-done
+ done
IFS=$as_save_IFS
fi
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
- { $as_echo "$as_me:$LINENO: result: $CC" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
$as_echo "$CC" >&6; }
else
- { $as_echo "$as_me:$LINENO: result: no" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
fi
if test -z "$CC"; then
# Extract the first word of "cc", so it can be a program name with args.
set dummy cc; ac_word=$2
-{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_CC+set}" = set; then
+if test "${ac_cv_prog_CC+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
ac_prog_rejected=yes
continue
fi
ac_cv_prog_CC="cc"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
-done
+ done
IFS=$as_save_IFS
if test $ac_prog_rejected = yes; then
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
- { $as_echo "$as_me:$LINENO: result: $CC" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
$as_echo "$CC" >&6; }
else
- { $as_echo "$as_me:$LINENO: result: no" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
fi
do
# Extract the first word of "$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:$LINENO: checking for $ac_word" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_CC+set}" = set; then
+if test "${ac_cv_prog_CC+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if test -n "$CC"; then
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
-done
+ done
IFS=$as_save_IFS
fi
fi
CC=$ac_cv_prog_CC
if test -n "$CC"; then
- { $as_echo "$as_me:$LINENO: result: $CC" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5
$as_echo "$CC" >&6; }
else
- { $as_echo "$as_me:$LINENO: result: no" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
fi
do
# Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
-{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
-if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if test -n "$ac_ct_CC"; then
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
ac_cv_prog_ac_ct_CC="$ac_prog"
- $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
break 2
fi
done
-done
+ done
IFS=$as_save_IFS
fi
fi
ac_ct_CC=$ac_cv_prog_ac_ct_CC
if test -n "$ac_ct_CC"; then
- { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5
$as_echo "$ac_ct_CC" >&6; }
else
- { $as_echo "$as_me:$LINENO: result: no" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
fi
else
case $cross_compiling:$ac_tool_warned in
yes:)
-{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+{ $as_echo "$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
fi
-test -z "$CC" && { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: no acceptable C compiler found in \$PATH
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
+as_fn_error "no acceptable C compiler found in \$PATH
+See \`config.log' for more details." "$LINENO" 5; }
# Provide some information about the compiler.
-$as_echo "$as_me:$LINENO: checking for C compiler version" >&5
+$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5
set X $ac_compile
ac_compiler=$2
-{ (ac_try="$ac_compiler --version >&5"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compiler --version >&5") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }
-{ (ac_try="$ac_compiler -v >&5"
+for ac_option in --version -v -V -qversion; do
+ { { ac_try="$ac_compiler $ac_option >&5"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compiler -v >&5") 2>&5
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compiler $ac_option >&5") 2>conftest.err
ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }
-{ (ac_try="$ac_compiler -V >&5"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compiler -V >&5") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }
+ if test -s conftest.err; then
+ sed '10a\
+... rest of stderr output deleted ...
+ 10q' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ fi
+ rm -f conftest.er1 conftest.err
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+done
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
# Try to create an executable without -o first, disregard a.out.
# It will help us diagnose broken compilers, and finding out an intuition
# of exeext.
-{ $as_echo "$as_me:$LINENO: checking for C compiler default output file name" >&5
-$as_echo_n "checking for C compiler default output file name... " >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5
+$as_echo_n "checking whether the C compiler works... " >&6; }
ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
# The possible output files:
done
rm -f $ac_rmfiles
-if { (ac_try="$ac_link_default"
+if { { ac_try="$ac_link_default"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
(eval "$ac_link_default") 2>&5
ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; then
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
# Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
# in a Makefile. We should not override ac_cv_exeext if it was cached,
# certainly right.
break;;
*.* )
- if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+ if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
then :; else
ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
fi
else
ac_file=''
fi
-
-{ $as_echo "$as_me:$LINENO: result: $ac_file" >&5
-$as_echo "$ac_file" >&6; }
-if test -z "$ac_file"; then
- $as_echo "$as_me: failed program was:" >&5
+if test -z "$ac_file"; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: C compiler cannot create executables
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: C compiler cannot create executables
-See \`config.log' for more details." >&2;}
- { (exit 77); exit 77; }; }; }
+{ as_fn_set_status 77
+as_fn_error "C compiler cannot create executables
+See \`config.log' for more details." "$LINENO" 5; }; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
fi
-
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5
+$as_echo_n "checking for C compiler default output file name... " >&6; }
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5
+$as_echo "$ac_file" >&6; }
ac_exeext=$ac_cv_exeext
-# Check that the compiler produces executables we can run. If not, either
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-{ $as_echo "$as_me:$LINENO: checking whether the C compiler works" >&5
-$as_echo_n "checking whether the C compiler works... " >&6; }
-# FIXME: These cross compiler hacks should be removed for Autoconf 3.0
-# If not cross compiling, check that we can run a simple program.
-if test "$cross_compiling" != yes; then
- if { ac_try='./$ac_file'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- cross_compiling=no
- else
- if test "$cross_compiling" = maybe; then
- cross_compiling=yes
- else
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run C compiled programs.
-If you meant to cross compile, use \`--host'.
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run C compiled programs.
-If you meant to cross compile, use \`--host'.
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
- fi
- fi
-fi
-{ $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-
rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
ac_clean_files=$ac_clean_files_save
-# Check that the compiler produces executables we can run. If not, either
-# the compiler is broken, or we cross compile.
-{ $as_echo "$as_me:$LINENO: checking whether we are cross compiling" >&5
-$as_echo_n "checking whether we are cross compiling... " >&6; }
-{ $as_echo "$as_me:$LINENO: result: $cross_compiling" >&5
-$as_echo "$cross_compiling" >&6; }
-
-{ $as_echo "$as_me:$LINENO: checking for suffix of executables" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5
$as_echo_n "checking for suffix of executables... " >&6; }
-if { (ac_try="$ac_link"
+if { { ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
(eval "$ac_link") 2>&5
ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; then
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
# If both `conftest.exe' and `conftest' are `present' (well, observable)
# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
# work properly (i.e., refer to `conftest.exe'), while it won't with
esac
done
else
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot compute suffix of executables: cannot compile and link
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
+as_fn_error "cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details." "$LINENO" 5; }
fi
-
-rm -f conftest$ac_cv_exeext
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5
+rm -f conftest conftest$ac_cv_exeext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5
$as_echo "$ac_cv_exeext" >&6; }
rm -f conftest.$ac_ext
EXEEXT=$ac_cv_exeext
ac_exeext=$EXEEXT
-{ $as_echo "$as_me:$LINENO: checking for suffix of object files" >&5
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdio.h>
+int
+main ()
+{
+FILE *f = fopen ("conftest.out", "w");
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files="$ac_clean_files conftest.out"
+# Check that the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+if test "$cross_compiling" != yes; then
+ { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }
+ if { ac_try='./conftest$ac_cv_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then
+ cross_compiling=no
+ else
+ if test "$cross_compiling" = maybe; then
+ cross_compiling=yes
+ else
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error "cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details." "$LINENO" 5; }
+ fi
+ fi
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out
+ac_clean_files=$ac_clean_files_save
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5
$as_echo_n "checking for suffix of object files... " >&6; }
-if test "${ac_cv_objext+set}" = set; then
+if test "${ac_cv_objext+set}" = set; then :
$as_echo_n "(cached) " >&6
else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
}
_ACEOF
rm -f conftest.o conftest.obj
-if { (ac_try="$ac_compile"
+if { { ac_try="$ac_compile"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
(eval "$ac_compile") 2>&5
ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; then
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; then :
for ac_file in conftest.o conftest.obj conftest.*; do
test -f "$ac_file" || continue;
case $ac_file in
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot compute suffix of object files: cannot compile
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
+as_fn_error "cannot compute suffix of object files: cannot compile
+See \`config.log' for more details." "$LINENO" 5; }
fi
-
rm -f conftest.$ac_cv_objext conftest.$ac_ext
fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_objext" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5
$as_echo "$ac_cv_objext" >&6; }
OBJEXT=$ac_cv_objext
ac_objext=$OBJEXT
-{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5
$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
-if test "${ac_cv_c_compiler_gnu+set}" = set; then
+if test "${ac_cv_c_compiler_gnu+set}" = set; then :
$as_echo_n "(cached) " >&6
else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
+if ac_fn_c_try_compile "$LINENO"; then :
ac_compiler_gnu=yes
else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_compiler_gnu=no
+ ac_compiler_gnu=no
fi
-
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
ac_cv_c_compiler_gnu=$ac_compiler_gnu
fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5
$as_echo "$ac_cv_c_compiler_gnu" >&6; }
if test $ac_compiler_gnu = yes; then
GCC=yes
fi
ac_test_CFLAGS=${CFLAGS+set}
ac_save_CFLAGS=$CFLAGS
-{ $as_echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5
$as_echo_n "checking whether $CC accepts -g... " >&6; }
-if test "${ac_cv_prog_cc_g+set}" = set; then
+if test "${ac_cv_prog_cc_g+set}" = set; then :
$as_echo_n "(cached) " >&6
else
ac_save_c_werror_flag=$ac_c_werror_flag
ac_c_werror_flag=yes
ac_cv_prog_cc_g=no
CFLAGS="-g"
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
+if ac_fn_c_try_compile "$LINENO"; then :
ac_cv_prog_cc_g=yes
else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- CFLAGS=""
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- :
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_c_werror_flag=$ac_save_c_werror_flag
- CFLAGS="-g"
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ CFLAGS=""
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ac_cv_prog_cc_g=yes
+if ac_fn_c_try_compile "$LINENO"; then :
+
else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+int
+main ()
+{
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_cv_prog_cc_g=yes
fi
-
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
-
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
-
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
ac_c_werror_flag=$ac_save_c_werror_flag
fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5
$as_echo "$ac_cv_prog_cc_g" >&6; }
if test "$ac_test_CFLAGS" = set; then
CFLAGS=$ac_save_CFLAGS
CFLAGS=
fi
fi
-{ $as_echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5
$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
-if test "${ac_cv_prog_cc_c89+set}" = set; then
+if test "${ac_cv_prog_cc_c89+set}" = set; then :
$as_echo_n "(cached) " >&6
else
ac_cv_prog_cc_c89=no
ac_save_CC=$CC
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <stdarg.h>
#include <stdio.h>
-Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
do
CC="$ac_save_CC $ac_arg"
- rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
+ if ac_fn_c_try_compile "$LINENO"; then :
ac_cv_prog_cc_c89=$ac_arg
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-
fi
-
rm -f core conftest.err conftest.$ac_objext
test "x$ac_cv_prog_cc_c89" != "xno" && break
done
# AC_CACHE_VAL
case "x$ac_cv_prog_cc_c89" in
x)
- { $as_echo "$as_me:$LINENO: result: none needed" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5
$as_echo "none needed" >&6; } ;;
xno)
- { $as_echo "$as_me:$LINENO: result: unsupported" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5
$as_echo "unsupported" >&6; } ;;
*)
CC="$CC $ac_cv_prog_cc_c89"
- { $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5
$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
esac
+if test "x$ac_cv_prog_cc_c89" != xno; then :
+fi
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
am_make=${MAKE-make}
cat > confinc << 'END'
am__doit:
- @echo done
+ @echo this is the am__doit target
.PHONY: am__doit
END
# If we don't find an include directive, just comment out the code.
-{ $as_echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5
$as_echo_n "checking for style of include used by $am_make... " >&6; }
am__include="#"
am__quote=
_am_result=none
# First try GNU make style include.
echo "include confinc" > confmf
-# We grep out `Entering directory' and `Leaving directory'
-# messages which can occur if `w' ends up in MAKEFLAGS.
-# In particular we don't look at `^make:' because GNU make might
-# be invoked under some other name (usually "gmake"), in which
-# case it prints its new name instead of `make'.
-if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then
- am__include=include
- am__quote=
- _am_result=GNU
-fi
+# Ignore all kinds of additional output from `make'.
+case `$am_make -s -f confmf 2> /dev/null` in #(
+*the\ am__doit\ target*)
+ am__include=include
+ am__quote=
+ _am_result=GNU
+ ;;
+esac
# Now try BSD make style include.
if test "$am__include" = "#"; then
echo '.include "confinc"' > confmf
- if test "`$am_make -s -f confmf 2> /dev/null`" = "done"; then
- am__include=.include
- am__quote="\""
- _am_result=BSD
- fi
+ case `$am_make -s -f confmf 2> /dev/null` in #(
+ *the\ am__doit\ target*)
+ am__include=.include
+ am__quote="\""
+ _am_result=BSD
+ ;;
+ esac
fi
-{ $as_echo "$as_me:$LINENO: result: $_am_result" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5
$as_echo "$_am_result" >&6; }
rm -f confinc confmf
# Check whether --enable-dependency-tracking was given.
-if test "${enable_dependency_tracking+set}" = set; then
+if test "${enable_dependency_tracking+set}" = set; then :
enableval=$enable_dependency_tracking;
fi
depcc="$CC" am_compiler_list=
-{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
$as_echo_n "checking dependency style of $depcc... " >&6; }
-if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
if test "$am_compiler_list" = ""; then
am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
fi
+ am__universal=false
+ case " $depcc " in #(
+ *\ -arch\ *\ -arch\ *) am__universal=true ;;
+ esac
+
for depmode in $am_compiler_list; do
# Setup a source with many dependencies, because some compilers
# like to wrap large dependency lists on column 80 (with \), and
done
echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this. Also, some Intel
+ # versions had trouble with output in subdirs
+ am__obj=sub/conftest.${OBJEXT-o}
+ am__minus_obj="-o $am__obj"
case $depmode in
+ gcc)
+ # This depmode causes a compiler race in universal mode.
+ test "$am__universal" = false || continue
+ ;;
nosideeffect)
# after this tag, mechanisms are not by side-effect, so they'll
# only be used when explicitly requested
break
fi
;;
+ msvisualcpp | msvcmsys)
+ # This compiler won't grok `-c -o', but also, the minuso test has
+ # not run yet. These depmodes are late enough in the game, and
+ # so weak that their functioning should not be impacted.
+ am__obj=conftest.${OBJEXT-o}
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+ ;;
none) break ;;
esac
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if depmode=$depmode \
- source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
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depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
- $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
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fi
-{ $as_echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5
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test -z "$as_dir" && as_dir=.
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break 2
fi
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IFS=$as_save_IFS
fi
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if test -n "$CXX"; then
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else
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case $cross_compiling:$ac_tool_warned in
yes:)
-{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
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- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
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-{ (ac_try="$ac_compiler -V >&5"
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ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
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-{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5
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-/* confdefs.h. */
-_ACEOF
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-cat >>conftest.$ac_ext <<_ACEOF
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/* end confdefs.h. */
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-/* confdefs.h. */
-_ACEOF
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-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
return 0;
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-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
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-cat >>conftest.$ac_ext <<_ACEOF
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-cat >>conftest.$ac_ext <<_ACEOF
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/* end confdefs.h. */
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return 0;
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- case $cross_compiling:$ac_tool_warned in
-yes:)
-{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
-$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
-
-# AC_PROG_INSTALL will generate an install target so that users may
-# just type 'make install' to install the software.
-# Find a good install program. We prefer a C program (faster),
-# so one script is as good as another. But avoid the broken or
-# incompatible versions:
-# SysV /etc/install, /usr/sbin/install
-# SunOS /usr/etc/install
-# IRIX /sbin/install
-# AIX /bin/install
-# AmigaOS /C/install, which installs bootblocks on floppy discs
-# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
-# AFS /usr/afsws/bin/install, which mishandles nonexistent args
-# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
-# OS/2's system install, which has a completely different semantic
-# ./install, which can be erroneously created by make from ./install.sh.
-# Reject install programs that cannot install multiple files.
-{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
-$as_echo_n "checking for a BSD-compatible install... " >&6; }
-if test -z "$INSTALL"; then
-if test "${ac_cv_path_install+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- # Account for people who put trailing slashes in PATH elements.
-case $as_dir/ in
- ./ | .// | /cC/* | \
- /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
- ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
- /usr/ucb/* ) ;;
- *)
- # OSF1 and SCO ODT 3.0 have their own names for install.
- # Don't use installbsd from OSF since it installs stuff as root
- # by default.
- for ac_prog in ginstall scoinst install; do
- for ac_exec_ext in '' $ac_executable_extensions; do
- if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
- if test $ac_prog = install &&
- grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
- # AIX install. It has an incompatible calling convention.
- :
- elif test $ac_prog = install &&
- grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
- # program-specific install script used by HP pwplus--don't use.
- :
- else
- rm -rf conftest.one conftest.two conftest.dir
- echo one > conftest.one
- echo two > conftest.two
- mkdir conftest.dir
- if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
- test -s conftest.one && test -s conftest.two &&
- test -s conftest.dir/conftest.one &&
- test -s conftest.dir/conftest.two
- then
- ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
- break 3
- fi
- fi
- fi
- done
- done
- ;;
-esac
-
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$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
-rm -rf conftest.one conftest.two conftest.dir
+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
+$as_echo "no" >&6; }
+fi
+
fi
- if test "${ac_cv_path_install+set}" = set; then
- INSTALL=$ac_cv_path_install
- else
- # As a last resort, use the slow shell script. Don't cache a
- # value for INSTALL within a source directory, because that will
- # break other packages using the cache if that directory is
- # removed, or if the value is a relative name.
- INSTALL=$ac_install_sh
+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 $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; 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 '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$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
-fi
-{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5
-$as_echo "$INSTALL" >&6; }
+done
+ done
+IFS=$as_save_IFS
-# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
-# It thinks the first close brace ends the variable substitution.
-test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+fi
+fi
+ac_ct_RANLIB=$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
+$as_echo "no" >&6; }
+fi
-test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+ if test "x$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 "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+# AC_PROG_INSTALL will generate an install target so that users may
+# just type 'make install' to install the software.
# use C++ compiler and linker
ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-{ $as_echo "$as_me:$LINENO: checking how to run the C++ preprocessor" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C++ preprocessor" >&5
$as_echo_n "checking how to run the C++ preprocessor... " >&6; }
if test -z "$CXXCPP"; then
- if test "${ac_cv_prog_CXXCPP+set}" = set; then
+ if test "${ac_cv_prog_CXXCPP+set}" = set; then :
$as_echo_n "(cached) " >&6
else
# Double quotes because CXXCPP needs to be expanded
# <limits.h> exists even on freestanding compilers.
# On the NeXT, cc -E runs the code through the compiler's parser,
# not just through cpp. "Syntax error" is here to catch this case.
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#ifdef __STDC__
# include <limits.h>
#endif
Syntax error
_ACEOF
-if { (ac_try="$ac_cpp conftest.$ac_ext"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } >/dev/null && {
- test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- }; then
- :
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+else
# Broken: fails on valid input.
continue
fi
-
rm -f conftest.err conftest.$ac_ext
# OK, works on sane cases. Now check whether nonexistent headers
# can be detected and how.
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <ac_nonexistent.h>
_ACEOF
-if { (ac_try="$ac_cpp conftest.$ac_ext"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } >/dev/null && {
- test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- }; then
+if ac_fn_cxx_try_cpp "$LINENO"; then :
# Broken: success on invalid input.
continue
else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
# Passes both tests.
ac_preproc_ok=:
break
fi
-
rm -f conftest.err conftest.$ac_ext
done
# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
rm -f conftest.err conftest.$ac_ext
-if $ac_preproc_ok; then
+if $ac_preproc_ok; then :
break
fi
else
ac_cv_prog_CXXCPP=$CXXCPP
fi
-{ $as_echo "$as_me:$LINENO: result: $CXXCPP" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXXCPP" >&5
$as_echo "$CXXCPP" >&6; }
ac_preproc_ok=false
for ac_cxx_preproc_warn_flag in '' yes
# <limits.h> exists even on freestanding compilers.
# On the NeXT, cc -E runs the code through the compiler's parser,
# not just through cpp. "Syntax error" is here to catch this case.
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#ifdef __STDC__
# include <limits.h>
#endif
Syntax error
_ACEOF
-if { (ac_try="$ac_cpp conftest.$ac_ext"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } >/dev/null && {
- test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- }; then
- :
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
+if ac_fn_cxx_try_cpp "$LINENO"; then :
+else
# Broken: fails on valid input.
continue
fi
-
rm -f conftest.err conftest.$ac_ext
# OK, works on sane cases. Now check whether nonexistent headers
# can be detected and how.
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <ac_nonexistent.h>
_ACEOF
-if { (ac_try="$ac_cpp conftest.$ac_ext"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } >/dev/null && {
- test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- }; then
+if ac_fn_cxx_try_cpp "$LINENO"; then :
# Broken: success on invalid input.
continue
else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
# Passes both tests.
ac_preproc_ok=:
break
fi
-
rm -f conftest.err conftest.$ac_ext
done
# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
rm -f conftest.err conftest.$ac_ext
-if $ac_preproc_ok; then
- :
+if $ac_preproc_ok; then :
+
else
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: C++ preprocessor \"$CXXCPP\" fails sanity check
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: C++ preprocessor \"$CXXCPP\" fails sanity check
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
+as_fn_error "C++ preprocessor \"$CXXCPP\" fails sanity check
+See \`config.log' for more details." "$LINENO" 5; }
fi
ac_ext=cpp
ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-{ $as_echo "$as_me:$LINENO: checking for grep that handles long lines and -e" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
$as_echo_n "checking for grep that handles long lines and -e... " >&6; }
-if test "${ac_cv_path_GREP+set}" = set; then
+if test "${ac_cv_path_GREP+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if test -z "$GREP"; then
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_prog in grep ggrep; do
+ for ac_prog in grep ggrep; do
for ac_exec_ext in '' $ac_executable_extensions; do
ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
{ test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
$as_echo 'GREP' >> "conftest.nl"
"$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
- ac_count=`expr $ac_count + 1`
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
if test $ac_count -gt ${ac_path_GREP_max-0}; then
# Best one so far, save it but keep looking for a better one
ac_cv_path_GREP="$ac_path_GREP"
$ac_path_GREP_found && break 3
done
done
-done
+ done
IFS=$as_save_IFS
if test -z "$ac_cv_path_GREP"; then
- { { $as_echo "$as_me:$LINENO: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
-$as_echo "$as_me: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
fi
else
ac_cv_path_GREP=$GREP
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5
$as_echo "$ac_cv_path_GREP" >&6; }
GREP="$ac_cv_path_GREP"
-{ $as_echo "$as_me:$LINENO: checking for egrep" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5
$as_echo_n "checking for egrep... " >&6; }
-if test "${ac_cv_path_EGREP+set}" = set; then
+if test "${ac_cv_path_EGREP+set}" = set; then :
$as_echo_n "(cached) " >&6
else
if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- for ac_prog in egrep; do
+ for ac_prog in egrep; do
for ac_exec_ext in '' $ac_executable_extensions; do
ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
{ test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
$as_echo 'EGREP' >> "conftest.nl"
"$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break
diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
- ac_count=`expr $ac_count + 1`
+ as_fn_arith $ac_count + 1 && ac_count=$as_val
if test $ac_count -gt ${ac_path_EGREP_max-0}; then
# Best one so far, save it but keep looking for a better one
ac_cv_path_EGREP="$ac_path_EGREP"
$ac_path_EGREP_found && break 3
done
done
-done
+ done
IFS=$as_save_IFS
if test -z "$ac_cv_path_EGREP"; then
- { { $as_echo "$as_me:$LINENO: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
-$as_echo "$as_me: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
fi
else
ac_cv_path_EGREP=$EGREP
fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5
$as_echo "$ac_cv_path_EGREP" >&6; }
EGREP="$ac_cv_path_EGREP"
-{ $as_echo "$as_me:$LINENO: checking for ANSI C header files" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
$as_echo_n "checking for ANSI C header files... " >&6; }
-if test "${ac_cv_header_stdc+set}" = set; then
+if test "${ac_cv_header_stdc+set}" = set; then :
$as_echo_n "(cached) " >&6
else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <stdlib.h>
#include <stdarg.h>
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
+if ac_fn_cxx_try_compile "$LINENO"; then :
ac_cv_header_stdc=yes
else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_header_stdc=no
+ ac_cv_header_stdc=no
fi
-
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
if test $ac_cv_header_stdc = yes; then
# SunOS 4.x string.h does not declare mem*, contrary to ANSI.
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <string.h>
_ACEOF
if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
- $EGREP "memchr" >/dev/null 2>&1; then
- :
+ $EGREP "memchr" >/dev/null 2>&1; then :
+
else
ac_cv_header_stdc=no
fi
if test $ac_cv_header_stdc = yes; then
# ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <stdlib.h>
_ACEOF
if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
- $EGREP "free" >/dev/null 2>&1; then
- :
+ $EGREP "free" >/dev/null 2>&1; then :
+
else
ac_cv_header_stdc=no
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
+ if test "$cross_compiling" = yes; then :
:
else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <ctype.h>
#include <stdlib.h>
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- :
-else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
+if ac_fn_cxx_try_run "$LINENO"; then :
-( exit $ac_status )
-ac_cv_header_stdc=no
+else
+ ac_cv_header_stdc=no
fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+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:$LINENO: result: $ac_cv_header_stdc" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5
$as_echo "$ac_cv_header_stdc" >&6; }
if test $ac_cv_header_stdc = yes; then
-cat >>confdefs.h <<\_ACEOF
-#define STDC_HEADERS 1
-_ACEOF
+$as_echo "#define STDC_HEADERS 1" >>confdefs.h
fi
# Checks for typedefs, structures, and compiler characteristics.
# 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`
-{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
-$as_echo_n "checking for $ac_header... " >&6; }
-if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
- $as_echo_n "(cached) " >&6
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_includes_default
-
-#include <$ac_header>
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- eval "$as_ac_Header=yes"
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- eval "$as_ac_Header=no"
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-ac_res=`eval 'as_val=${'$as_ac_Header'}
- $as_echo "$as_val"'`
- { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-as_val=`eval 'as_val=${'$as_ac_Header'}
- $as_echo "$as_val"'`
- if test "x$as_val" = x""yes; then
+do :
+ as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+ac_fn_cxx_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
+"
+eval as_val=\$$as_ac_Header
+ if test "x$as_val" = x""yes; then :
cat >>confdefs.h <<_ACEOF
#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
_ACEOF
done
-{ $as_echo "$as_me:$LINENO: checking for stdbool.h that conforms to C99" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for stdbool.h that conforms to C99" >&5
$as_echo_n "checking for stdbool.h that conforms to C99... " >&6; }
-if test "${ac_cv_header_stdbool_h+set}" = set; then
+if test "${ac_cv_header_stdbool_h+set}" = set; then :
$as_echo_n "(cached) " >&6
else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#include <stdbool.h>
*pq |= q;
*pq |= ! q;
- /* Refer to every declared value, to avoid compiler optimizations. */
- return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l
- + !m + !n + !o + !p + !q + !pq);
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ac_cv_header_stdbool_h=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_header_stdbool_h=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdbool_h" >&5
-$as_echo "$ac_cv_header_stdbool_h" >&6; }
-{ $as_echo "$as_me:$LINENO: checking for _Bool" >&5
-$as_echo_n "checking for _Bool... " >&6; }
-if test "${ac_cv_type__Bool+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- ac_cv_type__Bool=no
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_includes_default
-int
-main ()
-{
-if (sizeof (_Bool))
- return 0;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_includes_default
-int
-main ()
-{
-if (sizeof ((_Bool)))
- return 0;
+ /* Refer to every declared value, to avoid compiler optimizations. */
+ return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l
+ + !m + !n + !o + !p + !q + !pq);
+
;
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- :
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_type__Bool=yes
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+if ac_fn_cxx_try_compile "$LINENO"; then :
+ ac_cv_header_stdbool_h=yes
else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-
+ ac_cv_header_stdbool_h=no
fi
-
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_type__Bool" >&5
-$as_echo "$ac_cv_type__Bool" >&6; }
-if test "x$ac_cv_type__Bool" = x""yes; then
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdbool_h" >&5
+$as_echo "$ac_cv_header_stdbool_h" >&6; }
+ac_fn_cxx_check_type "$LINENO" "_Bool" "ac_cv_type__Bool" "$ac_includes_default"
+if test "x$ac_cv_type__Bool" = x""yes; then :
cat >>confdefs.h <<_ACEOF
#define HAVE__BOOL 1
if test $ac_cv_header_stdbool_h = yes; then
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_STDBOOL_H 1
-_ACEOF
+$as_echo "#define HAVE_STDBOOL_H 1" >>confdefs.h
fi
-{ $as_echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for an ANSI C-conforming const" >&5
$as_echo_n "checking for an ANSI C-conforming const... " >&6; }
-if test "${ac_cv_c_const+set}" = set; then
+if test "${ac_cv_c_const+set}" = set; then :
$as_echo_n "(cached) " >&6
else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
+if ac_fn_cxx_try_compile "$LINENO"; then :
ac_cv_c_const=yes
else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_c_const=no
+ ac_cv_c_const=no
fi
-
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_const" >&5
$as_echo "$ac_cv_c_const" >&6; }
if test $ac_cv_c_const = no; then
-cat >>confdefs.h <<\_ACEOF
-#define const /**/
-_ACEOF
-
-fi
-
-{ $as_echo "$as_me:$LINENO: checking for size_t" >&5
-$as_echo_n "checking for size_t... " >&6; }
-if test "${ac_cv_type_size_t+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- ac_cv_type_size_t=no
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_includes_default
-int
-main ()
-{
-if (sizeof (size_t))
- return 0;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_includes_default
-int
-main ()
-{
-if (sizeof ((size_t)))
- return 0;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- :
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
+$as_echo "#define const /**/" >>confdefs.h
- ac_cv_type_size_t=yes
fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-
-fi
+ac_fn_cxx_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default"
+if test "x$ac_cv_type_size_t" = x""yes; then :
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_size_t" >&5
-$as_echo "$ac_cv_type_size_t" >&6; }
-if test "x$ac_cv_type_size_t" = x""yes; then
- :
else
cat >>confdefs.h <<_ACEOF
ac_config_headers="$ac_config_headers src/config.h"
-
for ac_header in stdlib.h
-do
-as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
- { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
-$as_echo_n "checking for $ac_header... " >&6; }
-if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
- $as_echo_n "(cached) " >&6
-fi
-ac_res=`eval 'as_val=${'$as_ac_Header'}
- $as_echo "$as_val"'`
- { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-else
- # Is the header compilable?
-{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5
-$as_echo_n "checking $ac_header usability... " >&6; }
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_includes_default
-#include <$ac_header>
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ac_header_compiler=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_header_compiler=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
-$as_echo "$ac_header_compiler" >&6; }
-
-# Is the header present?
-{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5
-$as_echo_n "checking $ac_header presence... " >&6; }
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <$ac_header>
-_ACEOF
-if { (ac_try="$ac_cpp conftest.$ac_ext"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } >/dev/null && {
- test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- }; then
- ac_header_preproc=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_header_preproc=no
-fi
-
-rm -f conftest.err conftest.$ac_ext
-{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
-$as_echo "$ac_header_preproc" >&6; }
-
-# So? What about this header?
-case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in
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- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
-$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
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-$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
- ac_header_preproc=yes
- ;;
- no:yes:* )
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
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-$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
-$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5
-$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
-$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
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-$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
- ( cat <<\_ASBOX
-## ------------------------------ ##
-## Report this to clustalw@ucd.ie ##
-## ------------------------------ ##
-_ASBOX
- ) | sed "s/^/$as_me: WARNING: /" >&2
- ;;
-esac
-{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
-$as_echo_n "checking for $ac_header... " >&6; }
-if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
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- eval "$as_ac_Header=\$ac_header_preproc"
-fi
-ac_res=`eval 'as_val=${'$as_ac_Header'}
- $as_echo "$as_val"'`
- { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-
-fi
-as_val=`eval 'as_val=${'$as_ac_Header'}
- $as_echo "$as_val"'`
- if test "x$as_val" = x""yes; then
+do :
+ ac_fn_cxx_check_header_mongrel "$LINENO" "stdlib.h" "ac_cv_header_stdlib_h" "$ac_includes_default"
+if test "x$ac_cv_header_stdlib_h" = x""yes; then :
cat >>confdefs.h <<_ACEOF
-#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+#define HAVE_STDLIB_H 1
_ACEOF
fi
done
-{ $as_echo "$as_me:$LINENO: checking for GNU libc compatible malloc" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU libc compatible malloc" >&5
$as_echo_n "checking for GNU libc compatible malloc... " >&6; }
-if test "${ac_cv_func_malloc_0_nonnull+set}" = set; then
+if test "${ac_cv_func_malloc_0_nonnull+set}" = set; then :
$as_echo_n "(cached) " >&6
else
- if test "$cross_compiling" = yes; then
+ if test "$cross_compiling" = yes; then :
ac_cv_func_malloc_0_nonnull=no
else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
#if defined STDC_HEADERS || defined HAVE_STDLIB_H
# include <stdlib.h>
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
+if ac_fn_cxx_try_run "$LINENO"; then :
ac_cv_func_malloc_0_nonnull=yes
else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-( exit $ac_status )
-ac_cv_func_malloc_0_nonnull=no
+ ac_cv_func_malloc_0_nonnull=no
fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+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:$LINENO: result: $ac_cv_func_malloc_0_nonnull" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_malloc_0_nonnull" >&5
$as_echo "$ac_cv_func_malloc_0_nonnull" >&6; }
-if test $ac_cv_func_malloc_0_nonnull = yes; then
+if test $ac_cv_func_malloc_0_nonnull = yes; then :
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_MALLOC 1
-_ACEOF
+$as_echo "#define HAVE_MALLOC 1" >>confdefs.h
else
- cat >>confdefs.h <<\_ACEOF
-#define HAVE_MALLOC 0
-_ACEOF
+ $as_echo "#define HAVE_MALLOC 0" >>confdefs.h
case " $LIBOBJS " in
*" malloc.$ac_objext "* ) ;;
esac
-cat >>confdefs.h <<\_ACEOF
-#define malloc rpl_malloc
-_ACEOF
+$as_echo "#define malloc rpl_malloc" >>confdefs.h
fi
-
# enable hashing if requested (--with-mhash)
# will set HAVE_MHASH_H only
# Check whether --with-mhash was given.
-if test "${with_mhash+set}" = set; then
+if test "${with_mhash+set}" = set; then :
withval=$with_mhash; with_mhash=$withval
else
with_mhash=no
fi
if test "$with_mhash" = "yes"; then
-
-{ $as_echo "$as_me:$LINENO: checking for mhash_init in -lmhash" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for mhash_init in -lmhash" >&5
$as_echo_n "checking for mhash_init in -lmhash... " >&6; }
-if test "${ac_cv_lib_mhash_mhash_init+set}" = set; then
+if test "${ac_cv_lib_mhash_mhash_init+set}" = set; then :
$as_echo_n "(cached) " >&6
else
ac_check_lib_save_LIBS=$LIBS
LIBS="-lmhash $LIBS"
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
/* Override any GCC internal prototype to avoid an error.
char mhash_init ();
int
main ()
-{
-return mhash_init ();
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
- }; then
- ac_cv_lib_mhash_mhash_init=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_cv_lib_mhash_mhash_init=no
-fi
-
-rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
- conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
-fi
-{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_mhash_mhash_init" >&5
-$as_echo "$ac_cv_lib_mhash_mhash_init" >&6; }
-if test "x$ac_cv_lib_mhash_mhash_init" = x""yes; then
- cat >>confdefs.h <<_ACEOF
-#define HAVE_LIBMHASH 1
-_ACEOF
-
- LIBS="-lmhash $LIBS"
-
-else
- { { $as_echo "$as_me:$LINENO: error: mhash lib not found" >&5
-$as_echo "$as_me: error: mhash lib not found" >&2;}
- { (exit 1); exit 1; }; }
-fi
-
-
-for ac_header in mhash.h
-do
-as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
- { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
-$as_echo_n "checking for $ac_header... " >&6; }
-if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
- $as_echo_n "(cached) " >&6
-fi
-ac_res=`eval 'as_val=${'$as_ac_Header'}
- $as_echo "$as_val"'`
- { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-else
- # Is the header compilable?
-{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5
-$as_echo_n "checking $ac_header usability... " >&6; }
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-$ac_includes_default
-#include <$ac_header>
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ac_header_compiler=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_header_compiler=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
-$as_echo "$ac_header_compiler" >&6; }
-
-# Is the header present?
-{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5
-$as_echo_n "checking $ac_header presence... " >&6; }
-cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <$ac_header>
-_ACEOF
-if { (ac_try="$ac_cpp conftest.$ac_ext"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } >/dev/null && {
- test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
- test ! -s conftest.err
- }; then
- ac_header_preproc=yes
+{
+return mhash_init ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+ ac_cv_lib_mhash_mhash_init=yes
else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ac_header_preproc=no
+ ac_cv_lib_mhash_mhash_init=no
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mhash_mhash_init" >&5
+$as_echo "$ac_cv_lib_mhash_mhash_init" >&6; }
+if test "x$ac_cv_lib_mhash_mhash_init" = x""yes; then :
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBMHASH 1
+_ACEOF
-rm -f conftest.err conftest.$ac_ext
-{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
-$as_echo "$ac_header_preproc" >&6; }
+ LIBS="-lmhash $LIBS"
-# So? What about this header?
-case $ac_header_compiler:$ac_header_preproc:$ac_cxx_preproc_warn_flag in
- yes:no: )
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
-$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
-$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
- ac_header_preproc=yes
- ;;
- no:yes:* )
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
-$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5
-$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
-$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5
-$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
-$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
- { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
-$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
- ( cat <<\_ASBOX
-## ------------------------------ ##
-## Report this to clustalw@ucd.ie ##
-## ------------------------------ ##
-_ASBOX
- ) | sed "s/^/$as_me: WARNING: /" >&2
- ;;
-esac
-{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
-$as_echo_n "checking for $ac_header... " >&6; }
-if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
- $as_echo_n "(cached) " >&6
else
- eval "$as_ac_Header=\$ac_header_preproc"
+ as_fn_error "mhash lib not found" "$LINENO" 5
fi
-ac_res=`eval 'as_val=${'$as_ac_Header'}
- $as_echo "$as_val"'`
- { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
-fi
-as_val=`eval 'as_val=${'$as_ac_Header'}
- $as_echo "$as_val"'`
- if test "x$as_val" = x""yes; then
+ for ac_header in mhash.h
+do :
+ ac_fn_cxx_check_header_mongrel "$LINENO" "mhash.h" "ac_cv_header_mhash_h" "$ac_includes_default"
+if test "x$ac_cv_header_mhash_h" = x""yes; then :
cat >>confdefs.h <<_ACEOF
-#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+#define HAVE_MHASH_H 1
_ACEOF
else
- { { $as_echo "$as_me:$LINENO: error: mhash header not found" >&5
-$as_echo "$as_me: error: mhash header not found" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "mhash header not found" "$LINENO" 5
fi
done
case $ac_val in #(
*${as_nl}*)
case $ac_var in #(
- *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5
+ *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
esac
case $ac_var in #(
_ | IFS | as_nl) ;; #(
BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
- *) $as_unset $ac_var ;;
+ *) { eval $ac_var=; unset $ac_var;} ;;
esac ;;
esac
done
(set) 2>&1 |
case $as_nl`(ac_space=' '; set) 2>&1` in #(
*${as_nl}ac_space=\ *)
- # `set' does not quote correctly, so add quotes (double-quote
- # substitution turns \\\\ into \\, and sed turns \\ into \).
+ # `set' does not quote correctly, so add quotes: double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \.
sed -n \
"s/'/'\\\\''/g;
s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
if test -w "$cache_file"; then
test "x$cache_file" != "x/dev/null" &&
- { $as_echo "$as_me:$LINENO: updating cache $cache_file" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
$as_echo "$as_me: updating cache $cache_file" >&6;}
cat confcache >$cache_file
else
- { $as_echo "$as_me:$LINENO: not updating unwritable cache $cache_file" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
fi
fi
ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
# 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
# will be set to the directory where LIBOBJS objects are built.
- ac_libobjs="$ac_libobjs \${LIBOBJDIR}$ac_i\$U.$ac_objext"
- ac_ltlibobjs="$ac_ltlibobjs \${LIBOBJDIR}$ac_i"'$U.lo'
+ as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
done
LIBOBJS=$ac_libobjs
LTLIBOBJS=$ac_ltlibobjs
+ if test -n "$EXEEXT"; then
+ am__EXEEXT_TRUE=
+ am__EXEEXT_FALSE='#'
+else
+ am__EXEEXT_TRUE='#'
+ am__EXEEXT_FALSE=
+fi
+
if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
- { { $as_echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined.
-Usually this means the macro was only invoked conditionally." >&5
-$as_echo "$as_me: error: conditional \"AMDEP\" was never defined.
-Usually this means the macro was only invoked conditionally." >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
fi
if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
- { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined.
-Usually this means the macro was only invoked conditionally." >&5
-$as_echo "$as_me: error: conditional \"am__fastdepCC\" was never defined.
-Usually this means the macro was only invoked conditionally." >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
fi
if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
- { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined.
-Usually this means the macro was only invoked conditionally." >&5
-$as_echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined.
-Usually this means the macro was only invoked conditionally." >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." "$LINENO" 5
fi
: ${CONFIG_STATUS=./config.status}
ac_write_fail=0
ac_clean_files_save=$ac_clean_files
ac_clean_files="$ac_clean_files $CONFIG_STATUS"
-{ $as_echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5
+{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
-cat >$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+as_write_fail=0
+cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
#! $SHELL
# Generated by $as_me.
# Run this file to recreate the current configuration.
debug=false
ac_cs_recheck=false
ac_cs_silent=false
-SHELL=\${CONFIG_SHELL-$SHELL}
-_ACEOF
-cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
-## --------------------- ##
-## M4sh Initialization. ##
-## --------------------- ##
+SHELL=\${CONFIG_SHELL-$SHELL}
+export SHELL
+_ASEOF
+cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
# Be more Bourne compatible
DUALCASE=1; export DUALCASE # for MKS sh
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
emulate sh
NULLCMD=:
# Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
alias -g '${1+"$@"}'='"$@"'
setopt NO_GLOB_SUBST
else
- case `(set -o) 2>/dev/null` in
- *posix*) set -o posix ;;
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
esac
-
fi
-
-
-# PATH needs CR
-# Avoid depending upon Character Ranges.
-as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-as_cr_digits='0123456789'
-as_cr_alnum=$as_cr_Letters$as_cr_digits
-
as_nl='
'
export as_nl
as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
as_echo='printf %s\n'
as_echo_n='printf %s'
else
as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
as_echo_n_body='eval
arg=$1;
- case $arg in
+ case $arg in #(
*"$as_nl"*)
expr "X$arg" : "X\\(.*\\)$as_nl";
arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
}
fi
-# Support unset when possible.
-if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
- as_unset=unset
-else
- as_unset=false
-fi
-
# IFS
# We need space, tab and new line, in precisely that order. Quoting is
IFS=" "" $as_nl"
# Find who we are. Look in the path if we contain no directory separator.
-case $0 in
+case $0 in #((
*[\\/]* ) as_myself=$0 ;;
*) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
-done
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
IFS=$as_save_IFS
;;
fi
if test ! -f "$as_myself"; then
$as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
- { (exit 1); exit 1; }
+ exit 1
fi
-# Work around bugs in pre-3.0 UWIN ksh.
-for as_var in ENV MAIL MAILPATH
-do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
done
PS1='$ '
PS2='> '
LANGUAGE=C
export LANGUAGE
-# Required to use basename.
+# CDPATH.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+
+# as_fn_error ERROR [LINENO LOG_FD]
+# ---------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with status $?, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$?; test $as_status -eq 0 && as_status=1
+ if test "$3"; then
+ as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3
+ fi
+ $as_echo "$as_me: error: $1" >&2
+ as_fn_exit $as_status
+} # as_fn_error
+
+
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
+
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
+
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
+
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
+
+
if expr a : '\(a\)' >/dev/null 2>&1 &&
test "X`expr 00001 : '.*\(...\)'`" = X001; then
as_expr=expr
as_basename=false
fi
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
-# Name of the executable.
as_me=`$as_basename -- "$0" ||
$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
X"$0" : 'X\(//\)$' \| \
}
s/.*/./; q'`
-# CDPATH.
-$as_unset CDPATH
-
-
-
- as_lineno_1=$LINENO
- as_lineno_2=$LINENO
- test "x$as_lineno_1" != "x$as_lineno_2" &&
- test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
-
- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
- # uniformly replaced by the line number. The first 'sed' inserts a
- # line-number line after each line using $LINENO; the second 'sed'
- # does the real work. The second script uses 'N' to pair each
- # line-number line with the line containing $LINENO, and appends
- # trailing '-' during substitution so that $LINENO is not a special
- # case at line end.
- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
- # scripts with optimization help from Paolo Bonzini. Blame Lee
- # E. McMahon (1931-1989) for sed's syntax. :-)
- sed -n '
- p
- /[$]LINENO/=
- ' <$as_myself |
- sed '
- s/[$]LINENO.*/&-/
- t lineno
- b
- :lineno
- N
- :loop
- s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
- t loop
- s/-\n.*//
- ' >$as_me.lineno &&
- chmod +x "$as_me.lineno" ||
- { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
- { (exit 1); exit 1; }; }
-
- # Don't try to exec as it changes $[0], causing all sort of problems
- # (the dirname of $[0] is not the place where we might find the
- # original and so on. Autoconf is especially sensitive to this).
- . "./$as_me.lineno"
- # Exit status is that of the last command.
- exit
-}
-
-
-if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
- as_dirname=dirname
-else
- as_dirname=false
-fi
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
ECHO_C= ECHO_N= ECHO_T=
-case `echo -n x` in
+case `echo -n x` in #(((((
-n*)
- case `echo 'x\c'` in
+ case `echo 'xy\c'` in
*c*) ECHO_T=' ';; # ECHO_T is single tab character.
- *) ECHO_C='\c';;
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
esac;;
*)
ECHO_N='-n';;
esac
-if expr a : '\(a\)' >/dev/null 2>&1 &&
- test "X`expr 00001 : '.*\(...\)'`" = X001; then
- as_expr=expr
-else
- as_expr=false
-fi
rm -f conf$$ conf$$.exe conf$$.file
if test -d conf$$.dir; then
rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
rmdir conf$$.dir 2>/dev/null
+
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
+
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir"
+
+
+} # as_fn_mkdir_p
if mkdir -p . 2>/dev/null; then
- as_mkdir_p=:
+ as_mkdir_p='mkdir -p "$as_dir"'
else
test -d ./-p && rmdir ./-p
as_mkdir_p=false
if test -d "$1"; then
test -d "$1/.";
else
- case $1 in
+ case $1 in #(
-*)set "./$1";;
esac;
- case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
???[sx]*):;;*)false;;esac;fi
'\'' sh
'
exec 6>&1
+## ----------------------------------- ##
+## Main body of $CONFIG_STATUS script. ##
+## ----------------------------------- ##
+_ASEOF
+test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1
-# Save the log message, to keep $[0] and so on meaningful, and to
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# Save the log message, to keep $0 and so on meaningful, and to
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by clustalw $as_me 2.0.12, which was
-generated by GNU Autoconf 2.63. Invocation command line was
+This file was extended by clustalw $as_me 2.1, which was
+generated by GNU Autoconf 2.65. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
CONFIG_HEADERS = $CONFIG_HEADERS
cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
ac_cs_usage="\
-\`$as_me' instantiates files from templates according to the
-current configuration.
+\`$as_me' instantiates files and other configuration actions
+from templates according to the current configuration. Unless the files
+and actions are specified as TAGs, all are instantiated by default.
-Usage: $0 [OPTION]... [FILE]...
+Usage: $0 [OPTION]... [TAG]...
-h, --help print this help, then exit
-V, --version print version number and configuration settings, then exit
+ --config print configuration, then exit
-q, --quiet, --silent
do not print progress messages
-d, --debug don't remove temporary files
Configuration commands:
$config_commands
-Report bugs to <bug-autoconf@gnu.org>."
+Report bugs to <clustalw@ucd.ie>."
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-clustalw config.status 2.0.12
-configured by $0, generated by GNU Autoconf 2.63,
- with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
+clustalw config.status 2.1
+configured by $0, generated by GNU Autoconf 2.65,
+ with options \\"\$ac_cs_config\\"
-Copyright (C) 2008 Free Software Foundation, Inc.
+Copyright (C) 2009 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it."
ac_cs_recheck=: ;;
--version | --versio | --versi | --vers | --ver | --ve | --v | -V )
$as_echo "$ac_cs_version"; exit ;;
+ --config | --confi | --conf | --con | --co | --c )
+ $as_echo "$ac_cs_config"; exit ;;
--debug | --debu | --deb | --de | --d | -d )
debug=: ;;
--file | --fil | --fi | --f )
case $ac_optarg in
*\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
esac
- CONFIG_FILES="$CONFIG_FILES '$ac_optarg'"
+ as_fn_append CONFIG_FILES " '$ac_optarg'"
ac_need_defaults=false;;
--header | --heade | --head | --hea )
$ac_shift
case $ac_optarg in
*\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
esac
- CONFIG_HEADERS="$CONFIG_HEADERS '$ac_optarg'"
+ as_fn_append CONFIG_HEADERS " '$ac_optarg'"
ac_need_defaults=false;;
--he | --h)
# Conflict between --help and --header
- { $as_echo "$as_me: error: ambiguous option: $1
-Try \`$0 --help' for more information." >&2
- { (exit 1); exit 1; }; };;
+ as_fn_error "ambiguous option: \`$1'
+Try \`$0 --help' for more information.";;
--help | --hel | -h )
$as_echo "$ac_cs_usage"; exit ;;
-q | -quiet | --quiet | --quie | --qui | --qu | --q \
ac_cs_silent=: ;;
# This is an error.
- -*) { $as_echo "$as_me: error: unrecognized option: $1
-Try \`$0 --help' for more information." >&2
- { (exit 1); exit 1; }; } ;;
+ -*) as_fn_error "unrecognized option: \`$1'
+Try \`$0 --help' for more information." ;;
- *) ac_config_targets="$ac_config_targets $1"
+ *) as_fn_append ac_config_targets " $1"
ac_need_defaults=false ;;
esac
"src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
"src/clustalw_version.h") CONFIG_FILES="$CONFIG_FILES src/clustalw_version.h" ;;
- *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
-$as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
- { (exit 1); exit 1; }; };;
+ *) as_fn_error "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
esac
done
trap 'exit_status=$?
{ test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
' 0
- trap '{ (exit 1); exit 1; }' 1 2 13 15
+ trap 'as_fn_exit 1' 1 2 13 15
}
# Create a (secure) tmp directory for tmp files.
{
tmp=./conf$$-$RANDOM
(umask 077 && mkdir "$tmp")
-} ||
-{
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+} || as_fn_error "cannot create a temporary directory in ." "$LINENO" 5
# Set up the scripts for CONFIG_FILES section.
# No need to generate them if there are no CONFIG_FILES.
if test -n "$CONFIG_FILES"; then
-ac_cr='\r'
+ac_cr=`echo X | tr X '\015'`
+# On cygwin, bash can eat \r inside `` if the user requested igncr.
+# But we know of no other shell where ac_cr would be empty at this
+# point, so we can use a bashism as a fallback.
+if test "x$ac_cr" = x; then
+ eval ac_cr=\$\'\\r\'
+fi
ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
- ac_cs_awk_cr='\\r'
+ ac_cs_awk_cr='\r'
else
ac_cs_awk_cr=$ac_cr
fi
echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
echo "_ACEOF"
} >conf$$subs.sh ||
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-$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5
ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'`
ac_delim='%!_!# '
for ac_last_try in false false false false false :; do
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-$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5
ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
if test $ac_delim_n = $ac_delim_num; then
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-$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5
else
ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
fi
t delim
:nl
h
-s/\(.\{148\}\).*/\1/
+s/\(.\{148\}\)..*/\1/
t more1
s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
p
t nl
:delim
h
-s/\(.\{148\}\).*/\1/
+s/\(.\{148\}\)..*/\1/
t more2
s/["\\]/\\&/g; s/^/"/; s/$/"/
p
else
cat
fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
- || { { $as_echo "$as_me:$LINENO: error: could not setup config files machinery" >&5
-$as_echo "$as_me: error: could not setup config files machinery" >&2;}
- { (exit 1); exit 1; }; }
+ || as_fn_error "could not setup config files machinery" "$LINENO" 5
_ACEOF
# VPATH may cause trouble with some makes, so we remove $(srcdir),
if test -z "$ac_t"; then
break
elif $ac_last_try; then
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-$as_echo "$as_me: error: could not make $CONFIG_HEADERS" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "could not make $CONFIG_HEADERS" "$LINENO" 5
else
ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
fi
_ACAWK
_ACEOF
cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
- { { $as_echo "$as_me:$LINENO: error: could not setup config headers machinery" >&5
-$as_echo "$as_me: error: could not setup config headers machinery" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "could not setup config headers machinery" "$LINENO" 5
fi # test -n "$CONFIG_HEADERS"
esac
case $ac_mode$ac_tag in
:[FHL]*:*);;
- :L* | :C*:*) { { $as_echo "$as_me:$LINENO: error: invalid tag $ac_tag" >&5
-$as_echo "$as_me: error: invalid tag $ac_tag" >&2;}
- { (exit 1); exit 1; }; };;
+ :L* | :C*:*) as_fn_error "invalid tag \`$ac_tag'" "$LINENO" 5;;
:[FH]-) ac_tag=-:-;;
:[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
esac
[\\/$]*) false;;
*) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
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-$as_echo "$as_me: error: cannot find input file: $ac_f" >&2;}
- { (exit 1); exit 1; }; };;
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esac
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+ as_dir=$dirpart/$fdir; as_fn_mkdir_p
# echo "creating $dirpart/$file"
echo '# dummy' > "$dirpart/$file"
done
done # for ac_tag
-{ (exit 0); exit 0; }
+as_fn_exit 0
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-chmod +x $CONFIG_STATUS
ac_clean_files=$ac_clean_files_save
test $ac_write_fail = 0 ||
- { { $as_echo "$as_me:$LINENO: error: write failure creating $CONFIG_STATUS" >&5
-$as_echo "$as_me: error: write failure creating $CONFIG_STATUS" >&2;}
- { (exit 1); exit 1; }; }
+ as_fn_error "write failure creating $CONFIG_STATUS" "$LINENO" 5
# configure is writing to config.log, and then calls config.status.
exec 5>>config.log
# Use ||, not &&, to avoid exiting from the if with $? = 1, which
# would make configure fail if this is the last instruction.
- $ac_cs_success || { (exit 1); exit 1; }
+ $ac_cs_success || as_fn_exit $?
fi
if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
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+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
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fi
# after apllying any changes you will have to run
# $ autoreconf
#
-AC_INIT([clustalw], [2.0.12], [clustalw@ucd.ie])
+AC_INIT([clustalw], [2.1], [clustalw@ucd.ie])
#
# The AC_INIT macro can take any source file as an argument. It just
# checks that the file is there, which should, in turn, mean that the
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
-scriptversion=2007-03-29.01
+scriptversion=2009-04-28.21; # UTC
-# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software
-# Foundation, Inc.
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 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
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
-# 02110-1301, USA.
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
depmode=dashmstdout
fi
+cygpath_u="cygpath -u -f -"
+if test "$depmode" = msvcmsys; then
+ # This is just like msvisualcpp but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u="sed s,\\\\\\\\,/,g"
+ depmode=msvisualcpp
+fi
+
case "$depmode" in
gcc3)
## gcc 3 implements dependency tracking that does exactly what
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
tr '
-' ' ' >> $depfile
- echo >> $depfile
+' ' ' >> "$depfile"
+ echo >> "$depfile"
# The second pass generates a dummy entry for each header file.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
- >> $depfile
+ >> "$depfile"
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
if test -f "$tmpdepfile"; then
sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
# Add `dependent.h:' lines.
- sed -ne '2,${; s/^ *//; s/ \\*$//; s/$/:/; p;}' "$tmpdepfile" >> "$depfile"
+ sed -ne '2,${
+ s/^ *//
+ s/ \\*$//
+ s/$/:/
+ p
+ }' "$tmpdepfile" >> "$depfile"
else
echo "#dummy" > "$depfile"
fi
# Remove the call to Libtool.
if test "$libtool" = yes; then
- while test $1 != '--mode=compile'; do
+ while test "X$1" != 'X--mode=compile'; do
shift
done
shift
"$@" || exit $?
# Remove any Libtool call
if test "$libtool" = yes; then
- while test $1 != '--mode=compile'; do
+ while test "X$1" != 'X--mode=compile'; do
shift
done
shift
fi
# X makedepend
shift
- cleared=no
- for arg in "$@"; do
+ cleared=no eat=no
+ for arg
+ do
case $cleared in
no)
set ""; shift
cleared=yes ;;
esac
+ if test $eat = yes; then
+ eat=no
+ continue
+ fi
case "$arg" in
-D*|-I*)
set fnord "$@" "$arg"; shift ;;
# Strip any option that makedepend may not understand. Remove
# the object too, otherwise makedepend will parse it as a source file.
+ -arch)
+ eat=yes ;;
-*|$object)
;;
*)
set fnord "$@" "$arg"; shift ;;
esac
done
- obj_suffix="`echo $object | sed 's/^.*\././'`"
+ obj_suffix=`echo "$object" | sed 's/^.*\././'`
touch "$tmpdepfile"
${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
rm -f "$depfile"
# Remove the call to Libtool.
if test "$libtool" = yes; then
- while test $1 != '--mode=compile'; do
+ while test "X$1" != 'X--mode=compile'; do
shift
done
shift
msvisualcpp)
# Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout, regardless of -o,
- # because we must use -o when running libtool.
+ # always write the preprocessed file to stdout.
"$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
IFS=" "
for arg
do
case "$arg" in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
set fnord "$@"
shift
;;
esac
done
- "$@" -E |
- sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
+ "$@" -E 2>/dev/null |
+ sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
- . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
echo " " >> "$depfile"
- . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
rm -f "$tmpdepfile"
;;
+msvcmsys)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
none)
exec "$@"
;;
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
# End:
#!/bin/sh
# install - install a program, script, or datafile
-scriptversion=2006-12-25.00
+scriptversion=2009-04-28.21; # UTC
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-end: "$"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
# End:
-# Makefile.in generated by automake 1.10.2 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
# m4/Makefile. Generated from Makefile.in by configure.
# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 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.
pkgdatadir = $(datadir)/clustalw
-pkglibdir = $(libdir)/clustalw
pkgincludedir = $(includedir)/clustalw
+pkglibdir = $(libdir)/clustalw
+pkglibexecdir = $(libexecdir)/clustalw
am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = $(top_builddir)/src/config.h
CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
SOURCES =
DIST_SOURCES =
am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
$(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
*) f=$$p;; \
esac;
-am__strip_dir = `echo $$p | sed -e 's|^.*/||'`;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+ for p in $$list; do echo "$$p $$p"; done | \
+ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+ if (++n[$$2] == $(am__install_max)) \
+ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+ END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+ sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
am__installdirs = "$(DESTDIR)$(m4datadir)"
-m4dataDATA_INSTALL = $(INSTALL_DATA)
DATA = $(m4data_DATA)
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-ACLOCAL = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run aclocal-1.10
-AMTAR = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run tar
-AUTOCONF = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoconf
-AUTOHEADER = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoheader
-AUTOMAKE = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run automake-1.10
+ACLOCAL = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run aclocal-1.11
+AMTAR = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run tar
+AUTOCONF = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoconf
+AUTOHEADER = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoheader
+AUTOMAKE = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run automake-1.11
AWK = gawk
CC = gcc
CCDEPMODE = depmode=gcc3
CFLAGS = -g -O2
CLUSTALW_NAME = ClustalW
-CLUSTALW_VERSION = 2.0.12
+CLUSTALW_VERSION = 2.1
CPPFLAGS =
CXX = g++
CXXCPP = g++ -E
LIBOBJS =
LIBS =
LTLIBOBJS =
-MAKEINFO = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run makeinfo
+MAKEINFO = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run makeinfo
MKDIR_P = /bin/mkdir -p
OBJEXT = o
PACKAGE = clustalw
PACKAGE_BUGREPORT = clustalw@ucd.ie
PACKAGE_NAME = clustalw
-PACKAGE_STRING = clustalw 2.0.12
+PACKAGE_STRING = clustalw 2.1
PACKAGE_TARNAME = clustalw
-PACKAGE_VERSION = 2.0.12
+PACKAGE_URL =
+PACKAGE_VERSION = 2.1
PATH_SEPARATOR = :
RANLIB = ranlib
SET_MAKE =
SHELL = /bin/sh
STRIP =
-VERSION = 2.0.12
-abs_builddir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/m4
-abs_srcdir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/m4
-abs_top_builddir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw
-abs_top_srcdir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw
+VERSION = 2.1
+abs_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/m4
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc \
- alignment/Alignment.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- alignment/Sequence.h alignment/../general/userparams.h \
- alignment/../general/UserParameters.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
- alignment/../general/utils.h alignment/../general/Utility.h \
- /usr/include/errno.h /usr/include/bits/errno.h \
- /usr/include/linux/errno.h /usr/include/asm/errno.h \
- /usr/include/asm-x86_64/errno.h /usr/include/asm-generic/errno.h \
- /usr/include/asm-generic/errno-base.h alignment/../general/clustalw.h \
- alignment/../general/general.h alignment/../general/Array2D.h \
- alignment/../general/SquareMat.h alignment/../general/SymMatrix.h \
- alignment/../general/utils.h \
- alignment/../substitutionMatrix/globalmatrix.h \
- alignment/../substitutionMatrix/SubMatrix.h \
- alignment/../substitutionMatrix/../general/clustalw.h \
- alignment/../substitutionMatrix/../general/userparams.h \
- alignment/../substitutionMatrix/../general/utils.h \
- alignment/../substitutionMatrix/../general/Array2D.h \
- alignment/../general/VectorOutOfRange.h \
- alignment/../general/SequenceNotFoundException.h
+Alignment.o: alignment/Alignment.cpp config.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
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+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \
+ alignment/Alignment.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ alignment/Sequence.h alignment/../general/userparams.h \
+ alignment/../general/UserParameters.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ alignment/../general/utils.h alignment/../general/Utility.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \
+ /usr/include/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
+ /usr/include/asm-generic/errno-base.h alignment/../general/clustalw.h \
+ alignment/../general/general.h alignment/../general/Array2D.h \
+ alignment/../general/SquareMat.h alignment/../general/SymMatrix.h \
+ alignment/../general/utils.h \
+ alignment/../substitutionMatrix/globalmatrix.h \
+ alignment/../substitutionMatrix/SubMatrix.h \
+ alignment/../substitutionMatrix/../general/clustalw.h \
+ alignment/../substitutionMatrix/../general/userparams.h \
+ alignment/../substitutionMatrix/../general/utils.h \
+ alignment/../substitutionMatrix/../general/Array2D.h \
+ alignment/../general/VectorOutOfRange.h \
+ alignment/../general/SequenceNotFoundException.h
config.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:
/usr/include/bits/wordsize.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:
/usr/include/features.h:
/usr/include/gnu/stubs-64.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h:
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+ /usr/include/getopt.h \
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+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cassert \
+ /usr/include/assert.h alignment/Alignment.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
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+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
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+ /usr/include/asm-generic/errno-base.h alignment/../general/clustalw.h \
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+ alignment/../general/utils.h \
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+ alignment/../substitutionMatrix/../general/utils.h \
+ alignment/../substitutionMatrix/../general/Array2D.h \
+ alignment/../general/VectorOutOfRange.h \
+ alignment/../general/SequenceNotFoundException.h
config.h:
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config.h:
tree/AlignmentSteps.h:
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- fileInput/../alignment/Sequence.h fileInput/../general/userparams.h \
- fileInput/../general/utils.h fileInput/FileParser.h \
- fileInput/InFileStream.h fileInput/ClustalFileParser.h \
- fileInput/PearsonFileParser.h fileInput/PIRFileParser.h \
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- alignment/../substitutionMatrix/globalmatrix.h \
- general/ClustalWResources.h Help.h
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
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+ general/SquareMat.h \
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+ general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
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+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
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+ /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
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+ fileInput/../alignment/Alignment.h fileInput/../alignment/Sequence.h \
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config.h:
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- /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \
- /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
- /usr/include/bits/confname.h /usr/include/getopt.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \
- /usr/include/ctype.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \
- /usr/include/stdint.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
- /usr/include/wctype.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- general/clustalw.h general/general.h general/Array2D.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
- general/SquareMat.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
- /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc
+ClustalWResources.o: general/ClustalWResources.cpp config.h \
+ general/ClustalWResources.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ general/clustalw.h general/general.h general/Array2D.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ general/SquareMat.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc
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+ /usr/include/asm-generic/errno-base.h \
+ tree/../alignment/../general/clustalw.h \
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config.h:
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream
+DebugLog.o: general/DebugLog.cpp config.h general/DebugLog.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
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+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
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+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream
config.h:
general/DebugLog.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:
/usr/include/bits/wordsize.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:
/usr/include/features.h:
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- /usr/include/time.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
- /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
- fileInput/FileParser.h fileInput/../alignment/Sequence.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
- fileInput/../alignment/../general/userparams.h \
- fileInput/../alignment/../general/UserParameters.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
- /usr/include/wctype.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- fileInput/../alignment/../general/utils.h \
- fileInput/../alignment/../general/Utility.h /usr/include/errno.h \
- /usr/include/bits/errno.h /usr/include/linux/errno.h \
- /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \
- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- fileInput/../alignment/../general/clustalw.h \
- fileInput/../alignment/../general/general.h \
- fileInput/../alignment/../general/Array2D.h \
- fileInput/../alignment/../general/SquareMat.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- fileInput/../alignment/../general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
- /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- fileInput/../alignment/../general/utils.h \
- fileInput/../general/userparams.h fileInput/InFileStream.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc
+EMBLFileParser.o: fileInput/EMBLFileParser.cpp config.h \
+ fileInput/EMBLFileParser.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ fileInput/FileParser.h fileInput/../alignment/Sequence.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ fileInput/../alignment/../general/userparams.h \
+ fileInput/../alignment/../general/UserParameters.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- pairwise/../alignment/Sequence.h \
- pairwise/../alignment/../general/userparams.h \
- pairwise/../alignment/../general/UserParameters.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
- pairwise/../alignment/../general/utils.h \
- pairwise/../alignment/../general/Utility.h /usr/include/errno.h \
- /usr/include/bits/errno.h /usr/include/linux/errno.h \
- /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \
- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- pairwise/../alignment/../general/clustalw.h \
- pairwise/../alignment/../general/general.h \
- pairwise/../alignment/../general/Array2D.h \
- pairwise/../alignment/../general/SquareMat.h \
- pairwise/../alignment/../general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
- pairwise/../alignment/../general/utils.h \
- pairwise/../alignment/../substitutionMatrix/globalmatrix.h \
- pairwise/../alignment/../substitutionMatrix/SubMatrix.h \
- pairwise/../alignment/../substitutionMatrix/../general/clustalw.h \
- pairwise/../alignment/../substitutionMatrix/../general/userparams.h \
- pairwise/../alignment/../substitutionMatrix/../general/utils.h \
- pairwise/../alignment/../substitutionMatrix/../general/Array2D.h \
- pairwise/../alignment/../general/VectorOutOfRange.h \
- pairwise/../alignment/../general/SequenceNotFoundException.h
+FastPairwiseAlign.o: pairwise/FastPairwiseAlign.cpp config.h \
+ /usr/include/math.h /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h pairwise/FastPairwiseAlign.h \
+ pairwise/PairwiseAlignBase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ pairwise/../alignment/Alignment.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
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+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ pairwise/../alignment/Sequence.h \
+ pairwise/../alignment/../general/userparams.h \
+ pairwise/../alignment/../general/UserParameters.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ pairwise/../alignment/../general/utils.h \
+ pairwise/../alignment/../general/Utility.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \
+ /usr/include/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
+ /usr/include/asm-generic/errno-base.h \
+ pairwise/../alignment/../general/clustalw.h \
+ pairwise/../alignment/../general/general.h \
+ pairwise/../alignment/../general/Array2D.h \
+ pairwise/../alignment/../general/SquareMat.h \
+ pairwise/../alignment/../general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ pairwise/../alignment/../general/utils.h \
+ pairwise/../alignment/../substitutionMatrix/globalmatrix.h \
+ pairwise/../alignment/../substitutionMatrix/SubMatrix.h \
+ pairwise/../alignment/../substitutionMatrix/../general/clustalw.h \
+ pairwise/../alignment/../substitutionMatrix/../general/userparams.h \
+ pairwise/../alignment/../substitutionMatrix/../general/utils.h \
+ pairwise/../alignment/../substitutionMatrix/../general/Array2D.h \
+ pairwise/../alignment/../general/VectorOutOfRange.h \
+ pairwise/../alignment/../general/SequenceNotFoundException.h
config.h:
pairwise/PairwiseAlignBase.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:
-/usr/include/string.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:
-/usr/include/xlocale.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h:
-/usr/include/limits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h:
-/usr/include/bits/posix1_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h:
-/usr/include/bits/local_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h:
-/usr/include/linux/limits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h:
-/usr/include/bits/posix2_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h:
-/usr/include/bits/xopen_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h:
-/usr/include/bits/stdio_lim.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new:
-/usr/include/stdlib.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception:
-/usr/include/bits/waitflags.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:
-/usr/include/bits/waitstatus.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h:
-/usr/include/endian.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:
-/usr/include/bits/endian.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list:
-/usr/include/sys/types.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h:
-/usr/include/bits/types.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc:
-/usr/include/bits/typesizes.h:
+pairwise/../alignment/Alignment.h:
-/usr/include/time.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string:
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- fileInput/../alignment/../general/utils.h \
- fileInput/../alignment/../general/Utility.h /usr/include/errno.h \
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- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
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- fileInput/../alignment/../general/general.h \
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- fileInput/../alignment/../general/SquareMat.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
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- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
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- fileInput/../alignment/../general/utils.h \
- fileInput/../general/userparams.h fileInput/InFileStream.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc
+FileParser.o: fileInput/FileParser.cpp config.h fileInput/FileParser.h \
+ /usr/include/ctype.h /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/xlocale.h fileInput/../alignment/Sequence.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ fileInput/../alignment/../general/userparams.h \
+ fileInput/../alignment/../general/UserParameters.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ fileInput/../alignment/../general/utils.h \
+ fileInput/../alignment/../general/Utility.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \
+ /usr/include/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
+ /usr/include/asm-generic/errno-base.h \
+ fileInput/../alignment/../general/clustalw.h \
+ fileInput/../alignment/../general/general.h \
+ fileInput/../alignment/../general/Array2D.h \
+ fileInput/../alignment/../general/SquareMat.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- pairwise/../alignment/Sequence.h \
- pairwise/../alignment/../general/userparams.h \
- pairwise/../alignment/../general/UserParameters.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
- pairwise/../alignment/../general/utils.h \
- pairwise/../alignment/../general/Utility.h /usr/include/errno.h \
- /usr/include/bits/errno.h /usr/include/linux/errno.h \
- /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \
- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- pairwise/../alignment/../general/clustalw.h \
- pairwise/../alignment/../general/general.h \
- pairwise/../alignment/../general/Array2D.h \
- pairwise/../alignment/../general/SquareMat.h \
- pairwise/../alignment/../general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
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- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
- pairwise/../alignment/../general/utils.h \
- pairwise/../alignment/../substitutionMatrix/globalmatrix.h \
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- pairwise/../alignment/../substitutionMatrix/../general/clustalw.h \
- pairwise/../alignment/../substitutionMatrix/../general/userparams.h \
- pairwise/../alignment/../substitutionMatrix/../general/utils.h \
- pairwise/../alignment/../substitutionMatrix/../general/Array2D.h \
- pairwise/../alignment/../general/VectorOutOfRange.h \
- pairwise/../alignment/../general/SequenceNotFoundException.h
+FullPairwiseAlign.o: pairwise/FullPairwiseAlign.cpp config.h \
+ pairwise/FullPairwiseAlign.h pairwise/PairwiseAlignBase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
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+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ pairwise/../alignment/Alignment.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
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+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ pairwise/../alignment/Sequence.h \
+ pairwise/../alignment/../general/userparams.h \
+ pairwise/../alignment/../general/UserParameters.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ pairwise/../alignment/../general/utils.h \
+ pairwise/../alignment/../general/Utility.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \
+ /usr/include/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
+ /usr/include/asm-generic/errno-base.h \
+ pairwise/../alignment/../general/clustalw.h \
+ pairwise/../alignment/../general/general.h \
+ pairwise/../alignment/../general/Array2D.h \
+ pairwise/../alignment/../general/SquareMat.h \
+ pairwise/../alignment/../general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
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+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ pairwise/../alignment/../general/utils.h \
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+ pairwise/../alignment/../substitutionMatrix/SubMatrix.h \
+ pairwise/../alignment/../substitutionMatrix/../general/clustalw.h \
+ pairwise/../alignment/../substitutionMatrix/../general/userparams.h \
+ pairwise/../alignment/../substitutionMatrix/../general/utils.h \
+ pairwise/../alignment/../substitutionMatrix/../general/Array2D.h \
+ pairwise/../alignment/../general/VectorOutOfRange.h \
+ pairwise/../alignment/../general/SequenceNotFoundException.h
config.h:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h:
+pairwise/../alignment/../general/utils.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h:
+pairwise/../alignment/../general/Utility.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc:
+/usr/include/stdlib.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc:
+/usr/include/bits/waitflags.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale:
+/usr/include/bits/waitstatus.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc:
+/usr/include/sys/types.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo:
+/usr/include/sys/select.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream:
+/usr/include/bits/select.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc:
+/usr/include/bits/sigset.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional:
+/usr/include/sys/sysmacros.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept:
+/usr/include/alloca.h:
-pairwise/../alignment/Sequence.h:
+/usr/include/libio.h:
-pairwise/../alignment/../general/userparams.h:
+/usr/include/_G_config.h:
-pairwise/../alignment/../general/UserParameters.h:
+/usr/include/bits/stdio_lim.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream:
+/usr/include/bits/sys_errlist.h:
-pairwise/../alignment/../general/utils.h:
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-pairwise/../alignment/../general/Utility.h:
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/usr/include/errno.h:
/usr/include/asm/errno.h:
-/usr/include/asm-x86_64/errno.h:
-
/usr/include/asm-generic/errno.h:
/usr/include/asm-generic/errno-base.h:
pairwise/../alignment/../general/SymMatrix.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath:
/usr/include/math.h:
/usr/include/bits/mathinline.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc:
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pairwise/../alignment/../general/utils.h:
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- fileInput/GDEFileParser.h \
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- /usr/include/features.h /usr/include/sys/cdefs.h \
- /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \
- /usr/include/string.h /usr/include/xlocale.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \
- /usr/include/limits.h /usr/include/bits/posix1_lim.h \
- /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
- /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
- /usr/include/bits/stdio_lim.h \
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- /usr/include/stdlib.h /usr/include/bits/waitflags.h \
- /usr/include/bits/waitstatus.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/sys/types.h \
- /usr/include/bits/types.h /usr/include/bits/typesizes.h \
- /usr/include/time.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
- /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \
- /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \
- /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \
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- /usr/include/locale.h /usr/include/bits/locale.h \
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- /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \
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- /usr/include/bits/confname.h /usr/include/getopt.h \
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- /usr/include/ctype.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
- fileInput/FileParser.h fileInput/../alignment/Sequence.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
- fileInput/../alignment/../general/userparams.h \
- fileInput/../alignment/../general/UserParameters.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
- /usr/include/wctype.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- fileInput/../alignment/../general/utils.h \
- fileInput/../alignment/../general/Utility.h /usr/include/errno.h \
- /usr/include/bits/errno.h /usr/include/linux/errno.h \
- /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \
- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- fileInput/../alignment/../general/clustalw.h \
- fileInput/../alignment/../general/general.h \
- fileInput/../alignment/../general/Array2D.h \
- fileInput/../alignment/../general/SquareMat.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- fileInput/../alignment/../general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
- /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- fileInput/../alignment/../general/utils.h \
- fileInput/../general/userparams.h fileInput/InFileStream.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc
+GDEFileParser.o: fileInput/GDEFileParser.cpp config.h \
+ fileInput/GDEFileParser.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
- fileInput/InFileStream.h
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
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+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ fileInput/InFileStream.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h
config.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string:
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/usr/include/bits/wordsize.h:
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/usr/include/features.h:
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config.h:
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multipleAlign/../tree/AlignmentSteps.h:
multipleAlign/../tree/../alignment/Alignment.h:
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+ multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \
+ multipleAlign/../alignment/../general/VectorOutOfRange.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
- fileInput/FileParser.h fileInput/../alignment/Sequence.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
- fileInput/../alignment/../general/userparams.h \
- fileInput/../alignment/../general/UserParameters.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
- /usr/include/wctype.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- fileInput/../alignment/../general/utils.h \
- fileInput/../alignment/../general/Utility.h /usr/include/errno.h \
- /usr/include/bits/errno.h /usr/include/linux/errno.h \
- /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \
- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- fileInput/../alignment/../general/clustalw.h \
- fileInput/../alignment/../general/general.h \
- fileInput/../alignment/../general/Array2D.h \
- fileInput/../alignment/../general/SquareMat.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- fileInput/../alignment/../general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
- /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- fileInput/../alignment/../general/utils.h \
- fileInput/../general/userparams.h fileInput/InFileStream.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc
+MSFFileParser.o: fileInput/MSFFileParser.cpp config.h \
+ fileInput/MSFFileParser.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ fileInput/FileParser.h fileInput/../alignment/Sequence.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ fileInput/../alignment/../general/userparams.h \
+ fileInput/../alignment/../general/UserParameters.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ fileInput/../alignment/../general/utils.h \
+ fileInput/../alignment/../general/Utility.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \
+ /usr/include/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
+ /usr/include/asm-generic/errno-base.h \
+ fileInput/../alignment/../general/clustalw.h \
+ fileInput/../alignment/../general/general.h \
+ fileInput/../alignment/../general/Array2D.h \
+ fileInput/../alignment/../general/SquareMat.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ fileInput/../alignment/../general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ fileInput/../alignment/../general/utils.h \
+ fileInput/../general/userparams.h fileInput/InFileStream.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h
config.h:
fileInput/MSFFileParser.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:
/usr/include/bits/wordsize.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:
/usr/include/features.h:
/usr/include/gnu/stubs-64.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept:
fileInput/../alignment/../general/utils.h:
fileInput/InFileStream.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h:
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+ config.h multipleAlign/MyersMillerProfileAlign.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ multipleAlign/ProfileAlignAlgorithm.h \
+ multipleAlign/../alignment/Alignment.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
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+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
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+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ multipleAlign/../alignment/Sequence.h \
+ multipleAlign/../alignment/../general/userparams.h \
+ multipleAlign/../alignment/../general/UserParameters.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ multipleAlign/../alignment/../general/utils.h \
+ multipleAlign/../alignment/../general/Utility.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \
+ /usr/include/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
+ /usr/include/asm-generic/errno-base.h \
+ multipleAlign/../alignment/../general/clustalw.h \
+ multipleAlign/../alignment/../general/general.h \
+ multipleAlign/../alignment/../general/Array2D.h \
+ multipleAlign/../alignment/../general/SquareMat.h \
+ multipleAlign/../alignment/../general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
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+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ multipleAlign/../alignment/../general/utils.h \
+ multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \
+ multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \
+ multipleAlign/../alignment/../general/VectorOutOfRange.h \
+ multipleAlign/../alignment/../general/SequenceNotFoundException.h \
+ multipleAlign/ProfileStandard.h multipleAlign/ProfileBase.h \
+ multipleAlign/ProfileWithSub.h multipleAlign/Iteration.h \
+ multipleAlign/../general/clustalw.h
config.h:
multipleAlign/MyersMillerProfileAlign.h:
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config.h:
tree/NJTree.h:
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
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- tree/UPGMA/../../general/debuglogObject.h \
- tree/UPGMA/../../general/DebugLog.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \
- tree/UPGMA/../../general/clustalw.h tree/UPGMA/../../general/general.h \
- tree/UPGMA/../../general/Array2D.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
- tree/UPGMA/../../general/SquareMat.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- tree/UPGMA/../../general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
- /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc
+Node.o: tree/UPGMA/Node.cpp config.h tree/UPGMA/Node.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/limits \
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+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ tree/UPGMA/upgmadata.h tree/UPGMA/../../general/VectorUtility.h \
+ tree/UPGMA/../../general/debuglogObject.h \
+ tree/UPGMA/../../general/DebugLog.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \
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+ tree/UPGMA/../../general/Array2D.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ tree/UPGMA/../../general/SquareMat.h \
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+ /usr/include/alloca.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc
config.h:
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+ /usr/include/libio.h /usr/include/_G_config.h \
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+ /usr/include/bits/stdio.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \
+ general/utils.h general/Utility.h \
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h:
+general/utils.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h:
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/usr/include/errno.h:
/usr/include/asm/errno.h:
-/usr/include/asm-x86_64/errno.h:
-
/usr/include/asm-generic/errno.h:
/usr/include/asm-generic/errno-base.h:
general/Array2D.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream:
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general/SquareMat.h:
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-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional:
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general/SymMatrix.h:
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/usr/include/math.h:
/usr/include/bits/mathinline.h:
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general/userparams.h:
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- fileInput/PIRFileParser.h \
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- /usr/include/features.h /usr/include/sys/cdefs.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- fileInput/../alignment/../general/utils.h \
- fileInput/../alignment/../general/Utility.h /usr/include/errno.h \
- /usr/include/bits/errno.h /usr/include/linux/errno.h \
- /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \
- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- fileInput/../alignment/../general/clustalw.h \
- fileInput/../alignment/../general/general.h \
- fileInput/../alignment/../general/Array2D.h \
- fileInput/../alignment/../general/SquareMat.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
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- /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- fileInput/../alignment/../general/utils.h \
- fileInput/../general/userparams.h fileInput/InFileStream.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc
+PIRFileParser.o: fileInput/PIRFileParser.cpp config.h \
+ fileInput/PIRFileParser.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
- fileInput/FileParser.h fileInput/../alignment/Sequence.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
- fileInput/../alignment/../general/userparams.h \
- fileInput/../alignment/../general/UserParameters.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
- /usr/include/wctype.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- fileInput/../alignment/../general/utils.h \
- fileInput/../alignment/../general/Utility.h /usr/include/errno.h \
- /usr/include/bits/errno.h /usr/include/linux/errno.h \
- /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \
- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- fileInput/../alignment/../general/clustalw.h \
- fileInput/../alignment/../general/general.h \
- fileInput/../alignment/../general/Array2D.h \
- fileInput/../alignment/../general/SquareMat.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- fileInput/../alignment/../general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
- /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- fileInput/../alignment/../general/utils.h \
- fileInput/../general/userparams.h fileInput/InFileStream.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc
+PearsonFileParser.o: fileInput/PearsonFileParser.cpp config.h \
+ fileInput/PearsonFileParser.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ fileInput/FileParser.h fileInput/../alignment/Sequence.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ fileInput/../alignment/../general/userparams.h \
+ fileInput/../alignment/../general/UserParameters.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ fileInput/../alignment/../general/utils.h \
+ fileInput/../alignment/../general/Utility.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \
+ /usr/include/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
+ /usr/include/asm-generic/errno-base.h \
+ fileInput/../alignment/../general/clustalw.h \
+ fileInput/../alignment/../general/general.h \
+ fileInput/../alignment/../general/Array2D.h \
+ fileInput/../alignment/../general/SquareMat.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ fileInput/../alignment/../general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ fileInput/../alignment/../general/utils.h \
+ fileInput/../general/userparams.h fileInput/InFileStream.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- multipleAlign/../alignment/Sequence.h \
- multipleAlign/../alignment/../general/userparams.h \
- multipleAlign/../alignment/../general/UserParameters.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
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- /usr/include/bits/errno.h /usr/include/linux/errno.h \
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- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- multipleAlign/../alignment/../general/clustalw.h \
- multipleAlign/../alignment/../general/general.h \
- multipleAlign/../alignment/../general/Array2D.h \
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- multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \
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- multipleAlign/../alignment/../general/VectorOutOfRange.h \
- multipleAlign/../alignment/../general/SequenceNotFoundException.h \
- multipleAlign/ProfileBase.h
+ProfileStandard.o: multipleAlign/ProfileStandard.cpp config.h \
+ multipleAlign/ProfileStandard.h multipleAlign/../alignment/Alignment.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ multipleAlign/../alignment/../general/utils.h \
+ multipleAlign/../alignment/../general/Utility.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
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+ /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
+ /usr/include/asm-generic/errno-base.h \
+ multipleAlign/../alignment/../general/clustalw.h \
+ multipleAlign/../alignment/../general/general.h \
+ multipleAlign/../alignment/../general/Array2D.h \
+ multipleAlign/../alignment/../general/SquareMat.h \
+ multipleAlign/../alignment/../general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
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+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ multipleAlign/../alignment/../general/utils.h \
+ multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h \
+ multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/utils.h \
+ multipleAlign/../alignment/../substitutionMatrix/../general/Array2D.h \
+ multipleAlign/../alignment/../general/VectorOutOfRange.h \
+ multipleAlign/../alignment/../general/SequenceNotFoundException.h \
+ multipleAlign/ProfileBase.h
config.h:
multipleAlign/../alignment/Alignment.h:
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/usr/include/bits/wordsize.h:
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/usr/include/features.h:
/usr/include/gnu/stubs-64.h:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring:
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+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
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+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ multipleAlign/../alignment/Sequence.h \
+ multipleAlign/../alignment/../general/userparams.h \
+ multipleAlign/../alignment/../general/UserParameters.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept:
+/usr/include/alloca.h:
-multipleAlign/../alignment/Sequence.h:
+/usr/include/libio.h:
-multipleAlign/../alignment/../general/userparams.h:
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-multipleAlign/../alignment/../general/UserParameters.h:
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/usr/include/errno.h:
/usr/include/asm/errno.h:
-/usr/include/asm-x86_64/errno.h:
-
/usr/include/asm-generic/errno.h:
/usr/include/asm-generic/errno-base.h:
multipleAlign/../alignment/../general/SymMatrix.h:
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/usr/include/math.h:
/usr/include/bits/mathinline.h:
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multipleAlign/../alignment/../general/utils.h:
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- /usr/include/features.h /usr/include/sys/cdefs.h \
- /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \
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- /usr/include/time.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
- /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
- fileInput/FileParser.h fileInput/../alignment/Sequence.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
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- fileInput/../alignment/../general/UserParameters.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
- /usr/include/wctype.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- fileInput/../alignment/../general/utils.h \
- fileInput/../alignment/../general/Utility.h /usr/include/errno.h \
- /usr/include/bits/errno.h /usr/include/linux/errno.h \
- /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \
- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- fileInput/../alignment/../general/clustalw.h \
- fileInput/../alignment/../general/general.h \
- fileInput/../alignment/../general/Array2D.h \
- fileInput/../alignment/../general/SquareMat.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- fileInput/../alignment/../general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
- /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- fileInput/../alignment/../general/utils.h \
- fileInput/../general/userparams.h fileInput/InFileStream.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc
+RSFFileParser.o: fileInput/RSFFileParser.cpp config.h \
+ fileInput/RSFFileParser.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
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config.h:
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config.h:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h:
+tree/UPGMA/../../alignment/Sequence.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc:
+tree/UPGMA/../../alignment/../general/userparams.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc:
+/usr/include/stdlib.h:
-tree/UPGMA/../../alignment/Alignment.h:
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-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept:
+/usr/include/sys/select.h:
-tree/UPGMA/../../alignment/Sequence.h:
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-tree/UPGMA/../../alignment/../general/userparams.h:
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/usr/include/errno.h:
/usr/include/asm/errno.h:
-/usr/include/asm-x86_64/errno.h:
-
/usr/include/asm-generic/errno.h:
/usr/include/asm-generic/errno-base.h:
tree/UPGMA/../../alignment/../general/SymMatrix.h:
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tree/UPGMA/../../alignment/../general/utils.h:
tree/UPGMA/Node.h:
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+
tree/UPGMA/upgmadata.h:
tree/UPGMA/../../alignment/Alignment.h:
tree/UPGMA/../../general/clustalw.h:
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tree/UPGMA/RootedTreeOutput.h:
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- tree/UPGMA/RootedGuideTree.h tree/UPGMA/Node.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
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config.h:
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
- /usr/include/wctype.h \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \
- tree/UPGMA/RootedGuideTree.h tree/UPGMA/Node.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
- tree/UPGMA/upgmadata.h tree/UPGMA/../../alignment/Alignment.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- tree/UPGMA/../../alignment/Sequence.h \
- tree/UPGMA/../../alignment/../general/userparams.h \
- tree/UPGMA/../../alignment/../general/UserParameters.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
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- tree/UPGMA/../../alignment/../general/Utility.h /usr/include/errno.h \
- /usr/include/bits/errno.h /usr/include/linux/errno.h \
- /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \
- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- tree/UPGMA/../../alignment/../general/clustalw.h \
- tree/UPGMA/../../alignment/../general/general.h \
- tree/UPGMA/../../alignment/../general/Array2D.h \
- tree/UPGMA/../../alignment/../general/SquareMat.h \
- tree/UPGMA/../../alignment/../general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
- /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
- tree/UPGMA/../../alignment/../general/utils.h \
- tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h \
- tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h \
- tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h \
- tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h \
- tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h \
- tree/UPGMA/../../alignment/../substitutionMatrix/../general/Array2D.h \
- tree/UPGMA/../../alignment/../general/VectorOutOfRange.h \
- tree/UPGMA/../../alignment/../general/SequenceNotFoundException.h \
- tree/UPGMA/../../general/clustalw.h
+RootedTreeOutput.o: tree/UPGMA/RootedTreeOutput.cpp config.h \
+ tree/UPGMA/RootedTreeOutput.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \
+ tree/UPGMA/RootedGuideTree.h tree/UPGMA/Node.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/limits \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ tree/UPGMA/upgmadata.h tree/UPGMA/../../alignment/Alignment.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ tree/UPGMA/../../alignment/Sequence.h \
+ tree/UPGMA/../../alignment/../general/userparams.h \
+ tree/UPGMA/../../alignment/../general/UserParameters.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ tree/UPGMA/../../alignment/../general/utils.h \
+ tree/UPGMA/../../alignment/../general/Utility.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/errno.h \
+ /usr/include/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
+ /usr/include/asm-generic/errno-base.h \
+ tree/UPGMA/../../alignment/../general/clustalw.h \
+ tree/UPGMA/../../alignment/../general/general.h \
+ tree/UPGMA/../../alignment/../general/Array2D.h \
+ tree/UPGMA/../../alignment/../general/SquareMat.h \
+ tree/UPGMA/../../alignment/../general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ tree/UPGMA/../../alignment/../general/utils.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/../general/Array2D.h \
+ tree/UPGMA/../../alignment/../general/VectorOutOfRange.h \
+ tree/UPGMA/../../alignment/../general/SequenceNotFoundException.h \
+ tree/UPGMA/../../general/clustalw.h
config.h:
tree/UPGMA/RootedTreeOutput.h:
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+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h
config.h:
general/SymMatrix.h:
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+ tree/../alignment/Alignment.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
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+ tree/../alignment/Sequence.h tree/../alignment/../general/userparams.h \
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+ /usr/include/asm-generic/errno-base.h \
+ tree/../alignment/../general/clustalw.h \
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config.h:
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+UPGMAAlgorithm.o: tree/UPGMA/UPGMAAlgorithm.cpp config.h \
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+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ tree/UPGMA/upgmadata.h tree/UPGMA/../../general/clustalw.h \
+ tree/UPGMA/../../general/general.h tree/UPGMA/../../general/Array2D.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ tree/UPGMA/../../general/SquareMat.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ tree/UPGMA/../../general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h tree/UPGMA/../AlignmentSteps.h \
+ tree/UPGMA/RootedGuideTree.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \
+ tree/UPGMA/../../alignment/Alignment.h \
+ tree/UPGMA/../../alignment/Sequence.h \
+ tree/UPGMA/../../alignment/../general/userparams.h \
+ tree/UPGMA/../../alignment/../general/UserParameters.h \
+ tree/UPGMA/../../alignment/../general/utils.h \
+ tree/UPGMA/../../alignment/../general/Utility.h /usr/include/string.h \
+ /usr/include/errno.h /usr/include/bits/errno.h \
+ /usr/include/linux/errno.h /usr/include/asm/errno.h \
+ /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
+ tree/UPGMA/../../alignment/../general/clustalw.h \
+ tree/UPGMA/../../alignment/../general/general.h \
+ tree/UPGMA/../../alignment/../general/utils.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h \
+ tree/UPGMA/../../alignment/../substitutionMatrix/../general/Array2D.h \
+ tree/UPGMA/../../alignment/../general/VectorOutOfRange.h \
+ tree/UPGMA/../../alignment/../general/SequenceNotFoundException.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_list.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/list.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ctime \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \
+ tree/UPGMA/../../general/SymMatrix.h \
+ tree/UPGMA/../../general/debuglogObject.h \
+ tree/UPGMA/../../general/DebugLog.h
config.h:
tree/UPGMA/Node.h:
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/usr/include/bits/wordsize.h:
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/usr/include/features.h:
/usr/include/gnu/stubs-64.h:
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
- /usr/include/wctype.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
- tree/../alignment/Alignment.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- tree/../alignment/Sequence.h tree/../alignment/../general/userparams.h \
- tree/../alignment/../general/UserParameters.h \
- tree/../alignment/../general/utils.h \
- tree/../alignment/../general/Utility.h /usr/include/errno.h \
- /usr/include/bits/errno.h /usr/include/linux/errno.h \
- /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \
- /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- tree/../alignment/../general/clustalw.h \
- tree/../alignment/../general/general.h \
- tree/../alignment/../general/Array2D.h \
- tree/../alignment/../general/SquareMat.h \
- tree/../alignment/../general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
- /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
- tree/../alignment/../general/utils.h \
- tree/../alignment/../substitutionMatrix/globalmatrix.h \
- tree/../alignment/../substitutionMatrix/SubMatrix.h \
- tree/../alignment/../substitutionMatrix/../general/clustalw.h \
- tree/../alignment/../substitutionMatrix/../general/userparams.h \
- tree/../alignment/../substitutionMatrix/../general/utils.h \
- tree/../alignment/../substitutionMatrix/../general/Array2D.h \
- tree/../alignment/../general/VectorOutOfRange.h \
- tree/../alignment/../general/SequenceNotFoundException.h tree/NJTree.h \
- tree/ClusterTreeAlgorithm.h tree/../general/clustalw.h \
- tree/../general/userparams.h tree/ClusterTreeOutput.h \
- tree/../general/OutputFile.h tree/../general/utils.h \
- tree/RandomGenerator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc
+UnRootedClusterTree.o: tree/UnRootedClusterTree.cpp config.h \
+ tree/UnRootedClusterTree.h tree/ClusterTree.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ tree/../alignment/Alignment.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ tree/../alignment/Sequence.h tree/../alignment/../general/userparams.h \
+ tree/../alignment/../general/UserParameters.h \
+ tree/../alignment/../general/utils.h \
+ tree/../alignment/../general/Utility.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/errno.h \
+ /usr/include/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
+ /usr/include/asm-generic/errno-base.h \
+ tree/../alignment/../general/clustalw.h \
+ tree/../alignment/../general/general.h \
+ tree/../alignment/../general/Array2D.h \
+ tree/../alignment/../general/SquareMat.h \
+ tree/../alignment/../general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ tree/../alignment/../general/utils.h \
+ tree/../alignment/../substitutionMatrix/globalmatrix.h \
+ tree/../alignment/../substitutionMatrix/SubMatrix.h \
+ tree/../alignment/../substitutionMatrix/../general/clustalw.h \
+ tree/../alignment/../substitutionMatrix/../general/userparams.h \
+ tree/../alignment/../substitutionMatrix/../general/utils.h \
+ tree/../alignment/../substitutionMatrix/../general/Array2D.h \
+ tree/../alignment/../general/VectorOutOfRange.h \
+ tree/../alignment/../general/SequenceNotFoundException.h tree/NJTree.h \
+ tree/ClusterTreeAlgorithm.h tree/../general/clustalw.h \
+ tree/../general/userparams.h tree/ClusterTreeOutput.h \
+ tree/../general/OutputFile.h tree/../general/utils.h \
+ tree/RandomGenerator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc
config.h:
tree/ClusterTree.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream:
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-tree/../alignment/Alignment.h:
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/usr/include/asm-generic/errno.h:
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tree/../alignment/../general/SymMatrix.h:
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tree/../alignment/../general/utils.h:
tree/RandomGenerator.h:
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- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
- /usr/include/wctype.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- general/Utility.h /usr/include/errno.h /usr/include/bits/errno.h \
- /usr/include/linux/errno.h /usr/include/asm/errno.h \
- /usr/include/asm-x86_64/errno.h /usr/include/asm-generic/errno.h \
- /usr/include/asm-generic/errno-base.h general/clustalw.h \
- general/general.h general/Array2D.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
- general/SquareMat.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
- general/SymMatrix.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
- /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /usr/include/bits/mathinline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
- general/userparams.h general/UserParameters.h general/utils.h
+Utility.o: general/Utility.cpp config.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
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+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/algorithm \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algo.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
+ /usr/include/alloca.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/algorithmfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_heap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
+ general/Utility.h /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \
+ /usr/include/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
+ /usr/include/asm-generic/errno-base.h general/clustalw.h \
+ general/general.h general/Array2D.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
+ general/SquareMat.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
+ general/SymMatrix.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ general/userparams.h general/UserParameters.h general/utils.h
config.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:
/usr/include/bits/wordsize.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:
/usr/include/features.h:
/usr/include/gnu/stubs-64.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:
-/usr/include/string.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/wchar.h:
+
+/usr/include/stdio.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/wchar.h:
/usr/include/xlocale.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception:
-/usr/include/stdio.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h:
-/usr/include/bits/types.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h:
-/usr/include/bits/typesizes.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h:
-/usr/include/libio.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h:
-/usr/include/_G_config.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:
-/usr/include/wchar.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:
-/usr/include/bits/wchar.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h:
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- /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
- /usr/include/bits/stdio_lim.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \
- /usr/include/stdlib.h /usr/include/bits/waitflags.h \
- /usr/include/bits/waitstatus.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/sys/types.h \
- /usr/include/bits/types.h /usr/include/bits/typesizes.h \
- /usr/include/time.h /usr/include/sys/select.h \
- /usr/include/bits/select.h /usr/include/bits/sigset.h \
- /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
- /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \
- /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \
- /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \
- /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \
- /usr/include/locale.h /usr/include/bits/locale.h \
- /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \
- /usr/include/libintl.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \
- /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \
- /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \
- /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
- /usr/include/bits/confname.h /usr/include/getopt.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \
- /usr/include/ctype.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \
- /usr/include/stdint.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
- /usr/include/wctype.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc \
- /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream
+VectorOutOfRange.o: general/VectorOutOfRange.cpp config.h \
+ general/VectorOutOfRange.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
+ /usr/include/wctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream
config.h:
general/VectorOutOfRange.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:
/usr/include/bits/wordsize.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:
/usr/include/features.h:
/usr/include/gnu/stubs-64.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h:
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+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
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-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits:
-
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h:
+/usr/include/wctype.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h:
+alignment/Alignment.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h:
-/usr/include/wctype.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h:
+alignment/Sequence.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc:
+alignment/../general/userparams.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc:
+alignment/../general/UserParameters.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale:
+alignment/../general/utils.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc:
+alignment/../general/Utility.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream:
+/usr/include/stdlib.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc:
+/usr/include/bits/waitflags.h:
-alignment/Alignment.h:
+/usr/include/bits/waitstatus.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector:
+/usr/include/sys/types.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h:
+/usr/include/sys/select.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h:
+/usr/include/bits/select.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc:
+/usr/include/bits/sigset.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip:
+/usr/include/sys/sysmacros.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional:
+/usr/include/alloca.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept:
+/usr/include/libio.h:
-alignment/Sequence.h:
+/usr/include/_G_config.h:
-alignment/../general/userparams.h:
+/usr/include/bits/stdio_lim.h:
-alignment/../general/UserParameters.h:
+/usr/include/bits/sys_errlist.h:
-alignment/../general/utils.h:
+/usr/include/bits/stdio.h:
-alignment/../general/Utility.h:
+/usr/include/string.h:
/usr/include/errno.h:
/usr/include/asm/errno.h:
-/usr/include/asm-x86_64/errno.h:
-
/usr/include/asm-generic/errno.h:
/usr/include/asm-generic/errno-base.h:
alignment/../general/SymMatrix.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath:
/usr/include/math.h:
/usr/include/bits/mathinline.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc:
alignment/../general/utils.h:
fileInput/FileReader.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h:
+
fileInput/../alignment/Alignment.h:
fileInput/../alignment/Sequence.h:
fileInput/InFileStream.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc:
fileInput/ClustalFileParser.h:
interface/../alignment/AlignmentOutput.h:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/sstream:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/sstream.tcc:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc:
-/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cassert:
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cassert:
/usr/include/assert.h:
general/ClustalWResources.h:
general/Stats.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ctime:
userParameters->setSeqName(profile2Name);
userParameters->setProfile2Name(profile2Name);
+
FileReader readProfileFile;
+ cout << "before profileInput\n";
code = readProfileFile.profileInput(&alignmentObj);
+ cout << "after profileInput\n";
if(!userParameters->getInteractive())
{
else
cerr << "ERROR: Unhandled error code (" << code << ") returned from profileInput.\n";
// AW: should we really exit here? What if called from clustalx?
- exit(2);
+ // DD: fixed
+ if(!userParameters->getGui())
+ exit(2);
}
}
return code;
s.marker = "5";
s.title = "Help for output format options.";
- s.content = "Six output formats are offered. You can choose any (or all 6 if you wish). \n"
+ s.content = "Several output formats are offered. You can choose any (or all 6 if you wish). \n"
"\n"
"CLUSTAL format output is a self explanatory alignment format. It shows the\n"
"sequences aligned in blocks. It can be read in again at a later date to\n"
"alignments (e.g. PRETTY, PROFILEMAKE, PLOTALIGN). It is the same as the GCG\n"
".msf format files (multiple sequence file); new in version 7 of GCG.\n"
"\n"
+"Fasta output cis widely used because of it's simplicity. Each sequence name is\n"
+"preceeded by a '>'-sign. The sequence itself is printed out in the following lines\n"
+"\n"
"PHYLIP format output can be used for input to the PHYLIP package of Joe \n"
"Felsenstein. This is an extremely widely used package for doing every \n"
"imaginable form of phylogenetic analysis (MUCH more than the the modest intro-\n"
"-TYPE= :PROTEIN or DNA sequences\n"
"-NEGATIVE :protein alignment with negative values in matrix\n"
"-OUTFILE= :sequence alignment file name\n"
-"-OUTPUT= :GCG, GDE, PHYLIP, PIR or NEXUS\n"
+"-OUTPUT= :CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA\n"
"-OUTORDER= :INPUT or ALIGNED\n"
"-CASE :LOWER or UPPER (for GDE output only)\n"
"-SEQNOS= :OFF or ON (for Clustal output only)\n"
-# Makefile.in generated by automake 1.10.2 from Makefile.am.
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
# src/Makefile. Generated from Makefile.in by configure.
# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 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.
pkgdatadir = $(datadir)/clustalw
-pkglibdir = $(libdir)/clustalw
pkgincludedir = $(includedir)/clustalw
+pkglibdir = $(libdir)/clustalw
+pkglibexecdir = $(libexecdir)/clustalw
am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = config.h
CONFIG_CLEAN_FILES = clustalw_version.h
+CONFIG_CLEAN_VPATH_FILES =
am__installdirs = "$(DESTDIR)$(bindir)"
-binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
PROGRAMS = $(bin_PROGRAMS)
am_clustalw2_OBJECTS = FullPairwiseAlign.$(OBJEXT) \
FastPairwiseAlign.$(OBJEXT) MSFFileParser.$(OBJEXT) \
DEFAULT_INCLUDES = -I.
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
+am__mv = mv -f
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
CXXLD = $(CXX)
ps-recursive uninstall-recursive
RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
distclean-recursive maintainer-clean-recursive
+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
+ $(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
+ distdir
ETAGS = etags
CTAGS = ctags
DIST_SUBDIRS = $(SUBDIRS)
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run aclocal-1.10
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-AUTOMAKE = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run automake-1.10
+am__relativize = \
+ dir0=`pwd`; \
+ sed_first='s,^\([^/]*\)/.*$$,\1,'; \
+ sed_rest='s,^[^/]*/*,,'; \
+ sed_last='s,^.*/\([^/]*\)$$,\1,'; \
+ sed_butlast='s,/*[^/]*$$,,'; \
+ while test -n "$$dir1"; do \
+ first=`echo "$$dir1" | sed -e "$$sed_first"`; \
+ if test "$$first" != "."; then \
+ if test "$$first" = ".."; then \
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+ dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
+ else \
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+ if test "$$first2" = "$$first"; then \
+ dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
+ else \
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+AMTAR = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run tar
+AUTOCONF = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoconf
+AUTOHEADER = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run autoheader
+AUTOMAKE = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run automake-1.11
AWK = gawk
CC = gcc
CCDEPMODE = depmode=gcc3
CFLAGS = -g -O2
CLUSTALW_NAME = ClustalW
-CLUSTALW_VERSION = 2.0.12
+CLUSTALW_VERSION = 2.1
CPPFLAGS =
CXX = g++
CXXCPP = g++ -E
LIBOBJS =
LIBS =
LTLIBOBJS =
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+MAKEINFO = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/missing --run makeinfo
MKDIR_P = /bin/mkdir -p
OBJEXT = o
PACKAGE = clustalw
PACKAGE_BUGREPORT = clustalw@ucd.ie
PACKAGE_NAME = clustalw
-PACKAGE_STRING = clustalw 2.0.12
+PACKAGE_STRING = clustalw 2.1
PACKAGE_TARNAME = clustalw
-PACKAGE_VERSION = 2.0.12
+PACKAGE_URL =
+PACKAGE_VERSION = 2.1
PATH_SEPARATOR = :
RANLIB = ranlib
SET_MAKE =
SHELL = /bin/sh
STRIP =
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-abs_top_builddir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw
-abs_top_srcdir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw
+VERSION = 2.1
+abs_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/src
+abs_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/src
+abs_top_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw
+abs_top_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw
ac_ct_CC = gcc
ac_ct_CXX = g++
am__include = include
htmldir = ${docdir}
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infodir = ${datarootdir}/info
-install_sh = $(SHELL) /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/install-sh
+install_sh = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalw/install-sh
libdir = ${exec_prefix}/lib
libexecdir = ${exec_prefix}/libexec
localedir = ${datarootdir}/locale
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
- cd $(top_srcdir) && \
- $(AUTOMAKE) --foreign src/Makefile
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
+ $(am__cd) $(top_srcdir) && \
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cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4): $(am__aclocal_m4_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
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$(srcdir)/config.h.in: $(am__configure_deps)
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- $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \
- else :; fi; \
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TAGS: tags-recursive $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
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- tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \
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maintainer-clean-generic:
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html: html-recursive
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+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
/*
* This function checks to see if all names are different. It returns true if they
* are all different, and false if there are 2 the same.
+ * currently quadratic - would be nice to speed up
*/
bool Alignment::checkAllNamesDifferent(string *offendingSeq)
{
(*nexusOutFile) << "dimensions ntax=" << alignPtr->getNumSeqs()
<< " nchar=" << length << ";\n"; //- nige
(*nexusOutFile) << "format missing=?\n";
+
+ // removed - bugzilla bug 204
+ /*
(*nexusOutFile) << "symbols=\"";
for(i = 0; i <= userParameters->getMaxAA(); i++)
(*nexusOutFile) << userParameters->getAminoAcidCode(i);
}
(*nexusOutFile) << "\"\n";
+ */
+
(*nexusOutFile) << "interleave datatype=";
bool _dnaFlag = userParameters->getDNAFlag();
string _type = _dnaFlag ? "DNA " : "PROTEIN ";
#define CLUSTALW_NAME "ClustalW"
-#define CLUSTALW_VERSION "2.0.12"
+#define CLUSTALW_VERSION "2.1"
#endif
#define PACKAGE_NAME "clustalw"
/* Define to the full name and version of this package. */
-#define PACKAGE_STRING "clustalw 2.0.12"
+#define PACKAGE_STRING "clustalw 2.1"
/* Define to the one symbol short name of this package. */
#define PACKAGE_TARNAME "clustalw"
+/* Define to the home page for this package. */
+#define PACKAGE_URL ""
+
/* Define to the version of this package. */
-#define PACKAGE_VERSION "2.0.12"
+#define PACKAGE_VERSION "2.1"
/* Define to 1 if you have the ANSI C header files. */
#define STDC_HEADERS 1
/* Version number of package */
-#define VERSION "2.0.12"
+#define VERSION "2.1"
/* Define to empty if `const' does not conform to ANSI C. */
/* #undef const */
/* 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
}
- Sequence ClustalFileParser::getSeq(int seqNum, string *offendingSeq)
+Sequence ClustalFileParser::getSeq(int seqNum, string *offendingSeq)
{
char line[MAXLINE + 1];
line[0] = EOS;
}
freeFileResources(_fileIn);
+ // getSecStructure(vector<char>& gapPenaltyMask,
+ // vector<char>& secStructMask, string& secStructName, int &structPenalties, int length)
+
if ((int)characterSeq.length() > userParameters->getMaxAllowedSeqLength())
{
parseExitCode=SEQUENCETOOBIG;
void ClustalFileParser::getSecStructure(vector<char>& gapPenaltyMask,
vector<char>& secStructMask, string& secStructName, int &structPenalties, int length)
{
+ bool guigetss = false;
+ if(userParameters->getProfileNum() == 1 && userParameters->getStructPenalties1())
+ guigetss = true;
+ if(userParameters->getProfileNum() == 2 && userParameters->getStructPenalties2())
+ guigetss = true;
+
char title[MAXLINE + 1];
title[0] = '\0';
char line[MAXLINE + 1];
utilityObject->rTrim(sname);
utilityObject->blankToUnderscore(sname);
- if (userParameters->getInteractive())
+ if (userParameters->getInteractive() && !userParameters->getGui())
{
strcpy(title, "Found secondary structure in alignment file: ");
strcat(title, sname);
{
(*lin2) = 'y';
}
- if ((*lin2 != 'n') && (*lin2 != 'N'))
+ if (guigetss || ((*lin2 != 'n') && (*lin2 != 'N')))
{
structPenalties = SECST;
struct_index = ix;
utilityObject->rTrim(sname);
utilityObject->blankToUnderscore(sname);
- if (userParameters->getInteractive())
+ if (userParameters->getInteractive() && !userParameters->getGui())
{
strcpy(title, "Found gap penalty mask in alignment file: ");
strcat(title, sname);
{
(*lin2) = 'y';
}
- if ((*lin2 != 'n') && (*lin2 != 'N'))
+ if (guigetss || ((*lin2 != 'n') && (*lin2 != 'N')))
{
structPenalties = GMASK;
struct_index = ix;
}
if (!_fileIn->getline(line, MAXLINE + 1))
{
- freeFileResources(_fileIn);
+ freeFileResources(_fileIn);
return ;
}
}
*/
void EMBLFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask, string& secStructName, int &structPenalties, int length)
{
+ bool guigetss = false;
+ if(userParameters->getProfileNum() == 1 && userParameters->getStructPenalties1())
+ guigetss = true;
+ if(userParameters->getProfileNum() == 2 && userParameters->getStructPenalties2())
+ guigetss = true;
+
char _title[MAXLINE + 1];
char _line[MAXLINE + 1];
char _lin2[MAXLINE + 1];
sscanf(_line + 2, "%s", _feature);
if (strcmp(_feature, "HELIX") == 0 || strcmp(_feature, "STRAND") == 0)
{
- if (userParameters->getInteractive())
+ if (userParameters->getInteractive() && !userParameters->getGui())
{
strcpy(_title,
"Found secondary structure in alignment file: ");
{
(*_lin2) = 'y';
}
- if ((*_lin2 != 'n') && (*_lin2 != 'N'))
+ if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
{
structPenalties = SECST;
for (i = 0; i < length; i++)
{
(*_lin2) = 'y';
}
- if ((*_lin2 != 'n') && (*_lin2 != 'N'))
+ if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
{
structPenalties = GMASK;
for (i = 0; i < length; i++)
}
userParameters->setSeqName(line);
-
// NOTE I made a change here because the profile2Name was not stored!
if(userParameters->getProfileNum() == 2 && userParameters->getProfile2Name().empty())
if (noEmptySequence(seqRangeVector, offendingSeq) == false) {
return EMPTYSEQUENCE; // Error there are same names.
}
-
+
for (int i=0; i < (int)seqRangeVector.size(); i++) {
// Andreas Wilm (UCD): fixed wrong default output order
// which is important when no alignment (convert!) is done
}
else
{
+
// first seq to be read = profile1_nseqs + 1
int profile1NumOfSeqs = alignPtr->getNumSeqs();
code = readSeqs(alignPtr, profile1NumOfSeqs + 1, &offendingSeq);
void GDEFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
string& secStructName, int &structPenalties, int length)
{
+ bool guigetss = false;
+ if(userParameters->getProfileNum() == 1 && userParameters->getStructPenalties1())
+ guigetss = true;
+ if(userParameters->getProfileNum() == 2 && userParameters->getStructPenalties2())
+ guigetss = true;
+
char _title[MAXLINE + 1];
char _line[MAXLINE + 1];
char _lin2[MAXLINE + 1];
utilityObject->blankToUnderscore(_sname);
secStructName = string(_sname);
- if (userParameters->getInteractive())
+ if (userParameters->getInteractive() && !userParameters->getGui())
{
strcpy(_title, "Found secondary structure in alignment file: ");
strcat(_title, _sname);
{
(*_lin2) = 'y';
}
- if ((*_lin2 != 'n') && (*_lin2 != 'N'))
+ if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
{
structPenalties = SECST;
for (i = 0; i < length; i++)
utilityObject->blankToUnderscore(_sname);
secStructName = string(_sname);
- if (userParameters->getInteractive())
+ if (userParameters->getInteractive() && !userParameters->getGui())
{
strcpy(_title, "Found gap penalty mask in alignment file: ");
strcat(_title, _sname);
{
(*_lin2) = 'y';
}
- if ((*_lin2 != 'n') && (*_lin2 != 'N'))
+ if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
{
structPenalties = GMASK;
for (i = 0; i < length; i++)
while (_fileIn->getline(_line, MAXLINE + 1))
{
- if (utilityObject->blankLine(_line))
+ if (utilityObject->blankLineNumericLabel(_line))
{
_fileIn->close();
return _numSeqs;
void RSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
string& secStructName, int &structPenalties, int length)
{
+ bool guigetss = false;
+ if(userParameters->getProfileNum() == 1 && userParameters->getStructPenalties1())
+ guigetss = true;
+ if(userParameters->getProfileNum() == 2 && userParameters->getStructPenalties2())
+ guigetss = true;
+
char _title[MAXLINE + 1];
char _line[MAXLINE + 1];
char _lin2[MAXLINE + 1];
{
if (keyword(_line, "feature"))
{
- if (userParameters->getInteractive())
+ if (userParameters->getInteractive() && !userParameters->getGui())
{
strcpy(_title, "Found secondary structure in alignment file: ");
strcat(_title, _sname);
{
(*_lin2) = 'y';
}
- if ((*_lin2 != 'n') && (*_lin2 != 'N'))
+ if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
{
structPenalties = SECST;
secStructMask.assign(length, '.');
//revisionLevel = CLU_SHORT_VERSION_STRING;
revisionLevel = CLUSTALW_VERSION;
interactive = false;
+ gui = false;
seqName = "";
DNAGapOpen = 15.0;
interactive = value;
}
+void UserParameters::setGui(bool value)
+{
+ gui = value;
+}
+
void UserParameters::setGapOpen(float value)
{
gapOpen = value;
void setRevisionLevel(string value);
bool getInteractive(){return interactive;};
void setInteractive(bool value);
+ bool getGui(){return gui;};
+ void setGui(bool value);
float getGapOpen(){return gapOpen;};
void setGapOpen(float value);
float getGapExtend(){return gapExtend;};
string revisionLevel;
bool interactive;
+ bool gui;
float gapOpen;
float gapExtend;
float PWGapOpen;
/**
*
+ * @param line
+ * @return
+ */
+// Utility::blankLine thinks that a line like
+// 2125209 .......... .......... .......... .......... ..........
+// is blank, causing problems for countSeqs when sequence labels are numeric
+// this function will return false if there's a number and a bunch of dots (not ideal, i know)
+bool Utility::blankLineNumericLabel(char *line)
+{
+ int i;
+ int dots = 0;
+ bool isnumeric = false;
+
+ for (i = 0; line[i] != '\n' && line[i] != EOS; i++)
+ {
+ if (isdigit(line[i]) || isspace(line[i]) || (line[i] == '*') ||
+ (line[i] == ':') || (line[i] == '.'))
+ ;
+ else
+ {
+ return false;
+ }
+ if(line[i] == '.')
+ dots++;
+ if(isdigit(line[i]))
+ isnumeric = true;
+ }
+ if(isnumeric && dots > 10)
+ return false;
+ else
+ return true;
+}
+
+/**
+ *
* @param str
* @param path
*/
bool lineType(char *line, const char *code);
bool blankLine(char *line);
+ bool blankLineNumericLabel(char *line);
void getPath(string str, string *path);
seqNoArg = new StringArray(3);
seqNoRangeArg = new StringArray(3);
scoreArg = new StringArray(3);
- outputArg = new StringArray(7);
+ outputArg = new StringArray(8);
outputTreeArg = new StringArray(5);
outputSecStrArg = new StringArray(5);
cmdLineType = new StringArray(6);
(*outputArg)[3] = "phylip";
(*outputArg)[4] = "nexus";
(*outputArg)[5] = "fasta";
- (*outputArg)[6] = "";
+ (*outputArg)[6] = "clustal";
+ (*outputArg)[7] = "";
(*outputTreeArg)[0] = "nj";
(*outputTreeArg)[1] = "phylip";
#endif
if((*paramArg)[setOutput].length() > 0)
{
- temp = findMatch((*paramArg)[setOutput], outputArg, 6);
- if (temp >= 0 && temp <= 5)
+ temp = findMatch((*paramArg)[setOutput], outputArg, 7);
+ if (temp >= 0 && temp <= 6)
{
userParameters->setOutputClustal(false);
userParameters->setOutputGCG(false);
case 4: // NEXUS
userParameters->setOutputNexus(true);
break;
- case 5: // NEXUS
+ case 5: // FASTA
userParameters->setOutputFasta(true);
break;
+ case 6: // CLUSTAL
+ userParameters->setOutputClustal(true);
+ break;
default:
// FIXME AW: 1.83 behaves the same, but shouldnt
// we exit here?
void ClusterTree::overspillMessage(int overspill,int totalDists)
{
- std::stringstream ssOverSpill;
- ssOverSpill << overspill << " of the distances out of a total of " << totalDists
- << "\n were out of range for the distance correction." << "\n"
- << "\n SUGGESTIONS: 1) remove the most distant sequences"
- << "\n or 2) use the PHYLIP package"
- << "\n or 3) turn off the correction."
- << "\n Note: Use option 3 with caution! With this degree"
- << "\n of divergence you will have great difficulty"
- << "\n getting robust and reliable trees." << "\n\n";
+ std::ostringstream ssOverSpill;
+ std::ostringstream ssTotalDists;
string message;
- ssOverSpill >> message;
+
+ ssOverSpill << overspill;
+ message += ssOverSpill.str();
+ message += " of the distances out of a total of ";
+ ssTotalDists << totalDists;
+ message += ssTotalDists.str();
+ message += "\n were out of range for the distance correction.\n"
+ "\n SUGGESTIONS: 1) remove the most distant sequences"
+ "\n or 2) use the PHYLIP package"
+ "\n or 3) turn off the correction."
+ "\n Note: Use option 3 with caution! With this degree"
+ "\n of divergence you will have great difficulty"
+ "\n getting robust and reliable trees.\n\n";
+
clustalw::utilityObject->warning(message.c_str());
}
}
}
}
- if (nerrs > 0)
+ if (nerrs > 0 && !userParameters->getGui())
{
string errMess = "The following sequences are too divergent to be aligned:\n";
git://source.jalview.org / jabaws.git / commitdiff