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GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
License is intended to guarantee your freedom to share and change free
software--to make sure the software is free for all its users. This
General Public License applies to most of the Free Software
Foundation's software and to any other program whose authors commit to
using it. (Some other Free Software Foundation software is covered by
the GNU Library General Public License instead.) You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
this service if you wish), that you receive source code or can get it
if you want it, that you can change the software or use pieces of it
in new free programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid
anyone to deny you these rights or to ask you to surrender the rights.
These restrictions translate to certain responsibilities for you if you
distribute copies of the software, or if you modify it.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must give the recipients all the rights that
you have. You must make sure that they, too, receive or can get the
source code. And you must show them these terms so they know their
rights.
We protect your rights with two steps: (1) copyright the software, and
(2) offer you this license which gives you legal permission to copy,
distribute and/or modify the software.
Also, for each author's protection and ours, we want to make certain
that everyone understands that there is no warranty for this free
software. If the software is modified by someone else and passed on, we
want its recipients to know that what they have is not the original, so
that any problems introduced by others will not reflect on the original
authors' reputations.
Finally, any free program is threatened constantly by software
patents. We wish to avoid the danger that redistributors of a free
program will individually obtain patent licenses, in effect making the
program proprietary. To prevent this, we have made it clear that any
patent must be licensed for everyone's free use or not licensed at all.
The precise terms and conditions for copying, distribution and
modification follow.
GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains
a notice placed by the copyright holder saying it may be distributed
under the terms of this General Public License. The "Program", below,
refers to any such program or work, and a "work based on the Program"
means either the Program or any derivative work under copyright law:
that is to say, a work containing the Program or a portion of it,
either verbatim or with modifications and/or translated into another
language. (Hereinafter, translation is included without limitation in
the term "modification".) Each licensee is addressed as "you".
Activities other than copying, distribution and modification are not
covered by this License; they are outside its scope. The act of
running the Program is not restricted, and the output from the Program
is covered only if its contents constitute a work based on the
Program (independent of having been made by running the Program).
Whether that is true depends on what the Program does.
1. You may copy and distribute verbatim copies of the Program's
source code as you receive it, in any medium, provided that you
conspicuously and appropriately publish on each copy an appropriate
copyright notice and disclaimer of warranty; keep intact all the
notices that refer to this License and to the absence of any warranty;
and give any other recipients of the Program a copy of this License
along with the Program.
You may charge a fee for the physical act of transferring a copy, and
you may at your option offer warranty protection in exchange for a fee.
2. You may modify your copy or copies of the Program or any portion
of it, thus forming a work based on the Program, and copy and
distribute such modifications or work under the terms of Section 1
above, provided that you also meet all of these conditions:
a) You must cause the modified files to carry prominent notices
stating that you changed the files and the date of any change.
b) You must cause any work that you distribute or publish, that in
whole or in part contains or is derived from the Program or any
part thereof, to be licensed as a whole at no charge to all third
parties under the terms of this License.
c) If the modified program normally reads commands interactively
when run, you must cause it, when started running for such
interactive use in the most ordinary way, to print or display an
announcement including an appropriate copyright notice and a
notice that there is no warranty (or else, saying that you provide
a warranty) and that users may redistribute the program under
these conditions, and telling the user how to view a copy of this
License. (Exception: if the Program itself is interactive but
does not normally print such an announcement, your work based on
the Program is not required to print an announcement.)
These requirements apply to the modified work as a whole. If
identifiable sections of that work are not derived from the Program,
and can be reasonably considered independent and separate works in
themselves, then this License, and its terms, do not apply to those
sections when you distribute them as separate works. But when you
distribute the same sections as part of a whole which is a work based
on the Program, the distribution of the whole must be on the terms of
this License, whose permissions for other licensees extend to the
entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest
your rights to work written entirely by you; rather, the intent is to
exercise the right to control the distribution of derivative or
collective works based on the Program.
In addition, mere aggregation of another work not based on the Program
with the Program (or with a work based on the Program) on a volume of
a storage or distribution medium does not bring the other work under
the scope of this License.
3. You may copy and distribute the Program (or a work based on it,
under Section 2) in object code or executable form under the terms of
Sections 1 and 2 above provided that you also do one of the following:
a) Accompany it with the complete corresponding machine-readable
source code, which must be distributed under the terms of Sections
1 and 2 above on a medium customarily used for software interchange; or,
b) Accompany it with a written offer, valid for at least three
years, to give any third party, for a charge no more than your
cost of physically performing source distribution, a complete
machine-readable copy of the corresponding source code, to be
distributed under the terms of Sections 1 and 2 above on a medium
customarily used for software interchange; or,
c) Accompany it with the information you received as to the offer
to distribute corresponding source code. (This alternative is
allowed only for noncommercial distribution and only if you
received the program in object code or executable form with such
an offer, in accord with Subsection b above.)
The source code for a work means the preferred form of the work for
making modifications to it. For an executable work, complete source
code means all the source code for all modules it contains, plus any
associated interface definition files, plus the scripts used to
control compilation and installation of the executable. However, as a
special exception, the source code distributed need not include
anything that is normally distributed (in either source or binary
form) with the major components (compiler, kernel, and so on) of the
operating system on which the executable runs, unless that component
itself accompanies the executable.
If distribution of executable or object code is made by offering
access to copy from a designated place, then offering equivalent
access to copy the source code from the same place counts as
distribution of the source code, even though third parties are not
compelled to copy the source along with the object code.
4. You may not copy, modify, sublicense, or distribute the Program
except as expressly provided under this License. Any attempt
otherwise to copy, modify, sublicense or distribute the Program is
void, and will automatically terminate your rights under this License.
However, parties who have received copies, or rights, from you under
this License will not have their licenses terminated so long as such
parties remain in full compliance.
5. You are not required to accept this License, since you have not
signed it. However, nothing else grants you permission to modify or
distribute the Program or its derivative works. These actions are
prohibited by law if you do not accept this License. Therefore, by
modifying or distributing the Program (or any work based on the
Program), you indicate your acceptance of this License to do so, and
all its terms and conditions for copying, distributing or modifying
the Program or works based on it.
6. Each time you redistribute the Program (or any work based on the
Program), the recipient automatically receives a license from the
original licensor to copy, distribute or modify the Program subject to
these terms and conditions. You may not impose any further
restrictions on the recipients' exercise of the rights granted herein.
You are not responsible for enforcing compliance by third parties to
this License.
7. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot
distribute so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you
may not distribute the Program at all. For example, if a patent
license would not permit royalty-free redistribution of the Program by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Program.
If any portion of this section is held invalid or unenforceable under
any particular circumstance, the balance of the section is intended to
apply and the section as a whole is intended to apply in other
circumstances.
It is not the purpose of this section to induce you to infringe any
patents or other property right claims or to contest validity of any
such claims; this section has the sole purpose of protecting the
integrity of the free software distribution system, which is
implemented by public license practices. Many people have made
generous contributions to the wide range of software distributed
through that system in reliance on consistent application of that
system; it is up to the author/donor to decide if he or she is willing
to distribute software through any other system and a licensee cannot
impose that choice.
This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.
8. If the distribution and/or use of the Program is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Program under this License
may add an explicit geographical distribution limitation excluding
those countries, so that distribution is permitted only in or among
countries not thus excluded. In such case, this License incorporates
the limitation as if written in the body of this License.
9. The Free Software Foundation may publish revised and/or new versions
of the General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the Program
specifies a version number of this License which applies to it and "any
later version", you have the option of following the terms and conditions
either of that version or of any later version published by the Free
Software Foundation. If the Program does not specify a version number of
this License, you may choose any version ever published by the Free Software
Foundation.
10. If you wish to incorporate parts of the Program into other free
programs whose distribution conditions are different, write to the author
to ask for permission. For software which is copyrighted by the Free
Software Foundation, write to the Free Software Foundation; we sometimes
make exceptions for this. Our decision will be guided by the two goals
of preserving the free status of all derivatives of our free software and
of promoting the sharing and reuse of software generally.
NO WARRANTY
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
REPAIR OR CORRECTION.
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
<signature of Ty Coon>, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Library General
Public License instead of this License.
INSTALL deleted 100644 → 0
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Installation Instructions
*************************
Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004 Free
Software Foundation, Inc.
This file is free documentation; the Free Software Foundation gives
unlimited permission to copy, distribute and modify it.
Basic Installation
==================
These are generic installation instructions.
The `configure' shell script attempts to guess correct values for
various system-dependent variables used during compilation. It uses
those values to create a `Makefile' in each directory of the package.
It may also create one or more `.h' files containing system-dependent
definitions. Finally, it creates a shell script `config.status' that
you can run in the future to recreate the current configuration, and a
file `config.log' containing compiler output (useful mainly for
debugging `configure').
It can also use an optional file (typically called `config.cache'
and enabled with `--cache-file=config.cache' or simply `-C') that saves
the results of its tests to speed up reconfiguring. (Caching is
disabled by default to prevent problems with accidental use of stale
cache files.)
If you need to do unusual things to compile the package, please try
to figure out how `configure' could check whether to do them, and mail
diffs or instructions to the address given in the `README' so they can
be considered for the next release. If you are using the cache, and at
some point `config.cache' contains results you don't want to keep, you
may remove or edit it.
The file `configure.ac' (or `configure.in') is used to create
`configure' by a program called `autoconf'. You only need
`configure.ac' if you want to change it or regenerate `configure' using
a newer version of `autoconf'.
The simplest way to compile this package is:
1. `cd' to the directory containing the package's source code and type
`./configure' to configure the package for your system. If you're
using `csh' on an old version of System V, you might need to type
`sh ./configure' instead to prevent `csh' from trying to execute
`configure' itself.
Running `configure' takes awhile. While running, it prints some
messages telling which features it is checking for.
2. Type `make' to compile the package.
3. Optionally, type `make check' to run any self-tests that come with
the package.
4. Type `make install' to install the programs and any data files and
documentation.
5. You can remove the program binaries and object files from the
source code directory by typing `make clean'. To also remove the
files that `configure' created (so you can compile the package for
a different kind of computer), type `make distclean'. There is
also a `make maintainer-clean' target, but that is intended mainly
for the package's developers. If you use it, you may have to get
all sorts of other programs in order to regenerate files that came
with the distribution.
Compilers and Options
=====================
Some systems require unusual options for compilation or linking that the
`configure' script does not know about. Run `./configure --help' for
details on some of the pertinent environment variables.
You can give `configure' initial values for configuration parameters
by setting variables in the command line or in the environment. Here
is an example:
./configure CC=c89 CFLAGS=-O2 LIBS=-lposix
*Note Defining Variables::, for more details.
Compiling For Multiple Architectures
====================================
You can compile the package for more than one kind of computer at the
same time, by placing the object files for each architecture in their
own directory. To do this, you must use a version of `make' that
supports the `VPATH' variable, such as GNU `make'. `cd' to the
directory where you want the object files and executables to go and run
the `configure' script. `configure' automatically checks for the
source code in the directory that `configure' is in and in `..'.
If you have to use a `make' that does not support the `VPATH'
variable, you have to compile the package for one architecture at a
time in the source code directory. After you have installed the
package for one architecture, use `make distclean' before reconfiguring
for another architecture.
Installation Names
==================
By default, `make install' will install the package's files in
`/usr/local/bin', `/usr/local/man', etc. You can specify an
installation prefix other than `/usr/local' by giving `configure' the
option `--prefix=PREFIX'.
You can specify separate installation prefixes for
architecture-specific files and architecture-independent files. If you
give `configure' the option `--exec-prefix=PREFIX', the package will
use PREFIX as the prefix for installing programs and libraries.
Documentation and other data files will still use the regular prefix.
In addition, if you use an unusual directory layout you can give
options like `--bindir=DIR' to specify different values for particular
kinds of files. Run `configure --help' for a list of the directories
you can set and what kinds of files go in them.
If the package supports it, you can cause programs to be installed
with an extra prefix or suffix on their names by giving `configure' the
option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
Optional Features
=================
Some packages pay attention to `--enable-FEATURE' options to
`configure', where FEATURE indicates an optional part of the package.
They may also pay attention to `--with-PACKAGE' options, where PACKAGE
is something like `gnu-as' or `x' (for the X Window System). The
`README' should mention any `--enable-' and `--with-' options that the
package recognizes.
For packages that use the X Window System, `configure' can usually
find the X include and library files automatically, but if it doesn't,
you can use the `configure' options `--x-includes=DIR' and
`--x-libraries=DIR' to specify their locations.
Specifying the System Type
==========================
There may be some features `configure' cannot figure out automatically,
but needs to determine by the type of machine the package will run on.
Usually, assuming the package is built to be run on the _same_
architectures, `configure' can figure that out, but if it prints a
message saying it cannot guess the machine type, give it the
`--build=TYPE' option. TYPE can either be a short name for the system
type, such as `sun4', or a canonical name which has the form:
CPU-COMPANY-SYSTEM
where SYSTEM can have one of these forms:
OS KERNEL-OS
See the file `config.sub' for the possible values of each field. If
`config.sub' isn't included in this package, then this package doesn't
need to know the machine type.
If you are _building_ compiler tools for cross-compiling, you should
use the `--target=TYPE' option to select the type of system they will
produce code for.
If you want to _use_ a cross compiler, that generates code for a
platform different from the build platform, you should specify the
"host" platform (i.e., that on which the generated programs will
eventually be run) with `--host=TYPE'.
Sharing Defaults
================
If you want to set default values for `configure' scripts to share, you
can create a site shell script called `config.site' that gives default
values for variables like `CC', `cache_file', and `prefix'.
`configure' looks for `PREFIX/share/config.site' if it exists, then
`PREFIX/etc/config.site' if it exists. Or, you can set the
`CONFIG_SITE' environment variable to the location of the site script.
A warning: not all `configure' scripts look for a site script.
Defining Variables
==================
Variables not defined in a site shell script can be set in the
environment passed to `configure'. However, some packages may run
configure again during the build, and the customized values of these
variables may be lost. In order to avoid this problem, you should set
them in the `configure' command line, using `VAR=value'. For example:
./configure CC=/usr/local2/bin/gcc
will cause the specified gcc to be used as the C compiler (unless it is
overridden in the site shell script).
`configure' Invocation
======================
`configure' recognizes the following options to control how it operates.
`--help'
`-h'
Print a summary of the options to `configure', and exit.
`--version'
`-V'
Print the version of Autoconf used to generate the `configure'
script, and exit.
`--cache-file=FILE'
Enable the cache: use and save the results of the tests in FILE,
traditionally `config.cache'. FILE defaults to `/dev/null' to
disable caching.
`--config-cache'
`-C'
Alias for `--cache-file=config.cache'.
`--quiet'
`--silent'
`-q'
Do not print messages saying which checks are being made. To
suppress all normal output, redirect it to `/dev/null' (any error
messages will still be shown).
`--srcdir=DIR'
Look for the package's source code in directory DIR. Usually
`configure' can determine that directory automatically.
`configure' also accepts some other, not widely useful, options. Run
`configure --help' for more details.
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#!/bin/sh
mkdir -p config
autoreconf --force --install -I config -I m4
echo "Now run ./configure --prefix=$HOME && make install" && \
echo "Add --disable-shared to the configure line if building on Mac OS X"
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/* config.h.in. Generated from configure.ac by autoheader. */
/* Define to 1 if you have the <dlfcn.h> header file. */
#undef HAVE_DLFCN_H
/* Define to 1 if you have the <inttypes.h> header file. */
#undef HAVE_INTTYPES_H
/* Define to 1 if you have the <memory.h> header file. */
#undef HAVE_MEMORY_H
/* Define if OpenMP is enabled */
#undef HAVE_OPENMP
/* Define to 1 if you have the <stdint.h> header file. */
#undef HAVE_STDINT_H
/* Define to 1 if you have the <stdlib.h> header file. */
#undef HAVE_STDLIB_H
/* Define to 1 if you have the <strings.h> header file. */
#undef HAVE_STRINGS_H
/* Define to 1 if you have the <string.h> header file. */
#undef HAVE_STRING_H
/* Define to 1 if you have the <sys/stat.h> header file. */
#undef HAVE_SYS_STAT_H
/* Define to 1 if you have the <sys/types.h> header file. */
#undef HAVE_SYS_TYPES_H
/* Define to 1 if you have the <unistd.h> header file. */
#undef HAVE_UNISTD_H
/* Define to the address where bug reports for this package should be sent. */
#undef PACKAGE_BUGREPORT
/* Define to the full name of this package. */
#undef PACKAGE_NAME
/* Define to the full name and version of this package. */
#undef PACKAGE_STRING
/* Define to the one symbol short name of this package. */
#undef PACKAGE_TARNAME
/* Define to the version of this package. */
#undef PACKAGE_VERSION
/* Define to 1 if you have the ANSI C header files. */
#undef STDC_HEADERS
/* Define to 1 if you can safely include both <sys/time.h> and <time.h>. */
#undef TIME_WITH_SYS_TIME
/* Number of bits in a file offset, on hosts where this is settable. */
#undef _FILE_OFFSET_BITS
/* Define for large files, on AIX-style hosts. */
#undef _LARGE_FILES
/* Define to empty if `const' does not conform to ANSI C. */
#undef const
/* Define to `__inline__' or `__inline' if that's what the C compiler
calls it, or to nothing if 'inline' is not supported under any name. */
#ifndef __cplusplus
#undef inline
#endif
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configure.ac
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dnl Process this file with autoconf to produce a configure script.
AC_PREREQ([2.59])
AC_INIT(libGenome/gnDefs.h)
AC_CONFIG_AUX_DIR(config)
AC_CONFIG_MACRO_DIR([m4])
dnl Get the target and build system types and add appropriate options
AC_CANONICAL_TARGET
......@@ -96,7 +99,7 @@ AM_CONDITIONAL(DEBUG, test x$debug = xtrue)
AM_CONFIG_HEADER(config.h)
dnl Check for OpenMP
AX_OPENMP()
#AX_OPENMP()
AC_SUBST(OPENMP_CFLAGS)
dnl OpenMP checker only defines for C when compiling both C and C++
dnl OPENMP_CXXFLAGS=$OPENMP_CFLAGS
......
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#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
scriptversion=2004-05-31.23
# Copyright (C) 1999, 2000, 2003, 2004 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
# 02111-1307, USA.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.
case $1 in
'')
echo "$0: No command. Try \`$0 --help' for more information." 1>&2
exit 1;
;;
-h | --h*)
cat <<\EOF
Usage: depcomp [--help] [--version] PROGRAM [ARGS]
Run PROGRAMS ARGS to compile a file, generating dependencies
as side-effects.
Environment variables:
depmode Dependency tracking mode.
source Source file read by `PROGRAMS ARGS'.
object Object file output by `PROGRAMS ARGS'.
DEPDIR directory where to store dependencies.
depfile Dependency file to output.
tmpdepfile Temporary file to use when outputing dependencies.
libtool Whether libtool is used (yes/no).
Report bugs to <bug-automake@gnu.org>.
EOF
exit 0
;;
-v | --v*)
echo "depcomp $scriptversion"
exit 0
;;
esac
if test -z "$depmode" || test -z "$source" || test -z "$object"; then
echo "depcomp: Variables source, object and depmode must be set" 1>&2
exit 1
fi
# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
depfile=${depfile-`echo "$object" |
sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
rm -f "$tmpdepfile"
# Some modes work just like other modes, but use different flags. We
# parameterize here, but still list the modes in the big case below,
# to make depend.m4 easier to write. Note that we *cannot* use a case
# here, because this file can only contain one case statement.
if test "$depmode" = hp; then
# HP compiler uses -M and no extra arg.
gccflag=-M
depmode=gcc
fi
if test "$depmode" = dashXmstdout; then
# This is just like dashmstdout with a different argument.
dashmflag=-xM
depmode=dashmstdout
fi
case "$depmode" in
gcc3)
## gcc 3 implements dependency tracking that does exactly what
## we want. Yay! Note: for some reason libtool 1.4 doesn't like
## it if -MD -MP comes after the -MF stuff. Hmm.
"$@" -MT "$object" -MD -MP -MF "$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
mv "$tmpdepfile" "$depfile"
;;
gcc)
## There are various ways to get dependency output from gcc. Here's
## why we pick this rather obscure method:
## - Don't want to use -MD because we'd like the dependencies to end
## up in a subdir. Having to rename by hand is ugly.
## (We might end up doing this anyway to support other compilers.)
## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
## -MM, not -M (despite what the docs say).
## - Using -M directly means running the compiler twice (even worse
## than renaming).
if test -z "$gccflag"; then
gccflag=-MD,
fi
"$@" -Wp,"$gccflag$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
echo "$object : \\" > "$depfile"
alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
## The second -e expression handles DOS-style file names with drive letters.
sed -e 's/^[^:]*: / /' \
-e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
## This next piece of magic avoids the `deleted header file' problem.
## The problem is that when a header file which appears in a .P file
## is deleted, the dependency causes make to die (because there is
## typically no way to rebuild the header). We avoid this by adding
## dummy dependencies for each header file. Too bad gcc doesn't do
## this for us directly.
tr ' ' '
' < "$tmpdepfile" |
## Some versions of gcc put a space before the `:'. On the theory
## that the space means something, we add a space to the output as
## well.
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
hp)
# This case exists only to let depend.m4 do its work. It works by
# looking at the text of this script. This case will never be run,
# since it is checked for above.
exit 1
;;
sgi)
if test "$libtool" = yes; then
"$@" "-Wp,-MDupdate,$tmpdepfile"
else
"$@" -MDupdate "$tmpdepfile"
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
echo "$object : \\" > "$depfile"
# Clip off the initial element (the dependent). Don't try to be
# clever and replace this with sed code, as IRIX sed won't handle
# lines with more than a fixed number of characters (4096 in
# IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
# the IRIX cc adds comments like `#:fec' to the end of the
# dependency line.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
tr '
' ' ' >> $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/$/:/' \
>> $depfile
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
aix)
# The C for AIX Compiler uses -M and outputs the dependencies
# in a .u file. In older versions, this file always lives in the
# current directory. Also, the AIX compiler puts `$object:' at the
# start of each line; $object doesn't have directory information.
# Version 6 uses the directory in both cases.
stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'`
tmpdepfile="$stripped.u"
if test "$libtool" = yes; then
"$@" -Wc,-M
else
"$@" -M
fi
stat=$?
if test -f "$tmpdepfile"; then :
else
stripped=`echo "$stripped" | sed 's,^.*/,,'`
tmpdepfile="$stripped.u"
fi
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
if test -f "$tmpdepfile"; then
outname="$stripped.o"
# Each line is of the form `foo.o: dependent.h'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile"
sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile"
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
icc)
# Intel's C compiler understands `-MD -MF file'. However on
# icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
# ICC 7.0 will fill foo.d with something like
# foo.o: sub/foo.c
# foo.o: sub/foo.h
# which is wrong. We want:
# sub/foo.o: sub/foo.c
# sub/foo.o: sub/foo.h
# sub/foo.c:
# sub/foo.h:
# ICC 7.1 will output
# foo.o: sub/foo.c sub/foo.h
# and will wrap long lines using \ :
# foo.o: sub/foo.c ... \
# sub/foo.h ... \
# ...
"$@" -MD -MF "$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
# Each line is of the form `foo.o: dependent.h',
# or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
# Some versions of the HPUX 10.20 sed can't process this invocation
# correctly. Breaking it into two sed invocations is a workaround.
sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
tru64)
# The Tru64 compiler uses -MD to generate dependencies as a side
# effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
# At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
# dependencies in `foo.d' instead, so we check for that too.
# Subdirectories are respected.
dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
test "x$dir" = "x$object" && dir=
base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
# Dependencies are output in .lo.d with libtool 1.4.
# With libtool 1.5 they are output both in $dir.libs/$base.o.d
# and in $dir.libs/$base.o.d and $dir$base.o.d. We process the
# latter, because the former will be cleaned when $dir.libs is
# erased.
tmpdepfile1="$dir.libs/$base.lo.d"
tmpdepfile2="$dir$base.o.d"
tmpdepfile3="$dir.libs/$base.d"
"$@" -Wc,-MD
else
tmpdepfile1="$dir$base.o.d"
tmpdepfile2="$dir$base.d"
tmpdepfile3="$dir$base.d"
"$@" -MD
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
exit $stat
fi
if test -f "$tmpdepfile1"; then
tmpdepfile="$tmpdepfile1"
elif test -f "$tmpdepfile2"; then
tmpdepfile="$tmpdepfile2"
else
tmpdepfile="$tmpdepfile3"
fi
if test -f "$tmpdepfile"; then
sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
# That's a tab and a space in the [].
sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
else
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
#nosideeffect)
# This comment above is used by automake to tell side-effect
# dependency tracking mechanisms from slower ones.
dashmstdout)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout, regardless of -o.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
test -z "$dashmflag" && dashmflag=-M
# Require at least two characters before searching for `:'
# in the target name. This is to cope with DOS-style filenames:
# a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
"$@" $dashmflag |
sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
tr ' ' '
' < "$tmpdepfile" | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
dashXmstdout)
# This case only exists to satisfy depend.m4. It is never actually
# run, as this mode is specially recognized in the preamble.
exit 1
;;
makedepend)
"$@" || exit $?
# Remove any Libtool call
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# X makedepend
shift
cleared=no
for arg in "$@"; do
case $cleared in
no)
set ""; shift
cleared=yes ;;
esac
case "$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.
-*|$object)
;;
*)
set fnord "$@" "$arg"; shift ;;
esac
done
obj_suffix="`echo $object | sed 's/^.*\././'`"
touch "$tmpdepfile"
${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
sed '1,2d' "$tmpdepfile" | tr ' ' '
' | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile" "$tmpdepfile".bak
;;
cpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
"$@" -E |
sed -n '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
sed '$ s: \\$::' > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
cat < "$tmpdepfile" >> "$depfile"
sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
msvisualcpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout, regardless of -o,
# because we must use -o when running libtool.
"$@" || exit $?
IFS=" "
for arg
do
case "$arg" in
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
set fnord "$@"
shift
shift
;;
*)
set fnord "$@" "$arg"
shift
shift
;;
esac
done
"$@" -E |
sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
. "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
echo " " >> "$depfile"
. "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
rm -f "$tmpdepfile"
;;
none)
exec "$@"
;;
*)
echo "Unknown depmode $depmode" 1>&2
exit 1
;;
esac
exit 0
# Local Variables:
# mode: shell-script
# sh-indentation: 2
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-end: "$"
# End:
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libGenome/TestgnSeqConverter.cpp 0 → 100644
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#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnSequence.h"
#include "libGenome/gnFASSource.h"
#include "libGenome/gnGBKSource.h"
#include <iostream>
#include <string>
#include "libGenome/gnTranslator.h"
#include "libGenome/gnDebug.h"
#include "libGenome/gnDNASequence.h"
#include "libGenome/gnDebug.h"
void runTests(gnSequence& seq);
void runTests(gnSequence& seq){
cout << "Testing with sequence:\n";
cout << seq << endl;
seq.setReverseComplement(true);
cout << "Reverse Complement:\n";
cout << seq << endl;
seq.setReverseComplement(false);
cout << "Forward sequence:\n";
cout << seq << endl;
seq.setFilter(gnTranslator::DNAProteinTranslator);
cout << "Translated to protein sequence:\n";
cout << seq << endl;
seq.setReverseComplement(true);
cout << "Reverse complement translated to protein sequence:\n";
cout << seq << endl;
list<const gnBaseFilter*> filter_list;
filter_list.push_back(gnTranslator::DNAProteinTranslator);
filter_list.push_back(gnTranslator::ProteinDNATranslator);
seq.setFilterList(filter_list);
cout << "Reverse Comp translated to protein sequence and back to dna:\n";
cout << seq << endl;
};
int main(int argc, char* argv[]){
gnDNASequence seq = "ACGTTAGCGTAT";
gnDNASequence seq2 = "A";
seq2 += "CG";
seq2 += "TTA";
seq2 += "GCGT";
seq2 += "AT";
string blah;
DebugMsg("Hello World.\n");
runTests(seq);
cout << "And now for the same thing with the same sequence.\n";
cin >> blah;
runTests(seq2);
cin >> blah;
do{
cout << "Finally, enter a sequence file to play with: ";
cin >> blah;
}while(!seq.LoadSource(blah));
seq.setFilter(NULL);
gnFASSource::Write(seq, "test_rc.fas");
gnGBKSource::Write(seq, "test_rc.gbk");
return 0;
}
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libGenome/gnSourceFactory.cpp
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......@@ -39,6 +39,8 @@ gnSourceFactory::gnSourceFactory()
m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".SEQ", new gnSEQSource()));
m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".gbk", new gnGBKSource()));
m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".GBK", new gnGBKSource()));
m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".gb", new gnGBKSource()));
m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".GB", new gnGBKSource()));
m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".raw", new gnRAWSource()));
m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".RAW", new gnRAWSource()));
m_pDefaultSourceClass = new gnFASSource();
......@@ -288,13 +290,13 @@ gnBaseSource* gnSourceFactory::HasSource( string sourceStr, boolean searchPaths
boolean gnSourceFactory::PathExists( string path ) const{
#ifdef HAVE_UNISTD_H
standardizePathString( path );
char folder[FILENAME_MAX];
getcwd( folder, FILENAME_MAX );
char folder[FILENAME_MAX], *f2;
f2 = getcwd( folder, FILENAME_MAX );
if( chdir( path.c_str() ) ){
return false;
}
chdir( folder );
int err = chdir( folder );
#endif
return true;
}
......
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