initial commit

00boot

+#!/bin/sh
+
+## function to print error message and exit
+fail () {
+  echo "!!! $0: $1" >&2
+  exit 1
+}
+
+## check script is being run from top-level source directory
+test "$0" = "./00boot" || fail "must be run from top-level source directory"
+
+## remove M4 cache files
+rm -rf autom4te.cache/
+rm -f aclocal.m4
+
+# FIXME: autoreconf from Ubuntu 9.10 (and probably also from recent
+# Debian versions) automatically run libtoolize with the --copy option
+# therefore over writing the supplied libtool scripts with system
+# version. This can lead to unexpected build failures therefore to work
+# round this "feature" we set the LIBTOOLIZE enviroment variable to
+# point to the the true executable which bypasses the running of
+# libtoolize, this will not effect the vast majority of users and those
+# it will effect will know how to run libtoolize, if required.
+
+## run autoreconf
+AUTORECONF=${AUTORECONF:-"autoreconf"}
+echo "00boot: running ${AUTORECONF}"
+LIBTOOLIZE=true ${AUTORECONF} || fail "${AUTORECONF} failed"
+
+echo "
+==================================================
+00boot has been run successfully.
+Now run './configure' with appropriate options
+to configure CWSeaOptiFol.
+==================================================
+"

COPYING

+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 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 Lesser 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
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+These restrictions translate to certain responsibilities for you if you
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+
+  For example, if you distribute copies of such a program, whether
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+
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+(2) offer you this license which gives you legal permission to copy,
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+
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+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
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+
+  Finally, any free program is threatened constantly by software
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+
+                    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,
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+Activities other than copying, distribution and modification are not
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+running the Program is not restricted, and the output from the Program
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+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
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+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
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+  2. You may modify your copy or copies of the Program or any portion
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+
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+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
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+
+These requirements apply to the modified work as a whole.  If
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+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
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+
+  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
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+    a) Accompany it with the complete corresponding machine-readable
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+
+  4. You may not copy, modify, sublicense, or distribute the Program
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+
+  5. You are not required to accept this License, since you have not
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+
+  6. Each time you redistribute the Program (or any work based on the
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+
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+infringement or for any other reason (not limited to patent issues),
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+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
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+
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+This section is intended to make thoroughly clear what is believed to
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+  8. If the distribution and/or use of the Program is restricted in
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+
+  9. The Free Software Foundation may publish revised and/or new versions
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+
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+Software Foundation.  If the Program does not specify a version number of
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+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
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+
+                            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
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+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
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+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
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+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.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 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 Lesser General
+Public License instead of this License.

Makefile.am

+ACLOCAL_AMFLAGS = -I misc
+
+EXTRA_DIST = \
+	COPYING \
+	README \
+	README.bugs \
+	README.contrib \
+	cwseaoptifol.spec.in \
+	cwseaoptifol.spec
+
+SUBDIRS = \
+	debian \
+	misc \
+	src
+
+DISTCLEANFILES = config.lt
+
+if HAVE_GIT_REPO
+vcs-clean: maintainer-clean
+	-cd $(top_srcdir) && $(GIT) clean -Xdf
+endif
+
+all-local:
+	@echo "";\
+	echo "==================================================";\
+	echo "CWSeaOptiFol has now been successfully built.";\
+	echo "Now run 'make install' to install CWSeaOptiFol.";\
+	echo "==================================================";\
+	echo ""
+
+install-exec-local:
+	@echo "";\
+	echo "==================================================";\
+	echo "CWSeaOptiFol has now been successfully installed.";\
+	echo "Now you may want to setup your environment:";\
+	echo "";\
+	echo "* Bourne shell [bash] users: please add the line";\
+	echo "  . $(sysconfdir)/cwsof-user-env.sh";\
+	echo "  to your .profile file.";\
+	echo "";\
+	echo "* C-shell [tcsh] users: please add the line";\
+	echo "  source $(sysconfdir)/cwsof-user-env.csh";\
+	echo "  to your .login file.";\
+	echo "==================================================";\
+	echo ""

README

+LALApps - LIGO Scientific Collaboration Algorithm Library Applications
+
+Synopsis:
+
+        A collection of programs and other software for gravitational wave data
+        analysis.
+
+
+Notice:
+
+        We request that any academic report, publication, or other
+        academic disclosure of results derived from the use of this
+        software acknowledge the use of the software by an appropriate
+        acknowledgment or citation.
+
+
+Consult:
+
+        README.bugs             reporting problems with LAL
+        README.contrib          instructions for LAL developers
+
+
+Installation:
+
+        LALApps requires various pieces of software which can be installed
+        by following these directions:
+        http://www.lsc-group.phys.uwm.edu/daswg/docs/howto/lscsoft-install.html
+
+        Binary versions of these software packages, as well as the latest
+        released version of LALApps, can be obtained from:
+        http://www.lsc-group.phys.uwm.edu/daswg/download/repositories.html
+
+        Follow these directions to build both LAL and LALApps from source:
+        http://www.lsc-group.phys.uwm.edu/daswg/docs/howto/lal-install.html
+
+
+Other resources:
+
+        Binary releases of LALApps for various platforms:
+        http://www.lsc-group.phys.uwm.edu/daswg/download/repositories.html
+
+        LAL-Announce: LAL announcements including release announcements.
+        http://www.lsc-group.phys.uwm.edu/mailman/listinfo.cgi/lal-announce
+
+        LAL-Discuss: general LAL discussion forum (not for bug reports)
+        http://www.lsc-group.phys.uwm.edu/mailman/listinfo.cgi/lal-discuss
+
+        Please see the LALApps webpage for more information:
+        http://www.lsc-group.phys.uwm.edu/daswg/projects/lalapps.html

README.bugs

+The LAL and LALApps Bug Reporting System can be accessed at the URL
+
+        http://www.lsc-group.phys.uwm.edu/daswg/projects/lal/bugreport.html
+
+To enter the bug reporting system you will need a username and a password.
+Anyone can enter to create or query bug reports using:
+
+        Username: anonymous
+        Password: anonymous

README.contrib

+INSTRUCTIONS FOR CONTRIBUTORS
+
+LALApps is rather free-form. The golden rule is:
+
+  Your code must be ANSI C 89 for maximum portability
+
+If you like uniformity, I recommend that you copy what is already there.  If
+you like to do your own thing, that's fine too.  Here are the essential
+instructions.
+
+
+1. Sources:
+
+   Put your sources in a subdirectory, hereafter src/myprogdir, of the src
+   subdirectory.  Sources include all your .c files and all your .h files.
+   As a general rule, bundle a bunch of programs that are related (e.g., using
+   the same source files or pertaining to the same search type) into a single
+   subdirectory.
+
+   If you have created a new subdirectory within the src subdirectory, edit
+   the file src/Makefile.am to add the new directory (myprogdir) to the SUBDIRS
+   line.  Copy the file src/example/Makefile.am to src/myprogdir and edit it
+   to build the new program (see below).  Also add the new Makefile
+   (src/myprogdir/Makefile) to the AC_OUTPUT command at the end of the
+   configure.in file (in the top lalapps directory).
+
+   Edit the file src/myprogdir/Makefile.am so that your program is built.  The
+   program that is built should have a name like lalapps_myprog.  This is so
+   that you don't clobber another program that somewhat may have installed with
+   the same name.  Suppose your sources are myprog.c and myprog.h.  Then the
+   Makefile.am should have the line
+
+     lalapps_myprog_SOURCES = myprog.c myprog.h
+
+   Finally, be sure to add lalapps_myprog to the bin_PROGRAMS variable.
+
+   Note that the file src/myprogdir/Makefile.am should have a line like:
+
+     INCLUDES = -I$(top_srcdir)/src
+
+   if you need to include config.h, or the lines
+
+     INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/src/lalapps
+     LDADD = $(top_builddir)/src/lalapps/liblalapps.la
+
+   if you are also using the lalapps routines.
+
+
+2. Documentation:
+
+   Documentation is essential if you want anyone to use your program.  The
+   documentation is located in the doc subdirectory.
+
+   The way to document your program is to write a texfile to be included in the
+   lalapps texfile lalapps.tex.  You would write a texfile called myprog.tex.
+   It should start with:
+
+     \section{Program \texttt{lalapps\_myprog}}
+     \idx[Program]{lalapps\_myprog}
+
+   and go from there.
+
+   Then you need to get lalapps.tex to include it.  Down near the bottom of
+   the file lalapps.tex you should add the line
+
+     \include{myprog}
+
+   (the location is obvious).
+
+   Finally, edit the Makefile.am so that myprog.tex appears as one of the
+   TEXSOURCEFILES.
+
+   If you have figures, make sure that you have both a pdf and eps version.
+   If you only have an eps figure, myfig.eps, create a pdf version using the
+   command
+
+     epstopdf myfig
+
+   To load the figure in the documentation, use the LaTeX command
+
+     \includegraphics{myfig}
+
+   (note: no extension).  Also be sure that myfig.eps and myfig.pdf both appear
+   in the TEXSOURCEFILES line of Makefile.am.
+
+
+3. Manual pages: (optional)
+
+   If you want a man page installed for your program, put it in the man
+   subdirectory.  Also add it to the MANS line in the Makefile.am.
+
+
+4. Make sure it works:
+
+   Try building the program using
+
+     make
+
+   the documentation using
+
+     make dvi
+
+   and installing everything using
+
+     make install
+
+   then clean everything up using
+
+     make cvs-clean
+
+   If one of these things fails, and it is because of something you did,
+   fix it before committing your changes to the git repository.

configure.ac

+AC_PREREQ([2.63])
+AC_INIT([cwsof],[0.0.1.1],[miroslav.shaltev@aei.mpg.de])
+AC_CONFIG_HEADERS([src/config.h])
+AC_CONFIG_SRCDIR([src/cwsof.c])
+AC_CONFIG_AUX_DIR([misc])
+AC_CONFIG_MACRO_DIR([misc])
+AC_CONFIG_FILES([\
+  Makefile \
+  cwseaoptifol.spec \
+  debian/Makefile \
+  misc/Makefile \
+  src/Makefile \
+  src/FollowUp/Nomad/Makefile \
+  src/SearchOptimization/Makefile \
+])
+AM_INIT_AUTOMAKE([1.11 foreign color-tests parallel-tests])
+AH_TOP([
+#ifndef CONFIG_H
+#define CONFIG_H])
+AH_BOTTOM([
+#endif /* CONFIG_H */
+])
+
+AC_CANONICAL_HOST
+
+LALSUITE_ARG_VAR
+LALSUITE_DISTCHECK_CONFIGURE_FLAGS
+
+# check for git repo
+LALSUITE_CHECK_GIT_REPO
+
+LALAPPS_WITH_CC
+LALAPPS_WITH_LAL_PREFIX
+LALAPPS_WITH_EXTRA_CPPFLAGS
+LALAPPS_WITH_EXTRA_CFLAGS
+LALAPPS_WITH_EXTRA_LDFLAGS
+LALAPPS_WITH_EXTRA_LIBS
+
+LALSUITE_ENABLE_DEBUG
+
+LALSUITE_WITH_CUDA
+
+LALSUITE_ENABLE_GCC_FLAGS
+LALSUITE_ENABLE_NIGHTLY
+LALAPPS_ENABLE_CONDOR
+LALSUITE_ENABLE_BOINC
+LALAPPS_ENABLE_STATIC_BINARIES
+
+LALAPPS_ENABLE_MPI
+
+LALAPPS_ENABLE_FFTW
+LALAPPS_ENABLE_FRAME
+LALAPPS_ENABLE_METAIO
+LALAPPS_ENABLE_CFITSIO
+LALAPPS_ENABLE_NOMAD
+LALAPPS_ENABLE_PSS
+LALAPPS_ENABLE_GDS
+
+LALSUITE_ENABLE_LALFRAME
+LALSUITE_ENABLE_LALMETAIO
+LALSUITE_ENABLE_LALXML