[med-svn] [toppred] 01/02: Imported Upstream version 1.10
Andreas Tille
tille at debian.org
Sat Jan 31 11:56:36 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository toppred.
commit 54df7def0373cf31c097bf1866acf368fb1faf48
Author: Andreas Tille <tille at debian.org>
Date: Sat Jan 31 12:49:37 2015 +0100
Imported Upstream version 1.10
---
AUTHORS | 4 +
COPYING | 340 +++
ChangeLog | 287 +++
INSTALL | 236 ++
LICENSE | 340 +++
Makefile.am | 5 +
Makefile.in | 557 +++++
NEWS | 1 +
README | 28 +
TODO | 7 +
aclocal.m4 | 1045 ++++++++
config.guess | 1463 ++++++++++++
config.sub | 1579 ++++++++++++
configure | 5792 +++++++++++++++++++++++++++++++++++++++++++++
configure.in | 48 +
data/CYTEXT-scale | 24 +
data/GES-scale | 25 +
data/GVH-scale | 25 +
data/KD-scale | 25 +
data/Makefile.am | 3 +
data/Makefile.in | 319 +++
data/toppred.dtd | 101 +
depcomp | 530 +++++
doc/Makefile.am | 14 +
doc/Makefile.in | 352 +++
doc/toppred.1 | 341 +++
doc/toppred.pod | 257 ++
install-sh | 323 +++
m4/Makefile.am | 2 +
m4/Makefile.in | 290 +++
m4/aclibgd.m4 | 92 +
missing | 360 +++
mkinstalldirs | 158 ++
src/Makefile.am | 27 +
src/Makefile.in | 465 ++++
src/charge.c | 296 +++
src/charge.h | 41 +
src/config.h.in | 96 +
src/error.c | 44 +
src/error.h | 10 +
src/graph.c | 439 ++++
src/graph.h | 33 +
src/loop.c | 300 +++
src/loop.h | 55 +
src/main.c | 556 +++++
src/main.h | 26 +
src/mloutput.c | 161 ++
src/mloutput.h | 26 +
src/output.c | 132 ++
src/output.h | 19 +
src/params.h | 49 +
src/profile.c | 368 +++
src/profile.h | 38 +
src/seq-reader.c | 245 ++
src/seq-reader.h | 45 +
src/topology.c | 181 ++
src/topology.h | 41 +
src/topoprint.c | 296 +++
src/topoprint.h | 68 +
src/usage.c | 116 +
src/usage.h | 30 +
test/Makefile.am | 26 +
test/Makefile.in | 385 +++
test/construct_topos.test | 31 +
test/detect_segments.test | 31 +
test/first_seg.err | 0
test/first_seg.fasta | 4 +
test/first_seg.out | 67 +
test/hydro.test | 18 +
test/last_seg.err | 0
test/last_seg.fasta | 2 +
test/last_seg.out | 36 +
test/math.test | 15 +
test/min_seqlen.err | 0
test/min_seqlen.fasta | 2 +
test/min_seqlen.out | 35 +
test/more_calc.err | 1 +
test/more_calc.fasta | 8 +
test/more_calc.out | 256 ++
test/naming.test | 23 +
test/no_error.err | 0
test/no_seg.err | 0
test/no_seg.fasta | 2 +
test/no_seg.out | 23 +
test/only_put.err | 0
test/only_put.fasta | 2 +
test/only_put.out | 55 +
test/seq-test | 12 +
test/seq_anonymous.err | 1 +
test/seq_anonymous.fasta | 3 +
test/seq_zero_div.fasta | 2 +
test/seqlen.test | 17 +
test/too_many_put.err | 1 +
test/too_many_put.fasta | 24 +
test/too_many_put.out | 63 +
test/toppred.test | 15 +
96 files changed, 20336 insertions(+)
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..98fc7a3
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,4 @@
+
+Eric Deveaud <edeveaud at pasteur.fr>
+Katja Schuerer
+
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..d60c31a
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,340 @@
+ 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.
diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..6684d9d
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,287 @@
+2008-10-22 Eric Deveaud <edeveaud at raclette-tete1.calcul.pasteur.fr>
+
+ * configure.in: Changed version to 1.10
+
+2008-05-06 Nicolas Joly <njoly at pasteur.fr>
+
+ * doc/toppred.pod: Add missing option `-t none' in example
+ command.
+
+ * src/*.[ch]: Remove XML output, which was unused and broken too
+ often without notice ...
+ * doc/toppred.pod: Adjust.
+
+2008-04-18 Nicolas Joly <njoly at pasteur.fr>
+
+ * test/*.test: Enforce correct status value on success.
+
+2008-03-06 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/seq-reader.c: Allow starting blank lines on fasta formated
+ files.
+
+2008-02-19 Nicolas Joly <njoly at pasteur.fr>
+
+ * src/main.c: Remove unneeded newlines from fatal error messages.
+
+2008-02-01 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/seq-reader.c: Allow `*' (stop codon representation) while
+ sequence reading.
+
+2006-06-06 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/seq-reader.c: Fix anonymous detection and sequence name
+ parsing with pipes.
+
+2006-05-31 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * doc/toppred.pod: Man page update and correction.
+
+2006-05-31 Nicolas Joly <njoly at pasteur.fr>
+
+ * test/hydro.test: New file that checks all hydrophobicity scales.
+
+2006-05-30 Nicolas Joly <njoly at pasteur.fr>
+
+ * src/seq-reader.c: Do not push characters back on stream if
+ nothing was read previously.
+
+ * src/main.c: Do not close output file in sequence file processing
+ loop.
+
+2006-05-30 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/*.c, src/*.h: time stamp cleanup.
+
+ * src/main.c: Optional options `-g' and `-t' no more silently
+ ignored if needed support is missing.
+
+ * src/usage.c: gnuplot png color definition fix.
+
+ * src/seq-reader.c: Fix anonymous detection and related memory
+ overflow.
+
+ * src/profile.c: Fix file descriptor leak induced by mkstemp.
+
+2006-05-29 Nicolas Joly <njoly at pasteur.fr>
+
+ * doc/toppred.pod: Small spelling/formatting fixes.
+
+ * src/mloutput.c: Remove trailing space in XML output.
+ * src/main.c: Fix incorrect XML generation, by moving `toppreds'
+ end tag, out of file process loop.
+
+ * src/mloutput.c: Make HTML header looks a little better (no
+ functional change).
+
+ * src/output.[ch]: Remove local `dirname()' function, and prefer
+ the one from the system.
+ * src/main.c: Adjust accordingly.
+
+ * src/graph.c, src/mloutput.c, src/profile.c: Do not assume
+ `dirname()' return value has a trailing `/' character.
+
+2006-05-25 Nicolas Joly <njoly at pasteur.fr>
+
+ * src/main.c: Move cleanup outside of the processing loop to avoid
+ use of freed memory (data files and output dir) with multiple
+ input files.
+ * test/toppred.test: Exercize more than one input file.
+
+2004-05-17 Nicolas Joly <njoly at pasteur.fr>
+
+ * src/profile.c: hide gplot() function if gnuplot is missing.
+ * src/topology.c, src/loop.c: Use const where appropriate.
+
+2004-05-17 Katja Schuerer <schuerer at pasteur.fr>
+
+ * src/topology.c: Fix off by one index error in topologies
+ construction.
+
+2004-05-14 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/main.c: memory leak while freeing KS structures corrected in
+ case of too many topologies.
+ * src/main.c: memory liberation in case of no libgd.
+ NB: free(NULL) is allowed by the C iso guidelines.
+ * src/main.c: added internal -y flag in order to disable .hydro
+ file generation. (not documented).
+ * src/seq-reader.c: a bunch of header processing bugs correction.
+
+2004-05-03 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/graph.c: topologies graphic production code completly
+ rewrote.
+ * src/topology.c: removing the warning when no segment found.
+ * test/last_seg.err: modified to be coherent with no segment found
+ warning modification.
+ * test/more_calc.err: modified to be coherent with no segment
+ found warning modification.
+ * test/only_put.err: modified to be coherent with no segment found
+ warning modification.
+ * test/seq_float.err: modified to be coherent with no segment
+ found warning modification.
+
+2004-04-29 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/graph.c: correction of the graph representation. no longer
+ crash.
+
+2003-12-12 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/topology.c: modified warning message when no segment found
+ to be more accurate.
+
+2003-12-12 Nicolas Joly <njoly at pasteur.fr>
+
+ * test/*.test: New verbose mode (VERBOSE=x).
+
+2003-12-10 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/profile.c: changed aa2H from function to macro,
+ optimisation.
+ * src/seq-reader.c: modified sequence reading function.
+
+2003-12-09 Nicolas Joly <njoly at pasteur.fr>
+
+ * src/topoprint.c: Do not call `strlen()' on the same object 5
+ times.
+
+2001-11-21 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * configure.in: toppred is now in version 1.00.
+ * src/seq-reader.c: non ascii characters on sequences not more
+ allowed.
+ * src/*.c: corrected the -o result_file option behaviour. All
+ files are stored to the same directory than result_file.
+
+2001-10-15 Katja Schuerer <schuerer at pasteur.fr>
+
+ * test/detect_segments.test: test if all segments are detected.
+ * test/seqlen.test: test of sequences of critical lengths.
+ * test/construct_topos.test: test to verify the calculation of all
+ toplogies.
+ * src/topology.c: correct topology calculation -- skip topologies
+ without any segment.
+
+2001-10-05 Katja Schuerer <schuerer at pasteur.fr>
+
+ * data/toppred.dtd: add DTD file for xml output.
+ * src/mloutput.c: add function for xml output and transfer html
+ output functions to this file.
+ * src/output.c: transfer general output functions to this file.
+
+2001-09-12 Katja Schuerer <schuerer at pasteur.fr>
+
+ * src/loop.c: modify get_segment to allow a segment at beginning
+ of the sequence.
+ * src/loop.c: correct bug while translation of old segment
+ sructure to new segment structure (detection of segment at
+ beginning of the sequence).
+ * src/charge.c: correct floating point exceptions caused by zero
+ division in distance function.
+
+2001-09-10 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/seq-reader.c: corrected bug while reading long comments. id
+ and comment are now dynamically handled, anonymous sequence are
+ tagged as anonymous, and empty sequence causes program exit.
+
+2001-08-30 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/seq-reader.c: modified sequence aquisition, sequence is not
+ systematicaly converted to upcase.
+
+ * src/main.c: added web output format via -w option.
+
+2001-08-28 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/loop.c: corrected a Hplot reading values, that causes a
+ segmentation fault on some systems.
+
+2001-08-03 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/seq-reader.c: seq reader upcase the sequence, as donwcase
+ sequences are not useable.
+
+2001-07-26 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * doc/toppred.pod: manpage looks like a manpage now.
+
+2001-07-24 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/seq-reader.c: corrected a seq-reader bug.
+
+ * src/*.[ch] corrected the include localisation.
+
+2001-07-23 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/graph.c: corrected a bug in graph representation.
+
+2001-07-19 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/graph.c: added graphic topos output choice (-d option).
+
+2001-07-18 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * configure.in: the graphic topology representation is now
+ depending on the use/presence of the libgd.
+
+2001-07-18 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/graph.c: adapted graphic topos output to KS structs.
+
+2001-07-05 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/loop.c (calc_loop): added the penultimate aa checking.
+
+2001-06-27 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/loop.h: introduced loop_t and seg_t structures.
+
+ * src/loop.c : modified the loop / segments structure to fit for
+ the Katja topology calcul.
+
+2001-06-21 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/loop.c: modified calc_segments to take in account segments
+ in position 0 and segments inside a "plateau".
+
+2001-06-19 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/seq_reader.c: sequence reader corrected, now handle
+ correctly incorect format sequence files.
+
+2001-06-13 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/profile.c: added region drawing in produced plot.
+
+2001-06-12 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/profile.c: changed /tmp/gnuplot-file-definition, is now
+ unique. Added some cosmetics in seq.hydro file.
+
+2001-05-14 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * doc/toppred.pod: added documentation.
+
+2001-05-11 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/main.c: modified a bunch of tests.
+
+2001-05-10 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/main.c: added hydrophobic gnu-plotting routine supported
+ format are ps, ppm, and x11.
+
+2001-05-03 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/loop.c: some code cleanning.
+ * src/main.c: some code cleanning.
+
+2001-04-20 Eric Deveaud <edeveaud at pasteur.fr>
+
+ * src/main.c (main): beginning of work. Added hydrophobic values
+ load from file added sequence load from file
+
diff --git a/INSTALL b/INSTALL
new file mode 100644
index 0000000..23e5f25
--- /dev/null
+++ b/INSTALL
@@ -0,0 +1,236 @@
+Installation Instructions
+*************************
+
+Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005 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' installs the package's commands under
+`/usr/local/bin', include files under `/usr/local/include', etc. You
+can specify an installation prefix other than `/usr/local' by giving
+`configure' the option `--prefix=PREFIX'.
+
+ You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files. If you
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses
+PREFIX as the prefix for installing programs and libraries.
+Documentation and other data files 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 option `--target=TYPE' 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
+
+causes the specified `gcc' to be used as the C compiler (unless it is
+overridden in the site shell script). Here is a another example:
+
+ /bin/bash ./configure CONFIG_SHELL=/bin/bash
+
+Here the `CONFIG_SHELL=/bin/bash' operand causes subsequent
+configuration-related scripts to be executed by `/bin/bash'.
+
+`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.
+
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..d6a9326
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,340 @@
+GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/>
+ 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
+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.
+
+ {description}
+ Copyright (C) {year} {fullname}
+
+ 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.
+
diff --git a/Makefile.am b/Makefile.am
new file mode 100644
index 0000000..90aa1ba
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,5 @@
+SUBDIRS = . m4 src data doc test
+
+## Add m4 dir for autoconf extra definitions
+ACLOCAL_AMFLAGS = -I m4
+
diff --git a/Makefile.in b/Makefile.in
new file mode 100644
index 0000000..230e9a0
--- /dev/null
+++ b/Makefile.in
@@ -0,0 +1,557 @@
+# Makefile.in generated by automake 1.9.2 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+top_builddir = .
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+INSTALL = @INSTALL@
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
+ $(srcdir)/Makefile.in $(top_srcdir)/configure AUTHORS COPYING \
+ ChangeLog INSTALL NEWS TODO config.guess config.sub depcomp \
+ install-sh missing mkinstalldirs
+subdir = .
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/m4/aclibgd.m4 \
+ $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
+ configure.lineno configure.status.lineno
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_HEADER = $(top_builddir)/src/config.h
+CONFIG_CLEAN_FILES =
+SOURCES =
+DIST_SOURCES =
+RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
+ html-recursive info-recursive install-data-recursive \
+ install-exec-recursive install-info-recursive \
+ install-recursive installcheck-recursive installdirs-recursive \
+ pdf-recursive ps-recursive uninstall-info-recursive \
+ uninstall-recursive
+ETAGS = etags
+CTAGS = ctags
+DIST_SUBDIRS = $(SUBDIRS)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+distdir = $(PACKAGE)-$(VERSION)
+top_distdir = $(distdir)
+am__remove_distdir = \
+ { test ! -d $(distdir) \
+ || { find $(distdir) -type d ! -perm -200 -exec chmod u+w {} ';' \
+ && rm -fr $(distdir); }; }
+DIST_ARCHIVES = $(distdir).tar.gz
+GZIP_ENV = --best
+distuninstallcheck_listfiles = find . -type f -print
+distcleancheck_listfiles = find . -type f -print
+ACLOCAL = @ACLOCAL@
+AMDEP_FALSE = @AMDEP_FALSE@
+AMDEP_TRUE = @AMDEP_TRUE@
+AMTAR = @AMTAR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+GNUPLOT = @GNUPLOT@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LDFLAGS = @LDFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+OBJEXT = @OBJEXT@
+OS_CPPFLAGS = @OS_CPPFLAGS@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+POD2MAN = @POD2MAN@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+USE_GD_LIB_SRC_FALSE = @USE_GD_LIB_SRC_FALSE@
+USE_GD_LIB_SRC_TRUE = @USE_GD_LIB_SRC_TRUE@
+VERSION = @VERSION@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_STRIP = @ac_ct_STRIP@
+am__fastdepCC_FALSE = @am__fastdepCC_FALSE@
+am__fastdepCC_TRUE = @am__fastdepCC_TRUE@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+datadir = @datadir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localstatedir = @localstatedir@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+SUBDIRS = . m4 src data doc test
+ACLOCAL_AMFLAGS = -I m4
+all: all-recursive
+
+.SUFFIXES:
+am--refresh:
+ @:
+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
+ @for dep in $?; do \
+ case '$(am__configure_deps)' in \
+ *$$dep*) \
+ echo ' cd $(srcdir) && $(AUTOMAKE) --gnu '; \
+ cd $(srcdir) && $(AUTOMAKE) --gnu \
+ && exit 0; \
+ exit 1;; \
+ esac; \
+ done; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Makefile'; \
+ cd $(top_srcdir) && \
+ $(AUTOMAKE) --gnu Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ @case '$?' in \
+ *config.status*) \
+ echo ' $(SHELL) ./config.status'; \
+ $(SHELL) ./config.status;; \
+ *) \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
+ esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+ $(SHELL) ./config.status --recheck
+
+$(top_srcdir)/configure: $(am__configure_deps)
+ cd $(srcdir) && $(AUTOCONF)
+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
+ cd $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
+uninstall-info-am:
+
+# This directory's subdirectories are mostly independent; you can cd
+# into them and run `make' without going through this Makefile.
+# To change the values of `make' variables: instead of editing Makefiles,
+# (1) if the variable is set in `config.status', edit `config.status'
+# (which will cause the Makefiles to be regenerated when you run `make');
+# (2) otherwise, pass the desired values on the `make' command line.
+$(RECURSIVE_TARGETS):
+ @set fnord $$MAKEFLAGS; amf=$$2; \
+ dot_seen=no; \
+ target=`echo $@ | sed s/-recursive//`; \
+ list='$(SUBDIRS)'; for subdir in $$list; do \
+ echo "Making $$target in $$subdir"; \
+ if test "$$subdir" = "."; then \
+ dot_seen=yes; \
+ local_target="$$target-am"; \
+ else \
+ local_target="$$target"; \
+ fi; \
+ (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+ || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
+ done; \
+ if test "$$dot_seen" = "no"; then \
+ $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
+ fi; test -z "$$fail"
+
+mostlyclean-recursive clean-recursive distclean-recursive \
+maintainer-clean-recursive:
+ @set fnord $$MAKEFLAGS; amf=$$2; \
+ dot_seen=no; \
+ case "$@" in \
+ distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
+ *) list='$(SUBDIRS)' ;; \
+ esac; \
+ rev=''; for subdir in $$list; do \
+ if test "$$subdir" = "."; then :; else \
+ rev="$$subdir $$rev"; \
+ fi; \
+ done; \
+ rev="$$rev ."; \
+ target=`echo $@ | sed s/-recursive//`; \
+ for subdir in $$rev; do \
+ echo "Making $$target in $$subdir"; \
+ if test "$$subdir" = "."; then \
+ local_target="$$target-am"; \
+ else \
+ local_target="$$target"; \
+ fi; \
+ (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+ || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
+ done && test -z "$$fail"
+tags-recursive:
+ list='$(SUBDIRS)'; for subdir in $$list; do \
+ test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
+ done
+ctags-recursive:
+ list='$(SUBDIRS)'; for subdir in $$list; do \
+ test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
+ done
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ mkid -fID $$unique
+tags: TAGS
+
+TAGS: tags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ tags=; \
+ here=`pwd`; \
+ if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
+ include_option=--etags-include; \
+ empty_fix=.; \
+ else \
+ include_option=--include; \
+ empty_fix=; \
+ fi; \
+ list='$(SUBDIRS)'; for subdir in $$list; do \
+ if test "$$subdir" = .; then :; else \
+ test ! -f $$subdir/TAGS || \
+ tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \
+ fi; \
+ done; \
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
+ test -n "$$unique" || unique=$$empty_fix; \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ $$tags $$unique; \
+ fi
+ctags: CTAGS
+CTAGS: ctags-recursive $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ tags=; \
+ here=`pwd`; \
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ test -z "$(CTAGS_ARGS)$$tags$$unique" \
+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+ $$tags $$unique
+
+GTAGS:
+ here=`$(am__cd) $(top_builddir) && pwd` \
+ && cd $(top_srcdir) \
+ && gtags -i $(GTAGS_ARGS) $$here
+
+distclean-tags:
+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+ $(am__remove_distdir)
+ mkdir $(distdir)
+ $(mkdir_p) $(distdir)/m4
+ @srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
+ list='$(DISTFILES)'; for file in $$list; do \
+ case $$file in \
+ $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
+ $(top_srcdir)/*) file=`echo "$$file" | sed "s|^$$topsrcdirstrip/|$(top_builddir)/|"`;; \
+ esac; \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ dir=`echo "$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test "$$dir" != "$$file" && test "$$dir" != "."; then \
+ dir="/$$dir"; \
+ $(mkdir_p) "$(distdir)$$dir"; \
+ else \
+ dir=''; \
+ fi; \
+ if test -d $$d/$$file; then \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+ fi; \
+ cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+ else \
+ test -f $(distdir)/$$file \
+ || cp -p $$d/$$file $(distdir)/$$file \
+ || exit 1; \
+ fi; \
+ done
+ list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+ if test "$$subdir" = .; then :; else \
+ test -d "$(distdir)/$$subdir" \
+ || $(mkdir_p) "$(distdir)/$$subdir" \
+ || exit 1; \
+ distdir=`$(am__cd) $(distdir) && pwd`; \
+ top_distdir=`$(am__cd) $(top_distdir) && pwd`; \
+ (cd $$subdir && \
+ $(MAKE) $(AM_MAKEFLAGS) \
+ top_distdir="$$top_distdir" \
+ distdir="$$distdir/$$subdir" \
+ distdir) \
+ || exit 1; \
+ fi; \
+ done
+ -find $(distdir) -type d ! -perm -777 -exec chmod a+rwx {} \; -o \
+ ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
+ ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
+ ! -type d ! -perm -444 -exec $(SHELL) $(install_sh) -c -m a+r {} {} \; \
+ || chmod -R a+r $(distdir)
+dist-gzip: distdir
+ tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+ $(am__remove_distdir)
+
+dist-bzip2: distdir
+ tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2
+ $(am__remove_distdir)
+
+dist-tarZ: distdir
+ tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
+ $(am__remove_distdir)
+
+dist-shar: distdir
+ shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
+ $(am__remove_distdir)
+
+dist-zip: distdir
+ -rm -f $(distdir).zip
+ zip -rq $(distdir).zip $(distdir)
+ $(am__remove_distdir)
+
+dist dist-all: distdir
+ tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
+ $(am__remove_distdir)
+
+# This target untars the dist file and tries a VPATH configuration. Then
+# it guarantees that the distribution is self-contained by making another
+# tarfile.
+distcheck: dist
+ case '$(DIST_ARCHIVES)' in \
+ *.tar.gz*) \
+ GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\
+ *.tar.bz2*) \
+ bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\
+ *.tar.Z*) \
+ uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
+ *.shar.gz*) \
+ GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\
+ *.zip*) \
+ unzip $(distdir).zip ;;\
+ esac
+ chmod -R a-w $(distdir); chmod a+w $(distdir)
+ mkdir $(distdir)/_build
+ mkdir $(distdir)/_inst
+ chmod a-w $(distdir)
+ dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
+ && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
+ && cd $(distdir)/_build \
+ && ../configure --srcdir=.. --prefix="$$dc_install_base" \
+ $(DISTCHECK_CONFIGURE_FLAGS) \
+ && $(MAKE) $(AM_MAKEFLAGS) \
+ && $(MAKE) $(AM_MAKEFLAGS) dvi \
+ && $(MAKE) $(AM_MAKEFLAGS) check \
+ && $(MAKE) $(AM_MAKEFLAGS) install \
+ && $(MAKE) $(AM_MAKEFLAGS) installcheck \
+ && $(MAKE) $(AM_MAKEFLAGS) uninstall \
+ && $(MAKE) $(AM_MAKEFLAGS) distuninstallcheck_dir="$$dc_install_base" \
+ distuninstallcheck \
+ && chmod -R a-w "$$dc_install_base" \
+ && ({ \
+ (cd ../.. && umask 077 && mkdir "$$dc_destdir") \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" install \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" uninstall \
+ && $(MAKE) $(AM_MAKEFLAGS) DESTDIR="$$dc_destdir" \
+ distuninstallcheck_dir="$$dc_destdir" distuninstallcheck; \
+ } || { rm -rf "$$dc_destdir"; exit 1; }) \
+ && rm -rf "$$dc_destdir" \
+ && $(MAKE) $(AM_MAKEFLAGS) dist \
+ && rm -rf $(DIST_ARCHIVES) \
+ && $(MAKE) $(AM_MAKEFLAGS) distcleancheck
+ $(am__remove_distdir)
+ @(echo "$(distdir) archives ready for distribution: "; \
+ list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
+ sed -e '1{h;s/./=/g;p;x;}' -e '$${p;x;}'
+distuninstallcheck:
+ @cd $(distuninstallcheck_dir) \
+ && test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
+ || { echo "ERROR: files left after uninstall:" ; \
+ if test -n "$(DESTDIR)"; then \
+ echo " (check DESTDIR support)"; \
+ fi ; \
+ $(distuninstallcheck_listfiles) ; \
+ exit 1; } >&2
+distcleancheck: distclean
+ @if test '$(srcdir)' = . ; then \
+ echo "ERROR: distcleancheck can only run from a VPATH build" ; \
+ exit 1 ; \
+ fi
+ @test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
+ || { echo "ERROR: files left in build directory after distclean:" ; \
+ $(distcleancheck_listfiles) ; \
+ exit 1; } >&2
+check-am: all-am
+check: check-recursive
+all-am: Makefile
+installdirs: installdirs-recursive
+installdirs-am:
+install: install-recursive
+install-exec: install-exec-recursive
+install-data: install-data-recursive
+uninstall: uninstall-recursive
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-recursive
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+clean: clean-recursive
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-recursive
+ -rm -f $(am__CONFIG_DISTCLEAN_FILES)
+ -rm -f Makefile
+distclean-am: clean-am distclean-generic distclean-tags
+
+dvi: dvi-recursive
+
+dvi-am:
+
+html: html-recursive
+
+info: info-recursive
+
+info-am:
+
+install-data-am:
+
+install-exec-am:
+
+install-info: install-info-recursive
+
+install-man:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-recursive
+ -rm -f $(am__CONFIG_DISTCLEAN_FILES)
+ -rm -rf $(top_srcdir)/autom4te.cache
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-recursive
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-recursive
+
+pdf-am:
+
+ps: ps-recursive
+
+ps-am:
+
+uninstall-am: uninstall-info-am
+
+uninstall-info: uninstall-info-recursive
+
+.PHONY: $(RECURSIVE_TARGETS) CTAGS GTAGS all all-am am--refresh check \
+ check-am clean clean-generic clean-recursive ctags \
+ ctags-recursive dist dist-all dist-bzip2 dist-gzip dist-shar \
+ dist-tarZ dist-zip distcheck distclean distclean-generic \
+ distclean-recursive distclean-tags distcleancheck distdir \
+ distuninstallcheck dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am install-exec \
+ install-exec-am install-info install-info-am install-man \
+ install-strip installcheck installcheck-am installdirs \
+ installdirs-am maintainer-clean maintainer-clean-generic \
+ maintainer-clean-recursive mostlyclean mostlyclean-generic \
+ mostlyclean-recursive pdf pdf-am ps ps-am tags tags-recursive \
+ uninstall uninstall-am uninstall-info-am
+
+# 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:
diff --git a/NEWS b/NEWS
new file mode 100644
index 0000000..6edf1a1
--- /dev/null
+++ b/NEWS
@@ -0,0 +1 @@
+no news is good news !
diff --git a/README b/README
new file mode 100644
index 0000000..44e3e41
--- /dev/null
+++ b/README
@@ -0,0 +1,28 @@
+
+TOPPRED - Transmembrane topology prediction.
+
+This program is a new implementation of the original toppred program,
+based on G. von Heijne algorithm :
+
+"Membrane protein structure prediction. Hydrophobicity analysis and
+the positive-inside rule." J Mol Biol 1992 May 20;225(2):487-94.
+
+"TopPred II: an improved software for membrane protein structure
+predictions." CABIOS 10(6):685-6, 1994 Dec.
+
+This implementation can use 2 optionals programs in order to
+display graphical results:
+
+ - gnuplot version 3.7 patchlevel 1 or more
+ `gnuplot' can be used in order to display the
+ hydrophobicity profile of a given sequence.
+ see <http://www.gnuplot.info/>
+ - libgd with png support
+ `gd' library can be used in order to produce a
+ graphical representation of the calculated topologies.
+ see <http://www.boutell.com/gd>
+
+For installation, please see INSTALL note.
+
+Please report bugs, comments or suggestions to:
+Eric Deveaud: edeveaud at pasteur.fr
diff --git a/TODO b/TODO
new file mode 100644
index 0000000..49ab647
--- /dev/null
+++ b/TODO
@@ -0,0 +1,7 @@
+
+Assorted ToDo items :
+
+* Add tests to exercise `-g' and `-t' formats.
+* Cleanup Text/HTML output functions.
+* Unhandled conflict between `-O html' and `-o outfile'.
+
diff --git a/aclocal.m4 b/aclocal.m4
new file mode 100644
index 0000000..567b9fc
--- /dev/null
+++ b/aclocal.m4
@@ -0,0 +1,1045 @@
+# generated automatically by aclocal 1.9.2 -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004
+# Free Software Foundation, Inc.
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+# -*- Autoconf -*-
+# Copyright (C) 2002, 2003 Free Software Foundation, Inc.
+# Generated from amversion.in; do not edit by hand.
+
+# 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
+
+# AM_AUTOMAKE_VERSION(VERSION)
+# ----------------------------
+# Automake X.Y traces this macro to ensure aclocal.m4 has been
+# generated from the m4 files accompanying Automake X.Y.
+AC_DEFUN([AM_AUTOMAKE_VERSION], [am__api_version="1.9"])
+
+# AM_SET_CURRENT_AUTOMAKE_VERSION
+# -------------------------------
+# Call AM_AUTOMAKE_VERSION so it can be traced.
+# This function is AC_REQUIREd by AC_INIT_AUTOMAKE.
+AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
+ [AM_AUTOMAKE_VERSION([1.9.2])])
+
+# AM_AUX_DIR_EXPAND
+
+# Copyright (C) 2001, 2003 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.
+
+# For projects using AC_CONFIG_AUX_DIR([foo]), Autoconf sets
+# $ac_aux_dir to `$srcdir/foo'. In other projects, it is set to
+# `$srcdir', `$srcdir/..', or `$srcdir/../..'.
+#
+# Of course, Automake must honor this variable whenever it calls a
+# tool from the auxiliary directory. The problem is that $srcdir (and
+# therefore $ac_aux_dir as well) can be either absolute or relative,
+# depending on how configure is run. This is pretty annoying, since
+# it makes $ac_aux_dir quite unusable in subdirectories: in the top
+# source directory, any form will work fine, but in subdirectories a
+# relative path needs to be adjusted first.
+#
+# $ac_aux_dir/missing
+# fails when called from a subdirectory if $ac_aux_dir is relative
+# $top_srcdir/$ac_aux_dir/missing
+# fails if $ac_aux_dir is absolute,
+# fails when called from a subdirectory in a VPATH build with
+# a relative $ac_aux_dir
+#
+# The reason of the latter failure is that $top_srcdir and $ac_aux_dir
+# are both prefixed by $srcdir. In an in-source build this is usually
+# harmless because $srcdir is `.', but things will broke when you
+# start a VPATH build or use an absolute $srcdir.
+#
+# So we could use something similar to $top_srcdir/$ac_aux_dir/missing,
+# iff we strip the leading $srcdir from $ac_aux_dir. That would be:
+# am_aux_dir='\$(top_srcdir)/'`expr "$ac_aux_dir" : "$srcdir//*\(.*\)"`
+# and then we would define $MISSING as
+# MISSING="\${SHELL} $am_aux_dir/missing"
+# This will work as long as MISSING is not called from configure, because
+# unfortunately $(top_srcdir) has no meaning in configure.
+# However there are other variables, like CC, which are often used in
+# configure, and could therefore not use this "fixed" $ac_aux_dir.
+#
+# Another solution, used here, is to always expand $ac_aux_dir to an
+# absolute PATH. The drawback is that using absolute paths prevent a
+# configured tree to be moved without reconfiguration.
+
+AC_DEFUN([AM_AUX_DIR_EXPAND],
+[dnl Rely on autoconf to set up CDPATH properly.
+AC_PREREQ([2.50])dnl
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+])
+
+# AM_CONDITIONAL -*- Autoconf -*-
+
+# Copyright (C) 1997, 2000, 2001, 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.
+
+# serial 6
+
+# AM_CONDITIONAL(NAME, SHELL-CONDITION)
+# -------------------------------------
+# Define a conditional.
+AC_DEFUN([AM_CONDITIONAL],
+[AC_PREREQ(2.52)dnl
+ ifelse([$1], [TRUE], [AC_FATAL([$0: invalid condition: $1])],
+ [$1], [FALSE], [AC_FATAL([$0: invalid condition: $1])])dnl
+AC_SUBST([$1_TRUE])
+AC_SUBST([$1_FALSE])
+if $2; then
+ $1_TRUE=
+ $1_FALSE='#'
+else
+ $1_TRUE='#'
+ $1_FALSE=
+fi
+AC_CONFIG_COMMANDS_PRE(
+[if test -z "${$1_TRUE}" && test -z "${$1_FALSE}"; then
+ AC_MSG_ERROR([[conditional "$1" was never defined.
+Usually this means the macro was only invoked conditionally.]])
+fi])])
+
+# serial 7 -*- Autoconf -*-
+
+# Copyright (C) 1999, 2000, 2001, 2002, 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.
+
+
+# There are a few dirty hacks below to avoid letting `AC_PROG_CC' be
+# written in clear, in which case automake, when reading aclocal.m4,
+# will think it sees a *use*, and therefore will trigger all it's
+# C support machinery. Also note that it means that autoscan, seeing
+# CC etc. in the Makefile, will ask for an AC_PROG_CC use...
+
+
+
+# _AM_DEPENDENCIES(NAME)
+# ----------------------
+# See how the compiler implements dependency checking.
+# NAME is "CC", "CXX", "GCJ", or "OBJC".
+# We try a few techniques and use that to set a single cache variable.
+#
+# We don't AC_REQUIRE the corresponding AC_PROG_CC since the latter was
+# modified to invoke _AM_DEPENDENCIES(CC); we would have a circular
+# dependency, and given that the user is not expected to run this macro,
+# just rely on AC_PROG_CC.
+AC_DEFUN([_AM_DEPENDENCIES],
+[AC_REQUIRE([AM_SET_DEPDIR])dnl
+AC_REQUIRE([AM_OUTPUT_DEPENDENCY_COMMANDS])dnl
+AC_REQUIRE([AM_MAKE_INCLUDE])dnl
+AC_REQUIRE([AM_DEP_TRACK])dnl
+
+ifelse([$1], CC, [depcc="$CC" am_compiler_list=],
+ [$1], CXX, [depcc="$CXX" am_compiler_list=],
+ [$1], OBJC, [depcc="$OBJC" am_compiler_list='gcc3 gcc'],
+ [$1], GCJ, [depcc="$GCJ" am_compiler_list='gcc3 gcc'],
+ [depcc="$$1" am_compiler_list=])
+
+AC_CACHE_CHECK([dependency style of $depcc],
+ [am_cv_$1_dependencies_compiler_type],
+[if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_$1_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n ['s/^#*\([a-zA-Z0-9]*\))$/\1/p'] < ./depcomp`
+ fi
+ 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
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ case $depmode in
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ none) break ;;
+ esac
+ # 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.
+ if depmode=$depmode \
+ source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_$1_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_$1_dependencies_compiler_type=none
+fi
+])
+AC_SUBST([$1DEPMODE], [depmode=$am_cv_$1_dependencies_compiler_type])
+AM_CONDITIONAL([am__fastdep$1], [
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_$1_dependencies_compiler_type" = gcc3])
+])
+
+
+# AM_SET_DEPDIR
+# -------------
+# Choose a directory name for dependency files.
+# This macro is AC_REQUIREd in _AM_DEPENDENCIES
+AC_DEFUN([AM_SET_DEPDIR],
+[AC_REQUIRE([AM_SET_LEADING_DOT])dnl
+AC_SUBST([DEPDIR], ["${am__leading_dot}deps"])dnl
+])
+
+
+# AM_DEP_TRACK
+# ------------
+AC_DEFUN([AM_DEP_TRACK],
+[AC_ARG_ENABLE(dependency-tracking,
+[ --disable-dependency-tracking speeds up one-time build
+ --enable-dependency-tracking do not reject slow dependency extractors])
+if test "x$enable_dependency_tracking" != xno; then
+ am_depcomp="$ac_aux_dir/depcomp"
+ AMDEPBACKSLASH='\'
+fi
+AM_CONDITIONAL([AMDEP], [test "x$enable_dependency_tracking" != xno])
+AC_SUBST([AMDEPBACKSLASH])
+])
+
+# Generate code to set up dependency tracking. -*- Autoconf -*-
+
+# Copyright (C) 1999, 2000, 2001, 2002, 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.
+
+#serial 2
+
+# _AM_OUTPUT_DEPENDENCY_COMMANDS
+# ------------------------------
+AC_DEFUN([_AM_OUTPUT_DEPENDENCY_COMMANDS],
+[for mf in $CONFIG_FILES; do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # So let's grep whole file.
+ if grep '^#.*generated by automake' $mf > /dev/null 2>&1; then
+ dirpart=`AS_DIRNAME("$mf")`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`AS_DIRNAME(["$file"])`
+ AS_MKDIR_P([$dirpart/$fdir])
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+done
+])# _AM_OUTPUT_DEPENDENCY_COMMANDS
+
+
+# AM_OUTPUT_DEPENDENCY_COMMANDS
+# -----------------------------
+# This macro should only be invoked once -- use via AC_REQUIRE.
+#
+# This code is only required when automatic dependency tracking
+# is enabled. FIXME. This creates each `.P' file that we will
+# need in order to bootstrap the dependency handling code.
+AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
+[AC_CONFIG_COMMANDS([depfiles],
+ [test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS],
+ [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
+])
+
+# Like AC_CONFIG_HEADER, but automatically create stamp file. -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 2000, 2001, 2003 Free Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+# 02111-1307, USA.
+
+# serial 7
+
+# AM_CONFIG_HEADER is obsolete. It has been replaced by AC_CONFIG_HEADERS.
+AU_DEFUN([AM_CONFIG_HEADER], [AC_CONFIG_HEADERS($@)])
+
+# Do all the work for Automake. -*- Autoconf -*-
+
+# This macro actually does too much some checks are only needed if
+# your package does certain things. But this isn't really a big deal.
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 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.
+
+# serial 11
+
+# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
+# AM_INIT_AUTOMAKE([OPTIONS])
+# -----------------------------------------------
+# The call with PACKAGE and VERSION arguments is the old style
+# call (pre autoconf-2.50), which is being phased out. PACKAGE
+# and VERSION should now be passed to AC_INIT and removed from
+# the call to AM_INIT_AUTOMAKE.
+# We support both call styles for the transition. After
+# the next Automake release, Autoconf can make the AC_INIT
+# arguments mandatory, and then we can depend on a new Autoconf
+# release and drop the old call support.
+AC_DEFUN([AM_INIT_AUTOMAKE],
+[AC_PREREQ([2.58])dnl
+dnl Autoconf wants to disallow AM_ names. We explicitly allow
+dnl the ones we care about.
+m4_pattern_allow([^AM_[A-Z]+FLAGS$])dnl
+AC_REQUIRE([AM_SET_CURRENT_AUTOMAKE_VERSION])dnl
+AC_REQUIRE([AC_PROG_INSTALL])dnl
+# test to see if srcdir already configured
+if test "`cd $srcdir && pwd`" != "`pwd`" &&
+ test -f $srcdir/config.status; then
+ AC_MSG_ERROR([source directory already configured; run "make distclean" there first])
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
+ CYGPATH_W='cygpath -w'
+ else
+ CYGPATH_W=echo
+ fi
+fi
+AC_SUBST([CYGPATH_W])
+
+# Define the identity of the package.
+dnl Distinguish between old-style and new-style calls.
+m4_ifval([$2],
+[m4_ifval([$3], [_AM_SET_OPTION([no-define])])dnl
+ AC_SUBST([PACKAGE], [$1])dnl
+ AC_SUBST([VERSION], [$2])],
+[_AM_SET_OPTIONS([$1])dnl
+ AC_SUBST([PACKAGE], ['AC_PACKAGE_TARNAME'])dnl
+ AC_SUBST([VERSION], ['AC_PACKAGE_VERSION'])])dnl
+
+_AM_IF_OPTION([no-define],,
+[AC_DEFINE_UNQUOTED(PACKAGE, "$PACKAGE", [Name of package])
+ AC_DEFINE_UNQUOTED(VERSION, "$VERSION", [Version number of package])])dnl
+
+# Some tools Automake needs.
+AC_REQUIRE([AM_SANITY_CHECK])dnl
+AC_REQUIRE([AC_ARG_PROGRAM])dnl
+AM_MISSING_PROG(ACLOCAL, aclocal-${am__api_version})
+AM_MISSING_PROG(AUTOCONF, autoconf)
+AM_MISSING_PROG(AUTOMAKE, automake-${am__api_version})
+AM_MISSING_PROG(AUTOHEADER, autoheader)
+AM_MISSING_PROG(MAKEINFO, makeinfo)
+AM_PROG_INSTALL_SH
+AM_PROG_INSTALL_STRIP
+AC_REQUIRE([AM_PROG_MKDIR_P])dnl
+# We need awk for the "check" target. The system "awk" is bad on
+# some platforms.
+AC_REQUIRE([AC_PROG_AWK])dnl
+AC_REQUIRE([AC_PROG_MAKE_SET])dnl
+AC_REQUIRE([AM_SET_LEADING_DOT])dnl
+_AM_IF_OPTION([tar-ustar], [_AM_PROG_TAR([ustar])],
+ [_AM_IF_OPTION([tar-pax], [_AM_PROG_TAR([pax])],
+ [_AM_PROG_TAR([v7])])])
+_AM_IF_OPTION([no-dependencies],,
+[AC_PROVIDE_IFELSE([AC_PROG_CC],
+ [_AM_DEPENDENCIES(CC)],
+ [define([AC_PROG_CC],
+ defn([AC_PROG_CC])[_AM_DEPENDENCIES(CC)])])dnl
+AC_PROVIDE_IFELSE([AC_PROG_CXX],
+ [_AM_DEPENDENCIES(CXX)],
+ [define([AC_PROG_CXX],
+ defn([AC_PROG_CXX])[_AM_DEPENDENCIES(CXX)])])dnl
+])
+])
+
+
+# When config.status generates a header, we must update the stamp-h file.
+# This file resides in the same directory as the config header
+# that is generated. The stamp files are numbered to have different names.
+
+# Autoconf calls _AC_AM_CONFIG_HEADER_HOOK (when defined) in the
+# loop where config.status creates the headers, so we can generate
+# our stamp files there.
+AC_DEFUN([_AC_AM_CONFIG_HEADER_HOOK],
+[# Compute $1's index in $config_headers.
+_am_stamp_count=1
+for _am_header in $config_headers :; do
+ case $_am_header in
+ $1 | $1:* )
+ break ;;
+ * )
+ _am_stamp_count=`expr $_am_stamp_count + 1` ;;
+ esac
+done
+echo "timestamp for $1" >`AS_DIRNAME([$1])`/stamp-h[]$_am_stamp_count])
+
+# AM_PROG_INSTALL_SH
+# ------------------
+# Define $install_sh.
+
+# Copyright (C) 2001, 2003 Free Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+# 02111-1307, USA.
+
+AC_DEFUN([AM_PROG_INSTALL_SH],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+install_sh=${install_sh-"$am_aux_dir/install-sh"}
+AC_SUBST(install_sh)])
+
+# -*- Autoconf -*-
+# Copyright (C) 2003 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.
+
+# serial 1
+
+# Check whether the underlying file-system supports filenames
+# with a leading dot. For instance MS-DOS doesn't.
+AC_DEFUN([AM_SET_LEADING_DOT],
+[rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+ am__leading_dot=.
+else
+ am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+AC_SUBST([am__leading_dot])])
+
+# Check to see how 'make' treats includes. -*- Autoconf -*-
+
+# Copyright (C) 2001, 2002, 2003 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.
+
+# serial 2
+
+# AM_MAKE_INCLUDE()
+# -----------------
+# Check to see how make treats includes.
+AC_DEFUN([AM_MAKE_INCLUDE],
+[am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+ @echo done
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+AC_MSG_CHECKING([for style of include used by $am_make])
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# We grep out `Entering directory' and `Leaving directory'
+# messages which can occur if `w' ends up in MAKEFLAGS.
+# In particular we don't look at `^make:' because GNU make might
+# be invoked under some other name (usually "gmake"), in which
+# case it prints its new name instead of `make'.
+if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then
+ am__include=include
+ am__quote=
+ _am_result=GNU
+fi
+# 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
+fi
+AC_SUBST([am__include])
+AC_SUBST([am__quote])
+AC_MSG_RESULT([$_am_result])
+rm -f confinc confmf
+])
+
+# -*- Autoconf -*-
+
+
+# Copyright (C) 1997, 1999, 2000, 2001, 2003 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.
+
+# serial 3
+
+# AM_MISSING_PROG(NAME, PROGRAM)
+# ------------------------------
+AC_DEFUN([AM_MISSING_PROG],
+[AC_REQUIRE([AM_MISSING_HAS_RUN])
+$1=${$1-"${am_missing_run}$2"}
+AC_SUBST($1)])
+
+
+# AM_MISSING_HAS_RUN
+# ------------------
+# Define MISSING if not defined so far and test if it supports --run.
+# If it does, set am_missing_run to use it, otherwise, to nothing.
+AC_DEFUN([AM_MISSING_HAS_RUN],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing"
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
+else
+ am_missing_run=
+ AC_MSG_WARN([`missing' script is too old or missing])
+fi
+])
+
+# AM_PROG_MKDIR_P
+# ---------------
+# Check whether `mkdir -p' is supported, fallback to mkinstalldirs otherwise.
+
+# Copyright (C) 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.
+
+# Automake 1.8 used `mkdir -m 0755 -p --' to ensure that directories
+# created by `make install' are always world readable, even if the
+# installer happens to have an overly restrictive umask (e.g. 077).
+# This was a mistake. There are at least two reasons why we must not
+# use `-m 0755':
+# - it causes special bits like SGID to be ignored,
+# - it may be too restrictive (some setups expect 775 directories).
+#
+# Do not use -m 0755 and let people choose whatever they expect by
+# setting umask.
+#
+# We cannot accept any implementation of `mkdir' that recognizes `-p'.
+# Some implementations (such as Solaris 8's) are not thread-safe: if a
+# parallel make tries to run `mkdir -p a/b' and `mkdir -p a/c'
+# concurrently, both version can detect that a/ is missing, but only
+# one can create it and the other will error out. Consequently we
+# restrict ourselves to GNU make (using the --version option ensures
+# this.)
+AC_DEFUN([AM_PROG_MKDIR_P],
+[if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then
+ # We used to keeping the `.' as first argument, in order to
+ # allow $(mkdir_p) to be used without argument. As in
+ # $(mkdir_p) $(somedir)
+ # where $(somedir) is conditionally defined. However this is wrong
+ # for two reasons:
+ # 1. if the package is installed by a user who cannot write `.'
+ # make install will fail,
+ # 2. the above comment should most certainly read
+ # $(mkdir_p) $(DESTDIR)$(somedir)
+ # so it does not work when $(somedir) is undefined and
+ # $(DESTDIR) is not.
+ # To support the latter case, we have to write
+ # test -z "$(somedir)" || $(mkdir_p) $(DESTDIR)$(somedir),
+ # so the `.' trick is pointless.
+ mkdir_p='mkdir -p --'
+else
+ # On NextStep and OpenStep, the `mkdir' command does not
+ # recognize any option. It will interpret all options as
+ # directories to create, and then abort because `.' already
+ # exists.
+ for d in ./-p ./--version;
+ do
+ test -d $d && rmdir $d
+ done
+ # $(mkinstalldirs) is defined by Automake if mkinstalldirs exists.
+ if test -f "$ac_aux_dir/mkinstalldirs"; then
+ mkdir_p='$(mkinstalldirs)'
+ else
+ mkdir_p='$(install_sh) -d'
+ fi
+fi
+AC_SUBST([mkdir_p])])
+
+# Helper functions for option handling. -*- Autoconf -*-
+
+# Copyright (C) 2001, 2002, 2003 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.
+
+# serial 2
+
+# _AM_MANGLE_OPTION(NAME)
+# -----------------------
+AC_DEFUN([_AM_MANGLE_OPTION],
+[[_AM_OPTION_]m4_bpatsubst($1, [[^a-zA-Z0-9_]], [_])])
+
+# _AM_SET_OPTION(NAME)
+# ------------------------------
+# Set option NAME. Presently that only means defining a flag for this option.
+AC_DEFUN([_AM_SET_OPTION],
+[m4_define(_AM_MANGLE_OPTION([$1]), 1)])
+
+# _AM_SET_OPTIONS(OPTIONS)
+# ----------------------------------
+# OPTIONS is a space-separated list of Automake options.
+AC_DEFUN([_AM_SET_OPTIONS],
+[AC_FOREACH([_AM_Option], [$1], [_AM_SET_OPTION(_AM_Option)])])
+
+# _AM_IF_OPTION(OPTION, IF-SET, [IF-NOT-SET])
+# -------------------------------------------
+# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise.
+AC_DEFUN([_AM_IF_OPTION],
+[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
+
+#
+# Check to make sure that the build environment is sane.
+#
+
+# Copyright (C) 1996, 1997, 2000, 2001, 2003 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.
+
+# serial 3
+
+# AM_SANITY_CHECK
+# ---------------
+AC_DEFUN([AM_SANITY_CHECK],
+[AC_MSG_CHECKING([whether build environment is sane])
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# 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 $srcdir/configure conftest.file 2> /dev/null`
+ if test "$[*]" = "X"; then
+ # -L didn't work.
+ set X `ls -t $srcdir/configure conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$[*]" != "X $srcdir/configure conftest.file" \
+ && test "$[*]" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ AC_MSG_ERROR([ls -t appears to fail. Make sure there is not a broken
+alias in your environment])
+ fi
+
+ test "$[2]" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ AC_MSG_ERROR([newly created file is older than distributed files!
+Check your system clock])
+fi
+AC_MSG_RESULT(yes)])
+
+# AM_PROG_INSTALL_STRIP
+
+# Copyright (C) 2001, 2003 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.
+
+# One issue with vendor `install' (even GNU) is that you can't
+# specify the program used to strip binaries. This is especially
+# annoying in cross-compiling environments, where the build's strip
+# is unlikely to handle the host's binaries.
+# Fortunately install-sh will honor a STRIPPROG variable, so we
+# always use install-sh in `make install-strip', and initialize
+# STRIPPROG with the value of the STRIP variable (set by the user).
+AC_DEFUN([AM_PROG_INSTALL_STRIP],
+[AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
+# 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.
+dnl Don't test for $cross_compiling = yes, because it might be `maybe'.
+if test "$cross_compiling" != no; then
+ AC_CHECK_TOOL([STRIP], [strip], :)
+fi
+INSTALL_STRIP_PROGRAM="\${SHELL} \$(install_sh) -c -s"
+AC_SUBST([INSTALL_STRIP_PROGRAM])])
+
+# Check how to create a tarball. -*- Autoconf -*-
+
+# Copyright (C) 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.
+
+# serial 1
+
+
+# _AM_PROG_TAR(FORMAT)
+# --------------------
+# Check how to create a tarball in format FORMAT.
+# FORMAT should be one of `v7', `ustar', or `pax'.
+#
+# Substitute a variable $(am__tar) that is a command
+# writing to stdout a FORMAT-tarball containing the directory
+# $tardir.
+# tardir=directory && $(am__tar) > result.tar
+#
+# Substitute a variable $(am__untar) that extract such
+# a tarball read from stdin.
+# $(am__untar) < result.tar
+AC_DEFUN([_AM_PROG_TAR],
+[# Always define AMTAR for backward compatibility.
+AM_MISSING_PROG([AMTAR], [tar])
+m4_if([$1], [v7],
+ [am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'],
+ [m4_case([$1], [ustar],, [pax],,
+ [m4_fatal([Unknown tar format])])
+AC_MSG_CHECKING([how to create a $1 tar archive])
+# Loop over all known methods to create a tar archive until one works.
+_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
+_am_tools=${am_cv_prog_tar_$1-$_am_tools}
+# Do not fold the above two line into one, because Tru64 sh and
+# Solaris sh will not grok spaces in the rhs of `-'.
+for _am_tool in $_am_tools
+do
+ case $_am_tool in
+ gnutar)
+ for _am_tar in tar gnutar gtar;
+ do
+ AM_RUN_LOG([$_am_tar --version]) && break
+ done
+ am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
+ am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
+ am__untar="$_am_tar -xf -"
+ ;;
+ plaintar)
+ # Must skip GNU tar: if it does not support --format= it doesn't create
+ # ustar tarball either.
+ (tar --version) >/dev/null 2>&1 && continue
+ am__tar='tar chf - "$$tardir"'
+ am__tar_='tar chf - "$tardir"'
+ am__untar='tar xf -'
+ ;;
+ pax)
+ am__tar='pax -L -x $1 -w "$$tardir"'
+ am__tar_='pax -L -x $1 -w "$tardir"'
+ am__untar='pax -r'
+ ;;
+ cpio)
+ am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
+ am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
+ am__untar='cpio -i -H $1 -d'
+ ;;
+ none)
+ am__tar=false
+ am__tar_=false
+ am__untar=false
+ ;;
+ esac
+
+ # If the value was cached, stop now. We just wanted to have am__tar
+ # and am__untar set.
+ test -n "${am_cv_prog_tar_$1}" && break
+
+ # tar/untar a dummy directory, and stop if the command works
+ rm -rf conftest.dir
+ mkdir conftest.dir
+ echo GrepMe > conftest.dir/file
+ AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
+ rm -rf conftest.dir
+ if test -s conftest.tar; then
+ AM_RUN_LOG([$am__untar <conftest.tar])
+ grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
+ fi
+done
+rm -rf conftest.dir
+
+AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
+AC_MSG_RESULT([$am_cv_prog_tar_$1])])
+AC_SUBST([am__tar])
+AC_SUBST([am__untar])
+]) # _AM_PROG_TAR
+
+m4_include([m4/aclibgd.m4])
diff --git a/config.guess b/config.guess
new file mode 100755
index 0000000..917bbc5
--- /dev/null
+++ b/config.guess
@@ -0,0 +1,1463 @@
+#! /bin/sh
+# Attempt to guess a canonical system name.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004, 2005 Free Software Foundation, Inc.
+
+timestamp='2005-07-08'
+
+# This file is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
+# 02110-1301, 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 Per Bothner <per at bothner.com>.
+# Please send patches to <config-patches at gnu.org>. Submit a context
+# diff and a properly formatted ChangeLog entry.
+#
+# This script attempts to guess a canonical system name similar to
+# config.sub. If it succeeds, it prints the system name on stdout, and
+# exits with 0. Otherwise, it exits with 1.
+#
+# The plan is that this can be called by configure scripts if you
+# don't specify an explicit build system type.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION]
+
+Output the configuration name of the system \`$me' is run on.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.guess ($timestamp)
+
+Originally written by Per Bothner.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
+Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help" >&2
+ exit 1 ;;
+ * )
+ break ;;
+ esac
+done
+
+if test $# != 0; then
+ echo "$me: too many arguments$help" >&2
+ exit 1
+fi
+
+trap 'exit 1' 1 2 15
+
+# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
+# compiler to aid in system detection is discouraged as it requires
+# temporary files to be created and, as you can see below, it is a
+# headache to deal with in a portable fashion.
+
+# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
+# use `HOST_CC' if defined, but it is deprecated.
+
+# Portable tmp directory creation inspired by the Autoconf team.
+
+set_cc_for_build='
+trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ;
+trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
+: ${TMPDIR=/tmp} ;
+ { tmp=`(umask 077 && mktemp -d -q "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
+ { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
+ { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||
+ { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;
+dummy=$tmp/dummy ;
+tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;
+case $CC_FOR_BUILD,$HOST_CC,$CC in
+ ,,) echo "int x;" > $dummy.c ;
+ for c in cc gcc c89 c99 ; do
+ if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then
+ CC_FOR_BUILD="$c"; break ;
+ fi ;
+ done ;
+ if test x"$CC_FOR_BUILD" = x ; then
+ CC_FOR_BUILD=no_compiler_found ;
+ fi
+ ;;
+ ,,*) CC_FOR_BUILD=$CC ;;
+ ,*,*) CC_FOR_BUILD=$HOST_CC ;;
+esac ; set_cc_for_build= ;'
+
+# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
+# (ghazi at noc.rutgers.edu 1994-08-24)
+if (test -f /.attbin/uname) >/dev/null 2>&1 ; then
+ PATH=$PATH:/.attbin ; export PATH
+fi
+
+UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
+UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
+UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
+UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
+
+# Note: order is significant - the case branches are not exclusive.
+
+case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
+ *:NetBSD:*:*)
+ # NetBSD (nbsd) targets should (where applicable) match one or
+ # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*,
+ # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently
+ # switched to ELF, *-*-netbsd* would select the old
+ # object file format. This provides both forward
+ # compatibility and a consistent mechanism for selecting the
+ # object file format.
+ #
+ # Note: NetBSD doesn't particularly care about the vendor
+ # portion of the name. We always set it to "unknown".
+ sysctl="sysctl -n hw.machine_arch"
+ UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \
+ /usr/sbin/$sysctl 2>/dev/null || echo unknown)`
+ case "${UNAME_MACHINE_ARCH}" in
+ armeb) machine=armeb-unknown ;;
+ arm*) machine=arm-unknown ;;
+ sh3el) machine=shl-unknown ;;
+ sh3eb) machine=sh-unknown ;;
+ *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
+ esac
+ # The Operating System including object format, if it has switched
+ # to ELF recently, or will in the future.
+ case "${UNAME_MACHINE_ARCH}" in
+ arm*|i386|m68k|ns32k|sh3*|sparc|vax)
+ eval $set_cc_for_build
+ if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep __ELF__ >/dev/null
+ then
+ # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
+ # Return netbsd for either. FIX?
+ os=netbsd
+ else
+ os=netbsdelf
+ fi
+ ;;
+ *)
+ os=netbsd
+ ;;
+ esac
+ # The OS release
+ # Debian GNU/NetBSD machines have a different userland, and
+ # thus, need a distinct triplet. However, they do not need
+ # kernel version information, so it can be replaced with a
+ # suitable tag, in the style of linux-gnu.
+ case "${UNAME_VERSION}" in
+ Debian*)
+ release='-gnu'
+ ;;
+ *)
+ release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
+ ;;
+ esac
+ # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
+ # contains redundant information, the shorter form:
+ # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
+ echo "${machine}-${os}${release}"
+ exit ;;
+ *:OpenBSD:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
+ echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
+ exit ;;
+ *:ekkoBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
+ exit ;;
+ macppc:MirBSD:*:*)
+ echo powerppc-unknown-mirbsd${UNAME_RELEASE}
+ exit ;;
+ *:MirBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
+ exit ;;
+ alpha:OSF1:*:*)
+ case $UNAME_RELEASE in
+ *4.0)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
+ ;;
+ *5.*)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+ ;;
+ esac
+ # According to Compaq, /usr/sbin/psrinfo has been available on
+ # OSF/1 and Tru64 systems produced since 1995. I hope that
+ # covers most systems running today. This code pipes the CPU
+ # types through head -n 1, so we only detect the type of CPU 0.
+ ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
+ case "$ALPHA_CPU_TYPE" in
+ "EV4 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "EV4.5 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "LCA4 (21066/21068)")
+ UNAME_MACHINE="alpha" ;;
+ "EV5 (21164)")
+ UNAME_MACHINE="alphaev5" ;;
+ "EV5.6 (21164A)")
+ UNAME_MACHINE="alphaev56" ;;
+ "EV5.6 (21164PC)")
+ UNAME_MACHINE="alphapca56" ;;
+ "EV5.7 (21164PC)")
+ UNAME_MACHINE="alphapca57" ;;
+ "EV6 (21264)")
+ UNAME_MACHINE="alphaev6" ;;
+ "EV6.7 (21264A)")
+ UNAME_MACHINE="alphaev67" ;;
+ "EV6.8CB (21264C)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8AL (21264B)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8CX (21264D)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.9A (21264/EV69A)")
+ UNAME_MACHINE="alphaev69" ;;
+ "EV7 (21364)")
+ UNAME_MACHINE="alphaev7" ;;
+ "EV7.9 (21364A)")
+ UNAME_MACHINE="alphaev79" ;;
+ esac
+ # A Pn.n version is a patched version.
+ # A Vn.n version is a released version.
+ # A Tn.n version is a released field test version.
+ # A Xn.n version is an unreleased experimental baselevel.
+ # 1.2 uses "1.2" for uname -r.
+ echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ exit ;;
+ Alpha\ *:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # Should we change UNAME_MACHINE based on the output of uname instead
+ # of the specific Alpha model?
+ echo alpha-pc-interix
+ exit ;;
+ 21064:Windows_NT:50:3)
+ echo alpha-dec-winnt3.5
+ exit ;;
+ Amiga*:UNIX_System_V:4.0:*)
+ echo m68k-unknown-sysv4
+ exit ;;
+ *:[Aa]miga[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-amigaos
+ exit ;;
+ *:[Mm]orph[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-morphos
+ exit ;;
+ *:OS/390:*:*)
+ echo i370-ibm-openedition
+ exit ;;
+ *:z/VM:*:*)
+ echo s390-ibm-zvmoe
+ exit ;;
+ *:OS400:*:*)
+ echo powerpc-ibm-os400
+ exit ;;
+ arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
+ echo arm-acorn-riscix${UNAME_RELEASE}
+ exit ;;
+ arm:riscos:*:*|arm:RISCOS:*:*)
+ echo arm-unknown-riscos
+ exit ;;
+ SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
+ echo hppa1.1-hitachi-hiuxmpp
+ exit ;;
+ Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
+ # akee at wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
+ if test "`(/bin/universe) 2>/dev/null`" = att ; then
+ echo pyramid-pyramid-sysv3
+ else
+ echo pyramid-pyramid-bsd
+ fi
+ exit ;;
+ NILE*:*:*:dcosx)
+ echo pyramid-pyramid-svr4
+ exit ;;
+ DRS?6000:unix:4.0:6*)
+ echo sparc-icl-nx6
+ exit ;;
+ DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*)
+ case `/usr/bin/uname -p` in
+ sparc) echo sparc-icl-nx7; exit ;;
+ esac ;;
+ sun4H:SunOS:5.*:*)
+ echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
+ echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ i86pc:SunOS:5.*:*)
+ echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:6*:*)
+ # According to config.sub, this is the proper way to canonicalize
+ # SunOS6. Hard to guess exactly what SunOS6 will be like, but
+ # it's likely to be more like Solaris than SunOS4.
+ echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:*:*)
+ case "`/usr/bin/arch -k`" in
+ Series*|S4*)
+ UNAME_RELEASE=`uname -v`
+ ;;
+ esac
+ # Japanese Language versions have a version number like `4.1.3-JL'.
+ echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
+ exit ;;
+ sun3*:SunOS:*:*)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ exit ;;
+ sun*:*:4.2BSD:*)
+ UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
+ test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
+ case "`/bin/arch`" in
+ sun3)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ ;;
+ sun4)
+ echo sparc-sun-sunos${UNAME_RELEASE}
+ ;;
+ esac
+ exit ;;
+ aushp:SunOS:*:*)
+ echo sparc-auspex-sunos${UNAME_RELEASE}
+ exit ;;
+ # The situation for MiNT is a little confusing. The machine name
+ # can be virtually everything (everything which is not
+ # "atarist" or "atariste" at least should have a processor
+ # > m68000). The system name ranges from "MiNT" over "FreeMiNT"
+ # to the lowercase version "mint" (or "freemint"). Finally
+ # the system name "TOS" denotes a system which is actually not
+ # MiNT. But MiNT is downward compatible to TOS, so this should
+ # be no problem.
+ atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
+ echo m68k-milan-mint${UNAME_RELEASE}
+ exit ;;
+ hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
+ echo m68k-hades-mint${UNAME_RELEASE}
+ exit ;;
+ *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
+ echo m68k-unknown-mint${UNAME_RELEASE}
+ exit ;;
+ m68k:machten:*:*)
+ echo m68k-apple-machten${UNAME_RELEASE}
+ exit ;;
+ powerpc:machten:*:*)
+ echo powerpc-apple-machten${UNAME_RELEASE}
+ exit ;;
+ RISC*:Mach:*:*)
+ echo mips-dec-mach_bsd4.3
+ exit ;;
+ RISC*:ULTRIX:*:*)
+ echo mips-dec-ultrix${UNAME_RELEASE}
+ exit ;;
+ VAX*:ULTRIX*:*:*)
+ echo vax-dec-ultrix${UNAME_RELEASE}
+ exit ;;
+ 2020:CLIX:*:* | 2430:CLIX:*:*)
+ echo clipper-intergraph-clix${UNAME_RELEASE}
+ exit ;;
+ mips:*:*:UMIPS | mips:*:*:RISCos)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+#ifdef __cplusplus
+#include <stdio.h> /* for printf() prototype */
+ int main (int argc, char *argv[]) {
+#else
+ int main (argc, argv) int argc; char *argv[]; {
+#endif
+ #if defined (host_mips) && defined (MIPSEB)
+ #if defined (SYSTYPE_SYSV)
+ printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_SVR4)
+ printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
+ printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
+ #endif
+ #endif
+ exit (-1);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c &&
+ dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` &&
+ SYSTEM_NAME=`$dummy $dummyarg` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ echo mips-mips-riscos${UNAME_RELEASE}
+ exit ;;
+ Motorola:PowerMAX_OS:*:*)
+ echo powerpc-motorola-powermax
+ exit ;;
+ Motorola:*:4.3:PL8-*)
+ echo powerpc-harris-powermax
+ exit ;;
+ Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
+ echo powerpc-harris-powermax
+ exit ;;
+ Night_Hawk:Power_UNIX:*:*)
+ echo powerpc-harris-powerunix
+ exit ;;
+ m88k:CX/UX:7*:*)
+ echo m88k-harris-cxux7
+ exit ;;
+ m88k:*:4*:R4*)
+ echo m88k-motorola-sysv4
+ exit ;;
+ m88k:*:3*:R3*)
+ echo m88k-motorola-sysv3
+ exit ;;
+ AViiON:dgux:*:*)
+ # DG/UX returns AViiON for all architectures
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
+ if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
+ then
+ if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
+ [ ${TARGET_BINARY_INTERFACE}x = x ]
+ then
+ echo m88k-dg-dgux${UNAME_RELEASE}
+ else
+ echo m88k-dg-dguxbcs${UNAME_RELEASE}
+ fi
+ else
+ echo i586-dg-dgux${UNAME_RELEASE}
+ fi
+ exit ;;
+ M88*:DolphinOS:*:*) # DolphinOS (SVR3)
+ echo m88k-dolphin-sysv3
+ exit ;;
+ M88*:*:R3*:*)
+ # Delta 88k system running SVR3
+ echo m88k-motorola-sysv3
+ exit ;;
+ XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
+ echo m88k-tektronix-sysv3
+ exit ;;
+ Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
+ echo m68k-tektronix-bsd
+ exit ;;
+ *:IRIX*:*:*)
+ echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
+ exit ;;
+ ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
+ echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id
+ exit ;; # Note that: echo "'`uname -s`'" gives 'AIX '
+ i*86:AIX:*:*)
+ echo i386-ibm-aix
+ exit ;;
+ ia64:AIX:*:*)
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${UNAME_MACHINE}-ibm-aix${IBM_REV}
+ exit ;;
+ *:AIX:2:3)
+ if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <sys/systemcfg.h>
+
+ main()
+ {
+ if (!__power_pc())
+ exit(1);
+ puts("powerpc-ibm-aix3.2.5");
+ exit(0);
+ }
+EOF
+ if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy`
+ then
+ echo "$SYSTEM_NAME"
+ else
+ echo rs6000-ibm-aix3.2.5
+ fi
+ elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
+ echo rs6000-ibm-aix3.2.4
+ else
+ echo rs6000-ibm-aix3.2
+ fi
+ exit ;;
+ *:AIX:*:[45])
+ IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
+ if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
+ IBM_ARCH=rs6000
+ else
+ IBM_ARCH=powerpc
+ fi
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${IBM_ARCH}-ibm-aix${IBM_REV}
+ exit ;;
+ *:AIX:*:*)
+ echo rs6000-ibm-aix
+ exit ;;
+ ibmrt:4.4BSD:*|romp-ibm:BSD:*)
+ echo romp-ibm-bsd4.4
+ exit ;;
+ ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and
+ echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to
+ exit ;; # report: romp-ibm BSD 4.3
+ *:BOSX:*:*)
+ echo rs6000-bull-bosx
+ exit ;;
+ DPX/2?00:B.O.S.:*:*)
+ echo m68k-bull-sysv3
+ exit ;;
+ 9000/[34]??:4.3bsd:1.*:*)
+ echo m68k-hp-bsd
+ exit ;;
+ hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
+ echo m68k-hp-bsd4.4
+ exit ;;
+ 9000/[34678]??:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ case "${UNAME_MACHINE}" in
+ 9000/31? ) HP_ARCH=m68000 ;;
+ 9000/[34]?? ) HP_ARCH=m68k ;;
+ 9000/[678][0-9][0-9])
+ if [ -x /usr/bin/getconf ]; then
+ sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
+ sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+ case "${sc_cpu_version}" in
+ 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
+ 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
+ 532) # CPU_PA_RISC2_0
+ case "${sc_kernel_bits}" in
+ 32) HP_ARCH="hppa2.0n" ;;
+ 64) HP_ARCH="hppa2.0w" ;;
+ '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20
+ esac ;;
+ esac
+ fi
+ if [ "${HP_ARCH}" = "" ]; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+
+ #define _HPUX_SOURCE
+ #include <stdlib.h>
+ #include <unistd.h>
+
+ int main ()
+ {
+ #if defined(_SC_KERNEL_BITS)
+ long bits = sysconf(_SC_KERNEL_BITS);
+ #endif
+ long cpu = sysconf (_SC_CPU_VERSION);
+
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+ case CPU_PA_RISC2_0:
+ #if defined(_SC_KERNEL_BITS)
+ switch (bits)
+ {
+ case 64: puts ("hppa2.0w"); break;
+ case 32: puts ("hppa2.0n"); break;
+ default: puts ("hppa2.0"); break;
+ } break;
+ #else /* !defined(_SC_KERNEL_BITS) */
+ puts ("hppa2.0"); break;
+ #endif
+ default: puts ("hppa1.0"); break;
+ }
+ exit (0);
+ }
+EOF
+ (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
+ test -z "$HP_ARCH" && HP_ARCH=hppa
+ fi ;;
+ esac
+ if [ ${HP_ARCH} = "hppa2.0w" ]
+ then
+ eval $set_cc_for_build
+
+ # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
+ # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler
+ # generating 64-bit code. GNU and HP use different nomenclature:
+ #
+ # $ CC_FOR_BUILD=cc ./config.guess
+ # => hppa2.0w-hp-hpux11.23
+ # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
+ # => hppa64-hp-hpux11.23
+
+ if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
+ grep __LP64__ >/dev/null
+ then
+ HP_ARCH="hppa2.0w"
+ else
+ HP_ARCH="hppa64"
+ fi
+ fi
+ echo ${HP_ARCH}-hp-hpux${HPUX_REV}
+ exit ;;
+ ia64:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ echo ia64-hp-hpux${HPUX_REV}
+ exit ;;
+ 3050*:HI-UX:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <unistd.h>
+ int
+ main ()
+ {
+ long cpu = sysconf (_SC_CPU_VERSION);
+ /* The order matters, because CPU_IS_HP_MC68K erroneously returns
+ true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct
+ results, however. */
+ if (CPU_IS_PA_RISC (cpu))
+ {
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
+ default: puts ("hppa-hitachi-hiuxwe2"); break;
+ }
+ }
+ else if (CPU_IS_HP_MC68K (cpu))
+ puts ("m68k-hitachi-hiuxwe2");
+ else puts ("unknown-hitachi-hiuxwe2");
+ exit (0);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ echo unknown-hitachi-hiuxwe2
+ exit ;;
+ 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* )
+ echo hppa1.1-hp-bsd
+ exit ;;
+ 9000/8??:4.3bsd:*:*)
+ echo hppa1.0-hp-bsd
+ exit ;;
+ *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
+ echo hppa1.0-hp-mpeix
+ exit ;;
+ hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* )
+ echo hppa1.1-hp-osf
+ exit ;;
+ hp8??:OSF1:*:*)
+ echo hppa1.0-hp-osf
+ exit ;;
+ i*86:OSF1:*:*)
+ if [ -x /usr/sbin/sysversion ] ; then
+ echo ${UNAME_MACHINE}-unknown-osf1mk
+ else
+ echo ${UNAME_MACHINE}-unknown-osf1
+ fi
+ exit ;;
+ parisc*:Lites*:*:*)
+ echo hppa1.1-hp-lites
+ exit ;;
+ C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
+ echo c1-convex-bsd
+ exit ;;
+ C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit ;;
+ C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
+ echo c34-convex-bsd
+ exit ;;
+ C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
+ echo c38-convex-bsd
+ exit ;;
+ C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
+ echo c4-convex-bsd
+ exit ;;
+ CRAY*Y-MP:*:*:*)
+ echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*[A-Z]90:*:*:*)
+ echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
+ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
+ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
+ -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*TS:*:*:*)
+ echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*T3E:*:*:*)
+ echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*SV1:*:*:*)
+ echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ *:UNICOS/mp:*:*)
+ echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
+ FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+ echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
+ 5000:UNIX_System_V:4.*:*)
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
+ echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
+ i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
+ echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
+ exit ;;
+ sparc*:BSD/OS:*:*)
+ echo sparc-unknown-bsdi${UNAME_RELEASE}
+ exit ;;
+ *:BSD/OS:*:*)
+ echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
+ exit ;;
+ *:FreeBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+ exit ;;
+ i*:CYGWIN*:*)
+ echo ${UNAME_MACHINE}-pc-cygwin
+ exit ;;
+ i*:MINGW*:*)
+ echo ${UNAME_MACHINE}-pc-mingw32
+ exit ;;
+ i*:windows32*:*)
+ # uname -m includes "-pc" on this system.
+ echo ${UNAME_MACHINE}-mingw32
+ exit ;;
+ i*:PW*:*)
+ echo ${UNAME_MACHINE}-pc-pw32
+ exit ;;
+ x86:Interix*:[34]*)
+ echo i586-pc-interix${UNAME_RELEASE}|sed -e 's/\..*//'
+ exit ;;
+ [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
+ echo i${UNAME_MACHINE}-pc-mks
+ exit ;;
+ i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
+ # UNAME_MACHINE based on the output of uname instead of i386?
+ echo i586-pc-interix
+ exit ;;
+ i*:UWIN*:*)
+ echo ${UNAME_MACHINE}-pc-uwin
+ exit ;;
+ amd64:CYGWIN*:*:*)
+ echo x86_64-unknown-cygwin
+ exit ;;
+ p*:CYGWIN*:*)
+ echo powerpcle-unknown-cygwin
+ exit ;;
+ prep*:SunOS:5.*:*)
+ echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ *:GNU:*:*)
+ # the GNU system
+ echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+ exit ;;
+ *:GNU/*:*:*)
+ # other systems with GNU libc and userland
+ echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
+ exit ;;
+ i*86:Minix:*:*)
+ echo ${UNAME_MACHINE}-pc-minix
+ exit ;;
+ arm*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ cris:Linux:*:*)
+ echo cris-axis-linux-gnu
+ exit ;;
+ crisv32:Linux:*:*)
+ echo crisv32-axis-linux-gnu
+ exit ;;
+ frv:Linux:*:*)
+ echo frv-unknown-linux-gnu
+ exit ;;
+ ia64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ m32r*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ m68*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ mips:Linux:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #undef CPU
+ #undef mips
+ #undef mipsel
+ #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+ CPU=mipsel
+ #else
+ #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+ CPU=mips
+ #else
+ CPU=
+ #endif
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=`
+ test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+ ;;
+ mips64:Linux:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #undef CPU
+ #undef mips64
+ #undef mips64el
+ #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+ CPU=mips64el
+ #else
+ #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+ CPU=mips64
+ #else
+ CPU=
+ #endif
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=`
+ test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+ ;;
+ ppc:Linux:*:*)
+ echo powerpc-unknown-linux-gnu
+ exit ;;
+ ppc64:Linux:*:*)
+ echo powerpc64-unknown-linux-gnu
+ exit ;;
+ alpha:Linux:*:*)
+ case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
+ EV5) UNAME_MACHINE=alphaev5 ;;
+ EV56) UNAME_MACHINE=alphaev56 ;;
+ PCA56) UNAME_MACHINE=alphapca56 ;;
+ PCA57) UNAME_MACHINE=alphapca56 ;;
+ EV6) UNAME_MACHINE=alphaev6 ;;
+ EV67) UNAME_MACHINE=alphaev67 ;;
+ EV68*) UNAME_MACHINE=alphaev68 ;;
+ esac
+ objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null
+ if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
+ echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+ exit ;;
+ parisc:Linux:*:* | hppa:Linux:*:*)
+ # Look for CPU level
+ case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
+ PA7*) echo hppa1.1-unknown-linux-gnu ;;
+ PA8*) echo hppa2.0-unknown-linux-gnu ;;
+ *) echo hppa-unknown-linux-gnu ;;
+ esac
+ exit ;;
+ parisc64:Linux:*:* | hppa64:Linux:*:*)
+ echo hppa64-unknown-linux-gnu
+ exit ;;
+ s390:Linux:*:* | s390x:Linux:*:*)
+ echo ${UNAME_MACHINE}-ibm-linux
+ exit ;;
+ sh64*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ sh*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ sparc:Linux:*:* | sparc64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ x86_64:Linux:*:*)
+ echo x86_64-unknown-linux-gnu
+ exit ;;
+ i*86:Linux:*:*)
+ # The BFD linker knows what the default object file format is, so
+ # first see if it will tell us. cd to the root directory to prevent
+ # problems with other programs or directories called `ld' in the path.
+ # Set LC_ALL=C to ensure ld outputs messages in English.
+ ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \
+ | sed -ne '/supported targets:/!d
+ s/[ ][ ]*/ /g
+ s/.*supported targets: *//
+ s/ .*//
+ p'`
+ case "$ld_supported_targets" 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 $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <features.h>
+ #ifdef __ELF__
+ # ifdef __GLIBC__
+ # if __GLIBC__ >= 2
+ LIBC=gnu
+ # else
+ LIBC=gnulibc1
+ # endif
+ # else
+ LIBC=gnulibc1
+ # endif
+ #else
+ #ifdef __INTEL_COMPILER
+ LIBC=gnu
+ #else
+ LIBC=gnuaout
+ #endif
+ #endif
+ #ifdef __dietlibc__
+ LIBC=dietlibc
+ #endif
+EOF
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^LIBC=`
+ test x"${LIBC}" != x && {
+ echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
+ exit
+ }
+ test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; }
+ ;;
+ i*86:DYNIX/ptx:4*:*)
+ # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
+ # earlier versions are messed up and put the nodename in both
+ # sysname and nodename.
+ echo i386-sequent-sysv4
+ exit ;;
+ i*86:UNIX_SV:4.2MP:2.*)
+ # Unixware is an offshoot of SVR4, but it has its own version
+ # number series starting with 2...
+ # I am not positive that other SVR4 systems won't match this,
+ # I just have to hope. -- rms.
+ # Use sysv4.2uw... so that sysv4* matches it.
+ echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
+ exit ;;
+ i*86:OS/2:*:*)
+ # If we were able to find `uname', then EMX Unix compatibility
+ # is probably installed.
+ echo ${UNAME_MACHINE}-pc-os2-emx
+ exit ;;
+ i*86:XTS-300:*:STOP)
+ echo ${UNAME_MACHINE}-unknown-stop
+ exit ;;
+ i*86:atheos:*:*)
+ echo ${UNAME_MACHINE}-unknown-atheos
+ exit ;;
+ i*86:syllable:*:*)
+ echo ${UNAME_MACHINE}-pc-syllable
+ exit ;;
+ i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*)
+ echo i386-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ i*86:*DOS:*:*)
+ echo ${UNAME_MACHINE}-pc-msdosdjgpp
+ exit ;;
+ i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
+ UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
+ if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
+ echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL}
+ else
+ echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL}
+ fi
+ exit ;;
+ i*86:*:5:[678]*)
+ # UnixWare 7.x, OpenUNIX and OpenServer 6.
+ case `/bin/uname -X | grep "^Machine"` in
+ *486*) UNAME_MACHINE=i486 ;;
+ *Pentium) UNAME_MACHINE=i586 ;;
+ *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
+ esac
+ echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
+ exit ;;
+ i*86:*:3.2:*)
+ if test -f /usr/options/cb.name; then
+ UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
+ echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
+ elif /bin/uname -X 2>/dev/null >/dev/null ; then
+ UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
+ (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
+ (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
+ && UNAME_MACHINE=i586
+ (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
+ && UNAME_MACHINE=i686
+ (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
+ && UNAME_MACHINE=i686
+ echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
+ else
+ echo ${UNAME_MACHINE}-pc-sysv32
+ fi
+ exit ;;
+ pc:*:*:*)
+ # Left here for compatibility:
+ # uname -m prints for DJGPP always 'pc', but it prints nothing about
+ # the processor, so we play safe by assuming i386.
+ echo i386-pc-msdosdjgpp
+ exit ;;
+ Intel:Mach:3*:*)
+ echo i386-pc-mach3
+ exit ;;
+ paragon:*:*:*)
+ echo i860-intel-osf1
+ exit ;;
+ i860:*:4.*:*) # i860-SVR4
+ if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
+ echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
+ else # Add other i860-SVR4 vendors below as they are discovered.
+ echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4
+ fi
+ exit ;;
+ mini*:CTIX:SYS*5:*)
+ # "miniframe"
+ echo m68010-convergent-sysv
+ exit ;;
+ mc68k:UNIX:SYSTEM5:3.51m)
+ echo m68k-convergent-sysv
+ exit ;;
+ M680?0:D-NIX:5.3:*)
+ echo m68k-diab-dnix
+ exit ;;
+ M68*:*:R3V[5678]*:*)
+ test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;;
+ 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
+ OS_REL=''
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
+ 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4; exit; } ;;
+ m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
+ echo m68k-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ mc68030:UNIX_System_V:4.*:*)
+ echo m68k-atari-sysv4
+ exit ;;
+ TSUNAMI:LynxOS:2.*:*)
+ echo sparc-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ rs6000:LynxOS:2.*:*)
+ echo rs6000-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*)
+ echo powerpc-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ SM[BE]S:UNIX_SV:*:*)
+ echo mips-dde-sysv${UNAME_RELEASE}
+ exit ;;
+ RM*:ReliantUNIX-*:*:*)
+ echo mips-sni-sysv4
+ exit ;;
+ RM*:SINIX-*:*:*)
+ echo mips-sni-sysv4
+ exit ;;
+ *:SINIX-*:*:*)
+ if uname -p 2>/dev/null >/dev/null ; then
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ echo ${UNAME_MACHINE}-sni-sysv4
+ else
+ echo ns32k-sni-sysv
+ fi
+ exit ;;
+ PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+ # says <Richard.M.Bartel at ccMail.Census.GOV>
+ echo i586-unisys-sysv4
+ exit ;;
+ *:UNIX_System_V:4*:FTX*)
+ # From Gerald Hewes <hewes at openmarket.com>.
+ # How about differentiating between stratus architectures? -djm
+ echo hppa1.1-stratus-sysv4
+ exit ;;
+ *:*:*:FTX*)
+ # From seanf at swdc.stratus.com.
+ echo i860-stratus-sysv4
+ exit ;;
+ i*86:VOS:*:*)
+ # From Paul.Green at stratus.com.
+ echo ${UNAME_MACHINE}-stratus-vos
+ exit ;;
+ *:VOS:*:*)
+ # From Paul.Green at stratus.com.
+ echo hppa1.1-stratus-vos
+ exit ;;
+ mc68*:A/UX:*:*)
+ echo m68k-apple-aux${UNAME_RELEASE}
+ exit ;;
+ news*:NEWS-OS:6*:*)
+ echo mips-sony-newsos6
+ exit ;;
+ R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
+ if [ -d /usr/nec ]; then
+ echo mips-nec-sysv${UNAME_RELEASE}
+ else
+ echo mips-unknown-sysv${UNAME_RELEASE}
+ fi
+ exit ;;
+ BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
+ echo powerpc-be-beos
+ exit ;;
+ BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only.
+ echo powerpc-apple-beos
+ exit ;;
+ BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
+ echo i586-pc-beos
+ exit ;;
+ SX-4:SUPER-UX:*:*)
+ echo sx4-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-5:SUPER-UX:*:*)
+ echo sx5-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-6:SUPER-UX:*:*)
+ echo sx6-nec-superux${UNAME_RELEASE}
+ exit ;;
+ Power*:Rhapsody:*:*)
+ echo powerpc-apple-rhapsody${UNAME_RELEASE}
+ exit ;;
+ *:Rhapsody:*:*)
+ echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
+ exit ;;
+ *:Darwin:*:*)
+ UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
+ case $UNAME_PROCESSOR in
+ *86) UNAME_PROCESSOR=i686 ;;
+ unknown) UNAME_PROCESSOR=powerpc ;;
+ esac
+ echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
+ exit ;;
+ *:procnto*:*:* | *:QNX:[0123456789]*:*)
+ UNAME_PROCESSOR=`uname -p`
+ if test "$UNAME_PROCESSOR" = "x86"; then
+ UNAME_PROCESSOR=i386
+ UNAME_MACHINE=pc
+ fi
+ echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}
+ exit ;;
+ *:QNX:*:4*)
+ echo i386-pc-qnx
+ exit ;;
+ NSE-?:NONSTOP_KERNEL:*:*)
+ echo nse-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ NSR-?:NONSTOP_KERNEL:*:*)
+ echo nsr-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ *:NonStop-UX:*:*)
+ echo mips-compaq-nonstopux
+ exit ;;
+ BS2000:POSIX*:*:*)
+ echo bs2000-siemens-sysv
+ exit ;;
+ DS/*:UNIX_System_V:*:*)
+ echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}
+ exit ;;
+ *:Plan9:*:*)
+ # "uname -m" is not consistent, so use $cputype instead. 386
+ # is converted to i386 for consistency with other x86
+ # operating systems.
+ if test "$cputype" = "386"; then
+ UNAME_MACHINE=i386
+ else
+ UNAME_MACHINE="$cputype"
+ fi
+ echo ${UNAME_MACHINE}-unknown-plan9
+ exit ;;
+ *:TOPS-10:*:*)
+ echo pdp10-unknown-tops10
+ exit ;;
+ *:TENEX:*:*)
+ echo pdp10-unknown-tenex
+ exit ;;
+ KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
+ echo pdp10-dec-tops20
+ exit ;;
+ XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
+ echo pdp10-xkl-tops20
+ exit ;;
+ *:TOPS-20:*:*)
+ echo pdp10-unknown-tops20
+ exit ;;
+ *:ITS:*:*)
+ echo pdp10-unknown-its
+ exit ;;
+ SEI:*:*:SEIUX)
+ echo mips-sei-seiux${UNAME_RELEASE}
+ exit ;;
+ *:DragonFly:*:*)
+ echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+ exit ;;
+ *:*VMS:*:*)
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ case "${UNAME_MACHINE}" in
+ A*) echo alpha-dec-vms ; exit ;;
+ I*) echo ia64-dec-vms ; exit ;;
+ V*) echo vax-dec-vms ; exit ;;
+ esac ;;
+ *:XENIX:*:SysV)
+ echo i386-pc-xenix
+ exit ;;
+ i*86:skyos:*:*)
+ echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
+ exit ;;
+esac
+
+#echo '(No uname command or uname output not recognized.)' 1>&2
+#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
+
+eval $set_cc_for_build
+cat >$dummy.c <<EOF
+#ifdef _SEQUENT_
+# include <sys/types.h>
+# include <sys/utsname.h>
+#endif
+main ()
+{
+#if defined (sony)
+#if defined (MIPSEB)
+ /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed,
+ I don't know.... */
+ printf ("mips-sony-bsd\n"); exit (0);
+#else
+#include <sys/param.h>
+ printf ("m68k-sony-newsos%s\n",
+#ifdef NEWSOS4
+ "4"
+#else
+ ""
+#endif
+ ); exit (0);
+#endif
+#endif
+
+#if defined (__arm) && defined (__acorn) && defined (__unix)
+ printf ("arm-acorn-riscix\n"); exit (0);
+#endif
+
+#if defined (hp300) && !defined (hpux)
+ printf ("m68k-hp-bsd\n"); exit (0);
+#endif
+
+#if defined (NeXT)
+#if !defined (__ARCHITECTURE__)
+#define __ARCHITECTURE__ "m68k"
+#endif
+ int version;
+ version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
+ if (version < 4)
+ printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
+ else
+ printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
+ exit (0);
+#endif
+
+#if defined (MULTIMAX) || defined (n16)
+#if defined (UMAXV)
+ printf ("ns32k-encore-sysv\n"); exit (0);
+#else
+#if defined (CMU)
+ printf ("ns32k-encore-mach\n"); exit (0);
+#else
+ printf ("ns32k-encore-bsd\n"); exit (0);
+#endif
+#endif
+#endif
+
+#if defined (__386BSD__)
+ printf ("i386-pc-bsd\n"); exit (0);
+#endif
+
+#if defined (sequent)
+#if defined (i386)
+ printf ("i386-sequent-dynix\n"); exit (0);
+#endif
+#if defined (ns32000)
+ printf ("ns32k-sequent-dynix\n"); exit (0);
+#endif
+#endif
+
+#if defined (_SEQUENT_)
+ struct utsname un;
+
+ uname(&un);
+
+ if (strncmp(un.version, "V2", 2) == 0) {
+ printf ("i386-sequent-ptx2\n"); exit (0);
+ }
+ if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
+ printf ("i386-sequent-ptx1\n"); exit (0);
+ }
+ printf ("i386-sequent-ptx\n"); exit (0);
+
+#endif
+
+#if defined (vax)
+# if !defined (ultrix)
+# include <sys/param.h>
+# if defined (BSD)
+# if BSD == 43
+ printf ("vax-dec-bsd4.3\n"); exit (0);
+# else
+# if BSD == 199006
+ printf ("vax-dec-bsd4.3reno\n"); exit (0);
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# endif
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# else
+ printf ("vax-dec-ultrix\n"); exit (0);
+# endif
+#endif
+
+#if defined (alliant) && defined (i860)
+ printf ("i860-alliant-bsd\n"); exit (0);
+#endif
+
+ exit (1);
+}
+EOF
+
+$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&
+ { echo "$SYSTEM_NAME"; exit; }
+
+# Apollos put the system type in the environment.
+
+test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }
+
+# Convex versions that predate uname can use getsysinfo(1)
+
+if [ -x /usr/convex/getsysinfo ]
+then
+ case `getsysinfo -f cpu_type` in
+ c1*)
+ echo c1-convex-bsd
+ exit ;;
+ c2*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit ;;
+ c34*)
+ echo c34-convex-bsd
+ exit ;;
+ c38*)
+ echo c38-convex-bsd
+ exit ;;
+ c4*)
+ echo c4-convex-bsd
+ exit ;;
+ esac
+fi
+
+cat >&2 <<EOF
+$0: unable to guess system type
+
+This script, last modified $timestamp, has failed to recognize
+the operating system you are using. It is advised that you
+download the most up to date version of the config scripts from
+
+ http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
+and
+ http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub
+
+If the version you run ($0) is already up to date, please
+send the following data and any information you think might be
+pertinent to <config-patches at gnu.org> in order to provide the needed
+information to handle your system.
+
+config.guess timestamp = $timestamp
+
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null`
+
+hostinfo = `(hostinfo) 2>/dev/null`
+/bin/universe = `(/bin/universe) 2>/dev/null`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null`
+/bin/arch = `(/bin/arch) 2>/dev/null`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
+
+UNAME_MACHINE = ${UNAME_MACHINE}
+UNAME_RELEASE = ${UNAME_RELEASE}
+UNAME_SYSTEM = ${UNAME_SYSTEM}
+UNAME_VERSION = ${UNAME_VERSION}
+EOF
+
+exit 1
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff --git a/config.sub b/config.sub
new file mode 100755
index 0000000..1c366df
--- /dev/null
+++ b/config.sub
@@ -0,0 +1,1579 @@
+#! /bin/sh
+# Configuration validation subroutine script.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004, 2005 Free Software Foundation, Inc.
+
+timestamp='2005-07-08'
+
+# This file is (in principle) common to ALL GNU software.
+# The presence of a machine in this file suggests that SOME GNU software
+# can handle that machine. It does not imply ALL GNU software can.
+#
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
+# 02110-1301, 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.
+
+
+# Please send patches to <config-patches at gnu.org>. Submit a context
+# diff and a properly formatted ChangeLog entry.
+#
+# Configuration subroutine to validate and canonicalize a configuration type.
+# Supply the specified configuration type as an argument.
+# If it is invalid, we print an error message on stderr and exit with code 1.
+# Otherwise, we print the canonical config type on stdout and succeed.
+
+# This file is supposed to be the same for all GNU packages
+# and recognize all the CPU types, system types and aliases
+# that are meaningful with *any* GNU software.
+# Each package is responsible for reporting which valid configurations
+# it does not support. The user should be able to distinguish
+# a failure to support a valid configuration from a meaningless
+# configuration.
+
+# The goal of this file is to map all the various variations of a given
+# machine specification into a single specification in the form:
+# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
+# or in some cases, the newer four-part form:
+# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
+# It is wrong to echo any other type of specification.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION] CPU-MFR-OPSYS
+ $0 [OPTION] ALIAS
+
+Canonicalize a configuration name.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches at gnu.org>."
+
+version="\
+GNU config.sub ($timestamp)
+
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
+Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help"
+ exit 1 ;;
+
+ *local*)
+ # First pass through any local machine types.
+ echo $1
+ exit ;;
+
+ * )
+ break ;;
+ esac
+done
+
+case $# in
+ 0) echo "$me: missing argument$help" >&2
+ exit 1;;
+ 1) ;;
+ *) echo "$me: too many arguments$help" >&2
+ exit 1;;
+esac
+
+# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
+# Here we must recognize all the valid KERNEL-OS combinations.
+maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
+case $maybe_os in
+ nto-qnx* | linux-gnu* | linux-dietlibc | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | \
+ kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | storm-chaos* | os2-emx* | rtmk-nova*)
+ os=-$maybe_os
+ basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
+ ;;
+ *)
+ basic_machine=`echo $1 | sed 's/-[^-]*$//'`
+ if [ $basic_machine != $1 ]
+ then os=`echo $1 | sed 's/.*-/-/'`
+ else os=; fi
+ ;;
+esac
+
+### Let's recognize common machines as not being operating systems so
+### that things like config.sub decstation-3100 work. We also
+### recognize some manufacturers as not being operating systems, so we
+### can provide default operating systems below.
+case $os in
+ -sun*os*)
+ # Prevent following clause from handling this invalid input.
+ ;;
+ -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \
+ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \
+ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \
+ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
+ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
+ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
+ -apple | -axis | -knuth | -cray)
+ os=
+ basic_machine=$1
+ ;;
+ -sim | -cisco | -oki | -wec | -winbond)
+ os=
+ basic_machine=$1
+ ;;
+ -scout)
+ ;;
+ -wrs)
+ os=-vxworks
+ basic_machine=$1
+ ;;
+ -chorusos*)
+ os=-chorusos
+ basic_machine=$1
+ ;;
+ -chorusrdb)
+ os=-chorusrdb
+ basic_machine=$1
+ ;;
+ -hiux*)
+ os=-hiuxwe2
+ ;;
+ -sco5)
+ os=-sco3.2v5
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco4)
+ os=-sco3.2v4
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2.[4-9]*)
+ os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2v[4-9]*)
+ # Don't forget version if it is 3.2v4 or newer.
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco*)
+ os=-sco3.2v2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -udk*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -isc)
+ os=-isc2.2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -clix*)
+ basic_machine=clipper-intergraph
+ ;;
+ -isc*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -lynx*)
+ os=-lynxos
+ ;;
+ -ptx*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
+ ;;
+ -windowsnt*)
+ os=`echo $os | sed -e 's/windowsnt/winnt/'`
+ ;;
+ -psos*)
+ os=-psos
+ ;;
+ -mint | -mint[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+esac
+
+# Decode aliases for certain CPU-COMPANY combinations.
+case $basic_machine in
+ # Recognize the basic CPU types without company name.
+ # Some are omitted here because they have special meanings below.
+ 1750a | 580 \
+ | a29k \
+ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
+ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
+ | am33_2.0 \
+ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr \
+ | bfin \
+ | c4x | clipper \
+ | d10v | d30v | dlx | dsp16xx \
+ | fr30 | frv \
+ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
+ | i370 | i860 | i960 | ia64 \
+ | ip2k | iq2000 \
+ | m32r | m32rle | m68000 | m68k | m88k | maxq | mcore \
+ | mips | mipsbe | mipseb | mipsel | mipsle \
+ | mips16 \
+ | mips64 | mips64el \
+ | mips64vr | mips64vrel \
+ | mips64orion | mips64orionel \
+ | mips64vr4100 | mips64vr4100el \
+ | mips64vr4300 | mips64vr4300el \
+ | mips64vr5000 | mips64vr5000el \
+ | mips64vr5900 | mips64vr5900el \
+ | mipsisa32 | mipsisa32el \
+ | mipsisa32r2 | mipsisa32r2el \
+ | mipsisa64 | mipsisa64el \
+ | mipsisa64r2 | mipsisa64r2el \
+ | mipsisa64sb1 | mipsisa64sb1el \
+ | mipsisa64sr71k | mipsisa64sr71kel \
+ | mipstx39 | mipstx39el \
+ | mn10200 | mn10300 \
+ | ms1 \
+ | msp430 \
+ | ns16k | ns32k \
+ | or32 \
+ | pdp10 | pdp11 | pj | pjl \
+ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
+ | pyramid \
+ | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | shbe | shle | sh[1234]le | sh3ele \
+ | sh64 | sh64le \
+ | sparc | sparc64 | sparc64b | sparc86x | sparclet | sparclite \
+ | sparcv8 | sparcv9 | sparcv9b \
+ | strongarm \
+ | tahoe | thumb | tic4x | tic80 | tron \
+ | v850 | v850e \
+ | we32k \
+ | x86 | xscale | xscalee[bl] | xstormy16 | xtensa \
+ | z8k)
+ basic_machine=$basic_machine-unknown
+ ;;
+ m32c)
+ basic_machine=$basic_machine-unknown
+ ;;
+ m6811 | m68hc11 | m6812 | m68hc12)
+ # Motorola 68HC11/12.
+ basic_machine=$basic_machine-unknown
+ os=-none
+ ;;
+ m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k)
+ ;;
+
+ # We use `pc' rather than `unknown'
+ # because (1) that's what they normally are, and
+ # (2) the word "unknown" tends to confuse beginning users.
+ i*86 | x86_64)
+ basic_machine=$basic_machine-pc
+ ;;
+ # Object if more than one company name word.
+ *-*-*)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+ # Recognize the basic CPU types with company name.
+ 580-* \
+ | a29k-* \
+ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
+ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
+ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
+ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \
+ | avr-* \
+ | bfin-* | bs2000-* \
+ | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \
+ | clipper-* | craynv-* | cydra-* \
+ | d10v-* | d30v-* | dlx-* \
+ | elxsi-* \
+ | f30[01]-* | f700-* | fr30-* | frv-* | fx80-* \
+ | h8300-* | h8500-* \
+ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
+ | i*86-* | i860-* | i960-* | ia64-* \
+ | ip2k-* | iq2000-* \
+ | m32r-* | m32rle-* \
+ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
+ | m88110-* | m88k-* | maxq-* | mcore-* \
+ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
+ | mips16-* \
+ | mips64-* | mips64el-* \
+ | mips64vr-* | mips64vrel-* \
+ | mips64orion-* | mips64orionel-* \
+ | mips64vr4100-* | mips64vr4100el-* \
+ | mips64vr4300-* | mips64vr4300el-* \
+ | mips64vr5000-* | mips64vr5000el-* \
+ | mips64vr5900-* | mips64vr5900el-* \
+ | mipsisa32-* | mipsisa32el-* \
+ | mipsisa32r2-* | mipsisa32r2el-* \
+ | mipsisa64-* | mipsisa64el-* \
+ | mipsisa64r2-* | mipsisa64r2el-* \
+ | mipsisa64sb1-* | mipsisa64sb1el-* \
+ | mipsisa64sr71k-* | mipsisa64sr71kel-* \
+ | mipstx39-* | mipstx39el-* \
+ | mmix-* \
+ | ms1-* \
+ | msp430-* \
+ | none-* | np1-* | ns16k-* | ns32k-* \
+ | orion-* \
+ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
+ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
+ | pyramid-* \
+ | romp-* | rs6000-* \
+ | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | shbe-* \
+ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
+ | sparc-* | sparc64-* | sparc64b-* | sparc86x-* | sparclet-* \
+ | sparclite-* \
+ | sparcv8-* | sparcv9-* | sparcv9b-* | strongarm-* | sv1-* | sx?-* \
+ | tahoe-* | thumb-* \
+ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+ | tron-* \
+ | v850-* | v850e-* | vax-* \
+ | we32k-* \
+ | x86-* | x86_64-* | xps100-* | xscale-* | xscalee[bl]-* \
+ | xstormy16-* | xtensa-* \
+ | ymp-* \
+ | z8k-*)
+ ;;
+ m32c-*)
+ ;;
+ # Recognize the various machine names and aliases which stand
+ # for a CPU type and a company and sometimes even an OS.
+ 386bsd)
+ basic_machine=i386-unknown
+ os=-bsd
+ ;;
+ 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
+ basic_machine=m68000-att
+ ;;
+ 3b*)
+ basic_machine=we32k-att
+ ;;
+ a29khif)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ abacus)
+ basic_machine=abacus-unknown
+ ;;
+ adobe68k)
+ basic_machine=m68010-adobe
+ os=-scout
+ ;;
+ alliant | fx80)
+ basic_machine=fx80-alliant
+ ;;
+ altos | altos3068)
+ basic_machine=m68k-altos
+ ;;
+ am29k)
+ basic_machine=a29k-none
+ os=-bsd
+ ;;
+ amd64)
+ basic_machine=x86_64-pc
+ ;;
+ amd64-*)
+ basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ amdahl)
+ basic_machine=580-amdahl
+ os=-sysv
+ ;;
+ amiga | amiga-*)
+ basic_machine=m68k-unknown
+ ;;
+ amigaos | amigados)
+ basic_machine=m68k-unknown
+ os=-amigaos
+ ;;
+ amigaunix | amix)
+ basic_machine=m68k-unknown
+ os=-sysv4
+ ;;
+ apollo68)
+ basic_machine=m68k-apollo
+ os=-sysv
+ ;;
+ apollo68bsd)
+ basic_machine=m68k-apollo
+ os=-bsd
+ ;;
+ aux)
+ basic_machine=m68k-apple
+ os=-aux
+ ;;
+ balance)
+ basic_machine=ns32k-sequent
+ os=-dynix
+ ;;
+ c90)
+ basic_machine=c90-cray
+ os=-unicos
+ ;;
+ convex-c1)
+ basic_machine=c1-convex
+ os=-bsd
+ ;;
+ convex-c2)
+ basic_machine=c2-convex
+ os=-bsd
+ ;;
+ convex-c32)
+ basic_machine=c32-convex
+ os=-bsd
+ ;;
+ convex-c34)
+ basic_machine=c34-convex
+ os=-bsd
+ ;;
+ convex-c38)
+ basic_machine=c38-convex
+ os=-bsd
+ ;;
+ cray | j90)
+ basic_machine=j90-cray
+ os=-unicos
+ ;;
+ craynv)
+ basic_machine=craynv-cray
+ os=-unicosmp
+ ;;
+ cr16c)
+ basic_machine=cr16c-unknown
+ os=-elf
+ ;;
+ crds | unos)
+ basic_machine=m68k-crds
+ ;;
+ crisv32 | crisv32-* | etraxfs*)
+ basic_machine=crisv32-axis
+ ;;
+ cris | cris-* | etrax*)
+ basic_machine=cris-axis
+ ;;
+ crx)
+ basic_machine=crx-unknown
+ os=-elf
+ ;;
+ da30 | da30-*)
+ basic_machine=m68k-da30
+ ;;
+ decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn)
+ basic_machine=mips-dec
+ ;;
+ decsystem10* | dec10*)
+ basic_machine=pdp10-dec
+ os=-tops10
+ ;;
+ decsystem20* | dec20*)
+ basic_machine=pdp10-dec
+ os=-tops20
+ ;;
+ delta | 3300 | motorola-3300 | motorola-delta \
+ | 3300-motorola | delta-motorola)
+ basic_machine=m68k-motorola
+ ;;
+ delta88)
+ basic_machine=m88k-motorola
+ os=-sysv3
+ ;;
+ djgpp)
+ basic_machine=i586-pc
+ os=-msdosdjgpp
+ ;;
+ dpx20 | dpx20-*)
+ basic_machine=rs6000-bull
+ os=-bosx
+ ;;
+ dpx2* | dpx2*-bull)
+ basic_machine=m68k-bull
+ os=-sysv3
+ ;;
+ ebmon29k)
+ basic_machine=a29k-amd
+ os=-ebmon
+ ;;
+ elxsi)
+ basic_machine=elxsi-elxsi
+ os=-bsd
+ ;;
+ encore | umax | mmax)
+ basic_machine=ns32k-encore
+ ;;
+ es1800 | OSE68k | ose68k | ose | OSE)
+ basic_machine=m68k-ericsson
+ os=-ose
+ ;;
+ fx2800)
+ basic_machine=i860-alliant
+ ;;
+ genix)
+ basic_machine=ns32k-ns
+ ;;
+ gmicro)
+ basic_machine=tron-gmicro
+ os=-sysv
+ ;;
+ go32)
+ basic_machine=i386-pc
+ os=-go32
+ ;;
+ h3050r* | hiux*)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ h8300hms)
+ basic_machine=h8300-hitachi
+ os=-hms
+ ;;
+ h8300xray)
+ basic_machine=h8300-hitachi
+ os=-xray
+ ;;
+ h8500hms)
+ basic_machine=h8500-hitachi
+ os=-hms
+ ;;
+ harris)
+ basic_machine=m88k-harris
+ os=-sysv3
+ ;;
+ hp300-*)
+ basic_machine=m68k-hp
+ ;;
+ hp300bsd)
+ basic_machine=m68k-hp
+ os=-bsd
+ ;;
+ hp300hpux)
+ basic_machine=m68k-hp
+ os=-hpux
+ ;;
+ hp3k9[0-9][0-9] | hp9[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k2[0-9][0-9] | hp9k31[0-9])
+ basic_machine=m68000-hp
+ ;;
+ hp9k3[2-9][0-9])
+ basic_machine=m68k-hp
+ ;;
+ hp9k6[0-9][0-9] | hp6[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k7[0-79][0-9] | hp7[0-79][0-9])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k78[0-9] | hp78[0-9])
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][13679] | hp8[0-9][13679])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][0-9] | hp8[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hppa-next)
+ os=-nextstep3
+ ;;
+ hppaosf)
+ basic_machine=hppa1.1-hp
+ os=-osf
+ ;;
+ hppro)
+ basic_machine=hppa1.1-hp
+ os=-proelf
+ ;;
+ i370-ibm* | ibm*)
+ basic_machine=i370-ibm
+ ;;
+# I'm not sure what "Sysv32" means. Should this be sysv3.2?
+ i*86v32)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv32
+ ;;
+ i*86v4*)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv4
+ ;;
+ i*86v)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv
+ ;;
+ i*86sol2)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-solaris2
+ ;;
+ i386mach)
+ basic_machine=i386-mach
+ os=-mach
+ ;;
+ i386-vsta | vsta)
+ basic_machine=i386-unknown
+ os=-vsta
+ ;;
+ iris | iris4d)
+ basic_machine=mips-sgi
+ case $os in
+ -irix*)
+ ;;
+ *)
+ os=-irix4
+ ;;
+ esac
+ ;;
+ isi68 | isi)
+ basic_machine=m68k-isi
+ os=-sysv
+ ;;
+ m88k-omron*)
+ basic_machine=m88k-omron
+ ;;
+ magnum | m3230)
+ basic_machine=mips-mips
+ os=-sysv
+ ;;
+ merlin)
+ basic_machine=ns32k-utek
+ os=-sysv
+ ;;
+ mingw32)
+ basic_machine=i386-pc
+ os=-mingw32
+ ;;
+ miniframe)
+ basic_machine=m68000-convergent
+ ;;
+ *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+ mips3*-*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
+ ;;
+ mips3*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
+ ;;
+ monitor)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ morphos)
+ basic_machine=powerpc-unknown
+ os=-morphos
+ ;;
+ msdos)
+ basic_machine=i386-pc
+ os=-msdos
+ ;;
+ mvs)
+ basic_machine=i370-ibm
+ os=-mvs
+ ;;
+ ncr3000)
+ basic_machine=i486-ncr
+ os=-sysv4
+ ;;
+ netbsd386)
+ basic_machine=i386-unknown
+ os=-netbsd
+ ;;
+ netwinder)
+ basic_machine=armv4l-rebel
+ os=-linux
+ ;;
+ news | news700 | news800 | news900)
+ basic_machine=m68k-sony
+ os=-newsos
+ ;;
+ news1000)
+ basic_machine=m68030-sony
+ os=-newsos
+ ;;
+ news-3600 | risc-news)
+ basic_machine=mips-sony
+ os=-newsos
+ ;;
+ necv70)
+ basic_machine=v70-nec
+ os=-sysv
+ ;;
+ next | m*-next )
+ basic_machine=m68k-next
+ case $os in
+ -nextstep* )
+ ;;
+ -ns2*)
+ os=-nextstep2
+ ;;
+ *)
+ os=-nextstep3
+ ;;
+ esac
+ ;;
+ nh3000)
+ basic_machine=m68k-harris
+ os=-cxux
+ ;;
+ nh[45]000)
+ basic_machine=m88k-harris
+ os=-cxux
+ ;;
+ nindy960)
+ basic_machine=i960-intel
+ os=-nindy
+ ;;
+ mon960)
+ basic_machine=i960-intel
+ os=-mon960
+ ;;
+ nonstopux)
+ basic_machine=mips-compaq
+ os=-nonstopux
+ ;;
+ np1)
+ basic_machine=np1-gould
+ ;;
+ nsr-tandem)
+ basic_machine=nsr-tandem
+ ;;
+ op50n-* | op60c-*)
+ basic_machine=hppa1.1-oki
+ os=-proelf
+ ;;
+ openrisc | openrisc-*)
+ basic_machine=or32-unknown
+ ;;
+ os400)
+ basic_machine=powerpc-ibm
+ os=-os400
+ ;;
+ OSE68000 | ose68000)
+ basic_machine=m68000-ericsson
+ os=-ose
+ ;;
+ os68k)
+ basic_machine=m68k-none
+ os=-os68k
+ ;;
+ pa-hitachi)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ paragon)
+ basic_machine=i860-intel
+ os=-osf
+ ;;
+ pbd)
+ basic_machine=sparc-tti
+ ;;
+ pbb)
+ basic_machine=m68k-tti
+ ;;
+ pc532 | pc532-*)
+ basic_machine=ns32k-pc532
+ ;;
+ pentium | p5 | k5 | k6 | nexgen | viac3)
+ basic_machine=i586-pc
+ ;;
+ pentiumpro | p6 | 6x86 | athlon | athlon_*)
+ basic_machine=i686-pc
+ ;;
+ pentiumii | pentium2 | pentiumiii | pentium3)
+ basic_machine=i686-pc
+ ;;
+ pentium4)
+ basic_machine=i786-pc
+ ;;
+ pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
+ basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumpro-* | p6-* | 6x86-* | athlon-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentium4-*)
+ basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pn)
+ basic_machine=pn-gould
+ ;;
+ power) basic_machine=power-ibm
+ ;;
+ ppc) basic_machine=powerpc-unknown
+ ;;
+ ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppcle | powerpclittle | ppc-le | powerpc-little)
+ basic_machine=powerpcle-unknown
+ ;;
+ ppcle-* | powerpclittle-*)
+ basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64) basic_machine=powerpc64-unknown
+ ;;
+ ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64le | powerpc64little | ppc64-le | powerpc64-little)
+ basic_machine=powerpc64le-unknown
+ ;;
+ ppc64le-* | powerpc64little-*)
+ basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ps2)
+ basic_machine=i386-ibm
+ ;;
+ pw32)
+ basic_machine=i586-unknown
+ os=-pw32
+ ;;
+ rom68k)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ rm[46]00)
+ basic_machine=mips-siemens
+ ;;
+ rtpc | rtpc-*)
+ basic_machine=romp-ibm
+ ;;
+ s390 | s390-*)
+ basic_machine=s390-ibm
+ ;;
+ s390x | s390x-*)
+ basic_machine=s390x-ibm
+ ;;
+ sa29200)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ sb1)
+ basic_machine=mipsisa64sb1-unknown
+ ;;
+ sb1el)
+ basic_machine=mipsisa64sb1el-unknown
+ ;;
+ sei)
+ basic_machine=mips-sei
+ os=-seiux
+ ;;
+ sequent)
+ basic_machine=i386-sequent
+ ;;
+ sh)
+ basic_machine=sh-hitachi
+ os=-hms
+ ;;
+ sh64)
+ basic_machine=sh64-unknown
+ ;;
+ sparclite-wrs | simso-wrs)
+ basic_machine=sparclite-wrs
+ os=-vxworks
+ ;;
+ sps7)
+ basic_machine=m68k-bull
+ os=-sysv2
+ ;;
+ spur)
+ basic_machine=spur-unknown
+ ;;
+ st2000)
+ basic_machine=m68k-tandem
+ ;;
+ stratus)
+ basic_machine=i860-stratus
+ os=-sysv4
+ ;;
+ sun2)
+ basic_machine=m68000-sun
+ ;;
+ sun2os3)
+ basic_machine=m68000-sun
+ os=-sunos3
+ ;;
+ sun2os4)
+ basic_machine=m68000-sun
+ os=-sunos4
+ ;;
+ sun3os3)
+ basic_machine=m68k-sun
+ os=-sunos3
+ ;;
+ sun3os4)
+ basic_machine=m68k-sun
+ os=-sunos4
+ ;;
+ sun4os3)
+ basic_machine=sparc-sun
+ os=-sunos3
+ ;;
+ sun4os4)
+ basic_machine=sparc-sun
+ os=-sunos4
+ ;;
+ sun4sol2)
+ basic_machine=sparc-sun
+ os=-solaris2
+ ;;
+ sun3 | sun3-*)
+ basic_machine=m68k-sun
+ ;;
+ sun4)
+ basic_machine=sparc-sun
+ ;;
+ sun386 | sun386i | roadrunner)
+ basic_machine=i386-sun
+ ;;
+ sv1)
+ basic_machine=sv1-cray
+ os=-unicos
+ ;;
+ symmetry)
+ basic_machine=i386-sequent
+ os=-dynix
+ ;;
+ t3e)
+ basic_machine=alphaev5-cray
+ os=-unicos
+ ;;
+ t90)
+ basic_machine=t90-cray
+ os=-unicos
+ ;;
+ tic54x | c54x*)
+ basic_machine=tic54x-unknown
+ os=-coff
+ ;;
+ tic55x | c55x*)
+ basic_machine=tic55x-unknown
+ os=-coff
+ ;;
+ tic6x | c6x*)
+ basic_machine=tic6x-unknown
+ os=-coff
+ ;;
+ tx39)
+ basic_machine=mipstx39-unknown
+ ;;
+ tx39el)
+ basic_machine=mipstx39el-unknown
+ ;;
+ toad1)
+ basic_machine=pdp10-xkl
+ os=-tops20
+ ;;
+ tower | tower-32)
+ basic_machine=m68k-ncr
+ ;;
+ tpf)
+ basic_machine=s390x-ibm
+ os=-tpf
+ ;;
+ udi29k)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ ultra3)
+ basic_machine=a29k-nyu
+ os=-sym1
+ ;;
+ v810 | necv810)
+ basic_machine=v810-nec
+ os=-none
+ ;;
+ vaxv)
+ basic_machine=vax-dec
+ os=-sysv
+ ;;
+ vms)
+ basic_machine=vax-dec
+ os=-vms
+ ;;
+ vpp*|vx|vx-*)
+ basic_machine=f301-fujitsu
+ ;;
+ vxworks960)
+ basic_machine=i960-wrs
+ os=-vxworks
+ ;;
+ vxworks68)
+ basic_machine=m68k-wrs
+ os=-vxworks
+ ;;
+ vxworks29k)
+ basic_machine=a29k-wrs
+ os=-vxworks
+ ;;
+ w65*)
+ basic_machine=w65-wdc
+ os=-none
+ ;;
+ w89k-*)
+ basic_machine=hppa1.1-winbond
+ os=-proelf
+ ;;
+ xbox)
+ basic_machine=i686-pc
+ os=-mingw32
+ ;;
+ xps | xps100)
+ basic_machine=xps100-honeywell
+ ;;
+ ymp)
+ basic_machine=ymp-cray
+ os=-unicos
+ ;;
+ z8k-*-coff)
+ basic_machine=z8k-unknown
+ os=-sim
+ ;;
+ none)
+ basic_machine=none-none
+ os=-none
+ ;;
+
+# Here we handle the default manufacturer of certain CPU types. It is in
+# some cases the only manufacturer, in others, it is the most popular.
+ w89k)
+ basic_machine=hppa1.1-winbond
+ ;;
+ op50n)
+ basic_machine=hppa1.1-oki
+ ;;
+ op60c)
+ basic_machine=hppa1.1-oki
+ ;;
+ romp)
+ basic_machine=romp-ibm
+ ;;
+ mmix)
+ basic_machine=mmix-knuth
+ ;;
+ rs6000)
+ basic_machine=rs6000-ibm
+ ;;
+ vax)
+ basic_machine=vax-dec
+ ;;
+ pdp10)
+ # there are many clones, so DEC is not a safe bet
+ basic_machine=pdp10-unknown
+ ;;
+ pdp11)
+ basic_machine=pdp11-dec
+ ;;
+ we32k)
+ basic_machine=we32k-att
+ ;;
+ sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele)
+ basic_machine=sh-unknown
+ ;;
+ sparc | sparcv8 | sparcv9 | sparcv9b)
+ basic_machine=sparc-sun
+ ;;
+ cydra)
+ basic_machine=cydra-cydrome
+ ;;
+ orion)
+ basic_machine=orion-highlevel
+ ;;
+ orion105)
+ basic_machine=clipper-highlevel
+ ;;
+ mac | mpw | mac-mpw)
+ basic_machine=m68k-apple
+ ;;
+ pmac | pmac-mpw)
+ basic_machine=powerpc-apple
+ ;;
+ *-unknown)
+ # Make sure to match an already-canonicalized machine name.
+ ;;
+ *)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+
+# Here we canonicalize certain aliases for manufacturers.
+case $basic_machine in
+ *-digital*)
+ basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
+ ;;
+ *-commodore*)
+ basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
+ ;;
+ *)
+ ;;
+esac
+
+# Decode manufacturer-specific aliases for certain operating systems.
+
+if [ x"$os" != x"" ]
+then
+case $os in
+ # First match some system type aliases
+ # that might get confused with valid system types.
+ # -solaris* is a basic system type, with this one exception.
+ -solaris1 | -solaris1.*)
+ os=`echo $os | sed -e 's|solaris1|sunos4|'`
+ ;;
+ -solaris)
+ os=-solaris2
+ ;;
+ -svr4*)
+ os=-sysv4
+ ;;
+ -unixware*)
+ os=-sysv4.2uw
+ ;;
+ -gnu/linux*)
+ os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
+ ;;
+ # First accept the basic system types.
+ # The portable systems comes first.
+ # 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]*\
+ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \
+ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
+ | -aos* \
+ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
+ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
+ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* | -openbsd* \
+ | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
+ | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
+ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
+ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
+ | -chorusos* | -chorusrdb* \
+ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
+ | -mingw32* | -linux-gnu* | -linux-uclibc* | -uxpv* | -beos* | -mpeix* | -udk* \
+ | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
+ | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
+ | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
+ | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
+ | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
+ | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
+ | -skyos* | -haiku*)
+ # Remember, each alternative MUST END IN *, to match a version number.
+ ;;
+ -qnx*)
+ case $basic_machine in
+ x86-* | i*86-*)
+ ;;
+ *)
+ os=-nto$os
+ ;;
+ esac
+ ;;
+ -nto-qnx*)
+ ;;
+ -nto*)
+ os=`echo $os | sed -e 's|nto|nto-qnx|'`
+ ;;
+ -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \
+ | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \
+ | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*)
+ ;;
+ -mac*)
+ os=`echo $os | sed -e 's|mac|macos|'`
+ ;;
+ -linux-dietlibc)
+ os=-linux-dietlibc
+ ;;
+ -linux*)
+ os=`echo $os | sed -e 's|linux|linux-gnu|'`
+ ;;
+ -sunos5*)
+ os=`echo $os | sed -e 's|sunos5|solaris2|'`
+ ;;
+ -sunos6*)
+ os=`echo $os | sed -e 's|sunos6|solaris3|'`
+ ;;
+ -opened*)
+ os=-openedition
+ ;;
+ -os400*)
+ os=-os400
+ ;;
+ -wince*)
+ os=-wince
+ ;;
+ -osfrose*)
+ os=-osfrose
+ ;;
+ -osf*)
+ os=-osf
+ ;;
+ -utek*)
+ os=-bsd
+ ;;
+ -dynix*)
+ os=-bsd
+ ;;
+ -acis*)
+ os=-aos
+ ;;
+ -atheos*)
+ os=-atheos
+ ;;
+ -syllable*)
+ os=-syllable
+ ;;
+ -386bsd)
+ os=-bsd
+ ;;
+ -ctix* | -uts*)
+ os=-sysv
+ ;;
+ -nova*)
+ os=-rtmk-nova
+ ;;
+ -ns2 )
+ os=-nextstep2
+ ;;
+ -nsk*)
+ os=-nsk
+ ;;
+ # Preserve the version number of sinix5.
+ -sinix5.*)
+ os=`echo $os | sed -e 's|sinix|sysv|'`
+ ;;
+ -sinix*)
+ os=-sysv4
+ ;;
+ -tpf*)
+ os=-tpf
+ ;;
+ -triton*)
+ os=-sysv3
+ ;;
+ -oss*)
+ os=-sysv3
+ ;;
+ -svr4)
+ os=-sysv4
+ ;;
+ -svr3)
+ os=-sysv3
+ ;;
+ -sysvr4)
+ os=-sysv4
+ ;;
+ # This must come after -sysvr4.
+ -sysv*)
+ ;;
+ -ose*)
+ os=-ose
+ ;;
+ -es1800*)
+ os=-ose
+ ;;
+ -xenix)
+ os=-xenix
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ os=-mint
+ ;;
+ -aros*)
+ os=-aros
+ ;;
+ -kaos*)
+ os=-kaos
+ ;;
+ -zvmoe)
+ os=-zvmoe
+ ;;
+ -none)
+ ;;
+ *)
+ # Get rid of the `-' at the beginning of $os.
+ os=`echo $os | sed 's/[^-]*-//'`
+ echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+else
+
+# Here we handle the default operating systems that come with various machines.
+# The value should be what the vendor currently ships out the door with their
+# machine or put another way, the most popular os provided with the machine.
+
+# Note that if you're going to try to match "-MANUFACTURER" here (say,
+# "-sun"), then you have to tell the case statement up towards the top
+# that MANUFACTURER isn't an operating system. Otherwise, code above
+# will signal an error saying that MANUFACTURER isn't an operating
+# system, and we'll never get to this point.
+
+case $basic_machine in
+ *-acorn)
+ os=-riscix1.2
+ ;;
+ arm*-rebel)
+ os=-linux
+ ;;
+ arm*-semi)
+ os=-aout
+ ;;
+ c4x-* | tic4x-*)
+ os=-coff
+ ;;
+ # This must come before the *-dec entry.
+ pdp10-*)
+ os=-tops20
+ ;;
+ pdp11-*)
+ os=-none
+ ;;
+ *-dec | vax-*)
+ os=-ultrix4.2
+ ;;
+ m68*-apollo)
+ os=-domain
+ ;;
+ i386-sun)
+ os=-sunos4.0.2
+ ;;
+ m68000-sun)
+ os=-sunos3
+ # This also exists in the configure program, but was not the
+ # default.
+ # os=-sunos4
+ ;;
+ m68*-cisco)
+ os=-aout
+ ;;
+ mips*-cisco)
+ os=-elf
+ ;;
+ mips*-*)
+ os=-elf
+ ;;
+ or32-*)
+ os=-coff
+ ;;
+ *-tti) # must be before sparc entry or we get the wrong os.
+ os=-sysv3
+ ;;
+ sparc-* | *-sun)
+ os=-sunos4.1.1
+ ;;
+ *-be)
+ os=-beos
+ ;;
+ *-haiku)
+ os=-haiku
+ ;;
+ *-ibm)
+ os=-aix
+ ;;
+ *-knuth)
+ os=-mmixware
+ ;;
+ *-wec)
+ os=-proelf
+ ;;
+ *-winbond)
+ os=-proelf
+ ;;
+ *-oki)
+ os=-proelf
+ ;;
+ *-hp)
+ os=-hpux
+ ;;
+ *-hitachi)
+ os=-hiux
+ ;;
+ i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
+ os=-sysv
+ ;;
+ *-cbm)
+ os=-amigaos
+ ;;
+ *-dg)
+ os=-dgux
+ ;;
+ *-dolphin)
+ os=-sysv3
+ ;;
+ m68k-ccur)
+ os=-rtu
+ ;;
+ m88k-omron*)
+ os=-luna
+ ;;
+ *-next )
+ os=-nextstep
+ ;;
+ *-sequent)
+ os=-ptx
+ ;;
+ *-crds)
+ os=-unos
+ ;;
+ *-ns)
+ os=-genix
+ ;;
+ i370-*)
+ os=-mvs
+ ;;
+ *-next)
+ os=-nextstep3
+ ;;
+ *-gould)
+ os=-sysv
+ ;;
+ *-highlevel)
+ os=-bsd
+ ;;
+ *-encore)
+ os=-bsd
+ ;;
+ *-sgi)
+ os=-irix
+ ;;
+ *-siemens)
+ os=-sysv4
+ ;;
+ *-masscomp)
+ os=-rtu
+ ;;
+ f30[01]-fujitsu | f700-fujitsu)
+ os=-uxpv
+ ;;
+ *-rom68k)
+ os=-coff
+ ;;
+ *-*bug)
+ os=-coff
+ ;;
+ *-apple)
+ os=-macos
+ ;;
+ *-atari*)
+ os=-mint
+ ;;
+ *)
+ os=-none
+ ;;
+esac
+fi
+
+# Here we handle the case where we know the os, and the CPU type, but not the
+# manufacturer. We pick the logical manufacturer.
+vendor=unknown
+case $basic_machine in
+ *-unknown)
+ case $os in
+ -riscix*)
+ vendor=acorn
+ ;;
+ -sunos*)
+ vendor=sun
+ ;;
+ -aix*)
+ vendor=ibm
+ ;;
+ -beos*)
+ vendor=be
+ ;;
+ -hpux*)
+ vendor=hp
+ ;;
+ -mpeix*)
+ vendor=hp
+ ;;
+ -hiux*)
+ vendor=hitachi
+ ;;
+ -unos*)
+ vendor=crds
+ ;;
+ -dgux*)
+ vendor=dg
+ ;;
+ -luna*)
+ vendor=omron
+ ;;
+ -genix*)
+ vendor=ns
+ ;;
+ -mvs* | -opened*)
+ vendor=ibm
+ ;;
+ -os400*)
+ vendor=ibm
+ ;;
+ -ptx*)
+ vendor=sequent
+ ;;
+ -tpf*)
+ vendor=ibm
+ ;;
+ -vxsim* | -vxworks* | -windiss*)
+ vendor=wrs
+ ;;
+ -aux*)
+ vendor=apple
+ ;;
+ -hms*)
+ vendor=hitachi
+ ;;
+ -mpw* | -macos*)
+ vendor=apple
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ vendor=atari
+ ;;
+ -vos*)
+ vendor=stratus
+ ;;
+ esac
+ basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
+ ;;
+esac
+
+echo $basic_machine$os
+exit
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
diff --git a/configure b/configure
new file mode 100755
index 0000000..d90ccec
--- /dev/null
+++ b/configure
@@ -0,0 +1,5792 @@
+#! /bin/sh
+# Guess values for system-dependent variables and create Makefiles.
+# Generated by GNU Autoconf 2.59 for toppred 1.10.
+#
+# Copyright (C) 2003 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. ##
+## --------------------- ##
+
+# Be Bourne compatible
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then
+ set -o posix
+fi
+DUALCASE=1; export DUALCASE # for MKS sh
+
+# Support unset when possible.
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ as_unset=unset
+else
+ as_unset=false
+fi
+
+
+# Work around bugs in pre-3.0 UWIN ksh.
+$as_unset ENV MAIL MAILPATH
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+for as_var in \
+ LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \
+ LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \
+ LC_TELEPHONE LC_TIME
+do
+ if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then
+ eval $as_var=C; export $as_var
+ else
+ $as_unset $as_var
+ fi
+done
+
+# Required to use basename.
+if expr a : '\(a\)' >/dev/null 2>&1; 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 ||
+echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; }
+ /^X\/\(\/\/\)$/{ s//\1/; q; }
+ /^X\/\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+
+
+# PATH needs CR, and LINENO needs CR and PATH.
+# 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
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ echo "#! /bin/sh" >conf$$.sh
+ echo "exit 0" >>conf$$.sh
+ chmod +x conf$$.sh
+ if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
+ PATH_SEPARATOR=';'
+ else
+ PATH_SEPARATOR=:
+ fi
+ rm -f conf$$.sh
+fi
+
+
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null`
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x$as_lineno_3" = "x$as_lineno_2" || {
+ # Find who we are. Look in the path if we contain no path at all
+ # relative or not.
+ 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/$0 && break
+done
+
+ ;;
+ esac
+ # We did not find ourselves, most probably we were run as `sh COMMAND'
+ # in which case we are not to be found in the path.
+ if test "x$as_myself" = x; then
+ as_myself=$0
+ fi
+ if test ! -f "$as_myself"; then
+ { echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2
+ { (exit 1); exit 1; }; }
+ fi
+ case $CONFIG_SHELL in
+ '')
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for as_base in sh bash ksh sh5; do
+ case $as_dir in
+ /*)
+ if ("$as_dir/$as_base" -c '
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null`
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then
+ $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; }
+ $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; }
+ CONFIG_SHELL=$as_dir/$as_base
+ export CONFIG_SHELL
+ exec "$CONFIG_SHELL" "$0" ${1+"$@"}
+ fi;;
+ esac
+ done
+done
+;;
+ esac
+
+ # 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 before each line; the second 'sed' does the real
+ # work. The second script uses 'N' to pair each line-number line
+ # with the numbered line, and appends trailing '-' during
+ # substitution so that $LINENO is not a special case at line end.
+ # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
+ # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-)
+ sed '=' <$as_myself |
+ sed '
+ N
+ s,$,-,
+ : loop
+ s,^\(['$as_cr_digits']*\)\(.*\)[$]LINENO\([^'$as_cr_alnum'_]\),\1\2\1\3,
+ t loop
+ s,-$,,
+ s,^['$as_cr_digits']*\n,,
+ ' >$as_me.lineno &&
+ chmod +x $as_me.lineno ||
+ { echo "$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 $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensible to this).
+ . ./$as_me.lineno
+ # Exit status is that of the last command.
+ exit
+}
+
+
+case `echo "testing\c"; echo 1,2,3`,`echo -n testing; echo 1,2,3` in
+ *c*,-n*) ECHO_N= ECHO_C='
+' ECHO_T=' ' ;;
+ *c*,* ) ECHO_N=-n ECHO_C= ECHO_T= ;;
+ *) ECHO_N= ECHO_C='\c' ECHO_T= ;;
+esac
+
+if expr a : '\(a\)' >/dev/null 2>&1; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+rm -f conf$$ conf$$.exe conf$$.file
+echo >conf$$.file
+if ln -s conf$$.file conf$$ 2>/dev/null; then
+ # We could just check for DJGPP; but this test a) works b) is more generic
+ # and c) will remain valid once DJGPP supports symlinks (DJGPP 2.04).
+ if test -f conf$$.exe; then
+ # Don't use ln at all; we don't have any links
+ as_ln_s='cp -p'
+ else
+ as_ln_s='ln -s'
+ fi
+elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.file
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p=:
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+as_executable_p="test -f"
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+# IFS
+# We need space, tab and new line, in precisely that order.
+as_nl='
+'
+IFS=" $as_nl"
+
+# CDPATH.
+$as_unset CDPATH
+
+
+# Name of the host.
+# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
+# so uname gets run too.
+ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
+
+exec 6>&1
+
+#
+# Initializations.
+#
+ac_default_prefix=/usr/local
+ac_config_libobj_dir=.
+cross_compiling=no
+subdirs=
+MFLAGS=
+MAKEFLAGS=
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+# Maximum number of lines to put in a shell here document.
+# This variable seems obsolete. It should probably be removed, and
+# only ac_max_sed_lines should be used.
+: ${ac_max_here_lines=38}
+
+# Identity of this package.
+PACKAGE_NAME='toppred'
+PACKAGE_TARNAME='toppred'
+PACKAGE_VERSION='1.10'
+PACKAGE_STRING='toppred 1.10'
+PACKAGE_BUGREPORT=''
+
+# Factoring default headers for most tests.
+ac_includes_default="\
+#include <stdio.h>
+#if HAVE_SYS_TYPES_H
+# include <sys/types.h>
+#endif
+#if HAVE_SYS_STAT_H
+# include <sys/stat.h>
+#endif
+#if STDC_HEADERS
+# include <stdlib.h>
+# include <stddef.h>
+#else
+# if HAVE_STDLIB_H
+# include <stdlib.h>
+# endif
+#endif
+#if HAVE_STRING_H
+# if !STDC_HEADERS && HAVE_MEMORY_H
+# include <memory.h>
+# endif
+# include <string.h>
+#endif
+#if HAVE_STRINGS_H
+# include <strings.h>
+#endif
+#if HAVE_INTTYPES_H
+# include <inttypes.h>
+#else
+# if HAVE_STDINT_H
+# include <stdint.h>
+# endif
+#endif
+#if HAVE_UNISTD_H
+# include <unistd.h>
+#endif"
+
+ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INS [...]
+ac_subst_files=''
+
+# Initialize some variables set by options.
+ac_init_help=
+ac_init_version=false
+# The variables have the same names as the options, with
+# dashes changed to underlines.
+cache_file=/dev/null
+exec_prefix=NONE
+no_create=
+no_recursion=
+prefix=NONE
+program_prefix=NONE
+program_suffix=NONE
+program_transform_name=s,x,x,
+silent=
+site=
+srcdir=
+verbose=
+x_includes=NONE
+x_libraries=NONE
+
+# Installation directory options.
+# These are left unexpanded so users can "make install exec_prefix=/foo"
+# and all the variables that are supposed to be based on exec_prefix
+# by default will actually change.
+# Use braces instead of parens because sh, perl, etc. also accept them.
+bindir='${exec_prefix}/bin'
+sbindir='${exec_prefix}/sbin'
+libexecdir='${exec_prefix}/libexec'
+datadir='${prefix}/share'
+sysconfdir='${prefix}/etc'
+sharedstatedir='${prefix}/com'
+localstatedir='${prefix}/var'
+libdir='${exec_prefix}/lib'
+includedir='${prefix}/include'
+oldincludedir='/usr/include'
+infodir='${prefix}/info'
+mandir='${prefix}/man'
+
+ac_prev=
+for ac_option
+do
+ # If the previous option needs an argument, assign it.
+ if test -n "$ac_prev"; then
+ eval "$ac_prev=\$ac_option"
+ ac_prev=
+ continue
+ fi
+
+ ac_optarg=`expr "x$ac_option" : 'x[^=]*=\(.*\)'`
+
+ # Accept the important Cygnus configure options, so we can diagnose typos.
+
+ case $ac_option in
+
+ -bindir | --bindir | --bindi | --bind | --bin | --bi)
+ ac_prev=bindir ;;
+ -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
+ bindir=$ac_optarg ;;
+
+ -build | --build | --buil | --bui | --bu)
+ ac_prev=build_alias ;;
+ -build=* | --build=* | --buil=* | --bui=* | --bu=*)
+ build_alias=$ac_optarg ;;
+
+ -cache-file | --cache-file | --cache-fil | --cache-fi \
+ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
+ cache_file=$ac_optarg ;;
+
+ --config-cache | -C)
+ cache_file=config.cache ;;
+
+ -datadir | --datadir | --datadi | --datad | --data | --dat | --da)
+ ac_prev=datadir ;;
+ -datadir=* | --datadir=* | --datadi=* | --datad=* | --data=* | --dat=* \
+ | --da=*)
+ datadir=$ac_optarg ;;
+
+ -disable-* | --disable-*)
+ ac_feature=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_feature" : ".*[^-_$as_cr_alnum]" >/dev/null &&
+ { echo "$as_me: error: invalid feature name: $ac_feature" >&2
+ { (exit 1); exit 1; }; }
+ ac_feature=`echo $ac_feature | sed 's/-/_/g'`
+ eval "enable_$ac_feature=no" ;;
+
+ -enable-* | --enable-*)
+ ac_feature=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_feature" : ".*[^-_$as_cr_alnum]" >/dev/null &&
+ { echo "$as_me: error: invalid feature name: $ac_feature" >&2
+ { (exit 1); exit 1; }; }
+ ac_feature=`echo $ac_feature | sed 's/-/_/g'`
+ case $ac_option in
+ *=*) ac_optarg=`echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"`;;
+ *) ac_optarg=yes ;;
+ esac
+ eval "enable_$ac_feature='$ac_optarg'" ;;
+
+ -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
+ | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
+ | --exec | --exe | --ex)
+ ac_prev=exec_prefix ;;
+ -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \
+ | --exec-pref=* | --exec-pre=* | --exec-pr=* | --exec-p=* | --exec-=* \
+ | --exec=* | --exe=* | --ex=*)
+ exec_prefix=$ac_optarg ;;
+
+ -gas | --gas | --ga | --g)
+ # Obsolete; use --with-gas.
+ with_gas=yes ;;
+
+ -help | --help | --hel | --he | -h)
+ ac_init_help=long ;;
+ -help=r* | --help=r* | --hel=r* | --he=r* | -hr*)
+ ac_init_help=recursive ;;
+ -help=s* | --help=s* | --hel=s* | --he=s* | -hs*)
+ ac_init_help=short ;;
+
+ -host | --host | --hos | --ho)
+ ac_prev=host_alias ;;
+ -host=* | --host=* | --hos=* | --ho=*)
+ host_alias=$ac_optarg ;;
+
+ -includedir | --includedir | --includedi | --included | --include \
+ | --includ | --inclu | --incl | --inc)
+ ac_prev=includedir ;;
+ -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \
+ | --includ=* | --inclu=* | --incl=* | --inc=*)
+ includedir=$ac_optarg ;;
+
+ -infodir | --infodir | --infodi | --infod | --info | --inf)
+ ac_prev=infodir ;;
+ -infodir=* | --infodir=* | --infodi=* | --infod=* | --info=* | --inf=*)
+ infodir=$ac_optarg ;;
+
+ -libdir | --libdir | --libdi | --libd)
+ ac_prev=libdir ;;
+ -libdir=* | --libdir=* | --libdi=* | --libd=*)
+ libdir=$ac_optarg ;;
+
+ -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \
+ | --libexe | --libex | --libe)
+ ac_prev=libexecdir ;;
+ -libexecdir=* | --libexecdir=* | --libexecdi=* | --libexecd=* | --libexec=* \
+ | --libexe=* | --libex=* | --libe=*)
+ libexecdir=$ac_optarg ;;
+
+ -localstatedir | --localstatedir | --localstatedi | --localstated \
+ | --localstate | --localstat | --localsta | --localst \
+ | --locals | --local | --loca | --loc | --lo)
+ ac_prev=localstatedir ;;
+ -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \
+ | --localstate=* | --localstat=* | --localsta=* | --localst=* \
+ | --locals=* | --local=* | --loca=* | --loc=* | --lo=*)
+ localstatedir=$ac_optarg ;;
+
+ -mandir | --mandir | --mandi | --mand | --man | --ma | --m)
+ ac_prev=mandir ;;
+ -mandir=* | --mandir=* | --mandi=* | --mand=* | --man=* | --ma=* | --m=*)
+ mandir=$ac_optarg ;;
+
+ -nfp | --nfp | --nf)
+ # Obsolete; use --without-fp.
+ with_fp=no ;;
+
+ -no-create | --no-create | --no-creat | --no-crea | --no-cre \
+ | --no-cr | --no-c | -n)
+ no_create=yes ;;
+
+ -no-recursion | --no-recursion | --no-recursio | --no-recursi \
+ | --no-recurs | --no-recur | --no-recu | --no-rec | --no-re | --no-r)
+ no_recursion=yes ;;
+
+ -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \
+ | --oldinclude | --oldinclud | --oldinclu | --oldincl | --oldinc \
+ | --oldin | --oldi | --old | --ol | --o)
+ ac_prev=oldincludedir ;;
+ -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \
+ | --oldinclude=* | --oldinclud=* | --oldinclu=* | --oldincl=* | --oldinc=* \
+ | --oldin=* | --oldi=* | --old=* | --ol=* | --o=*)
+ oldincludedir=$ac_optarg ;;
+
+ -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
+ ac_prev=prefix ;;
+ -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
+ prefix=$ac_optarg ;;
+
+ -program-prefix | --program-prefix | --program-prefi | --program-pref \
+ | --program-pre | --program-pr | --program-p)
+ ac_prev=program_prefix ;;
+ -program-prefix=* | --program-prefix=* | --program-prefi=* \
+ | --program-pref=* | --program-pre=* | --program-pr=* | --program-p=*)
+ program_prefix=$ac_optarg ;;
+
+ -program-suffix | --program-suffix | --program-suffi | --program-suff \
+ | --program-suf | --program-su | --program-s)
+ ac_prev=program_suffix ;;
+ -program-suffix=* | --program-suffix=* | --program-suffi=* \
+ | --program-suff=* | --program-suf=* | --program-su=* | --program-s=*)
+ program_suffix=$ac_optarg ;;
+
+ -program-transform-name | --program-transform-name \
+ | --program-transform-nam | --program-transform-na \
+ | --program-transform-n | --program-transform- \
+ | --program-transform | --program-transfor \
+ | --program-transfo | --program-transf \
+ | --program-trans | --program-tran \
+ | --progr-tra | --program-tr | --program-t)
+ ac_prev=program_transform_name ;;
+ -program-transform-name=* | --program-transform-name=* \
+ | --program-transform-nam=* | --program-transform-na=* \
+ | --program-transform-n=* | --program-transform-=* \
+ | --program-transform=* | --program-transfor=* \
+ | --program-transfo=* | --program-transf=* \
+ | --program-trans=* | --program-tran=* \
+ | --progr-tra=* | --program-tr=* | --program-t=*)
+ program_transform_name=$ac_optarg ;;
+
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ silent=yes ;;
+
+ -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
+ ac_prev=sbindir ;;
+ -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
+ | --sbi=* | --sb=*)
+ sbindir=$ac_optarg ;;
+
+ -sharedstatedir | --sharedstatedir | --sharedstatedi \
+ | --sharedstated | --sharedstate | --sharedstat | --sharedsta \
+ | --sharedst | --shareds | --shared | --share | --shar \
+ | --sha | --sh)
+ ac_prev=sharedstatedir ;;
+ -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \
+ | --sharedstated=* | --sharedstate=* | --sharedstat=* | --sharedsta=* \
+ | --sharedst=* | --shareds=* | --shared=* | --share=* | --shar=* \
+ | --sha=* | --sh=*)
+ sharedstatedir=$ac_optarg ;;
+
+ -site | --site | --sit)
+ ac_prev=site ;;
+ -site=* | --site=* | --sit=*)
+ site=$ac_optarg ;;
+
+ -srcdir | --srcdir | --srcdi | --srcd | --src | --sr)
+ ac_prev=srcdir ;;
+ -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*)
+ srcdir=$ac_optarg ;;
+
+ -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \
+ | --syscon | --sysco | --sysc | --sys | --sy)
+ ac_prev=sysconfdir ;;
+ -sysconfdir=* | --sysconfdir=* | --sysconfdi=* | --sysconfd=* | --sysconf=* \
+ | --syscon=* | --sysco=* | --sysc=* | --sys=* | --sy=*)
+ sysconfdir=$ac_optarg ;;
+
+ -target | --target | --targe | --targ | --tar | --ta | --t)
+ ac_prev=target_alias ;;
+ -target=* | --target=* | --targe=* | --targ=* | --tar=* | --ta=* | --t=*)
+ target_alias=$ac_optarg ;;
+
+ -v | -verbose | --verbose | --verbos | --verbo | --verb)
+ verbose=yes ;;
+
+ -version | --version | --versio | --versi | --vers | -V)
+ ac_init_version=: ;;
+
+ -with-* | --with-*)
+ ac_package=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_package" : ".*[^-_$as_cr_alnum]" >/dev/null &&
+ { echo "$as_me: error: invalid package name: $ac_package" >&2
+ { (exit 1); exit 1; }; }
+ ac_package=`echo $ac_package| sed 's/-/_/g'`
+ case $ac_option in
+ *=*) ac_optarg=`echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"`;;
+ *) ac_optarg=yes ;;
+ esac
+ eval "with_$ac_package='$ac_optarg'" ;;
+
+ -without-* | --without-*)
+ ac_package=`expr "x$ac_option" : 'x-*without-\(.*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_package" : ".*[^-_$as_cr_alnum]" >/dev/null &&
+ { echo "$as_me: error: invalid package name: $ac_package" >&2
+ { (exit 1); exit 1; }; }
+ ac_package=`echo $ac_package | sed 's/-/_/g'`
+ eval "with_$ac_package=no" ;;
+
+ --x)
+ # Obsolete; use --with-x.
+ with_x=yes ;;
+
+ -x-includes | --x-includes | --x-include | --x-includ | --x-inclu \
+ | --x-incl | --x-inc | --x-in | --x-i)
+ ac_prev=x_includes ;;
+ -x-includes=* | --x-includes=* | --x-include=* | --x-includ=* | --x-inclu=* \
+ | --x-incl=* | --x-inc=* | --x-in=* | --x-i=*)
+ x_includes=$ac_optarg ;;
+
+ -x-libraries | --x-libraries | --x-librarie | --x-librari \
+ | --x-librar | --x-libra | --x-libr | --x-lib | --x-li | --x-l)
+ ac_prev=x_libraries ;;
+ -x-libraries=* | --x-libraries=* | --x-librarie=* | --x-librari=* \
+ | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
+ x_libraries=$ac_optarg ;;
+
+ -*) { echo "$as_me: error: unrecognized option: $ac_option
+Try \`$0 --help' for more information." >&2
+ { (exit 1); exit 1; }; }
+ ;;
+
+ *=*)
+ ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null &&
+ { echo "$as_me: error: invalid variable name: $ac_envvar" >&2
+ { (exit 1); exit 1; }; }
+ ac_optarg=`echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"`
+ eval "$ac_envvar='$ac_optarg'"
+ export $ac_envvar ;;
+
+ *)
+ # FIXME: should be removed in autoconf 3.0.
+ echo "$as_me: WARNING: you should use --build, --host, --target" >&2
+ expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null &&
+ echo "$as_me: WARNING: invalid host type: $ac_option" >&2
+ : ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}
+ ;;
+
+ esac
+done
+
+if test -n "$ac_prev"; then
+ ac_option=--`echo $ac_prev | sed 's/_/-/g'`
+ { echo "$as_me: error: missing argument to $ac_option" >&2
+ { (exit 1); exit 1; }; }
+fi
+
+# Be sure to have absolute paths.
+for ac_var in exec_prefix prefix
+do
+ eval ac_val=$`echo $ac_var`
+ case $ac_val in
+ [\\/$]* | ?:[\\/]* | NONE | '' ) ;;
+ *) { echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2
+ { (exit 1); exit 1; }; };;
+ esac
+done
+
+# Be sure to have absolute paths.
+for ac_var in bindir sbindir libexecdir datadir sysconfdir sharedstatedir \
+ localstatedir libdir includedir oldincludedir infodir mandir
+do
+ eval ac_val=$`echo $ac_var`
+ case $ac_val in
+ [\\/$]* | ?:[\\/]* ) ;;
+ *) { echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2
+ { (exit 1); exit 1; }; };;
+ esac
+done
+
+# There might be people who depend on the old broken behavior: `$host'
+# used to hold the argument of --host etc.
+# FIXME: To remove some day.
+build=$build_alias
+host=$host_alias
+target=$target_alias
+
+# FIXME: To remove some day.
+if test "x$host_alias" != x; then
+ if test "x$build_alias" = x; then
+ cross_compiling=maybe
+ echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host.
+ If a cross compiler is detected then cross compile mode will be used." >&2
+ elif test "x$build_alias" != "x$host_alias"; then
+ cross_compiling=yes
+ fi
+fi
+
+ac_tool_prefix=
+test -n "$host_alias" && ac_tool_prefix=$host_alias-
+
+test "$silent" = yes && exec 6>/dev/null
+
+
+# Find the source files, if location was not specified.
+if test -z "$srcdir"; then
+ ac_srcdir_defaulted=yes
+ # Try the directory containing this script, then its parent.
+ ac_confdir=`(dirname "$0") 2>/dev/null ||
+$as_expr X"$0" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$0" : 'X\(//\)[^/]' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$0" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ srcdir=$ac_confdir
+ if test ! -r $srcdir/$ac_unique_file; then
+ srcdir=..
+ fi
+else
+ ac_srcdir_defaulted=no
+fi
+if test ! -r $srcdir/$ac_unique_file; then
+ if test "$ac_srcdir_defaulted" = yes; then
+ { echo "$as_me: error: cannot find sources ($ac_unique_file) in $ac_confdir or .." >&2
+ { (exit 1); exit 1; }; }
+ else
+ { echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2
+ { (exit 1); exit 1; }; }
+ fi
+fi
+(cd $srcdir && test -r ./$ac_unique_file) 2>/dev/null ||
+ { echo "$as_me: error: sources are in $srcdir, but \`cd $srcdir' does not work" >&2
+ { (exit 1); exit 1; }; }
+srcdir=`echo "$srcdir" | sed 's%\([^\\/]\)[\\/]*$%\1%'`
+ac_env_build_alias_set=${build_alias+set}
+ac_env_build_alias_value=$build_alias
+ac_cv_env_build_alias_set=${build_alias+set}
+ac_cv_env_build_alias_value=$build_alias
+ac_env_host_alias_set=${host_alias+set}
+ac_env_host_alias_value=$host_alias
+ac_cv_env_host_alias_set=${host_alias+set}
+ac_cv_env_host_alias_value=$host_alias
+ac_env_target_alias_set=${target_alias+set}
+ac_env_target_alias_value=$target_alias
+ac_cv_env_target_alias_set=${target_alias+set}
+ac_cv_env_target_alias_value=$target_alias
+ac_env_CC_set=${CC+set}
+ac_env_CC_value=$CC
+ac_cv_env_CC_set=${CC+set}
+ac_cv_env_CC_value=$CC
+ac_env_CFLAGS_set=${CFLAGS+set}
+ac_env_CFLAGS_value=$CFLAGS
+ac_cv_env_CFLAGS_set=${CFLAGS+set}
+ac_cv_env_CFLAGS_value=$CFLAGS
+ac_env_LDFLAGS_set=${LDFLAGS+set}
+ac_env_LDFLAGS_value=$LDFLAGS
+ac_cv_env_LDFLAGS_set=${LDFLAGS+set}
+ac_cv_env_LDFLAGS_value=$LDFLAGS
+ac_env_CPPFLAGS_set=${CPPFLAGS+set}
+ac_env_CPPFLAGS_value=$CPPFLAGS
+ac_cv_env_CPPFLAGS_set=${CPPFLAGS+set}
+ac_cv_env_CPPFLAGS_value=$CPPFLAGS
+ac_env_CPP_set=${CPP+set}
+ac_env_CPP_value=$CPP
+ac_cv_env_CPP_set=${CPP+set}
+ac_cv_env_CPP_value=$CPP
+
+#
+# Report the --help message.
+#
+if test "$ac_init_help" = "long"; then
+ # Omit some internal or obsolete options to make the list less imposing.
+ # This message is too long to be a string in the A/UX 3.1 sh.
+ cat <<_ACEOF
+\`configure' configures toppred 1.10 to adapt to many kinds of systems.
+
+Usage: $0 [OPTION]... [VAR=VALUE]...
+
+To assign environment variables (e.g., CC, CFLAGS...), specify them as
+VAR=VALUE. See below for descriptions of some of the useful variables.
+
+Defaults for the options are specified in brackets.
+
+Configuration:
+ -h, --help display this help and exit
+ --help=short display options specific to this package
+ --help=recursive display the short help of all the included packages
+ -V, --version display version information and exit
+ -q, --quiet, --silent do not print \`checking...' messages
+ --cache-file=FILE cache test results in FILE [disabled]
+ -C, --config-cache alias for \`--cache-file=config.cache'
+ -n, --no-create do not create output files
+ --srcdir=DIR find the sources in DIR [configure dir or \`..']
+
+_ACEOF
+
+ cat <<_ACEOF
+Installation directories:
+ --prefix=PREFIX install architecture-independent files in PREFIX
+ [$ac_default_prefix]
+ --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX
+ [PREFIX]
+
+By default, \`make install' will install all the files in
+\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify
+an installation prefix other than \`$ac_default_prefix' using \`--prefix',
+for instance \`--prefix=\$HOME'.
+
+For better control, use the options below.
+
+Fine tuning of the installation directories:
+ --bindir=DIR user executables [EPREFIX/bin]
+ --sbindir=DIR system admin executables [EPREFIX/sbin]
+ --libexecdir=DIR program executables [EPREFIX/libexec]
+ --datadir=DIR read-only architecture-independent data [PREFIX/share]
+ --sysconfdir=DIR read-only single-machine data [PREFIX/etc]
+ --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
+ --localstatedir=DIR modifiable single-machine data [PREFIX/var]
+ --libdir=DIR object code libraries [EPREFIX/lib]
+ --includedir=DIR C header files [PREFIX/include]
+ --oldincludedir=DIR C header files for non-gcc [/usr/include]
+ --infodir=DIR info documentation [PREFIX/info]
+ --mandir=DIR man documentation [PREFIX/man]
+_ACEOF
+
+ cat <<\_ACEOF
+
+Program names:
+ --program-prefix=PREFIX prepend PREFIX to installed program names
+ --program-suffix=SUFFIX append SUFFIX to installed program names
+ --program-transform-name=PROGRAM run sed PROGRAM on installed program names
+
+System types:
+ --build=BUILD configure for building on BUILD [guessed]
+ --host=HOST cross-compile to build programs to run on HOST [BUILD]
+_ACEOF
+fi
+
+if test -n "$ac_init_help"; then
+ case $ac_init_help in
+ short | recursive ) echo "Configuration of toppred 1.10:";;
+ esac
+ cat <<\_ACEOF
+
+Optional Features:
+ --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
+ --enable-FEATURE[=ARG] include FEATURE [ARG=yes]
+ --disable-dependency-tracking speeds up one-time build
+ --enable-dependency-tracking do not reject slow dependency extractors
+
+Optional Packages:
+ --with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
+ --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
+ --with-libgd=DIR root directory path of libgd installation
+ defaults to /usr and /usr/local
+ --without-libgd to disable libgd usage completely (not yet implemented)
+
+Some influential environment variables:
+ CC C compiler command
+ CFLAGS C compiler flags
+ LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
+ nonstandard directory <lib dir>
+ CPPFLAGS C/C++ preprocessor flags, e.g. -I<include dir> if you have
+ headers in a nonstandard directory <include dir>
+ CPP C preprocessor
+
+Use these variables to override the choices made by `configure' or to help
+it to find libraries and programs with nonstandard names/locations.
+
+_ACEOF
+fi
+
+if test "$ac_init_help" = "recursive"; then
+ # If there are subdirs, report their specific --help.
+ ac_popdir=`pwd`
+ for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
+ test -d $ac_dir || continue
+ ac_builddir=.
+
+if test "$ac_dir" != .; then
+ ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
+ # A "../" for each directory in $ac_dir_suffix.
+ ac_top_builddir=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,../,g'`
+else
+ ac_dir_suffix= ac_top_builddir=
+fi
+
+case $srcdir in
+ .) # No --srcdir option. We are building in place.
+ ac_srcdir=.
+ if test -z "$ac_top_builddir"; then
+ ac_top_srcdir=.
+ else
+ ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'`
+ fi ;;
+ [\\/]* | ?:[\\/]* ) # Absolute path.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir ;;
+ *) # Relative path.
+ ac_srcdir=$ac_top_builddir$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_builddir$srcdir ;;
+esac
+
+# Do not use `cd foo && pwd` to compute absolute paths, because
+# the directories may not exist.
+case `pwd` in
+.) ac_abs_builddir="$ac_dir";;
+*)
+ case "$ac_dir" in
+ .) ac_abs_builddir=`pwd`;;
+ [\\/]* | ?:[\\/]* ) ac_abs_builddir="$ac_dir";;
+ *) ac_abs_builddir=`pwd`/"$ac_dir";;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_top_builddir=${ac_top_builddir}.;;
+*)
+ case ${ac_top_builddir}. in
+ .) ac_abs_top_builddir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_top_builddir=${ac_top_builddir}.;;
+ *) ac_abs_top_builddir=$ac_abs_builddir/${ac_top_builddir}.;;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_srcdir=$ac_srcdir;;
+*)
+ case $ac_srcdir in
+ .) ac_abs_srcdir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_srcdir=$ac_srcdir;;
+ *) ac_abs_srcdir=$ac_abs_builddir/$ac_srcdir;;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_top_srcdir=$ac_top_srcdir;;
+*)
+ case $ac_top_srcdir in
+ .) ac_abs_top_srcdir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_top_srcdir=$ac_top_srcdir;;
+ *) ac_abs_top_srcdir=$ac_abs_builddir/$ac_top_srcdir;;
+ esac;;
+esac
+
+ cd $ac_dir
+ # Check for guested configure; otherwise get Cygnus style 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
+ elif test -f $ac_srcdir/configure.ac ||
+ test -f $ac_srcdir/configure.in; then
+ echo
+ $ac_configure --help
+ else
+ echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
+ fi
+ cd $ac_popdir
+ done
+fi
+
+test -n "$ac_init_help" && exit 0
+if $ac_init_version; then
+ cat <<\_ACEOF
+toppred configure 1.10
+generated by GNU Autoconf 2.59
+
+Copyright (C) 2003 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 0
+fi
+exec 5>config.log
+cat >&5 <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by toppred $as_me 1.10, which was
+generated by GNU Autoconf 2.59. Invocation command line was
+
+ $ $0 $@
+
+_ACEOF
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown`
+
+/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
+hostinfo = `(hostinfo) 2>/dev/null || echo unknown`
+/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
+/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
+
+_ASUNAME
+
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ echo "PATH: $as_dir"
+done
+
+} >&5
+
+cat >&5 <<_ACEOF
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+_ACEOF
+
+
+# Keep a trace of the command line.
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Strip out --silent because we don't want to record it for future runs.
+# Also quote any args containing shell meta-characters.
+# Make two passes to allow for proper duplicate-argument suppression.
+ac_configure_args=
+ac_configure_args0=
+ac_configure_args1=
+ac_sep=
+ac_must_keep_next=false
+for ac_pass in 1 2
+do
+ for ac_arg
+ do
+ case $ac_arg in
+ -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ continue ;;
+ *" "*|*" "*|*[\[\]\~\#\$\^\&\*\(\)\{\}\\\|\;\<\>\?\"\']*)
+ ac_arg=`echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ case $ac_pass in
+ 1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;;
+ 2)
+ ac_configure_args1="$ac_configure_args1 '$ac_arg'"
+ if test $ac_must_keep_next = true; then
+ ac_must_keep_next=false # Got value, back to normal.
+ else
+ case $ac_arg in
+ *=* | --config-cache | -C | -disable-* | --disable-* \
+ | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
+ | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
+ | -with-* | --with-* | -without-* | --without-* | --x)
+ case "$ac_configure_args0 " in
+ "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
+ esac
+ ;;
+ -* ) ac_must_keep_next=true ;;
+ esac
+ fi
+ ac_configure_args="$ac_configure_args$ac_sep'$ac_arg'"
+ # Get rid of the leading space.
+ ac_sep=" "
+ ;;
+ esac
+ done
+done
+$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; }
+$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; }
+
+# When interrupted or exit'd, cleanup temporary files, and complete
+# config.log. We remove comments because anyway the quotes in there
+# would cause problems or look ugly.
+# WARNING: Be sure not to use single quotes in there, as some shells,
+# such as our DU 5.0 friend, will then `close' the trap.
+trap 'exit_status=$?
+ # Save into config.log some information that might help in debugging.
+ {
+ echo
+
+ cat <<\_ASBOX
+## ---------------- ##
+## Cache variables. ##
+## ---------------- ##
+_ASBOX
+ echo
+ # The following way of writing the cache mishandles newlines in values,
+{
+ (set) 2>&1 |
+ case `(ac_space='"'"' '"'"'; set | grep ac_space) 2>&1` in
+ *ac_space=\ *)
+ sed -n \
+ "s/'"'"'/'"'"'\\\\'"'"''"'"'/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='"'"'\\2'"'"'/p"
+ ;;
+ *)
+ sed -n \
+ "s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1=\\2/p"
+ ;;
+ esac;
+}
+ echo
+
+ cat <<\_ASBOX
+## ----------------- ##
+## Output variables. ##
+## ----------------- ##
+_ASBOX
+ echo
+ for ac_var in $ac_subst_vars
+ do
+ eval ac_val=$`echo $ac_var`
+ echo "$ac_var='"'"'$ac_val'"'"'"
+ done | sort
+ echo
+
+ if test -n "$ac_subst_files"; then
+ cat <<\_ASBOX
+## ------------- ##
+## Output files. ##
+## ------------- ##
+_ASBOX
+ echo
+ for ac_var in $ac_subst_files
+ do
+ eval ac_val=$`echo $ac_var`
+ echo "$ac_var='"'"'$ac_val'"'"'"
+ done | sort
+ echo
+ fi
+
+ if test -s confdefs.h; then
+ cat <<\_ASBOX
+## ----------- ##
+## confdefs.h. ##
+## ----------- ##
+_ASBOX
+ echo
+ sed "/^$/d" confdefs.h | sort
+ echo
+ fi
+ test "$ac_signal" != 0 &&
+ echo "$as_me: caught signal $ac_signal"
+ echo "$as_me: exit $exit_status"
+ } >&5
+ rm -f core *.core &&
+ rm -rf conftest* confdefs* conf$$* $ac_clean_files &&
+ exit $exit_status
+ ' 0
+for ac_signal in 1 2 13 15; do
+ trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal
+done
+ac_signal=0
+
+# confdefs.h avoids OS command line length limits that DEFS can exceed.
+rm -rf conftest* confdefs.h
+# AIX cpp loses on an empty file, so make sure it contains at least a newline.
+echo >confdefs.h
+
+# Predefined preprocessor variables.
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_NAME "$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
+
+
+# Let the site file select an alternate cache file if it wants to.
+# Prefer explicitly selected file to automatically selected ones.
+if test -z "$CONFIG_SITE"; then
+ if test "x$prefix" != xNONE; then
+ CONFIG_SITE="$prefix/share/config.site $prefix/etc/config.site"
+ else
+ CONFIG_SITE="$ac_default_prefix/share/config.site $ac_default_prefix/etc/config.site"
+ fi
+fi
+for ac_site_file in $CONFIG_SITE; do
+ if test -r "$ac_site_file"; then
+ { echo "$as_me:$LINENO: loading site script $ac_site_file" >&5
+echo "$as_me: loading site script $ac_site_file" >&6;}
+ sed 's/^/| /' "$ac_site_file" >&5
+ . "$ac_site_file"
+ fi
+done
+
+if test -r "$cache_file"; then
+ # Some versions of bash will fail to source /dev/null (special
+ # files actually), so we avoid doing that.
+ if test -f "$cache_file"; then
+ { echo "$as_me:$LINENO: loading cache $cache_file" >&5
+echo "$as_me: loading cache $cache_file" >&6;}
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) . $cache_file;;
+ *) . ./$cache_file;;
+ esac
+ fi
+else
+ { echo "$as_me:$LINENO: creating cache $cache_file" >&5
+echo "$as_me: creating cache $cache_file" >&6;}
+ >$cache_file
+fi
+
+# Check that the precious variables saved in the cache have kept the same
+# value.
+ac_cache_corrupted=false
+for ac_var in `(set) 2>&1 |
+ sed -n 's/^ac_env_\([a-zA-Z_0-9]*\)_set=.*/\1/p'`; do
+ eval ac_old_set=\$ac_cv_env_${ac_var}_set
+ eval ac_new_set=\$ac_env_${ac_var}_set
+ eval ac_old_val="\$ac_cv_env_${ac_var}_value"
+ eval ac_new_val="\$ac_env_${ac_var}_value"
+ case $ac_old_set,$ac_new_set in
+ set,)
+ { echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,set)
+ { echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5
+echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,);;
+ *)
+ if test "x$ac_old_val" != "x$ac_new_val"; then
+ { echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5
+echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
+ { echo "$as_me:$LINENO: former value: $ac_old_val" >&5
+echo "$as_me: former value: $ac_old_val" >&2;}
+ { echo "$as_me:$LINENO: current value: $ac_new_val" >&5
+echo "$as_me: current value: $ac_new_val" >&2;}
+ ac_cache_corrupted=:
+ fi;;
+ esac
+ # Pass precious variables to config.status.
+ if test "$ac_new_set" = set; then
+ case $ac_new_val in
+ *" "*|*" "*|*[\[\]\~\#\$\^\&\*\(\)\{\}\\\|\;\<\>\?\"\']*)
+ ac_arg=$ac_var=`echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+ *) ac_arg=$ac_var=$ac_new_val ;;
+ esac
+ case " $ac_configure_args " in
+ *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
+ *) ac_configure_args="$ac_configure_args '$ac_arg'" ;;
+ esac
+ fi
+done
+if $ac_cache_corrupted; then
+ { echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5
+echo "$as_me: error: changes in the environment can compromise the build" >&2;}
+ { { echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5
+echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+am__api_version="1.9"
+ac_aux_dir=
+for ac_dir in $srcdir $srcdir/.. $srcdir/../..; do
+ if test -f $ac_dir/install-sh; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install-sh -c"
+ break
+ elif test -f $ac_dir/install.sh; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install.sh -c"
+ break
+ elif test -f $ac_dir/shtool; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/shtool install -c"
+ break
+ fi
+done
+if test -z "$ac_aux_dir"; then
+ { { echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&5
+echo "$as_me: error: cannot find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+ac_config_guess="$SHELL $ac_aux_dir/config.guess"
+ac_config_sub="$SHELL $ac_aux_dir/config.sub"
+ac_configure="$SHELL $ac_aux_dir/configure" # This should be Cygnus configure.
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
+echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6
+if test -z "$INSTALL"; then
+if test "${ac_cv_path_install+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ as_save_IFS=$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 $as_executable_p "$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
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+done
+
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. We don't cache a
+ # path for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the path is relative.
+ INSTALL=$ac_install_sh
+ fi
+fi
+echo "$as_me:$LINENO: result: $INSTALL" >&5
+echo "${ECHO_T}$INSTALL" >&6
+
+# 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='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+echo "$as_me:$LINENO: checking whether build environment is sane" >&5
+echo $ECHO_N "checking whether build environment is sane... $ECHO_C" >&6
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# 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 $srcdir/configure conftest.file 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t $srcdir/configure conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$*" != "X $srcdir/configure conftest.file" \
+ && test "$*" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ { { echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken
+alias in your environment" >&5
+echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken
+alias in your environment" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+
+ test "$2" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ { { echo "$as_me:$LINENO: error: newly created file is older than distributed files!
+Check your system clock" >&5
+echo "$as_me: error: newly created file is older than distributed files!
+Check your system clock" >&2;}
+ { (exit 1); exit 1; }; }
+fi
+echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+test "$program_prefix" != NONE &&
+ program_transform_name="s,^,$program_prefix,;$program_transform_name"
+# Use a double $ so make ignores it.
+test "$program_suffix" != NONE &&
+ program_transform_name="s,\$,$program_suffix,;$program_transform_name"
+# Double any \ or $. echo might interpret backslashes.
+# By default was `s,x,x', remove it if useless.
+cat <<\_ACEOF >conftest.sed
+s/[\\$]/&&/g;s/;s,x,x,$//
+_ACEOF
+program_transform_name=`echo $program_transform_name | sed -f conftest.sed`
+rm conftest.sed
+
+# 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"
+# Use eval to expand $SHELL
+if eval "$MISSING --run true"; then
+ am_missing_run="$MISSING --run "
+else
+ am_missing_run=
+ { echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5
+echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
+fi
+
+if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then
+ # We used to keeping the `.' as first argument, in order to
+ # allow $(mkdir_p) to be used without argument. As in
+ # $(mkdir_p) $(somedir)
+ # where $(somedir) is conditionally defined. However this is wrong
+ # for two reasons:
+ # 1. if the package is installed by a user who cannot write `.'
+ # make install will fail,
+ # 2. the above comment should most certainly read
+ # $(mkdir_p) $(DESTDIR)$(somedir)
+ # so it does not work when $(somedir) is undefined and
+ # $(DESTDIR) is not.
+ # To support the latter case, we have to write
+ # test -z "$(somedir)" || $(mkdir_p) $(DESTDIR)$(somedir),
+ # so the `.' trick is pointless.
+ mkdir_p='mkdir -p --'
+else
+ # On NextStep and OpenStep, the `mkdir' command does not
+ # recognize any option. It will interpret all options as
+ # directories to create, and then abort because `.' already
+ # exists.
+ for d in ./-p ./--version;
+ do
+ test -d $d && rmdir $d
+ done
+ # $(mkinstalldirs) is defined by Automake if mkinstalldirs exists.
+ if test -f "$ac_aux_dir/mkinstalldirs"; then
+ mkdir_p='$(mkinstalldirs)'
+ else
+ mkdir_p='$(install_sh) -d'
+ fi
+fi
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_AWK+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$AWK"; then
+ ac_cv_prog_AWK="$AWK" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_AWK="$ac_prog"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
+ echo "$as_me:$LINENO: result: $AWK" >&5
+echo "${ECHO_T}$AWK" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+ test -n "$AWK" && break
+done
+
+echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+echo $ECHO_N "checking whether ${MAKE-make} sets \$(MAKE)... $ECHO_C" >&6
+set dummy ${MAKE-make}; ac_make=`echo "$2" | sed 'y,:./+-,___p_,'`
+if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\" = set"; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.make <<\_ACEOF
+all:
+ @echo 'ac_maketemp="$(MAKE)"'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
+eval `${MAKE-make} -f conftest.make 2>/dev/null | grep temp=`
+if test -n "$ac_maketemp"; then
+ eval ac_cv_prog_make_${ac_make}_set=yes
+else
+ eval ac_cv_prog_make_${ac_make}_set=no
+fi
+rm -f conftest.make
+fi
+if eval "test \"`echo '$ac_cv_prog_make_'${ac_make}_set`\" = yes"; then
+ echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+ SET_MAKE=
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+ am__leading_dot=.
+else
+ am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+# test to see if srcdir already configured
+if test "`cd $srcdir && pwd`" != "`pwd`" &&
+ test -f $srcdir/config.status; then
+ { { echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5
+echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+# test whether we have cygpath
+if test -z "$CYGPATH_W"; then
+ if (cygpath --version) >/dev/null 2>/dev/null; then
+ CYGPATH_W='cygpath -w'
+ else
+ CYGPATH_W=echo
+ fi
+fi
+
+
+# Define the identity of the package.
+ PACKAGE='toppred'
+ VERSION='1.10'
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE "$PACKAGE"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define VERSION "$VERSION"
+_ACEOF
+
+# Some tools Automake needs.
+
+ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"}
+
+
+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
+
+
+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
+
+
+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
+
+
+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+
+install_sh=${install_sh-"$am_aux_dir/install-sh"}
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$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=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_STRIP+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ echo "$as_me:$LINENO: result: $STRIP" >&5
+echo "${ECHO_T}$STRIP" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}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=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+ test -z "$ac_cv_prog_ac_ct_STRIP" && ac_cv_prog_ac_ct_STRIP=":"
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5
+echo "${ECHO_T}$ac_ct_STRIP" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+ STRIP=$ac_ct_STRIP
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+fi
+INSTALL_STRIP_PROGRAM="\${SHELL} \$(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.
+
+AMTAR=${AMTAR-"${am_missing_run}tar"}
+
+am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -'
+
+
+
+
+
+ ac_config_headers="$ac_config_headers src/config.h"
+
+
+# Checks for programs.
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+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=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_CC+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_CC="${ac_tool_prefix}gcc"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_ac_ct_CC="gcc"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+echo "${ECHO_T}$ac_ct_CC" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+ CC=$ac_ct_CC
+else
+ CC="$ac_cv_prog_CC"
+fi
+
+if test -z "$CC"; then
+ if test -n "$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=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_CC+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_CC="${ac_tool_prefix}cc"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_ac_ct_CC="cc"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+echo "${ECHO_T}$ac_ct_CC" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+ CC=$ac_ct_CC
+else
+ CC="$ac_cv_prog_CC"
+fi
+
+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=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_CC+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $# != 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+ fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+fi
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in cl
+ 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=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_CC+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ echo "$as_me:$LINENO: result: $CC" >&5
+echo "${ECHO_T}$CC" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+ test -n "$CC" && break
+ done
+fi
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in cl
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_ac_ct_CC="$ac_prog"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+echo "${ECHO_T}$ac_ct_CC" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+ test -n "$ac_ct_CC" && break
+done
+
+ CC=$ac_ct_CC
+fi
+
+fi
+
+
+test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&5
+echo "$as_me: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }
+
+# Provide some information about the compiler.
+echo "$as_me:$LINENO:" \
+ "checking for C compiler version" >&5
+ac_compiler=`set X $ac_compile; echo $2`
+{ (eval echo "$as_me:$LINENO: \"$ac_compiler --version </dev/null >&5\"") >&5
+ (eval $ac_compiler --version </dev/null >&5) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (eval echo "$as_me:$LINENO: \"$ac_compiler -v </dev/null >&5\"") >&5
+ (eval $ac_compiler -v </dev/null >&5) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (eval echo "$as_me:$LINENO: \"$ac_compiler -V </dev/null >&5\"") >&5
+ (eval $ac_compiler -V </dev/null >&5) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+
+cat >conftest.$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
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files a.out a.exe b.out"
+# 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.
+echo "$as_me:$LINENO: checking for C compiler default output file name" >&5
+echo $ECHO_N "checking for C compiler default output file name... $ECHO_C" >&6
+ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
+if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5
+ (eval $ac_link_default) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ # Find the output, starting from the most likely. This scheme is
+# not robust to junk in `.', hence go to wildcards (a.*) only as a last
+# resort.
+
+# Be careful to initialize this variable, since it used to be cached.
+# Otherwise an old cache value of `no' led to `EXEEXT = no' in a Makefile.
+ac_cv_exeext=
+# b.out is created by i960 compilers.
+for ac_file in a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out
+do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj )
+ ;;
+ conftest.$ac_ext )
+ # This is the source file.
+ ;;
+ [ab].out )
+ # We found the default executable, but exeext='' is most
+ # certainly right.
+ break;;
+ *.* )
+ ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ # FIXME: I believe we export ac_cv_exeext for Libtool,
+ # but it would be cool to find out if it's true. Does anybody
+ # maintain Libtool? --akim.
+ export ac_cv_exeext
+ break;;
+ * )
+ break;;
+ esac
+done
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { echo "$as_me:$LINENO: error: C compiler cannot create executables
+See \`config.log' for more details." >&5
+echo "$as_me: error: C compiler cannot create executables
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }
+fi
+
+ac_exeext=$ac_cv_exeext
+echo "$as_me:$LINENO: result: $ac_file" >&5
+echo "${ECHO_T}$ac_file" >&6
+
+# Check the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+echo "$as_me:$LINENO: checking whether the C compiler works" >&5
+echo $ECHO_N "checking whether the C compiler works... $ECHO_C" >&6
+# FIXME: These cross compiler hacks should be removed for Autoconf 3.0
+# If not cross compiling, check that we can run a simple program.
+if test "$cross_compiling" != yes; then
+ if { ac_try='./$ac_file'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ 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
+ { { 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
+echo "$as_me: error: cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ fi
+fi
+echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+
+rm -f a.out a.exe conftest$ac_cv_exeext b.out
+ac_clean_files=$ac_clean_files_save
+# Check the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+echo "$as_me:$LINENO: checking whether we are cross compiling" >&5
+echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6
+echo "$as_me:$LINENO: result: $cross_compiling" >&5
+echo "${ECHO_T}$cross_compiling" >&6
+
+echo "$as_me:$LINENO: checking for suffix of executables" >&5
+echo $ECHO_N "checking for suffix of executables... $ECHO_C" >&6
+if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ # If both `conftest.exe' and `conftest' are `present' (well, observable)
+# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
+# work properly (i.e., refer to `conftest.exe'), while it won't with
+# `rm'.
+for ac_file in conftest.exe conftest conftest.*; do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) ;;
+ *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ export ac_cv_exeext
+ break;;
+ * ) break;;
+ esac
+done
+else
+ { { echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+rm -f conftest$ac_cv_exeext
+echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5
+echo "${ECHO_T}$ac_cv_exeext" >&6
+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+echo "$as_me:$LINENO: checking for suffix of object files" >&5
+echo $ECHO_N "checking for suffix of object files... $ECHO_C" >&6
+if test "${ac_cv_objext+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$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.o conftest.obj
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ for ac_file in `(ls conftest.o conftest.obj; ls conftest.*) 2>/dev/null`; do
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg ) ;;
+ *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
+ break;;
+ esac
+done
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile
+See \`config.log' for more details." >&5
+echo "$as_me: error: cannot compute suffix of object files: cannot compile
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+rm -f conftest.$ac_cv_objext conftest.$ac_ext
+fi
+echo "$as_me:$LINENO: result: $ac_cv_objext" >&5
+echo "${ECHO_T}$ac_cv_objext" >&6
+OBJEXT=$ac_cv_objext
+ac_objext=$OBJEXT
+echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5
+echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6
+if test "${ac_cv_c_compiler_gnu+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_compiler_gnu=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_compiler_gnu=no
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5
+echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6
+GCC=`test $ac_compiler_gnu = yes && echo yes`
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+CFLAGS="-g"
+echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5
+echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6
+if test "${ac_cv_prog_cc_g+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$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.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_prog_cc_g=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_cv_prog_cc_g=no
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5
+echo "${ECHO_T}$ac_cv_prog_cc_g" >&6
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5
+echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6
+if test "${ac_cv_prog_cc_stdc+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ ac_cv_prog_cc_stdc=no
+ac_save_CC=$CC
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std1 is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std1. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+# Don't try gcc -ansi; that turns off useful extensions and
+# breaks some systems' header files.
+# AIX -qlanglvl=ansi
+# Ultrix and OSF/1 -std1
+# HP-UX 10.20 and later -Ae
+# HP-UX older versions -Aa -D_HPUX_SOURCE
+# SVR4 -Xc -D__EXTENSIONS__
+for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_prog_cc_stdc=$ac_arg
+break
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+fi
+rm -f conftest.err conftest.$ac_objext
+done
+rm -f conftest.$ac_ext conftest.$ac_objext
+CC=$ac_save_CC
+
+fi
+
+case "x$ac_cv_prog_cc_stdc" in
+ x|xno)
+ echo "$as_me:$LINENO: result: none needed" >&5
+echo "${ECHO_T}none needed" >&6 ;;
+ *)
+ echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5
+echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6
+ CC="$CC $ac_cv_prog_cc_stdc" ;;
+esac
+
+# Some people use a C++ compiler to compile C. Since we use `exit',
+# in C++ we need to declare it. In case someone uses the same compiler
+# for both compiling C and C++ we need to have the C++ compiler decide
+# the declaration of exit, since it's the most demanding environment.
+cat >conftest.$ac_ext <<_ACEOF
+#ifndef __cplusplus
+ choke me
+#endif
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ for ac_declaration in \
+ '' \
+ 'extern "C" void std::exit (int) throw (); using std::exit;' \
+ 'extern "C" void std::exit (int); using std::exit;' \
+ 'extern "C" void exit (int) throw ();' \
+ 'extern "C" void exit (int);' \
+ 'void exit (int);'
+do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_declaration
+#include <stdlib.h>
+int
+main ()
+{
+exit (42);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ :
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+continue
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_declaration
+int
+main ()
+{
+exit (42);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ break
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+done
+rm -f conftest*
+if test -n "$ac_declaration"; then
+ echo '#ifdef __cplusplus' >>confdefs.h
+ echo $ac_declaration >>confdefs.h
+ echo '#endif' >>confdefs.h
+fi
+
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+DEPDIR="${am__leading_dot}deps"
+
+ ac_config_commands="$ac_config_commands depfiles"
+
+
+am_make=${MAKE-make}
+cat > confinc << 'END'
+am__doit:
+ @echo done
+.PHONY: am__doit
+END
+# If we don't find an include directive, just comment out the code.
+echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5
+echo $ECHO_N "checking for style of include used by $am_make... $ECHO_C" >&6
+am__include="#"
+am__quote=
+_am_result=none
+# First try GNU make style include.
+echo "include confinc" > confmf
+# We grep out `Entering directory' and `Leaving directory'
+# messages which can occur if `w' ends up in MAKEFLAGS.
+# In particular we don't look at `^make:' because GNU make might
+# be invoked under some other name (usually "gmake"), in which
+# case it prints its new name instead of `make'.
+if test "`$am_make -s -f confmf 2> /dev/null | grep -v 'ing directory'`" = "done"; then
+ am__include=include
+ am__quote=
+ _am_result=GNU
+fi
+# 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
+fi
+
+
+echo "$as_me:$LINENO: result: $_am_result" >&5
+echo "${ECHO_T}$_am_result" >&6
+rm -f confinc confmf
+
+# Check whether --enable-dependency-tracking or --disable-dependency-tracking was given.
+if test "${enable_dependency_tracking+set}" = set; then
+ enableval="$enable_dependency_tracking"
+
+fi;
+if test "x$enable_dependency_tracking" != xno; then
+ am_depcomp="$ac_aux_dir/depcomp"
+ AMDEPBACKSLASH='\'
+fi
+
+
+if test "x$enable_dependency_tracking" != xno; then
+ AMDEP_TRUE=
+ AMDEP_FALSE='#'
+else
+ AMDEP_TRUE='#'
+ AMDEP_FALSE=
+fi
+
+
+
+
+depcc="$CC" am_compiler_list=
+
+echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
+echo $ECHO_N "checking dependency style of $depcc... $ECHO_C" >&6
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ 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
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ case $depmode in
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ none) break ;;
+ esac
+ # 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.
+ if depmode=$depmode \
+ source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5
+echo "${ECHO_T}$am_cv_CC_dependencies_compiler_type" >&6
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+
+
+if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+# Extract the first word of "pod2man", so it can be a program name with args.
+set dummy pod2man; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_POD2MAN+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$POD2MAN"; then
+ ac_cv_prog_POD2MAN="$POD2MAN" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_POD2MAN="pod2man"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+ test -z "$ac_cv_prog_POD2MAN" && ac_cv_prog_POD2MAN=":"
+fi
+fi
+POD2MAN=$ac_cv_prog_POD2MAN
+if test -n "$POD2MAN"; then
+ echo "$as_me:$LINENO: result: $POD2MAN" >&5
+echo "${ECHO_T}$POD2MAN" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+# Extract the first word of "gnuplot", so it can be a program name with args.
+set dummy gnuplot; ac_word=$2
+echo "$as_me:$LINENO: checking for $ac_word" >&5
+echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
+if test "${ac_cv_prog_GNUPLOT+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test -n "$GNUPLOT"; then
+ ac_cv_prog_GNUPLOT="$GNUPLOT" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
+ ac_cv_prog_GNUPLOT="gnuplot"
+ echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+
+fi
+fi
+GNUPLOT=$ac_cv_prog_GNUPLOT
+if test -n "$GNUPLOT"; then
+ echo "$as_me:$LINENO: result: $GNUPLOT" >&5
+echo "${ECHO_T}$GNUPLOT" >&6
+else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+fi
+
+if test "$GNUPLOT" = "gnuplot"; then
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_GNUPLOT 1
+_ACEOF
+
+else
+ { echo "$as_me:$LINENO: WARNING: gnuplot not found, Hydrophobic profile will be unavailable" >&5
+echo "$as_me: WARNING: gnuplot not found, Hydrophobic profile will be unavailable" >&2;}
+fi
+
+# Checks for libraries.
+
+
+echo "$as_me:$LINENO: checking for pow in -lm" >&5
+echo $ECHO_N "checking for pow in -lm... $ECHO_C" >&6
+if test "${ac_cv_lib_m_pow+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lm $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+/* Override any gcc2 internal prototype to avoid an error. */
+#ifdef __cplusplus
+extern "C"
+#endif
+/* We use char because int might match the return type of a gcc2
+ builtin and then its argument prototype would still apply. */
+char pow ();
+int
+main ()
+{
+pow ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+ (eval $ac_link) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest$ac_exeext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_lib_m_pow=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_cv_lib_m_pow=no
+fi
+rm -f conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+echo "$as_me:$LINENO: result: $ac_cv_lib_m_pow" >&5
+echo "${ECHO_T}$ac_cv_lib_m_pow" >&6
+if test $ac_cv_lib_m_pow = yes; then
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBM 1
+_ACEOF
+
+ LIBS="-lm $LIBS"
+
+fi
+
+
+# Checks for header files.
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5
+echo $ECHO_N "checking how to run the C preprocessor... $ECHO_C" >&6
+# On Suns, sometimes $CPP names a directory.
+if test -n "$CPP" && test -d "$CPP"; then
+ CPP=
+fi
+if test -z "$CPP"; then
+ if test "${ac_cv_prog_CPP+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ # Double quotes because CPP needs to be expanded
+ for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+ (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null; then
+ if test -s conftest.err; then
+ ac_cpp_err=$ac_c_preproc_warn_flag
+ ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+ else
+ ac_cpp_err=
+ fi
+else
+ ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+ :
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether non-existent headers
+ # can be detected and how.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+ (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null; then
+ if test -s conftest.err; then
+ ac_cpp_err=$ac_c_preproc_warn_flag
+ ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+ else
+ ac_cpp_err=
+ fi
+else
+ ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+ # Broken: success on invalid input.
+continue
+else
+ echo "$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 $ac_preproc_ok; then
+ break
+fi
+
+ done
+ ac_cv_prog_CPP=$CPP
+
+fi
+ CPP=$ac_cv_prog_CPP
+else
+ ac_cv_prog_CPP=$CPP
+fi
+echo "$as_me:$LINENO: result: $CPP" >&5
+echo "${ECHO_T}$CPP" >&6
+ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+ (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null; then
+ if test -s conftest.err; then
+ ac_cpp_err=$ac_c_preproc_warn_flag
+ ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+ else
+ ac_cpp_err=
+ fi
+else
+ ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+ :
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Broken: fails on valid input.
+continue
+fi
+rm -f conftest.err conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether non-existent headers
+ # can be detected and how.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+ (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null; then
+ if test -s conftest.err; then
+ ac_cpp_err=$ac_c_preproc_warn_flag
+ ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+ else
+ ac_cpp_err=
+ fi
+else
+ ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+ # Broken: success on invalid input.
+continue
+else
+ echo "$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 $ac_preproc_ok; then
+ :
+else
+ { { echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&5
+echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+echo "$as_me:$LINENO: checking for egrep" >&5
+echo $ECHO_N "checking for egrep... $ECHO_C" >&6
+if test "${ac_cv_prog_egrep+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if echo a | (grep -E '(a|b)') >/dev/null 2>&1
+ then ac_cv_prog_egrep='grep -E'
+ else ac_cv_prog_egrep='egrep'
+ fi
+fi
+echo "$as_me:$LINENO: result: $ac_cv_prog_egrep" >&5
+echo "${ECHO_T}$ac_cv_prog_egrep" >&6
+ EGREP=$ac_cv_prog_egrep
+
+
+echo "$as_me:$LINENO: checking for ANSI C header files" >&5
+echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6
+if test "${ac_cv_header_stdc+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <float.h>
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_header_stdc=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_cv_header_stdc=no
+fi
+rm -f conftest.err conftest.$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
+/* end confdefs.h. */
+#include <string.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "memchr" >/dev/null 2>&1; then
+ :
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <stdlib.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "free" >/dev/null 2>&1; then
+ :
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
+ if test "$cross_compiling" = yes; then
+ :
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ctype.h>
+#if ((' ' & 0x0FF) == 0x020)
+# define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
+#else
+# define ISLOWER(c) \
+ (('a' <= (c) && (c) <= 'i') \
+ || ('j' <= (c) && (c) <= 'r') \
+ || ('s' <= (c) && (c) <= 'z'))
+# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
+#endif
+
+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
+int
+main ()
+{
+ int i;
+ for (i = 0; i < 256; i++)
+ if (XOR (islower (i), ISLOWER (i))
+ || toupper (i) != TOUPPER (i))
+ exit(2);
+ exit (0);
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ :
+else
+ echo "$as_me: program exited with status $ac_status" >&5
+echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_header_stdc=no
+fi
+rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+fi
+fi
+echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5
+echo "${ECHO_T}$ac_cv_header_stdc" >&6
+if test $ac_cv_header_stdc = yes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define STDC_HEADERS 1
+_ACEOF
+
+fi
+
+# On IRIX 5.3, sys/types and inttypes.h are conflicting.
+
+
+
+
+
+
+
+
+
+for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
+ inttypes.h stdint.h unistd.h
+do
+as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh`
+echo "$as_me:$LINENO: checking for $ac_header" >&5
+echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6
+if eval "test \"\${$as_ac_Header+set}\" = set"; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$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.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ eval "$as_ac_Header=yes"
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+eval "$as_ac_Header=no"
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5
+echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6
+if test `eval echo '${'$as_ac_Header'}'` = yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+
+
+
+
+for ac_header in errno.h stdlib.h string.h unistd.h
+do
+as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh`
+if eval "test \"\${$as_ac_Header+set}\" = set"; then
+ echo "$as_me:$LINENO: checking for $ac_header" >&5
+echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6
+if eval "test \"\${$as_ac_Header+set}\" = set"; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+fi
+echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5
+echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6
+else
+ # Is the header compilable?
+echo "$as_me:$LINENO: checking $ac_header usability" >&5
+echo $ECHO_N "checking $ac_header usability... $ECHO_C" >&6
+cat >conftest.$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.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_header_compiler=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_header_compiler=no
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+echo "${ECHO_T}$ac_header_compiler" >&6
+
+# Is the header present?
+echo "$as_me:$LINENO: checking $ac_header presence" >&5
+echo $ECHO_N "checking $ac_header presence... $ECHO_C" >&6
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <$ac_header>
+_ACEOF
+if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5
+ (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null; then
+ if test -s conftest.err; then
+ ac_cpp_err=$ac_c_preproc_warn_flag
+ ac_cpp_err=$ac_cpp_err$ac_c_werror_flag
+ else
+ ac_cpp_err=
+ fi
+else
+ ac_cpp_err=yes
+fi
+if test -z "$ac_cpp_err"; then
+ ac_header_preproc=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_preproc=no
+fi
+rm -f conftest.err conftest.$ac_ext
+echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+echo "${ECHO_T}$ac_header_preproc" >&6
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+ yes:no: )
+ { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
+echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
+echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
+ ac_header_preproc=yes
+ ;;
+ no:yes:* )
+ { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
+echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
+ { echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5
+echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;}
+ { echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
+echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
+ { echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5
+echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;}
+ { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
+echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
+ { echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
+echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
+ (
+ cat <<\_ASBOX
+## ---------------------------------- ##
+## Report this to the toppred lists. ##
+## ---------------------------------- ##
+_ASBOX
+ ) |
+ sed "s/^/$as_me: WARNING: /" >&2
+ ;;
+esac
+echo "$as_me:$LINENO: checking for $ac_header" >&5
+echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6
+if eval "test \"\${$as_ac_Header+set}\" = set"; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ eval "$as_ac_Header=\$ac_header_preproc"
+fi
+echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5
+echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6
+
+fi
+if test `eval echo '${'$as_ac_Header'}'` = yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+# Checks for typedefs, structures, and compiler characteristics.
+echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5
+echo $ECHO_N "checking for an ANSI C-conforming const... $ECHO_C" >&6
+if test "${ac_cv_c_const+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+/* FIXME: Include the comments suggested by Paul. */
+#ifndef __cplusplus
+ /* Ultrix mips cc rejects this. */
+ typedef int charset[2];
+ const charset x;
+ /* SunOS 4.1.1 cc rejects this. */
+ char const *const *ccp;
+ char **p;
+ /* NEC SVR4.0.2 mips cc rejects this. */
+ struct point {int x, y;};
+ static struct point const zero = {0,0};
+ /* AIX XL C 1.02.0.0 rejects this.
+ It does not let you subtract one const X* pointer from another in
+ an arm of an if-expression whose if-part is not a constant
+ expression */
+ const char *g = "string";
+ ccp = &g + (g ? g-g : 0);
+ /* HPUX 7.0 cc rejects these. */
+ ++ccp;
+ p = (char**) ccp;
+ ccp = (char const *const *) p;
+ { /* SCO 3.2v4 cc rejects this. */
+ char *t;
+ char const *s = 0 ? (char *) 0 : (char const *) 0;
+
+ *t++ = 0;
+ }
+ { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */
+ int x[] = {25, 17};
+ const int *foo = &x[0];
+ ++foo;
+ }
+ { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */
+ typedef const int *iptr;
+ iptr p = 0;
+ ++p;
+ }
+ { /* AIX XL C 1.02.0.0 rejects this saying
+ "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */
+ struct s { int j; const int *ap[3]; };
+ struct s *b; b->j = 5;
+ }
+ { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */
+ const int foo = 10;
+ }
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_c_const=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_cv_c_const=no
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5
+echo "${ECHO_T}$ac_cv_c_const" >&6
+if test $ac_cv_c_const = no; then
+
+cat >>confdefs.h <<\_ACEOF
+#define const
+_ACEOF
+
+fi
+
+echo "$as_me:$LINENO: checking for size_t" >&5
+echo $ECHO_N "checking for size_t... $ECHO_C" >&6
+if test "${ac_cv_type_size_t+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+if ((size_t *) 0)
+ return 0;
+if (sizeof (size_t))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_type_size_t=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_cv_type_size_t=no
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+echo "$as_me:$LINENO: result: $ac_cv_type_size_t" >&5
+echo "${ECHO_T}$ac_cv_type_size_t" >&6
+if test $ac_cv_type_size_t = yes; then
+ :
+else
+
+cat >>confdefs.h <<_ACEOF
+#define size_t unsigned
+_ACEOF
+
+fi
+
+echo "$as_me:$LINENO: checking whether struct tm is in sys/time.h or time.h" >&5
+echo $ECHO_N "checking whether struct tm is in sys/time.h or time.h... $ECHO_C" >&6
+if test "${ac_cv_struct_tm+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <sys/types.h>
+#include <time.h>
+
+int
+main ()
+{
+struct tm *tp; tp->tm_sec;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_struct_tm=time.h
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ac_cv_struct_tm=sys/time.h
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+echo "$as_me:$LINENO: result: $ac_cv_struct_tm" >&5
+echo "${ECHO_T}$ac_cv_struct_tm" >&6
+if test $ac_cv_struct_tm = sys/time.h; then
+
+cat >>confdefs.h <<\_ACEOF
+#define TM_IN_SYS_TIME 1
+_ACEOF
+
+fi
+
+
+# Checks for library functions.
+# AC_FUNC_MALLOC # tru64 problem
+echo "$as_me:$LINENO: checking whether lstat dereferences a symlink specified with a trailing slash" >&5
+echo $ECHO_N "checking whether lstat dereferences a symlink specified with a trailing slash... $ECHO_C" >&6
+if test "${ac_cv_func_lstat_dereferences_slashed_symlink+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ rm -f conftest.sym conftest.file
+echo >conftest.file
+if test "$as_ln_s" = "ln -s" && ln -s conftest.file conftest.sym; then
+ if test "$cross_compiling" = yes; then
+ ac_cv_func_lstat_dereferences_slashed_symlink=no
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+struct stat sbuf;
+ /* Linux will dereference the symlink and fail.
+ That is better in the sense that it means we will not
+ have to compile and use the lstat wrapper. */
+ exit (lstat ("conftest.sym/", &sbuf) ? 0 : 1);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_func_lstat_dereferences_slashed_symlink=yes
+else
+ echo "$as_me: program exited with status $ac_status" >&5
+echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_func_lstat_dereferences_slashed_symlink=no
+fi
+rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+else
+ # If the `ln -s' command failed, then we probably don't even
+ # have an lstat function.
+ ac_cv_func_lstat_dereferences_slashed_symlink=no
+fi
+rm -f conftest.sym conftest.file
+
+fi
+echo "$as_me:$LINENO: result: $ac_cv_func_lstat_dereferences_slashed_symlink" >&5
+echo "${ECHO_T}$ac_cv_func_lstat_dereferences_slashed_symlink" >&6
+
+test $ac_cv_func_lstat_dereferences_slashed_symlink = yes &&
+
+cat >>confdefs.h <<_ACEOF
+#define LSTAT_FOLLOWS_SLASHED_SYMLINK 1
+_ACEOF
+
+
+if test $ac_cv_func_lstat_dereferences_slashed_symlink = no; then
+ case $LIBOBJS in
+ "lstat.$ac_objext" | \
+ *" lstat.$ac_objext" | \
+ "lstat.$ac_objext "* | \
+ *" lstat.$ac_objext "* ) ;;
+ *) LIBOBJS="$LIBOBJS lstat.$ac_objext" ;;
+esac
+
+fi
+
+echo "$as_me:$LINENO: checking whether stat accepts an empty string" >&5
+echo $ECHO_N "checking whether stat accepts an empty string... $ECHO_C" >&6
+if test "${ac_cv_func_stat_empty_string_bug+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ if test "$cross_compiling" = yes; then
+ ac_cv_func_stat_empty_string_bug=yes
+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
+int
+main ()
+{
+struct stat sbuf;
+ exit (stat ("", &sbuf) ? 1 : 0);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_func_stat_empty_string_bug=yes
+else
+ echo "$as_me: program exited with status $ac_status" >&5
+echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_func_stat_empty_string_bug=no
+fi
+rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+fi
+echo "$as_me:$LINENO: result: $ac_cv_func_stat_empty_string_bug" >&5
+echo "${ECHO_T}$ac_cv_func_stat_empty_string_bug" >&6
+if test $ac_cv_func_stat_empty_string_bug = yes; then
+ case $LIBOBJS in
+ "stat.$ac_objext" | \
+ *" stat.$ac_objext" | \
+ "stat.$ac_objext "* | \
+ *" stat.$ac_objext "* ) ;;
+ *) LIBOBJS="$LIBOBJS stat.$ac_objext" ;;
+esac
+
+
+cat >>confdefs.h <<_ACEOF
+#define HAVE_STAT_EMPTY_STRING_BUG 1
+_ACEOF
+
+fi
+
+
+
+
+
+
+for ac_func in pow sqrt strchr strerror strrchr
+do
+as_ac_var=`echo "ac_cv_func_$ac_func" | $as_tr_sh`
+echo "$as_me:$LINENO: checking for $ac_func" >&5
+echo $ECHO_N "checking for $ac_func... $ECHO_C" >&6
+if eval "test \"\${$as_ac_var+set}\" = set"; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $ac_func (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any gcc2 internal prototype to avoid an error. */
+#ifdef __cplusplus
+extern "C"
+{
+#endif
+/* We use char because int might match the return type of a gcc2
+ builtin and then its argument prototype would still apply. */
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined (__stub_$ac_func) || defined (__stub___$ac_func)
+choke me
+#else
+char (*f) () = $ac_func;
+#endif
+#ifdef __cplusplus
+}
+#endif
+
+int
+main ()
+{
+return f != $ac_func;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+ (eval $ac_link) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest$ac_exeext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ eval "$as_ac_var=yes"
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+eval "$as_ac_var=no"
+fi
+rm -f conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_var'}'`" >&5
+echo "${ECHO_T}`eval echo '${'$as_ac_var'}'`" >&6
+if test `eval echo '${'$as_ac_var'}'` = yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+
+# Checks for png driver
+#
+# Handle user hints
+#
+
+ echo "$as_me:$LINENO: checking if libgd is wanted" >&5
+echo $ECHO_N "checking if libgd is wanted... $ECHO_C" >&6
+
+
+# Check whether --with-libgd or --without-libgd was given.
+if test "${with_libgd+set}" = set; then
+ withval="$with_libgd"
+
+ #
+ # Run this if -with or -without was specified
+ #
+ if test "$withval" != no ; then
+ echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+ LIBGD_WANTED=yes
+ if test "$withval" != yes ; then
+ LIBGD_HOME_DIR="$withval"
+ fi
+ else
+ LIBGD_WANTED=no
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+ fi
+
+else
+
+ # Nothing was said I assume libgd is needed
+
+ LIBGD_WANTED=yes
+ echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+
+fi;
+
+
+
+# just do the job if libgd is wanted
+if test $LIBGD_WANTED = yes; then
+
+ # save the state at begining
+ _old_LDFLAGS=$LDFLAGS
+ _old_CPPFLAGS=$CPPFLAGS
+
+ # perform search in various directory.
+ echo "$as_me:$LINENO: checking for libgd with png support" >&5
+echo $ECHO_N "checking for libgd with png support... $ECHO_C" >&6
+ for _search_dir_to_inc in "$LIBGD_HOME_DIR" /usr /usr/local ; do
+
+ LDFLAGS="$_old_LDFLAGS -L${_search_dir_to_inc}/lib"
+ CPPFLAGS="$_old_CPPFLAGS -I${_search_dir_to_inc}/include"
+
+
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include "gd.h"
+int
+main ()
+{
+ gdImagePtr im;
+ FILE *pngout;
+ gdImagePng(im, pngout);
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } &&
+ { ac_try='test -z "$ac_c_werror_flag"
+ || test ! -s conftest.err'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; } &&
+ { ac_try='test -s conftest.$ac_objext'
+ { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5
+ (eval $ac_try) 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ _compil_ok="yes"
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+fi
+rm -f conftest.err conftest.$ac_objext conftest.$ac_ext
+ if test "$_compil_ok" = yes ; then
+ break
+ fi
+ done
+
+ # if OK, then just add the library to $LIBS,
+ # else reset to the initial state
+
+ if test "$_compil_ok" = yes ; then
+ echo "$as_me:$LINENO: result: yes" >&5
+echo "${ECHO_T}yes" >&6
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_LIBGD 1
+_ACEOF
+
+ LIBS="$LIBS -lgd -lpng -lz"
+ if test -z "$_search_dir_to_inc" ; then
+ LDFLAGS=$_old_LDFLAGS
+ CPPFLAGS=$_old_CPPFLAGS
+ fi
+ else
+ echo "$as_me:$LINENO: result: no" >&5
+echo "${ECHO_T}no" >&6
+ { echo "$as_me:$LINENO: WARNING: libgd not found, graphic topologies will be unavailable" >&5
+echo "$as_me: WARNING: libgd not found, graphic topologies will be unavailable" >&2;}
+ fi
+
+
+if test "$_compil_ok"; then
+ USE_GD_LIB_SRC_TRUE=
+ USE_GD_LIB_SRC_FALSE='#'
+else
+ USE_GD_LIB_SRC_TRUE='#'
+ USE_GD_LIB_SRC_FALSE=
+fi
+
+ # if libgd is not wanted, disable some piece of code
+ # still to implement
+ # I'm thinking about
+ # setting up a #define and check for it in the code.
+
+fi
+
+
+# Host specific stuff
+OS_CPPFLAGS=""
+# Make sure we can run config.sub.
+$ac_config_sub sun4 >/dev/null 2>&1 ||
+ { { echo "$as_me:$LINENO: error: cannot run $ac_config_sub" >&5
+echo "$as_me: error: cannot run $ac_config_sub" >&2;}
+ { (exit 1); exit 1; }; }
+
+echo "$as_me:$LINENO: checking build system type" >&5
+echo $ECHO_N "checking build system type... $ECHO_C" >&6
+if test "${ac_cv_build+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ ac_cv_build_alias=$build_alias
+test -z "$ac_cv_build_alias" &&
+ ac_cv_build_alias=`$ac_config_guess`
+test -z "$ac_cv_build_alias" &&
+ { { echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5
+echo "$as_me: error: cannot guess build type; you must specify one" >&2;}
+ { (exit 1); exit 1; }; }
+ac_cv_build=`$ac_config_sub $ac_cv_build_alias` ||
+ { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_build_alias failed" >&5
+echo "$as_me: error: $ac_config_sub $ac_cv_build_alias failed" >&2;}
+ { (exit 1); exit 1; }; }
+
+fi
+echo "$as_me:$LINENO: result: $ac_cv_build" >&5
+echo "${ECHO_T}$ac_cv_build" >&6
+build=$ac_cv_build
+build_cpu=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'`
+build_vendor=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'`
+build_os=`echo $ac_cv_build | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'`
+
+
+echo "$as_me:$LINENO: checking host system type" >&5
+echo $ECHO_N "checking host system type... $ECHO_C" >&6
+if test "${ac_cv_host+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ ac_cv_host_alias=$host_alias
+test -z "$ac_cv_host_alias" &&
+ ac_cv_host_alias=$ac_cv_build_alias
+ac_cv_host=`$ac_config_sub $ac_cv_host_alias` ||
+ { { echo "$as_me:$LINENO: error: $ac_config_sub $ac_cv_host_alias failed" >&5
+echo "$as_me: error: $ac_config_sub $ac_cv_host_alias failed" >&2;}
+ { (exit 1); exit 1; }; }
+
+fi
+echo "$as_me:$LINENO: result: $ac_cv_host" >&5
+echo "${ECHO_T}$ac_cv_host" >&6
+host=$ac_cv_host
+host_cpu=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'`
+host_vendor=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'`
+host_os=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'`
+
+
+case $host in
+ *-*osf*)
+ OS_CPPFLAGS="-D_XOPEN_SOURCE_EXTENDED"
+ break
+esac
+
+
+ ac_config_files="$ac_config_files Makefile m4/Makefile src/Makefile data/Makefile doc/Makefile test/Makefile"
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems. If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, don't put newlines in cache variables' values.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+{
+ (set) 2>&1 |
+ case `(ac_space=' '; set | grep ac_space) 2>&1` in
+ *ac_space=\ *)
+ # `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"
+ ;;
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n \
+ "s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1=\\2/p"
+ ;;
+ esac;
+} |
+ sed '
+ t clear
+ : clear
+ s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
+ t end
+ /^ac_cv_env/!s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+ : end' >>confcache
+if diff $cache_file confcache >/dev/null 2>&1; then :; else
+ if test -w $cache_file; then
+ test "x$cache_file" != "x/dev/null" && echo "updating cache $cache_file"
+ cat confcache >$cache_file
+ else
+ echo "not updating unwritable cache $cache_file"
+ fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+# VPATH may cause trouble with some makes, so we remove $(srcdir),
+# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=/{
+s/:*\$(srcdir):*/:/;
+s/:*\${srcdir}:*/:/;
+s/:*@srcdir@:*/:/;
+s/^\([^=]*=[ ]*\):*/\1/;
+s/:*$//;
+s/^[^=]*=[ ]*$//;
+}'
+fi
+
+DEFS=-DHAVE_CONFIG_H
+
+ac_libobjs=
+ac_ltlibobjs=
+for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
+ # 1. Remove the extension, and $U if already installed.
+ ac_i=`echo "$ac_i" |
+ sed 's/\$U\././;s/\.o$//;s/\.obj$//'`
+ # 2. Add them.
+ ac_libobjs="$ac_libobjs $ac_i\$U.$ac_objext"
+ ac_ltlibobjs="$ac_ltlibobjs $ac_i"'$U.lo'
+done
+LIBOBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
+ { { echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+echo "$as_me: error: conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+ { { echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+echo "$as_me: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+if test -z "${USE_GD_LIB_SRC_TRUE}" && test -z "${USE_GD_LIB_SRC_FALSE}"; then
+ { { echo "$as_me:$LINENO: error: conditional \"USE_GD_LIB_SRC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+echo "$as_me: error: conditional \"USE_GD_LIB_SRC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+: ${CONFIG_STATUS=./config.status}
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5
+echo "$as_me: creating $CONFIG_STATUS" >&6;}
+cat >$CONFIG_STATUS <<_ACEOF
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+SHELL=\${CONFIG_SHELL-$SHELL}
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+## --------------------- ##
+## M4sh Initialization. ##
+## --------------------- ##
+
+# Be Bourne compatible
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then
+ set -o posix
+fi
+DUALCASE=1; export DUALCASE # for MKS sh
+
+# Support unset when possible.
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ as_unset=unset
+else
+ as_unset=false
+fi
+
+
+# Work around bugs in pre-3.0 UWIN ksh.
+$as_unset ENV MAIL MAILPATH
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+for as_var in \
+ LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \
+ LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \
+ LC_TELEPHONE LC_TIME
+do
+ if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then
+ eval $as_var=C; export $as_var
+ else
+ $as_unset $as_var
+ fi
+done
+
+# Required to use basename.
+if expr a : '\(a\)' >/dev/null 2>&1; 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 ||
+echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; }
+ /^X\/\(\/\/\)$/{ s//\1/; q; }
+ /^X\/\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+
+
+# PATH needs CR, and LINENO needs CR and PATH.
+# 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
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ echo "#! /bin/sh" >conf$$.sh
+ echo "exit 0" >>conf$$.sh
+ chmod +x conf$$.sh
+ if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
+ PATH_SEPARATOR=';'
+ else
+ PATH_SEPARATOR=:
+ fi
+ rm -f conf$$.sh
+fi
+
+
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null`
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x$as_lineno_3" = "x$as_lineno_2" || {
+ # Find who we are. Look in the path if we contain no path at all
+ # relative or not.
+ 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/$0 && break
+done
+
+ ;;
+ esac
+ # We did not find ourselves, most probably we were run as `sh COMMAND'
+ # in which case we are not to be found in the path.
+ if test "x$as_myself" = x; then
+ as_myself=$0
+ fi
+ if test ! -f "$as_myself"; then
+ { { echo "$as_me:$LINENO: error: cannot find myself; rerun with an absolute path" >&5
+echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ case $CONFIG_SHELL in
+ '')
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for as_base in sh bash ksh sh5; do
+ case $as_dir in
+ /*)
+ if ("$as_dir/$as_base" -c '
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null`
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then
+ $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; }
+ $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; }
+ CONFIG_SHELL=$as_dir/$as_base
+ export CONFIG_SHELL
+ exec "$CONFIG_SHELL" "$0" ${1+"$@"}
+ fi;;
+ esac
+ done
+done
+;;
+ esac
+
+ # 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 before each line; the second 'sed' does the real
+ # work. The second script uses 'N' to pair each line-number line
+ # with the numbered line, and appends trailing '-' during
+ # substitution so that $LINENO is not a special case at line end.
+ # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
+ # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-)
+ sed '=' <$as_myself |
+ sed '
+ N
+ s,$,-,
+ : loop
+ s,^\(['$as_cr_digits']*\)\(.*\)[$]LINENO\([^'$as_cr_alnum'_]\),\1\2\1\3,
+ t loop
+ s,-$,,
+ s,^['$as_cr_digits']*\n,,
+ ' >$as_me.lineno &&
+ chmod +x $as_me.lineno ||
+ { { echo "$as_me:$LINENO: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&5
+echo "$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 $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensible to this).
+ . ./$as_me.lineno
+ # Exit status is that of the last command.
+ exit
+}
+
+
+case `echo "testing\c"; echo 1,2,3`,`echo -n testing; echo 1,2,3` in
+ *c*,-n*) ECHO_N= ECHO_C='
+' ECHO_T=' ' ;;
+ *c*,* ) ECHO_N=-n ECHO_C= ECHO_T= ;;
+ *) ECHO_N= ECHO_C='\c' ECHO_T= ;;
+esac
+
+if expr a : '\(a\)' >/dev/null 2>&1; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+rm -f conf$$ conf$$.exe conf$$.file
+echo >conf$$.file
+if ln -s conf$$.file conf$$ 2>/dev/null; then
+ # We could just check for DJGPP; but this test a) works b) is more generic
+ # and c) will remain valid once DJGPP supports symlinks (DJGPP 2.04).
+ if test -f conf$$.exe; then
+ # Don't use ln at all; we don't have any links
+ as_ln_s='cp -p'
+ else
+ as_ln_s='ln -s'
+ fi
+elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.file
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p=:
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+as_executable_p="test -f"
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+# IFS
+# We need space, tab and new line, in precisely that order.
+as_nl='
+'
+IFS=" $as_nl"
+
+# CDPATH.
+$as_unset CDPATH
+
+exec 6>&1
+
+# Open the log real soon, to keep \$[0] and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling. Logging --version etc. is OK.
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
+## Running $as_me. ##
+_ASBOX
+} >&5
+cat >&5 <<_CSEOF
+
+This file was extended by toppred $as_me 1.10, which was
+generated by GNU Autoconf 2.59. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+_CSEOF
+echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5
+echo >&5
+_ACEOF
+
+# Files that config.status was made for.
+if test -n "$ac_config_files"; then
+ echo "config_files=\"$ac_config_files\"" >>$CONFIG_STATUS
+fi
+
+if test -n "$ac_config_headers"; then
+ echo "config_headers=\"$ac_config_headers\"" >>$CONFIG_STATUS
+fi
+
+if test -n "$ac_config_links"; then
+ echo "config_links=\"$ac_config_links\"" >>$CONFIG_STATUS
+fi
+
+if test -n "$ac_config_commands"; then
+ echo "config_commands=\"$ac_config_commands\"" >>$CONFIG_STATUS
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+
+ac_cs_usage="\
+\`$as_me' instantiates files from templates according to the
+current configuration.
+
+Usage: $0 [OPTIONS] [FILE]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number, then exit
+ -q, --quiet do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+ --header=FILE[:TEMPLATE]
+ instantiate the configuration header FILE
+
+Configuration files:
+$config_files
+
+Configuration headers:
+$config_headers
+
+Configuration commands:
+$config_commands
+
+Report bugs to <bug-autoconf at gnu.org>."
+_ACEOF
+
+cat >>$CONFIG_STATUS <<_ACEOF
+ac_cs_version="\\
+toppred config.status 1.10
+configured by $0, generated by GNU Autoconf 2.59,
+ with options \\"`echo "$ac_configure_args" | sed 's/[\\""\`\$]/\\\\&/g'`\\"
+
+Copyright (C) 2003 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+srcdir=$srcdir
+INSTALL="$INSTALL"
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+# If no file are specified by the user, then we need to provide default
+# value. By we need to know if files were specified by the user.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=*)
+ ac_option=`expr "x$1" : 'x\([^=]*\)='`
+ ac_optarg=`expr "x$1" : 'x[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ -*)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ *) # This is not an option, so the user has probably given explicit
+ # arguments.
+ ac_option=$1
+ ac_need_defaults=false;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --vers* | -V )
+ echo "$ac_cs_version"; exit 0 ;;
+ --he | --h)
+ # Conflict between --help and --header
+ { { echo "$as_me:$LINENO: error: ambiguous option: $1
+Try \`$0 --help' for more information." >&5
+echo "$as_me: error: ambiguous option: $1
+Try \`$0 --help' for more information." >&2;}
+ { (exit 1); exit 1; }; };;
+ --help | --hel | -h )
+ echo "$ac_cs_usage"; exit 0 ;;
+ --debug | --d* | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ CONFIG_FILES="$CONFIG_FILES $ac_optarg"
+ ac_need_defaults=false;;
+ --header | --heade | --head | --hea )
+ $ac_shift
+ CONFIG_HEADERS="$CONFIG_HEADERS $ac_optarg"
+ ac_need_defaults=false;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) { { echo "$as_me:$LINENO: error: unrecognized option: $1
+Try \`$0 --help' for more information." >&5
+echo "$as_me: error: unrecognized option: $1
+Try \`$0 --help' for more information." >&2;}
+ { (exit 1); exit 1; }; } ;;
+
+ *) ac_config_targets="$ac_config_targets $1" ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF
+if \$ac_cs_recheck; then
+ echo "running $SHELL $0 " $ac_configure_args \$ac_configure_extra_args " --no-create --no-recursion" >&6
+ exec $SHELL $0 $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+fi
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<_ACEOF
+#
+# INIT-COMMANDS section.
+#
+
+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
+
+_ACEOF
+
+
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+for ac_config_target in $ac_config_targets
+do
+ case "$ac_config_target" in
+ # Handling of arguments.
+ "Makefile" ) CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+ "m4/Makefile" ) CONFIG_FILES="$CONFIG_FILES m4/Makefile" ;;
+ "src/Makefile" ) CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+ "data/Makefile" ) CONFIG_FILES="$CONFIG_FILES data/Makefile" ;;
+ "doc/Makefile" ) CONFIG_FILES="$CONFIG_FILES doc/Makefile" ;;
+ "test/Makefile" ) CONFIG_FILES="$CONFIG_FILES test/Makefile" ;;
+ "depfiles" ) CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "src/config.h" ) CONFIG_HEADERS="$CONFIG_HEADERS src/config.h" ;;
+ *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
+echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
+ { (exit 1); exit 1; }; };;
+ esac
+done
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers
+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason to put it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Create a temporary directory, and hook for its removal unless debugging.
+$debug ||
+{
+ trap 'exit_status=$?; rm -rf $tmp && exit $exit_status' 0
+ trap '{ (exit 1); exit 1; }' 1 2 13 15
+}
+
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d -q "./confstatXXXXXX") 2>/dev/null` &&
+ test -n "$tmp" && test -d "$tmp"
+} ||
+{
+ tmp=./confstat$$-$RANDOM
+ (umask 077 && mkdir $tmp)
+} ||
+{
+ echo "$me: cannot create a temporary directory in ." >&2
+ { (exit 1); exit 1; }
+}
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<_ACEOF
+
+#
+# CONFIG_FILES section.
+#
+
+# No need to generate the scripts if there are no CONFIG_FILES.
+# This happens for instance when ./config.status config.h
+if test -n "\$CONFIG_FILES"; then
+ # Protect against being on the right side of a sed subst in config.status.
+ sed 's/,@/@@/; s/@,/@@/; s/,;t t\$/@;t t/; /@;t t\$/s/[\\\\&,]/\\\\&/g;
+ s/@@/,@/; s/@@/@,/; s/@;t t\$/,;t t/' >\$tmp/subs.sed <<\\CEOF
+s, at SHELL@,$SHELL,;t t
+s, at PATH_SEPARATOR@,$PATH_SEPARATOR,;t t
+s, at PACKAGE_NAME@,$PACKAGE_NAME,;t t
+s, at PACKAGE_TARNAME@,$PACKAGE_TARNAME,;t t
+s, at PACKAGE_VERSION@,$PACKAGE_VERSION,;t t
+s, at PACKAGE_STRING@,$PACKAGE_STRING,;t t
+s, at PACKAGE_BUGREPORT@,$PACKAGE_BUGREPORT,;t t
+s, at exec_prefix@,$exec_prefix,;t t
+s, at prefix@,$prefix,;t t
+s, at program_transform_name@,$program_transform_name,;t t
+s, at bindir@,$bindir,;t t
+s, at sbindir@,$sbindir,;t t
+s, at libexecdir@,$libexecdir,;t t
+s, at datadir@,$datadir,;t t
+s, at sysconfdir@,$sysconfdir,;t t
+s, at sharedstatedir@,$sharedstatedir,;t t
+s, at localstatedir@,$localstatedir,;t t
+s, at libdir@,$libdir,;t t
+s, at includedir@,$includedir,;t t
+s, at oldincludedir@,$oldincludedir,;t t
+s, at infodir@,$infodir,;t t
+s, at mandir@,$mandir,;t t
+s, at build_alias@,$build_alias,;t t
+s, at host_alias@,$host_alias,;t t
+s, at target_alias@,$target_alias,;t t
+s, at DEFS@,$DEFS,;t t
+s, at ECHO_C@,$ECHO_C,;t t
+s, at ECHO_N@,$ECHO_N,;t t
+s, at ECHO_T@,$ECHO_T,;t t
+s, at LIBS@,$LIBS,;t t
+s, at INSTALL_PROGRAM@,$INSTALL_PROGRAM,;t t
+s, at INSTALL_SCRIPT@,$INSTALL_SCRIPT,;t t
+s, at INSTALL_DATA@,$INSTALL_DATA,;t t
+s, at CYGPATH_W@,$CYGPATH_W,;t t
+s, at PACKAGE@,$PACKAGE,;t t
+s, at VERSION@,$VERSION,;t t
+s, at ACLOCAL@,$ACLOCAL,;t t
+s, at AUTOCONF@,$AUTOCONF,;t t
+s, at AUTOMAKE@,$AUTOMAKE,;t t
+s, at AUTOHEADER@,$AUTOHEADER,;t t
+s, at MAKEINFO@,$MAKEINFO,;t t
+s, at install_sh@,$install_sh,;t t
+s, at STRIP@,$STRIP,;t t
+s, at ac_ct_STRIP@,$ac_ct_STRIP,;t t
+s, at INSTALL_STRIP_PROGRAM@,$INSTALL_STRIP_PROGRAM,;t t
+s, at mkdir_p@,$mkdir_p,;t t
+s, at AWK@,$AWK,;t t
+s, at SET_MAKE@,$SET_MAKE,;t t
+s, at am__leading_dot@,$am__leading_dot,;t t
+s, at AMTAR@,$AMTAR,;t t
+s, at am__tar@,$am__tar,;t t
+s, at am__untar@,$am__untar,;t t
+s, at CC@,$CC,;t t
+s, at CFLAGS@,$CFLAGS,;t t
+s, at LDFLAGS@,$LDFLAGS,;t t
+s, at CPPFLAGS@,$CPPFLAGS,;t t
+s, at ac_ct_CC@,$ac_ct_CC,;t t
+s, at EXEEXT@,$EXEEXT,;t t
+s, at OBJEXT@,$OBJEXT,;t t
+s, at DEPDIR@,$DEPDIR,;t t
+s, at am__include@,$am__include,;t t
+s, at am__quote@,$am__quote,;t t
+s, at AMDEP_TRUE@,$AMDEP_TRUE,;t t
+s, at AMDEP_FALSE@,$AMDEP_FALSE,;t t
+s, at AMDEPBACKSLASH@,$AMDEPBACKSLASH,;t t
+s, at CCDEPMODE@,$CCDEPMODE,;t t
+s, at am__fastdepCC_TRUE@,$am__fastdepCC_TRUE,;t t
+s, at am__fastdepCC_FALSE@,$am__fastdepCC_FALSE,;t t
+s, at POD2MAN@,$POD2MAN,;t t
+s, at GNUPLOT@,$GNUPLOT,;t t
+s, at CPP@,$CPP,;t t
+s, at EGREP@,$EGREP,;t t
+s, at LIBOBJS@,$LIBOBJS,;t t
+s, at USE_GD_LIB_SRC_TRUE@,$USE_GD_LIB_SRC_TRUE,;t t
+s, at USE_GD_LIB_SRC_FALSE@,$USE_GD_LIB_SRC_FALSE,;t t
+s, at build@,$build,;t t
+s, at build_cpu@,$build_cpu,;t t
+s, at build_vendor@,$build_vendor,;t t
+s, at build_os@,$build_os,;t t
+s, at host@,$host,;t t
+s, at host_cpu@,$host_cpu,;t t
+s, at host_vendor@,$host_vendor,;t t
+s, at host_os@,$host_os,;t t
+s, at OS_CPPFLAGS@,$OS_CPPFLAGS,;t t
+s, at LTLIBOBJS@,$LTLIBOBJS,;t t
+CEOF
+
+_ACEOF
+
+ cat >>$CONFIG_STATUS <<\_ACEOF
+ # Split the substitutions into bite-sized pieces for seds with
+ # small command number limits, like on Digital OSF/1 and HP-UX.
+ ac_max_sed_lines=48
+ ac_sed_frag=1 # Number of current file.
+ ac_beg=1 # First line for current file.
+ ac_end=$ac_max_sed_lines # Line after last line for current file.
+ ac_more_lines=:
+ ac_sed_cmds=
+ while $ac_more_lines; do
+ if test $ac_beg -gt 1; then
+ sed "1,${ac_beg}d; ${ac_end}q" $tmp/subs.sed >$tmp/subs.frag
+ else
+ sed "${ac_end}q" $tmp/subs.sed >$tmp/subs.frag
+ fi
+ if test ! -s $tmp/subs.frag; then
+ ac_more_lines=false
+ else
+ # The purpose of the label and of the branching condition is to
+ # speed up the sed processing (if there are no `@' at all, there
+ # is no need to browse any of the substitutions).
+ # These are the two extra sed commands mentioned above.
+ (echo ':t
+ /@[a-zA-Z_][a-zA-Z_0-9]*@/!b' && cat $tmp/subs.frag) >$tmp/subs-$ac_sed_frag.sed
+ if test -z "$ac_sed_cmds"; then
+ ac_sed_cmds="sed -f $tmp/subs-$ac_sed_frag.sed"
+ else
+ ac_sed_cmds="$ac_sed_cmds | sed -f $tmp/subs-$ac_sed_frag.sed"
+ fi
+ ac_sed_frag=`expr $ac_sed_frag + 1`
+ ac_beg=$ac_end
+ ac_end=`expr $ac_end + $ac_max_sed_lines`
+ fi
+ done
+ if test -z "$ac_sed_cmds"; then
+ ac_sed_cmds=cat
+ fi
+fi # test -n "$CONFIG_FILES"
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF
+for ac_file in : $CONFIG_FILES; do test "x$ac_file" = x: && continue
+ # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in".
+ case $ac_file in
+ - | *:- | *:-:* ) # input from stdin
+ cat >$tmp/stdin
+ ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'`
+ ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;;
+ *:* ) ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'`
+ ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;;
+ * ) ac_file_in=$ac_file.in ;;
+ esac
+
+ # Compute @srcdir@, @top_srcdir@, and @INSTALL@ for subdirectories.
+ ac_dir=`(dirname "$ac_file") 2>/dev/null ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ { if $as_mkdir_p; then
+ mkdir -p "$ac_dir"
+ else
+ as_dir="$ac_dir"
+ as_dirs=
+ while test ! -d "$as_dir"; do
+ as_dirs="$as_dir $as_dirs"
+ as_dir=`(dirname "$as_dir") 2>/dev/null ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ done
+ test ! -n "$as_dirs" || mkdir $as_dirs
+ fi || { { echo "$as_me:$LINENO: error: cannot create directory \"$ac_dir\"" >&5
+echo "$as_me: error: cannot create directory \"$ac_dir\"" >&2;}
+ { (exit 1); exit 1; }; }; }
+
+ ac_builddir=.
+
+if test "$ac_dir" != .; then
+ ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
+ # A "../" for each directory in $ac_dir_suffix.
+ ac_top_builddir=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,../,g'`
+else
+ ac_dir_suffix= ac_top_builddir=
+fi
+
+case $srcdir in
+ .) # No --srcdir option. We are building in place.
+ ac_srcdir=.
+ if test -z "$ac_top_builddir"; then
+ ac_top_srcdir=.
+ else
+ ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'`
+ fi ;;
+ [\\/]* | ?:[\\/]* ) # Absolute path.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir ;;
+ *) # Relative path.
+ ac_srcdir=$ac_top_builddir$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_builddir$srcdir ;;
+esac
+
+# Do not use `cd foo && pwd` to compute absolute paths, because
+# the directories may not exist.
+case `pwd` in
+.) ac_abs_builddir="$ac_dir";;
+*)
+ case "$ac_dir" in
+ .) ac_abs_builddir=`pwd`;;
+ [\\/]* | ?:[\\/]* ) ac_abs_builddir="$ac_dir";;
+ *) ac_abs_builddir=`pwd`/"$ac_dir";;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_top_builddir=${ac_top_builddir}.;;
+*)
+ case ${ac_top_builddir}. in
+ .) ac_abs_top_builddir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_top_builddir=${ac_top_builddir}.;;
+ *) ac_abs_top_builddir=$ac_abs_builddir/${ac_top_builddir}.;;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_srcdir=$ac_srcdir;;
+*)
+ case $ac_srcdir in
+ .) ac_abs_srcdir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_srcdir=$ac_srcdir;;
+ *) ac_abs_srcdir=$ac_abs_builddir/$ac_srcdir;;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_top_srcdir=$ac_top_srcdir;;
+*)
+ case $ac_top_srcdir in
+ .) ac_abs_top_srcdir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_top_srcdir=$ac_top_srcdir;;
+ *) ac_abs_top_srcdir=$ac_abs_builddir/$ac_top_srcdir;;
+ esac;;
+esac
+
+
+ case $INSTALL in
+ [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
+ *) ac_INSTALL=$ac_top_builddir$INSTALL ;;
+ esac
+
+ if test x"$ac_file" != x-; then
+ { echo "$as_me:$LINENO: creating $ac_file" >&5
+echo "$as_me: creating $ac_file" >&6;}
+ rm -f "$ac_file"
+ fi
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ if test x"$ac_file" = x-; then
+ configure_input=
+ else
+ configure_input="$ac_file. "
+ fi
+ configure_input=$configure_input"Generated from `echo $ac_file_in |
+ sed 's,.*/,,'` by configure."
+
+ # First look for the input files in the build tree, otherwise in the
+ # src tree.
+ ac_file_inputs=`IFS=:
+ for f in $ac_file_in; do
+ case $f in
+ -) echo $tmp/stdin ;;
+ [\\/$]*)
+ # Absolute (can't be DOS-style, as IFS=:)
+ test -f "$f" || { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5
+echo "$as_me: error: cannot find input file: $f" >&2;}
+ { (exit 1); exit 1; }; }
+ echo "$f";;
+ *) # Relative
+ if test -f "$f"; then
+ # Build tree
+ echo "$f"
+ elif test -f "$srcdir/$f"; then
+ # Source tree
+ echo "$srcdir/$f"
+ else
+ # /dev/null tree
+ { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5
+echo "$as_me: error: cannot find input file: $f" >&2;}
+ { (exit 1); exit 1; }; }
+ fi;;
+ esac
+ done` || { (exit 1); exit 1; }
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF
+ sed "$ac_vpsub
+$extrasub
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s, at configure_input@,$configure_input,;t t
+s, at srcdir@,$ac_srcdir,;t t
+s, at abs_srcdir@,$ac_abs_srcdir,;t t
+s, at top_srcdir@,$ac_top_srcdir,;t t
+s, at abs_top_srcdir@,$ac_abs_top_srcdir,;t t
+s, at builddir@,$ac_builddir,;t t
+s, at abs_builddir@,$ac_abs_builddir,;t t
+s, at top_builddir@,$ac_top_builddir,;t t
+s, at abs_top_builddir@,$ac_abs_top_builddir,;t t
+s, at INSTALL@,$ac_INSTALL,;t t
+" $ac_file_inputs | (eval "$ac_sed_cmds") >$tmp/out
+ rm -f $tmp/stdin
+ if test x"$ac_file" != x-; then
+ mv $tmp/out $ac_file
+ else
+ cat $tmp/out
+ rm -f $tmp/out
+ fi
+
+done
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF
+
+#
+# CONFIG_HEADER section.
+#
+
+# These sed commands are passed to sed as "A NAME B NAME C VALUE D", where
+# NAME is the cpp macro being defined and VALUE is the value it is being given.
+#
+# ac_d sets the value in "#define NAME VALUE" lines.
+ac_dA='s,^\([ ]*\)#\([ ]*define[ ][ ]*\)'
+ac_dB='[ ].*$,\1#\2'
+ac_dC=' '
+ac_dD=',;t'
+# ac_u turns "#undef NAME" without trailing blanks into "#define NAME VALUE".
+ac_uA='s,^\([ ]*\)#\([ ]*\)undef\([ ][ ]*\)'
+ac_uB='$,\1#\2define\3'
+ac_uC=' '
+ac_uD=',;t'
+
+for ac_file in : $CONFIG_HEADERS; do test "x$ac_file" = x: && continue
+ # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in".
+ case $ac_file in
+ - | *:- | *:-:* ) # input from stdin
+ cat >$tmp/stdin
+ ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'`
+ ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;;
+ *:* ) ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'`
+ ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;;
+ * ) ac_file_in=$ac_file.in ;;
+ esac
+
+ test x"$ac_file" != x- && { echo "$as_me:$LINENO: creating $ac_file" >&5
+echo "$as_me: creating $ac_file" >&6;}
+
+ # First look for the input files in the build tree, otherwise in the
+ # src tree.
+ ac_file_inputs=`IFS=:
+ for f in $ac_file_in; do
+ case $f in
+ -) echo $tmp/stdin ;;
+ [\\/$]*)
+ # Absolute (can't be DOS-style, as IFS=:)
+ test -f "$f" || { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5
+echo "$as_me: error: cannot find input file: $f" >&2;}
+ { (exit 1); exit 1; }; }
+ # Do quote $f, to prevent DOS paths from being IFS'd.
+ echo "$f";;
+ *) # Relative
+ if test -f "$f"; then
+ # Build tree
+ echo "$f"
+ elif test -f "$srcdir/$f"; then
+ # Source tree
+ echo "$srcdir/$f"
+ else
+ # /dev/null tree
+ { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5
+echo "$as_me: error: cannot find input file: $f" >&2;}
+ { (exit 1); exit 1; }; }
+ fi;;
+ esac
+ done` || { (exit 1); exit 1; }
+ # Remove the trailing spaces.
+ sed 's/[ ]*$//' $ac_file_inputs >$tmp/in
+
+_ACEOF
+
+# Transform confdefs.h into two sed scripts, `conftest.defines' and
+# `conftest.undefs', that substitutes the proper values into
+# config.h.in to produce config.h. The first handles `#define'
+# templates, and the second `#undef' templates.
+# And first: Protect against being on the right side of a sed subst in
+# config.status. Protect against being in an unquoted here document
+# in config.status.
+rm -f conftest.defines conftest.undefs
+# Using a here document instead of a string reduces the quoting nightmare.
+# Putting comments in sed scripts is not portable.
+#
+# `end' is used to avoid that the second main sed command (meant for
+# 0-ary CPP macros) applies to n-ary macro definitions.
+# See the Autoconf documentation for `clear'.
+cat >confdef2sed.sed <<\_ACEOF
+s/[\\&,]/\\&/g
+s,[\\$`],\\&,g
+t clear
+: clear
+s,^[ ]*#[ ]*define[ ][ ]*\([^ (][^ (]*\)\(([^)]*)\)[ ]*\(.*\)$,${ac_dA}\1${ac_dB}\1\2${ac_dC}\3${ac_dD},gp
+t end
+s,^[ ]*#[ ]*define[ ][ ]*\([^ ][^ ]*\)[ ]*\(.*\)$,${ac_dA}\1${ac_dB}\1${ac_dC}\2${ac_dD},gp
+: end
+_ACEOF
+# If some macros were called several times there might be several times
+# the same #defines, which is useless. Nevertheless, we may not want to
+# sort them, since we want the *last* AC-DEFINE to be honored.
+uniq confdefs.h | sed -n -f confdef2sed.sed >conftest.defines
+sed 's/ac_d/ac_u/g' conftest.defines >conftest.undefs
+rm -f confdef2sed.sed
+
+# This sed command replaces #undef with comments. This is necessary, for
+# example, in the case of _POSIX_SOURCE, which is predefined and required
+# on some systems where configure will not decide to define it.
+cat >>conftest.undefs <<\_ACEOF
+s,^[ ]*#[ ]*undef[ ][ ]*[a-zA-Z_][a-zA-Z_0-9]*,/* & */,
+_ACEOF
+
+# Break up conftest.defines because some shells have a limit on the size
+# of here documents, and old seds have small limits too (100 cmds).
+echo ' # Handle all the #define templates only if necessary.' >>$CONFIG_STATUS
+echo ' if grep "^[ ]*#[ ]*define" $tmp/in >/dev/null; then' >>$CONFIG_STATUS
+echo ' # If there are no defines, we may have an empty if/fi' >>$CONFIG_STATUS
+echo ' :' >>$CONFIG_STATUS
+rm -f conftest.tail
+while grep . conftest.defines >/dev/null
+do
+ # Write a limited-size here document to $tmp/defines.sed.
+ echo ' cat >$tmp/defines.sed <<CEOF' >>$CONFIG_STATUS
+ # Speed up: don't consider the non `#define' lines.
+ echo '/^[ ]*#[ ]*define/!b' >>$CONFIG_STATUS
+ # Work around the forget-to-reset-the-flag bug.
+ echo 't clr' >>$CONFIG_STATUS
+ echo ': clr' >>$CONFIG_STATUS
+ sed ${ac_max_here_lines}q conftest.defines >>$CONFIG_STATUS
+ echo 'CEOF
+ sed -f $tmp/defines.sed $tmp/in >$tmp/out
+ rm -f $tmp/in
+ mv $tmp/out $tmp/in
+' >>$CONFIG_STATUS
+ sed 1,${ac_max_here_lines}d conftest.defines >conftest.tail
+ rm -f conftest.defines
+ mv conftest.tail conftest.defines
+done
+rm -f conftest.defines
+echo ' fi # grep' >>$CONFIG_STATUS
+echo >>$CONFIG_STATUS
+
+# Break up conftest.undefs because some shells have a limit on the size
+# of here documents, and old seds have small limits too (100 cmds).
+echo ' # Handle all the #undef templates' >>$CONFIG_STATUS
+rm -f conftest.tail
+while grep . conftest.undefs >/dev/null
+do
+ # Write a limited-size here document to $tmp/undefs.sed.
+ echo ' cat >$tmp/undefs.sed <<CEOF' >>$CONFIG_STATUS
+ # Speed up: don't consider the non `#undef'
+ echo '/^[ ]*#[ ]*undef/!b' >>$CONFIG_STATUS
+ # Work around the forget-to-reset-the-flag bug.
+ echo 't clr' >>$CONFIG_STATUS
+ echo ': clr' >>$CONFIG_STATUS
+ sed ${ac_max_here_lines}q conftest.undefs >>$CONFIG_STATUS
+ echo 'CEOF
+ sed -f $tmp/undefs.sed $tmp/in >$tmp/out
+ rm -f $tmp/in
+ mv $tmp/out $tmp/in
+' >>$CONFIG_STATUS
+ sed 1,${ac_max_here_lines}d conftest.undefs >conftest.tail
+ rm -f conftest.undefs
+ mv conftest.tail conftest.undefs
+done
+rm -f conftest.undefs
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ if test x"$ac_file" = x-; then
+ echo "/* Generated by configure. */" >$tmp/config.h
+ else
+ echo "/* $ac_file. Generated by configure. */" >$tmp/config.h
+ fi
+ cat $tmp/in >>$tmp/config.h
+ rm -f $tmp/in
+ if test x"$ac_file" != x-; then
+ if diff $ac_file $tmp/config.h >/dev/null 2>&1; then
+ { echo "$as_me:$LINENO: $ac_file is unchanged" >&5
+echo "$as_me: $ac_file is unchanged" >&6;}
+ else
+ ac_dir=`(dirname "$ac_file") 2>/dev/null ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ { if $as_mkdir_p; then
+ mkdir -p "$ac_dir"
+ else
+ as_dir="$ac_dir"
+ as_dirs=
+ while test ! -d "$as_dir"; do
+ as_dirs="$as_dir $as_dirs"
+ as_dir=`(dirname "$as_dir") 2>/dev/null ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ done
+ test ! -n "$as_dirs" || mkdir $as_dirs
+ fi || { { echo "$as_me:$LINENO: error: cannot create directory \"$ac_dir\"" >&5
+echo "$as_me: error: cannot create directory \"$ac_dir\"" >&2;}
+ { (exit 1); exit 1; }; }; }
+
+ rm -f $ac_file
+ mv $tmp/config.h $ac_file
+ fi
+ else
+ cat $tmp/config.h
+ rm -f $tmp/config.h
+ fi
+# Compute $ac_file's index in $config_headers.
+_am_stamp_count=1
+for _am_header in $config_headers :; do
+ case $_am_header in
+ $ac_file | $ac_file:* )
+ break ;;
+ * )
+ _am_stamp_count=`expr $_am_stamp_count + 1` ;;
+ esac
+done
+echo "timestamp for $ac_file" >`(dirname $ac_file) 2>/dev/null ||
+$as_expr X$ac_file : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X$ac_file : 'X\(//\)[^/]' \| \
+ X$ac_file : 'X\(//\)$' \| \
+ X$ac_file : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X$ac_file |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`/stamp-h$_am_stamp_count
+done
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF
+
+#
+# CONFIG_COMMANDS section.
+#
+for ac_file in : $CONFIG_COMMANDS; do test "x$ac_file" = x: && continue
+ ac_dest=`echo "$ac_file" | sed 's,:.*,,'`
+ ac_source=`echo "$ac_file" | sed 's,[^:]*:,,'`
+ ac_dir=`(dirname "$ac_dest") 2>/dev/null ||
+$as_expr X"$ac_dest" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_dest" : 'X\(//\)[^/]' \| \
+ X"$ac_dest" : 'X\(//\)$' \| \
+ X"$ac_dest" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$ac_dest" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ { if $as_mkdir_p; then
+ mkdir -p "$ac_dir"
+ else
+ as_dir="$ac_dir"
+ as_dirs=
+ while test ! -d "$as_dir"; do
+ as_dirs="$as_dir $as_dirs"
+ as_dir=`(dirname "$as_dir") 2>/dev/null ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ done
+ test ! -n "$as_dirs" || mkdir $as_dirs
+ fi || { { echo "$as_me:$LINENO: error: cannot create directory \"$ac_dir\"" >&5
+echo "$as_me: error: cannot create directory \"$ac_dir\"" >&2;}
+ { (exit 1); exit 1; }; }; }
+
+ ac_builddir=.
+
+if test "$ac_dir" != .; then
+ ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
+ # A "../" for each directory in $ac_dir_suffix.
+ ac_top_builddir=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,../,g'`
+else
+ ac_dir_suffix= ac_top_builddir=
+fi
+
+case $srcdir in
+ .) # No --srcdir option. We are building in place.
+ ac_srcdir=.
+ if test -z "$ac_top_builddir"; then
+ ac_top_srcdir=.
+ else
+ ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'`
+ fi ;;
+ [\\/]* | ?:[\\/]* ) # Absolute path.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir ;;
+ *) # Relative path.
+ ac_srcdir=$ac_top_builddir$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_builddir$srcdir ;;
+esac
+
+# Do not use `cd foo && pwd` to compute absolute paths, because
+# the directories may not exist.
+case `pwd` in
+.) ac_abs_builddir="$ac_dir";;
+*)
+ case "$ac_dir" in
+ .) ac_abs_builddir=`pwd`;;
+ [\\/]* | ?:[\\/]* ) ac_abs_builddir="$ac_dir";;
+ *) ac_abs_builddir=`pwd`/"$ac_dir";;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_top_builddir=${ac_top_builddir}.;;
+*)
+ case ${ac_top_builddir}. in
+ .) ac_abs_top_builddir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_top_builddir=${ac_top_builddir}.;;
+ *) ac_abs_top_builddir=$ac_abs_builddir/${ac_top_builddir}.;;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_srcdir=$ac_srcdir;;
+*)
+ case $ac_srcdir in
+ .) ac_abs_srcdir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_srcdir=$ac_srcdir;;
+ *) ac_abs_srcdir=$ac_abs_builddir/$ac_srcdir;;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_top_srcdir=$ac_top_srcdir;;
+*)
+ case $ac_top_srcdir in
+ .) ac_abs_top_srcdir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_top_srcdir=$ac_top_srcdir;;
+ *) ac_abs_top_srcdir=$ac_abs_builddir/$ac_top_srcdir;;
+ esac;;
+esac
+
+
+ { echo "$as_me:$LINENO: executing $ac_dest commands" >&5
+echo "$as_me: executing $ac_dest commands" >&6;}
+ case $ac_dest in
+ depfiles ) test x"$AMDEP_TRUE" != x"" || for mf in $CONFIG_FILES; do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # So let's grep whole file.
+ if grep '^#.*generated by automake' $mf > /dev/null 2>&1; then
+ dirpart=`(dirname "$mf") 2>/dev/null ||
+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$mf" : 'X\(//\)[^/]' \| \
+ X"$mf" : 'X\(//\)$' \| \
+ X"$mf" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$mf" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ else
+ continue
+ fi
+ # Extract the definition of DEPDIR, am__include, and am__quote
+ # from the Makefile without running `make'.
+ DEPDIR=`sed -n 's/^DEPDIR = //p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n 's/^U = //p' < "$mf"`
+ # Find all dependency output files, they are included files with
+ # $(DEPDIR) in their names. We invoke sed twice because it is the
+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
+ for file in `sed -n "
+ s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`(dirname "$file") 2>/dev/null ||
+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$file" : 'X\(//\)[^/]' \| \
+ X"$file" : 'X\(//\)$' \| \
+ X"$file" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ { if $as_mkdir_p; then
+ mkdir -p $dirpart/$fdir
+ else
+ as_dir=$dirpart/$fdir
+ as_dirs=
+ while test ! -d "$as_dir"; do
+ as_dirs="$as_dir $as_dirs"
+ as_dir=`(dirname "$as_dir") 2>/dev/null ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ done
+ test ! -n "$as_dirs" || mkdir $as_dirs
+ fi || { { echo "$as_me:$LINENO: error: cannot create directory $dirpart/$fdir" >&5
+echo "$as_me: error: cannot create directory $dirpart/$fdir" >&2;}
+ { (exit 1); exit 1; }; }; }
+
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+done
+ ;;
+ esac
+done
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF
+
+{ (exit 0); exit 0; }
+_ACEOF
+chmod +x $CONFIG_STATUS
+ac_clean_files=$ac_clean_files_save
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded. So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status. When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+ ac_cs_success=:
+ ac_config_status_args=
+ test "$silent" = yes &&
+ ac_config_status_args="$ac_config_status_args --quiet"
+ exec 5>/dev/null
+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+ 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.
+ $ac_cs_success || { (exit 1); exit 1; }
+fi
+
diff --git a/configure.in b/configure.in
new file mode 100644
index 0000000..dae5dea
--- /dev/null
+++ b/configure.in
@@ -0,0 +1,48 @@
+# Process this file with autoconf to produce a configure script.
+AC_INIT([toppred], [1.10])
+AM_INIT_AUTOMAKE
+AM_CONFIG_HEADER([src/config.h])
+
+# Checks for programs.
+AC_PROG_CC
+AC_CHECK_PROG(POD2MAN, pod2man, pod2man, :)
+AC_CHECK_PROG(GNUPLOT, gnuplot, gnuplot)
+if test "$GNUPLOT" = "gnuplot"; then
+ AC_DEFINE(HAVE_GNUPLOT, 1, is gnuplot present)
+else
+ AC_MSG_WARN([gnuplot not found, Hydrophobic profile will be unavailable])
+fi
+
+# Checks for libraries.
+AC_CHECK_LIB(m, pow)
+
+# Checks for header files.
+AC_HEADER_STDC
+AC_CHECK_HEADERS([errno.h stdlib.h string.h unistd.h])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_C_CONST
+AC_TYPE_SIZE_T
+AC_STRUCT_TM
+
+# Checks for library functions.
+# AC_FUNC_MALLOC # tru64 problem
+AC_FUNC_STAT
+AC_CHECK_FUNCS([pow sqrt strchr strerror strrchr])
+
+# Checks for png driver
+GD_CHECK
+
+# Host specific stuff
+OS_CPPFLAGS=""
+AC_CANONICAL_HOST
+case $host in
+ *-*osf*)
+ OS_CPPFLAGS="-D_XOPEN_SOURCE_EXTENDED"
+ break
+esac
+AC_SUBST([OS_CPPFLAGS])
+
+AC_CONFIG_FILES([Makefile m4/Makefile src/Makefile data/Makefile doc/Makefile
+ test/Makefile])
+AC_OUTPUT
diff --git a/data/CYTEXT-scale b/data/CYTEXT-scale
new file mode 100644
index 0000000..66494d8
--- /dev/null
+++ b/data/CYTEXT-scale
@@ -0,0 +1,24 @@
+#___________________________________________________________________________
+#
+# aa cyt ext sd
+#___________________________________________________________________________
+A 8.387 8.097 3.7
+C 3.226 0 2.3
+D 7.419 6.005 2.2
+E 7.742 5.533 3.0
+F 2.581 3.171 1.9
+G 7.419 8.907 3.4
+H 0.968 1.417 1.6
+I 5.484 4.926 2.5
+K 5.484 5.533 3.4
+L 9.032 7.422 3.4
+M 3.226 3.171 1.4
+N 3.871 4.858 2.3
+P 4.194 6.545 3.2
+Q 3.548 3.306 2.4
+R 9.032 5.938 3.3
+S 4.516 6.883 2.8
+T 6.129 5.263 2.6
+V 4.516 8.165 2.5
+W 0.968 1.282 1.2
+Y 2.258 3.576 1.8
diff --git a/data/GES-scale b/data/GES-scale
new file mode 100644
index 0000000..61d82c8
--- /dev/null
+++ b/data/GES-scale
@@ -0,0 +1,25 @@
+# ___________________________________________________________________________
+#
+# Hphobe Values Goldman Engelman Steitz
+# Ann Rev Biophys. Biophys. Chem. 1986 15/ 321 53
+#___________________________________________________________________________
+A 1.6
+C 2.0
+D -9.2
+E -8.2
+F 3.7
+G 1.0
+H -3.0
+I 3.1
+K -8.8
+L 2.8
+M 3.4
+N -4.8
+P -0.2
+Q -4.1
+R -12.3
+S 0.6
+T 1.2
+V 2.6
+W 1.9
+Y -0.7
diff --git a/data/GVH-scale b/data/GVH-scale
new file mode 100644
index 0000000..b428c1a
--- /dev/null
+++ b/data/GVH-scale
@@ -0,0 +1,25 @@
+#___________________________________________________________________________
+#
+# Hphobe Values Gunnar von Heijne
+# Gunnar von Heijne J. Mol/ Biol (1992) 225, 487-494
+#___________________________________________________________________________
+A 0.267
+C 1.806
+D -2.303
+E -2.442
+F 0.427
+G 0.160
+H -2.189
+I 0.971
+K -2.996
+L 0.623
+M 0.136
+N -1.988
+P -0.451
+Q -1.814
+R -2.749
+S -0.119
+T -0.083
+V 0.721
+W -0.875
+Y -0.386
diff --git a/data/KD-scale b/data/KD-scale
new file mode 100644
index 0000000..6871794
--- /dev/null
+++ b/data/KD-scale
@@ -0,0 +1,25 @@
+#___________________________________________________________________________
+#
+# Hphobe Values Kyte & Doolittle
+# Kyte and Doolittle, J.Mol.Biol.157 (1982) 105-132
+#___________________________________________________________________________
+A 1.8
+C .5
+D -3.5
+E -3.5
+F 2.8
+G -0.4
+H -3.2
+I 4.5
+K -3.9
+L 3.8
+M 1.9
+N -3.5
+P -1.6
+Q -3.5
+R -4.5
+S -0.8
+T -0.7
+V 4.2
+W -0.9
+Y -1.3
diff --git a/data/Makefile.am b/data/Makefile.am
new file mode 100644
index 0000000..f8959a9
--- /dev/null
+++ b/data/Makefile.am
@@ -0,0 +1,3 @@
+pkgdata_DATA = GES-scale GVH-scale KD-scale CYTEXT-scale toppred.dtd
+
+EXTRA_DIST = $(pkgdata_DATA)
diff --git a/data/Makefile.in b/data/Makefile.in
new file mode 100644
index 0000000..8417f82
--- /dev/null
+++ b/data/Makefile.in
@@ -0,0 +1,319 @@
+# Makefile.in generated by automake 1.9.2 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+top_builddir = ..
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+INSTALL = @INSTALL@
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+subdir = data
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/m4/aclibgd.m4 \
+ $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_HEADER = $(top_builddir)/src/config.h
+CONFIG_CLEAN_FILES =
+SOURCES =
+DIST_SOURCES =
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+ *) f=$$p;; \
+ esac;
+am__strip_dir = `echo $$p | sed -e 's|^.*/||'`;
+am__installdirs = "$(DESTDIR)$(pkgdatadir)"
+pkgdataDATA_INSTALL = $(INSTALL_DATA)
+DATA = $(pkgdata_DATA)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMDEP_FALSE = @AMDEP_FALSE@
+AMDEP_TRUE = @AMDEP_TRUE@
+AMTAR = @AMTAR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+GNUPLOT = @GNUPLOT@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LDFLAGS = @LDFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+OBJEXT = @OBJEXT@
+OS_CPPFLAGS = @OS_CPPFLAGS@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+POD2MAN = @POD2MAN@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+USE_GD_LIB_SRC_FALSE = @USE_GD_LIB_SRC_FALSE@
+USE_GD_LIB_SRC_TRUE = @USE_GD_LIB_SRC_TRUE@
+VERSION = @VERSION@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_STRIP = @ac_ct_STRIP@
+am__fastdepCC_FALSE = @am__fastdepCC_FALSE@
+am__fastdepCC_TRUE = @am__fastdepCC_TRUE@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+datadir = @datadir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localstatedir = @localstatedir@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+pkgdata_DATA = GES-scale GVH-scale KD-scale CYTEXT-scale toppred.dtd
+EXTRA_DIST = $(pkgdata_DATA)
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
+ @for dep in $?; do \
+ case '$(am__configure_deps)' in \
+ *$$dep*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
+ && exit 0; \
+ exit 1;; \
+ esac; \
+ done; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu data/Makefile'; \
+ cd $(top_srcdir) && \
+ $(AUTOMAKE) --gnu data/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ @case '$?' in \
+ *config.status*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+ *) \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure: $(am__configure_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+uninstall-info-am:
+install-pkgdataDATA: $(pkgdata_DATA)
+ @$(NORMAL_INSTALL)
+ test -z "$(pkgdatadir)" || $(mkdir_p) "$(DESTDIR)$(pkgdatadir)"
+ @list='$(pkgdata_DATA)'; for p in $$list; do \
+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ f=$(am__strip_dir) \
+ echo " $(pkgdataDATA_INSTALL) '$$d$$p' '$(DESTDIR)$(pkgdatadir)/$$f'"; \
+ $(pkgdataDATA_INSTALL) "$$d$$p" "$(DESTDIR)$(pkgdatadir)/$$f"; \
+ done
+
+uninstall-pkgdataDATA:
+ @$(NORMAL_UNINSTALL)
+ @list='$(pkgdata_DATA)'; for p in $$list; do \
+ f=$(am__strip_dir) \
+ echo " rm -f '$(DESTDIR)$(pkgdatadir)/$$f'"; \
+ rm -f "$(DESTDIR)$(pkgdatadir)/$$f"; \
+ done
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
+ list='$(DISTFILES)'; for file in $$list; do \
+ case $$file in \
+ $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
+ $(top_srcdir)/*) file=`echo "$$file" | sed "s|^$$topsrcdirstrip/|$(top_builddir)/|"`;; \
+ esac; \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ dir=`echo "$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test "$$dir" != "$$file" && test "$$dir" != "."; then \
+ dir="/$$dir"; \
+ $(mkdir_p) "$(distdir)$$dir"; \
+ else \
+ dir=''; \
+ fi; \
+ if test -d $$d/$$file; then \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+ fi; \
+ cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+ else \
+ test -f $(distdir)/$$file \
+ || cp -p $$d/$$file $(distdir)/$$file \
+ || exit 1; \
+ fi; \
+ done
+check-am: all-am
+check: check-am
+all-am: Makefile $(DATA)
+installdirs:
+ for dir in "$(DESTDIR)$(pkgdatadir)"; do \
+ test -z "$$dir" || $(mkdir_p) "$$dir"; \
+ done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+ -rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+info: info-am
+
+info-am:
+
+install-data-am: install-pkgdataDATA
+
+install-exec-am:
+
+install-info: install-info-am
+
+install-man:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-info-am uninstall-pkgdataDATA
+
+.PHONY: all all-am check check-am clean clean-generic distclean \
+ distclean-generic distdir dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am install-exec \
+ install-exec-am install-info install-info-am install-man \
+ install-pkgdataDATA install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am uninstall \
+ uninstall-am uninstall-info-am uninstall-pkgdataDATA
+
+# 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:
diff --git a/data/toppred.dtd b/data/toppred.dtd
new file mode 100644
index 0000000..0a92e23
--- /dev/null
+++ b/data/toppred.dtd
@@ -0,0 +1,101 @@
+<!-- DTD for toppred output -->
+<!ELEMENT toppreds (parameters?, toppred+)>
+
+<!ELEMENT toppred (parameters?, sequence?, annotation?, plot?, tmsummary, topologies?)>
+
+<!-- parameters of the toppred algorithm -->
+<!ELEMENT parameters (corewindow, wedgewindow, certain, putative, distsegments, looplength, eucaryotes, hydrophobycity)>
+
+<!ELEMENT corewindow (#PCDATA)>
+<!ATTLIST corewindow
+ default (true|false) "false">
+<!ELEMENT wedgewindow (#PCDATA)>
+<!ATTLIST wedgewindow
+ default (true|false) "false">
+<!ELEMENT certain (#PCDATA)>
+<!ATTLIST certain
+ default (true|false) "false">
+<!ELEMENT putative (#PCDATA)>
+<!ATTLIST putative
+ default (true|false) "false">
+<!ELEMENT distsegments (#PCDATA)>
+<!ATTLIST distsegments
+ default (true|false) "false">
+<!ELEMENT looplength (#PCDATA)>
+<!ATTLIST distsegments
+ default (true|false) "false">
+<!ELEMENT kingdom (#PCDATA)>
+<!ATTLIST kingdom
+ default (true|false) "false">
+<!ELEMENT hydrophobycity (#PCDATA)>
+<!ATTLIST hydrophobycity
+ default (true|false) "false">
+
+<!-- programme results -->
+<!ELEMENT results (sequence)+>
+
+
+<!ATTLIST sequence
+ id ID #IMPLIED
+ len CDATA #IMPLIED>
+
+<!ELEMENT annotation (#PCDATA)>
+
+<!ELEMENT plot EMPTY>
+<!ATTLIST plot
+ hydro CDATA #REQUIRED
+ gplot CDATA #IMPLIED>
+
+<!ELEMENT tmsummary (segment*)>
+<!ATTLIST tmsummary
+ segments CDATA "0">
+
+
+<!ELEMENT segment EMPTY>
+<!ATTLIST segment
+ start CDATA #REQUIRED
+ stop CDATA #IMPLIED
+ hp CDATA #REQUIRED
+ type (putative|certain) "certain">
+
+<!ELEMENT topologies (toppology+)>
+<!ATTLIST topologies
+ maxtopos CDATA #IMPLIED
+ topoprint CDATA #IMPLIED>
+
+<!ELEMENT topology (loop?, (transmem, loop)+, transmem?)>
+<!ATTLIST topology
+ nr ID #IMPLIED
+ prob CDATA #IMPLIED
+ darglys CDATA #REQUIRED
+ dcytext CDATA #IMPLIED
+ dncharge CDATA #IMPLIED
+ dnnegpos CDATA #IMPLIED
+ image CDATA #IMPLIED
+ orient CDATA #IMPLIED>
+
+<!ELEMENT transmem EMPTY>
+<!ATTLIST transmem
+ start CDATA #REQUIRED
+ stop CDATA #IMPLIED
+ prob CDATA #IMPLIED
+ hp CDATA #REQUIRED>
+
+<!ELEMENT loop EMPTY>
+<!ATTLIST loop
+ type (ext|cyt|unknown) "unknown"
+ start CDATA #REQUIRED
+ stop CDATA #IMPLIED
+ darglys CDATA #REQUIRED
+ dcytext CDATA #IMPLIED
+ decisive (darglys|dcytext) "darglys">
+
+
+
+
+
+
+
+
+
+
diff --git a/depcomp b/depcomp
new file mode 100755
index 0000000..04701da
--- /dev/null
+++ b/depcomp
@@ -0,0 +1,530 @@
+#! /bin/sh
+# depcomp - compile a program generating dependencies as side-effects
+
+scriptversion=2005-07-09.11
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005 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., 51 Franklin Street, Fifth Floor, Boston, MA
+# 02110-1301, 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 at 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 at gnu.org>.
+EOF
+ exit $?
+ ;;
+ -v | --v*)
+ echo "depcomp $scriptversion"
+ exit $?
+ ;;
+esac
+
+if test -z "$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
+ # With Tru64 cc, shared objects can also be used to make a
+ # static library. This mecanism is used in libtool 1.4 series to
+ # handle both shared and static libraries in a single compilation.
+ # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
+ #
+ # With libtool 1.5 this exception was removed, and libtool now
+ # generates 2 separate objects for the 2 libraries. These two
+ # compilations output dependencies in in $dir.libs/$base.o.d and
+ # in $dir$base.o.d. We have to check for both files, because
+ # one of the two compilations can be disabled. We should prefer
+ # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+ # automatically cleaned when .libs/ is deleted, while ignoring
+ # the former would cause a distcleancheck panic.
+ tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
+ tmpdepfile2=$dir$base.o.d # libtool 1.5
+ tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
+ tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
+ "$@" -Wc,-MD
+ else
+ tmpdepfile1=$dir$base.o.d
+ tmpdepfile2=$dir$base.d
+ tmpdepfile3=$dir$base.d
+ tmpdepfile4=$dir$base.d
+ "$@" -MD
+ fi
+
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ 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 -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+ -e '/^#line [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:
diff --git a/doc/Makefile.am b/doc/Makefile.am
new file mode 100644
index 0000000..fe5acc9
--- /dev/null
+++ b/doc/Makefile.am
@@ -0,0 +1,14 @@
+SUFFIXES = .pod .1
+
+man_MANS = toppred.1
+
+EXTRA_DIST = $(man_MANS) toppred.pod
+
+PODARGS = --center='User Manuals' --release='Unix'
+
+.pod.1:
+ $(POD2MAN) $(PODARGS) $< > $@ && touch $@
+
+## Maintainer parano checks
+parano:
+ (for p in *.pod; do podchecker --warnings --warnings $$p; done)
diff --git a/doc/Makefile.in b/doc/Makefile.in
new file mode 100644
index 0000000..efab90c
--- /dev/null
+++ b/doc/Makefile.in
@@ -0,0 +1,352 @@
+# Makefile.in generated by automake 1.9.2 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+top_builddir = ..
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+INSTALL = @INSTALL@
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+subdir = doc
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/m4/aclibgd.m4 \
+ $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_HEADER = $(top_builddir)/src/config.h
+CONFIG_CLEAN_FILES =
+SOURCES =
+DIST_SOURCES =
+man1dir = $(mandir)/man1
+am__installdirs = "$(DESTDIR)$(man1dir)"
+NROFF = nroff
+MANS = $(man_MANS)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMDEP_FALSE = @AMDEP_FALSE@
+AMDEP_TRUE = @AMDEP_TRUE@
+AMTAR = @AMTAR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+GNUPLOT = @GNUPLOT@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LDFLAGS = @LDFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+OBJEXT = @OBJEXT@
+OS_CPPFLAGS = @OS_CPPFLAGS@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+POD2MAN = @POD2MAN@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+USE_GD_LIB_SRC_FALSE = @USE_GD_LIB_SRC_FALSE@
+USE_GD_LIB_SRC_TRUE = @USE_GD_LIB_SRC_TRUE@
+VERSION = @VERSION@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_STRIP = @ac_ct_STRIP@
+am__fastdepCC_FALSE = @am__fastdepCC_FALSE@
+am__fastdepCC_TRUE = @am__fastdepCC_TRUE@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+datadir = @datadir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localstatedir = @localstatedir@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+SUFFIXES = .pod .1
+man_MANS = toppred.1
+EXTRA_DIST = $(man_MANS) toppred.pod
+PODARGS = --center='User Manuals' --release='Unix'
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .pod .1
+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
+ @for dep in $?; do \
+ case '$(am__configure_deps)' in \
+ *$$dep*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
+ && exit 0; \
+ exit 1;; \
+ esac; \
+ done; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/Makefile'; \
+ cd $(top_srcdir) && \
+ $(AUTOMAKE) --gnu doc/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ @case '$?' in \
+ *config.status*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+ *) \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure: $(am__configure_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+uninstall-info-am:
+install-man1: $(man1_MANS) $(man_MANS)
+ @$(NORMAL_INSTALL)
+ test -z "$(man1dir)" || $(mkdir_p) "$(DESTDIR)$(man1dir)"
+ @list='$(man1_MANS) $(dist_man1_MANS) $(nodist_man1_MANS)'; \
+ l2='$(man_MANS) $(dist_man_MANS) $(nodist_man_MANS)'; \
+ for i in $$l2; do \
+ case "$$i" in \
+ *.1*) list="$$list $$i" ;; \
+ esac; \
+ done; \
+ for i in $$list; do \
+ if test -f $(srcdir)/$$i; then file=$(srcdir)/$$i; \
+ else file=$$i; fi; \
+ ext=`echo $$i | sed -e 's/^.*\\.//'`; \
+ case "$$ext" in \
+ 1*) ;; \
+ *) ext='1' ;; \
+ esac; \
+ inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
+ inst=`echo $$inst | sed -e 's/^.*\///'`; \
+ inst=`echo $$inst | sed '$(transform)'`.$$ext; \
+ echo " $(INSTALL_DATA) '$$file' '$(DESTDIR)$(man1dir)/$$inst'"; \
+ $(INSTALL_DATA) "$$file" "$(DESTDIR)$(man1dir)/$$inst"; \
+ done
+uninstall-man1:
+ @$(NORMAL_UNINSTALL)
+ @list='$(man1_MANS) $(dist_man1_MANS) $(nodist_man1_MANS)'; \
+ l2='$(man_MANS) $(dist_man_MANS) $(nodist_man_MANS)'; \
+ for i in $$l2; do \
+ case "$$i" in \
+ *.1*) list="$$list $$i" ;; \
+ esac; \
+ done; \
+ for i in $$list; do \
+ ext=`echo $$i | sed -e 's/^.*\\.//'`; \
+ case "$$ext" in \
+ 1*) ;; \
+ *) ext='1' ;; \
+ esac; \
+ inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
+ inst=`echo $$inst | sed -e 's/^.*\///'`; \
+ inst=`echo $$inst | sed '$(transform)'`.$$ext; \
+ echo " rm -f '$(DESTDIR)$(man1dir)/$$inst'"; \
+ rm -f "$(DESTDIR)$(man1dir)/$$inst"; \
+ done
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
+ list='$(DISTFILES)'; for file in $$list; do \
+ case $$file in \
+ $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
+ $(top_srcdir)/*) file=`echo "$$file" | sed "s|^$$topsrcdirstrip/|$(top_builddir)/|"`;; \
+ esac; \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ dir=`echo "$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test "$$dir" != "$$file" && test "$$dir" != "."; then \
+ dir="/$$dir"; \
+ $(mkdir_p) "$(distdir)$$dir"; \
+ else \
+ dir=''; \
+ fi; \
+ if test -d $$d/$$file; then \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+ fi; \
+ cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+ else \
+ test -f $(distdir)/$$file \
+ || cp -p $$d/$$file $(distdir)/$$file \
+ || exit 1; \
+ fi; \
+ done
+check-am: all-am
+check: check-am
+all-am: Makefile $(MANS)
+installdirs:
+ for dir in "$(DESTDIR)$(man1dir)"; do \
+ test -z "$$dir" || $(mkdir_p) "$$dir"; \
+ done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+ -rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+info: info-am
+
+info-am:
+
+install-data-am: install-man
+
+install-exec-am:
+
+install-info: install-info-am
+
+install-man: install-man1
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-info-am uninstall-man
+
+uninstall-man: uninstall-man1
+
+.PHONY: all all-am check check-am clean clean-generic distclean \
+ distclean-generic distdir dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am install-exec \
+ install-exec-am install-info install-info-am install-man \
+ install-man1 install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am uninstall \
+ uninstall-am uninstall-info-am uninstall-man uninstall-man1
+
+
+.pod.1:
+ $(POD2MAN) $(PODARGS) $< > $@ && touch $@
+
+parano:
+ (for p in *.pod; do podchecker --warnings --warnings $$p; done)
+# 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:
diff --git a/doc/toppred.1 b/doc/toppred.1
new file mode 100644
index 0000000..5e65bb6
--- /dev/null
+++ b/doc/toppred.1
@@ -0,0 +1,341 @@
+.\" Automatically generated by Pod::Man v1.37, Pod::Parser v1.3
+.\"
+.\" Standard preamble:
+.\" ========================================================================
+.de Sh \" Subsection heading
+.br
+.if t .Sp
+.ne 5
+.PP
+\fB\\$1\fR
+.PP
+..
+.de Sp \" Vertical space (when we can't use .PP)
+.if t .sp .5v
+.if n .sp
+..
+.de Vb \" Begin verbatim text
+.ft CW
+.nf
+.ne \\$1
+..
+.de Ve \" End verbatim text
+.ft R
+.fi
+..
+.\" Set up some character translations and predefined strings. \*(-- will
+.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
+.\" double quote, and \*(R" will give a right double quote. | will give a
+.\" real vertical bar. \*(C+ will give a nicer C++. Capital omega is used to
+.\" do unbreakable dashes and therefore won't be available. \*(C` and \*(C'
+.\" expand to `' in nroff, nothing in troff, for use with C<>.
+.tr \(*W-|\(bv\*(Tr
+.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
+.ie n \{\
+. ds -- \(*W-
+. ds PI pi
+. if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
+. if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch
+. ds L" ""
+. ds R" ""
+. ds C` ""
+. ds C' ""
+'br\}
+.el\{\
+. ds -- \|\(em\|
+. ds PI \(*p
+. ds L" ``
+. ds R" ''
+'br\}
+.\"
+.\" If the F register is turned on, we'll generate index entries on stderr for
+.\" titles (.TH), headers (.SH), subsections (.Sh), items (.Ip), and index
+.\" entries marked with X<> in POD. Of course, you'll have to process the
+.\" output yourself in some meaningful fashion.
+.if \nF \{\
+. de IX
+. tm Index:\\$1\t\\n%\t"\\$2"
+..
+. nr % 0
+. rr F
+.\}
+.\"
+.\" For nroff, turn off justification. Always turn off hyphenation; it makes
+.\" way too many mistakes in technical documents.
+.hy 0
+.if n .na
+.\"
+.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
+.\" Fear. Run. Save yourself. No user-serviceable parts.
+. \" fudge factors for nroff and troff
+.if n \{\
+. ds #H 0
+. ds #V .8m
+. ds #F .3m
+. ds #[ \f1
+. ds #] \fP
+.\}
+.if t \{\
+. ds #H ((1u-(\\\\n(.fu%2u))*.13m)
+. ds #V .6m
+. ds #F 0
+. ds #[ \&
+. ds #] \&
+.\}
+. \" simple accents for nroff and troff
+.if n \{\
+. ds ' \&
+. ds ` \&
+. ds ^ \&
+. ds , \&
+. ds ~ ~
+. ds /
+.\}
+.if t \{\
+. ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
+. ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
+. ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
+. ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
+. ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
+. ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
+.\}
+. \" troff and (daisy-wheel) nroff accents
+.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
+.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
+.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
+.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
+.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
+.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
+.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
+.ds ae a\h'-(\w'a'u*4/10)'e
+.ds Ae A\h'-(\w'A'u*4/10)'E
+. \" corrections for vroff
+.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
+.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
+. \" for low resolution devices (crt and lpr)
+.if \n(.H>23 .if \n(.V>19 \
+\{\
+. ds : e
+. ds 8 ss
+. ds o a
+. ds d- d\h'-1'\(ga
+. ds D- D\h'-1'\(hy
+. ds th \o'bp'
+. ds Th \o'LP'
+. ds ae ae
+. ds Ae AE
+.\}
+.rm #[ #] #H #V #F C
+.\" ========================================================================
+.\"
+.IX Title "TOPPRED 1"
+.TH TOPPRED 1 "2008-05-06" "Unix" "User Manuals"
+.SH "NAME"
+.IP "\fBtoppred\fR \- Transmembrane topology prediction." 4
+.IX Item "toppred - Transmembrane topology prediction."
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+.PD 0
+.IP "\fBtoppred\fR [options] <\fIseq data\fR> ..." 4
+.IX Item "toppred [options] <seq data> ..."
+.PD
+.SH "OPTIONS"
+.IX Header "OPTIONS"
+Following command line options are allowed:
+.IP "\-c \fIvalue\fR" 4
+.IX Item "-c value"
+Use \fIvalue\fR as certain cut-off value. Default is 1.
+.IP "\-d \fIval\fR" 4
+.IX Item "-d val"
+Use \fIval\fR as critical distance between 2 transmembrane segments.
+If 2 calculated segments are separated by a distance smaller than
+\&\fIval\fR amino-acids only the segment with best hydrophobicity value is
+taken in account. Default is 2.
+.IP "\-e" 4
+.IX Item "-e"
+switch the cyt-ext calculus to Eucaryotes. Default is Procaryotes.
+.IP "\-g \fIformat\fR" 4
+.IX Item "-g format"
+Produce or display hydrophobic profile in specified \fIformat\fR.
+Currently the supported values for format are:
+.RS 4
+.IP "\fBx11\fR : display the graph on screen (default)." 1
+.IX Item "x11 : display the graph on screen (default)."
+.PD 0
+.IP "\fBps\fR : produce a .ps file." 1
+.IX Item "ps : produce a .ps file."
+.IP "\fBpng\fR : produce a .png file." 1
+.IX Item "png : produce a .png file."
+.IP "\fBppm\fR : produce a .ppm file." 1
+.IX Item "ppm : produce a .ppm file."
+.IP "\fBnone\fR : no profile is produced." 1
+.IX Item "none : no profile is produced."
+.RE
+.RS 4
+.PD
+.Sp
+\&\fBWarning:\fR this option and the related values are \fBonly\fR available
+if toppred is compiled with the gnuplot support.
+.RE
+.IP "\-h" 4
+.IX Item "-h"
+Usage display.
+.IP "\-H \fIfile\fR" 4
+.IX Item "-H file"
+Load hydrophobicity scale from \fIfile\fR, default is GES\-scale.
+Accepted values are either:
+.RS 4
+.IP "\fBKD-scale\fR : (Kyte and Doolittle, J. Mol. Biol (1982) 157, 105\-132 )" 1
+.IX Item "KD-scale : (Kyte and Doolittle, J. Mol. Biol (1982) 157, 105-132 )"
+.PD 0
+.IP "\fBGES-scale\fR : (Goldman Engelman Steitz Ann. Rev. Biophys. Biophys. Chem. 1986 15/ 321 53)" 1
+.IX Item "GES-scale : (Goldman Engelman Steitz Ann. Rev. Biophys. Biophys. Chem. 1986 15/ 321 53)"
+.IP "\fBGVH-scale\fR : (Gunnar von Heijne J. Mol. Biol. (1992) 225, 487\-494)" 1
+.IX Item "GVH-scale : (Gunnar von Heijne J. Mol. Biol. (1992) 225, 487-494)"
+.IP "either your own hydrophobicity scale file. In this case the hydrophobicity scale file must be located in the working directory." 1
+.IX Item "either your own hydrophobicity scale file. In this case the hydrophobicity scale file must be located in the working directory."
+.RE
+.RS 4
+.PD
+.Sp
+In order to use your own hydrophobicity scale file, see the format of
+the supported scale files in the toppred data directory on your
+system; look in \fI/usr/share/toppred/\fRor \fI/usr/local/share/toppred/\fR,
+or ask your system administrator.
+.RE
+.IP "\-n \fIvalue\fR" 4
+.IX Item "-n value"
+Use \fIvalue\fR as a core window length, default is 11.
+.IP "\-o \fIfile\fR" 4
+.IX Item "-o file"
+Place the output into \fIfile\fR, and store all other files to the same
+directory than \fIfile\fR.
+.IP "\-O \fIformat\fR" 4
+.IX Item "-O format"
+Print output in the specified \fIformat\fR. Supported values are: \fBold\fR:
+old toppred output format, \fBnew\fR: new toppred output format (the
+default value), \fBhtml\fR: produce an html page per sequence, note that
+if not specified hydrophobic profile and topologies representation are
+forced in png format.
+.IP "\-p \fIvalue\fR" 4
+.IX Item "-p value"
+Use \fIvalue\fR as putative cut\-off, default is 0.6.
+.IP "\-q \fIvalue\fR" 4
+.IX Item "-q value"
+Use \fIvalue\fR as wedge window length, default is 5.
+.IP "\-s \fIvalue\fR" 4
+.IX Item "-s value"
+Use \fIvalue\fR as critical loop length. If a loop between 2
+transmembrane segments has a length greater than \fIval\fR the Lys/Arg
+ratio is not taken in account to determine the topologies. Default is
+60.
+.IP "\-t \fIformat\fR" 4
+.IX Item "-t format"
+Produce images of the topologies in specified \fIformat\fR. Currently the
+supported values for format are: \fBpng\fR: produces images of the
+topologies in png format, \fBnone\fR: no graphic representation of the
+topologies is produced. Default is png.
+.Sp
+\&\fBWarning:\fR this option and the related values are \fBonly\fR available
+if toppred is compiled with the libgdb support.
+.IP "\-v" 4
+.IX Item "-v"
+Display the version number.
+.SH "FORMAT"
+.IX Header "FORMAT"
+\&\fBtoppred\fR only handles fasta sequence format as input.
+.PP
+\&\fBtoppred\fR handles 2 output format via the \fB\-O\fR flag.
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+\&\fBtoppred\fR is a program to determine the topology of a transmembrane
+protein based on G. von Heijne algorithm.
+.PP
+\&\*(L"Membrane protein structure prediction. Hydrophobicity analysis
+and the positive-inside rule.\*(R"
+J. Mol. Biol. 1992 225,487\-494.
+.PP
+Each sequence from \fIseq data\fR in fasta format is processed, and
+\&\fBtoppred\fR generate the Hydrophobycity profile of the sequence, and
+the corresponding hydrophobycities values in the file
+<\fBsequence-ID\fR>\fB.hydro\fR.
+.PP
+Furthermore, the predicted topologies are represented as png images.
+Each topology is stored in file
+<\fBsequence-ID\fR>\fB\-\fR<\fBnumber\fR>\fB.png\fR
+.PP
+The hydrophobicity profile is computed using a window formed by a core
+rectangular window of size n, flanked by 2 triangular windows of size
+q. \s-1NB\s0 rectangular and triangular mean that the ponderation values
+inside those windows are respectively constant and variable.
+.PP
+The hydrophobicity profile is computed using the following window
+.PP
+.Vb 7
+\& -> n <-
+\& ___________
+\& /| |\e
+\& / | | \e
+\& /__|_________|__\e
+\& -> q <- -> q <-
+\& -> l = n + 2q <-
+.Ve
+.PP
+Thus one can use a rectangular window by setting q to 0.
+.PP
+\&\fBtoppred\fR produces the following output files, depending on the
+command line options
+.IP "\fBfoo.hydro\fR" 4
+.IX Item "foo.hydro"
+File containing the hydrophobic values for the sequence \fBfoo\fR.
+.IP "\fBfoo.ps\fR, \fBfoo.ppm\fR, \fBfoo.png\fR" 4
+.IX Item "foo.ps, foo.ppm, foo.png"
+Image representing the hydrophobic profile for the sequence \fBfoo\fR in
+postcript, ppm or png format depending on the \-g option value
+specified on command line, respectively \-g ps, \-g ppm or \-g png.
+.IP "\fBfoo\-1.png\fR ... \fBfoo\-n.png\fR" 4
+.IX Item "foo-1.png ... foo-n.png"
+Image representing the graphic representation of the predicted
+topology \fB1\fR... \fBn\fR for the sequence \fBfoo\fR in png format if the \-t
+png option is given on the command line.
+.SH "ENVIRONMENT"
+.IX Header "ENVIRONMENT"
+\&\fB\s-1TOPPREDDATA\s0\fR could be used to specify an alternate toppred data
+folder
+.SH "EXAMPLES"
+.IX Header "EXAMPLES"
+Consider the fasta formated sequence \fBfoo\fR in file \fBbar\fR.
+.IP "\fBtoppred\fR \fIbar\fR" 4
+.IX Item "toppred bar"
+Process all sequences in fasta format from \fIbar\fR, display for each
+sequence the hydrophobicity profile, produce the corresponding
+\&\fBfoo.hydro\fR and the corresponding \fBfoo\fR\fB\-\fR<\fB#\fR>\fB.png\fR
+graphical topologies representation as png images.
+.IP "\fBtoppred\fR \-g ps \fIbar\fR" 4
+.IX Item "toppred -g ps bar"
+Same as previous, except that instead of displaying the hydrophobicity
+profile on screen, this one is produced in a postcript format image
+\&\fBfoo.ps\fR
+.IP "\fBtoppred\fR \-g none \fIbar\fR" 4
+.IX Item "toppred -g none bar"
+Same a previous, except that the hydrophobicity profile is not
+displayed neither produced.
+.IP "\fBtoppred\fR \-g none \-t none \fIbar\fR" 4
+.IX Item "toppred -g none -t none bar"
+Same a previous, except that neither the hydrophobicity profile
+neither the graphical topologies representation are not produced
+.IP "\fBtoppred\fR \-H KD-scale \fIbar\fR" 4
+.IX Item "toppred -H KD-scale bar"
+Use \s-1KD\s0 scale instead of default \s-1GES\s0 scale, while processing sequences.
+.IP "\fBtoppred\fR \-O html \-g png \-t none \-o result \fIbar\fR" 4
+.IX Item "toppred -O html -g png -t none -o result bar"
+Write html outpout in file \fIresult\fR, furthermore the hydrophobicity
+profile is produced in \s-1PNG\s0 format and graphics topologies are not
+produced.
+.IP "cat \fIbar\fR | \fBtoppred\fR \-" 4
+.IX Item "cat bar | toppred -"
+\&\fBtoppred\fR is able to read data from stdin.
+.SH "AUTHORS"
+.IX Header "AUTHORS"
+Eric Deveaud <edeveaud at pasteur.fr>, Institut Pasteur and
+Katja Schuerer.
diff --git a/doc/toppred.pod b/doc/toppred.pod
new file mode 100644
index 0000000..7eb9dff
--- /dev/null
+++ b/doc/toppred.pod
@@ -0,0 +1,257 @@
+=pod
+
+=head1 NAME
+
+=over 4
+
+=item B<toppred> - Transmembrane topology prediction.
+
+=back
+
+=head1 SYNOPSIS
+
+=over 4
+
+=item B<toppred> [options] E<lt>F<seq data>E<gt> ...
+
+=back
+
+=head1 OPTIONS
+
+Following command line options are allowed:
+
+=over 4
+
+=item -c F<value>
+
+Use F<value> as certain cut-off value. Default is 1.
+
+=item -d F<val>
+
+Use F<val> as critical distance between 2 transmembrane segments.
+If 2 calculated segments are separated by a distance smaller than
+F<val> amino-acids only the segment with best hydrophobicity value is
+taken in account. Default is 2.
+
+=item -e
+
+switch the cyt-ext calculus to Eucaryotes. Default is Procaryotes.
+
+=item -g F<format>
+
+Produce or display hydrophobic profile in specified F<format>.
+Currently the supported values for format are:
+
+=over 1
+
+=item B<x11> : display the graph on screen (default).
+
+=item B<ps> : produce a .ps file.
+
+=item B<png> : produce a .png file.
+
+=item B<ppm> : produce a .ppm file.
+
+=item B<none> : no profile is produced.
+
+=back
+
+B<Warning:> this option and the related values are B<only> available
+if toppred is compiled with the gnuplot support.
+
+=item -h
+
+Usage display.
+
+=item -H F<file>
+
+Load hydrophobicity scale from F<file>, default is GES-scale.
+Accepted values are either:
+
+=over 1
+
+=item B<KD-scale> : (Kyte and Doolittle, J. Mol. Biol (1982) 157, 105-132 )
+
+=item B<GES-scale> : (Goldman Engelman Steitz Ann. Rev. Biophys. Biophys. Chem. 1986 15/ 321 53)
+
+=item B<GVH-scale> : (Gunnar von Heijne J. Mol. Biol. (1992) 225, 487-494)
+
+=item either your own hydrophobicity scale file. In this case the
+hydrophobicity scale file must be located in the working directory.
+
+=back
+
+In order to use your own hydrophobicity scale file, see the format of
+the supported scale files in the toppred data directory on your
+system; look in F</usr/share/toppred/>or F</usr/local/share/toppred/>,
+or ask your system administrator.
+
+=item -n F<value>
+
+Use F<value> as a core window length, default is 11.
+
+=item -o F<file>
+
+Place the output into F<file>, and store all other files to the same
+directory than F<file>.
+
+=item -O F<format>
+
+Print output in the specified F<format>. Supported values are: B<old>:
+old toppred output format, B<new>: new toppred output format (the
+default value), B<html>: produce an html page per sequence, note that
+if not specified hydrophobic profile and topologies representation are
+forced in png format.
+
+=item -p F<value>
+
+Use F<value> as putative cut-off, default is 0.6.
+
+=item -q F<value>
+
+Use F<value> as wedge window length, default is 5.
+
+=item -s F<value>
+
+Use F<value> as critical loop length. If a loop between 2
+transmembrane segments has a length greater than F<val> the Lys/Arg
+ratio is not taken in account to determine the topologies. Default is
+60.
+
+=item -t F<format>
+
+Produce images of the topologies in specified F<format>. Currently the
+supported values for format are: B<png>: produces images of the
+topologies in png format, B<none>: no graphic representation of the
+topologies is produced. Default is png.
+
+B<Warning:> this option and the related values are B<only> available
+if toppred is compiled with the libgdb support.
+
+=item -v
+
+Display the version number.
+
+=back
+
+=head1 FORMAT
+
+B<toppred> only handles fasta sequence format as input.
+
+B<toppred> handles 2 output format via the B<-O> flag.
+
+
+=head1 DESCRIPTION
+
+B<toppred> is a program to determine the topology of a transmembrane
+protein based on G. von Heijne algorithm.
+
+"Membrane protein structure prediction. Hydrophobicity analysis
+and the positive-inside rule."
+J. Mol. Biol. 1992 225,487-494.
+
+Each sequence from F<seq data> in fasta format is processed, and
+B<toppred> generate the Hydrophobycity profile of the sequence, and
+the corresponding hydrophobycities values in the file
+E<lt>B<sequence-ID>E<gt>B<.hydro>.
+
+Furthermore, the predicted topologies are represented as png images.
+Each topology is stored in file
+E<lt>B<sequence-ID>E<gt>B<->E<lt>B<number>E<gt>B<.png>
+
+The hydrophobicity profile is computed using a window formed by a core
+rectangular window of size n, flanked by 2 triangular windows of size
+q. NB rectangular and triangular mean that the ponderation values
+inside those windows are respectively constant and variable.
+
+The hydrophobicity profile is computed using the following window
+
+ -> n <-
+ ___________
+ /| |\
+ / | | \
+ /__|_________|__\
+ -> q <- -> q <-
+ -> l = n + 2q <-
+
+Thus one can use a rectangular window by setting q to 0.
+
+B<toppred> produces the following output files, depending on the
+command line options
+
+=over 4
+
+=item B<foo.hydro>
+
+File containing the hydrophobic values for the sequence B<foo>.
+
+=item B<foo.ps>, B<foo.ppm>, B<foo.png>
+
+Image representing the hydrophobic profile for the sequence B<foo> in
+postcript, ppm or png format depending on the -g option value
+specified on command line, respectively -g ps, -g ppm or -g png.
+
+=item B<foo-1.png> ... B<foo-n.png>
+
+Image representing the graphic representation of the predicted
+topology B<1>... B<n> for the sequence B<foo> in png format if the -t
+png option is given on the command line.
+
+=back
+
+=head1 ENVIRONMENT
+
+B<TOPPREDDATA> could be used to specify an alternate toppred data
+folder
+
+=head1 EXAMPLES
+
+Consider the fasta formated sequence B<foo> in file B<bar>.
+
+=over 4
+
+=item B<toppred> F<bar>
+
+Process all sequences in fasta format from F<bar>, display for each
+sequence the hydrophobicity profile, produce the corresponding
+B<foo.hydro> and the corresponding B<foo>B<->E<lt>B<#>E<gt>B<.png>
+graphical topologies representation as png images.
+
+=item B<toppred> -g ps F<bar>
+
+Same as previous, except that instead of displaying the hydrophobicity
+profile on screen, this one is produced in a postcript format image
+B<foo.ps>
+
+=item B<toppred> -g none F<bar>
+
+Same a previous, except that the hydrophobicity profile is not
+displayed neither produced.
+
+=item B<toppred> -g none -t none F<bar>
+
+Same a previous, except that neither the hydrophobicity profile
+neither the graphical topologies representation are not produced
+
+=item B<toppred> -H KD-scale F<bar>
+
+Use KD scale instead of default GES scale, while processing sequences.
+
+=item B<toppred> -O html -g png -t none -o result F<bar>
+
+Write html outpout in file F<result>, furthermore the hydrophobicity
+profile is produced in PNG format and graphics topologies are not
+produced.
+
+=item cat F<bar> | B<toppred> -
+
+B<toppred> is able to read data from stdin.
+
+=back
+
+=head1 AUTHORS
+
+Eric Deveaud E<lt>edeveaud at pasteur.frE<gt>, Institut Pasteur and
+Katja Schuerer.
+
+=cut
diff --git a/install-sh b/install-sh
new file mode 100755
index 0000000..4d4a951
--- /dev/null
+++ b/install-sh
@@ -0,0 +1,323 @@
+#!/bin/sh
+# install - install a program, script, or datafile
+
+scriptversion=2005-05-14.22
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
+#
+# Copyright (C) 1994 X Consortium
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch. It can only install one file at a time, a restriction
+# shared with many OS's install programs.
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit="${DOITPROG-}"
+
+# put in absolute paths if you don't have them in your path; or use env. vars.
+
+mvprog="${MVPROG-mv}"
+cpprog="${CPPROG-cp}"
+chmodprog="${CHMODPROG-chmod}"
+chownprog="${CHOWNPROG-chown}"
+chgrpprog="${CHGRPPROG-chgrp}"
+stripprog="${STRIPPROG-strip}"
+rmprog="${RMPROG-rm}"
+mkdirprog="${MKDIRPROG-mkdir}"
+
+chmodcmd="$chmodprog 0755"
+chowncmd=
+chgrpcmd=
+stripcmd=
+rmcmd="$rmprog -f"
+mvcmd="$mvprog"
+src=
+dst=
+dir_arg=
+dstarg=
+no_target_directory=
+
+usage="Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
+ or: $0 [OPTION]... SRCFILES... DIRECTORY
+ or: $0 [OPTION]... -t DIRECTORY SRCFILES...
+ or: $0 [OPTION]... -d DIRECTORIES...
+
+In the 1st form, copy SRCFILE to DSTFILE.
+In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
+In the 4th, create DIRECTORIES.
+
+Options:
+-c (ignored)
+-d create directories instead of installing files.
+-g GROUP $chgrpprog installed files to GROUP.
+-m MODE $chmodprog installed files to MODE.
+-o USER $chownprog installed files to USER.
+-s $stripprog installed files.
+-t DIRECTORY install into DIRECTORY.
+-T report an error if DSTFILE is a directory.
+--help display this help and exit.
+--version display version info and exit.
+
+Environment variables override the default commands:
+ CHGRPPROG CHMODPROG CHOWNPROG CPPROG MKDIRPROG MVPROG RMPROG STRIPPROG
+"
+
+while test -n "$1"; do
+ case $1 in
+ -c) shift
+ continue;;
+
+ -d) dir_arg=true
+ shift
+ continue;;
+
+ -g) chgrpcmd="$chgrpprog $2"
+ shift
+ shift
+ continue;;
+
+ --help) echo "$usage"; exit $?;;
+
+ -m) chmodcmd="$chmodprog $2"
+ shift
+ shift
+ continue;;
+
+ -o) chowncmd="$chownprog $2"
+ shift
+ shift
+ continue;;
+
+ -s) stripcmd=$stripprog
+ shift
+ continue;;
+
+ -t) dstarg=$2
+ shift
+ shift
+ continue;;
+
+ -T) no_target_directory=true
+ shift
+ continue;;
+
+ --version) echo "$0 $scriptversion"; exit $?;;
+
+ *) # When -d is used, all remaining arguments are directories to create.
+ # When -t is used, the destination is already specified.
+ test -n "$dir_arg$dstarg" && break
+ # Otherwise, the last argument is the destination. Remove it from $@.
+ for arg
+ do
+ if test -n "$dstarg"; then
+ # $@ is not empty: it contains at least $arg.
+ set fnord "$@" "$dstarg"
+ shift # fnord
+ fi
+ shift # arg
+ dstarg=$arg
+ done
+ break;;
+ esac
+done
+
+if test -z "$1"; then
+ if test -z "$dir_arg"; then
+ echo "$0: no input file specified." >&2
+ exit 1
+ fi
+ # It's OK to call `install-sh -d' without argument.
+ # This can happen when creating conditional directories.
+ exit 0
+fi
+
+for src
+do
+ # Protect names starting with `-'.
+ case $src in
+ -*) src=./$src ;;
+ esac
+
+ if test -n "$dir_arg"; then
+ dst=$src
+ src=
+
+ if test -d "$dst"; then
+ mkdircmd=:
+ chmodcmd=
+ else
+ mkdircmd=$mkdirprog
+ fi
+ else
+ # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
+ # might cause directories to be created, which would be especially bad
+ # if $src (and thus $dsttmp) contains '*'.
+ if test ! -f "$src" && test ! -d "$src"; then
+ echo "$0: $src does not exist." >&2
+ exit 1
+ fi
+
+ if test -z "$dstarg"; then
+ echo "$0: no destination specified." >&2
+ exit 1
+ fi
+
+ dst=$dstarg
+ # Protect names starting with `-'.
+ case $dst in
+ -*) dst=./$dst ;;
+ esac
+
+ # If destination is a directory, append the input filename; won't work
+ # if double slashes aren't ignored.
+ if test -d "$dst"; then
+ if test -n "$no_target_directory"; then
+ echo "$0: $dstarg: Is a directory" >&2
+ exit 1
+ fi
+ dst=$dst/`basename "$src"`
+ fi
+ fi
+
+ # This sed command emulates the dirname command.
+ dstdir=`echo "$dst" | sed -e 's,/*$,,;s,[^/]*$,,;s,/*$,,;s,^$,.,'`
+
+ # Make sure that the destination directory exists.
+
+ # Skip lots of stat calls in the usual case.
+ if test ! -d "$dstdir"; then
+ defaultIFS='
+ '
+ IFS="${IFS-$defaultIFS}"
+
+ oIFS=$IFS
+ # Some sh's can't handle IFS=/ for some reason.
+ IFS='%'
+ set x `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
+ shift
+ IFS=$oIFS
+
+ pathcomp=
+
+ while test $# -ne 0 ; do
+ pathcomp=$pathcomp$1
+ shift
+ if test ! -d "$pathcomp"; then
+ $mkdirprog "$pathcomp"
+ # mkdir can fail with a `File exist' error in case several
+ # install-sh are creating the directory concurrently. This
+ # is OK.
+ test -d "$pathcomp" || exit
+ fi
+ pathcomp=$pathcomp/
+ done
+ fi
+
+ if test -n "$dir_arg"; then
+ $doit $mkdircmd "$dst" \
+ && { test -z "$chowncmd" || $doit $chowncmd "$dst"; } \
+ && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } \
+ && { test -z "$stripcmd" || $doit $stripcmd "$dst"; } \
+ && { test -z "$chmodcmd" || $doit $chmodcmd "$dst"; }
+
+ else
+ dstfile=`basename "$dst"`
+
+ # Make a couple of temp file names in the proper directory.
+ dsttmp=$dstdir/_inst.$$_
+ rmtmp=$dstdir/_rm.$$_
+
+ # Trap to clean up those temp files at exit.
+ trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
+ trap '(exit $?); exit' 1 2 13 15
+
+ # Copy the file name to the temp name.
+ $doit $cpprog "$src" "$dsttmp" &&
+
+ # and set any options; do chmod last to preserve setuid bits.
+ #
+ # If any of these fail, we abort the whole thing. If we want to
+ # ignore errors from any of these, just make sure not to ignore
+ # errors from the above "$doit $cpprog $src $dsttmp" command.
+ #
+ { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } \
+ && { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } \
+ && { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } \
+ && { test -z "$chmodcmd" || $doit $chmodcmd "$dsttmp"; } &&
+
+ # Now rename the file to the real destination.
+ { $doit $mvcmd -f "$dsttmp" "$dstdir/$dstfile" 2>/dev/null \
+ || {
+ # The rename failed, perhaps because mv can't rename something else
+ # to itself, or perhaps because mv is so ancient that it does not
+ # support -f.
+
+ # Now remove or move aside any old file at destination location.
+ # We try this two ways since rm can't unlink itself on some
+ # systems and the destination file might be busy for other
+ # reasons. In this case, the final cleanup might fail but the new
+ # file should still install successfully.
+ {
+ if test -f "$dstdir/$dstfile"; then
+ $doit $rmcmd -f "$dstdir/$dstfile" 2>/dev/null \
+ || $doit $mvcmd -f "$dstdir/$dstfile" "$rmtmp" 2>/dev/null \
+ || {
+ echo "$0: cannot unlink or rename $dstdir/$dstfile" >&2
+ (exit 1); exit 1
+ }
+ else
+ :
+ fi
+ } &&
+
+ # Now rename the file to the real destination.
+ $doit $mvcmd "$dsttmp" "$dstdir/$dstfile"
+ }
+ }
+ fi || { (exit 1); exit 1; }
+done
+
+# The final little trick to "correctly" pass the exit status to the exit trap.
+{
+ (exit 0); exit 0
+}
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff --git a/m4/Makefile.am b/m4/Makefile.am
new file mode 100644
index 0000000..cf32e83
--- /dev/null
+++ b/m4/Makefile.am
@@ -0,0 +1,2 @@
+# EXTRA_DIST = chek_pngdriver.m4
+EXTRA_DIST = aclibgd.m4
diff --git a/m4/Makefile.in b/m4/Makefile.in
new file mode 100644
index 0000000..80a057d
--- /dev/null
+++ b/m4/Makefile.in
@@ -0,0 +1,290 @@
+# Makefile.in generated by automake 1.9.2 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+top_builddir = ..
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+INSTALL = @INSTALL@
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+subdir = m4
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/m4/aclibgd.m4 \
+ $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_HEADER = $(top_builddir)/src/config.h
+CONFIG_CLEAN_FILES =
+SOURCES =
+DIST_SOURCES =
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMDEP_FALSE = @AMDEP_FALSE@
+AMDEP_TRUE = @AMDEP_TRUE@
+AMTAR = @AMTAR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+GNUPLOT = @GNUPLOT@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LDFLAGS = @LDFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+OBJEXT = @OBJEXT@
+OS_CPPFLAGS = @OS_CPPFLAGS@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+POD2MAN = @POD2MAN@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+USE_GD_LIB_SRC_FALSE = @USE_GD_LIB_SRC_FALSE@
+USE_GD_LIB_SRC_TRUE = @USE_GD_LIB_SRC_TRUE@
+VERSION = @VERSION@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_STRIP = @ac_ct_STRIP@
+am__fastdepCC_FALSE = @am__fastdepCC_FALSE@
+am__fastdepCC_TRUE = @am__fastdepCC_TRUE@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+datadir = @datadir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localstatedir = @localstatedir@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+
+# EXTRA_DIST = chek_pngdriver.m4
+EXTRA_DIST = aclibgd.m4
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
+ @for dep in $?; do \
+ case '$(am__configure_deps)' in \
+ *$$dep*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
+ && exit 0; \
+ exit 1;; \
+ esac; \
+ done; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu m4/Makefile'; \
+ cd $(top_srcdir) && \
+ $(AUTOMAKE) --gnu m4/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ @case '$?' in \
+ *config.status*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+ *) \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure: $(am__configure_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+uninstall-info-am:
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
+ list='$(DISTFILES)'; for file in $$list; do \
+ case $$file in \
+ $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
+ $(top_srcdir)/*) file=`echo "$$file" | sed "s|^$$topsrcdirstrip/|$(top_builddir)/|"`;; \
+ esac; \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ dir=`echo "$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test "$$dir" != "$$file" && test "$$dir" != "."; then \
+ dir="/$$dir"; \
+ $(mkdir_p) "$(distdir)$$dir"; \
+ else \
+ dir=''; \
+ fi; \
+ if test -d $$d/$$file; then \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+ fi; \
+ cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+ else \
+ test -f $(distdir)/$$file \
+ || cp -p $$d/$$file $(distdir)/$$file \
+ || exit 1; \
+ fi; \
+ done
+check-am: all-am
+check: check-am
+all-am: Makefile
+installdirs:
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+ -rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-exec-am:
+
+install-info: install-info-am
+
+install-man:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-info-am
+
+.PHONY: all all-am check check-am clean clean-generic distclean \
+ distclean-generic distdir dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am install-exec \
+ install-exec-am install-info install-info-am install-man \
+ install-strip installcheck installcheck-am installdirs \
+ maintainer-clean maintainer-clean-generic mostlyclean \
+ mostlyclean-generic pdf pdf-am ps ps-am uninstall uninstall-am \
+ uninstall-info-am
+
+# 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:
diff --git a/m4/aclibgd.m4 b/m4/aclibgd.m4
new file mode 100644
index 0000000..e852f2b
--- /dev/null
+++ b/m4/aclibgd.m4
@@ -0,0 +1,92 @@
+dnl libgd checker for autoconf.
+dnl
+dnl Cheks for the gd/png/zlib library and all necessary stuff.
+dnl
+
+AC_DEFUN([GD_CHECK],
+#
+# Handle user hints
+#
+[
+ AC_MSG_CHECKING([if libgd is wanted])
+
+ AC_ARG_WITH([libgd],
+ [ --with-libgd=DIR root directory path of libgd installation
+ defaults to /usr and /usr/local
+ --without-libgd to disable libgd usage completely (not yet implemented)],
+ [
+ #
+ # Run this if -with or -without was specified
+ #
+ if test "$withval" != no ; then
+ AC_MSG_RESULT(yes)
+ LIBGD_WANTED=yes
+ if test "$withval" != yes ; then
+ LIBGD_HOME_DIR="$withval"
+ fi
+ else
+ LIBGD_WANTED=no
+ AC_MSG_RESULT(no)
+ fi]
+ ,[
+ # Nothing was said I assume libgd is needed
+
+ LIBGD_WANTED=yes
+ AC_MSG_RESULT(yes)
+ ])
+
+
+
+# just do the job if libgd is wanted
+if test $LIBGD_WANTED = yes; then
+
+ # save the state at begining
+ _old_LDFLAGS=$LDFLAGS
+ _old_CPPFLAGS=$CPPFLAGS
+
+ # perform search in various directory.
+ AC_MSG_CHECKING([for libgd with png support])
+ for _search_dir_to_inc in "$LIBGD_HOME_DIR" /usr /usr/local ; do
+
+ LDFLAGS="$_old_LDFLAGS -L${_search_dir_to_inc}/lib"
+ CPPFLAGS="$_old_CPPFLAGS -I${_search_dir_to_inc}/include"
+
+
+ AC_TRY_COMPILE([#include "gd.h"] ,
+ [ gdImagePtr im;
+ FILE *pngout;
+ gdImagePng(im, pngout);
+ ] ,
+ _compil_ok="yes" )
+ if test "$_compil_ok" = yes ; then
+ break
+ fi
+ done
+
+ # if OK, then just add the library to $LIBS,
+ # else reset to the initial state
+
+ if test "$_compil_ok" = yes ; then
+ AC_MSG_RESULT([yes])
+ AC_DEFINE(HAVE_LIBGD, 1, is libgd present)
+ LIBS="$LIBS -lgd -lpng -lz"
+ if test -z "$_search_dir_to_inc" ; then
+ LDFLAGS=$_old_LDFLAGS
+ CPPFLAGS=$_old_CPPFLAGS
+ fi
+ else
+ AC_MSG_RESULT([no])
+ AC_MSG_WARN([libgd not found, graphic topologies will be unavailable])
+ fi
+ AM_CONDITIONAL(USE_GD_LIB_SRC, test "$_compil_ok")
+ # if libgd is not wanted, disable some piece of code
+ # still to implement
+ # I'm thinking about
+ # setting up a #define and check for it in the code.
+
+fi
+])
+
+
+
+
diff --git a/missing b/missing
new file mode 100755
index 0000000..894e786
--- /dev/null
+++ b/missing
@@ -0,0 +1,360 @@
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2005-06-08.21
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005
+# Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
+
+# 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., 51 Franklin Street, Fifth Floor, Boston, MA
+# 02110-1301, 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.
+
+if test $# -eq 0; then
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+fi
+
+run=:
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+ configure_ac=configure.ac
+else
+ configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case "$1" in
+--run)
+ # Try to run requested program, and just exit if it succeeds.
+ run=
+ shift
+ "$@" && exit 0
+ # Exit code 63 means version mismatch. This often happens
+ # when the user try to use an ancient version of a tool on
+ # a file that requires a minimum version. In this case we
+ # we should proceed has if the program had been absent, or
+ # if --run hadn't been passed.
+ if test $? = 63; then
+ run=:
+ msg="probably too old"
+ fi
+ ;;
+
+ -h|--h|--he|--hel|--help)
+ echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+ -h, --help display this help and exit
+ -v, --version output version information and exit
+ --run try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ help2man touch the output file
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ tar try tar, gnutar, gtar, then tar without non-portable flags
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Send bug reports to <bug-automake at gnu.org>."
+ exit $?
+ ;;
+
+ -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+ echo "missing $scriptversion (GNU Automake)"
+ exit $?
+ ;;
+
+ -*)
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+ ;;
+
+esac
+
+# Now exit if we have it, but it failed. Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program).
+case "$1" in
+ lex|yacc)
+ # Not GNU programs, they don't have --version.
+ ;;
+
+ tar)
+ if test -n "$run"; then
+ echo 1>&2 "ERROR: \`tar' requires --run"
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ exit 1
+ fi
+ ;;
+
+ *)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ # Could not run --version or --help. This is probably someone
+ # running `$TOOL --version' or `$TOOL --help' to check whether
+ # $TOOL exists and not knowing $TOOL uses missing.
+ exit 1
+ fi
+ ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case "$1" in
+ aclocal*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acinclude.m4' or \`${configure_ac}'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`${configure_ac}'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acconfig.h' or \`${configure_ac}'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case "$f" in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ autom4te)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them.
+ You can get \`$1' as part of \`Autoconf' from any GNU
+ archive site."
+
+ file=`echo "$*" | sed -n 's/.*--output[ =]*\([^ ]*\).*/\1/p'`
+ test -z "$file" && file=`echo "$*" | sed -n 's/.*-o[ ]*\([^ ]*\).*/\1/p'`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo "#! /bin/sh"
+ echo "# Created by GNU Automake missing as a replacement of"
+ echo "# $ $@"
+ echo "exit 0"
+ chmod +x $file
+ exit 1
+ fi
+ ;;
+
+ bison|yacc)
+ echo 1>&2 "\
+WARNING: \`$1' $msg. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if [ $# -ne 1 ]; then
+ eval LASTARG="\${$#}"
+ case "$LASTARG" in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if [ ! -f y.tab.h ]; then
+ echo >y.tab.h
+ fi
+ if [ ! -f y.tab.c ]; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex|flex)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if [ $# -ne 1 ]; then
+ eval LASTARG="\${$#}"
+ case "$LASTARG" in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if [ ! -f lex.yy.c ]; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ help2man)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a dependency of a manual page. You may need the
+ \`Help2man' package in order for those modifications to take
+ effect. You can get \`Help2man' from any GNU archive site."
+
+ file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
+ if test -z "$file"; then
+ file=`echo "$*" | sed -n 's/.*--output=\([^ ]*\).*/\1/p'`
+ fi
+ if [ -f "$file" ]; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo ".ab help2man is required to generate this page"
+ exit 1
+ fi
+ ;;
+
+ makeinfo)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ # The file to touch is that specified with -o ...
+ file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
+ if test -z "$file"; then
+ # ... or it is the one specified with @setfilename ...
+ infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '/^@setfilename/ { s/.* \([^ ]*\) *$/\1/; p; q; }' $infile`
+ # ... or it is derived from the source name (dir/f.texi becomes f.info)
+ test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+ fi
+ # If the file does not exist, the user really needs makeinfo;
+ # let's fail without touching anything.
+ test -f $file || exit 1
+ touch $file
+ ;;
+
+ tar)
+ shift
+
+ # We have already tried tar in the generic part.
+ # Look for gnutar/gtar before invocation to avoid ugly error
+ # messages.
+ if (gnutar --version > /dev/null 2>&1); then
+ gnutar "$@" && exit 0
+ fi
+ if (gtar --version > /dev/null 2>&1); then
+ gtar "$@" && exit 0
+ fi
+ firstarg="$1"
+ if shift; then
+ case "$firstarg" in
+ *o*)
+ firstarg=`echo "$firstarg" | sed s/o//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ case "$firstarg" in
+ *h*)
+ firstarg=`echo "$firstarg" | sed s/h//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ fi
+
+ echo 1>&2 "\
+WARNING: I can't seem to be able to run \`tar' with the given arguments.
+ You may want to install GNU tar or Free paxutils, or check the
+ command line arguments."
+ exit 1
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequisites for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff --git a/mkinstalldirs b/mkinstalldirs
new file mode 100755
index 0000000..259dbfc
--- /dev/null
+++ b/mkinstalldirs
@@ -0,0 +1,158 @@
+#! /bin/sh
+# mkinstalldirs --- make directory hierarchy
+
+scriptversion=2005-06-29.22
+
+# Original author: Noah Friedman <friedman at prep.ai.mit.edu>
+# Created: 1993-05-16
+# Public domain.
+#
+# This file is maintained in Automake, please report
+# bugs to <bug-automake at gnu.org> or send patches to
+# <automake-patches at gnu.org>.
+
+errstatus=0
+dirmode=
+
+usage="\
+Usage: mkinstalldirs [-h] [--help] [--version] [-m MODE] DIR ...
+
+Create each directory DIR (with mode MODE, if specified), including all
+leading file name components.
+
+Report bugs to <bug-automake at gnu.org>."
+
+# process command line arguments
+while test $# -gt 0 ; do
+ case $1 in
+ -h | --help | --h*) # -h for help
+ echo "$usage"
+ exit $?
+ ;;
+ -m) # -m PERM arg
+ shift
+ test $# -eq 0 && { echo "$usage" 1>&2; exit 1; }
+ dirmode=$1
+ shift
+ ;;
+ --version)
+ echo "$0 $scriptversion"
+ exit $?
+ ;;
+ --) # stop option processing
+ shift
+ break
+ ;;
+ -*) # unknown option
+ echo "$usage" 1>&2
+ exit 1
+ ;;
+ *) # first non-opt arg
+ break
+ ;;
+ esac
+done
+
+for file
+do
+ if test -d "$file"; then
+ shift
+ else
+ break
+ fi
+done
+
+case $# in
+ 0) exit 0 ;;
+esac
+
+# Solaris 8's mkdir -p isn't thread-safe. If you mkdir -p a/b and
+# mkdir -p a/c at the same time, both will detect that a is missing,
+# one will create a, then the other will try to create a and die with
+# a "File exists" error. This is a problem when calling mkinstalldirs
+# from a parallel make. We use --version in the probe to restrict
+# ourselves to GNU mkdir, which is thread-safe.
+case $dirmode in
+ '')
+ if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then
+ echo "mkdir -p -- $*"
+ exec mkdir -p -- "$@"
+ else
+ # On NextStep and OpenStep, the `mkdir' command does not
+ # recognize any option. It will interpret all options as
+ # directories to create, and then abort because `.' already
+ # exists.
+ test -d ./-p && rmdir ./-p
+ test -d ./--version && rmdir ./--version
+ fi
+ ;;
+ *)
+ if mkdir -m "$dirmode" -p --version . >/dev/null 2>&1 &&
+ test ! -d ./--version; then
+ echo "mkdir -m $dirmode -p -- $*"
+ exec mkdir -m "$dirmode" -p -- "$@"
+ else
+ # Clean up after NextStep and OpenStep mkdir.
+ for d in ./-m ./-p ./--version "./$dirmode";
+ do
+ test -d $d && rmdir $d
+ done
+ fi
+ ;;
+esac
+
+for file
+do
+ case $file in
+ /*) pathcomp=/ ;;
+ *) pathcomp= ;;
+ esac
+ oIFS=$IFS
+ IFS=/
+ set fnord $file
+ shift
+ IFS=$oIFS
+
+ for d
+ do
+ test "x$d" = x && continue
+
+ pathcomp=$pathcomp$d
+ case $pathcomp in
+ -*) pathcomp=./$pathcomp ;;
+ esac
+
+ if test ! -d "$pathcomp"; then
+ echo "mkdir $pathcomp"
+
+ mkdir "$pathcomp" || lasterr=$?
+
+ if test ! -d "$pathcomp"; then
+ errstatus=$lasterr
+ else
+ if test ! -z "$dirmode"; then
+ echo "chmod $dirmode $pathcomp"
+ lasterr=
+ chmod "$dirmode" "$pathcomp" || lasterr=$?
+
+ if test ! -z "$lasterr"; then
+ errstatus=$lasterr
+ fi
+ fi
+ fi
+ fi
+
+ pathcomp=$pathcomp/
+ done
+done
+
+exit $errstatus
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:
diff --git a/src/Makefile.am b/src/Makefile.am
new file mode 100644
index 0000000..466fce2
--- /dev/null
+++ b/src/Makefile.am
@@ -0,0 +1,27 @@
+
+AM_CPPFLAGS = -DDATADIR=\"$(pkgdatadir)\" $(OS_CPPFLAGS)
+
+bin_PROGRAMS = toppred
+
+if USE_GD_LIB_SRC
+extra_src=graph.c
+extra_header=graph.h
+else
+extra_src=
+extra_header=
+endif
+
+EXTRA_DIST = graph.c graph.h
+
+toppred_SOURCES = error.c main.c usage.c profile.c seq-reader.c loop.c \
+ charge.c topology.c topoprint.c output.c mloutput.c $(extra_src)
+
+noinst_HEADERS = error.h main.h usage.h profile.h seq-reader.h loop.h \
+ params.h charge.h topology.h topoprint.h output.h mloutput.h \
+ $(extra_header)
+
+## Maintainer parano check
+LINTDEFS = $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS)
+
+parano:
+ $(LINT) $(LINTFLAGS) $(LINTDEFS) $(toppred_SOURCES)
diff --git a/src/Makefile.in b/src/Makefile.in
new file mode 100644
index 0000000..8f4b788
--- /dev/null
+++ b/src/Makefile.in
@@ -0,0 +1,465 @@
+# Makefile.in generated by automake 1.9.2 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+
+
+SOURCES = $(toppred_SOURCES)
+
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+top_builddir = ..
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+INSTALL = @INSTALL@
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+bin_PROGRAMS = toppred$(EXEEXT)
+subdir = src
+DIST_COMMON = $(am__noinst_HEADERS_DIST) $(srcdir)/Makefile.am \
+ $(srcdir)/Makefile.in $(srcdir)/config.h.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/m4/aclibgd.m4 \
+ $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_HEADER = config.h
+CONFIG_CLEAN_FILES =
+am__installdirs = "$(DESTDIR)$(bindir)"
+binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
+PROGRAMS = $(bin_PROGRAMS)
+am__toppred_SOURCES_DIST = error.c main.c usage.c profile.c \
+ seq-reader.c loop.c charge.c topology.c topoprint.c output.c \
+ mloutput.c graph.c
+ at USE_GD_LIB_SRC_TRUE@am__objects_1 = graph.$(OBJEXT)
+am_toppred_OBJECTS = error.$(OBJEXT) main.$(OBJEXT) usage.$(OBJEXT) \
+ profile.$(OBJEXT) seq-reader.$(OBJEXT) loop.$(OBJEXT) \
+ charge.$(OBJEXT) topology.$(OBJEXT) topoprint.$(OBJEXT) \
+ output.$(OBJEXT) mloutput.$(OBJEXT) $(am__objects_1)
+toppred_OBJECTS = $(am_toppred_OBJECTS)
+toppred_LDADD = $(LDADD)
+DEFAULT_INCLUDES = -I. -I$(srcdir) -I.
+depcomp = $(SHELL) $(top_srcdir)/depcomp
+am__depfiles_maybe = depfiles
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+SOURCES = $(toppred_SOURCES)
+DIST_SOURCES = $(am__toppred_SOURCES_DIST)
+am__noinst_HEADERS_DIST = error.h main.h usage.h profile.h \
+ seq-reader.h loop.h params.h charge.h topology.h topoprint.h \
+ output.h mloutput.h graph.h
+HEADERS = $(noinst_HEADERS)
+ETAGS = etags
+CTAGS = ctags
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMDEP_FALSE = @AMDEP_FALSE@
+AMDEP_TRUE = @AMDEP_TRUE@
+AMTAR = @AMTAR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+GNUPLOT = @GNUPLOT@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LDFLAGS = @LDFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+OBJEXT = @OBJEXT@
+OS_CPPFLAGS = @OS_CPPFLAGS@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+POD2MAN = @POD2MAN@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+USE_GD_LIB_SRC_FALSE = @USE_GD_LIB_SRC_FALSE@
+USE_GD_LIB_SRC_TRUE = @USE_GD_LIB_SRC_TRUE@
+VERSION = @VERSION@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_STRIP = @ac_ct_STRIP@
+am__fastdepCC_FALSE = @am__fastdepCC_FALSE@
+am__fastdepCC_TRUE = @am__fastdepCC_TRUE@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+datadir = @datadir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localstatedir = @localstatedir@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+AM_CPPFLAGS = -DDATADIR=\"$(pkgdatadir)\" $(OS_CPPFLAGS)
+ at USE_GD_LIB_SRC_FALSE@extra_src =
+ at USE_GD_LIB_SRC_TRUE@extra_src = graph.c
+ at USE_GD_LIB_SRC_FALSE@extra_header =
+ at USE_GD_LIB_SRC_TRUE@extra_header = graph.h
+EXTRA_DIST = graph.c graph.h
+toppred_SOURCES = error.c main.c usage.c profile.c seq-reader.c loop.c \
+ charge.c topology.c topoprint.c output.c mloutput.c $(extra_src)
+
+noinst_HEADERS = error.h main.h usage.h profile.h seq-reader.h loop.h \
+ params.h charge.h topology.h topoprint.h output.h mloutput.h \
+ $(extra_header)
+
+LINTDEFS = $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS)
+all: config.h
+ $(MAKE) $(AM_MAKEFLAGS) all-am
+
+.SUFFIXES:
+.SUFFIXES: .c .o .obj
+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
+ @for dep in $?; do \
+ case '$(am__configure_deps)' in \
+ *$$dep*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
+ && exit 0; \
+ exit 1;; \
+ esac; \
+ done; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
+ cd $(top_srcdir) && \
+ $(AUTOMAKE) --gnu src/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ @case '$?' in \
+ *config.status*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+ *) \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure: $(am__configure_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+config.h: stamp-h1
+ @if test ! -f $@; then \
+ rm -f stamp-h1; \
+ $(MAKE) stamp-h1; \
+ else :; fi
+
+stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
+ @rm -f stamp-h1
+ cd $(top_builddir) && $(SHELL) ./config.status src/config.h
+$(srcdir)/config.h.in: $(am__configure_deps)
+ cd $(top_srcdir) && $(AUTOHEADER)
+ rm -f stamp-h1
+ touch $@
+
+distclean-hdr:
+ -rm -f config.h stamp-h1
+install-binPROGRAMS: $(bin_PROGRAMS)
+ @$(NORMAL_INSTALL)
+ test -z "$(bindir)" || $(mkdir_p) "$(DESTDIR)$(bindir)"
+ @list='$(bin_PROGRAMS)'; for p in $$list; do \
+ p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
+ if test -f $$p \
+ ; then \
+ f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
+ echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \
+ $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \
+ else :; fi; \
+ done
+
+uninstall-binPROGRAMS:
+ @$(NORMAL_UNINSTALL)
+ @list='$(bin_PROGRAMS)'; for p in $$list; do \
+ f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
+ echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \
+ rm -f "$(DESTDIR)$(bindir)/$$f"; \
+ done
+
+clean-binPROGRAMS:
+ -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+toppred$(EXEEXT): $(toppred_OBJECTS) $(toppred_DEPENDENCIES)
+ @rm -f toppred$(EXEEXT)
+ $(LINK) $(toppred_LDFLAGS) $(toppred_OBJECTS) $(toppred_LDADD) $(LIBS)
+
+mostlyclean-compile:
+ -rm -f *.$(OBJEXT)
+
+distclean-compile:
+ -rm -f *.tab.c
+
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/charge.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/error.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/graph.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/loop.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/main.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/mloutput.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/output.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/profile.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/seq-reader.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/topology.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/topoprint.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/usage.Po at am__quote@
+
+.c.o:
+ at am__fastdepCC_TRUE@ if $(COMPILE) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.Tpo" -c -o $@ $<; \
+ at am__fastdepCC_TRUE@ then mv -f "$(DEPDIR)/$*.Tpo" "$(DEPDIR)/$*.Po"; else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; fi
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
+
+.c.obj:
+ at am__fastdepCC_TRUE@ if $(COMPILE) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.Tpo" -c -o $@ `$(CYGPATH_W) '$<'`; \
+ at am__fastdepCC_TRUE@ then mv -f "$(DEPDIR)/$*.Tpo" "$(DEPDIR)/$*.Po"; else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; fi
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(COMPILE) -c `$(CYGPATH_W) '$<'`
+uninstall-info-am:
+
+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ mkid -fID $$unique
+tags: TAGS
+
+TAGS: $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ tags=; \
+ here=`pwd`; \
+ list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
+ test -n "$$unique" || unique=$$empty_fix; \
+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+ $$tags $$unique; \
+ fi
+ctags: CTAGS
+CTAGS: $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
+ $(TAGS_FILES) $(LISP)
+ tags=; \
+ here=`pwd`; \
+ list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
+ unique=`for i in $$list; do \
+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+ done | \
+ $(AWK) ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ test -z "$(CTAGS_ARGS)$$tags$$unique" \
+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+ $$tags $$unique
+
+GTAGS:
+ here=`$(am__cd) $(top_builddir) && pwd` \
+ && cd $(top_srcdir) \
+ && gtags -i $(GTAGS_ARGS) $$here
+
+distclean-tags:
+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+
+distdir: $(DISTFILES)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
+ list='$(DISTFILES)'; for file in $$list; do \
+ case $$file in \
+ $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
+ $(top_srcdir)/*) file=`echo "$$file" | sed "s|^$$topsrcdirstrip/|$(top_builddir)/|"`;; \
+ esac; \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ dir=`echo "$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test "$$dir" != "$$file" && test "$$dir" != "."; then \
+ dir="/$$dir"; \
+ $(mkdir_p) "$(distdir)$$dir"; \
+ else \
+ dir=''; \
+ fi; \
+ if test -d $$d/$$file; then \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+ fi; \
+ cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+ else \
+ test -f $(distdir)/$$file \
+ || cp -p $$d/$$file $(distdir)/$$file \
+ || exit 1; \
+ fi; \
+ done
+check-am: all-am
+check: check-am
+all-am: Makefile $(PROGRAMS) $(HEADERS) config.h
+installdirs:
+ for dir in "$(DESTDIR)$(bindir)"; do \
+ test -z "$$dir" || $(mkdir_p) "$$dir"; \
+ done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
+
+distclean: distclean-am
+ -rm -rf ./$(DEPDIR)
+ -rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+ distclean-hdr distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-exec-am: install-binPROGRAMS
+
+install-info: install-info-am
+
+install-man:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -rf ./$(DEPDIR)
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS uninstall-info-am
+
+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
+ clean-generic ctags distclean distclean-compile \
+ distclean-generic distclean-hdr distclean-tags distdir dvi \
+ dvi-am html html-am info info-am install install-am \
+ install-binPROGRAMS install-data install-data-am install-exec \
+ install-exec-am install-info install-info-am install-man \
+ install-strip installcheck installcheck-am installdirs \
+ maintainer-clean maintainer-clean-generic mostlyclean \
+ mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
+ tags uninstall uninstall-am uninstall-binPROGRAMS \
+ uninstall-info-am
+
+
+parano:
+ $(LINT) $(LINTFLAGS) $(LINTDEFS) $(toppred_SOURCES)
+# 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:
diff --git a/src/charge.c b/src/charge.c
new file mode 100644
index 0000000..1f12c9f
--- /dev/null
+++ b/src/charge.c
@@ -0,0 +1,296 @@
+/* -----------------------------------------------------------------
+ file : /home/schuerer/toppred_com/src/top_loop.c
+
+ author : Schuerer
+ description :
+
+
+-------------------------------------------------------------------- */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+#include <ctype.h>
+
+#ifdef STDC_HEADERS
+#include <stdlib.h>
+#include <string.h>
+#endif
+
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+
+#ifdef HAVE_LIBM
+#include <math.h>
+#endif
+
+#include "charge.h"
+#include "error.h"
+
+
+#define MAXSIZE 5
+
+/* internal function prototypes */
+static int is_aa(int c);
+
+/* calc the Arg+Lys content of a loop
+
+ to calculate over :
+ _____ _____
+ ... |\ /| ...
+ _____|_\ /_|_____
+ |<------->| */
+int countkr (char *seq, int soff, int eoff) {
+
+ int c = 0;
+ int i;
+
+ if (soff == -1) return 0; /* undefined sequence element */
+
+ if (soff < 0)
+ error_fatal (seq, "start position smaller than zero");
+ if (eoff > strlen (seq))
+ error_fatal (seq, "end position greater than sequence lenght");
+
+ /* if (eoff - soff > 70) return 0; peut etre un niveau plus haut */
+
+ for(i=soff; i<eoff; i++)
+ if (seq[i] == 'K' || seq[i] == 'R') c++;
+
+ return c;
+}
+
+/* calc the number of negative aa (Asp+Glu)
+ in a subsequence (soff, eoff) of seq
+
+ to calculate over :
+ _____ _____
+ ... |\ /| ...
+ _____|_\ /_|_____
+ |<------->| */
+int countneg (char *seq, int soff, int eoff) {
+
+ int c = 0;
+ int i;
+
+ if (soff == -1) return 0; /* undefined sequence element */
+
+ if (soff < 0)
+ error_fatal (seq, "start position smaller than zero");
+ if (eoff > strlen (seq)){
+ error_fatal (seq, "end position greater than sequence lenght");
+ }
+ for(i=soff; i<eoff; i++)
+ if (seq[i] == 'D' || seq[i] == 'E') c++;
+
+ return c;
+}
+
+/* charge of N-terminus =
+ 1 if Met start is cleaved after translation
+ 0 other one */
+int ncharge (char *seq, int kingdom) {
+
+ if (kingdom == EUKARYOTE) return 1;
+ if (strlen(seq) > 2 && strchr("KRLFI", seq[1]) == NULL) return 1;
+ return 0;
+}
+
+/* calc the difference between the cyt ext compositions
+ a value of smaller than zero indicates a cytoplasmatic location
+ should only be used for loops longer than 50 aa
+ FEBS Lett. 303:141-46 (1992)
+
+ to calculate over :
+ _____ _____
+ ... |\ /| ...
+ _____|_\ /_|_____
+ |<->| */
+double distance (char *seq, int soff, int eoff, scale_t *scale) {
+
+ double *cyt = scale->cyt;
+ double *ext = scale->ext;
+ double *sd = scale->sd;
+
+ int i;
+ int naa[26];
+ double freq, sumcyt, sumext, temp;
+
+ if (soff == eoff) return 0.0;
+
+ for (i=0; i<26; i++) naa[i] = 0;
+ for (i=soff; i<eoff; i++) naa[seq[i] - 'A']++;
+
+ sumext = sumcyt = 0.0;
+ for (i=0; i<26; i++) {
+ if (is_aa (i + 'A')) {
+ freq = naa[i] * 100.0 / (eoff - soff);
+ temp = (cyt[i] - freq) / sd[i];
+ sumcyt += temp * temp;
+ temp = (ext[i] - freq) / sd[i];
+ sumext += temp * temp;
+ }
+ }
+
+ return sqrt(sumcyt) - sqrt(sumext);
+}
+
+
+/* calc the net charge difference of the N-terminal segment including 15 aa
+ up- and 15 aa downward
+ Hartmann et al., PNAS
+
+ to calculate over :
+ __________
+ /| S0 |\
+ | 15 aa |/_|__________|_\| 15 aa |
+ |<-------->| |<-------->| */
+int nterminus (char *seq, int soff, int eoff, int delta) {
+
+ int start, end, charge;
+ int i, len;
+
+ charge = 0;
+ /* calc charge avant the segment */
+ start = soff - 15;
+ start = (start < 0) ? 0 : start;
+ end = soff + delta;
+
+ for (i=start; i<end; i++)
+ if (strchr("KR", seq[i]) != NULL) charge++;
+ else if (strchr("DE", seq[i]) != NULL) charge--;
+
+ /* calc charge after the segment */
+ start = eoff - 1 - delta;
+ end = eoff - 1 + 15;
+ len = strlen(seq);
+ end = (end > len) ? len : end;
+
+ for (i=start; i<end; i++)
+ if (strchr("KR", seq[i]) != NULL) charge--;
+ else if (strchr("DE", seq[i]) != NULL) charge++;
+
+ return charge;
+}
+
+static int is_aa(int aa) {
+
+ char c;
+ c = (char)aa;
+
+ if ((c >= 'A') && (c <= 'Z'))
+ if (strchr("BJOUXZ", c) == NULL)
+ return TRUE;
+
+ return FALSE;
+
+}
+
+/* retreive cyt-ext scale datas from file */
+int read_cytext_datas (char *file, scale_t *scales) {
+
+ double *cyt = scales->cyt;
+ double *ext = scales->ext;
+ double *sd = scales->sd;
+
+ int i;
+ char *BUFF, *p, *q, *val;
+ int aa;
+
+ FILE *IN;
+
+ /* we initialise the storage to 0 */
+ for(i = 0; i < 26; i++) {
+ cyt[i] = ext[i] = sd[i] = 0;
+ }
+
+ if ((IN = fopen(file, "r")) == NULL)
+ error_fatal(file, NULL);
+
+ if((BUFF = (char *)malloc(BUFFLEN)) == NULL)
+ error_fatal("memory", NULL);
+
+ if((val = (char *)malloc(sizeof(char) * (MAXSIZE + 1))) == NULL)
+ error_fatal("memory", NULL);
+
+ while (fgets(BUFF, BUFFLEN, IN) != NULL) {
+
+ /* we skip the comment lines */
+ if (*BUFF == '\0')
+ continue;
+
+ if (*BUFF == '#')
+ continue;
+
+ p = BUFF;
+
+ /* get aa definition */
+ aa = (int)*p;
+ if (!is_aa(aa)){
+ error_warn(file, "Unknown aminoacid.");
+ continue;
+ }
+
+ p++;
+
+ while (*p != '\0' && isalpha((int)*p)) p++;
+ while (*p != '\0' && isspace((int)*p)) p++;
+
+ if(*p == '\0')
+ error_fatal(file, "Incorrect format.");
+
+
+ /* get cyt value */
+ q = val;
+ *q = '\0';
+ while (*p != '\0' && !isspace((int)*p)) {
+ *q++ = *p++; }
+ *q = '\0';
+ cyt[aa - 'A'] = atof(val);
+
+ while (*p != '\0' && isspace((int)*p)) p++;
+ /* get ext value */
+ q = val;
+ *q = '\0';
+ while (*p != '\0' && !isspace((int)*p)) {
+ *q++ = *p++; }
+ *q = '\0';
+ ext[aa - 'A'] = atof(val);
+
+ while (*p != '\0' && isspace((int)*p)) p++;
+ /* get ext value */
+ q = val;
+ *q = '\0';
+ while (*p != '\0' && !isspace((int)*p)) {
+ *q++ = *p++; }
+ *q = '\0';
+ sd[aa - 'A'] = atof(val);
+
+ }
+
+ if(fclose(IN) == EOF)
+ error_fatal(file, NULL);
+
+ free(BUFF);
+ free(val);
+
+ /* print_Hphobes_datas(hphobes_datas); */
+
+ return 0;
+}
+
+/* determine the N-terminus orientation */
+char *orientation(double val) {
+ if (val > 0.0) return "N-in";
+ else if (val < 0.0) return "N-out";
+ else return "undecided";
+}
+
+/* determine the N-terminus orientation */
+char *new_orientation(double val) {
+ if (val > 0.0) return "N-in";
+ else if (val < 0.0) return "N-out";
+ else return "?";
+}
diff --git a/src/charge.h b/src/charge.h
new file mode 100644
index 0000000..f0a0850
--- /dev/null
+++ b/src/charge.h
@@ -0,0 +1,41 @@
+/* File: /home/edeveaud/Work/toppred/src/charge.h
+ * Author: Katja Schuerer
+ */
+
+
+#ifndef __CHARGE_H_
+#define __CHARGE_H_
+
+
+#include "params.h"
+
+#define EUKARYOTE 1
+#define PROKARYOTE 2
+
+/* retreive cyt-ext scale datas from file */
+int read_cytext_datas (char *file, scale_t *scales);
+
+/* calc the Arg+Lys content over a subsequence from soff to eoff */
+int countkr (char *seq, int soff, int eoff);
+
+/* calc the Asp+Glu content over a subsequence from soff to eoff */
+int countneg (char *seq, int soff, int eoff);
+
+/* calc the charge of the N-terminus, depend on cleavage of Met start */
+int ncharge (char *seq, int kingdom);
+
+/* calc the difference of cyt-ext values of a subsequence */
+double distance (char *seq, int soff, int eoff, scale_t *scale);
+
+/* calc the charge difference over adjacent loops of the first segment
+ including 15 aa at each side */
+int nterminus (char *seq, int soff, int eoff, int delta);
+
+/* determine the N-terminus orientation */
+char *orientation(double val);
+
+/* determine the N-terminus orientation
+ if undecided return "?" */
+char *new_orientation(double val);
+
+#endif /* __CHARGE_H_ */
diff --git a/src/config.h.in b/src/config.h.in
new file mode 100644
index 0000000..407d599
--- /dev/null
+++ b/src/config.h.in
@@ -0,0 +1,96 @@
+/* src/config.h.in. Generated from configure.in by autoheader. */
+
+/* Define to 1 if you have the <errno.h> header file. */
+#undef HAVE_ERRNO_H
+
+/* is gnuplot present */
+#undef HAVE_GNUPLOT
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#undef HAVE_INTTYPES_H
+
+/* is libgd present */
+#undef HAVE_LIBGD
+
+/* Define to 1 if you have the `m' library (-lm). */
+#undef HAVE_LIBM
+
+/* Define to 1 if you have the <memory.h> header file. */
+#undef HAVE_MEMORY_H
+
+/* Define to 1 if you have the `pow' function. */
+#undef HAVE_POW
+
+/* Define to 1 if you have the `sqrt' function. */
+#undef HAVE_SQRT
+
+/* Define to 1 if `stat' has the bug that it succeeds when given the
+ zero-length file name argument. */
+#undef HAVE_STAT_EMPTY_STRING_BUG
+
+/* 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 `strchr' function. */
+#undef HAVE_STRCHR
+
+/* Define to 1 if you have the `strerror' function. */
+#undef HAVE_STRERROR
+
+/* 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 `strrchr' function. */
+#undef HAVE_STRRCHR
+
+/* 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 1 if `lstat' dereferences a symlink specified with a trailing
+ slash. */
+#undef LSTAT_FOLLOWS_SLASHED_SYMLINK
+
+/* Name of package */
+#undef PACKAGE
+
+/* Define to the address where bug reports for this package should be sent. */
+#undef PACKAGE_BUGREPORT
+
+/* Define to the full name of this package. */
+#undef PACKAGE_NAME
+
+/* Define to the full name and version of this package. */
+#undef PACKAGE_STRING
+
+/* Define to the one symbol short name of this package. */
+#undef PACKAGE_TARNAME
+
+/* Define to the 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 your <sys/time.h> declares `struct tm'. */
+#undef TM_IN_SYS_TIME
+
+/* Version number of package */
+#undef VERSION
+
+/* Define to empty if `const' does not conform to ANSI C. */
+#undef const
+
+/* Define to `unsigned' if <sys/types.h> does not define. */
+#undef size_t
diff --git a/src/error.c b/src/error.c
new file mode 100644
index 0000000..e62ecc3
--- /dev/null
+++ b/src/error.c
@@ -0,0 +1,44 @@
+/* error.c - Error functions */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef STDC_HEADERS
+#include <stdlib.h>
+#include <string.h>
+#endif
+
+#include <errno.h>
+
+#include "error.h"
+
+#ifndef HAVE_STRERROR
+char *strerror(int errnum) {
+ extern char *sys_errlist[];
+ extern int sys_nerr;
+
+ if (errnum > 0 && errnum < sys_nerr) {
+ return sys_errlist[errnum]; }
+
+ return (char *)"Unknown error type"; }
+#endif /* HAVE_STRERROR */
+
+
+/* Abort on fatal error */
+void error_fatal(const char *str, const char *err) {
+
+ if (err == NULL) { err = strerror(errno); }
+ (void)fprintf(stderr, "Fatal: %s: %s\n", str, err);
+
+ exit(EXIT_FAILURE); }
+
+/* Warn for non fatal error */
+void error_warn(const char *str, const char *err) {
+
+ if (err == NULL) { err = strerror(errno); }
+ (void)fprintf(stderr, "Warning: %s: %s\n", str, err);
+
+ return; }
diff --git a/src/error.h b/src/error.h
new file mode 100644
index 0000000..54ca298
--- /dev/null
+++ b/src/error.h
@@ -0,0 +1,10 @@
+/* error.h - Error functions */
+
+#ifndef __ERROR_H_
+#define __ERROR_H_
+
+/* Functions prototypes */
+void error_fatal(const char *str, const char *err);
+void error_warn(const char *str, const char *err);
+
+#endif /* __ERROR_H_ */
diff --git a/src/graph.c b/src/graph.c
new file mode 100644
index 0000000..c9bde2d
--- /dev/null
+++ b/src/graph.c
@@ -0,0 +1,439 @@
+/* File: /home/edeveaud/Work/toppred/src/graph.c
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef STDC_HEADERS
+#include <stdlib.h>
+#include <string.h>
+#endif
+
+#include <graph.h>
+#include <gd.h>
+#include <gdfontl.h>
+#include <gdfontg.h>
+
+
+#include "error.h"
+#include "topology.h"
+
+
+static int TM_COLOR;
+static int TM_BORDER;
+static int MBR_COLOR;
+static int PUT_COLOR;
+static int MBR_BORDER;
+static int FONT_COLOR;
+static int LOOP_COLOR;
+
+static float COEFF;
+
+static FILE *file_maker(char *title, char *dir, int num) ;
+
+static gdImagePtr init_img(char *title, int num) ;
+
+static int *loop_tweaker (elprint_t *element, int n) ;
+
+static void draw_segment(gdImagePtr img, int pos, int n, int kind) ;
+
+static void draw_loop(gdImagePtr img, int x1,int x2, int length, int real,
+ int kr, int kind, int first_last) ;
+
+static void print_legend(gdImagePtr img,char *legend) ;
+
+void topo_graph_print (topoprint_t *topo, int n, param_t *params, seq_t *seq) {
+
+ char *seq_name;
+ int i,j;
+ int *loop_length;
+ int ll, real, kr, loc,first_last;
+ int num;
+ int x1, x2;
+ char *legend, *p;
+ char *legend_text = "Segments included:";
+ char *dir_name;
+ FILE *pngout;
+ gdImagePtr img;
+ elprint_t *element;
+
+ /* could we draw */
+ if((n-1)/2 >MAX_SEGMENTS){
+ error_warn("graphic_topo", "too many segments to be represented, skipped");
+ return;
+ }
+
+ /* tweaking the values to avoid drawing overlaping segments */
+ element = topo->elps;
+ if ((loop_length = loop_tweaker(element, n)) == NULL) {
+ error_warn("graphic_topo", "could not display topologies");
+ return;
+ }
+
+ /* generating image holder file */
+ dir_name = params->out_dir;
+ seq_name=seq->id;
+ num = topo->nr;
+ pngout = file_maker(seq_name, dir_name, num);
+
+ /* allocate image */
+ img = init_img(seq_name, num);
+
+ /* there is at least n/2 -1 segment included
+ * each one is at max 2 char long + 1 for space
+ * thus generous legend size is */
+ i = strlen(legend_text) + n*3;
+ if((legend = (char *)malloc(sizeof(char) * (i+1))) == NULL){
+ error_fatal("memory", NULL);
+ }
+ p =legend;
+ (void)sprintf(p, "%s", legend_text);
+ p+=strlen(legend_text);
+
+
+ /* draw topologie segments and loops */
+ if ( topo->kr <= 0) loc = CYT;
+ else loc = EXT;
+
+ x1 = x2 = 0;
+ j = 0;
+ for (i=0; i<n; i++) {
+ if (i%2) {
+ draw_segment(img, x2, element[i].tm.nr, (int)element[i].tm.prob);
+ (void)sprintf(p, "%3d", element[i].tm.nr);
+ p+=3;
+ }
+ else {
+ x2 = x1 + loop_length[j];
+ ll = element[i].lo.len;
+ real = loop_length[j];
+ kr = element[i].lo.kr;
+ if (i == 0) first_last = FIRST;
+ else if (i == n-1) first_last = LAST;
+ else first_last = INNER;
+ draw_loop(img, x1, x2, ll, real, kr, loc,first_last ) ;
+ x1 = x2;
+ loc *= -1;
+ j++;
+ }
+ }
+
+ print_legend(img, legend);
+
+ /* dropping image to file */
+ gdImagePng(img, pngout);
+ gdImageDestroy(img);
+
+ if(fclose(pngout) == EOF) {
+ error_fatal("closing file", NULL);
+ }
+
+ /* memory cleaning */
+ free(legend);
+ free(loop_length);
+
+ return;
+}
+
+
+static void print_legend(gdImagePtr img,char *legend) {
+ gdFontPtr font;
+ font = gdFontGiant;
+ gdImageString(img, font, 10, 50, (unsigned char *)legend, FONT_COLOR);
+
+ return;
+}
+
+static void draw_loop(gdImagePtr img, int x1, int x2, int length, int real, int kr, int loc, int first_last) {
+
+ /* loop position */
+ int xc , yc;
+ int l, start, stop;
+ /* legend related */
+ gdFontPtr font;
+ char *legend1, *legend2;
+ int xf1, xf2, yf1, yf2;
+
+ font = gdFontLarge;
+
+ /* positioning the loop params */
+ l = (int)(COEFF * real);
+ yc = Y_CENTER - ((SEG_H /2) * loc);
+ if (first_last == INNER) {
+ xc = (int)(((x1 + x2)/2.0) * COEFF) + MARGIN;
+ start = 180 - ((1 - loc) * 90);
+ stop = start + 180;
+ }
+ else if (first_last == FIRST) {
+ xc = MARGIN;
+ start = 270 - ((1 - loc) * 135);
+ stop = start + 90;
+ l *= 2;
+ gdImageChar(img, font, xc , yc, 'N', FONT_COLOR) ;
+ }
+ else { /* first_last == LAST */
+ xc = (int)(((x1 + x2)/2.0) * COEFF) + l/2 + MARGIN;
+ start = 180 - ((1 - loc) * 45);
+ stop = start + 90;
+ l *= 2;
+ gdImageChar(img, font, xc , yc, 'C', FONT_COLOR) ;
+ }
+
+ /* draw the loop */
+ gdImageArc(img, xc, yc, l,LOOP_H, start, stop, LOOP_COLOR);
+
+
+ /* now deal with the loop legend */
+ if((legend1 = (char *)malloc(10)) == NULL){ error_fatal("memory", NULL); }
+ if((legend2 = (char *)malloc(10)) == NULL){ error_fatal("memory", NULL); }
+
+ (void)sprintf(legend1, "Ll = %d", length);
+ (void)sprintf(legend2, "KR = %d", kr);
+
+ /* legend position */
+ if (first_last == INNER) {
+ xf1 = xc - strlen(legend1)*font->w/2;
+ xf2 = xc - strlen(legend2)*font->w/2;
+ }
+ else if (first_last == FIRST) {
+ xf1 = xc ;
+ xf2 = xc ;
+ }
+ else {
+ xf1 = xc - strlen(legend1)*font->w;
+ xf2 = xc - strlen(legend2)*font->w;
+ }
+ yf1 = Y_CENTER - (loc * (LOOP_H + SEG_H - font->h/2));
+ yf2 = yf1 + 2*font->h/2;
+
+ /* plot the loop legend */
+ gdImageString(img, font, xf1, yf1, (unsigned char *)legend1, FONT_COLOR);
+ gdImageString(img, font, xf2, yf2, (unsigned char *)legend2, FONT_COLOR);
+
+ free(legend1);
+ free(legend2);
+
+ return;
+}
+
+/* segment representation routine */
+static void draw_segment(gdImagePtr img, int pos, int n, int kind) {
+
+ /* segment position */
+ int x;
+ int x1, x2, y1, y2;
+ int w, l;
+ int color;
+
+ /* legend related */
+ int xf, yf;
+ int num_l, num_h;
+ char *tag;
+ gdFontPtr font;
+ font = gdFontLarge;
+
+ x = (int)(pos * COEFF) + MARGIN;
+
+ /* segment coordinate */
+ x1 = x - (SEG_L/2);
+ x2 = x + (SEG_L/2);
+ y1 = Y_CENTER - (int)((SEG_H - SEG_L) / 2);
+ y2 = Y_CENTER + (int)((SEG_H - SEG_L) / 2);
+ w = l = SEG_L + 2;
+
+ /* segment color attribution */
+ if (kind == 1){ color = PUT_COLOR; }
+ else { color = TM_COLOR; }
+
+ /* draw the segment border and fill it*/
+ gdImageLine(img, x1, y1, x1, y2, TM_BORDER);
+ gdImageLine(img, x2, y1, x2, y2, TM_BORDER);
+ gdImageArc(img, x, y1, w, l, 180, 0, TM_BORDER);
+ gdImageArc(img, x, y2, w, l, 0, 180, TM_BORDER);
+ gdImageFillToBorder(img, x, Y_CENTER, TM_BORDER, color);
+
+ /* tag segment with is number */
+ if((tag = (char *)malloc(3*sizeof(char))) == NULL) {
+ error_fatal("memory", NULL);
+ }
+ (void)sprintf(tag, "%d", n);
+
+ num_l=(strlen(tag) * font->w) /2 ;
+ num_h = font->h / 2;
+ xf = x - num_l;
+ yf = Y_CENTER - num_h;
+
+ gdImageString(img, font, xf, yf, (unsigned char *)tag, FONT_COLOR);
+ free(tag);
+}
+
+/* tweaking the loop length values in order to avoid some overlaping segments
+ * drawing
+ * segment are drawn with a fixed width, we must check that the loop
+ * representation is long enough to avoid some segment collision.
+ * eg: shorter loop lenght are forced to be represented at least with
+ * a lenght compatible with segment width
+ * see below
+ * _ ____
+ * | | | |
+ * _____ ___ ___
+ * / / \ \ / \ / \
+ * | | | | | | |
+ * | | | | | | |
+ * \_\_/_/ \___/ \___/
+ *
+ * loop length < SEG_L loop_lenght forced to SEG_L
+ */
+
+static int *loop_tweaker (elprint_t *element, int n){
+
+ int check , cont, graph_len;
+ int i, j, ll;
+ int *loop_length;
+ i = n - ((n-1)/2);
+ if ((loop_length = malloc(i * sizeof(int))) == NULL) {
+ error_fatal("memory", NULL);
+ }
+ for (i=0, j=0; i<n; i+=2, j++ ) {
+ loop_length[j] = element[i].lo.len;
+ }
+
+
+ check = 10;
+ j = n - ((n-1)/2);
+ while (check > 0) {
+ cont = 1;
+ check--;
+ graph_len = 0;
+
+ for (i = 0; i< j; i++) { graph_len += loop_length[i]; }
+ if ( graph_len == 0) graph_len = 1;
+ COEFF = (float)(800 - 40)/ graph_len;
+ for (i = 0; i<j; i++) {
+ ll = loop_length[i]*COEFF;
+ if (ll < 20) {
+ cont = 0;
+ loop_length[i] = (int)(20/COEFF)+1;
+ }
+ }
+ if (cont == 1) {break;}
+ }
+
+ if (check <= 0) {
+ free (loop_length);
+ return NULL;
+ }
+
+ return loop_length;
+}
+
+/* prepare the png file wich will host the image */
+static FILE *file_maker(char *title, char *dir, int num) {
+
+ char *file_name, *p;
+ int path_len;
+ FILE *pngout;
+
+ /* preparing filename and allocating the result file ptr*/
+ path_len =sizeof(char) * (strlen(dir) + 1 + strlen(title) + 6 + 5 + 2 + 1 );
+ if((file_name=(char *)malloc(path_len)) == NULL){
+ error_fatal("memory", NULL);
+ }
+ p = file_name;
+ (void)sprintf(p, "%s/%s-%d.png",dir, title, num);
+
+ if ((pngout = fopen(file_name, "wb")) == NULL) {
+ error_fatal("topos", NULL);
+ }
+
+ free(file_name);
+ return pngout;
+}
+
+
+/* allocate the image holder, and plot the legends and common drawing */
+static gdImagePtr init_img(char *title, int num) {
+ int y1, y2;
+ int xf, yf, text_l, text_h;
+
+ char *cyto, *extra;
+ char *struct_num;
+ char *certain, *put;
+ char *loop, *kr;
+
+ gdImagePtr img;
+ gdFontPtr font, sfont;
+
+ img = gdImageCreate(IMAGE_LENGTH, IMAGE_HEIGTH);
+ font = gdFontGiant;
+ sfont = gdFontLarge;
+
+
+ /* colors are given in RGB see /usr/lib/X11/rgb.txt */
+ TM_COLOR = gdImageColorAllocate(img, 255, 255, 255); /* white */
+ TM_BORDER = FONT_COLOR = gdImageColorAllocate(img, 0, 0, 0); /* black */
+ MBR_COLOR = gdImageColorAllocate(img, 219, 219, 219); /* grey86 */
+ MBR_BORDER = LOOP_COLOR = gdImageColorAllocate(img, 3, 3, 3); /* grey1 */
+ PUT_COLOR = gdImageColorAllocate(img, 161, 161, 161); /* grey63 */
+
+ y1 = Y_CENTER - (int)(SEG_H / 4);
+ y2 = Y_CENTER + (int)(SEG_H / 4);
+
+ /* plot the membrane */
+ gdImageFilledRectangle(img, 0, y1, IMAGE_LENGTH , y2, MBR_COLOR);
+ gdImageLine(img, 0, y1, IMAGE_LENGTH, y1, MBR_BORDER);
+ gdImageLine(img, 0, y2, IMAGE_LENGTH, y2, MBR_BORDER);
+
+ /* title and legend */
+
+ /* localisation legend */
+ cyto = "CYTOPLASM";
+ extra = "EXTRACELLULAR";
+ text_h = font->h / 2;
+
+ /* cytoplasm legend */
+ text_l = (strlen(cyto) * font->w) /2 ;
+ xf = X_CENTER - text_l;
+ yf = (int)(IMAGE_HEIGTH * 2.0/9.0) - text_h;
+ gdImageString(img, font, xf, yf, (unsigned char *)cyto, FONT_COLOR);
+
+ /* extracellular legend */
+ text_l = (strlen(extra) * font->w) /2 ;
+ xf = X_CENTER - text_l;
+ yf = (int)(IMAGE_HEIGTH * 8.0/9.0) - text_h;
+ gdImageString(img, font, xf, yf, (unsigned char *)extra, FONT_COLOR);
+
+ /* title generation */
+ gdImageString(img, font, 10, 10, (unsigned char *)title, FONT_COLOR);
+ if((struct_num = (char *)malloc(14+3)) == NULL){
+ error_fatal("memory", NULL);
+ }
+ (void)sprintf(struct_num, "Structure no. %d", num);
+
+ gdImageString(img, font, 10, 30, (unsigned char *)struct_num, FONT_COLOR);
+ free(struct_num);
+
+ /* color meaning legend */
+ gdImageRectangle(img, 600, 30, 620, 50, TM_BORDER);
+ gdImageFilledRectangle(img, 600, 60, 620, 80, PUT_COLOR);
+ gdImageRectangle(img, 600, 60, 620, 80, TM_BORDER);
+
+ certain = "Segment Certain";
+ put = "Segment Putative";
+ gdImageString(img, sfont, 630, 32, (unsigned char *)put, FONT_COLOR);
+ gdImageString(img, sfont, 630, 62, (unsigned char *)certain, FONT_COLOR);
+
+ /* cellular localisation legend */
+ loop = "Ll: Loop length";
+ kr = "KR: Number of Lys and Arg";
+ gdImageString(img, font, 10, 350, (unsigned char *)loop, FONT_COLOR);
+ gdImageString(img, font, 10, 370, (unsigned char *)kr, FONT_COLOR);
+
+ /* positionnning the Margin */
+ return img;
+
+}
diff --git a/src/graph.h b/src/graph.h
new file mode 100644
index 0000000..a218d61
--- /dev/null
+++ b/src/graph.h
@@ -0,0 +1,33 @@
+/* File: /home/edeveaud/Work/toppred/src/top-graph.h
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+ */
+
+
+#ifndef __GRAPH_H__
+#define __GRAPH_H__
+
+
+#include "topoprint.h"
+
+
+#define IMAGE_LENGTH 800 /* image size is fixed */
+#define IMAGE_HEIGTH 400
+#define Y_CENTER IMAGE_HEIGTH/2
+#define X_CENTER IMAGE_LENGTH/2
+#define SEG_L 20 /* segment representation is fixed */
+#define SEG_H 60
+#define LOOP_H 40
+#define MARGIN 20
+#define MAX_SEGMENTS 37 /* maximum segments we can represent */
+
+#define CYT -1
+#define MBR 0
+#define EXT +1
+
+#define FIRST -1
+#define LAST 1
+#define INNER 0
+
+void topo_graph_print (topoprint_t *topo, int n, param_t *params, seq_t *seq);
+
+#endif /* __GRAPH_H__ */
diff --git a/src/loop.c b/src/loop.c
new file mode 100644
index 0000000..bd10525
--- /dev/null
+++ b/src/loop.c
@@ -0,0 +1,300 @@
+/* File: /home/edeveaud/Work/toppred/src/loop.c
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef STDC_HEADERS
+#include <stdlib.h>
+#endif
+
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+
+#include "loop.h"
+#include "error.h"
+
+
+
+/* eliminate segments overlapping */
+static int purge_segments(segment_t **seg, param_t params, int nbr);
+
+/* sort segments by Hvalues, used by purge_segments*/
+static int seg_H_sort(const void *p1, const void *p2);
+/* sort segments by positions, used by purge_segments*/
+static int seg_pos_sort(const void *p1, const void *p2);
+
+/* sort segments regardin their Hydrophobicity */
+static int seg_H_sort(const void *p1, const void *p2) {
+ const segment_t *seg1, *seg2 ;
+
+ seg1 = (const segment_t *)p1;
+ seg2 = (const segment_t *)p2;
+
+ if(seg1->max > seg2->max)
+ return -1 ;
+
+ if(seg1->max < seg2->max)
+ return 1;
+
+ return 0 ;
+}
+
+
+/* get segments from the hydrophobicity profile
+ * extract all maximum whose value is greater than the putative cut-of value
+ * on the curve, and check for their compliance to the
+ * parameters, ie eliminate overlaping segments
+ * allocte the correspondig structure, and returns the number of "correct"
+ * segments found
+ */
+int get_segments(double *Hplot, segment_t **res,int nb, param_t params) {
+
+ int n;
+ int i, n_tot;
+ size_t len;
+ double p_cut;
+ double prev, curr, next;
+
+ segment_t curr_seg;
+ segment_t *pos, *p;
+
+ p_cut = params.p_cut;
+ len = sizeof(segment_t);
+ prev = curr = next = 0.0;
+ pos = p = NULL;
+
+ if ((pos = (segment_t *)malloc(MAXSEGMENT*len)) == NULL)
+ error_fatal("Memory", NULL);
+
+ n_tot = MAXSEGMENT;
+
+ p = pos;
+ i = 0;
+ n = 0;
+ while(i < nb ) {
+ /* take segment at beginning of the sequence */
+ if (i == 0) prev = params.p_cut - 1.0;
+ else prev = Hplot[i-1];
+ curr = Hplot[i];
+ /* take segment at end of the sequence */
+ if (i == nb-1) next = curr - 1.0;
+ else next = Hplot[i+1];
+ /* <= and >= allow to get segments in position 0 */
+ /* and to get segments at the begining of a "plateau" */
+ if((curr > p_cut) && ((prev <= curr) && (curr >= next))) {
+ curr_seg.max = curr;
+ curr_seg.pos = i;
+ curr_seg.keep = 1;
+ /* resize the segment holder if needed */
+ if (n >= n_tot) {
+ n_tot = n_tot + MAXSEGMENT;
+ if ((pos=(segment_t *)realloc(pos, n_tot*len)) == NULL)
+ error_fatal("Memory", "Reallocating segment holder");
+ p = pos + n;
+ }
+ *p=curr_seg;
+ n++;
+ p++;
+ } /* end if max */
+ i++;
+ } /* end while */
+
+ if (n != 0) {
+ qsort(pos, (size_t)n, len, seg_H_sort) ;
+ n = purge_segments(&pos, params, n);
+
+ /* allocating the real segment holder */
+ if ((pos = (segment_t *)realloc(pos, n*len)) == NULL)
+ error_fatal("Memory", "resizing results");
+ }
+
+ *res = pos;
+ return n;
+}
+
+
+/* clean all the "incorretc" segments,
+ * overlaping ones,
+ * contiguous ones */
+static int purge_segments(segment_t **seg, param_t params, int nbr) {
+
+ int i, j;
+ int n, len;
+ int pos1, pos2;
+ int tmspacer;
+ segment_t *p, *q;
+
+ n = 0;
+ tmspacer = params.tmspacer;
+
+ /* don't allow transmembrane segments to be contiguous*/
+ len = (2* params.q) + params.n + tmspacer;
+ i = j = 0;
+ p = q = * seg;
+ for (i = 0; i <nbr; i++) {
+ pos1 = p->pos;
+ q = *seg;
+ for (j=0; j< nbr; j++) {
+ pos2 = q->pos;
+
+ if(p->keep == FALSE){
+ q++;
+ continue;
+ }
+
+ if((pos2 < pos1) && (pos1 - len < pos2)){
+ q->keep = FALSE;
+ q++;
+ continue;
+ }
+
+ if((pos2 > pos1) && (pos1 + len > pos2)) {
+ q->keep = FALSE;
+ q++;
+ continue;
+ }
+ q++;
+ }/*end for j */
+
+ p++;
+ }/*end for i */
+
+ p = *seg;
+ n = 0;
+ for(i = 0; i < nbr; i++, n++, p++){
+ if(p->keep == 0){
+ p->pos = 9999999;
+ n--;
+ }
+ }
+ q = *seg;
+ qsort(q, (size_t)nbr, sizeof(segment_t), seg_pos_sort) ;
+
+ return n;
+}
+
+
+static int seg_pos_sort(const void *p1, const void *p2) {
+ const segment_t *seg1, *seg2;
+
+ seg1 = (const segment_t *)p1;
+ seg2 = (const segment_t *)p2;
+
+ if(seg1->pos > seg2->pos)
+ return 1 ;
+
+ if(seg1->pos < seg2->pos)
+ return -1;
+
+ return 0 ;
+
+}
+
+/* allocate seg_t and loop_t structures from the segment_t structure
+ * and returns the number of loops */
+int calc_loop(seq_t *sequence, segment_t **segment, loop_t **loopKS,
+ seg_t **segKS, param_t params, int nbr)
+{
+ loop_t *l_res, *l;
+ seg_t *s_res, *s;
+ segment_t *seg;
+
+ int i, n, q_win;
+ int start, stop, x, y;
+ int state;
+ int win_len;
+ int seq_len;
+ char *seq;
+
+ start = stop = 0;
+
+ win_len = (2*params.q) + params.n; /* full window length */
+ q_win = params.q; /* flanking region length */
+
+ seq = sequence->seq;
+ seq_len = sequence->size;
+ seg = *segment;
+ state = -1;
+
+ n = nbr+1;
+
+ if ((l_res = (loop_t *)malloc(n*sizeof(loop_t))) == NULL){
+ error_fatal("memory", "allocating loops");
+ }
+ if ((s_res = (seg_t *)malloc(nbr*sizeof(seg_t))) == NULL) {
+ error_fatal("memory", "allocating segments");
+ }
+ l = l_res;
+ s = s_res;
+
+ if(seg[0].pos == 0) { /* sequence starts with a segment */
+ l[0].start = -1;
+ l++;
+ state = 1;
+ }
+
+ for(i = 0; i < nbr; i++, seg++) {
+
+ /* we are in a loop */
+ if(state == -1){
+ x = start = stop;
+ y = stop = seg->pos;
+
+ l->start = start;
+ l->stop = stop;
+ if ((start - q_win) >= 0){
+ x = start - q_win;
+ }
+ if ((stop + q_win) <= seq_len) {
+ y = stop + q_win;
+ }
+ l->delta = countkr(seq, x, y);
+ state *= -1;
+ l++;
+ }
+ /* we are now in a menbrane segment */
+ if(state == 1);{
+ start = stop;
+ stop = start + win_len;
+ s->start = start;
+ s->stop = stop;
+ s->H = seg->max;
+ if (seg->max >= params.c_cut) {
+ s->kind = CERTAIN; /* 1 */
+ s->probTM = 1.0;
+ }
+ else {
+ s->kind = PUTATIVE; /* 0 */
+ s->probTM = (seg->max - params.p_cut) / (params.c_cut - params.p_cut);
+ }
+ x = start + q_win;
+ y = stop - q_win;
+ s->delta = countkr(seq, x, y);
+ s++;
+ state *= -1;
+ }
+ }
+
+ /* dealing with the last segment if it exists */
+ if (stop < seq_len ) {
+ start = stop;
+ stop = sequence->size;
+ l->start = start;
+ l->stop = stop;
+ l->delta = countkr(seq, start - q_win, stop);
+ }
+ else { /* sequence ends with a segment */
+ l->start = -1;
+ }
+
+ *segKS = s_res;
+ *loopKS = l_res;
+
+ return n++;
+}
diff --git a/src/loop.h b/src/loop.h
new file mode 100644
index 0000000..280eb05
--- /dev/null
+++ b/src/loop.h
@@ -0,0 +1,55 @@
+/* File: /home/edeveaud/Work/toppred/src/loop.h
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+ */
+
+
+#ifndef __LOOP_H_
+#define __LOOP_H_
+
+
+
+#include "params.h"
+#include "charge.h"
+#include "seq-reader.h"
+
+
+
+typedef struct segment_S {
+ double max;
+ int pos;
+ int stop;
+ int keep;
+}segment_t;
+
+
+typedef struct seg_S {
+ int start;
+ int stop;
+ int kind;
+ int delta;
+ double H;
+ double probTM;
+} seg_t;
+
+
+typedef struct loop_S {
+ int start;
+ int stop;
+ int delta;
+} loop_t;
+
+#define MAXSEGMENT 20
+#define TMSPACER 2
+#define PUTATIVE 0
+#define CERTAIN 1
+#define LOOP -1
+
+#define MAXSIZE 5
+
+/* retrieve the position of ech peak on the curve, with is associated
+ H value */
+int get_segments(double *Hplot, segment_t **res,int nb, param_t params);
+
+int calc_loop(seq_t *sequence, segment_t **segment, loop_t **loop,
+ seg_t **seg, param_t params, int nbr);
+#endif /* __LOOP_H_ */
diff --git a/src/main.c b/src/main.c
new file mode 100644
index 0000000..7bfe872
--- /dev/null
+++ b/src/main.c
@@ -0,0 +1,556 @@
+/* File: /home/edeveaud/Work/toppred/src/main.c
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef STDC_HEADERS
+#include <stdlib.h>
+#include <string.h>
+#endif
+
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+
+#include <libgen.h>
+#include <math.h>
+
+#include <sys/stat.h>
+#include <sys/types.h>
+
+#ifdef HAVE_LIBGD
+#include "graph.h"
+#endif
+
+/* #include "params.h" */
+#include "main.h"
+#include "error.h"
+#include "usage.h"
+#include "seq-reader.h"
+#include "profile.h"
+#include "loop.h"
+#include "topology.h"
+#include "topoprint.h"
+#include "output.h"
+#include "mloutput.h"
+
+static char *prog;
+
+static void process_seq(FILE *IN, param_t params);
+
+int main(int argc, char **argv) {
+
+ /* variables and initialisation */
+ param_t params;
+ int i, uplot;
+ char *out_file, *p;
+ FILE *IN;
+ char *data_dir;
+ char *buf;
+ size_t len;
+
+ /* default values */
+ out_file = NULL;
+ params.web = 0;
+ params.n = 11;
+ params.q = 5;
+ params.p_cut = 0.6; /* 0.5; */
+ params.c_cut = 1.0;
+ params.n_topos = 16;
+ params.seg_len = 60; /* 70; */
+ params.OUT = stdout;
+ params.gplot = TRUE;
+ params.hydro_file = TRUE;
+ params.plot_format = "x11";
+ params.plot_pause = "";
+ params.output = NEW;
+ params.topo_format = "png";
+ params.tmspacer = 2;
+ params.kingdom = PROKARYOTE;
+ uplot = FALSE;
+
+ /* check to see if a TOPPREDDATA environment variable is available */
+ /* yes overwritte the DATADIR default, and use it*/
+ if ((data_dir = getenv("TOPPREDDATA")) == NULL){
+ data_dir = DATADIR;
+ }
+
+ params.data_file = "GES-scale";
+ params.ce_file = "CYTEXT-scale";
+
+ /* get progname */
+ prog = argv[0];
+ if((p = strrchr(prog, '/')) != NULL)
+ prog = ++p;
+
+
+ /* check syntax option on command line */
+ i = 0;
+ while((i = getopt(argc, argv, "c:d:eg:hH:n:N:o:O:p:q:s:t:vy")) != -1) {
+ switch(i) {
+
+ case 'c':
+ params.c_cut = atof(optarg);
+ break;
+
+ case 'd':
+ params.tmspacer = atoi(optarg);
+ break;
+
+ case 'e':
+ params.kingdom = EUKARYOTE;
+ break;
+
+ case 'g':
+#ifdef HAVE_GNUPLOT
+ params.gplot = TRUE;
+ params.plot_format = optarg;
+ uplot = TRUE;
+#else
+ if (strcmp(optarg, "none") != 0) {
+ (void)fprintf(stderr, "Missing gnuplot support: -g option unavailable");
+ return EXIT_FAILURE;
+ }
+ params.gplot = FALSE;
+ params.plot_format = "none";
+#endif /* HAVE_GNUPLOT */
+ break;
+
+ case 'h':
+ usage(prog);
+ return EXIT_SUCCESS;
+
+ case 'H':
+ params.data_file = optarg;
+ break;
+
+ case 'n':
+ params.n = atoi(optarg);
+ break;
+
+ case 'N':
+ params.n_topos = atoi(optarg);
+ break;
+
+ case 'o':
+ out_file = optarg;
+ break;
+
+ case 'O':
+ params.output = check_output_format(prog, optarg);
+ break;
+
+ case 'p':
+ params.p_cut = atof(optarg);
+ break;
+
+ case 'q':
+ params.q = atoi(optarg);
+ break;
+
+ case 's':
+ params.seg_len = atoi(optarg);
+ break;
+
+ case 't':
+#ifdef HAVE_LIBGD
+ params.topo_format = optarg;
+#else
+ if (strcmp(optarg, "none") != 0) {
+ (void)fprintf(stderr, "Missing libgd support: -t option unavailable");
+ return EXIT_FAILURE;
+ }
+ params.topo_format = "none";
+#endif
+ break;
+
+ case 'v':
+ (void)fprintf(stdout, "%s (%s %s)\n", prog, PACKAGE, VERSION);
+ return EXIT_SUCCESS;
+
+ case 'y':
+ params.hydro_file = FALSE;
+ break;
+
+ default :
+ usage(prog);
+ return EXIT_FAILURE;
+ }
+ }
+
+ /* change default values for different output formats */
+ if (params.output == HTML && !uplot) {
+ params.plot_format = PNG;
+ }
+
+ /* checking validity of arguments */
+ if (params.n < 0)
+ error_fatal(prog, "n should be a positive number.");
+ if (params.q < 0)
+ error_fatal(prog, "q should be a positive number.");
+ if(params.n + params.q == 0)
+ error_fatal(prog, "Humm, n or q can be null, but not simultaneously.");
+ if(params.c_cut < params.p_cut)
+ error_fatal(prog, "certain cutoff should be greater than putative cutoff.");
+ if(params.seg_len <= 0)
+ error_fatal(prog, "critical segment length s should be a positive integer.");
+ if(params.tmspacer <=0)
+ error_fatal(prog, "critical tm distance should be a positive integer.");
+ if(params.n_topos <= 0)
+ error_fatal(prog, "N should be a positive number.");
+
+ /* output file */
+ if(out_file != NULL && (params.OUT = fopen(out_file, "w")) == NULL)
+ error_fatal(out_file, NULL);
+
+ /* get the directory holder for files*/
+ params.out_dir = strdup(dirname(out_file));
+
+ /* check the plot format */
+ check_plot_format(prog, ¶ms);
+
+ /* check the topo format */
+ check_topo_format(prog, ¶ms);
+
+ /* check if there's some files to deal with */
+ if (optind >= argc) {
+ usage(prog);
+ return EXIT_FAILURE;
+ }
+
+ /* load the hphobes values once */
+ len = strlen(data_dir) + 1 + strlen(params.data_file) + 1;
+ if ((buf = (char *)malloc(len)) == NULL)
+ error_fatal("memory", NULL);
+ (void)snprintf(buf, len, "%s/%s", data_dir, params.data_file);
+ read_Hphobes_datas(buf, params.Hdatas);
+ free(buf);
+
+ /* load cyt-ext values from cefile */
+ len = strlen(data_dir) + 1 + strlen(params.ce_file) + 1;
+ if ((buf = (char *)malloc(len)) == NULL)
+ error_fatal("memory", NULL);
+ (void)snprintf(buf, len, "%s/%s", data_dir, params.ce_file);
+ (void) read_cytext_datas (buf, &(params.scales));
+ free(buf);
+
+ /* print parameter values */
+
+ switch (params.output) {
+ case HTML:
+ break;
+ case OLD:
+ old_print_firstparameters(¶ms);
+ break;
+ default: /* NEW */
+ new_print_parameters(¶ms);
+ }
+
+ IN = stdin;
+ /* process all the input files */
+ for (i = optind; i <argc; i++) {
+ if (*argv[i] != '-' && (IN = fopen(argv[i], "r")) == NULL)
+ error_fatal(argv[i], NULL);
+
+ if (params.output == OLD) {
+ (void) fprintf (params.OUT, "Using sequence file: %s\n\n", argv[i]);
+ }
+
+ process_seq(IN, params);
+
+ if(fclose(IN) !=0)
+ error_fatal(argv[i], NULL);
+
+ }
+
+ if(out_file != NULL && (fclose(params.OUT) == EOF)){
+ error_fatal(out_file, NULL); }
+
+ free(params.out_dir);
+
+ return 0;
+}
+
+
+static void process_seq(FILE *IN, param_t params) {
+
+ int i, s;
+ int nb_plot;
+ int ntopos, maxtopos;
+ size_t len;
+ double *Hprofile;
+ seq_t seq;
+ segment_t *segments;
+ loop_t *KSloop;
+ seg_t *KSseg;
+ elem_t KSelem;
+ topo_t *KStopo;
+ int nel2prn;
+ topoprint_t topo2prn;
+ FILE *OUT;
+ int skip;
+ char *alphabet;
+ char *err_msg;
+
+ OUT = params.OUT;
+ Hprofile = NULL;
+ segments = NULL;
+
+
+ alphabet = alphabet_maker(DEFAULT_ALPHABET);
+ while(read_seq(IN, &seq, alphabet) !=0) {
+
+/**** verify sequence ****/
+ skip = 0;
+
+ if(seq.size > MAXSEQLEN) {
+ err_msg = "sequence too long -- skipped";
+ skip = 1;
+ }
+ if(seq.size < ((2 * params.q) + params.n)) {
+ err_msg = "sequence too short -- skipped";
+ skip = 1;
+ }
+ if(seq.size == 0) {
+ err_msg = "empty sequence -- skipped";
+ skip = 1;
+ }
+
+ if(skip) {
+ error_warn(seq.id, err_msg);
+ free_seq(&seq);
+ continue;
+ }
+
+/**** print sequence ****/
+ switch (params.output) {
+ case HTML:
+ OUT = params.OUT = init_html (seq.id, params.out_dir);
+ html_header (OUT, seq.id);
+ html_parameters (OUT, ¶ms);
+ /* sequence is printed below the plot */
+ break;
+ case OLD:
+ default:
+ (void) fprintf(OUT, "\nSequence : %s (%d res)\n", seq.id, seq.size);
+ print_sequence(OUT, seq.seq);
+ (void) fprintf(OUT, "\n");
+ }
+
+ if (params.output == OLD) { old_print_secondparameters(¶ms); }
+
+/**** generation profile ****/
+
+ /* allocate memory of the hydrophobic profile */
+ nb_plot = seq.size - ((2 * params.q) + params.n) + 1;
+ len = nb_plot * sizeof(double);
+ if ((Hprofile = (double *)malloc(len)) == NULL) {
+ error_fatal("memory", NULL);
+ }
+
+ /* calc Hval for all window positions */
+ calc_profile(&seq, params, Hprofile);
+
+ /***** find transmembran segments *****/
+ s = get_segments(Hprofile, &segments, nb_plot , params);
+
+/***** produce profile plot with transmembran segment indication *****/
+
+ /* we produce the hydrophobic profile datas */
+ if (params.hydro_file == TRUE)
+ plot_values(Hprofile, &seq, params);
+
+ switch (params.output) {
+ case HTML:
+ html_plot(OUT, seq.id, ¶ms);
+ html_sequence (OUT, &seq);
+ break;
+ /* case OLD: */
+ /* default: */ /* NEW */
+ }
+
+#ifdef HAVE_GNUPLOT
+ if(!params.plot_outfile && strlen(params.plot_pause) != 0) {
+ (void)fprintf(stdout, "hit return to continue\n");
+ }
+ /* produce de gnuplot image */
+ if(params.gplot){
+ gplot(Hprofile, &segments, &seq, s, params);
+ }
+#endif
+
+/**** transform segments structure to segment-loop structure ****/
+
+ if (s != 0) {
+ (void)calc_loop(&seq, &segments, &KSloop, &KSseg, params, s);
+ }
+
+ /* as profile and segments-storage struct is no longer needed purge it */
+ free(Hprofile);
+ free(segments);
+
+/**** print transmembran segment summary ****/
+
+ switch (params.output) {
+ case OLD:
+ break;
+ case HTML:
+ (void)fprintf (OUT, "<H4><CENTER>Transmembran segments</CENTER></H4>\n");
+ start_phrase();
+ default:
+ (void) fprintf(OUT, "Found: %d segments\n\n", s);
+ if (params.output == HTML) { end_phrase(); start_phrase(); }
+ if (s) { print_tmsummary(OUT, s, KSseg); }
+ }
+
+ if (params.output == HTML) { end_phrase(); }
+
+/**** construct topologies ****/
+
+ if (s != 0) {
+
+ KSelem.nsegs = s;
+ KSelem.nputatives = 0;
+ for (i=0; i< s; i++)
+ if(KSseg[i].kind == 0) KSelem.nputatives++;
+ KSelem.segs = KSseg;
+ KSelem.loops = KSloop;
+
+ if (KSelem.nputatives > MAXPUTATIVES_CALC) {
+ error_warn(seq.id,
+ "too many putative segments to calculate best topologies");
+ }
+ else {
+
+ maxtopos = ntopos = (int) pow(2.0, (double) KSelem.nputatives);
+
+/**** print topology summary ****/
+
+ if (params.output == HTML) {
+ (void) fprintf (OUT, "<H4><CENTER>Topologies</CENTER></H4>\n");
+ start_phrase();
+ }
+
+
+ (void)fprintf(OUT, "\nTotal of %d structures are to be tested\n\n",
+ maxtopos);
+ if (params.output == OLD) {
+ (void) fprintf (OUT, "\n");
+ old_print_tmsummary(OUT, s, KSseg, seq.seq);
+ }
+
+ if (params.output == HTML) { end_phrase(); start_phrase(); }
+
+ if (ntopos > params.n_topos) {
+ error_warn(seq.id, "more topologies than printed");
+ ntopos = params.n_topos;
+ }
+
+/**** calculate topologies and stock the ntopos best ones ****/
+
+ if ((KStopo = (topo_t *) malloc (ntopos*sizeof(topo_t))) == NULL)
+ error_fatal("memory", NULL);
+
+ ntopos = tp_calc(KStopo, &KSelem, &seq, ¶ms);
+ /* sort topologies by highest Arg+Lys bias */
+ qsort((void *)KStopo, (size_t)ntopos, sizeof(topo_t), tp_compare);
+
+/**** print the best topologies ****/
+
+ /* allocate memory for max number of structure elements to print */
+ nel2prn = 2*KSelem.nsegs + 1;
+ if ((topo2prn.elps = (elprint_t *) malloc (nel2prn*sizeof(elprint_t))) == NULL)
+ error_fatal("memory", NULL);
+ topo2prn.image = NULL;
+
+ for (i=0; i<ntopos; i++) {
+ /* construct all topology information */
+ topo2prn.nr = i+1;
+ topo2prn.putatives = KStopo[i].putatives;
+ topo2prn.kr = KStopo[i].kr;
+ nel2prn = tp_decode (&topo2prn, &KSelem, &seq, ¶ms);
+
+/**** print topology image ****/
+#ifdef HAVE_LIBGD
+ if(strcmp(params.topo_format, "none") != 0) {
+ int image_len = strlen(seq.id) + strlen(params.topo_format) + 6 + 3;
+ if ((topo2prn.image = (char *) realloc (topo2prn.image, image_len*sizeof(char))) == NULL)
+ error_fatal("memory", NULL);
+ (void)sprintf(topo2prn.image, "%s-%d.%s",
+ seq.id, topo2prn.nr, params.topo_format);
+
+ /* graphic print go here */
+ (void)topo_graph_print(&topo2prn, nel2prn, ¶ms, &seq);
+ }
+#endif
+
+/**** printing nongraphic output ****/
+
+ switch (params.output) {
+ case HTML:
+ html_topology (&topo2prn, nel2prn, ¶ms);
+ break;
+ case OLD:
+ (void)fprintf(OUT, "\n-----------------------------------------------------------------------\n");
+ tp_toppred_fprintf (&topo2prn, nel2prn, ¶ms);
+ break;
+ default: /* NEW */
+ tp_new_print (&topo2prn, nel2prn, ¶ms);
+ }
+
+ } /* end for */
+
+/**** nettoyage ****/
+
+ /* free element structure for printing */
+ if (topo2prn.image != NULL) {
+ free(topo2prn.image);
+ }
+ free(topo2prn.elps);
+ free(KStopo);
+
+ } /* end else of if (KSelem.nputatives > MAXPUTATIVES_CALC) */
+
+ /* free KS structs even if no topologie calculated */
+ free(KSloop);
+ free(KSseg);
+
+ } /* end if (s != 0) */
+
+ /* freeing the seq-storage struct */
+ free_seq(&seq);
+
+ /* print sequence end informations and close html output file */
+
+ switch(params.output) {
+ case OLD:
+ (void)fprintf(OUT, "\n-----------------------------------------------------------------------\n");
+ break;
+ case HTML:
+ (void)fprintf(OUT, "\n");
+ (void)fprintf(OUT, "</BODY>\n");
+ (void)fprintf(OUT, "</HTML>\n");
+ break;
+ /* default : */
+ }
+
+ if (params.output == HTML) {
+ if (fclose(params.OUT) == EOF) {
+ error_fatal(prog, NULL);
+ }
+ OUT=stdout;
+ }
+
+ }/* end while j=read_seq */
+
+ free(alphabet);
+
+ return;
+}
+
+
diff --git a/src/main.h b/src/main.h
new file mode 100644
index 0000000..4f88fe7
--- /dev/null
+++ b/src/main.h
@@ -0,0 +1,26 @@
+/* File: /home/edeveaud/Work/toppred/src/main.h
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+ */
+
+
+#ifndef __MAIN_H_
+#define __MAIN_H_
+
+
+
+
+#define MAXSEQLEN 30000
+
+
+#ifndef DATADIR
+#define DATADIR "/usr/local/share/"PACKAGE
+#endif
+
+
+#endif /* __MAIN_H_ */
+
+
+
+
+
+
diff --git a/src/mloutput.c b/src/mloutput.c
new file mode 100644
index 0000000..96f1b7a
--- /dev/null
+++ b/src/mloutput.c
@@ -0,0 +1,161 @@
+/* -----------------------------------------------------------------
+ file : /home/schuerer/toppred/src/mloutput.c
+
+ author : Schuerer
+ description :
+
+
+-------------------------------------------------------------------- */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "error.h"
+#include "config.h"
+#include "usage.h"
+
+#include "output.h"
+#include "mloutput.h"
+
+/* internal macros */
+
+/* internal prototypes */
+
+FILE *init_html(char *name, char *dir) {
+ char *filename;
+ FILE *OUT;
+ int len;
+
+ len = strlen(dir) + 1 + strlen(name) + 5;
+
+ if ((filename = malloc((size_t)len+1)) == NULL) {
+ error_fatal("html output file", NULL); }
+
+ (void)sprintf(filename, "%s/%s.html", dir, name);
+
+ if ((OUT = fopen(filename, "w")) == NULL) {
+ error_fatal(filename, NULL); }
+
+ free(filename);
+
+ return OUT; }
+
+
+void html_header (FILE *OUT, char *name) {
+
+ (void)fprintf(OUT, "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0//EN\"\n");
+ (void)fprintf(OUT, " \"http://www.w3.org/TR/REC-html40/strict.dtd\">\n");
+ (void)fprintf(OUT, "<HTML>\n");
+
+ (void)fprintf(OUT, "<HEAD>\n");
+ (void)fprintf(OUT, "<META http-equiv=\"Content-Type\" content=\"text/html;");
+ (void)fprintf(OUT, " charset=iso-8859-1\">\n");
+ (void)fprintf(OUT, "<TITLE>Toppred prediction %s</TITLE>\n", name);
+ (void)fprintf(OUT, "</HEAD>\n");
+
+ (void)fprintf(OUT, "<BODY>\n");
+ (void)fprintf(OUT, "<H1><CENTER>Toppred prediction %s</CENTER></H1>\n", name);
+ (void)fprintf(OUT, "<PRE>\n");
+
+ return; }
+
+
+void html_parameters (FILE *OUT, param_t *p) {
+
+ (void) fprintf (OUT, "<H4><CENTER>Algorithm specific parameters</CENTER></H4>\n\n");
+ (void) fprintf (OUT, "<PRE>\n");
+ new_print_parameters (p);
+ (void) fprintf (OUT, "</PRE>\n");
+
+}
+
+void html_sequence (FILE *OUT, seq_t *seq) {
+
+ (void)fprintf(OUT, "<H4><CENTER>Sequence</CENTER></H4>\n");
+ start_phrase();
+ (void) fprintf(OUT, "Sequence : %s (%d res)\n", seq->id, seq->size);
+ print_sequence(OUT, seq->seq);
+ end_phrase();
+
+}
+
+void html_plot (FILE *OUT, char *seqname, param_t *p) {
+
+ (void)fprintf(OUT, "<H4><CENTER>Hydrophobicity plot</CENTER></H4>\n");
+ (void)fprintf(OUT, "<P><CENTER>\n");
+#ifdef HAVE_GNUPLOT
+ if (p->gplot && p->plot_outfile && !strcmp(p->plot_outfile, PNG)) {
+ (void)fprintf(OUT, "<IMG SRC=\"./%s.png\">\n", seqname);
+ }
+#endif
+ (void)fprintf(OUT, "<PRE>\n");
+ (void)fprintf(OUT, "<P>\n");
+ (void)fprintf(OUT, "<A HREF=\"./%s.hydro\">view hydrophobic values</A>\n",
+ seqname);
+ (void)fprintf(OUT, "</P>\n");
+ (void)fprintf(OUT, "</CENTER></P>\n");
+
+}
+
+void html_topology (topoprint_t *topo, int nel, param_t *para) {
+
+ FILE *OUT = para->OUT;
+ int clen = para->seg_len;
+ elprint_t *el = topo->elps;
+ int i;
+
+ /* header */
+ (void) fprintf (OUT, "%8s %6s %6s %6s %4s %4s %8s %8s %8s %8s\n",
+ "HEADER ", "START", "STOP", "LEN",
+ "PROB", "HP",
+ "DARGLYS", "DCYTEXT", "DNCHARGE", "DNNEGPOS");
+
+
+ /* topo summary */
+ (void) fprintf (OUT, "%8s ", "TOPOLOGY");
+#ifdef HAVE_LIBGD
+ if (!strcmp(para->topo_format, PNG)) {
+ (void) fprintf (OUT, "<A HREF=\"./%s\">%3d</A>", topo->image, topo->nr);
+ }
+ else {
+ (void) fprintf (OUT, "%3d", topo->nr);
+ }
+#else
+ (void) fprintf (OUT, "%3d", topo->nr);
+#endif
+
+ (void) fprintf (OUT, " %3.2f %6.2f %6.2f %8.2f %8.2f\n",
+ topo->prob, (double) topo->kr,
+ topo->cytext, (double) topo->nterm, topo->negpos);
+
+ (void) fprintf (OUT, "%8s %7s %7s %8s\n",
+ "TOPOLOGY",
+ new_orientation((double) (topo->kr+topo->ncharge)),
+ new_orientation(topo->cytext * (-1.0)),
+ new_orientation((double) topo->nterm));
+
+ /* topo elements */
+ for (i=0; i<nel; i++) {
+ if (i%2) { /* tmsegment (index impair) */
+ (void) fprintf(OUT, "%8s %6d %6d %6d %4.2f %4.2f\n",
+ el[i].tm.type, el[i].tm.start+1, el[i].tm.stop,
+ el[i].tm.len, el[i].tm.prob, el[i].tm.H);
+ }
+ else { /* loop (index pair) */
+ if (el[i].lo.len > clen) { /* cytext value is significant */
+ (void) fprintf(OUT, "%8s %6d %6d %6d (%6.2f) %6.2f\n",
+ el[i].lo.type, el[i].lo.start+1, el[i].lo.stop,
+ el[i].lo.len, (double) el[i].lo.kr, el[i].lo.cytext);
+ }
+ else if (el[i].lo.len != 0) { /* kr value is significant */
+ (void) fprintf(OUT, "%8s %6d %6d %6d %6.2f (%6.2f)\n",
+ el[i].lo.type, el[i].lo.start+1, el[i].lo.stop,
+ el[i].lo.len, (double) el[i].lo.kr, el[i].lo.cytext);
+ }
+ }
+ }
+
+ (void) fprintf(OUT, "\n");
+
+ return;
+}
diff --git a/src/mloutput.h b/src/mloutput.h
new file mode 100644
index 0000000..76e1185
--- /dev/null
+++ b/src/mloutput.h
@@ -0,0 +1,26 @@
+/* File: /home/schuerer/toppred/src/mloutput.h
+ * Author: Schuerer
+ */
+
+#ifndef __MLOUTPUT_H_
+#define __MLOUTPUT_H_
+
+#include <stdlib.h>
+#include "loop.h"
+#include "params.h"
+#include "topoprint.h"
+#include "seq-reader.h"
+
+/* html output functions */
+#define start_phrase() (void) fprintf(OUT, "<PRE><P>\n")
+#define end_phrase() (void) fprintf(OUT, "</P></PRE>\n")
+
+FILE *init_html(char *name, char *dir);
+void html_header (FILE *OUT, char *name);
+void html_parameters (FILE *OUT, param_t *p);
+
+void html_sequence (FILE *OUT, seq_t *seq);
+void html_plot (FILE *OUT, char *seqname, param_t *p);
+void html_topology (topoprint_t *topo, int nel, param_t *para);
+
+#endif /* _MLOUTPUT_H_ */
diff --git a/src/output.c b/src/output.c
new file mode 100644
index 0000000..63e1d21
--- /dev/null
+++ b/src/output.c
@@ -0,0 +1,132 @@
+/* -----------------------------------------------------------------
+ file : /home/schuerer/toppred/src/baseprint.c
+
+ author : Schuerer
+ description :
+
+
+-------------------------------------------------------------------- */
+
+#include <stdio.h>
+#include <string.h>
+#include "output.h"
+
+#include "error.h"
+
+/* internal macros */
+
+/* internal prototypes */
+
+void print_sequence (FILE *OUT, char *seq) {
+
+ int k;
+ char *sq;
+
+ sq = seq;
+ k = 1;
+ while(*sq){
+ (void)fputc(*sq, OUT);
+ sq++;
+ k++;
+ if(k>60) {
+ (void)fputc('\n', OUT);
+ k=1;
+ }
+ }
+ (void) fputc('\n', OUT);
+}
+
+void print_tmsummary (FILE *OUT, int nseg, seg_t *KSseg) {
+
+ char *type;
+ int i;
+
+ (void)fprintf(OUT, "Candidate membrane-spanning segments:\n\n");
+ (void)fprintf(OUT, " Helix Begin - End Score Certainity\n");
+ for(i=0; i< nseg; i++) {
+ type = NULL;
+ (void)fprintf(OUT, "%6d %5i - %-5i %-6.3f",
+ i+1, KSseg[i].start+1, KSseg[i].stop, KSseg[i].H);
+ if(KSseg[i].kind == 0) type = "Putative";
+ if(KSseg[i].kind == 1) type = "Certain";
+ (void)fprintf(OUT, "%s\n", type);
+ }
+}
+
+void new_print_parameters (param_t *p) {
+
+ FILE *OUT = p->OUT;
+ char *scale;
+ char *cytext;
+
+ scale = p->data_file;
+ cytext = p->ce_file;
+
+ (void) fprintf (OUT, "Algorithm specific parameters: \n\n");
+
+ (void) fprintf (OUT, "Full window size : %d\n", 2*p->q+p->n);
+ (void) fprintf (OUT, "Core window size : %d\n", p->n);
+ (void) fprintf (OUT, "Wedge window size: %d\n", p->q);
+ (void) fprintf (OUT, "Using hydrophobicity file: %s\n\n", scale);
+
+ (void) fprintf (OUT, "Cutoff for certain transmembrane segments: %.2f\n",
+ p->c_cut);
+ (void) fprintf (OUT, "Cutoff for putative transmembrane segments: %.2f\n",
+ p->p_cut);
+ (void) fprintf (OUT, "Critical distance between 2 transmembrane segments: %d\n\n",
+ p->tmspacer);
+
+ (void) fprintf (OUT, "Critical loop length: %d\n\n", p->seg_len);
+ (void) fprintf (OUT, "Kingdom: %s\n\n",
+ (p->kingdom == PROKARYOTE) ? "procaryote" : "eucaryote");
+ (void) fprintf (OUT, "Using cyt/ext file: %s\n\n", cytext);
+ /* (void) fprintf (OUT, "\nCharge-pair energy: 0\n"); mettre en variable */
+
+}
+
+void old_print_firstparameters (param_t *p) {
+
+ FILE *OUT = p->OUT;
+ char *scale, *cytext;
+
+ (void) fprintf (OUT, "\n");
+
+ cytext = p->ce_file;
+ scale = p->data_file;
+ (void) fprintf (OUT, "Using hydrophobicity file: %s\n", scale);
+ (void) fprintf (OUT, "Using cyt/ext file: %s\n", cytext);
+}
+
+void old_print_tmsummary (FILE *OUT, int nseg, seg_t *KSseg, char *seq) {
+
+ char *type;
+ int i;
+
+ (void)fprintf(OUT, "Candidate membrane-spanning segments:\n\n");
+ (void)fprintf(OUT, " Helix Begin End Score Certainity\n");
+ for(i=0; i< nseg; i++) {
+ type = NULL;
+ (void)fprintf(OUT, "%6d %5i %-5i %-6.3f",
+ i+1, KSseg[i].start+1, KSseg[i].stop, KSseg[i].H);
+ if(KSseg[i].kind == 0) type = "Putative";
+ if(KSseg[i].kind == 1) type = "Certain";
+ (void)fprintf(OUT, "%s\n", type);
+ }
+}
+
+void old_print_secondparameters (param_t *p) {
+
+ FILE *OUT = p->OUT;
+
+ (void) fprintf (OUT, "\n(p)rokaryotic or (e)ukaryotic: %c\n\n",
+ (p->kingdom == PROKARYOTE) ? 'p' : 'e');
+
+ (void) fprintf (OUT, "\nCharge-pair energy: 0\n\n"); /* mettre en variable */
+ (void) fprintf (OUT, "Length of full window (odd number!): %d\n\n", 2*p->q+p->n);
+ (void) fprintf (OUT, "Length of core window (odd number!): %d\n\n", p->n);
+ (void) fprintf (OUT, "Number of residues to add to each end of helix: 1\n\n");
+ (void) fprintf (OUT, "Critical length: %d\n\n", p->seg_len);
+ (void) fprintf (OUT, "Upper cutoff for candidates: %.2f\n\n", p->c_cut);
+ (void) fprintf (OUT, "Lower cutoff for candidates: %.2f", p->p_cut);
+
+}
diff --git a/src/output.h b/src/output.h
new file mode 100644
index 0000000..8fc5378
--- /dev/null
+++ b/src/output.h
@@ -0,0 +1,19 @@
+/* File: /home/schuerer/toppred/src/output.h
+ * Author: Schuerer
+ */
+
+#ifndef __OUTPUT_H_
+#define __OUTPUT_H_
+
+#include <stdlib.h>
+#include "loop.h"
+
+void new_print_parameters (param_t *p);
+void old_print_firstparameters (param_t *p);
+void old_print_secondparameters (param_t *p);
+
+void print_sequence (FILE *OUT, char *seq);
+void print_tmsummary (FILE *OUT, int nseg, seg_t *KSseg);
+void old_print_tmsummary (FILE *OUT, int nseg, seg_t *KSseg,char *seq);
+
+#endif /* __OUTPUT_H_ */
diff --git a/src/params.h b/src/params.h
new file mode 100644
index 0000000..36880ab
--- /dev/null
+++ b/src/params.h
@@ -0,0 +1,49 @@
+/* File: /home/edeveaud/Work/toppred/src/params.h
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+ */
+
+
+#ifndef __PARAMS_H_
+#define __PARAMS_H_
+
+typedef struct scale_S {
+
+ double cyt[26];
+ double ext[26];
+ double sd[26];
+
+} scale_t;
+
+typedef struct param_S {
+ double Hdatas[26];
+ double c_cut; /* certain cut-off */
+ double p_cut; /* putative cut-off */
+ int n; /* core window */
+ int q; /* wedge window */
+ int seg_len; /* segment lentgh */
+ int kingdom; /* kingdom of species to which the sequence belongs */
+ int n_topos; /* numbers of topologies to calculate/print */
+ int gplot; /* to produce the ps Hphobe profile file or not */
+ int hydro_file; /* to produce the hydro file or not */
+ char *out_dir; /* where to store results files */
+ FILE *OUT; /* where to display the results */
+ scale_t scales; /* cyt-ext-sd scale file */
+
+ char *plot_pause;
+ char *topo_format;/* wich format to produce for the topo images */
+ char *data_file; /* hydrophobicity scale */
+ char *ce_file; /* cyt-ext-sd scale file */
+ char *plot_format; /* wich format to produce */
+ char *plot_outfile; /* prefix for the plot file */
+
+ int output; /* output format */
+ int tmspacer; /* critical tm distance */
+ int web; /* for web output format */
+} param_t;
+
+#define BUFFLEN 100
+#define TRUE 1
+#define FALSE 0
+
+
+#endif
diff --git a/src/profile.c b/src/profile.c
new file mode 100644
index 0000000..9d82b32
--- /dev/null
+++ b/src/profile.c
@@ -0,0 +1,368 @@
+/* File: /home/edeveaud/Work/toppred/src/profile.c
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+*/
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef STDC_HEADERS
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+#endif
+
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+
+#include <ctype.h>
+
+#include "profile.h"
+#include "error.h"
+#include "output.h"
+
+/* as sequence verification was performed before. Thus I don't care
+ about checking, it is assumed all char (aa) submited will be
+ correct and is comprise between correc t bounds. */
+#define aa2H(c,d) (d)[(c)-'A']
+
+/* check aa syntax from sequence based on IUPAC alphabet */
+static int is_aa(int aa);
+
+
+/* retreive Hphobes datas from file */
+void read_Hphobes_datas (char *file, double *hphobes_datas)
+{
+
+ int i, indx;
+ char *BUFF, *p, *q, *val;
+ int aa;
+ double Hval;
+
+ FILE *IN;
+
+ /* we initialise the storage to 0 */
+ for(i = 0; i < 26; i++)
+ hphobes_datas[i] = 0;
+
+ if ((IN = fopen(file, "r")) == NULL)
+ error_fatal(file, NULL);
+
+ if((BUFF = (char *)malloc(sizeof(char)*BUFFLEN)) == NULL)
+ error_fatal("memory", NULL);
+
+ if((val = (char *)malloc(sizeof(char)*(MAXSIZE + 1))) == NULL)
+ error_fatal("memory", NULL);
+
+ while (fgets(BUFF, BUFFLEN, IN) != NULL) {
+
+ /* we skip the comment lines */
+ if (*BUFF == '\0')
+ continue;
+
+ if (*BUFF == '#')
+ continue;
+
+ indx = -1;
+ p = BUFF;
+
+ /* get aa definition */
+ aa = (int)*p;
+ if (!is_aa(aa)){
+ error_warn(file, "Unknown aminoacid.");
+ continue;
+ }
+
+ p++;
+
+ while (*p != '\0' && isalpha((int)*p)) p++;
+ while (*p != '\0' && isspace((int)*p)) p++;
+
+ if(*p == '\0')
+ error_fatal(file, "Incorrect format.");
+
+ /* get hydrophobic value */
+ q = val;
+ *q = '\0';
+ while (*p != '\0' && !isspace((int)*p)) {
+ *q++ = *p++; }
+ *q = '\0';
+
+ /*store the datas */
+ Hval = atof(val);
+ indx = (aa -'A');
+ hphobes_datas[indx] = Hval;
+ }
+
+ if(fclose(IN) == EOF){
+ error_fatal(file, NULL);
+ }
+
+ free(BUFF);
+ free(val);
+
+ return ;
+}
+
+
+
+
+/* retrieve the hydropbobic calcul for each positions */
+/* ___________________________________________________________________________
+ *
+ * based on G. von Heijne J. Mol. Biol. 1992 225,487-494
+ *
+ * --> l=2q+1 <--
+ * +--------+
+ * +----| |----+
+ * +----+--------+----+
+ * --> l=2n+1 <--
+ *
+ * for each given window position on sequence, i,
+ * the hydrophobicity value of the window is calculated this way
+ * heach hi for a given aa on the window is multiplied by Wi
+ * Wi = | 1/S 1<= i <= (n - q + 1)
+ * | (n - q + 1)/S (n - q + 1) < i < (n + q + 1)
+ * | (2n + 2 - i)/S (n + q + 1) <= i <= (2n + 1)
+ * with S = (1 + n)^2 - q^2
+ * ___________________________________________________________________________
+ *
+ * rewritten in order to use n as length of the center window and q
+ * as length of the wedge window
+ *
+ * ie
+ * --> l=n <--
+ * +--------+
+ * +----| |----+
+ * +----+--------+----+
+ * --> l=q <-- --> l=q <--
+ *
+ * --> l=2q+n <--
+ *
+ * thus ponderation calculus become
+ *
+ * Wi = | 1/S 1<= i <= q
+ * | (q + 1)/S (q + 1) < i < (q + n)
+ * | (2q + n + 1 - i)/S (q + n +1) <= i <= (q + 2n)
+ * with S = (q + 1)* (n + q)
+ */
+
+void calc_profile(seq_t *seq_holder, param_t params, double *profile) {
+
+ char *seq, *p;
+ int i, j, n, q;
+ int R1, R2;
+ int L, size;
+ double S;
+ double Hval;
+ double *Hdatas;
+ double d, wi;
+
+ n = params.n; /* 11 */
+ q = params.q; /* 5 */
+ Hdatas = params.Hdatas;
+
+ L = (2*q)+n;
+ size = seq_holder->size - L ;
+ seq = seq_holder->seq;
+ p = seq;
+
+ S = (double) ((q+1)*(n+q));
+
+ R1 = q;
+ R2 = n + q + 1;
+ for(i = 0; i<= size; i++ ) { /* loop on sequence */
+ Hval = 0.0;
+ d = 0.0;
+ p = seq+i;
+
+ for(j = 1; j<= R1; j++) { /*loop on window 1*/
+ wi = ((double) j) / S;
+ d = aa2H(p[j-1], Hdatas) * wi;
+ Hval = Hval + d;
+ }
+
+ wi = ((double) (q + 1)) / S;
+ for(j=R1+1 ; j < R2; j++){ /*loop on window 2*/
+ d = aa2H(p[j-1], Hdatas) * wi;
+ Hval = Hval + d;
+ }
+
+
+ for(j = R2; j<= L; j++) { /*loop on window 3*/
+ wi = ((double) (2 * q + n + 1 - j)) / S;
+ d = aa2H(p[j-1], Hdatas) * wi;
+ Hval = Hval + d;
+ }
+ profile[i] = Hval;
+ }
+}
+
+
+
+/* print hydrophobic values, in a useable manner */
+void plot_values(double *plot, seq_t *seq, param_t params) {
+
+ char *id, *filename, *dir;
+ FILE *OUT;
+ time_t timer;
+ int size;
+ char *scale;
+ int core_win, full_win;
+ int len;
+ int i;
+
+ id = seq->id;
+ size = seq->size;
+ dir = params.out_dir;
+ scale = params.data_file;
+
+ core_win = params.n;
+ full_win = core_win + (2 * params.q);
+
+ /* setting the creation time */
+ if (time(&timer) == (time_t) -1) error_warn("time", NULL);
+
+ /* creating the output file-name and associated FILE */
+ len = strlen(dir) + 1 + strlen(id) + 6 + 1;
+ if ((filename = (char *)malloc((size_t)len)) == NULL){
+ error_fatal("memory", NULL);
+ }
+ (void)sprintf(filename, "%s/%s.hydro",dir, id);
+ if((OUT=fopen(filename, "w")) == NULL){
+ error_fatal(filename, NULL);
+ }
+
+ /* generating header */
+ (void)fprintf(OUT, "# sequence:\t%s (%d res.)\n", id, size);
+ (void)fprintf(OUT, "# hydrophobicity values generated: %s", ctime(&timer));
+ (void)fprintf(OUT, "# core window: %d\n", core_win);
+ (void)fprintf(OUT, "# full window: %d\n", full_win);
+ (void)fprintf(OUT, "# using values from file: %s\n", scale);
+ (void)fprintf(OUT, "# Position Hydrophobicity\n");
+
+ for(i = 0 ; i <= size - full_win; i++) {
+ (void)fprintf(OUT, "%d\t%6.2f\n", i+1, plot[i]);
+ }
+ if(fclose(OUT) == EOF){
+ error_fatal(filename, NULL);
+ }
+
+ free(filename);
+}
+
+
+/* return TRUE if c is one of the 20 amino acid known on IUPAC */
+int is_aa(int aa) {
+ char c;
+ c = (char)aa;
+
+ if ((c >= 'A') && (c <= 'Z'))
+ if (strchr("BJOUXZ", c) == NULL)
+ return TRUE;
+
+ return FALSE;
+}
+
+
+#ifdef HAVE_GNUPLOT
+void gplot (double *plot, segment_t **segments, seq_t *seq, int nbr,
+ param_t params) {
+
+ char *id, *plot_format, *plot_outfile, *dir;
+ int size, x_max;
+ FILE *OUT;
+ double p_cut, c_cut;
+ double y_max, y_min, val;
+ double *p;
+ segment_t *seg;
+ char tempfilename[]=TEMPFILENAME;
+
+ char *gnuplot_command;
+ int j, i, win_len;
+ dir = params.out_dir;
+
+ p_cut = params.p_cut;
+ c_cut = params.c_cut;
+
+ id = seq->id;
+ size = seq->size;
+
+ i = nbr;
+ /* win_len = params.n + (2 * params.q) + 1; */
+ win_len = params.n + (2 * params.q);
+ seg = *segments;
+
+ /* generate tempory file name */
+ if((j = mkstemp(tempfilename)) == -1){
+ error_fatal("generating temporary file", NULL);
+ }
+
+ if ((OUT = fdopen(j, "w")) == NULL) {
+ error_fatal("writing temporary file", NULL);
+ }
+
+ plot_format = params.plot_format;
+ plot_outfile = params.plot_outfile;
+
+ /* getting axis range */
+ y_min = y_max = val = 0;
+ x_max = size - win_len + 1;
+ p = plot;
+ for(i = 0; i < size - win_len - 1; i++, p++) {
+ val = *p;
+ if (y_max < val) y_max = val;
+ if (y_min > val) y_min = val;
+ }
+ y_min = y_min - 0.25;
+ y_max = y_max + 0.5;
+
+ /* writting gnuplot file definition */
+ (void)fprintf(OUT, "set title '%s'\n", id);
+ (void)fprintf(OUT, "set time\n");
+ (void)fprintf(OUT, "set xlabel 'start position of window in sequence'\n");
+ (void)fprintf(OUT, "set ylabel 'hydrophobicity value'\n");
+ (void)fprintf(OUT, "set key right bottom\n");
+ (void)fprintf(OUT, "%s\n", plot_format);
+ if(plot_outfile){
+ (void)fprintf(OUT, "set output \"%s/%s.%s\"\n",dir, id, plot_outfile);
+ }
+ /* setting plot axis */
+ (void)fprintf(OUT, "set xrange [%d:%d]\n", 0, x_max);
+ (void)fprintf(OUT, "set yrange [%.1f:%.1f]\n", y_min, y_max);
+ (void)fprintf(OUT, "set y2range [%.1f:%.1f]\n", y_min - y_max, 0.2);
+
+ /* tagging the tm segments */
+ for(i = 0; i < nbr; i++, seg++) {
+ int x;
+ x = seg->pos;
+ (void)fprintf(OUT, "set arrow from second %d,0 to second %d,-0.2 nohead lw 2\n", x, x);
+ }
+
+ (void)fprintf(OUT, "plot %f title 'Upper cutoff', %f title 'Lower cutoff', '%s/%s.hydro' title 'hydrophobicity' with lines\n", c_cut, p_cut, dir, id);
+ (void)fprintf(OUT, "%s\n", params.plot_pause);
+
+ if(fclose(OUT) == EOF) {
+ error_fatal("gpl file 3", NULL);
+ }
+
+ /* gnuplot command */
+ if((gnuplot_command = (char*)malloc(sizeof(char) *(TEMPFILENAMELEN + 8 +1))) == NULL)
+ error_fatal ("memory", NULL);
+ (void)sprintf(gnuplot_command, "gnuplot %s", tempfilename);
+
+ if(system(gnuplot_command) == -1){
+ error_fatal("plotting" , NULL);
+ }
+
+ free(gnuplot_command);
+
+ if (unlink(tempfilename) == -1) {
+ error_fatal("gpl file", "deleting");
+ }
+
+}
+#endif /* HAVE_GNUPLOT */
diff --git a/src/profile.h b/src/profile.h
new file mode 100644
index 0000000..5552ba7
--- /dev/null
+++ b/src/profile.h
@@ -0,0 +1,38 @@
+/* File: /home/edeveaud/Work/toppred/src/profile.h
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+ */
+
+
+#ifndef __PROFILE_H_
+#define __PROFILE_H_
+
+#include "params.h"
+#include "seq-reader.h"
+#include "loop.h"
+
+
+
+/* WARNING if changing TEMPFILENAME value, adjust TEMPFILENAMELEN */
+#define TEMPFILENAME "/tmp/top-XXXXXX"
+#define TEMPFILENAMELEN 15
+
+
+
+/* retreive Hphobes datas from file */
+void read_Hphobes_datas (char *file, double *hphobes_datas);
+
+
+/* print hydrophobic values, in a useable manner */
+void plot_values(double *plot, seq_t *seq, param_t params);
+
+/* retrieve the hydropbobic calcul for each positions */
+void calc_profile(seq_t *seq, param_t params, double *res);
+void calc_profile_bug(seq_t *seq_holder, param_t params, double *profile);
+
+#ifdef HAVE_GNUPLOT
+/* display or produce the hydrophobic profile using gnuplot */
+void gplot (double *plot, segment_t **segments, seq_t *seq, int i,
+ param_t params);
+#endif /* HAVE_GNUPLOT */
+
+#endif
diff --git a/src/seq-reader.c b/src/seq-reader.c
new file mode 100644
index 0000000..8a1fe28
--- /dev/null
+++ b/src/seq-reader.c
@@ -0,0 +1,245 @@
+/* File: /home/edeveaud/Work/dnatool/src/readseq.c
+ * Author: Eric Deveaud <edeveaud at pasteur.fr>
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef STDC_HEADERS
+#include <stdlib.h>
+#include <string.h>
+#endif
+
+#include <ctype.h>
+
+#include "seq-reader.h"
+#include "error.h"
+
+
+
+static void process_header(seq_t *seq, char *header) ;
+static int clean_buff(char **buffer, char *alphabet) ;
+
+
+int read_seq (FILE *IN, seq_t *seq_holder, char *alphabet) {
+
+ char *BUFF, *stock, *p, *q;
+ int i, state, l;
+ size_t buffsize, bufflen, seq_len;
+
+ /* check if there is something to read */
+ if ((i = fgetc(IN)) == EOF && feof(IN) != 0) {
+ return NO_SEQ; }
+
+ ungetc(i, IN);
+
+ state = SEQ_NONE;
+ seq_len = bufflen = 0;
+ buffsize = BUFFSIZE;
+ seq_holder->seq = NULL;
+
+ if ((BUFF = (char *) malloc(sizeof(char) * buffsize+1 )) == NULL)
+ error_fatal ("memory1" , NULL);
+ if ((stock = (char *) malloc(sizeof(char) * buffsize+1 )) == NULL)
+ error_fatal ("memory2" , NULL);
+
+ *stock = '\0';
+ q = stock;
+
+ while ((i = fgetc(IN)) != EOF) {
+ /* skip empty lines */
+ if (isspace(i)) {continue;}
+
+ if ( ungetc(i, IN) == EOF ) error_fatal ("ungetc", NULL);
+
+ /* end entry or start entry */
+ if ( i == '>' ) {
+ if (state == SEQ_NONE ) state = HEADER;
+ if (state == SEQ) break ;
+ }
+
+ if (fgets(BUFF, BUFFSIZE + 1, IN) == NULL) break;
+
+ /* header processing */
+ if ( state == HEADER ) {
+
+ /* memcopy with '/0' inclusion */
+ memcpy(q, BUFF, BUFFSIZE+1);
+ /* is header line completly read */
+ if (strrchr(BUFF, '\n') == NULL) {
+ if((stock = realloc(stock, buffsize + BUFFSIZE + 1)) == NULL)
+ error_fatal("realloc", NULL);
+ q = stock + buffsize ;
+ buffsize += BUFFSIZE ;
+ continue;
+ }
+ process_header(seq_holder, stock);
+ state = SEQ;
+ buffsize = BUFFSIZE;
+ p = stock;
+ *p ='\0';
+ continue;
+ }
+
+ if ( state == SEQ || state == DUMP ){
+ /* we clean the buffer before any further use */
+ if ((l = clean_buff(&BUFF, alphabet)) == -1)
+ error_fatal(seq_holder->id, "sequence contain spurious characters");
+ }
+
+ if (state == SEQ ) {
+ bufflen = l;
+ /* is stock buffer long enough */
+ if ( seq_len + bufflen >= buffsize ) {
+ buffsize += BUFFSIZE;
+ if ((stock = realloc(stock, sizeof(char) * buffsize+1)) == NULL)
+ error_fatal("Memory3", "Reallocating seq");
+ }
+ q = stock + seq_len;
+ strncpy (q, BUFF, bufflen);
+ seq_len += bufflen;
+ }
+
+ if ( state == SEQ_NONE ) {
+ error_fatal("Sequence", "is NOT fasta formated");
+ }
+ }
+
+
+ free(BUFF);
+ if ( state == SEQ ) {
+ *(stock+seq_len) = '\0';
+ seq_holder->seq = stock;
+ }
+ seq_holder->size = seq_len;
+
+ return state;
+
+}
+
+char *alphabet_maker (char *alphabet) {
+
+ char *res, *p;
+ int j;
+
+ if ((res = calloc(255, sizeof(char))) == NULL) {
+ error_fatal("memory", NULL);
+ }
+
+ p = alphabet;
+ while(*p) {
+ j = (int)*p;
+ if ( islower(j) ){
+ res[j] = toupper((int)*p);
+ res[j-32] = toupper((int)*p);
+ }
+ else{
+ res[j] = *p;
+ res[j+32] = *p;
+ }
+ p++;
+ }
+
+ return res;
+}
+
+
+static void process_header(seq_t *seq, char *header) {
+ char *id, *comm, *p, *q;
+ int i, n, l;
+
+ n = 0;
+ p = header;
+
+ /* skip > */
+ p++;
+
+ while(*p && isascii((int)*p) && !isspace((int)*p)) {
+ p++; n++;
+ }
+
+ /* check if sequence is named or not */
+ if (n == 1 && strchr( ".,;", (int)header[1])) n = 0;
+ l = ( n == 0) ? 9 : n;
+
+ if((id = malloc(sizeof(char)*(l+1))) == NULL){
+ error_fatal("memory", NULL);
+ }
+ p = header;
+ p++;
+
+ /* check if sequence is named or not */
+ if ( n == 0 ){
+ error_warn("anonymous sequence",
+ "name will be forced to \"anonymous\"");
+ snprintf(id,10, "anonymous");
+ }
+ else {
+ q = id;
+ for (i=0; i<n; i++) {
+ /* replace all non alnum character by '_' */
+ if (isalnum((int)*p)) *q++ = *p++;
+ else { *q++ = '_'; p++; }
+ }
+ *q = '\0';
+ }
+
+
+ /* skip spaces */
+ while(*p && (isspace((int)*p))) { p++; n++; }
+
+ /* get comment */
+
+ if((comm = malloc(sizeof(char) * (strlen(header) - n))) == NULL){
+ error_fatal("memory", "COMLEN");
+ }
+ q = comm;
+ while(*p && *p != '\n') { *q++ = *p++; }
+ *q = '\0';
+
+ seq->id = id;
+ seq->comment = comm;
+}
+
+
+
+static signed int clean_buff(char **buffer, char *alphabet) {
+ char *p, *c;
+ int bufflen;
+
+ p = *buffer;
+ c = *buffer;
+ bufflen = 0;
+ while (*p && *p != '\n') {
+ if (isspace ((int)*p)) { p++; continue; }
+ if( alphabet[(int)*p] != '\0') {
+ *c++ = alphabet[(int)*p];
+ p++;
+ bufflen++;
+ }
+ else {
+ if (isalpha((int)*p) || *p == '*') {
+ char err_aa[2];
+ err_aa[0] = *p;
+ err_aa[1] = '\0';
+ error_warn(err_aa, "not a valid aa, skipped");
+ p++;
+ }
+ else {
+ return -1;
+ }
+ }
+ }
+ *c = '\0';
+
+ return bufflen;
+}
+
+void free_seq(seq_t *seq) {
+ free(seq->id);
+ free(seq->comment);
+ if ( seq->seq != NULL ) free(seq->seq);
+}
diff --git a/src/seq-reader.h b/src/seq-reader.h
new file mode 100644
index 0000000..164b148
--- /dev/null
+++ b/src/seq-reader.h
@@ -0,0 +1,45 @@
+/* File: /home/edeveaud/Work/dnatool/src/readseq.h
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+ */
+
+
+#ifndef __SEQ_READER_H_
+#define __SEQ_READER_H_
+
+/* sequence size switch between memory and file processing */
+#define MAX_MEM_SIZE 1000000
+
+/* default allowed characters in sequence */
+#define DEFAULT_ALPHABET "ARNDCQEGHILKMFPSTWYV"
+
+#define BUFFSIZE 100
+#define SEQ_NONE -1
+#define HEADER 0
+#define SEQ 1
+#define DUMP 2
+
+#define NO_SEQ 0
+#define SEQ_OK 1
+#define SEQ_OVERMEM 2
+
+
+
+typedef struct seq_S {
+ char *id;
+ char *comment;
+ char *seq;
+ size_t size;
+} seq_t;
+
+
+
+/* retreive sequence in fasta format from file descriptor */
+int read_seq(FILE *IN, seq_t *seq_holder, char *alphabet) ;
+
+/* generate alphabet table used to check the sequences */
+char *alphabet_maker (char *alphabet) ;
+
+/* free the sequence holder */
+void free_seq(seq_t *seq) ;
+
+#endif /* __SEQ_READER_ */
diff --git a/src/topology.c b/src/topology.c
new file mode 100644
index 0000000..79205b2
--- /dev/null
+++ b/src/topology.c
@@ -0,0 +1,181 @@
+/* -----------------------------------------------------------------
+ file : /home/schuerer/toppred_com/src/top_topology.c
+ author : Schuerer
+ description :
+
+
+-------------------------------------------------------------------- */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef STDC_HEADERS
+#include <stdlib.h>
+#endif
+
+#ifdef HAVE_LIBM
+#include <math.h>
+#endif
+
+#include "error.h"
+
+#include "topology.h"
+
+#include "charge.h"
+
+
+/* calculation of the total kr bias or each possible topology
+ stockage of the para->tmax best topologies */
+int tp_calc (topo_t *topos, elem_t *elems, seq_t *seq_h, param_t *para) {
+
+ int tmax = para->n_topos;
+ int cllen = para->seg_len;
+
+ int nsegments = elems->nsegs;
+ seg_t *segments = elems->segs;
+ loop_t *loops = elems->loops;
+ int ntopos = (int) pow(2.0, (double) elems->nputatives);
+
+ int i, k, n, saved;
+ int kr, kr_l, start_l, side, first_tm;
+ double probtm;
+ int putatives, integrate, kingdom;
+ char * seq;
+
+ seq = seq_h->seq;
+
+ kingdom = para->kingdom;
+
+ saved = 0; k = 0;
+ for (n=0; n < ntopos; n++) {
+ putatives = n; side = 1;
+ /* init kr with 1 if N-terminal met is cleaved elsewhere 0 */
+ kr = 0;
+ kr_l = 0; start_l = 0;
+ probtm = 1.0;
+ first_tm = 1;
+ for (i=0; i < nsegments; i++) {
+
+ /* segmentment integrated ? */
+ if (segments[i].kind == PUTATIVE) {
+ integrate = putatives % 2;
+ putatives /= 2;
+ }
+ else integrate = 1;
+
+ /* calculation of global transmembrane probability */
+ if (integrate) probtm *= segments[i].probTM;
+
+ /* calculation of total kr bias */
+ if (loops[i].start != -1) kr_l += loops[i].delta;
+ if(integrate) {
+ if (loops[i].start != -1 && loops[i].stop - start_l <= cllen) {
+ kr += kr_l * side;
+ if (first_tm) kr += ncharge(seq, kingdom);
+ }
+
+ side *= (-1);
+ kr_l = 0;
+ start_l = segments[i].stop;
+ first_tm = 0;
+ }
+ else kr_l += segments[i].delta;
+
+ } /* end for to calculate total kr bias */
+ if (loops[nsegments].start == -1 &&
+ segments[nsegments-1].stop - start_l <= cllen )
+ kr += kr_l * side;
+ else if (loops[nsegments].stop - start_l <= cllen)
+ kr += (kr_l + loops[nsegments].delta) * side;
+
+ /* if there is at least one segment save the topology */
+ if (!first_tm) {
+ /* find topology with minimum kr bias to replace */
+ if (saved >= tmax) {
+ k = 0;
+ for (i=1; i<tmax; i++)
+ if (abs(topos[i].kr) < abs(topos[k].kr)) k = i;
+ }
+ else { k = saved; saved++;}
+ /* init topology object */
+ topos[k].putatives = n;
+ topos[k].kr = kr;
+ topos[k].prob = probtm;
+ }
+ }
+
+ return saved;
+}
+
+/* sort topologies in increasing order */
+int tp_compare (const void *first, const void *second) {
+ const topo_t *topof = (const topo_t *) first;
+ const topo_t *topos = (const topo_t *) second;
+
+ int res = abs(topos->kr) - abs(topof->kr);
+
+ if (res) { return (abs(topos->kr) - abs(topof->kr)); }
+ if (topof->prob > topos->prob) return -1;
+ return 1;
+}
+
+
+/* extract loops and segments as 2 distinct structures */
+/*
+void KS_wrap (KSsegment_t *segs, KSloop_t *loops,
+ boucle_t *boucle, int n) {
+ int i, s, l;
+ boucle_t *p;
+
+ KSseg_t seg;
+ KSloop_t loop;
+
+ i = s = l = 0;
+ seg = NULL;
+ loop = NULL;
+
+ P = boucle;
+ getting the sizes for both struct to create
+ for(i = 0; i< n; i++) {
+ if(p[i].kind == PUTATIVE || p[i].kind == CERTAIN) {
+ s++;
+ }
+ else {
+ l++;
+ }
+ }
+
+ allocate both structures
+ if ((seg = (KSseg_t)malloc(sizeof(KSseg_t) *s)) == NULL) {
+ error_fatal("memory", NULL);
+ }
+ if ((loop = (KSloop_t)malloc(sizeof(KSloop_t) *s)) == NULL) {
+ error_fatal("memory", NULL);
+ }
+ s = l = 0;
+ for(i = 0; i < n; i++) {
+ if(p[i].kind == LOOP) {
+ loop[l].start = p[i].start;
+ loop[l].stop = p[i].stop;
+ loop[l].charge = p[i].delta;
+ l++;
+ } end if LOOP
+
+ else { it's a segment...
+ seg[s].start = p[i].start;
+ seg[s].stop = p[i].stop;
+ seg[s].kind = p[i].kind;
+ seg[s].hpval = p[i].H;
+ seg[s].charge = p[i].delta;
+ }
+
+ } end for
+
+ segs = seg;
+ loops =loop;
+
+}
+*/
diff --git a/src/topology.h b/src/topology.h
new file mode 100644
index 0000000..860147b
--- /dev/null
+++ b/src/topology.h
@@ -0,0 +1,41 @@
+/* File: /home/edeveaud/Work/toppred/src/topology.h
+ * Author: Katja Schuerer
+ */
+
+#ifndef __TOP_TOPOLOGY_
+#define __TOP_TOPOLOGY_
+
+
+#include "params.h"
+#include "loop.h"
+
+
+typedef struct topo {
+ int putatives; /* je sais pas */
+ int kr; /* total Arg + Lys bias */
+ double prob; /* global transmembrane probability */
+ int cytext; /* total cyt - ext difference */
+} topo_t;
+
+typedef struct elem {
+ int nputatives; /* number of putative segments */
+ int nsegs; /* number of all segements */
+
+ seg_t *segs; /* segment structures */
+ loop_t *loops; /* loop structures */
+} elem_t;
+
+#define CYTOPLASMIC 1
+#define PERIPLASMIC -1
+#define INDETERMINED 0
+#define MAXPUTATIVES_CALC 10
+
+int tp_calc (topo_t *topos, elem_t *elems, seq_t *seq, param_t *para);
+int tp_compare (const void *first, const void *second);
+
+#endif
+
+
+
+
+
diff --git a/src/topoprint.c b/src/topoprint.c
new file mode 100644
index 0000000..7d2677a
--- /dev/null
+++ b/src/topoprint.c
@@ -0,0 +1,296 @@
+/* -----------------------------------------------------------------
+ file : /home/schuerer/toppred/src/topoprint.c
+
+ author : Schuerer
+ description :
+
+
+-------------------------------------------------------------------- */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef STDC_HEADERS
+#include <stdlib.h>
+#include <string.h>
+#endif
+
+#include "topoprint.h"
+#include "loop.h"
+
+
+/* init topology_t object with topo_t informations */
+
+/* transforme topologie as topo_t object to topology_t with
+ informations of all elements */
+int tp_decode (topoprint_t *topo, elem_t *elems, seq_t *sq, param_t *para)
+{
+ int putatives = topo->putatives;
+ seg_t *segments = elems->segs;
+ int nsegments = elems->nsegs;
+
+ scale_t *scales = &(para->scales);
+ int clen = para->seg_len;
+
+ char *seq = sq->seq;
+ size_t len;
+
+ int krstart, krstop;
+ double pos , neg;
+ int type_loop, triangle, last_stop, first;
+ int integrate, k, i, nel, side, kingdom;
+
+ elprint_t *el = topo->elps;
+ loprint_t *lo;
+ tmprint_t *tm;
+
+ len = strlen(seq);
+
+ triangle = para->q;
+ type_loop = (topo->kr > 0) ? 1 : (topo->kr < 0) ? -1 : 0;
+ last_stop = 0;
+ k=0;
+ kingdom = para->kingdom;
+ for(i=0; i<nsegments; i++) {
+
+ /* segment integrated ? */
+ integrate = 1;
+ if (segments[i].kind == PUTATIVE)
+ { integrate = putatives % 2 ; putatives /= 2; }
+
+ /* */
+ if (integrate)
+ {
+ /* loop */
+ lo = &(el[k].lo);
+ lo->type = (type_loop == 1) ? "CYT_LOOP" : (type_loop == -1) ? "EXT_LOOP" : "LOOP";
+ lo->start = last_stop;
+ lo->stop = segments[i].start;
+ krstart = (lo->start - triangle < 0) ? 0 : lo->start - triangle;
+ krstop = (lo->stop + triangle > len) ? len : lo->stop + triangle;
+ lo->len = lo->stop - lo->start;
+ if (lo->len != 0) {
+ lo->kr = countkr (seq, krstart, krstop);
+ lo->cytext = distance (seq, lo->start, lo->stop, scales);
+ }
+ else { lo->kr =0; lo->cytext = 0.0; }
+
+ /* segment */
+ k++;
+ tm = &(el[k].tm);
+ tm->type = "TRANSMEM";
+ tm->nr = i+1;
+ tm->start = segments[i].start;
+ tm->stop = segments[i].stop;
+ tm->len = tm->stop - tm->start;
+ tm->prob = segments[i].probTM;
+ /* tm->type_seg = (segments[i].kind == CERTAIN) ? "certain" : "putative"; */
+ tm->H = segments[i].H;
+
+ /* init next loop and segment */
+ k++;
+ type_loop *= -1;
+ last_stop = tm->stop;
+ } /* end if */
+ } /* end for */
+
+ /* last loop */
+ lo = &(el[k].lo);
+ lo->type = (type_loop == 1) ? "CYT_LOOP" : (type_loop == -1) ? "EXT_LOOP" : "LOOP";
+ lo->start = last_stop;
+ lo->stop = len;
+ krstart = (lo->start - triangle < 0) ? 0 : lo->start - triangle;
+ krstop = (lo->stop + triangle > len) ? len : lo->stop + triangle;
+ lo->len = lo->stop - lo->start;
+ if (lo->len != 0) {
+ lo->kr = countkr (seq, krstart, krstop);
+ lo->cytext = distance (seq, lo->start, lo->stop, scales);
+ }
+ else { lo->kr =0; lo->cytext = 0.0; }
+
+ /* topology summary */
+ nel = k+1; side = 1;
+ topo->prob = 1.0;
+ topo->cytext = 0.0;
+ for (i=0; i<nel; i++) {
+ if (i%2) {/* tm segment (index impair) */
+ topo->prob = (el[i].tm.prob < topo->prob) ? el[i].tm.prob : topo->prob;
+ side *= -1;
+ }
+ else { /* loop (index pair) */
+ if (el[i].lo.len > clen) topo->cytext += el[i].lo.cytext * (double) side;
+ }
+ }
+
+ first = el[1].tm.nr - 1;
+ topo->nterm = nterminus(seq, segments[first].start, segments[first].stop, para->q);
+
+ topo->ncharge = (el[0].lo.start != -1 && el[0].lo.len <= clen) ?
+ ncharge(seq, kingdom) : 0;
+ topo->pos = pos = el[0].lo.kr;
+ topo->neg = neg = countneg(seq, el[0].lo.start, el[0].lo.stop);
+ if (neg+pos == 0) topo->negpos = 0.0;
+ else topo->negpos = ((double) (neg - pos))/((double) (neg+pos));
+
+ return nel;
+}
+
+
+void tp_new_print (topoprint_t *topo, int nel, param_t *para) {
+
+ FILE *OUT = para->OUT;
+ int clen = para->seg_len;
+ elprint_t *el = topo->elps;
+ int i;
+
+ /* header */
+ (void) fprintf (OUT, "%8s %6s %6s %6s %4s %4s %8s %8s %8s %8s\n",
+ "HEADER ", "START", "STOP", "LEN",
+ "PROB", "HP",
+ "DARGLYS", "DCYTEXT", "DNCHARGE", "DNNEGPOS");
+
+
+ /* topo summary */
+ if (para->web == 1)
+ {
+ (void) fprintf (OUT, "%8s <A HREF=\"./%s-%d.png\">%3d</A> %3.2f %6.2f %6.2f %8.2f %8.2f\n",
+ "TOPOLOGY", topo->image, topo->nr, topo->nr, topo->prob,
+ (double) topo->kr,
+ topo->cytext, (double) topo->nterm, topo->negpos);
+ }
+ else {
+ (void) fprintf (OUT, "%8s %3d %3.2f %6.2f %6.2f %8.2f %8.2f\n",
+ "TOPOLOGY", topo->nr, topo->prob,
+ (double) topo->kr,
+ topo->cytext, (double) topo->nterm, topo->negpos);
+ }
+ (void) fprintf (OUT, "%8s %7s %7s %8s\n",
+ "TOPOLOGY",
+ new_orientation((double) (topo->kr+topo->ncharge)),
+ new_orientation(topo->cytext * (-1.0)),
+ new_orientation((double) topo->nterm));
+
+ /* topo elements */
+ for (i=0; i<nel; i++) {
+ if (i%2) { /* tmsegment (index impair) */
+ (void) fprintf(OUT, "%8s %6d %6d %6d %4.2f %4.2f\n",
+ el[i].tm.type, el[i].tm.start+1, el[i].tm.stop,
+ el[i].tm.len, el[i].tm.prob, el[i].tm.H);
+ }
+ else { /* loop (index pair) */
+ if (el[i].lo.len > clen) { /* cytext value is significant */
+ (void) fprintf(OUT, "%8s %6d %6d %6d (%6.2f) %6.2f\n",
+ el[i].lo.type, el[i].lo.start+1, el[i].lo.stop,
+ el[i].lo.len, (double) el[i].lo.kr, el[i].lo.cytext);
+ }
+ else if (el[i].lo.len != 0) { /* kr value is significant */
+ (void) fprintf(OUT, "%8s %6d %6d %6d %6.2f (%6.2f)\n",
+ el[i].lo.type, el[i].lo.start+1, el[i].lo.stop,
+ el[i].lo.len, (double) el[i].lo.kr, el[i].lo.cytext);
+ }
+ }
+ }
+
+ /* end topology */
+ (void) fprintf(OUT, "//\n");
+
+ return;
+}
+
+
+void tp_toppred_fprintf (topoprint_t *topo, int nel, param_t *para) {
+
+ FILE *OUT = para->OUT;
+ int clen = para->seg_len;
+ elprint_t *el = topo->elps;
+ int i;
+
+ (void) fprintf(OUT, "Structure %d\n\n", topo->nr);
+
+ /* element information of the structure */
+ (void) fprintf(OUT, "Transmembrane segments included in this structure:\n");
+
+ /* number of included segments */
+ (void) fprintf(OUT, " Segment ");
+ for (i=0; i<nel; i++) {
+ if (i%2) { /* tmsegment (index impair) */
+ (void) fprintf(OUT, "%6d", el[i].tm.nr);
+ }
+ }
+ (void) fprintf(OUT, "\n");
+
+ /* loop length */
+ (void) fprintf(OUT, " Loop length");
+ for(i=0; i<nel; i++) {
+ if (!(i%2)) { /* loop (index pair) */
+ (void) fprintf(OUT, "%6d", el[i].lo.len);
+ }
+ }
+ (void) fprintf(OUT, "\n");
+
+ /* k+r profile */
+ (void) fprintf(OUT, " K+R profile");
+
+ for(i=0; i<nel; i++) {
+ if ((i%4) == 0) { /* loop (index pair) */
+ if (el[i].lo.len <= clen) { (void) fprintf(OUT, "%6.2f", (!i) ? (double) (el[i].lo.kr+topo->ncharge) : (double) el[i].lo.kr); }
+ else { (void) fprintf(OUT, "%6s", "+"); }
+ }
+ if ((i%4) == 2) { (void) fprintf(OUT, " "); }
+ }
+ (void) fprintf(OUT, "\n");
+
+ (void) fprintf(OUT, " ");
+ for(i=0; i<nel; i++) {
+ if ((i%4) == 0) { (void) fprintf(OUT, " "); }
+ else if ((i%4) == 2) {
+ if (el[i].lo.len <= clen) { (void) fprintf(OUT, "%6.2f", (double) el[i].lo.kr); }
+ else { (void) fprintf(OUT, "%6s", "+"); }
+ }
+ }
+ (void) fprintf(OUT, "\n");
+
+ /* cyt-ext profile */
+ (void) fprintf(OUT, "CYT-EXT prof");
+
+ for(i=0; i<nel; i++) {
+ if ((i%4) == 0) { /* loop (index pair) */
+ if (el[i].lo.len > clen) { (void) fprintf(OUT, "%6.2f", el[i].lo.cytext); }
+ else { (void) fprintf(OUT, "%6s", "-"); }
+ }
+ if ((i%4) == 2) { (void) fprintf(OUT, " "); }
+ }
+ (void) fprintf(OUT, "\n");
+
+ (void) fprintf(OUT, " ");
+ for(i=0; i<nel; i++) {
+ if ((i%4) == 0) { (void) fprintf(OUT, " "); }
+ else if ((i%4) == 2) {
+ if (el[i].lo.len > clen) { (void) fprintf(OUT, "%6.2f", el[i].lo.cytext); }
+ else { (void) fprintf(OUT, "%6s", "-"); }
+ }
+ }
+ (void) fprintf(OUT, "\n");
+
+ (void) fprintf(OUT, "For CYT-EXT profile neg. values indicate cytoplasmic preference.\n\n");
+
+ /* topology summary */
+
+ (void) fprintf(OUT, "\nK+R difference: %.2f\n", (double) (topo->kr));
+ (void) fprintf(OUT, "Tm probability: %.2f\n", topo->prob);
+ (void) fprintf(OUT, "-> Orientation: %s\n", orientation((double) (topo->kr)));
+ (void) fprintf(OUT, "\nCharge-difference over N-terminal Tm (+-15 residues): %.2f\n", (double) topo->nterm);
+ (void) fprintf (OUT, "%20s: %.4f\n", "(NEG-POS)/(NEG+POS)", topo->negpos);
+
+ (void) fprintf (OUT, "%20s: %.4f\n", "NEG", (double) topo->neg);
+ (void) fprintf (OUT, "%20s: %.4f\n", "POS", (double) topo->pos);
+
+ (void) fprintf(OUT, "-> Orientation: %s\n", orientation((double)topo->nterm));
+ (void) fprintf(OUT, "\nCYT-EXT difference: %6.2f\n", topo->cytext);
+ (void) fprintf(OUT, "-> Orientation: %s\n", orientation(topo->cytext * (-1.0)));
+
+ return;
+}
diff --git a/src/topoprint.h b/src/topoprint.h
new file mode 100644
index 0000000..c79b484
--- /dev/null
+++ b/src/topoprint.h
@@ -0,0 +1,68 @@
+/* File: /home/edeveaud/Work/toppred/src/topoprint.h
+ * Author: Katja Schuerer
+ */
+
+#ifndef __TOP_TOPOPRINT_
+#define __TOP_TOPOPRINT_
+
+#include "params.h"
+
+#include "topology.h"
+
+/* types for full length topology printing */
+
+typedef struct tmprint
+{
+ int nr;
+ int start;
+ int stop;
+ int len;
+ double prob;
+ double H;
+ char *type;
+} tmprint_t;
+
+typedef struct loprint
+{
+ int start;
+ int stop;
+ int len;
+ int kr;
+ double cytext;
+ char *type;
+} loprint_t;
+
+typedef union elprint
+{
+ loprint_t lo;
+ tmprint_t tm;
+} elprint_t;
+
+typedef struct topoprint
+{
+ double prob;
+ double cytext;
+ int pos;
+ int neg;
+ double negpos;
+ int nr;
+ int putatives;
+ int kr;
+ int nterm;
+ elprint_t *elps;
+ char *image;
+ int ncharge;
+} topoprint_t;
+
+/* transforme topologie as topo_t object to topology_t with
+ informatigons of all elements */
+int tp_decode (topoprint_t *topo, elem_t *elems, seq_t *sq, param_t *para);
+
+void tp_toppred_fprintf (topoprint_t *topo, int nel, param_t *para);
+
+/* print topology information in new output format */
+void tp_new_print (topoprint_t *topo, int nel, param_t *para);
+
+#endif
+
+
diff --git a/src/usage.c b/src/usage.c
new file mode 100644
index 0000000..b2acb9f
--- /dev/null
+++ b/src/usage.c
@@ -0,0 +1,116 @@
+/* File: /home/edeveaud/Work/toppred/src/usage.c
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifdef STDC_HEADERS
+#include <stdlib.h>
+#include <string.h>
+#endif
+
+#include <stdio.h>
+
+#include "usage.h"
+#include "error.h"
+
+
+void usage(char *prog) {
+ FILE *PERR = stderr;
+ (void)fprintf(PERR, "usage: %s [options] <file>\n", prog);
+
+ (void)fprintf(PERR, " -c <val> ... Use <val> as certain cut-off.\n");
+
+ (void)fprintf(PERR, " -d <val> ... Use <val> as critical distance between 2 transmembrane\n");
+ (void)fprintf(PERR, " segments.\n");
+
+ (void)fprintf(PERR, " -e ... For use with Eucaryotes.\n");
+
+#ifdef HAVE_GNUPLOT
+ (void)fprintf(PERR, " -g <format> ... Display or produce Hydropphobic profile, in the specified\n");
+ (void)fprintf(PERR, " <format> (ps, png, ppm, x11 and none).\n");
+#endif /* HAVE_GNUPLOT */
+
+ (void)fprintf(PERR, " -h ... Print this message and exit.\n");
+
+ (void)fprintf(PERR, " -H <file> ... Use Hydrophobycitie values from <file>.\n");
+
+ (void)fprintf(PERR, " -n <val> ... Use <val> as core window length.\n");
+
+ (void)fprintf(PERR, " -o <file> ... Place the output into <file>.\n");
+
+ (void)fprintf(PERR, " -O <format> ... Print output in the specified\n");
+ (void)fprintf(PERR, " <format> (old, new (default), html).\n");
+ (void)fprintf(PERR, " -p <val> ... Use <val> as putative cut-off.\n");
+
+ (void)fprintf(PERR, " -q <val> ... Use <val> as wedge window length.\n");
+
+ (void)fprintf(PERR, " -s <val> ... Use <val> as critical loop length.\n");
+
+#ifdef HAVE_LIBGD
+ (void)fprintf(PERR, " -t <format> ... Produce images of the topologies in the specified\n");
+ (void)fprintf(PERR, " <format> (png and none).\n");
+#endif
+
+ (void)fprintf(PERR, " -v ... Print version number and exit.\n");
+}
+
+int check_output_format(char *prog, char *format) {
+
+ if (strcmp (format, "html") == 0) { return HTML; }
+ if (strcmp (format, "old") == 0) { return OLD; }
+ if (strcmp (format, "new") == 0) { return NEW; }
+
+ error_fatal(prog, "supported format are currently new, old and html");
+
+ return 1;
+}
+
+
+void check_plot_format(char *prog, param_t *params) {
+ char *format;
+ format = params->plot_format;
+
+ if(strcmp (format, PS) == 0) {
+ params->plot_format = "set term postscript color solid\n";
+ params->plot_outfile = "ps";
+ return;
+ }
+ else if (strcmp (format, PNG) == 0) {
+ params->plot_format= "set term png medium";
+ params->plot_outfile = "png";
+ return;
+ }
+ else if(strcmp (format, NONE) == 0) {
+ params->gplot = FALSE;
+ params->plot_format = NULL;
+ return;
+ }
+ else if(strcmp (format, X11) == 0) {
+ params->plot_format = "" ;
+ params->plot_outfile = NULL;
+ params->plot_pause = "pause -1";
+ return;
+ }
+ else if(strcmp (format, PPM) == 0) {
+ params->plot_format = "set term pbm medium color";
+ params->plot_outfile = "ppm";
+ return;
+ }
+ else{error_fatal(prog,
+ "supported format are currently ps, png, ppm, x11 and none");
+ }
+}
+
+void check_topo_format(char *prog, param_t *params) {
+ char *format;
+ format = params->topo_format;
+
+ if((strcmp (format, PNG) != 0) && (strcmp (format, NONE) !=0 )) {
+ error_fatal(prog,
+ "supported format are currently png and none");
+ }
+}
diff --git a/src/usage.h b/src/usage.h
new file mode 100644
index 0000000..dea9d99
--- /dev/null
+++ b/src/usage.h
@@ -0,0 +1,30 @@
+/* File: /home/edeveaud/Work/toppred/src/usage.h
+ * Author: Eric Deveaud edeveaud at pasteur.fr
+ */
+
+
+#ifndef __USAGE_H_
+#define __USAGE_H_
+
+#include "params.h"
+
+#define PS "ps"
+#define PNG "png"
+#define PPM "ppm"
+#define NONE "none"
+#define X11 "x11"
+
+/* output format */
+#define NEW 1
+#define OLD 2
+#define HTML 3
+
+/* usage display */
+void usage(char *prog);
+
+/* check plot format */
+int check_output_format(char *prog, char *format);
+void check_plot_format(char *prog, param_t *params);
+void check_topo_format(char *prog, param_t *params);
+
+#endif
diff --git a/test/Makefile.am b/test/Makefile.am
new file mode 100644
index 0000000..74b1576
--- /dev/null
+++ b/test/Makefile.am
@@ -0,0 +1,26 @@
+TESTS = toppred.test hydro.test \
+ detect_segments.test seqlen.test construct_topos.test \
+ naming.test math.test
+# float.test naming.test
+
+SEQS = seq-test \
+ first_seg.fasta last_seg.fasta no_seg.fasta \
+ min_seqlen.fasta \
+ too_many_put.fasta more_calc.fasta only_put.fasta \
+ seq_anonymous.fasta seq_zero_div.fasta
+# seq_float.fasta seq_float2.fasta seq_float3.fasta
+
+
+OUT = first_seg.out last_seg.out no_seg.out \
+ min_seqlen.out \
+ too_many_put.out more_calc.out only_put.out
+
+ERR = first_seg.err last_seg.err no_seg.err \
+ min_seqlen.err seq_anonymous.err \
+ too_many_put.err more_calc.err only_put.err \
+ no_error.err
+
+
+EXTRA_DIST = $(TESTS) $(SEQS) $(OUT) $(ERR)
+
+CLEANFILES = *.hydro *_tmp.out *_tmp.err *.png
diff --git a/test/Makefile.in b/test/Makefile.in
new file mode 100644
index 0000000..46a44f6
--- /dev/null
+++ b/test/Makefile.in
@@ -0,0 +1,385 @@
+# Makefile.in generated by automake 1.9.2 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+ at SET_MAKE@
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+top_builddir = ..
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+INSTALL = @INSTALL@
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+subdir = test
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/m4/aclibgd.m4 \
+ $(top_srcdir)/configure.in
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_HEADER = $(top_builddir)/src/config.h
+CONFIG_CLEAN_FILES =
+SOURCES =
+DIST_SOURCES =
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMDEP_FALSE = @AMDEP_FALSE@
+AMDEP_TRUE = @AMDEP_TRUE@
+AMTAR = @AMTAR@
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
+AWK = @AWK@
+CC = @CC@
+CCDEPMODE = @CCDEPMODE@
+CFLAGS = @CFLAGS@
+CPP = @CPP@
+CPPFLAGS = @CPPFLAGS@
+CYGPATH_W = @CYGPATH_W@
+DEFS = @DEFS@
+DEPDIR = @DEPDIR@
+ECHO_C = @ECHO_C@
+ECHO_N = @ECHO_N@
+ECHO_T = @ECHO_T@
+EGREP = @EGREP@
+EXEEXT = @EXEEXT@
+GNUPLOT = @GNUPLOT@
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+LDFLAGS = @LDFLAGS@
+LIBOBJS = @LIBOBJS@
+LIBS = @LIBS@
+LTLIBOBJS = @LTLIBOBJS@
+MAKEINFO = @MAKEINFO@
+OBJEXT = @OBJEXT@
+OS_CPPFLAGS = @OS_CPPFLAGS@
+PACKAGE = @PACKAGE@
+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_NAME = @PACKAGE_NAME@
+PACKAGE_STRING = @PACKAGE_STRING@
+PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_VERSION = @PACKAGE_VERSION@
+PATH_SEPARATOR = @PATH_SEPARATOR@
+POD2MAN = @POD2MAN@
+SET_MAKE = @SET_MAKE@
+SHELL = @SHELL@
+STRIP = @STRIP@
+USE_GD_LIB_SRC_FALSE = @USE_GD_LIB_SRC_FALSE@
+USE_GD_LIB_SRC_TRUE = @USE_GD_LIB_SRC_TRUE@
+VERSION = @VERSION@
+ac_ct_CC = @ac_ct_CC@
+ac_ct_STRIP = @ac_ct_STRIP@
+am__fastdepCC_FALSE = @am__fastdepCC_FALSE@
+am__fastdepCC_TRUE = @am__fastdepCC_TRUE@
+am__include = @am__include@
+am__leading_dot = @am__leading_dot@
+am__quote = @am__quote@
+am__tar = @am__tar@
+am__untar = @am__untar@
+bindir = @bindir@
+build = @build@
+build_alias = @build_alias@
+build_cpu = @build_cpu@
+build_os = @build_os@
+build_vendor = @build_vendor@
+datadir = @datadir@
+exec_prefix = @exec_prefix@
+host = @host@
+host_alias = @host_alias@
+host_cpu = @host_cpu@
+host_os = @host_os@
+host_vendor = @host_vendor@
+includedir = @includedir@
+infodir = @infodir@
+install_sh = @install_sh@
+libdir = @libdir@
+libexecdir = @libexecdir@
+localstatedir = @localstatedir@
+mandir = @mandir@
+mkdir_p = @mkdir_p@
+oldincludedir = @oldincludedir@
+prefix = @prefix@
+program_transform_name = @program_transform_name@
+sbindir = @sbindir@
+sharedstatedir = @sharedstatedir@
+sysconfdir = @sysconfdir@
+target_alias = @target_alias@
+TESTS = toppred.test hydro.test \
+ detect_segments.test seqlen.test construct_topos.test \
+ naming.test math.test
+
+# float.test naming.test
+SEQS = seq-test \
+ first_seg.fasta last_seg.fasta no_seg.fasta \
+ min_seqlen.fasta \
+ too_many_put.fasta more_calc.fasta only_put.fasta \
+ seq_anonymous.fasta seq_zero_div.fasta
+
+# seq_float.fasta seq_float2.fasta seq_float3.fasta
+OUT = first_seg.out last_seg.out no_seg.out \
+ min_seqlen.out \
+ too_many_put.out more_calc.out only_put.out
+
+ERR = first_seg.err last_seg.err no_seg.err \
+ min_seqlen.err seq_anonymous.err \
+ too_many_put.err more_calc.err only_put.err \
+ no_error.err
+
+EXTRA_DIST = $(TESTS) $(SEQS) $(OUT) $(ERR)
+CLEANFILES = *.hydro *_tmp.out *_tmp.err *.png
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
+ @for dep in $?; do \
+ case '$(am__configure_deps)' in \
+ *$$dep*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
+ && exit 0; \
+ exit 1;; \
+ esac; \
+ done; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu test/Makefile'; \
+ cd $(top_srcdir) && \
+ $(AUTOMAKE) --gnu test/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ @case '$?' in \
+ *config.status*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+ *) \
+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+ cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+ esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure: $(am__configure_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4): $(am__aclocal_m4_deps)
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+uninstall-info-am:
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+check-TESTS: $(TESTS)
+ @failed=0; all=0; xfail=0; xpass=0; skip=0; \
+ srcdir=$(srcdir); export srcdir; \
+ list='$(TESTS)'; \
+ if test -n "$$list"; then \
+ for tst in $$list; do \
+ if test -f ./$$tst; then dir=./; \
+ elif test -f $$tst; then dir=; \
+ else dir="$(srcdir)/"; fi; \
+ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
+ all=`expr $$all + 1`; \
+ case " $(XFAIL_TESTS) " in \
+ *" $$tst "*) \
+ xpass=`expr $$xpass + 1`; \
+ failed=`expr $$failed + 1`; \
+ echo "XPASS: $$tst"; \
+ ;; \
+ *) \
+ echo "PASS: $$tst"; \
+ ;; \
+ esac; \
+ elif test $$? -ne 77; then \
+ all=`expr $$all + 1`; \
+ case " $(XFAIL_TESTS) " in \
+ *" $$tst "*) \
+ xfail=`expr $$xfail + 1`; \
+ echo "XFAIL: $$tst"; \
+ ;; \
+ *) \
+ failed=`expr $$failed + 1`; \
+ echo "FAIL: $$tst"; \
+ ;; \
+ esac; \
+ else \
+ skip=`expr $$skip + 1`; \
+ echo "SKIP: $$tst"; \
+ fi; \
+ done; \
+ if test "$$failed" -eq 0; then \
+ if test "$$xfail" -eq 0; then \
+ banner="All $$all tests passed"; \
+ else \
+ banner="All $$all tests behaved as expected ($$xfail expected failures)"; \
+ fi; \
+ else \
+ if test "$$xpass" -eq 0; then \
+ banner="$$failed of $$all tests failed"; \
+ else \
+ banner="$$failed of $$all tests did not behave as expected ($$xpass unexpected passes)"; \
+ fi; \
+ fi; \
+ dashes="$$banner"; \
+ skipped=""; \
+ if test "$$skip" -ne 0; then \
+ skipped="($$skip tests were not run)"; \
+ test `echo "$$skipped" | wc -c` -le `echo "$$banner" | wc -c` || \
+ dashes="$$skipped"; \
+ fi; \
+ report=""; \
+ if test "$$failed" -ne 0 && test -n "$(PACKAGE_BUGREPORT)"; then \
+ report="Please report to $(PACKAGE_BUGREPORT)"; \
+ test `echo "$$report" | wc -c` -le `echo "$$banner" | wc -c` || \
+ dashes="$$report"; \
+ fi; \
+ dashes=`echo "$$dashes" | sed s/./=/g`; \
+ echo "$$dashes"; \
+ echo "$$banner"; \
+ test -z "$$skipped" || echo "$$skipped"; \
+ test -z "$$report" || echo "$$report"; \
+ echo "$$dashes"; \
+ test "$$failed" -eq 0; \
+ else :; fi
+
+distdir: $(DISTFILES)
+ @srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
+ list='$(DISTFILES)'; for file in $$list; do \
+ case $$file in \
+ $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
+ $(top_srcdir)/*) file=`echo "$$file" | sed "s|^$$topsrcdirstrip/|$(top_builddir)/|"`;; \
+ esac; \
+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+ dir=`echo "$$file" | sed -e 's,/[^/]*$$,,'`; \
+ if test "$$dir" != "$$file" && test "$$dir" != "."; then \
+ dir="/$$dir"; \
+ $(mkdir_p) "$(distdir)$$dir"; \
+ else \
+ dir=''; \
+ fi; \
+ if test -d $$d/$$file; then \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+ fi; \
+ cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+ else \
+ test -f $(distdir)/$$file \
+ || cp -p $$d/$$file $(distdir)/$$file \
+ || exit 1; \
+ fi; \
+ done
+check-am: all-am
+ $(MAKE) $(AM_MAKEFLAGS) check-TESTS
+check: check-am
+all-am: Makefile
+installdirs:
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+ -test -z "$(CLEANFILES)" || rm -f $(CLEANFILES)
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+ -rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-exec-am:
+
+install-info: install-info-am
+
+install-man:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-info-am
+
+.PHONY: all all-am check check-TESTS check-am clean clean-generic \
+ distclean distclean-generic distdir dvi dvi-am html html-am \
+ info info-am install install-am install-data install-data-am \
+ install-exec install-exec-am install-info install-info-am \
+ install-man install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-generic pdf pdf-am ps ps-am uninstall \
+ uninstall-am uninstall-info-am
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/test/construct_topos.test b/test/construct_topos.test
new file mode 100755
index 0000000..3bd2391
--- /dev/null
+++ b/test/construct_topos.test
@@ -0,0 +1,31 @@
+#! /bin/sh
+
+### Set verbose mode
+test "x$VERBOSE" = "xx" && set -x
+
+### Set environnement
+TOPPREDDATA=$srcdir/../data; export TOPPREDDATA
+TOPPREDOPT='-g none -t none'
+
+### calculation of all topologies is impossible
+base='too_many_put'
+../src/toppred $TOPPREDOPT $srcdir/${base}.fasta >${base}_tmp.out 2>${base}_tmp.err || exit 1
+
+diff ${base}_tmp.out $srcdir/${base}.out >/dev/null || exit 1
+diff ${base}_tmp.err $srcdir/${base}.err >/dev/null || exit 1
+
+### more topologies than printed
+base='more_calc'
+../src/toppred $TOPPREDOPT $srcdir/${base}.fasta >${base}_tmp.out 2>${base}_tmp.err || exit 1
+
+diff ${base}_tmp.out $srcdir/${base}.out >/dev/null || exit 1
+diff ${base}_tmp.err $srcdir/${base}.err >/dev/null || exit 1
+
+### found only putative segments -> skip topo without segments
+base='only_put'
+../src/toppred $TOPPREDOPT $srcdir/${base}.fasta >${base}_tmp.out 2>${base}_tmp.err || exit 1
+
+diff ${base}_tmp.out $srcdir/${base}.out >/dev/null || exit 1
+diff ${base}_tmp.err $srcdir/${base}.err >/dev/null || exit 1
+
+exit 0
diff --git a/test/detect_segments.test b/test/detect_segments.test
new file mode 100755
index 0000000..a6ba050
--- /dev/null
+++ b/test/detect_segments.test
@@ -0,0 +1,31 @@
+#! /bin/sh
+
+### Set verbose mode
+test "x$VERBOSE" = "xx" && set -x
+
+### Set environnement
+TOPPREDDATA=$srcdir/../data; export TOPPREDDATA
+TOPPREDOPT=' -g none -t none'
+
+### detect segment at the beginning of the sequence
+base='first_seg'
+../src/toppred $TOPPREDOPT $srcdir/${base}.fasta >${base}_tmp.out 2>${base}_tmp.err || exit 1
+
+diff ${base}_tmp.out $srcdir/${base}.out >/dev/null || exit 1
+diff ${base}_tmp.err $srcdir/${base}.err >/dev/null || exit 1
+
+### detect segment at the end of the sequence
+base='last_seg'
+../src/toppred $TOPPREDOPT $srcdir/${base}.fasta >${base}_tmp.out 2>${base}_tmp.err || exit 1
+
+diff ${base}_tmp.out $srcdir/${base}.out >/dev/null || exit 1
+diff ${base}_tmp.err $srcdir/${base}.err >/dev/null || exit 1
+
+### no segment found
+base='no_seg'
+../src/toppred $TOPPREDOPT $srcdir/${base}.fasta >${base}_tmp.out 2>${base}_tmp.err || exit 1
+
+diff ${base}_tmp.out $srcdir/${base}.out >/dev/null || exit 1
+diff ${base}_tmp.err $srcdir/${base}.err >/dev/null || exit 1
+
+exit 0
diff --git a/test/first_seg.err b/test/first_seg.err
new file mode 100644
index 0000000..e69de29
diff --git a/test/first_seg.fasta b/test/first_seg.fasta
new file mode 100644
index 0000000..36ccbf4
--- /dev/null
+++ b/test/first_seg.fasta
@@ -0,0 +1,4 @@
+>first TMsegment starts at position 1
+VAKLFADAGLVCITSFISPYTRRRR
+VAKLFADAGLVCITSFISPYTRRRR
+VAKLFAIIIIIIIIIIISPYTRRRR
\ No newline at end of file
diff --git a/test/first_seg.out b/test/first_seg.out
new file mode 100644
index 0000000..7f701f6
--- /dev/null
+++ b/test/first_seg.out
@@ -0,0 +1,67 @@
+Algorithm specific parameters:
+
+Full window size : 21
+Core window size : 11
+Wedge window size: 5
+Using hydrophobicity file: GES-scale
+
+Cutoff for certain transmembrane segments: 1.00
+Cutoff for putative transmembrane segments: 0.60
+Critical distance between 2 transmembrane segments: 2
+
+Critical loop length: 60
+
+Kingdom: procaryote
+
+Using cyt/ext file: CYTEXT-scale
+
+
+Sequence : first (75 res)
+VAKLFADAGLVCITSFISPYTRRRRVAKLFADAGLVCITSFISPYTRRRRVAKLFAIIII
+IIIIIIISPYTRRRR
+
+Found: 3 segments
+
+Candidate membrane-spanning segments:
+
+ Helix Begin - End Score Certainity
+ 1 1 - 21 0.960 Putative
+ 2 26 - 46 0.960 Putative
+ 3 51 - 71 2.310 Certain
+
+Total of 4 structures are to be tested
+
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 1 1.00 7.00 0.00 1.00 -0.69
+TOPOLOGY N-in ? N-in
+CYT_LOOP 1 50 50 11.00 ( -0.15)
+TRANSMEM 51 71 21 1.00 2.31
+EXT_LOOP 72 75 4 4.00 ( -1.01)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 2 0.90 -6.00 0.00 -3.00 0.00
+TOPOLOGY N-out ? N-out
+TRANSMEM 1 21 21 0.90 0.96
+CYT_LOOP 22 50 29 10.00 ( -0.60)
+TRANSMEM 51 71 21 1.00 2.31
+EXT_LOOP 72 75 4 4.00 ( -1.01)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 3 0.90 5.00 0.00 0.00 -0.71
+TOPOLOGY N-in ? ?
+CYT_LOOP 1 25 25 6.00 ( -0.15)
+TRANSMEM 26 46 21 0.90 0.96
+EXT_LOOP 47 50 4 5.00 ( -1.01)
+TRANSMEM 51 71 21 1.00 2.31
+CYT_LOOP 72 75 4 4.00 ( -1.01)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 4 0.90 -4.00 0.00 -3.00 0.00
+TOPOLOGY N-out ? N-out
+TRANSMEM 1 21 21 0.90 0.96
+CYT_LOOP 22 25 4 5.00 ( -1.01)
+TRANSMEM 26 46 21 0.90 0.96
+EXT_LOOP 47 50 4 5.00 ( -1.01)
+TRANSMEM 51 71 21 1.00 2.31
+CYT_LOOP 72 75 4 4.00 ( -1.01)
+//
diff --git a/test/hydro.test b/test/hydro.test
new file mode 100755
index 0000000..7db8094
--- /dev/null
+++ b/test/hydro.test
@@ -0,0 +1,18 @@
+#! /bin/sh
+
+### Set verbose mode
+test "x$VERBOSE" = "xx" && set -x
+
+## Environnement
+TOPPREDDATA=$srcdir/../data; export TOPPREDDATA
+
+## Check hydrophobicity files
+hyd='GES-scale GVH-scale KD-scale'
+for h in $hyd; do
+ ../src/toppred -g none -t none -H $h -o toppred.out $srcdir/seq-test >/dev/null || exit 1
+ grep "^Using hydrophobicity file: $h" toppred.out >/dev/null || exit 1
+done
+
+rm -f toppred.out
+
+exit 0
diff --git a/test/last_seg.err b/test/last_seg.err
new file mode 100644
index 0000000..e69de29
diff --git a/test/last_seg.fasta b/test/last_seg.fasta
new file mode 100644
index 0000000..783578c
--- /dev/null
+++ b/test/last_seg.fasta
@@ -0,0 +1,2 @@
+>last TMsegment ends at end of the sequence
+RRRRRRRRRRVAKLFADAGLVCITSFISPYT
\ No newline at end of file
diff --git a/test/last_seg.out b/test/last_seg.out
new file mode 100644
index 0000000..4cb8ca3
--- /dev/null
+++ b/test/last_seg.out
@@ -0,0 +1,36 @@
+Algorithm specific parameters:
+
+Full window size : 21
+Core window size : 11
+Wedge window size: 5
+Using hydrophobicity file: GES-scale
+
+Cutoff for certain transmembrane segments: 1.00
+Cutoff for putative transmembrane segments: 0.60
+Critical distance between 2 transmembrane segments: 2
+
+Critical loop length: 60
+
+Kingdom: procaryote
+
+Using cyt/ext file: CYTEXT-scale
+
+
+Sequence : last (31 res)
+RRRRRRRRRRVAKLFADAGLVCITSFISPYT
+
+Found: 1 segments
+
+Candidate membrane-spanning segments:
+
+ Helix Begin - End Score Certainity
+ 1 11 - 31 0.960 Putative
+
+Total of 2 structures are to be tested
+
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 1 0.90 11.00 0.00 11.00 -1.00
+TOPOLOGY N-in ? N-in
+CYT_LOOP 1 10 10 11.00 ( -1.01)
+TRANSMEM 11 31 21 0.90 0.96
+//
diff --git a/test/math.test b/test/math.test
new file mode 100755
index 0000000..4600328
--- /dev/null
+++ b/test/math.test
@@ -0,0 +1,15 @@
+#! /bin/sh
+
+### Set verbose mode
+test "x$VERBOSE" = "xx" && set -x
+
+## check gnuplot availability
+(gnuplot --version) >/dev/null 2>&1 || exit 77
+
+### Set environnement
+TOPPREDDATA=$srcdir/../data; export TOPPREDDATA
+
+## Call program
+../src/toppred -g png $srcdir/seq_zero_div.fasta >/dev/null 2>&1
+
+exit 0
diff --git a/test/min_seqlen.err b/test/min_seqlen.err
new file mode 100644
index 0000000..e69de29
diff --git a/test/min_seqlen.fasta b/test/min_seqlen.fasta
new file mode 100644
index 0000000..d15bac2
--- /dev/null
+++ b/test/min_seqlen.fasta
@@ -0,0 +1,2 @@
+>window size (default) equal to sequence length
+VAKLFADAIIIIITSFISPYT
\ No newline at end of file
diff --git a/test/min_seqlen.out b/test/min_seqlen.out
new file mode 100644
index 0000000..6a47933
--- /dev/null
+++ b/test/min_seqlen.out
@@ -0,0 +1,35 @@
+Algorithm specific parameters:
+
+Full window size : 21
+Core window size : 11
+Wedge window size: 5
+Using hydrophobicity file: GES-scale
+
+Cutoff for certain transmembrane segments: 1.00
+Cutoff for putative transmembrane segments: 0.60
+Critical distance between 2 transmembrane segments: 2
+
+Critical loop length: 60
+
+Kingdom: procaryote
+
+Using cyt/ext file: CYTEXT-scale
+
+
+Sequence : window (21 res)
+VAKLFADAIIIIITSFISPYT
+
+Found: 1 segments
+
+Candidate membrane-spanning segments:
+
+ Helix Begin - End Score Certainity
+ 1 1 - 21 1.210 Certain
+
+Total of 1 structures are to be tested
+
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 1 1.00 0.00 0.00 1.00 0.00
+TOPOLOGY N-in ? N-in
+TRANSMEM 1 21 21 1.00 1.21
+//
diff --git a/test/more_calc.err b/test/more_calc.err
new file mode 100644
index 0000000..98d97a3
--- /dev/null
+++ b/test/more_calc.err
@@ -0,0 +1 @@
+Warning: more: more topologies than printed
diff --git a/test/more_calc.fasta b/test/more_calc.fasta
new file mode 100644
index 0000000..7c9bbfd
--- /dev/null
+++ b/test/more_calc.fasta
@@ -0,0 +1,8 @@
+>more topologies calculated than printed
+RRRRRRRVAKLFADAAAAAAASFISPYTRRRRRRR
+RRRRVAKLFADAGLVCITSFISPYTRRRRRR
+TTTTTTTTTRRRRRRRRRRVAKLFADSSYGLVCITSFISPYTRRRRRR
+VAKLFSDSGLVCITSFISPYTRRRRRRRV
+KKKKKKKKKRVRRRRRRRVAKLFADGLSSVCITSFISPYTRRRRRRRV
+RVRRRRRKKVAKLFADSGLVCIYTSFISPYRRRRRRRV
+RVRRRRRRREEEEEEEEEVAKLFADSPSGELVCITSFIASPYTRRRRRRRV
\ No newline at end of file
diff --git a/test/more_calc.out b/test/more_calc.out
new file mode 100644
index 0000000..ec754e3
--- /dev/null
+++ b/test/more_calc.out
@@ -0,0 +1,256 @@
+Algorithm specific parameters:
+
+Full window size : 21
+Core window size : 11
+Wedge window size: 5
+Using hydrophobicity file: GES-scale
+
+Cutoff for certain transmembrane segments: 1.00
+Cutoff for putative transmembrane segments: 0.60
+Critical distance between 2 transmembrane segments: 2
+
+Critical loop length: 60
+
+Kingdom: procaryote
+
+Using cyt/ext file: CYTEXT-scale
+
+
+Sequence : more (280 res)
+RRRRRRRVAKLFADAAAAAAASFISPYTRRRRRRRRRRRVAKLFADAGLVCITSFISPYT
+RRRRRRTTTTTTTTTRRRRRRRRRRVAKLFADSSYGLVCITSFISPYTRRRRRRVAKLFS
+DSGLVCITSFISPYTRRRRRRRVKKKKKKKKKRVRRRRRRRVAKLFADGLSSVCITSFIS
+PYTRRRRRRRVRVRRRRRKKVAKLFADSGLVCIYTSFISPYRRRRRRRVRVRRRRRRREE
+EEEEEEEVAKLFADSPSGELVCITSFIASPYTRRRRRRRV
+
+Found: 7 segments
+
+Candidate membrane-spanning segments:
+
+ Helix Begin - End Score Certainity
+ 1 8 - 28 0.767 Putative
+ 2 40 - 60 0.960 Putative
+ 3 89 - 109 0.952 Putative
+ 4 115 - 135 0.835 Putative
+ 5 163 - 183 0.899 Putative
+ 6 201 - 221 0.774 Putative
+ 7 252 - 272 0.680 Putative
+
+Total of 128 structures are to be tested
+
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 1 0.42 -46.00 0.00 -4.00 -1.00
+TOPOLOGY N-out ? N-out
+EXT_LOOP 1 7 7 8.00 ( -1.01)
+TRANSMEM 8 28 21 0.42 0.77
+CYT_LOOP 29 88 60 29.00 ( -0.95)
+TRANSMEM 89 109 21 0.88 0.95
+EXT_LOOP 110 114 5 7.00 ( -1.01)
+TRANSMEM 115 135 21 0.59 0.84
+CYT_LOOP 136 162 27 25.00 ( -0.55)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 200 17 16.00 ( -0.71)
+TRANSMEM 201 221 21 0.43 0.77
+CYT_LOOP 222 280 59 23.00 ( -0.86)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 2 0.20 -46.00 -0.76 -4.00 -1.00
+TOPOLOGY N-out N-in N-out
+EXT_LOOP 1 7 7 8.00 ( -1.01)
+TRANSMEM 8 28 21 0.42 0.77
+CYT_LOOP 29 88 60 29.00 ( -0.95)
+TRANSMEM 89 109 21 0.88 0.95
+EXT_LOOP 110 114 5 7.00 ( -1.01)
+TRANSMEM 115 135 21 0.59 0.84
+CYT_LOOP 136 162 27 25.00 ( -0.55)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 251 68 ( 32.00) -0.76
+TRANSMEM 252 272 21 0.20 0.68
+CYT_LOOP 273 280 8 7.00 ( -0.73)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 3 0.42 -44.00 -0.45 -4.00 -1.00
+TOPOLOGY N-out N-in N-out
+EXT_LOOP 1 7 7 8.00 ( -1.01)
+TRANSMEM 8 28 21 0.42 0.77
+CYT_LOOP 29 88 60 29.00 ( -0.95)
+TRANSMEM 89 109 21 0.88 0.95
+EXT_LOOP 110 200 91 ( 48.00) -0.45
+TRANSMEM 201 221 21 0.43 0.77
+CYT_LOOP 222 280 59 23.00 ( -0.86)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 4 0.43 43.00 0.60 6.00 -0.90
+TOPOLOGY N-in N-out N-in
+CYT_LOOP 1 39 39 20.00 ( -0.79)
+TRANSMEM 40 60 21 0.90 0.96
+EXT_LOOP 61 200 140 ( 65.00) -0.60
+TRANSMEM 201 221 21 0.43 0.77
+CYT_LOOP 222 280 59 23.00 ( -0.86)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 5 0.42 43.00 0.54 -4.00 -1.00
+TOPOLOGY N-in N-out N-out
+CYT_LOOP 1 7 7 8.00 ( -1.01)
+TRANSMEM 8 28 21 0.42 0.77
+EXT_LOOP 29 39 11 12.00 ( -1.01)
+TRANSMEM 40 60 21 0.90 0.96
+CYT_LOOP 61 114 54 24.00 ( -0.83)
+TRANSMEM 115 135 21 0.59 0.84
+EXT_LOOP 136 200 65 ( 41.00) -0.54
+TRANSMEM 201 221 21 0.43 0.77
+CYT_LOOP 222 280 59 23.00 ( -0.86)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 6 0.43 42.00 0.00 6.00 -0.90
+TOPOLOGY N-in ? N-in
+CYT_LOOP 1 39 39 20.00 ( -0.79)
+TRANSMEM 40 60 21 0.90 0.96
+EXT_LOOP 61 88 28 17.00 ( -0.99)
+TRANSMEM 89 109 21 0.88 0.95
+CYT_LOOP 110 162 53 32.00 ( -0.44)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 200 17 16.00 ( -0.71)
+TRANSMEM 201 221 21 0.43 0.77
+CYT_LOOP 222 280 59 23.00 ( -0.86)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 7 0.20 42.00 0.76 6.00 -0.90
+TOPOLOGY N-in N-out N-in
+CYT_LOOP 1 39 39 20.00 ( -0.79)
+TRANSMEM 40 60 21 0.90 0.96
+EXT_LOOP 61 88 28 17.00 ( -0.99)
+TRANSMEM 89 109 21 0.88 0.95
+CYT_LOOP 110 162 53 32.00 ( -0.44)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 251 68 ( 32.00) -0.76
+TRANSMEM 252 272 21 0.20 0.68
+CYT_LOOP 273 280 8 7.00 ( -0.73)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 8 0.42 40.00 0.83 -4.00 -1.00
+TOPOLOGY N-in N-out N-out
+CYT_LOOP 1 7 7 8.00 ( -1.01)
+TRANSMEM 8 28 21 0.42 0.77
+EXT_LOOP 29 114 86 ( 36.00) -0.83
+TRANSMEM 115 135 21 0.59 0.84
+CYT_LOOP 136 162 27 25.00 ( -0.55)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 200 17 16.00 ( -0.71)
+TRANSMEM 201 221 21 0.43 0.77
+CYT_LOOP 222 280 59 23.00 ( -0.86)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 9 0.20 40.00 1.58 -4.00 -1.00
+TOPOLOGY N-in N-out N-out
+CYT_LOOP 1 7 7 8.00 ( -1.01)
+TRANSMEM 8 28 21 0.42 0.77
+EXT_LOOP 29 114 86 ( 36.00) -0.83
+TRANSMEM 115 135 21 0.59 0.84
+CYT_LOOP 136 162 27 25.00 ( -0.55)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 251 68 ( 32.00) -0.76
+TRANSMEM 252 272 21 0.20 0.68
+CYT_LOOP 273 280 8 7.00 ( -0.73)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 10 0.43 -39.00 -0.86 4.00 -0.90
+TOPOLOGY N-out N-in N-in
+EXT_LOOP 1 88 88 ( 37.00) -0.86
+TRANSMEM 89 109 21 0.88 0.95
+CYT_LOOP 110 162 53 32.00 ( -0.44)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 200 17 16.00 ( -0.71)
+TRANSMEM 201 221 21 0.43 0.77
+CYT_LOOP 222 280 59 23.00 ( -0.86)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 11 0.42 -39.00 -0.66 -4.00 -1.00
+TOPOLOGY N-out N-in N-out
+EXT_LOOP 1 7 7 8.00 ( -1.01)
+TRANSMEM 8 28 21 0.42 0.77
+CYT_LOOP 29 88 60 29.00 ( -0.95)
+TRANSMEM 89 109 21 0.88 0.95
+EXT_LOOP 110 114 5 7.00 ( -1.01)
+TRANSMEM 115 135 21 0.59 0.84
+CYT_LOOP 136 162 27 25.00 ( -0.55)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 280 97 ( 39.00) -0.66
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 12 0.20 -39.00 -1.62 4.00 -0.90
+TOPOLOGY N-out N-in N-in
+EXT_LOOP 1 88 88 ( 37.00) -0.86
+TRANSMEM 89 109 21 0.88 0.95
+CYT_LOOP 110 162 53 32.00 ( -0.44)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 251 68 ( 32.00) -0.76
+TRANSMEM 252 272 21 0.20 0.68
+CYT_LOOP 273 280 8 7.00 ( -0.73)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 13 0.42 38.00 0.00 -4.00 -1.00
+TOPOLOGY N-in ? N-out
+CYT_LOOP 1 7 7 8.00 ( -1.01)
+TRANSMEM 8 28 21 0.42 0.77
+EXT_LOOP 29 39 11 12.00 ( -1.01)
+TRANSMEM 40 60 21 0.90 0.96
+CYT_LOOP 61 88 28 17.00 ( -0.99)
+TRANSMEM 89 109 21 0.88 0.95
+EXT_LOOP 110 114 5 7.00 ( -1.01)
+TRANSMEM 115 135 21 0.59 0.84
+CYT_LOOP 136 162 27 25.00 ( -0.55)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 200 17 16.00 ( -0.71)
+TRANSMEM 201 221 21 0.43 0.77
+CYT_LOOP 222 280 59 23.00 ( -0.86)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 14 0.20 38.00 0.76 -4.00 -1.00
+TOPOLOGY N-in N-out N-out
+CYT_LOOP 1 7 7 8.00 ( -1.01)
+TRANSMEM 8 28 21 0.42 0.77
+EXT_LOOP 29 39 11 12.00 ( -1.01)
+TRANSMEM 40 60 21 0.90 0.96
+CYT_LOOP 61 88 28 17.00 ( -0.99)
+TRANSMEM 89 109 21 0.88 0.95
+EXT_LOOP 110 114 5 7.00 ( -1.01)
+TRANSMEM 115 135 21 0.59 0.84
+CYT_LOOP 136 162 27 25.00 ( -0.55)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 251 68 ( 32.00) -0.76
+TRANSMEM 252 272 21 0.20 0.68
+CYT_LOOP 273 280 8 7.00 ( -0.73)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 15 0.42 36.00 0.45 -4.00 -1.00
+TOPOLOGY N-in N-out N-out
+CYT_LOOP 1 7 7 8.00 ( -1.01)
+TRANSMEM 8 28 21 0.42 0.77
+EXT_LOOP 29 39 11 12.00 ( -1.01)
+TRANSMEM 40 60 21 0.90 0.96
+CYT_LOOP 61 88 28 17.00 ( -0.99)
+TRANSMEM 89 109 21 0.88 0.95
+EXT_LOOP 110 200 91 ( 48.00) -0.45
+TRANSMEM 201 221 21 0.43 0.77
+CYT_LOOP 222 280 59 23.00 ( -0.86)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 16 0.20 24.00 0.00 -4.00 -1.00
+TOPOLOGY N-in ? N-out
+CYT_LOOP 1 7 7 8.00 ( -1.01)
+TRANSMEM 8 28 21 0.42 0.77
+EXT_LOOP 29 39 11 12.00 ( -1.01)
+TRANSMEM 40 60 21 0.90 0.96
+CYT_LOOP 61 88 28 17.00 ( -0.99)
+TRANSMEM 89 109 21 0.88 0.95
+EXT_LOOP 110 114 5 7.00 ( -1.01)
+TRANSMEM 115 135 21 0.59 0.84
+CYT_LOOP 136 162 27 25.00 ( -0.55)
+TRANSMEM 163 183 21 0.75 0.90
+EXT_LOOP 184 200 17 16.00 ( -0.71)
+TRANSMEM 201 221 21 0.43 0.77
+CYT_LOOP 222 251 30 16.00 ( -1.04)
+TRANSMEM 252 272 21 0.20 0.68
+EXT_LOOP 273 280 8 7.00 ( -0.73)
+//
diff --git a/test/naming.test b/test/naming.test
new file mode 100755
index 0000000..95336e3
--- /dev/null
+++ b/test/naming.test
@@ -0,0 +1,23 @@
+#! /bin/sh
+
+### Set verbose mode
+test "x$VERBOSE" = "xx" && set -x
+
+### Set environnement
+TOPPREDDATA=$srcdir/../data; export TOPPREDDATA
+TOPPREDOPT='-g none -t none'
+
+### is anonymous detection correct
+base='seq_anonymous'
+../src/toppred $TOPPREDOPT $srcdir/${base}.fasta >${base}_tmp.out 2>${base}_tmp.err || exit 1
+
+diff ${base}_tmp.err $srcdir/${base}.err >/dev/null || exit 1
+
+# what with named sequence
+base='seq-test'
+../src/toppred $TOPPREDOPT $srcdir/${base} >${base}_tmp.out 2>${base}_tmp.err || exit 1
+
+grep Q60967 ${base}_tmp.out >/dev/null 2>/dev/null || exit 1
+diff ${base}_tmp.err $srcdir/no_error.err >/dev/null || exit 1
+
+exit 0
diff --git a/test/no_error.err b/test/no_error.err
new file mode 100644
index 0000000..e69de29
diff --git a/test/no_seg.err b/test/no_seg.err
new file mode 100644
index 0000000..e69de29
diff --git a/test/no_seg.fasta b/test/no_seg.fasta
new file mode 100644
index 0000000..dad8395
--- /dev/null
+++ b/test/no_seg.fasta
@@ -0,0 +1,2 @@
+>no segment
+RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR
\ No newline at end of file
diff --git a/test/no_seg.out b/test/no_seg.out
new file mode 100644
index 0000000..da724df
--- /dev/null
+++ b/test/no_seg.out
@@ -0,0 +1,23 @@
+Algorithm specific parameters:
+
+Full window size : 21
+Core window size : 11
+Wedge window size: 5
+Using hydrophobicity file: GES-scale
+
+Cutoff for certain transmembrane segments: 1.00
+Cutoff for putative transmembrane segments: 0.60
+Critical distance between 2 transmembrane segments: 2
+
+Critical loop length: 60
+
+Kingdom: procaryote
+
+Using cyt/ext file: CYTEXT-scale
+
+
+Sequence : no (42 res)
+RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR
+
+Found: 0 segments
+
diff --git a/test/only_put.err b/test/only_put.err
new file mode 100644
index 0000000..e69de29
diff --git a/test/only_put.fasta b/test/only_put.fasta
new file mode 100644
index 0000000..ffadef3
--- /dev/null
+++ b/test/only_put.fasta
@@ -0,0 +1,2 @@
+>only putative segments
+RRRVAKLFADAGLVCITSFISPYTRRRRRRRRRRRRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRRR
\ No newline at end of file
diff --git a/test/only_put.out b/test/only_put.out
new file mode 100644
index 0000000..c5c2b3a
--- /dev/null
+++ b/test/only_put.out
@@ -0,0 +1,55 @@
+Algorithm specific parameters:
+
+Full window size : 21
+Core window size : 11
+Wedge window size: 5
+Using hydrophobicity file: GES-scale
+
+Cutoff for certain transmembrane segments: 1.00
+Cutoff for putative transmembrane segments: 0.60
+Critical distance between 2 transmembrane segments: 2
+
+Critical loop length: 60
+
+Kingdom: procaryote
+
+Using cyt/ext file: CYTEXT-scale
+
+
+Sequence : only (72 res)
+RRRVAKLFADAGLVCITSFISPYTRRRRRRRRRRRRRRRRRRVAKLFADAGLVCITSFIS
+PYTRRRRRRRRR
+
+Found: 2 segments
+
+Candidate membrane-spanning segments:
+
+ Helix Begin - End Score Certainity
+ 1 4 - 24 0.960 Putative
+ 2 43 - 63 0.960 Putative
+
+Total of 4 structures are to be tested
+
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 1 0.90 -24.00 0.00 -10.00 -1.00
+TOPOLOGY N-out ? N-out
+EXT_LOOP 1 3 3 4.00 ( -1.01)
+TRANSMEM 4 24 21 0.90 0.96
+CYT_LOOP 25 72 48 28.00 ( -0.93)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 2 0.90 14.00 0.00 7.00 -0.92
+TOPOLOGY N-in ? N-in
+CYT_LOOP 1 42 42 23.00 ( -0.90)
+TRANSMEM 43 63 21 0.90 0.96
+EXT_LOOP 64 72 9 9.00 ( -1.01)
+//
+HEADER START STOP LEN PROB HP DARGLYS DCYTEXT DNCHARGE DNNEGPOS
+TOPOLOGY 3 0.90 -6.00 0.00 -10.00 -1.00
+TOPOLOGY N-out ? N-out
+EXT_LOOP 1 3 3 4.00 ( -1.01)
+TRANSMEM 4 24 21 0.90 0.96
+CYT_LOOP 25 42 18 19.00 ( -1.01)
+TRANSMEM 43 63 21 0.90 0.96
+EXT_LOOP 64 72 9 9.00 ( -1.01)
+//
diff --git a/test/seq-test b/test/seq-test
new file mode 100644
index 0000000..a938bdd
--- /dev/null
+++ b/test/seq-test
@@ -0,0 +1,12 @@
+>Q60967 PPS1_MOUSE
+MEIPGSLCKKVKLSNNAQNWGMQRATNVTYQAHHVSRNKRGQVVGTRGGFRGCTVWLTGL
+SGAGKTTVSMALEEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLF
+ADAGLVCITSFISPYTQDRNNARQIHEGASLPFFEVFVDAPLHVCEQRDVKGLYKKARAG
+EIKGFTGIDSEYEKPEAPELVLKTDSCDVNDCVQQVVELLQERDIVPVDASYEVKELYVP
+ENKLHLAKTDAEALPALKINKVDMQWVQVLAEGWATPLNGFMREREYLQCLHFDCLLDGG
+VINLSVPIVLTATHEDKERLDGCTAFALVYEGRRVAILRNPEFFEHRKEERCARQWGTTC
+KNHPYIKMVLEQGDWLIGGDLQVLDRIYWNDGLDQYRLTPTELKQKFKDMNADAVFAFQL
+RNPVHNGHALLMQDTHKQLLERGYRRPVLLLHPLGGWTKDDDVPLMWRMKQHAAVLEEGI
+LDPETTVVAIFPSPMMYAGPTEVQWHCRARMVAGANFYIVGRDPAGMPHPETGKDLYEPT
+HGAKVLTMAPGLITLEIVPFRVAAYNKKKKRMDYYDSEHHEDFEFISGTRMRKLAREGQK
+PPEGFMAPKAWTVLVEYYKSLEKA
diff --git a/test/seq_anonymous.err b/test/seq_anonymous.err
new file mode 100644
index 0000000..9cc9581
--- /dev/null
+++ b/test/seq_anonymous.err
@@ -0,0 +1 @@
+Warning: anonymous sequence: name will be forced to "anonymous"
diff --git a/test/seq_anonymous.fasta b/test/seq_anonymous.fasta
new file mode 100644
index 0000000..02c0ee4
--- /dev/null
+++ b/test/seq_anonymous.fasta
@@ -0,0 +1,3 @@
+> unamed sequence
+MASTKRKHCALLIVVFWAIICLLVVYAAGPSTEDEDASTPALLIVVFWAIICLLVVYAAH
+STGKKRRKK
diff --git a/test/seq_zero_div.fasta b/test/seq_zero_div.fasta
new file mode 100644
index 0000000..95fc219
--- /dev/null
+++ b/test/seq_zero_div.fasta
@@ -0,0 +1,2 @@
+>, 23 aa.
+XGVSELLISTAVQGILFALLGAX
diff --git a/test/seqlen.test b/test/seqlen.test
new file mode 100755
index 0000000..f1f9b86
--- /dev/null
+++ b/test/seqlen.test
@@ -0,0 +1,17 @@
+#! /bin/sh
+
+### Set verbose mode
+test "x$VERBOSE" = "xx" && set -x
+
+### Set environnement
+TOPPREDDATA=$srcdir/../data; export TOPPREDDATA
+TOPPREDOPT='-g none -t none'
+
+### sequence length equal to window size
+base='min_seqlen'
+../src/toppred $TOPPREDOPT $srcdir/${base}.fasta >${base}_tmp.out 2>${base}_tmp.err || exit 1
+
+diff ${base}_tmp.out $srcdir/min_seqlen.out >/dev/null || exit 1
+diff ${base}_tmp.err $srcdir/min_seqlen.err >/dev/null || exit 1
+
+exit 0
diff --git a/test/too_many_put.err b/test/too_many_put.err
new file mode 100644
index 0000000..3267408
--- /dev/null
+++ b/test/too_many_put.err
@@ -0,0 +1 @@
+Warning: too: too many putative segments to calculate best topologies
diff --git a/test/too_many_put.fasta b/test/too_many_put.fasta
new file mode 100644
index 0000000..6011b9e
--- /dev/null
+++ b/test/too_many_put.fasta
@@ -0,0 +1,24 @@
+>too many putative segments to calculate all topologies
+RRRRRRRVAKLFADAAAAAAASFISPYTRRRRRRR
+RRRRRRRVAKLFADAGLVCITSFISPYTRRRRRR
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRR
+RVRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVR
+VRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVRVRR
+RRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RVRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
+RRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRV
\ No newline at end of file
diff --git a/test/too_many_put.out b/test/too_many_put.out
new file mode 100644
index 0000000..10d6926
--- /dev/null
+++ b/test/too_many_put.out
@@ -0,0 +1,63 @@
+Algorithm specific parameters:
+
+Full window size : 21
+Core window size : 11
+Wedge window size: 5
+Using hydrophobicity file: GES-scale
+
+Cutoff for certain transmembrane segments: 1.00
+Cutoff for putative transmembrane segments: 0.60
+Critical distance between 2 transmembrane segments: 2
+
+Critical loop length: 60
+
+Kingdom: procaryote
+
+Using cyt/ext file: CYTEXT-scale
+
+
+Sequence : too (867 res)
+RRRRRRRVAKLFADAAAAAAASFISPYTRRRRRRRRRRRRRRVAKLFADAGLVCITSFIS
+PYTRRRRRRRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVRVRRRRRRRVAKL
+FADAGLVCITSFISPYTRRRRRRRVRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRR
+RRVRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVRVRRRRRRRVAKLFADAGL
+VCITSFISPYTRRRRRRRVRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVRVR
+RRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVRVRRRRRRRVAKLFADAGLVCITSF
+ISPYTRRRRRRRVRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVRVRRRRRRR
+VAKLFADAGLVCITSFISPYTRRRRRRRVRVRVRRRRRRRVAKLFADAGLVCITSFISPY
+TRRRRRRRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVRVRRRRRRRVAKLFA
+DAGLVCITSFISPYTRRRRRRRVRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRR
+VRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVRVRRRRRRRVAKLFADAGLVC
+ITSFISPYTRRRRRRRVRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVRVRRR
+RRRRVAKLFADAGLVCITSFISPYTRRRRRRRVRVRRRRRRRVAKLFADAGLVCITSFIS
+PYTRRRRRRRVRVRVRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVRRRRRRRVA
+KLFADAGLVCITSFISPYTRRRRRRRV
+
+Found: 23 segments
+
+Candidate membrane-spanning segments:
+
+ Helix Begin - End Score Certainity
+ 1 8 - 28 0.767 Putative
+ 2 43 - 63 0.960 Putative
+ 3 79 - 99 0.960 Putative
+ 4 117 - 137 0.960 Putative
+ 5 155 - 175 0.960 Putative
+ 6 193 - 213 0.960 Putative
+ 7 231 - 251 0.960 Putative
+ 8 269 - 289 0.960 Putative
+ 9 307 - 327 0.960 Putative
+ 10 345 - 365 0.960 Putative
+ 11 383 - 403 0.960 Putative
+ 12 421 - 441 0.960 Putative
+ 13 461 - 481 0.960 Putative
+ 14 497 - 517 0.960 Putative
+ 15 535 - 555 0.960 Putative
+ 16 573 - 593 0.960 Putative
+ 17 611 - 631 0.960 Putative
+ 18 649 - 669 0.960 Putative
+ 19 687 - 707 0.960 Putative
+ 20 725 - 745 0.960 Putative
+ 21 763 - 783 0.960 Putative
+ 22 803 - 823 0.960 Putative
+ 23 839 - 859 0.960 Putative
diff --git a/test/toppred.test b/test/toppred.test
new file mode 100755
index 0000000..3cf8a02
--- /dev/null
+++ b/test/toppred.test
@@ -0,0 +1,15 @@
+#! /bin/sh
+
+### Set verbose mode
+test "x$VERBOSE" = "xx" && set -x
+
+## Environnement
+TOPPREDDATA=$srcdir/../data; export TOPPREDDATA
+
+## Simple sequence test
+../src/toppred -g none -t none $srcdir/seq-test >/dev/null || exit 1
+
+## Check with more than one input file
+../src/toppred -g none -t none $srcdir/seq-test $srcdir/seq-test >/dev/null || exit 1
+
+exit 0
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/toppred.git
More information about the debian-med-commit
mailing list