pax_global_header00006660000000000000000000000064124202053170014506gustar00rootroot0000000000000052 comment=1f1a408b55114f285ce5d1f3e722c63e48461e74 toppred-1.10/000077500000000000000000000000001242020531700131045ustar00rootroot00000000000000toppred-1.10/AUTHORS000066400000000000000000000000701242020531700141510ustar00rootroot00000000000000 Eric Deveaud Katja Schuerer toppred-1.10/COPYING000066400000000000000000000431101242020531700141360ustar00rootroot00000000000000 GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. toppred-1.10/ChangeLog000066400000000000000000000211631242020531700146610ustar00rootroot000000000000002008-10-22 Eric Deveaud * configure.in: Changed version to 1.10 2008-05-06 Nicolas Joly * 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 * test/*.test: Enforce correct status value on success. 2008-03-06 Eric Deveaud * src/seq-reader.c: Allow starting blank lines on fasta formated files. 2008-02-19 Nicolas Joly * src/main.c: Remove unneeded newlines from fatal error messages. 2008-02-01 Eric Deveaud * src/seq-reader.c: Allow `*' (stop codon representation) while sequence reading. 2006-06-06 Eric Deveaud * src/seq-reader.c: Fix anonymous detection and sequence name parsing with pipes. 2006-05-31 Eric Deveaud * doc/toppred.pod: Man page update and correction. 2006-05-31 Nicolas Joly * test/hydro.test: New file that checks all hydrophobicity scales. 2006-05-30 Nicolas Joly * 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 * 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 * 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 * 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 * 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 * src/topology.c: Fix off by one index error in topologies construction. 2004-05-14 Eric Deveaud * 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 * 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 * src/graph.c: correction of the graph representation. no longer crash. 2003-12-12 Eric Deveaud * src/topology.c: modified warning message when no segment found to be more accurate. 2003-12-12 Nicolas Joly * test/*.test: New verbose mode (VERBOSE=x). 2003-12-10 Eric Deveaud * src/profile.c: changed aa2H from function to macro, optimisation. * src/seq-reader.c: modified sequence reading function. 2003-12-09 Nicolas Joly * src/topoprint.c: Do not call `strlen()' on the same object 5 times. 2001-11-21 Eric Deveaud * 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 * 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 * 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 * 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 * 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 * 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 * src/loop.c: corrected a Hplot reading values, that causes a segmentation fault on some systems. 2001-08-03 Eric Deveaud * src/seq-reader.c: seq reader upcase the sequence, as donwcase sequences are not useable. 2001-07-26 Eric Deveaud * doc/toppred.pod: manpage looks like a manpage now. 2001-07-24 Eric Deveaud * src/seq-reader.c: corrected a seq-reader bug. * src/*.[ch] corrected the include localisation. 2001-07-23 Eric Deveaud * src/graph.c: corrected a bug in graph representation. 2001-07-19 Eric Deveaud * src/graph.c: added graphic topos output choice (-d option). 2001-07-18 Eric Deveaud * configure.in: the graphic topology representation is now depending on the use/presence of the libgd. 2001-07-18 Eric Deveaud * src/graph.c: adapted graphic topos output to KS structs. 2001-07-05 Eric Deveaud * src/loop.c (calc_loop): added the penultimate aa checking. 2001-06-27 Eric Deveaud * 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 * src/loop.c: modified calc_segments to take in account segments in position 0 and segments inside a "plateau". 2001-06-19 Eric Deveaud * src/seq_reader.c: sequence reader corrected, now handle correctly incorect format sequence files. 2001-06-13 Eric Deveaud * src/profile.c: added region drawing in produced plot. 2001-06-12 Eric Deveaud * src/profile.c: changed /tmp/gnuplot-file-definition, is now unique. Added some cosmetics in seq.hydro file. 2001-05-14 Eric Deveaud * doc/toppred.pod: added documentation. 2001-05-11 Eric Deveaud * src/main.c: modified a bunch of tests. 2001-05-10 Eric Deveaud * src/main.c: added hydrophobic gnu-plotting routine supported format are ps, ppm, and x11. 2001-05-03 Eric Deveaud * src/loop.c: some code cleanning. * src/main.c: some code cleanning. 2001-04-20 Eric Deveaud * src/main.c (main): beginning of work. Added hydrophobic values load from file added sequence load from file toppred-1.10/INSTALL000066400000000000000000000224321242020531700141400ustar00rootroot00000000000000Installation 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. 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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. toppred-1.10/LICENSE000066400000000000000000000431531242020531700141170ustar00rootroot00000000000000GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it 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. toppred-1.10/Makefile.am000066400000000000000000000001501242020531700151340ustar00rootroot00000000000000SUBDIRS = . m4 src data doc test ## Add m4 dir for autoconf extra definitions ACLOCAL_AMFLAGS = -I m4 toppred-1.10/Makefile.in000066400000000000000000000427651242020531700151670ustar00rootroot00000000000000# 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. @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 = . 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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 - libgd with png support `gd' library can be used in order to produce a graphical representation of the calculated topologies. see For installation, please see INSTALL note. 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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. 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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 /* 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 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 #include int main () { #if defined(_SC_KERNEL_BITS) long bits = sysconf(_SC_KERNEL_BITS); #endif long cpu = sysconf (_SC_CPU_VERSION); switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0"); break; case CPU_PA_RISC1_1: puts ("hppa1.1"); break; case CPU_PA_RISC2_0: #if defined(_SC_KERNEL_BITS) switch (bits) { case 64: puts ("hppa2.0w"); break; case 32: puts ("hppa2.0n"); break; default: puts ("hppa2.0"); break; } break; #else /* !defined(_SC_KERNEL_BITS) */ puts ("hppa2.0"); break; #endif default: puts ("hppa1.0"); break; } exit (0); } EOF (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` test -z "$HP_ARCH" && HP_ARCH=hppa fi ;; esac if [ ${HP_ARCH} = "hppa2.0w" ] then eval $set_cc_for_build # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler # generating 64-bit code. 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 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. 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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 #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' /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 echo i586-unisys-sysv4 exit ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm echo hppa1.1-stratus-sysv4 exit ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. echo i860-stratus-sysv4 exit ;; i*86:VOS:*:*) # From Paul.Green@stratus.com. echo ${UNAME_MACHINE}-stratus-vos exit ;; *:VOS:*:*) # From Paul.Green@stratus.com. echo hppa1.1-stratus-vos exit ;; mc68*:A/UX:*:*) echo m68k-apple-aux${UNAME_RELEASE} exit ;; news*:NEWS-OS:6*:*) echo mips-sony-newsos6 exit ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then echo mips-nec-sysv${UNAME_RELEASE} else echo mips-unknown-sysv${UNAME_RELEASE} fi exit ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. echo powerpc-apple-beos exit ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; 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 < # include #endif main () { #if defined (sony) #if defined (MIPSEB) /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, I don't know.... */ printf ("mips-sony-bsd\n"); exit (0); #else #include printf ("m68k-sony-newsos%s\n", #ifdef NEWSOS4 "4" #else "" #endif ); exit (0); #endif #endif #if defined (__arm) && defined (__acorn) && defined (__unix) printf ("arm-acorn-riscix\n"); exit (0); #endif #if defined (hp300) && !defined (hpux) printf ("m68k-hp-bsd\n"); exit (0); #endif #if defined (NeXT) #if !defined (__ARCHITECTURE__) #define __ARCHITECTURE__ "m68k" #endif int version; version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; if (version < 4) printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); else printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); exit (0); #endif #if defined (MULTIMAX) || defined (n16) #if defined (UMAXV) printf ("ns32k-encore-sysv\n"); exit (0); #else #if defined (CMU) printf ("ns32k-encore-mach\n"); exit (0); #else printf ("ns32k-encore-bsd\n"); exit (0); #endif #endif #endif #if defined (__386BSD__) printf ("i386-pc-bsd\n"); exit (0); #endif #if defined (sequent) #if defined (i386) printf ("i386-sequent-dynix\n"); exit (0); #endif #if defined (ns32000) printf ("ns32k-sequent-dynix\n"); exit (0); #endif #endif #if defined (_SEQUENT_) struct utsname un; uname(&un); if (strncmp(un.version, "V2", 2) == 0) { printf ("i386-sequent-ptx2\n"); exit (0); } if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ printf ("i386-sequent-ptx1\n"); exit (0); } printf ("i386-sequent-ptx\n"); exit (0); #endif #if defined (vax) # if !defined (ultrix) # include # if defined (BSD) # if BSD == 43 printf ("vax-dec-bsd4.3\n"); exit (0); # else # if BSD == 199006 printf ("vax-dec-bsd4.3reno\n"); exit (0); # else printf ("vax-dec-bsd\n"); exit (0); # endif # endif # else printf ("vax-dec-bsd\n"); exit (0); # endif # else printf ("vax-dec-ultrix\n"); exit (0); # endif #endif #if defined (alliant) && defined (i860) printf ("i860-alliant-bsd\n"); exit (0); #endif exit (1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } # Apollos put the system type in the environment. test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; } # Convex versions that predate uname can use getsysinfo(1) if [ -x /usr/convex/getsysinfo ] then case `getsysinfo -f cpu_type` in c1*) echo c1-convex-bsd exit ;; c2*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; c34*) echo c34-convex-bsd exit ;; c38*) echo c38-convex-bsd exit ;; c4*) echo c4-convex-bsd exit ;; esac fi cat >&2 < in order to provide the needed information to handle your system. config.guess timestamp = $timestamp uname -m = `(uname -m) 2>/dev/null || echo unknown` uname -r = `(uname -r) 2>/dev/null || echo unknown` uname -s = `(uname -s) 2>/dev/null || echo unknown` uname -v = `(uname -v) 2>/dev/null || echo unknown` /usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` /bin/uname -X = `(/bin/uname -X) 2>/dev/null` hostinfo = `(hostinfo) 2>/dev/null` /bin/universe = `(/bin/universe) 2>/dev/null` /usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` /bin/arch = `(/bin/arch) 2>/dev/null` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` UNAME_MACHINE = ${UNAME_MACHINE} UNAME_RELEASE = ${UNAME_RELEASE} UNAME_SYSTEM = ${UNAME_SYSTEM} UNAME_VERSION = ${UNAME_VERSION} EOF exit 1 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" # End: toppred-1.10/config.sub000077500000000000000000000757771242020531700151160ustar00rootroot00000000000000#! /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 . 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 $0 [OPTION] ALIAS Canonicalize a configuration name. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.sub ($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. 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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. 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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 &5\"") >&5 (eval $ac_compiler --version &5) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } { (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 (eval $ac_compiler -v &5) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } { (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 (eval $ac_compiler -V &5) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); 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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 to if __STDC__ is defined, since # 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 #else # include #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 _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 to if __STDC__ is defined, since # 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 #else # include #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 _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 #include #include #include 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 _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 _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 #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 #include 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. 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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 . 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'. 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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: toppred-1.10/doc/toppred.1000066400000000000000000000275711242020531700154240ustar00rootroot00000000000000.\" 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++. 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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 , Institut Pasteur and Katja Schuerer. toppred-1.10/doc/toppred.pod000066400000000000000000000147111242020531700160360ustar00rootroot00000000000000=pod =head1 NAME =over 4 =item B - Transmembrane topology prediction. =back =head1 SYNOPSIS =over 4 =item B [options] EFE ... =back =head1 OPTIONS Following command line options are allowed: =over 4 =item -c F Use F as certain cut-off value. Default is 1. =item -d F Use F as critical distance between 2 transmembrane segments. If 2 calculated segments are separated by a distance smaller than F 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 Produce or display hydrophobic profile in specified F. Currently the supported values for format are: =over 1 =item B : display the graph on screen (default). =item B : produce a .ps file. =item B : produce a .png file. =item B : produce a .ppm file. =item B : no profile is produced. =back B this option and the related values are B available if toppred is compiled with the gnuplot support. =item -h Usage display. =item -H F Load hydrophobicity scale from F, default is GES-scale. Accepted values are either: =over 1 =item B : (Kyte and Doolittle, J. Mol. Biol (1982) 157, 105-132 ) =item B : (Goldman Engelman Steitz Ann. Rev. Biophys. Biophys. Chem. 1986 15/ 321 53) =item B : (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 For F, or ask your system administrator. =item -n F Use F as a core window length, default is 11. =item -o F Place the output into F, and store all other files to the same directory than F. =item -O F Print output in the specified F. Supported values are: B: old toppred output format, B: new toppred output format (the default value), B: produce an html page per sequence, note that if not specified hydrophobic profile and topologies representation are forced in png format. =item -p F Use F as putative cut-off, default is 0.6. =item -q F Use F as wedge window length, default is 5. =item -s F Use F as critical loop length. If a loop between 2 transmembrane segments has a length greater than F the Lys/Arg ratio is not taken in account to determine the topologies. Default is 60. =item -t F Produce images of the topologies in specified F. Currently the supported values for format are: B: produces images of the topologies in png format, B: no graphic representation of the topologies is produced. Default is png. B this option and the related values are B available if toppred is compiled with the libgdb support. =item -v Display the version number. =back =head1 FORMAT B only handles fasta sequence format as input. B handles 2 output format via the B<-O> flag. =head1 DESCRIPTION B 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 in fasta format is processed, and B generate the Hydrophobycity profile of the sequence, and the corresponding hydrophobycities values in the file EBEB<.hydro>. Furthermore, the predicted topologies are represented as png images. Each topology is stored in file EBEB<->EBEB<.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 produces the following output files, depending on the command line options =over 4 =item B File containing the hydrophobic values for the sequence B. =item B, B, B Image representing the hydrophobic profile for the sequence B 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 ... B Image representing the graphic representation of the predicted topology B<1>... B for the sequence B in png format if the -t png option is given on the command line. =back =head1 ENVIRONMENT B could be used to specify an alternate toppred data folder =head1 EXAMPLES Consider the fasta formated sequence B in file B. =over 4 =item B F Process all sequences in fasta format from F, display for each sequence the hydrophobicity profile, produce the corresponding B and the corresponding BB<->EB<#>EB<.png> graphical topologies representation as png images. =item B -g ps F Same as previous, except that instead of displaying the hydrophobicity profile on screen, this one is produced in a postcript format image B =item B -g none F Same a previous, except that the hydrophobicity profile is not displayed neither produced. =item B -g none -t none F Same a previous, except that neither the hydrophobicity profile neither the graphical topologies representation are not produced =item B -H KD-scale F Use KD scale instead of default GES scale, while processing sequences. =item B -O html -g png -t none -o result F Write html outpout in file F, furthermore the hydrophobicity profile is produced in PNG format and graphics topologies are not produced. =item cat F | B - B is able to read data from stdin. =back =head1 AUTHORS Eric Deveaud Eedeveaud@pasteur.frE, Institut Pasteur and Katja Schuerer. =cut toppred-1.10/install-sh000077500000000000000000000220211242020531700151050ustar00rootroot00000000000000#!/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. 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(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| */ 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 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| |<-------->| */ 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 len) ? len : end; for (i=start; i= '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 "?"; } toppred-1.10/src/charge.h000066400000000000000000000022051242020531700152740ustar00rootroot00000000000000/* 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_ */ toppred-1.10/src/config.h.in000066400000000000000000000046521242020531700157250ustar00rootroot00000000000000/* src/config.h.in. Generated from configure.in by autoheader. */ /* Define to 1 if you have the header file. */ #undef HAVE_ERRNO_H /* is gnuplot present */ #undef HAVE_GNUPLOT /* Define to 1 if you have the 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 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 header file. */ #undef HAVE_STDINT_H /* Define to 1 if you have the header file. */ #undef HAVE_STDLIB_H /* Define to 1 if you have the `strchr' function. */ #undef HAVE_STRCHR /* Define to 1 if you have the `strerror' function. */ #undef HAVE_STRERROR /* Define to 1 if you have the header file. */ #undef HAVE_STRINGS_H /* Define to 1 if you have the header file. */ #undef HAVE_STRING_H /* Define to 1 if you have the `strrchr' function. */ #undef HAVE_STRRCHR /* Define to 1 if you have the header file. */ #undef HAVE_SYS_STAT_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_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 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 does not define. */ #undef size_t toppred-1.10/src/error.c000066400000000000000000000015431242020531700151730ustar00rootroot00000000000000/* error.c - Error functions */ #ifdef HAVE_CONFIG_H #include #endif #include #ifdef STDC_HEADERS #include #include #endif #include #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; } toppred-1.10/src/error.h000066400000000000000000000003431242020531700151750ustar00rootroot00000000000000/* 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_ */ toppred-1.10/src/graph.c000066400000000000000000000262171242020531700151500ustar00rootroot00000000000000/* File: /home/edeveaud/Work/toppred/src/graph.c * Author: Eric Deveaud edeveaud@pasteur.fr */ #ifdef HAVE_CONFIG_H #include #endif #include #ifdef STDC_HEADERS #include #include #endif #include #include #include #include #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; iw/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 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; ih / 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; } toppred-1.10/src/graph.h000066400000000000000000000013601242020531700151450ustar00rootroot00000000000000/* File: /home/edeveaud/Work/toppred/src/top-graph.h * Author: Eric Deveaud edeveaud@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__ */ toppred-1.10/src/loop.c000066400000000000000000000145021242020531700150120ustar00rootroot00000000000000/* File: /home/edeveaud/Work/toppred/src/loop.c * Author: Eric Deveaud edeveaud@pasteur.fr */ #ifdef HAVE_CONFIG_H #include #endif #include #ifdef STDC_HEADERS #include #endif #ifdef HAVE_UNISTD_H #include #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 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++; } toppred-1.10/src/loop.h000066400000000000000000000016341242020531700150210ustar00rootroot00000000000000/* File: /home/edeveaud/Work/toppred/src/loop.h * Author: Eric Deveaud edeveaud@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_ */ toppred-1.10/src/main.c000066400000000000000000000320151242020531700147640ustar00rootroot00000000000000/* File: /home/edeveaud/Work/toppred/src/main.c * Author: Eric Deveaud edeveaud@pasteur.fr */ #ifdef HAVE_CONFIG_H #include #endif #include #ifdef STDC_HEADERS #include #include #endif #ifdef HAVE_UNISTD_H #include #endif #include #include #include #include #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 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, "

Transmembran segments

\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, "

Topologies

\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 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, "\n"); (void)fprintf(OUT, "\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; } toppred-1.10/src/main.h000066400000000000000000000004451242020531700147730ustar00rootroot00000000000000/* File: /home/edeveaud/Work/toppred/src/main.h * Author: Eric Deveaud edeveaud@pasteur.fr */ #ifndef __MAIN_H_ #define __MAIN_H_ #define MAXSEQLEN 30000 #ifndef DATADIR #define DATADIR "/usr/local/share/"PACKAGE #endif #endif /* __MAIN_H_ */ toppred-1.10/src/mloutput.c000066400000000000000000000106161242020531700157340ustar00rootroot00000000000000/* ----------------------------------------------------------------- file : /home/schuerer/toppred/src/mloutput.c author : Schuerer description : -------------------------------------------------------------------- */ #include #include #include #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, "\n"); (void)fprintf(OUT, "\n"); (void)fprintf(OUT, "\n"); (void)fprintf(OUT, "\n"); (void)fprintf(OUT, "Toppred prediction %s\n", name); (void)fprintf(OUT, "\n"); (void)fprintf(OUT, "\n"); (void)fprintf(OUT, "

Toppred prediction %s

\n", name); (void)fprintf(OUT, "
\n");

  return; }


void html_parameters (FILE *OUT, param_t *p) {

  (void) fprintf (OUT, "
Algorithm specific parameters
\n\n");
  (void) fprintf (OUT, "
\n");
  new_print_parameters (p);
  (void) fprintf (OUT, "
\n");

}

void html_sequence (FILE *OUT, seq_t *seq) {

  (void)fprintf(OUT, "
Sequence
\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, "
Hydrophobicity plot
\n");
  (void)fprintf(OUT, "
\n");
#ifdef HAVE_GNUPLOT
  if (p->gplot && p->plot_outfile && !strcmp(p->plot_outfile, PNG)) {
    (void)fprintf(OUT, "\n", seqname);
  }
#endif
  (void)fprintf(OUT, "
\n");
  (void)fprintf(OUT, "
\n");
  (void)fprintf(OUT, "view hydrophobic values\n",
		seqname);
  (void)fprintf(OUT, "
\n");
  (void)fprintf(OUT, "
\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, "%3d", 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 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;
}
toppred-1.10/src/mloutput.h000066400000000000000000000013171242020531700157370ustar00rootroot00000000000000/*   File:                /home/schuerer/toppred/src/mloutput.h
 *   Author:              Schuerer
 */

#ifndef __MLOUTPUT_H_
#define __MLOUTPUT_H_

#include 
#include "loop.h"
#include "params.h"
#include "topoprint.h"
#include "seq-reader.h"

/* html output functions */
#define start_phrase() (void) fprintf(OUT, "
\n")
#define end_phrase()   (void) fprintf(OUT, "
\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_ */
toppred-1.10/src/output.c000066400000000000000000000072211242020531700154010ustar00rootroot00000000000000/* -----------------------------------------------------------------
 file      : /home/schuerer/toppred/src/baseprint.c

 author    : Schuerer
 description :


-------------------------------------------------------------------- */

#include 
#include 
#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);

}
toppred-1.10/src/output.h000066400000000000000000000010021242020531700153750ustar00rootroot00000000000000/*   File:                /home/schuerer/toppred/src/output.h
 *   Author:              Schuerer
 */

#ifndef __OUTPUT_H_
#define __OUTPUT_H_

#include 
#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_ */
toppred-1.10/src/params.h000066400000000000000000000025431242020531700153330ustar00rootroot00000000000000/*   File:                /home/edeveaud/Work/toppred/src/params.h
 *   Author:              Eric Deveaud edeveaud@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
toppred-1.10/src/profile.c000066400000000000000000000212051242020531700154770ustar00rootroot00000000000000/*   File:                /home/edeveaud/Work/toppred/src/profile.c
 *   Author:              Eric Deveaud edeveaud@pasteur.fr
*/

#ifdef HAVE_CONFIG_H
#include 
#endif

#include 

#ifdef STDC_HEADERS
#include 
#include 
#include 
#endif

#ifdef HAVE_UNISTD_H
#include 
#endif

#include 

#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 */
toppred-1.10/src/profile.h000066400000000000000000000017411242020531700155070ustar00rootroot00000000000000/*   File:                /home/edeveaud/Work/toppred/src/profile.h
 *   Author:              Eric Deveaud edeveaud@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
toppred-1.10/src/seq-reader.c000066400000000000000000000116151242020531700160730ustar00rootroot00000000000000/*   File:                /home/edeveaud/Work/dnatool/src/readseq.c
 *   Author:              Eric Deveaud 
 */

#ifdef HAVE_CONFIG_H
#include 
#endif

#include 

#ifdef STDC_HEADERS
#include 
#include 
#endif

#include 

#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; iid = 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);
}
toppred-1.10/src/seq-reader.h000066400000000000000000000016241242020531700160770ustar00rootroot00000000000000/*   File:                /home/edeveaud/Work/dnatool/src/readseq.h
 *   Author:              Eric Deveaud edeveaud@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_ */
toppred-1.10/src/topology.c000066400000000000000000000101301242020531700157060ustar00rootroot00000000000000/* -----------------------------------------------------------------
 file      : /home/schuerer/toppred_com/src/top_topology.c
 author    : Schuerer
 description :


-------------------------------------------------------------------- */

#ifdef HAVE_CONFIG_H
#include 
#endif

#include 

#ifdef STDC_HEADERS
#include 
#endif

#ifdef HAVE_LIBM
#include 
#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; ikr) - 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;

}
*/
toppred-1.10/src/topology.h000066400000000000000000000015401242020531700157200ustar00rootroot00000000000000/*   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





toppred-1.10/src/topoprint.c000066400000000000000000000211451242020531700161000ustar00rootroot00000000000000/* -----------------------------------------------------------------
 file      : /home/schuerer/toppred/src/topoprint.c

 author    : Schuerer
 description :


-------------------------------------------------------------------- */

#ifdef HAVE_CONFIG_H
#include 
#endif

#include 

#ifdef STDC_HEADERS
#include 
#include 
#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; itype = (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; iprob = (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 %3d                  %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 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; incharge) : (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 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 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;
}
toppred-1.10/src/topoprint.h000066400000000000000000000022031242020531700160770ustar00rootroot00000000000000/*   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


toppred-1.10/src/usage.c000066400000000000000000000065141242020531700151510ustar00rootroot00000000000000/*   File:                /home/edeveaud/Work/toppred/src/usage.c
 *   Author:              Eric Deveaud edeveaud@pasteur.fr
 */


#ifdef HAVE_CONFIG_H
#include 
#endif

#ifdef STDC_HEADERS
#include 
#include 
#endif

#include 

#include "usage.h"
#include "error.h"


void usage(char *prog) {
  FILE *PERR = stderr;
  (void)fprintf(PERR, "usage: %s [options] \n", prog);

  (void)fprintf(PERR, "  -c     ... Use  as certain cut-off.\n");

  (void)fprintf(PERR, "  -d     ... Use  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  ... Display or produce Hydropphobic profile, in the specified\n");
  (void)fprintf(PERR, "                   (ps, png, ppm, x11 and none).\n");
#endif /* HAVE_GNUPLOT */

  (void)fprintf(PERR, "  -h          ... Print this message and exit.\n");

  (void)fprintf(PERR, "  -H    ... Use Hydrophobycitie values from .\n");

  (void)fprintf(PERR, "  -n     ... Use  as core window length.\n");

  (void)fprintf(PERR, "  -o    ... Place the output into .\n");

  (void)fprintf(PERR, "  -O  ... Print output in the specified\n");
  (void)fprintf(PERR, "                   (old, new (default), html).\n");
  (void)fprintf(PERR, "  -p     ... Use  as putative cut-off.\n");

  (void)fprintf(PERR, "  -q     ... Use  as wedge window length.\n");

  (void)fprintf(PERR, "  -s     ... Use  as critical loop length.\n");

#ifdef HAVE_LIBGD
  (void)fprintf(PERR, "  -t  ... Produce images of the topologies in the specified\n");
  (void)fprintf(PERR, "                   (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");
  }
}
toppred-1.10/src/usage.h000066400000000000000000000011041242020531700151440ustar00rootroot00000000000000/*   File:                /home/edeveaud/Work/toppred/src/usage.h
 *   Author:              Eric Deveaud edeveaud@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
toppred-1.10/test/000077500000000000000000000000001242020531700140635ustar00rootroot00000000000000toppred-1.10/test/Makefile.am000066400000000000000000000014331242020531700161200ustar00rootroot00000000000000TESTS = 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
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	naming.test math.test

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       min_seqlen.fasta \
       too_many_put.fasta more_calc.fasta only_put.fasta \
       seq_anonymous.fasta seq_zero_div.fasta

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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)
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installcheck: installcheck-am
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	$(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 \
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	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:
toppred-1.10/test/construct_topos.test000077500000000000000000000020101242020531700202300ustar00rootroot00000000000000#! /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
toppred-1.10/test/detect_segments.test000077500000000000000000000017521242020531700201510ustar00rootroot00000000000000#! /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
toppred-1.10/test/first_seg.err000066400000000000000000000000001242020531700165500ustar00rootroot00000000000000toppred-1.10/test/first_seg.fasta000066400000000000000000000001631242020531700170700ustar00rootroot00000000000000>first TMsegment starts at position 1
VAKLFADAGLVCITSFISPYTRRRR
VAKLFADAGLVCITSFISPYTRRRR
VAKLFAIIIIIIIIIIISPYTRRRRtoppred-1.10/test/first_seg.out000066400000000000000000000047141242020531700166070ustar00rootroot00000000000000Algorithm 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)
//
toppred-1.10/test/hydro.test000077500000000000000000000006361242020531700161210ustar00rootroot00000000000000#! /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
toppred-1.10/test/last_seg.err000066400000000000000000000000001242020531700163640ustar00rootroot00000000000000toppred-1.10/test/last_seg.fasta000066400000000000000000000001131242020531700166770ustar00rootroot00000000000000>last TMsegment ends at end of the sequence
RRRRRRRRRRVAKLFADAGLVCITSFISPYTtoppred-1.10/test/last_seg.out000066400000000000000000000016331242020531700164200ustar00rootroot00000000000000Algorithm 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
//
toppred-1.10/test/math.test000077500000000000000000000004621242020531700157220ustar00rootroot00000000000000#! /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
toppred-1.10/test/min_seqlen.err000066400000000000000000000000001242020531700167150ustar00rootroot00000000000000toppred-1.10/test/min_seqlen.fasta000066400000000000000000000001051242020531700172310ustar00rootroot00000000000000>window size (default) equal to sequence length
VAKLFADAIIIIITSFISPYTtoppred-1.10/test/min_seqlen.out000066400000000000000000000015301242020531700167450ustar00rootroot00000000000000Algorithm 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
//
toppred-1.10/test/more_calc.err000066400000000000000000000000541242020531700165200ustar00rootroot00000000000000Warning: more: more topologies than printed
toppred-1.10/test/more_calc.fasta000066400000000000000000000005071242020531700170310ustar00rootroot00000000000000>more topologies calculated than printed
RRRRRRRVAKLFADAAAAAAASFISPYTRRRRRRR
RRRRVAKLFADAGLVCITSFISPYTRRRRRR
TTTTTTTTTRRRRRRRRRRVAKLFADSSYGLVCITSFISPYTRRRRRR
VAKLFSDSGLVCITSFISPYTRRRRRRRV
KKKKKKKKKRVRRRRRRRVAKLFADGLSSVCITSFISPYTRRRRRRRV
RVRRRRRKKVAKLFADSGLVCIYTSFISPYRRRRRRRV
RVRRRRRRREEEEEEEEEVAKLFADSPSGELVCITSFIASPYTRRRRRRRVtoppred-1.10/test/more_calc.out000066400000000000000000000276551242020531700165570ustar00rootroot00000000000000Algorithm 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)
//
toppred-1.10/test/naming.test000077500000000000000000000012061242020531700162370ustar00rootroot00000000000000#! /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
toppred-1.10/test/no_error.err000066400000000000000000000000001242020531700164100ustar00rootroot00000000000000toppred-1.10/test/no_seg.err000066400000000000000000000000001242020531700160350ustar00rootroot00000000000000toppred-1.10/test/no_seg.fasta000066400000000000000000000000671242020531700163600ustar00rootroot00000000000000>no segment 
RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRtoppred-1.10/test/no_seg.out000066400000000000000000000007121242020531700160660ustar00rootroot00000000000000Algorithm 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

toppred-1.10/test/only_put.err000066400000000000000000000000001242020531700164340ustar00rootroot00000000000000toppred-1.10/test/only_put.fasta000066400000000000000000000001401242020531700167470ustar00rootroot00000000000000>only putative segments
RRRVAKLFADAGLVCITSFISPYTRRRRRRRRRRRRRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRRRtoppred-1.10/test/only_put.out000066400000000000000000000035711242020531700164730ustar00rootroot00000000000000Algorithm 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)
//
toppred-1.10/test/seq-test000066400000000000000000000012171242020531700155540ustar00rootroot00000000000000>Q60967 PPS1_MOUSE 
MEIPGSLCKKVKLSNNAQNWGMQRATNVTYQAHHVSRNKRGQVVGTRGGFRGCTVWLTGL
SGAGKTTVSMALEEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLF
ADAGLVCITSFISPYTQDRNNARQIHEGASLPFFEVFVDAPLHVCEQRDVKGLYKKARAG
EIKGFTGIDSEYEKPEAPELVLKTDSCDVNDCVQQVVELLQERDIVPVDASYEVKELYVP
ENKLHLAKTDAEALPALKINKVDMQWVQVLAEGWATPLNGFMREREYLQCLHFDCLLDGG
VINLSVPIVLTATHEDKERLDGCTAFALVYEGRRVAILRNPEFFEHRKEERCARQWGTTC
KNHPYIKMVLEQGDWLIGGDLQVLDRIYWNDGLDQYRLTPTELKQKFKDMNADAVFAFQL
RNPVHNGHALLMQDTHKQLLERGYRRPVLLLHPLGGWTKDDDVPLMWRMKQHAAVLEEGI
LDPETTVVAIFPSPMMYAGPTEVQWHCRARMVAGANFYIVGRDPAGMPHPETGKDLYEPT
HGAKVLTMAPGLITLEIVPFRVAAYNKKKKRMDYYDSEHHEDFEFISGTRMRKLAREGQK
PPEGFMAPKAWTVLVEYYKSLEKA
toppred-1.10/test/seq_anonymous.err000066400000000000000000000001001242020531700174640ustar00rootroot00000000000000Warning: anonymous sequence: name will be forced to "anonymous"
toppred-1.10/test/seq_anonymous.fasta000066400000000000000000000001331242020531700200000ustar00rootroot00000000000000>   unamed sequence
MASTKRKHCALLIVVFWAIICLLVVYAAGPSTEDEDASTPALLIVVFWAIICLLVVYAAH
STGKKRRKK
toppred-1.10/test/seq_zero_div.fasta000066400000000000000000000000421242020531700175700ustar00rootroot00000000000000>, 23 aa.
XGVSELLISTAVQGILFALLGAX
toppred-1.10/test/seqlen.test000077500000000000000000000007141242020531700162600ustar00rootroot00000000000000#! /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
toppred-1.10/test/too_many_put.err000066400000000000000000000001061242020531700173070ustar00rootroot00000000000000Warning: too: too many putative segments to calculate best topologies
toppred-1.10/test/too_many_put.fasta000066400000000000000000000016611242020531700176240ustar00rootroot00000000000000>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
RRRRRRRVAKLFADAGLVCITSFISPYTRRRRRRRVtoppred-1.10/test/too_many_put.out000066400000000000000000000042351242020531700173350ustar00rootroot00000000000000Algorithm 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
toppred-1.10/test/toppred.test000077500000000000000000000005511242020531700164450ustar00rootroot00000000000000#! /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