Commit 54df7def authored by Andreas Tille's avatar Andreas Tille

Imported Upstream version 1.10

parents
Eric Deveaud <edeveaud@pasteur.fr>
Katja Schuerer
This diff is collapsed.
2008-10-22 Eric Deveaud <edeveaud@raclette-tete1.calcul.pasteur.fr>
* configure.in: Changed version to 1.10
2008-05-06 Nicolas Joly <njoly@pasteur.fr>
* doc/toppred.pod: Add missing option `-t none' in example
command.
* src/*.[ch]: Remove XML output, which was unused and broken too
often without notice ...
* doc/toppred.pod: Adjust.
2008-04-18 Nicolas Joly <njoly@pasteur.fr>
* test/*.test: Enforce correct status value on success.
2008-03-06 Eric Deveaud <edeveaud@pasteur.fr>
* src/seq-reader.c: Allow starting blank lines on fasta formated
files.
2008-02-19 Nicolas Joly <njoly@pasteur.fr>
* src/main.c: Remove unneeded newlines from fatal error messages.
2008-02-01 Eric Deveaud <edeveaud@pasteur.fr>
* src/seq-reader.c: Allow `*' (stop codon representation) while
sequence reading.
2006-06-06 Eric Deveaud <edeveaud@pasteur.fr>
* src/seq-reader.c: Fix anonymous detection and sequence name
parsing with pipes.
2006-05-31 Eric Deveaud <edeveaud@pasteur.fr>
* doc/toppred.pod: Man page update and correction.
2006-05-31 Nicolas Joly <njoly@pasteur.fr>
* test/hydro.test: New file that checks all hydrophobicity scales.
2006-05-30 Nicolas Joly <njoly@pasteur.fr>
* src/seq-reader.c: Do not push characters back on stream if
nothing was read previously.
* src/main.c: Do not close output file in sequence file processing
loop.
2006-05-30 Eric Deveaud <edeveaud@pasteur.fr>
* src/*.c, src/*.h: time stamp cleanup.
* src/main.c: Optional options `-g' and `-t' no more silently
ignored if needed support is missing.
* src/usage.c: gnuplot png color definition fix.
* src/seq-reader.c: Fix anonymous detection and related memory
overflow.
* src/profile.c: Fix file descriptor leak induced by mkstemp.
2006-05-29 Nicolas Joly <njoly@pasteur.fr>
* doc/toppred.pod: Small spelling/formatting fixes.
* src/mloutput.c: Remove trailing space in XML output.
* src/main.c: Fix incorrect XML generation, by moving `toppreds'
end tag, out of file process loop.
* src/mloutput.c: Make HTML header looks a little better (no
functional change).
* src/output.[ch]: Remove local `dirname()' function, and prefer
the one from the system.
* src/main.c: Adjust accordingly.
* src/graph.c, src/mloutput.c, src/profile.c: Do not assume
`dirname()' return value has a trailing `/' character.
2006-05-25 Nicolas Joly <njoly@pasteur.fr>
* src/main.c: Move cleanup outside of the processing loop to avoid
use of freed memory (data files and output dir) with multiple
input files.
* test/toppred.test: Exercize more than one input file.
2004-05-17 Nicolas Joly <njoly@pasteur.fr>
* src/profile.c: hide gplot() function if gnuplot is missing.
* src/topology.c, src/loop.c: Use const where appropriate.
2004-05-17 Katja Schuerer <schuerer@pasteur.fr>
* src/topology.c: Fix off by one index error in topologies
construction.
2004-05-14 Eric Deveaud <edeveaud@pasteur.fr>
* src/main.c: memory leak while freeing KS structures corrected in
case of too many topologies.
* src/main.c: memory liberation in case of no libgd.
NB: free(NULL) is allowed by the C iso guidelines.
* src/main.c: added internal -y flag in order to disable .hydro
file generation. (not documented).
* src/seq-reader.c: a bunch of header processing bugs correction.
2004-05-03 Eric Deveaud <edeveaud@pasteur.fr>
* src/graph.c: topologies graphic production code completly
rewrote.
* src/topology.c: removing the warning when no segment found.
* test/last_seg.err: modified to be coherent with no segment found
warning modification.
* test/more_calc.err: modified to be coherent with no segment
found warning modification.
* test/only_put.err: modified to be coherent with no segment found
warning modification.
* test/seq_float.err: modified to be coherent with no segment
found warning modification.
2004-04-29 Eric Deveaud <edeveaud@pasteur.fr>
* src/graph.c: correction of the graph representation. no longer
crash.
2003-12-12 Eric Deveaud <edeveaud@pasteur.fr>
* src/topology.c: modified warning message when no segment found
to be more accurate.
2003-12-12 Nicolas Joly <njoly@pasteur.fr>
* test/*.test: New verbose mode (VERBOSE=x).
2003-12-10 Eric Deveaud <edeveaud@pasteur.fr>
* src/profile.c: changed aa2H from function to macro,
optimisation.
* src/seq-reader.c: modified sequence reading function.
2003-12-09 Nicolas Joly <njoly@pasteur.fr>
* src/topoprint.c: Do not call `strlen()' on the same object 5
times.
2001-11-21 Eric Deveaud <edeveaud@pasteur.fr>
* configure.in: toppred is now in version 1.00.
* src/seq-reader.c: non ascii characters on sequences not more
allowed.
* src/*.c: corrected the -o result_file option behaviour. All
files are stored to the same directory than result_file.
2001-10-15 Katja Schuerer <schuerer@pasteur.fr>
* test/detect_segments.test: test if all segments are detected.
* test/seqlen.test: test of sequences of critical lengths.
* test/construct_topos.test: test to verify the calculation of all
toplogies.
* src/topology.c: correct topology calculation -- skip topologies
without any segment.
2001-10-05 Katja Schuerer <schuerer@pasteur.fr>
* data/toppred.dtd: add DTD file for xml output.
* src/mloutput.c: add function for xml output and transfer html
output functions to this file.
* src/output.c: transfer general output functions to this file.
2001-09-12 Katja Schuerer <schuerer@pasteur.fr>
* src/loop.c: modify get_segment to allow a segment at beginning
of the sequence.
* src/loop.c: correct bug while translation of old segment
sructure to new segment structure (detection of segment at
beginning of the sequence).
* src/charge.c: correct floating point exceptions caused by zero
division in distance function.
2001-09-10 Eric Deveaud <edeveaud@pasteur.fr>
* src/seq-reader.c: corrected bug while reading long comments. id
and comment are now dynamically handled, anonymous sequence are
tagged as anonymous, and empty sequence causes program exit.
2001-08-30 Eric Deveaud <edeveaud@pasteur.fr>
* src/seq-reader.c: modified sequence aquisition, sequence is not
systematicaly converted to upcase.
* src/main.c: added web output format via -w option.
2001-08-28 Eric Deveaud <edeveaud@pasteur.fr>
* src/loop.c: corrected a Hplot reading values, that causes a
segmentation fault on some systems.
2001-08-03 Eric Deveaud <edeveaud@pasteur.fr>
* src/seq-reader.c: seq reader upcase the sequence, as donwcase
sequences are not useable.
2001-07-26 Eric Deveaud <edeveaud@pasteur.fr>
* doc/toppred.pod: manpage looks like a manpage now.
2001-07-24 Eric Deveaud <edeveaud@pasteur.fr>
* src/seq-reader.c: corrected a seq-reader bug.
* src/*.[ch] corrected the include localisation.
2001-07-23 Eric Deveaud <edeveaud@pasteur.fr>
* src/graph.c: corrected a bug in graph representation.
2001-07-19 Eric Deveaud <edeveaud@pasteur.fr>
* src/graph.c: added graphic topos output choice (-d option).
2001-07-18 Eric Deveaud <edeveaud@pasteur.fr>
* configure.in: the graphic topology representation is now
depending on the use/presence of the libgd.
2001-07-18 Eric Deveaud <edeveaud@pasteur.fr>
* src/graph.c: adapted graphic topos output to KS structs.
2001-07-05 Eric Deveaud <edeveaud@pasteur.fr>
* src/loop.c (calc_loop): added the penultimate aa checking.
2001-06-27 Eric Deveaud <edeveaud@pasteur.fr>
* src/loop.h: introduced loop_t and seg_t structures.
* src/loop.c : modified the loop / segments structure to fit for
the Katja topology calcul.
2001-06-21 Eric Deveaud <edeveaud@pasteur.fr>
* src/loop.c: modified calc_segments to take in account segments
in position 0 and segments inside a "plateau".
2001-06-19 Eric Deveaud <edeveaud@pasteur.fr>
* src/seq_reader.c: sequence reader corrected, now handle
correctly incorect format sequence files.
2001-06-13 Eric Deveaud <edeveaud@pasteur.fr>
* src/profile.c: added region drawing in produced plot.
2001-06-12 Eric Deveaud <edeveaud@pasteur.fr>
* src/profile.c: changed /tmp/gnuplot-file-definition, is now
unique. Added some cosmetics in seq.hydro file.
2001-05-14 Eric Deveaud <edeveaud@pasteur.fr>
* doc/toppred.pod: added documentation.
2001-05-11 Eric Deveaud <edeveaud@pasteur.fr>
* src/main.c: modified a bunch of tests.
2001-05-10 Eric Deveaud <edeveaud@pasteur.fr>
* src/main.c: added hydrophobic gnu-plotting routine supported
format are ps, ppm, and x11.
2001-05-03 Eric Deveaud <edeveaud@pasteur.fr>
* src/loop.c: some code cleanning.
* src/main.c: some code cleanning.
2001-04-20 Eric Deveaud <edeveaud@pasteur.fr>
* src/main.c (main): beginning of work. Added hydrophobic values
load from file added sequence load from file
Installation Instructions
*************************
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SUBDIRS = . m4 src data doc test
## Add m4 dir for autoconf extra definitions
ACLOCAL_AMFLAGS = -I m4
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no news is good news !
TOPPRED - Transmembrane topology prediction.
This program is a new implementation of the original toppred program,
based on G. von Heijne algorithm :
"Membrane protein structure prediction. Hydrophobicity analysis and
the positive-inside rule." J Mol Biol 1992 May 20;225(2):487-94.
"TopPred II: an improved software for membrane protein structure
predictions." CABIOS 10(6):685-6, 1994 Dec.
This implementation can use 2 optionals programs in order to
display graphical results:
- gnuplot version 3.7 patchlevel 1 or more
`gnuplot' can be used in order to display the
hydrophobicity profile of a given sequence.
see <http://www.gnuplot.info/>
- libgd with png support
`gd' library can be used in order to produce a
graphical representation of the calculated topologies.
see <http://www.boutell.com/gd>
For installation, please see INSTALL note.
Please report bugs, comments or suggestions to:
Eric Deveaud: edeveaud@pasteur.fr
Assorted ToDo items :
* Add tests to exercise `-g' and `-t' formats.
* Cleanup Text/HTML output functions.
* Unhandled conflict between `-O html' and `-o outfile'.
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# Process this file with autoconf to produce a configure script.
AC_INIT([toppred], [1.10])
AM_INIT_AUTOMAKE
AM_CONFIG_HEADER([src/config.h])
# Checks for programs.
AC_PROG_CC
AC_CHECK_PROG(POD2MAN, pod2man, pod2man, :)
AC_CHECK_PROG(GNUPLOT, gnuplot, gnuplot)
if test "$GNUPLOT" = "gnuplot"; then
AC_DEFINE(HAVE_GNUPLOT, 1, is gnuplot present)
else
AC_MSG_WARN([gnuplot not found, Hydrophobic profile will be unavailable])
fi
# Checks for libraries.
AC_CHECK_LIB(m, pow)
# Checks for header files.
AC_HEADER_STDC
AC_CHECK_HEADERS([errno.h stdlib.h string.h unistd.h])
# Checks for typedefs, structures, and compiler characteristics.
AC_C_CONST
AC_TYPE_SIZE_T
AC_STRUCT_TM
# Checks for library functions.
# AC_FUNC_MALLOC # tru64 problem
AC_FUNC_STAT
AC_CHECK_FUNCS([pow sqrt strchr strerror strrchr])
# Checks for png driver
GD_CHECK
# Host specific stuff
OS_CPPFLAGS=""
AC_CANONICAL_HOST
case $host in
*-*osf*)
OS_CPPFLAGS="-D_XOPEN_SOURCE_EXTENDED"
break
esac
AC_SUBST([OS_CPPFLAGS])
AC_CONFIG_FILES([Makefile m4/Makefile src/Makefile data/Makefile doc/Makefile
test/Makefile])
AC_OUTPUT
#___________________________________________________________________________
#
# aa cyt ext sd
#___________________________________________________________________________
A 8.387 8.097 3.7
C 3.226 0 2.3
D 7.419 6.005 2.2
E 7.742 5.533 3.0
F 2.581 3.171 1.9
G 7.419 8.907 3.4
H 0.968 1.417 1.6
I 5.484 4.926 2.5
K 5.484 5.533 3.4
L 9.032 7.422 3.4
M 3.226 3.171 1.4
N 3.871 4.858 2.3
P 4.194 6.545 3.2
Q 3.548 3.306 2.4
R 9.032 5.938 3.3
S 4.516 6.883 2.8
T 6.129 5.263 2.6
V 4.516 8.165 2.5
W 0.968 1.282 1.2
Y 2.258 3.576 1.8
# ___________________________________________________________________________
#
# Hphobe Values Goldman Engelman Steitz
# Ann Rev Biophys. Biophys. Chem. 1986 15/ 321 53
#___________________________________________________________________________
A 1.6
C 2.0
D -9.2
E -8.2
F 3.7
G 1.0
H -3.0
I 3.1
K -8.8
L 2.8
M 3.4
N -4.8
P -0.2
Q -4.1
R -12.3
S 0.6
T 1.2
V 2.6
W 1.9
Y -0.7
#___________________________________________________________________________
#
# Hphobe Values Gunnar von Heijne
# Gunnar von Heijne J. Mol/ Biol (1992) 225, 487-494
#___________________________________________________________________________
A 0.267
C 1.806
D -2.303
E -2.442
F 0.427
G 0.160
H -2.189
I 0.971
K -2.996
L 0.623
M 0.136
N -1.988
P -0.451
Q -1.814
R -2.749
S -0.119
T -0.083
V 0.721
W -0.875
Y -0.386
#___________________________________________________________________________
#
# Hphobe Values Kyte & Doolittle
# Kyte and Doolittle, J.Mol.Biol.157 (1982) 105-132
#___________________________________________________________________________
A 1.8
C .5
D -3.5
E -3.5
F 2.8
G -0.4
H -3.2
I 4.5
K -3.9
L 3.8
M 1.9
N -3.5
P -1.6
Q -3.5
R -4.5
S -0.8
T -0.7
V 4.2
W -0.9
Y -1.3
pkgdata_DATA = GES-scale GVH-scale KD-scale CYTEXT-scale toppred.dtd