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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