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 (tp_decode): 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
	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, 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


