2011-03-28  Nicolas Joly  <njoly@pasteur.fr>

	* src/fasta.c: Fix a bug that prevented empty lines to be skipped.
	* test/sequence.sh: Exercise it.

2010-02-01  Nicolas Joly  <njoly@pasteur.fr>

	* src/prose.c: Do not leak memory, for a nul match. Avoid some
	other infinite loops with nul matches.

	* test/report.sh: New file to exercise report option.

	* src/prose.c: Do only try to match once if pattern starts with an
	anchor.
	* test/pattern.sh: Exercise it.

	* test/pattern.sh: Use prosite ending anchor character in tests,
	not the regex one.

2010-01-12  Nicolas Joly  <njoly@pasteur.fr>

	* src/prose.c: Do not choke on empty sequence.
	* test/sequence.sh: exercise it.

2010-01-11  Nicolas Joly  <njoly@pasteur.fr>

	* src/pat.c: Be robust against pattern list files without newline
	at EOF.
	* test/test_list.sh: Rename file from here ...
	* test/patlists.sh: ... to here, and exercise it.

2009-09-16  Nicolas Joly  <njoly@pasteur.fr>

	* test/test_intern.sh: Prefer cmp(1) tool instead of diff(1).

	* src/prose.c: Avoid an infinite loop when a pattern match returns
	a zero-length string, by rejecting it.
	* test/pattern.sh: Exercise it.

2009-09-15  Nicolas Joly  <njoly@pasteur.fr>

	* src/prose.c: Do not output cryptic regcomp error message, but
	rather custom ones.

2009-09-14  Nicolas Joly  <njoly@pasteur.fr>

	* test/pattern.sh: New file, to exercise Prosite pattern syntax.

2009-04-29  Nicolas Joly  <njoly@pasteur.fr>

	* src/prose.c: Properly allocate/free memory used for Prosite
	databank file.

2009-04-07  Nicolas Joly  <njoly@pasteur.fr>

	* src/prose.c: Do not read sequence from standard input anymore.
	* doc/prose.pod, test/casesrch.sh: Adjust accordingly.

2009-04-06  Nicolas Joly  <njoly@pasteur.fr>

	* src/fasta.c: Be robust against sequence in file without newline
	at EOF.
	* test/sequence.sh: Exercise it.

2009-04-03  Nicolas Joly  <njoly@pasteur.fr>

	* src/fasta.c: Full rewrite of fasta formatted sequence parsing;
	the old code was very badly handling anonymous sequences.
	* src/prose.c: Adjust accordingly.
	* test/sequence.sh: New file to exercise sequence parsing.

2008-02-12  Nicolas Joly  <njoly@pasteur.fr>

	* src/prose.c: Fix uninitialised variable.

	* src/fasta.c: Do not abort if last sequence line is missing its
	newline.

2008-02-11  Nicolas Joly  <njoly@pasteur.fr>

	* src/getpara.c: Kill it, by moving its content from here ...
	* src/prose.c: ... to here.

2007-07-02  Nicolas Joly  <njoly@pasteur.fr>

	* utils/prose+.pl: Major code cleanup, to make it functional
	again.

2007-06-29  Nicolas Joly  <njoly@pasteur.fr>

	* utils/prose+.pl: Add a default value for PROSITE documentation
	directory.

	* utils/prose+.pod: Small update.

	* src/prose.c: Add `REG_BASIC' definition for systems that don't
	have it.

2007-06-17  Nicolas Joly  <njoly@pasteur.fr>

	* src/getpara.[ch]: Cleanup param structure. Merge multiple
	boolean fields in a common new one; define all corresponding flag
	values.
	* src/prose.c: Adjust accordingly.

2007-06-16  Nicolas Joly  <njoly@pasteur.fr>

	* doc/prose.pod: Improve report option example formatting.

2006-12-22  Nicolas Joly  <njoly@pasteur.fr>

	* src/prosite.[ch]: Switch from Extended Regular Expressions (ERE)
	to Basic Regular Expressions (BRE). PROSITE syntax do not strictly
	require ERE, BRE support is enough. And this shows a small speedup
	in expressions searches (about 4%).
	* src/prose.c: Adjust.

	* src/translate.c: Move function to translate patterns (from
	PROSITE syntax into Regular Experssion) ...
	* src/prosite.c: ... here.
	* src/prose.c: Adjust accordingly.

	* src/prose.c: Check for successful PROSITE databank file access,
	before using it.

2006-12-21  Nicolas Joly  <njoly@pasteur.fr>

	* src/getpara.c: Add missing include for `tolower()' protoype.

	* src/error.[ch]: Use `const' where appropriate (function
	arguments).

2006-12-21  Nicolas Joly  <njoly@pasteur.fr>

	* test/prosite.sh: Check for documentation pattern (-d) option.

2006-12-20  Nicolas Joly  <njoly@pasteur.fr>

	* src/prosite.[ch]: New files for PROSITE databank specific
	functions.
	* src/prose.c: Use them.

	* src/pat.c: Remove now unused PROSITE specific functions from
	here.

2006-11-30  Nicolas Joly  <njoly@pasteur.fr>

	* src/prose.c: Remove undocumented option (-e) to handle regular
	expression input, instead of PROSITE patterns.

2006-11-29  Nicolas Joly  <njoly@pasteur.fr>

	* src/*.c: Remove option (-w) to check the syntax of PROSITE
	patterns.
	* doc/prose.pod: Adjust accordingly.

	* src/prose.c: Use case-insensitive regular expressions searches
	(intead of upper-casing both sequence and pattern).

	* test/casesrch.sh: New test file, to exercize case
	sensitive/insensitive searches.

	* test/Makefile.am: New maintainer targets to update test sequence
	and PROSITE databank sample file.

	* test/*: Many other assorted updates.

2006-11-28  Nicolas Joly  <njoly@pasteur.fr>

	* test/prose.sh: New file, for basic checks (options, ...).

2006-01-30  Nicolas Joly  <njoly@pasteur.fr>

	* configure.in: Do not check for perl executable if no utilities
	are needed.

2006-01-27  Nicolas Joly  <njoly@pasteur.fr>

	* test/test_intern.sh: Remove temporary file here ...
	* test/Makefile.am: ... instead of here.

	* test/*.sh: Add VERBOSE mode.

	* doc/prose.pod, utils/prose+.pod: Spelling fixes.

2006-01-27  Nicolas Joly  <njoly@pasteur.fr>

	* doc/prose.pod: POD syntax warnings fixes.

2002-05-02  Katja Schuerer  <schuerer@pasteur.fr>

	* src/prose.c: change pattern reporting, prose reports now not
	only the longest match of the pattern (as normal when searching
	regular expression) but can report the longest, the shortest
	(default) or all submatches.

2002-02-12  Katja Schuerer  <schuerer@pasteur.fr>

	* src/prose.c, src/getpara.c: Add -d option to print the ID + DO
	documentation instead of the pattern AC number.

2001-11-15  Katja Schuerer  <schuerer@pasteur.fr>

	* src/fasta.c: Change sequence reading to jump empty lines.

2001-10-16  Katja Schuerer  <schuerer@pasteur.fr>

	* src/prose.c: By default, no verification of all pattern and
	search case-insensitive, add options to verify all pattern and
	search case-sensitive.

	* src/prose.c: Add options to search directly with regex pattern
	not documented in the manpage.

