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2007-04-11	cjfields	convert to Test::More	commit \| commitdiff \| tree
2007-04-11	cjfields	Convert to Test::More	commit \| commitdiff \| tree
2007-04-11	cjfields	convert to Test::More	commit \| commitdiff \| tree
2007-04-11	cjfields	convert to Test::More	commit \| commitdiff \| tree
2007-04-11	cjfields	select_noncont() sorts numerically by default (fixed...	commit \| commitdiff \| tree
2007-04-11	cjfields	bug 2264, 2265	commit \| commitdiff \| tree
2007-04-05	cjfields	bug 2263	commit \| commitdiff \| tree
2007-04-02	cjfields	write_seq() is not implemented	commit \| commitdiff \| tree
2007-04-02	cjfields	bug 2246	commit \| commitdiff \| tree
2007-04-02	cjfields	bug 2237	commit \| commitdiff \| tree
2007-03-30	cjfields	Small bug which botches some report parsing	commit \| commitdiff \| tree
2007-03-29	cjfields	Fix '.' being appended to scientific_name	commit \| commitdiff \| tree
2007-03-28	cjfields	is(), not ok()	commit \| commitdiff \| tree
2007-03-27	cjfields	reroute data flow through data_handler() for centralized...	commit \| commitdiff \| tree
2007-03-26	cjfields	pass data in chunks using element_hash()	commit \| commitdiff \| tree
2007-03-26	cjfields	tests changes and additions	commit \| commitdiff \| tree
2007-03-26	cjfields	add warnings for unsupported methods	commit \| commitdiff \| tree
2007-03-26	cjfields	rnamotif fixes	commit \| commitdiff \| tree
2007-03-26	cjfields	parsing fixes	commit \| commitdiff \| tree
2007-03-22	cjfields	bug 2246 tentative fix	commit \| commitdiff \| tree
2007-03-22	cjfields	bug 2245 (enhancement to allow relative paths for index...	commit \| commitdiff \| tree
2007-03-22	cjfields	fix some tests	commit \| commitdiff \| tree
2007-03-22	cjfields	test data for BIC tests	commit \| commitdiff \| tree
2007-03-21	cjfields	Removing redundant module; passes flat.t	commit \| commitdiff \| tree
2007-03-21	cjfields	bug 2242	commit \| commitdiff \| tree
2007-03-21	cjfields	Now passes v3 tests (at least the v3 output we have...)	commit \| commitdiff \| tree
2007-03-21	cjfields	Neil & Co.'s modified Signalp parser (bug 2203) - passes...	commit \| commitdiff \| tree
2007-03-20	cjfields	Changed throw() due to verbose output from Infernal...	commit \| commitdiff \| tree
2007-03-19	cjfields	TargetP parser, data, and tests	commit \| commitdiff \| tree
2007-03-19	cjfields	bug 2240	commit \| commitdiff \| tree
2007-03-16	cjfields	getter/setter for comment type (not implemented yet)	commit \| commitdiff \| tree
2007-03-16	cjfields	tests (write_seq() for drivers not implemented yet)	commit \| commitdiff \| tree
2007-03-16	cjfields	seq format drivers and single handler module for GenBank...	commit \| commitdiff \| tree
2007-03-16	cjfields	Handler-based parsing interface	commit \| commitdiff \| tree
2007-03-15	cjfields	Move to Test::More	commit \| commitdiff \| tree
2007-03-15	cjfields	moved to Test::More	commit \| commitdiff \| tree
2007-03-15	cjfields	move to Test::More	commit \| commitdiff \| tree
2007-03-15	cjfields	new signalp parser (need to merge code and tests for...	commit \| commitdiff \| tree
2007-03-15	cjfields	signalp test data	commit \| commitdiff \| tree
2007-03-15	cjfields	new signalp tests; change to Test::More	commit \| commitdiff \| tree
2007-03-14	cjfields	Move to Test::More	commit \| commitdiff \| tree
2007-03-14	cjfields	Fix which checks for BLAST header for text/tabular...	commit \| commitdiff \| tree
2007-03-13	cjfields	Bug 2221	commit \| commitdiff \| tree
2007-03-13	cjfields	TandemRepeatsFinder parser (bug 2233)	commit \| commitdiff \| tree
2007-03-08	cjfields	switch to XML::SAX (not heavily tested); this module...	commit \| commitdiff \| tree
2007-03-08	cjfields	params use '-'	commit \| commitdiff \| tree
2007-03-08	cjfields	add simple bracket_string() tests	commit \| commitdiff \| tree
2007-03-08	cjfields	D* tests to Test::More	commit \| commitdiff \| tree
2007-03-08	cjfields	Finish converting C* tests to Test::More	commit \| commitdiff \| tree
2007-03-08	cjfields	removed tests from old bracket_string method (will...	commit \| commitdiff \| tree
2007-03-08	cjfields	change to Test::More	commit \| commitdiff \| tree
2007-03-08	cjfields	change to Test::More	commit \| commitdiff \| tree
2007-03-08	cjfields	convert to Test::More	commit \| commitdiff \| tree
2007-03-08	cjfields	move to Test::More	commit \| commitdiff \| tree
2007-03-07	cjfields	bug 2221; this should catch most translate data out...	commit \| commitdiff \| tree
2007-03-07	cjfields	Added data to spaces.nex for NEXUS TreeIO tests, no...	commit \| commitdiff \| tree
2007-03-07	cjfields	this should deal with all varieties of translate lines...	commit \| commitdiff \| tree
2007-03-07	cjfields	Bug 2221	commit \| commitdiff \| tree
2007-03-07	cjfields	bug 2205	commit \| commitdiff \| tree
2007-03-06	cjfields	perltidy and untabify (no bug fix for 2221 yet)	commit \| commitdiff \| tree
2007-03-06	cjfields	change to Test::More; added some tests for bug 2221...	commit \| commitdiff \| tree
2007-03-02	cjfields	additional spliced_seq tests (per Jay Hannah)	commit \| commitdiff \| tree
2007-02-27	cjfields	Add doi() get/setter	commit \| commitdiff \| tree
2007-02-27	cjfields	move to Test::More	commit \| commitdiff \| tree
2007-02-26	cjfields	Some POD fixes for bracket_string and sort_by_start	commit \| commitdiff \| tree
2007-02-26	cjfields	Made bracket_string a class method	commit \| commitdiff \| tree
2007-02-26	cjfields	remove bracket_strings (moving to SimpleAlign)	commit \| commitdiff \| tree
2007-02-22	cjfields	Bug 2215	commit \| commitdiff \| tree
2007-02-20	cjfields	Removed per Chris Mungall's request	commit \| commitdiff \| tree
2007-02-19	cjfields	Typo; add CVS tag	commit \| commitdiff \| tree
2007-02-17	cjfields	infernal parsing fixes	commit \| commitdiff \| tree
2007-02-16	cjfields	Remove XEMBL tests (no longer active)	commit \| commitdiff \| tree
2007-02-16	cjfields	Add deprecation warning	commit \| commitdiff \| tree
2007-02-16	cjfields	Removed extraneous line.	commit \| commitdiff \| tree
2007-02-15	cjfields	Add back per sac's request...	commit \| commitdiff \| tree
2007-02-15	cjfields	XEMBL no longer is available	commit \| commitdiff \| tree
2007-02-15	cjfields	No longer needed; tests should use Glimmer*.out and...	commit \| commitdiff \| tree
2007-02-15	cjfields	Bug 2206 - updates to allow all Glimmer formats to...	commit \| commitdiff \| tree
2007-02-15	cjfields	Fix for remote DB sort order change	commit \| commitdiff \| tree
2007-02-10	cjfields	XML::SAX 0.15 is req'd; may not need Bundle for XML...	commit \| commitdiff \| tree
2007-02-08	cjfields	fixed saxparser(), made tests stricter(!)	commit \| commitdiff \| tree
2007-02-08	cjfields	blastxml should now return all description data for...	commit \| commitdiff \| tree
2007-02-04	cjfields	our->my; fix GI error	commit \| commitdiff \| tree
2007-02-04	cjfields	erpin, rnamotif SearchIO-based parsers with some tests...	commit \| commitdiff \| tree
2007-02-04	cjfields	use quotemeta JIC for regexes	commit \| commitdiff \| tree
2007-02-04	cjfields	small changes	commit \| commitdiff \| tree
2007-02-04	cjfields	RNA-based SearchIO stuff (keep separate from SearchIO...	commit \| commitdiff \| tree
2007-02-04	cjfields	cmsearch (Infernal) SearchIO-based parser; HSP model...	commit \| commitdiff \| tree
2007-02-04	cjfields	Add private sub for getting GI/accession/version if...	commit \| commitdiff \| tree
2007-02-02	cjfields	Move to Test::More	commit \| commitdiff \| tree
2007-02-01	cjfields	bug 2189	commit \| commitdiff \| tree
2007-01-30	cjfields	XML::SAX::Expat (v. 0.38) works for XML parsing now...	commit \| commitdiff \| tree
2007-01-30	cjfields	Added tests for sort_by_start	commit \| commitdiff \| tree
2007-01-30	cjfields	Grr... remove Data::Dumper (from debugging)	commit \| commitdiff \| tree
2007-01-30	cjfields	tests for bug 2195	commit \| commitdiff \| tree
2007-01-30	cjfields	Bug 2195	commit \| commitdiff \| tree
2007-01-30	cjfields	Bugs 2197, 2092	commit \| commitdiff \| tree
2007-01-29	cjfields	Bug 2198	commit \| commitdiff \| tree
2007-01-29	cjfields	Bug 2197	commit \| commitdiff \| tree
2007-01-27	cjfields	small tweak to get rid of warning	commit \| commitdiff \| tree
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