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2007-01-16	cjfields	fix filehandle issue for NEXUS parsing	commit \| commitdiff \| tree
2007-01-16	cjfields	file handle tests (NEXUS still doesn't work)	commit \| commitdiff \| tree
2007-01-16	cjfields	fix for filehandle IO	commit \| commitdiff \| tree
2007-01-16	cjfields	Bug 2185	commit \| commitdiff \| tree
2007-01-11	cjfields	Bug 2182	commit \| commitdiff \| tree
2007-01-11	cjfields	revert rnamotif.t changes (committed accidentally along...	commit \| commitdiff \| tree
2007-01-11	cjfields	removed extraneous (now wrong) comment	commit \| commitdiff \| tree
2007-01-11	cjfields	Bug 2182	commit \| commitdiff \| tree
2007-01-08	cjfields	bug 2172	commit \| commitdiff \| tree
2007-01-07	cjfields	small changes	commit \| commitdiff \| tree
2007-01-07	cjfields	POD changes	commit \| commitdiff \| tree
2006-12-31	cjfields	bug 2167	commit \| commitdiff \| tree
2006-12-30	cjfields	small change reg. HTML::Entities	commit \| commitdiff \| tree
2006-12-30	cjfields	small changes	commit \| commitdiff \| tree
2006-12-30	cjfields	Bug 2166	commit \| commitdiff \| tree
2006-12-30	cjfields	Removed debugging cruft	commit \| commitdiff \| tree
2006-12-30	cjfields	tentative fix for bug 2166	commit \| commitdiff \| tree
2006-12-28	cjfields	Moving BLAST XML SAX methods to separate class	commit \| commitdiff \| tree
2006-12-21	cjfields	XML::SAX::PurePerl works with older BLAST XML report...	commit \| commitdiff \| tree
2006-12-21	cjfields	add tests for 'unisave', move to Test::More, minor...	commit \| commitdiff \| tree
2006-12-21	cjfields	added 'unisave'	commit \| commitdiff \| tree
2006-12-20	cjfields	Bug fix for env_proxy	commit \| commitdiff \| tree
2006-12-13	cjfields	If parser overheats, turn off and back slowly away...	commit \| commitdiff \| tree
2006-12-13	cjfields	Very experimental Infernal (cmsearch) parser.	commit \| commitdiff \| tree
2006-12-12	cjfields	small change for phase test	commit \| commitdiff \| tree
2006-12-12	cjfields	Add convenience parameter '-phase' to spliced_seq()	commit \| commitdiff \| tree
2006-12-12	cjfields	spliced_seq() phase tests	commit \| commitdiff \| tree
2006-12-06	cjfields	Update from wiki	commit \| commitdiff \| tree
2006-12-06	cjfields	Update from wiki	commit \| commitdiff \| tree
2006-12-05	cjfields	Grr...refix Bug 2159	commit \| commitdiff \| tree
2006-12-05	cjfields	bug 2159	commit \| commitdiff \| tree
2006-12-05	cjfields	Bug 2160	commit \| commitdiff \| tree
2006-11-30	cjfields	change for block to a map	commit \| commitdiff \| tree
2006-11-30	cjfields	Bug 2152	commit \| commitdiff \| tree
2006-11-27	cjfields	throw, not warn, since this dies 99% of the time anyway...	commit \| commitdiff \| tree
2006-11-27	cjfields	small fixes for AnnotationFactory	commit \| commitdiff \| tree
2006-11-26	cjfields	Bug 2124	commit \| commitdiff \| tree
2006-11-26	cjfields	Bug 2151	commit \| commitdiff \| tree
2006-11-23	cjfields	Bug 2146	commit \| commitdiff \| tree
2006-11-23	cjfields	Bug 2146	commit \| commitdiff \| tree
2006-11-16	cjfields	Convert to Test::More	commit \| commitdiff \| tree
2006-11-16	cjfields	Convert to Test::More	commit \| commitdiff \| tree
2006-11-16	cjfields	Bug 2145	commit \| commitdiff \| tree
2006-11-14	cjfields	Add CVS tags, move dependencies to new file	commit \| commitdiff \| tree
2006-11-14	cjfields	New INSTALL.WIN doc (from wiki)	commit \| commitdiff \| tree
2006-11-14	cjfields	Add POD	commit \| commitdiff \| tree
2006-11-13	cjfields	bug 2139; change to Test::More	commit \| commitdiff \| tree
2006-11-13	cjfields	Bug 2139	commit \| commitdiff \| tree
2006-11-13	cjfields	typo (bug 2141)	commit \| commitdiff \| tree
2006-11-13	cjfields	change test file data	commit \| commitdiff \| tree
2006-11-11	cjfields	ARP tests	commit \| commitdiff \| tree
2006-11-11	cjfields	Simple ARP parser	commit \| commitdiff \| tree
2006-11-10	cjfields	use single quotes for system calls to prevent interpolation	commit \| commitdiff \| tree
2006-11-10	cjfields	Changed or removed VERSION	commit \| commitdiff \| tree
2006-11-09	cjfields	delete output test files	commit \| commitdiff \| tree
2006-11-09	cjfields	Add xmfa alignment tests	commit \| commitdiff \| tree
2006-11-09	cjfields	add xmfa write_aln() method, stk and xmfa file extensions...	commit \| commitdiff \| tree
2006-11-09	cjfields	using 'our'	commit \| commitdiff \| tree
2006-11-09	cjfields	first pass at xmfa parser (next_aln() implemented only)	commit \| commitdiff \| tree
2006-11-09	cjfields	Bug 2134 (change output to conform with rel. 9 ID changes)	commit \| commitdiff \| tree
2006-11-09	cjfields	Bug 2134 (added tests for new swiss format); changed...	commit \| commitdiff \| tree
2006-11-09	cjfields	Bug 2134 (fix parsing)	commit \| commitdiff \| tree
2006-11-09	cjfields	Changed name	commit \| commitdiff \| tree
2006-11-08	cjfields	Bug 2134	commit \| commitdiff \| tree
2006-11-08	cjfields	Some modules don't define VERSION, default to 0	commit \| commitdiff \| tree
2006-11-08	cjfields	Remove extraneous debugging staatements	commit \| commitdiff \| tree
2006-11-08	cjfields	typo	commit \| commitdiff \| tree
2006-11-08	cjfields	Using DBLinks for database refs	commit \| commitdiff \| tree
2006-11-07	cjfields	Additional fun stuff; write_aln() test added; may move...	commit \| commitdiff \| tree
2006-11-06	cjfields	more Stockholm tests; skipping two for now (dropping...	commit \| commitdiff \| tree
2006-11-06	cjfields	Add alignment meta string output	commit \| commitdiff \| tree
2006-11-06	cjfields	remove old initialization parameter; will add builder...	commit \| commitdiff \| tree
2006-11-06	cjfields	Add sequence-based meta output	commit \| commitdiff \| tree
2006-11-06	cjfields	stockholm alignment tests	commit \| commitdiff \| tree
2006-11-06	cjfields	Add experimental stockholm write_aln() support	commit \| commitdiff \| tree
2006-11-05	cjfields	Use Test::More	commit \| commitdiff \| tree
2006-11-01	cjfields	Implement AnnotatableI (for alignment-specific annotation)	commit \| commitdiff \| tree
2006-10-31	cjfields	remove redundant sub_Location_by_order()	commit \| commitdiff \| tree
2006-10-31	cjfields	Bug 2130	commit \| commitdiff \| tree
2006-10-28	cjfields	remove extraneous use statement	commit \| commitdiff \| tree
2006-10-26	cjfields	Bullet-proof some tests	commit \| commitdiff \| tree
2006-10-24	cjfields	Bug 2060	commit \| commitdiff \| tree
2006-10-24	cjfields	our $VERSION (perl 5.6.1-ish)	commit \| commitdiff \| tree
2006-10-20	cjfields	Typo	commit \| commitdiff \| tree
2006-10-19	cjfields	Bug 2101 (tentative fix)	commit \| commitdiff \| tree
2006-10-17	cjfields	Change to Test::More; skip XML tests if problems arise...	commit \| commitdiff \| tree
2006-10-11	cjfields	Bug 2121	commit \| commitdiff \| tree
2006-10-10	cjfields	Bug 2120	commit \| commitdiff \| tree
2006-10-05	cjfields	Updates to POD and egquery (getting it up to speed)	commit \| commitdiff \| tree
2006-10-05	cjfields	Fixes to get EGQuery working correctly	commit \| commitdiff \| tree
2006-10-04	cjfields	Added tests for new DocSum methods; will probably cut...	commit \| commitdiff \| tree
2006-10-04	cjfields	POD cleanup (thanks Sendu), remove some debugging stuff...	commit \| commitdiff \| tree
2006-10-04	cjfields	ESummary tests	commit \| commitdiff \| tree
2006-10-04	cjfields	Fixes for tests	commit \| commitdiff \| tree
2006-10-03	cjfields	About to add a few tests for Esummary (not implemented...	commit \| commitdiff \| tree
2006-10-03	cjfields	Add POD	commit \| commitdiff \| tree
2006-10-03	cjfields	Adding methods to DocSum and esummary (still experimental)	commit \| commitdiff \| tree
2006-10-03	cjfields	Add simple docsum container object for esummary	commit \| commitdiff \| tree
2006-10-03	cjfields	Setting DB from cookie is bad for elink; it should...	commit \| commitdiff \| tree
2006-10-03	cjfields	Force IDs to be an array at all times	commit \| commitdiff \| tree
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