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2008-12-10	cjfields	update deprecation list	commit \| commitdiff \| tree
2008-12-10	cjfields	remove Bio::Graphics (separate package now)	commit \| commitdiff \| tree
2008-12-10	cjfields	[bug 2637]	commit \| commitdiff \| tree
2008-12-10	cjfields	Remove dependencies for Bio::Graphics and deprecated...	commit \| commitdiff \| tree
2008-12-09	cjfields	Squash warning	commit \| commitdiff \| tree
2008-12-09	cjfields	diag() only on verbose	commit \| commitdiff \| tree
2008-12-09	cjfields	Fix last loop tests, move some to can_ok	commit \| commitdiff \| tree
2008-12-09	cjfields	Modify to test new temp classes and ensure that added...	commit \| commitdiff \| tree
2008-12-09	cjfields	update Mauricio's email	commit \| commitdiff \| tree
2008-12-08	cjfields	Update Roy's email	commit \| commitdiff \| tree
2008-12-08	cjfields	Roy's email (and bioperl.org not bioperl.edu)	commit \| commitdiff \| tree
2008-12-08	cjfields	Updated emails	commit \| commitdiff \| tree
2008-12-07	cjfields	[bug 2699]	commit \| commitdiff \| tree
2008-12-05	cjfields	Need to retrieve the tree for output	commit \| commitdiff \| tree
2008-12-05	cjfields	[bug 2450]	commit \| commitdiff \| tree
2008-12-04	cjfields	Make Target a true DBLink	commit \| commitdiff \| tree
2008-12-04	cjfields	Directory is no longer needed (Heikki split this up...	commit \| commitdiff \| tree
2008-12-03	cjfields	add force_nse tests	commit \| commitdiff \| tree
2008-12-03	cjfields	leave ID undefined if it isn't present, but allow the...	commit \| commitdiff \| tree
2008-12-03	cjfields	Remove files accidently added from last commit	commit \| commitdiff \| tree
2008-12-03	cjfields	Reorganize Tools tests (needs some more splitting)	commit \| commitdiff \| tree
2008-12-03	cjfields	Remove (tests are redundant, in Consed.t)	commit \| commitdiff \| tree
2008-12-03	cjfields	Merge tests and remove redundant file	commit \| commitdiff \| tree
2008-12-03	cjfields	Update test count	commit \| commitdiff \| tree
2008-12-03	cjfields	Merge tests	commit \| commitdiff \| tree
2008-12-03	cjfields	Remove redundant file	commit \| commitdiff \| tree
2008-12-03	cjfields	Remove old files	commit \| commitdiff \| tree
2008-12-03	cjfields	Start Tools move	commit \| commitdiff \| tree
2008-12-03	cjfields	small updates:	commit \| commitdiff \| tree
2008-12-03	cjfields	forgot to increment test count	commit \| commitdiff \| tree
2008-12-03	cjfields	Add a couple of tests for seq_id (small but significant...	commit \| commitdiff \| tree
2008-12-02	cjfields	[bug 2450]	commit \| commitdiff \| tree
2008-12-02	cjfields	[bug 2450]	commit \| commitdiff \| tree
2008-12-02	cjfields	[bug 2450]	commit \| commitdiff \| tree
2008-12-02	cjfields	[bug 2450]	commit \| commitdiff \| tree
2008-12-02	cjfields	some pod updates	commit \| commitdiff \| tree
2008-12-02	cjfields	[bug 2450]	commit \| commitdiff \| tree
2008-12-02	cjfields	fix erroneously renamed stockholm tests	commit \| commitdiff \| tree
2008-12-02	cjfields	small pod fix	commit \| commitdiff \| tree
2008-11-30	cjfields	silence GuessSeqFormat.t warnings (not sure if old...	commit \| commitdiff \| tree
2008-11-28	cjfields	rearrange to avoid unnecessary warnings	commit \| commitdiff \| tree
2008-11-28	cjfields	Add warning for missing data (real bug)	commit \| commitdiff \| tree
2008-11-28	cjfields	hash ref, not a hash	commit \| commitdiff \| tree
2008-11-28	cjfields	test file name and test # correction	commit \| commitdiff \| tree
2008-11-28	cjfields	correct test file name	commit \| commitdiff \| tree
2008-11-28	cjfields	'::', not ':'	commit \| commitdiff \| tree
2008-11-28	cjfields	rename (recursive tests think this is a test file)	commit \| commitdiff \| tree
2008-11-28	cjfields	recurse into test subdirectories (means any non-test...	commit \| commitdiff \| tree
2008-11-28	cjfields	remove redundant copy	commit \| commitdiff \| tree
2008-11-28	cjfields	move into directory structure	commit \| commitdiff \| tree
2008-11-28	cjfields	move into directory structure (DaveM++)	commit \| commitdiff \| tree
2008-11-26	cjfields	[bug 2567]	commit \| commitdiff \| tree
2008-11-26	cjfields	Redundant; file was renamed SearchIO_blast_pull.t.	commit \| commitdiff \| tree
2008-11-26	cjfields	[bug 2686]	commit \| commitdiff \| tree
2008-11-26	cjfields	fix subversion tags	commit \| commitdiff \| tree
2008-11-25	cjfields	po, not poa	commit \| commitdiff \| tree
2008-11-25	cjfields	fix undefined value warnings	commit \| commitdiff \| tree
2008-11-25	cjfields	[bug 2686]	commit \| commitdiff \| tree
2008-11-25	cjfields	[bug 2641, 2642]	commit \| commitdiff \| tree
2008-11-25	cjfields	split up AlignIO tests	commit \| commitdiff \| tree
2008-11-25	cjfields	[bug 2682]	commit \| commitdiff \| tree
2008-11-25	cjfields	[bug 2630]	commit \| commitdiff \| tree
2008-11-24	cjfields	[bug 2633]	commit \| commitdiff \| tree
2008-11-24	cjfields	[bug 2663]	commit \| commitdiff \| tree
2008-11-24	cjfields	[bug 2663]	commit \| commitdiff \| tree
2008-11-24	cjfields	[bug 2630]	commit \| commitdiff \| tree
2008-11-24	cjfields	[bug 2262]	commit \| commitdiff \| tree
2008-11-24	cjfields	[bug 2630]	commit \| commitdiff \| tree
2008-11-18	cjfields	* Double-checked data, tested results were wrong	commit \| commitdiff \| tree
2008-11-18	cjfields	* seq_inds is not defined for Model-based HSPs	commit \| commitdiff \| tree
2008-11-18	cjfields	* fix POD	commit \| commitdiff \| tree
2008-11-17	cjfields	* 'highly' (and I get r15000!)	commit \| commitdiff \| tree
2008-11-17	cjfields	Remove redundant test files	commit \| commitdiff \| tree
2008-11-17	cjfields	[tests]	commit \| commitdiff \| tree
2008-11-17	cjfields	move results2hash test utility sub to SearchUtils	commit \| commitdiff \| tree
2008-11-16	cjfields	[bug 2663]	commit \| commitdiff \| tree
2008-11-16	cjfields	perltidy	commit \| commitdiff \| tree
2008-11-16	cjfields	[bug 2635]	commit \| commitdiff \| tree
2008-11-14	cjfields	[bug 2656]	commit \| commitdiff \| tree
2008-11-11	cjfields	remove debugging lines	commit \| commitdiff \| tree
2008-11-11	cjfields	remove fixed verbose flag	commit \| commitdiff \| tree
2008-11-11	cjfields	[bug 2650]	commit \| commitdiff \| tree
2008-11-11	cjfields	Clarify result_count (discussions on mail list per...	commit \| commitdiff \| tree
2008-11-11	cjfields	[bug 2632]	commit \| commitdiff \| tree
2008-11-10	cjfields	[bug 2645]	commit \| commitdiff \| tree
2008-11-04	cjfields	wrap text	commit \| commitdiff \| tree
2008-11-04	cjfields	* parse 'Features in this part of subject sequence...	commit \| commitdiff \| tree
2008-11-04	cjfields	* parse 'Features in this part of subject sequence...	commit \| commitdiff \| tree
2008-10-30	cjfields	[bug 2632]	commit \| commitdiff \| tree
2008-10-29	cjfields	fix seq_inds(); wasn't calling identical residues for...	commit \| commitdiff \| tree
2008-10-29	cjfields	[bug 2633]	commit \| commitdiff \| tree
2008-10-28	cjfields	[bug 2630]	commit \| commitdiff \| tree
2008-10-26	cjfields	Fix unlink() warning	commit \| commitdiff \| tree
2008-10-26	cjfields	end = start if only start is passed	commit \| commitdiff \| tree
2008-10-26	cjfields	use valid_Location to check Location state	commit \| commitdiff \| tree
2008-10-26	cjfields	add docs for LocationI method valid_Location	commit \| commitdiff \| tree
2008-10-26	cjfields	[bug 2621]	commit \| commitdiff \| tree
2008-10-26	cjfields	[bug 2621]	commit \| commitdiff \| tree
2008-10-26	cjfields	[bug 2624]	commit \| commitdiff \| tree
2008-10-26	cjfields	[bug 2621]	commit \| commitdiff \| tree
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