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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
2008-10-25	cjfields	bullet-proof prototype test	commit \| commitdiff \| tree
2008-10-22	cjfields	fix file properties	commit \| commitdiff \| tree
2008-10-22	cjfields	new module for parsing vecscreen -f 3 output, courtesy...	commit \| commitdiff \| tree
2008-10-15	cjfields	add -source for ARP	commit \| commitdiff \| tree
2008-10-15	cjfields	[bug 2563]	commit \| commitdiff \| tree
2008-10-10	cjfields	typo	commit \| commitdiff \| tree
2008-10-10	cjfields	[bug 2519]	commit \| commitdiff \| tree
2008-10-10	cjfields	[bug 2519]	commit \| commitdiff \| tree
2008-10-07	cjfields	add svn tag	commit \| commitdiff \| tree
2008-10-07	cjfields	TODO's work	commit \| commitdiff \| tree
2008-10-07	cjfields	[bug 2612]	commit \| commitdiff \| tree
2008-10-07	cjfields	[bug 2612]	commit \| commitdiff \| tree
2008-10-02	cjfields	clean up XMFA parsing, allow spaces in parsing (ende...	commit \| commitdiff \| tree
2008-09-27	cjfields	[BUG] bug 2598	commit \| commitdiff \| tree
2008-09-26	cjfields	[BUG] bugfix for # 2598 (add 'J')	commit \| commitdiff \| tree
2008-09-26	cjfields	[BUG] bug 2593	commit \| commitdiff \| tree
2008-09-26	cjfields	[BUG] fix bug 2595	commit \| commitdiff \| tree
2008-09-18	cjfields	Use 'warning_like' for instances where a regex match...	commit \| commitdiff \| tree
2008-09-17	cjfields	* No longer a stub	commit \| commitdiff \| tree
2008-09-17	cjfields	1965 + 6 -1 = 1970, not 1999	commit \| commitdiff \| tree
2008-09-17	cjfields	passing TODO's (?!?)	commit \| commitdiff \| tree
2008-09-17	cjfields	update tests (seq length change in record verified)	commit \| commitdiff \| tree
2008-09-17	cjfields	set -end to coorespond to sequence end	commit \| commitdiff \| tree
2008-09-16	cjfields	test result changed (start always < end)	commit \| commitdiff \| tree
2008-09-16	cjfields	Fix nexus issues with seq. ambiguity symbol '.'	commit \| commitdiff \| tree
2008-09-16	cjfields	MEGA now resets $GAP_SYMBOLS and $OTHER_SYMBOLS to...	commit \| commitdiff \| tree
2008-09-16	cjfields	Test data matches new XMFA example	commit \| commitdiff \| tree
2008-09-16	cjfields	* XMFA alignment doesn't correspond to XMFA spec (http...	commit \| commitdiff \| tree
2008-09-16	cjfields	fix xmfa.pm parsing oops	commit \| commitdiff \| tree
2008-09-16	cjfields	make LocatableSeq::end() consistent	commit \| commitdiff \| tree
2008-09-16	cjfields	* fix start/end/strand	commit \| commitdiff \| tree
2008-09-16	cjfields	typo	commit \| commitdiff \| tree
2008-09-15	cjfields	remove debugging statement	commit \| commitdiff \| tree
2008-09-15	cjfields	partial fix for arp (-end now works and counts ? as...	commit \| commitdiff \| tree
2008-09-15	cjfields	-end parameter does not take gaps into account	commit \| commitdiff \| tree
2008-09-15	cjfields	* always warn about passing wrong end() coordinate	commit \| commitdiff \| tree
2008-09-14	cjfields	Create Data::Stag node lazily; always use node() to...	commit \| commitdiff \| tree
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