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2008-03-28	cjfields	* revert symbol passing (forgot query and hit have...	commit \| commitdiff \| tree
2008-03-28	cjfields	* Allow gap symbol to be set	commit \| commitdiff \| tree
2008-03-27	cjfields	remove extraneous comment	commit \| commitdiff \| tree
2008-03-27	cjfields	using seq_inds() with 'gaps' now repeats sequence indices...	commit \| commitdiff \| tree
2008-03-27	cjfields	Collapse repeated sequence indices into one position	commit \| commitdiff \| tree
2008-03-27	cjfields	Marc's bug from mail list; repeat the seq position...	commit \| commitdiff \| tree
2008-03-25	cjfields	bug 2473 (with tests)	commit \| commitdiff \| tree
2008-03-04	cjfields	bug 1707	commit \| commitdiff \| tree
2008-03-03	cjfields	bug 2465	commit \| commitdiff \| tree
2008-03-03	cjfields	bug 2449	commit \| commitdiff \| tree
2008-03-03	cjfields	some more for bug 2349	commit \| commitdiff \| tree
2008-03-03	cjfields	partial fix for bug 2439	commit \| commitdiff \| tree
2008-03-02	cjfields	Bug 2378	commit \| commitdiff \| tree
2008-03-01	cjfields	fix undef. variable issue when no ancestor indicated...	commit \| commitdiff \| tree
2008-03-01	cjfields	add some flexibility for name length, defaulting to 10	commit \| commitdiff \| tree
2008-03-01	cjfields	bug 2356 (check for correct number with multiple trees)	commit \| commitdiff \| tree
2008-03-01	cjfields	bug 2356	commit \| commitdiff \| tree
2008-03-01	cjfields	add driver/handler support (will clean these up more...	commit \| commitdiff \| tree
2008-03-01	cjfields	add some docs	commit \| commitdiff \| tree
2008-03-01	cjfields	added prototype-checking method (bug 2179)	commit \| commitdiff \| tree
2008-03-01	cjfields	clean up inheritance tree; add remote database test	commit \| commitdiff \| tree
2008-02-29	cjfields	Add in support for grabbing most current data via ftp...	commit \| commitdiff \| tree
2008-02-29	cjfields	parser for neo/prototype format from REBASE	commit \| commitdiff \| tree
2008-02-29	cjfields	bug 2179	commit \| commitdiff \| tree
2008-02-29	cjfields	bug 2128	commit \| commitdiff \| tree
2008-02-29	cjfields	Note about XML format (related to bug 2018)	commit \| commitdiff \| tree
2008-02-28	cjfields	fix Handler tests	commit \| commitdiff \| tree
2008-02-28	cjfields	* Implement StructureValue-like get_all_values() (flattened...	commit \| commitdiff \| tree
2008-02-28	cjfields	add Data::Stag to require (may change to recommend...	commit \| commitdiff \| tree
2008-02-28	cjfields	minor word wrapping for error message	commit \| commitdiff \| tree
2008-02-28	cjfields	bug 1825	commit \| commitdiff \| tree
2008-02-28	cjfields	bug 1825: updating swiss.pm/tests to try out TagTree...	commit \| commitdiff \| tree
2008-02-28	cjfields	check tagtree in collection	commit \| commitdiff \| tree
2008-02-28	cjfields	More tests	commit \| commitdiff \| tree
2008-02-27	cjfields	bug 2462	commit \| commitdiff \| tree
2008-02-27	cjfields	Change name to TagTree	commit \| commitdiff \| tree
2008-02-27	cjfields	changes and additions (can't fairly implement StructureValue...	commit \| commitdiff \| tree
2008-02-27	cjfields	Add some tests, more to follow upon implementation...	commit \| commitdiff \| tree
2008-02-27	cjfields	Remove Data::Stag cruft (use a reimplementation instead)	commit \| commitdiff \| tree
2008-02-27	cjfields	StructuredTag - AnnotationI which uses Data::Stag for...	commit \| commitdiff \| tree
2008-02-27	cjfields	add error message for callbacks if no code reference	commit \| commitdiff \| tree
2008-02-26	cjfields	bug 2458	commit \| commitdiff \| tree
2008-02-26	cjfields	Russell's fixes	commit \| commitdiff \| tree
2008-02-24	cjfields	GN changes	commit \| commitdiff \| tree
2008-02-22	cjfields	revert last commit (good catch Sendu)	commit \| commitdiff \| tree
2008-02-21	cjfields	run tests directly in Build.PL (don't pass code refs...	commit \| commitdiff \| tree
2008-02-21	cjfields	TODO now works	commit \| commitdiff \| tree
2008-02-21	cjfields	fall back to empty set	commit \| commitdiff \| tree
2008-02-21	cjfields	now deprecated	commit \| commitdiff \| tree
2008-02-21	cjfields	Sequence gained a nucleotide	commit \| commitdiff \| tree
2008-02-21	cjfields	bug 2438. 'X' can't be completely disambiguated from...	commit \| commitdiff \| tree
2008-02-21	cjfields	add file test, unlink if already present	commit \| commitdiff \| tree
2008-02-21	cjfields	add Graph::Directed to requirements for tests	commit \| commitdiff \| tree
2008-02-21	cjfields	fix CUTG tests	commit \| commitdiff \| tree
2008-02-21	cjfields	Now passes tests; added warnings for no returned exons...	commit \| commitdiff \| tree
2008-02-20	cjfields	tests for bug 2453	commit \| commitdiff \| tree
2008-02-20	cjfields	Bug 2453; needs tests	commit \| commitdiff \| tree
2008-02-20	cjfields	Oops! Bug 2453 again.	commit \| commitdiff \| tree
2008-02-20	cjfields	small fix for bug 2453, but see bugzilla for reasons...	commit \| commitdiff \| tree
2008-02-20	cjfields	bug 2452	commit \| commitdiff \| tree
2008-02-19	cjfields	TODO now works	commit \| commitdiff \| tree
2008-02-13	cjfields	update interface documentation	commit \| commitdiff \| tree
2008-02-13	cjfields	not 1.5.3 (modules don't work anymore)	commit \| commitdiff \| tree
2008-02-12	cjfields	missing getter/setter added	commit \| commitdiff \| tree
2008-02-12	cjfields	bug 2440	commit \| commitdiff \| tree
2008-02-11	cjfields	remove comment (make sure tempfile/tempdirs stored...	commit \| commitdiff \| tree
2008-02-11	cjfields	Fix for bug 2413. Shouldn't we delegate all IO-related...	commit \| commitdiff \| tree
2008-02-10	cjfields	test commit msgs from /usr/local/bin	commit \| commitdiff \| tree
2008-02-10	cjfields	checking svn post commits to list	commit \| commitdiff \| tree
2008-02-07	cjfields	bug 2445: clean up hit table regex to skip N (Bernd...	commit \| commitdiff \| tree
2008-02-05	cjfields	changed URL	commit \| commitdiff \| tree
2008-02-05	cjfields	handles Bio::Taxon as well as Bio::Species now (might...	commit \| commitdiff \| tree
2008-02-05	cjfields	* small rnamotif fix	commit \| commitdiff \| tree
2008-02-05	cjfields	bug 2444 (HSP::significance returning wrong value)	commit \| commitdiff \| tree
2008-02-05	cjfields	bug 2438; 'X' no longer completely ambiguous	commit \| commitdiff \| tree
2008-02-05	cjfields	bug 2415	commit \| commitdiff \| tree
2008-02-05	cjfields	bug 2442	commit \| commitdiff \| tree
2008-02-04	cjfields	Fixed bits/raw_score issue related to GenericHit changes...	commit \| commitdiff \| tree
2008-01-31	cjfields	bug 2436; add option for 'mismatch' (no match w/o gaps)	commit \| commitdiff \| tree
2008-01-30	cjfields	Add simple method to retrieve parameter settings	commit \| commitdiff \| tree
2008-01-25	cjfields	Returned value from EntrezGene is different	commit \| commitdiff \| tree
2008-01-24	cjfields	Stefan's fix for entrezgene which includes a fix for...	commit \| commitdiff \| tree
2008-01-22	cjfields	revert last commit; problem more serious than initially...	commit \| commitdiff \| tree
2008-01-21	cjfields	get rid of annoying 'pseudohashes' error; tests now...	commit \| commitdiff \| tree
2008-01-21	cjfields	Use db settings for both BioDBGFF and BioDBSeqFeature_mysql...	commit \| commitdiff \| tree
2008-01-17	cjfields	remove format option for EMBL just in case...	commit \| commitdiff \| tree
2008-01-17	cjfields	bug 2433	commit \| commitdiff \| tree
2008-01-17	cjfields	Starter cross_match tests and sample data. Needs...	commit \| commitdiff \| tree
2008-01-17	cjfields	Tentative fix for bug 2427	commit \| commitdiff \| tree
2008-01-17	cjfields	bug 2423	commit \| commitdiff \| tree
2008-01-17	cjfields	bug 2431	commit \| commitdiff \| tree
2008-01-15	cjfields	Bug 2426	commit \| commitdiff \| tree
2008-01-14	cjfields	test post-commit after fsfs transfer (2nd try)	commit \| commitdiff \| tree
2008-01-14	cjfields	test commits after fsfs transfer	commit \| commitdiff \| tree
2008-01-07	cjfields	Test	commit \| commitdiff \| tree
2007-12-06	cjfields	small fix for VERSIONing issue, POD fixes	commit \| commitdiff \| tree
2007-11-29	cjfields	bug 2333; first pass at PSIBLAST XML parsing	commit \| commitdiff \| tree
2007-11-29	cjfields	Match HSP, not hit table	commit \| commitdiff \| tree
2007-11-29	cjfields	more memory-friendly	commit \| commitdiff \| tree
2007-11-28	cjfields	WUBLAST signif gets pvalue, NCBI BLAST signif gets...	commit \| commitdiff \| tree
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