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2011-03-17	Robert Buels	add test for leading whitespace before exonerate query...	commit \| commitdiff \| tree
2011-03-17	Robert Buels	fix big performance regression in which _load_module...	commit \| commitdiff \| tree
2011-03-17	Robert Buels	improved Bio::SeqFeature::Generic::has_tag performance...	commit \| commitdiff \| tree
2011-03-17	Robert Buels	improved _rearrange performance by 30%	commit \| commitdiff \| tree
2011-03-08	Robert Buels	bugfix to Bio::Tools::RepeatMasker, reverse matches...	commit \| commitdiff \| tree
2011-03-08	Robert Buels	localize $_ if you are going to modify it in a lib...	commit \| commitdiff \| tree
2011-02-24	Robert Buels	add a couple more tests for new phase accessor	commit \| commitdiff \| tree
2011-02-24	Robert Buels	add phase attr to Bio::SeqFeatureI, to match Bio::SeqFeature...	commit \| commitdiff \| tree
2010-11-22	Robert Buels	add seq() method to PrimaryQual, which is similar to...	commit \| commitdiff \| tree
2010-11-18	Robert Buels	add .qual file ext to file extension guessing in SeqIO...	commit \| commitdiff \| tree
2010-07-30	Robert Buels	dir in maint for working on dynamiting the monolith	commit \| commitdiff \| tree
2010-07-26	Robert Buels	StandAloneBlast.t should allow different types of quoting	commit \| commitdiff \| tree
2010-07-26	Robert Buels	whitespace cleanup in WrapperBase.pm code	commit \| commitdiff \| tree
2010-07-20	Robert Buels	broke t/Assembly/Assembly.t into 3 sane test files	commit \| commitdiff \| tree
2010-07-20	Duke Leto	Fix some failing InterPro tests, since the number of...	commit \| commitdiff \| tree
2010-07-20	Duke Leto	Add tests for the exceptions thrown by invalid Bio...	commit \| commitdiff \| tree
2010-07-20	Robert Buels	more perltidy	commit \| commitdiff \| tree
2010-07-20	Robert Buels	added 'Region' interpro type. recently-added test...	commit \| commitdiff \| tree
2010-07-20	Robert Buels	more perltidy	commit \| commitdiff \| tree
2010-07-20	Robert Buels	more perltidy	commit \| commitdiff \| tree
2010-07-20	Robert Buels	added a little defensive error checking when adding...	commit \| commitdiff \| tree
2010-07-20	Robert Buels	interpro parser now throws an error when it cannot...	commit \| commitdiff \| tree
2010-07-20	Robert Buels	perltidy on SimpleOntologyEngine.pm using bioperl perltidy...	commit \| commitdiff \| tree
2010-07-20	Robert Buels	moved platform detection out of inner loop of Bio:...	commit \| commitdiff \| tree
2010-07-20	Duke Leto	Add a small InterPro XML file that shows the parsing bug	commit \| commitdiff \| tree
2010-07-20	Duke Leto	Add test case for parsing interpro XML	commit \| commitdiff \| tree
2010-07-20	Duke Leto	Fix bug which prevents the parsing of the InterPro...	commit \| commitdiff \| tree
2010-06-07	Robert Buels	Merge branch 'master' of github.com:bioperl/bioperl...	commit \| commitdiff \| tree
2010-06-07	Robert Buels	Merge branch 'topic/longest_orf' into moster	commit \| commitdiff \| tree
2010-06-07	Robert Buels	PrimarySeqI.pm whitespace cleanup	commit \| commitdiff \| tree
2010-06-07	Robert Buels	clarified some translate() POD	commit \| commitdiff \| tree
2010-06-07	Robert Buels	added comment (not pod) block for internal _codon_is...	commit \| commitdiff \| tree
2010-06-05	Robert Buels	clean up stray whitespace in Assembly.t	commit \| commitdiff \| tree
2010-06-05	Robert Buels	added more intensive tests for longest-orf-finding...	commit \| commitdiff \| tree
2010-06-05	Robert Buels	tweaked translate() args format, removed -longest_orf...	commit \| commitdiff \| tree
2010-06-05	Robert Buels	another translate() docpatch for better rendering on...	commit \| commitdiff \| tree
2010-06-05	Robert Buels	more sane (maintainable) format for translate() option...	commit \| commitdiff \| tree
2010-05-25	Robert Buels	test fix: if this translate() is supposed to die, it...	commit \| commitdiff \| tree
2010-05-25	Robert Buels	docpatch to examples/longorf.pl	commit \| commitdiff \| tree
2010-05-21	Robert Buels	added comment with the bases used in the codon table...	commit \| commitdiff \| tree
2010-05-21	Robert Buels	fixed support for also including partial ORFs at the...	commit \| commitdiff \| tree
2010-05-21	Robert Buels	test for partial-orf warning should require the ORF...	commit \| commitdiff \| tree
2010-05-21	Robert Buels	updated topic/longest_orf from master	commit \| commitdiff \| tree
2010-05-21	Robert Buels	orf finder getting closer to passing...	commit \| commitdiff \| tree
2010-05-21	Robert Buels	more tests for the orf finder	commit \| commitdiff \| tree
2010-05-21	Robert Buels	_find_orfs now recognizes orfs that reach the end of...	commit \| commitdiff \| tree
2010-05-21	Robert Buels	test for ORF missing-stop-codon warning should be more...	commit \| commitdiff \| tree
2010-05-21	Robert Buels	whitespace correction	commit \| commitdiff \| tree
2010-05-21	Robert Buels	test fix: if this translate() is supposed to die, it...	commit \| commitdiff \| tree
2010-05-21	Robert Buels	refactored ORF finding in Bio::PrimarySeqI, in order...	commit \| commitdiff \| tree
2010-05-21	Robert Buels	tightened and cleaned up perl in Bio::Tools::CodonTable...	commit \| commitdiff \| tree
2010-05-21	Robert Buels	Bio::Tools::CodonTable whitespace cleanup	commit \| commitdiff \| tree
2010-05-20	Robert Buels	docpatch to examples/longorf.pl	commit \| commitdiff \| tree
2010-05-20	Robert Buels	docpatch to examples/longorf.pl	commit \| commitdiff \| tree
2010-05-20	Robert Buels	if Bio::DB::Taxonomy::entrez cannot load XML::Twig...	commit \| commitdiff \| tree

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