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2012-10-31	Florent Angly	Changes file update	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Changes update	commit \| commitdiff \| tree
2012-10-31	Florent Angly	-direct valid only once	commit \| commitdiff \| tree
2012-10-31	Florent Angly	subseq() speedup	commit \| commitdiff \| tree
2012-10-31	Florent Angly	More length() tests and some POD update	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Removed some code redundancy	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Bio::PrimarySeqI speedup	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Cosmetic changeS	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Cosmetic changes	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Avoid new() just to revcom() a sequence	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Subseq() optimisation	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Testing subseq() more thoroughly	commit \| commitdiff \| tree
2012-10-31	Florent Angly	More tests for validate_seq()	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Testing validate_seq() and -ref_to_seq	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Constructor -ref_to_seq fix	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Small changes in seq() for clarity	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Small fix in validation error message	commit \| commitdiff \| tree
2012-10-31	Florent Angly	PrimarySeq::seq() modularization	commit \| commitdiff \| tree
2012-10-31	Florent Angly	Removed unneeded method	commit \| commitdiff \| tree
2012-10-31	Florent Angly	POD update and more consitent variable names	commit \| commitdiff \| tree
2012-10-30	Florent Angly	PrimarySeq direct mode fix/improvement	commit \| commitdiff \| tree
2012-10-30	Florent Angly	Small POD and tests updates	commit \| commitdiff \| tree
2012-10-30	Florent Angly	Doc fixes	commit \| commitdiff \| tree
2012-10-30	Florent Angly	More tests for PrimarySeq	commit \| commitdiff \| tree
2012-10-30	Florent Angly	Fixes issue in EncodedSeq	commit \| commitdiff \| tree
2012-10-30	Florent Angly	Cosmetic changes	commit \| commitdiff \| tree
2012-10-30	Florent Angly	Consistent indentation	commit \| commitdiff \| tree
2012-10-30	Florent Angly	SeqFastaSpeedFactory fix	commit \| commitdiff \| tree
2012-10-30	Florent Angly	Consistent indentation	commit \| commitdiff \| tree
2012-10-30	Florent Angly	Bio::PrimarySeq::length() optimizations	commit \| commitdiff \| tree
2012-10-30	Florent Angly	More tests for Bio::PrimarySeq::length()	commit \| commitdiff \| tree
2012-10-30	Florent Angly	POD updated and beautification	commit \| commitdiff \| tree
2012-10-30	Florent Angly	More tests for Bio::PrimarySeq::length()	commit \| commitdiff \| tree
2012-10-30	Florent Angly	Added tests for Bio::PrimarySeq::length()	commit \| commitdiff \| tree
2012-10-10	Florent Angly	Better 0-length sequence support for Bio::DB::Qual...	commit \| commitdiff \| tree
2012-10-10	Florent Angly	Better support for 0-length sequences	commit \| commitdiff \| tree
2012-09-24	Florent Angly	Merge branch 'master' of github.com:bioperl/bioperl...	commit \| commitdiff \| tree
2012-09-24	Florent Angly	Fixed an untested regression in Bio::DB::Fasta	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Regexp to match RNA on request only	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Fixed indentation	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Reversed problematic commit 8334d175ffba095a9447038d421cac0d...	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Merge branch 'amplicons'	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Merge branch 'master' of github.com:bioperl/bioperl...	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Removed some comments	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Compound ID can now includ the strand	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Bio::DB::IndexedBase compliance with Bio::DB:SeqI and...	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Fixed typo	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Fixed silly error	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Updated Bio::DB::SeqI POD according to info in Bio...	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Updated Changes file	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Explicit variable name instead of Bio/DB/Qual.pm	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Handle RNA and IUPAC characters in Bio::DB::Fasta	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Updated Changes file	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Better alphabet detection method that honors IUPAC...	commit \| commitdiff \| tree
2012-09-10	Florent Angly	Fasta and Qual only use the IndexedBase base	commit \| commitdiff \| tree
2012-09-10	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-09	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Fixed bug introduced in recent commit	commit \| commitdiff \| tree
2012-09-09	Florent Angly	makeid logic in IndexedBase	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Added error checks on Fasta into Qual	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Small simplificatiosn	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Test -makeid option	commit \| commitdiff \| tree
2012-09-09	Florent Angly	More streamlining	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Support for specifying sequence strand	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Using the _parse_compound_id() method	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Removed a test because method length() does not take...	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Storing number of residues in index file	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Fix to avoid a warning	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Variable name changes	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Small changes	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Renamed function more appropriately	commit \| commitdiff \| tree
2012-09-09	Florent Angly	More methods in IndexedBase	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Misleading variable name	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Cosmetic changes	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Small changes	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Fixed a couple of typos and worked on consistent indentaion	commit \| commitdiff \| tree
2012-09-09	Florent Angly	Sub to parse compound IDs	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Fixed bug affecting Bio::DB::SeqFeature	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Fixing some failing tests	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Renamed test files for consistency	commit \| commitdiff \| tree
2012-09-08	Florent Angly	POD reorganization	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Fixed test	commit \| commitdiff \| tree
2012-09-08	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Test header()	commit \| commitdiff \| tree
2012-09-08	Florent Angly	fh() moved to _fh() in IndexedBase	commit \| commitdiff \| tree
2012-09-08	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-08	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-08	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-08	Florent Angly	Improved tests	commit \| commitdiff \| tree
2012-09-07	Florent Angly	POD update	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Big POD update	commit \| commitdiff \| tree
2012-09-07	Florent Angly	New option to remove index file when done	commit \| commitdiff \| tree
2012-09-07	Florent Angly	More improvements	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Some more streamlining	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Moved get_seq_stream to IndexedBase	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Migrating more code to IndexedBase	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Code simplification	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Small POD change	commit \| commitdiff \| tree
2012-09-07	Florent Angly	Misc changes	commit \| commitdiff \| tree
2012-09-07	Florent Angly	User can supply an arbitrary name for the index file	commit \| commitdiff \| tree
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