Core 0.6.0 0.6.1 delta

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These are detailed notes on changes made between release-06 and bioperl-06-1.

Bio::DB::GenBank: Bug 133 fixed; Bug 133 fixed; Fixed comments in Bio::DB::GenBank.pm about what it inherits off.; Fixed comments in Bio::DB::GenBank.pm > about what it inherits off.; Documentation correction

Bio::Index::Abstract: Fixed bug in Bio::Index::Abstract::_open_dbm_file; Fixes in Bio::Index::Abstract scripts/bpfetch.pl and t/Index.t; Corrected wrong logic in _check_file_sizes ('=' to '=='); Fixes to FTHelper propagated from main branch

Bio::Index::AbstractSeq: Documentation correction; Documentation tweak; Documentation tweak

Bio::Root::Utilities: Create_filehandle() checks whether the client is a ref. Safer.

Bio::SeqFeature::Generic: Fixed documentation in Bio::SeqFeature::Generic; Propagated fixes to documentatioin in Bio::SeqFeature::Generic to stable branch

Bio::SeqIO: Added Bio/SeqIO/ace.pm and tests; Bad checkin previously with merge messages

Bio::SeqIO::FTHelper: Minor fix to FThelper.pm; Fixed bug which threw exceptions when 1 bp long features were present on the complement. Regexp was too strict.; Moved redundant code from next_seq to a new method _parse_loc. Fixed regexp, no more throw()s upon unexpected/unparseable features, but warnings.; Made the location setting code in _generic_seqfeature better aware of unknown ends. If there is no position (like ? in SwissProt), the respective end will not be set.; Propagated Hilmar's SeqIO changes from main branch; Minor fixes to SeqIO::embl and SeqIO.t '; Fixed patterns in _parse_loc(). Fixes bug #235 and another one which was not reported. Tested briefly against GenBank and SwissProt, seems to work (tests should be added to t/SeqIO.t). Added documentation.; Fixes to FTHelper; Fixes to FTHelper propagated from main branch

Bio::SeqIO::embl: Updated README; Added feature-rich entry and an entry with a "weird" location feature.; Fixes for Feature table parsing in SeqIO embl, genbank, and swiss and changed storing of sub_species to be backwards compatible; Small fixes in Bio::SeqIO::embl and removed duff code from Bio::SeqIO::swiss; Propagated SeqIO changes over from branch-06; Added setting of display_id before further parse (lets you see the offending seq entry).; Propagated Hilmar's SeqIO changes from main branch; Minor fixes to SeqIO::embl and SeqIO.t '

Bio::SeqIO::fasta: Fix to Bio::SeqIO::fasta to reduce memory overhead; Fix to Bio::SeqIO::fasta to reduce memory usage; Bug 132, 204 fixed; Bug 132, 204 fixed - desc multiline problem in write_seq

Bio::SeqIO::gcg: PR#204; Fixed line 252 bug == instead of = as from jitterbug reoport all sequences were validating as correct even if they aren't, except for those which had a valid checksum of 0; Bug 132, 204 fixed - desc multiline problem in write_seq; Fixes to FTHelper

Bio::SeqIO::genbank: Updated README; Added fixed by <Hilmar.Lapp@pharma.novartis.com>; Changed using patch provided by <Hilmar.Lapp@pharma.novartis.com>; Added feature-rich entry and an entry with a "weird" location feature.; Fixes for Feature table parsing in SeqIO embl, genbank, and swiss and changed storing of sub_species to be backwards compatible; Propagated SeqIO changes over from branch-06; Fixed a bug in species parsing once again (was re-introduced by someone propagating from the branch) :| . Similarly another change setting display_id().; Fix to Bio/SeqIO/genbank.pm read_GenBank_Species; Propagated Hilmar's SeqIO changes from main branch

Bio::SeqIO::swiss: Updated README; Fixes for Feature table parsing in SeqIO embl, genbank, and swiss and changed storing of sub_species to be backwards compatible; Small fixes in Bio::SeqIO::embl and removed duff code from Bio::SeqIO::swiss; Propagated SeqIO changes over from branch-06; Fixed a missing \ in the docu of read_FTHelper, added setting of display_id() before parse, provided initial implementation of read_FTHelper. No write of features yet.; Next_seq() was very broken, fixed it. Note that before this, entry boundaries were silently overread, with entries getting lost without notice. In addition, fixed the code added to read_FTHelper. Seems to work now, but haven't tested entire SwissProt yet.; Added code to remove trailing dot for species.; Synched Bio::Species with main branch. Fixed t/Species.t; Added test for IO::Scalar in Makefile.PL; Propagated Hilmar's SeqIO changes from main branch

Bio::Species: Corrects bug report #226. (Some functions accessed the @classification array, and some did not, and some external modules thought to be cleverer than this module. Should work now, but read the documentation of classification() for the changes that this implies. Test script added as well.); Orrects bug report #226. (Some functions accessed the @classification array, and some did not, and some external modules thought to be cleverer than this module. Should work now, but read the documentation of classification() for the changes that this implies. Test script added as well.); Fixes for Feature table parsing in SeqIO embl, genbank, and swiss and changed storing of sub_species to be backwards compatible; Propagated SeqIO changes over from branch-06; Corrected a small bug (call to subspecies(): missing underscore).; Synched Bio::Species with main branch. Fixed t/Species.t

Makefile.PL: Fixed info regarding a new web page describing external modules. Corrected the link to our external module FTP area. cdagdigian.; updated info and links to web page and FTP URL for third party external modules. cdagdigian. Also fixed this in branch-06/.; Added test for IO::Scalar in Makefile.PL; Added test for IO::Scalar in Makefile.PL

scripts/bpfetch.pl: Changed scripts/bpfetch.pl to check for Bio::DB::RandomAccessI compliance instead of Bio::DB::BioSeqI compliance; Fixes in Bio::Index::Abstract scripts/bpfetch.pl and t/Index.t