Core 0.4.4 0.5.0 delta

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These are detailed notes on changes made between release-0-04-4 and release-0-05.

Bio::DB::Abstract
Moved things over to BioSeqI
Bio::DB::Ace
Added in Ace stuff No edits on GenBank...
Fixed Ace.pm with lincoln
Bio::DB::BioSeqI
Moved things over to BioSeqI
Bio::DB::GenBank
Updated the socket code to trap for errors (server and otherwise), and return undef. Also added the (redundant) get_Seq_by_acc() function.
Fixed the SeqIO stuff
Split out GenPept from GenBank. Cleaned up socket code to be in a separate function (code reuse, yay) Added functions get_Stream_by_id/acc -> returns a SeqIO object when passed a reference to an array of ids/acc's.
Moved things over to BioSeqI
Added Batch Entrez support. Pretty nifty.
Bio::DB::GenPept
Split out GenPept from GenBank. Cleaned up socket code to be in a separate function (code reuse, yay) Added functions get_Stream_by_id/acc -> returns a SeqIO object when passed a reference to an array of ids/acc's.
Moved things over to BioSeqI
Docs change
Added Batch Entrez support. Pretty nifty.
Bio::Index::Abstract
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Added Fasta.pm for index Fasta flat files
Implemented selection of DB_File or SDBM_File
Added embl parser, throw exceptions on failure
Added bpfetch stuff and bpindex fixed alot of other bugs
Got index stuff to work
Fixed Makefile.PL, added more docs to Abstract.pm and SwissPfam.pm etc....
Bio::Index::EMBL
Added embl parser, throw exceptions on failure
Added bpfetch stuff and bpindex fixed alot of other bugs
Got index stuff to work
Fixed out stuff...
Bio::Index::Fasta
Added Fasta.pm for index Fasta flat files
Implemented selection of DB_File or SDBM_File
Added embl parser, throw exceptions on failure
Added bpfetch stuff and bpindex fixed alot of other bugs
Bio::Index::SwissPfam
Beefed up SimpleAlign tests for Pfam format Added swisspfam indexer and test suite
Completed implementation of fetch method
Fixed Makefile.PL, added more docs to Abstract.pm and SwissPfam.pm etc....
Bio::Root::Err
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Bio::Root::Global
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Improved handling of Newline character 'tasting' in Utilities. IOManager::read uses gzip -cd to access compressed files instead of creating/destroying temp files. Global.pm checks for ENV{NEWLINE} to allow explicit setting of newline character(s).
Taste_file() is now only performed on uncompressed files, NOT on STDIN or on filehandles produced by gzip -cd (can't seek 0 on these after tasting. Some docs added/updated.
Bio::Root::IOManager
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Improved handling of Newline character 'tasting' in Utilities. IOManager::read uses gzip -cd to access compressed files instead of creating/destroying temp files. Global.pm checks for ENV{NEWLINE} to allow explicit setting of newline character(s).
Fixed a timeout related bug in read().
Taste_file() is now only performed on uncompressed files, NOT on STDIN or on filehandles produced by gzip -cd (can't seek 0 on these after tasting. Some docs added/updated.
Bio::Root::Object
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Taste_file() is now only performed on uncompressed files, NOT on STDIN or on filehandles produced by gzip -cd (can't seek 0 on these after tasting. Some docs added/updated.
Bio::Root::Utilities
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Improved handling of Newline character 'tasting' in Utilities. IOManager::read uses gzip -cd to access compressed files instead of creating/destroying temp files. Global.pm checks for ENV{NEWLINE} to allow explicit setting of newline character(s).
Taste_file() is now only performed on uncompressed files, NOT on STDIN or on filehandles produced by gzip -cd (can't seek 0 on these after tasting. Some docs added/updated.
Bio::SearchDist
Fixed search distribution, sequence bugs and removed seqfeature
Added bpfetch stuff and bpindex fixed alot of other bugs
Bio::Seq
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Fixed search distribution, sequence bugs and removed seqfeature
Bio::SeqFeature
Fixed search distribution, sequence bugs and removed seqfeature
Bio::SeqIO
Fixed the SeqIO stuff
Bio::SeqIO::EMBL
Fixed the SeqIO stuff
Fixed $fh->eof() calls to eof $fh - now it all works with \*STDIN sorta filehandles as well as true FileHandle/IO::File typeof filehandles.
Bio::SeqIO::Fasta
Fixed the SeqIO stuff
Edited the fasta regex so that a second read on a filehandle will be accepted as well. See comments within code.
Found another hitch in Fasta's parsing logic: if there were newlines inserted between records, the slurping mechanism failed. Now we catch for blank lines and jump back to grab the first character of the nextline. This will hold for any number of blank lines (the first time I've ever had a need for a goto statement).
Had to strip out my debugging print's
Implemented a temporary buffer to store "read" characters that we didn't really want to read (yet). This works through _pushbuffer() and _popbuffer(). Result: Now we're real picky (again) about our Fasta format being in Fasta format, without changing algorithms or diddling $/.
Fixed $fh->eof() calls to eof $fh - now it all works with \*STDIN sorta filehandles as well as true FileHandle/IO::File typeof filehandles.
Bio::SeqIO::GCG
Checking in GCG.pm for the first time.
Added bpfetch stuff and bpindex fixed alot of other bugs
Fixed $fh->eof() calls to eof $fh - now it all works with \*STDIN sorta filehandles as well as true FileHandle/IO::File typeof filehandles.
Bio::SeqIO::Raw
Fixed the SeqIO stuff
inserted standard header lines at top of file
Fixed $fh->eof() calls to eof $fh - now it all works with \*STDIN sorta filehandles as well as true FileHandle/IO::File typeof filehandles.
Bio::SimpleAlign
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Small bug fixes plus two new methods (percentage_identity, read_Prodom)
Bio::Tools::Blast
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
New parsing strategy. Should solve the memory usage problems. Still needs testing.
Fixed some residual parsing bugs. Now passes all tests in t/Blast.t. Updated some docs but there is still more doc updating to do...
Fixes in Blast.pm: fixed bug that caused the ultimate hit to be missed (reported by Richard Copley). Also changed self->{'_get_stats'} to Blast->{'_get_stats'}. Touched up some docs.
Bio::Tools::Fasta
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Bio::Tools::IUPAC
Added the IUPAC.pm to Bio::Tools Its scalable, works for both nucleotide and amino acid sequences, it streams like SeqIO. What else could you want?
Fixes to IUPAC
Added AUTOLOAD subroutine to pass along calls to underlying Seq.pm object. Also now we change the desc() to tack on our uniqueness signature.
Bio::Tools::RestrictionEnzyme
Removing whitespace from enzyme name when making standard enzymes.
Bio::Tools::SeqAnal
Minor changes
Bio::Tools::Sigcleave
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Bio::Tools::WWW
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Bio::Tools::pSW
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Added bpfetch stuff and bpindex fixed alot of other bugs
Bio::UnivAln
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Makefile.PL
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
Added check for LWP in Makefile.PL. Updated version number to 0.05
Fixed Makefile.PL, added more docs to Abstract.pm and SwissPfam.pm etc....
Added AcePerl support
bioback.pod
Added in back end dos
Got index stuff to work
bioperl.pod
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
examples/psw.pl
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
examples/rev_and_trans.pl
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
examples/seq_pattern.pl
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
examples/simplealign.pl
Merged release-0-04-bug with the trunk. All test successful. Still need to add back Sigcleave files.
scripts/bpfetch.pl
Added bpfetch stuff and bpindex fixed alot of other bugs
Added swisspfam stuff to manifest and added more comments to bpfetch.pl
Got index stuff to work
Extended bpfetch to cope with acedb databases as well
Minor change
scripts/bpindex.pl
Added bpfetch stuff and bpindex fixed alot of other bugs
Fixed Makefile.PL, added more docs to Abstract.pm and SwissPfam.pm etc....
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