Core 0.4.4 0.5.0 delta

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....