Core 0.4.3 0.4.4 delta

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These are detailed notes on changes made between release-0-04-3 and release-0-04-4.

Bio::DB::Abstract
Added the GenBank.pm DB module for retrieving nucleotide and protein sequences from GenBank (uses Tools::WWW and LWP:Simple qw(get)) and currently returns a Seq object (perhaps an EMBL-SeqIO parsed Entry/?? object soon).
Removed AutoLoader usage.
Bio::DB::GenBank
This is the GenBank.pm module, uses Bio::Tools::WWW and LWP::Simple qw(get) to retrieve nucleotide/protein entries (in genbank format) from GenBank, via Entrez. Returns a Seq object.
Removed AutoLoader usage.
Overhauled a bit to use IO::Socket instead of LWP and Bio::SeqIO instead of Seq->parse_genbank(). Probably not functional yet.
Getting things to work still using IO::Socket. Perhaps painfully.
Added documentation. Yee haw.
Made a small fix to SeqIO::Fasta.pm - it was grabbing the next character from the filehandle (getc($fh)) and checking to see if it's a '>' (if so, quit), and if not, just add it willy nilly to the sequence. However, it's possible that this character is neither '>' nor /\w/ (like if its a space or newline or such). In this case, we shouldn't add it. And now DB::GenBank.pm works ducky.
Bio::Index::Abstract
Better lisp added index/abstract.pm
Bio::Root::Global
Added NEWLINE global. Changed default timeout to 20 seconds.
Changes for the 0.04.4 release (see the Changes file in the central distribution).
Declaring TIMEOUT_SECS to avoid warnings with -w (only with 5.003).
Bio::Root::IOManager
Added NEWLINE global. Changed default timeout to 20 seconds.
Changes for the 0.04.4 release (see the Changes file in the central distribution).
Bumped up VERSION number and moved modification notes to bottom of file.
Bio::Root::Object
Changes for the 0.04.4 release (see the Changes file in the central distribution).
Bio::Root::Utilities
Added NEWLINE global. Changed default timeout to 20 seconds.
Changes for the 0.04.4 release (see the Changes file in the central distribution).
Declaring $buffer in taste_file() to prevent uninitialized warning (5.003 only).
Bio::SearchDist
Added in SeqFeature
Bio::Seq
Added parse_genbank to deal with individual sequence files coming from an Entrez query.
Fixed type() so that it always returns a string and no longer stores an uninformative 'unknown' string.
Bio::SeqFeature
Moved SeqFeature down one, added in EMBL.pm
Bio::SeqIO
Added in SeqIO system
Changed SeqIO stuff for new mechanism
Added in test suite for seqio, fixed things to work ;)
Fixed docs
Bio::SeqIO::EMBL
Moved SeqFeature down one, added in EMBL.pm
Added in test suite for seqio, fixed things to work ;)
Bio::SeqIO::Fasta
Added in SeqIO system
Changed SeqIO stuff for new mechanism
Added in test suite for seqio, fixed things to work ;)
Made a small fix to SeqIO::Fasta.pm - it was grabbing the next character from the filehandle (getc($fh)) and checking to see if it's a '>' (if so, quit), and if not, just add it willy nilly to the sequence. However, it's possible that this character is neither '>' nor /\w/ (like if its a space or newline or such). In this case, we shouldn't add it. And now DB::GenBank.pm works ducky.
Changed $c =~ /[\n\l\r\f\s]/ to $c =~ /\W/ - no big deal.
Fixed up uc($c)
Bio::SeqIO::Handler
Added in SeqIO system
Changed SeqIO stuff for new mechanism
Added in test suite for seqio, fixed things to work ;)
Bio::SeqIO::Raw
First commit of SeqIO::Raw.pm basically it is SeqIO::Fasta.pm with a few trivial modifications.
Bio::SimpleAlign
Fixed a write_fasta bug and beefed up the test suite thingy
Added RCS Id tag.
Bio::Tools::Blast
Minor formatting of docs
Fixed a variety of bugs the most glaring of which was in postclient.pl. See the CHANGES file for Blast version 0.075 in the bioperl 0.04.4 release.
Bio::Tools::Fasta
Fixed bug regarding call to the former Util->get_newline_char and fixed num_seqs().
Makefile.PL
Updating for 0.04.4
SeqFeature.pm
Added in SeqFeature
Moved SeqFeature down one, added in EMBL.pm
bioperl.lisp
Better lisp added index/abstract.pm
examples/psw.pl
Fixed bugs in the blast examples and in root_object/utilities.pl. Added RCS revision line (Id) and changed shebang lines to /usr/bin/perl (more standard).
examples/rev_and_trans.pl
Fixed bugs in the blast examples and in root_object/utilities.pl. Added RCS revision line (Id) and changed shebang lines to /usr/bin/perl (more standard).
examples/seq_pattern.pl
Fixed bugs in the blast examples and in root_object/utilities.pl. Added RCS revision line (Id) and changed shebang lines to /usr/bin/perl (more standard).
examples/simplealign.pl
Fixed bugs in the blast examples and in root_object/utilities.pl. Added RCS revision line (Id) and changed shebang lines to /usr/bin/perl (more standard).
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