Core 0.5.0 0.5.1 delta

These are detailed notes on changes made between release-0-05 and release-0-05-1.

Bio::AnnSeq

Added AnnSeq, SeqFeatureI, generics stuff

Added in EMBL parsing and stuff

Bio::AnnSeqI

Added AnnSeq, SeqFeatureI, generics stuff

Added in EMBL parsing and stuff

Bio::Annotation

Added in annotation stuff

Bio::RangeI

Added in EMBL parsing and stuff

Bio::Root::Object

Fixed uninitialized error in _display_stats() as suggested by Jason Stewart in PR#49

Bio::Search::Hit::Fasta

Initiation of the Search/ morass err project.

Processor for Fasta is now 98% functional!

Bio::Search::Hit::HitI

Initiation of the Search/ morass err project.

Try #2

Bio::Search::Processor

Initiation of the Search/ morass err project.

Processor for Fasta is now 98% functional!

Bio::Search::Result::Fasta

Initiation of the Search/ morass err project.

Processor for Fasta is now 98% functional!

Bio::Search::Result::ResultI

Initiation of the Search/ morass err project.

Try #2

Bio::SeqFeature::Generic

Added AnnSeq, SeqFeatureI, generics stuff

Stuff... ?

Fixes to SeqFeature

Bio::SeqFeatureI

Added AnnSeq, SeqFeatureI, generics stuff

Bio::SeqIO::EMBL

Removed extraneous DESTROY subs in SeqIO modules

Bio::SeqIO::Fasta

Updated SeqIO/Fasta.pm to deal with superfamily numbers (only if requested with the -superfamily tag set to something embodying truth. Added ScoringMatrix.pm and associated matrix files. Yee haw!

Simple little bug with sfnums fixed.

Superfamily fixup for Fasta.pm. New amino acid priors for ScoringMatrix.pm, as per Stephen Altschul

Regex fix.

Removed extraneous DESTROY subs in SeqIO modules

Bio::SeqIO::GCG

Removed extraneous DESTROY subs in SeqIO modules

Bio::SeqIO::Handler

Removed extraneous DESTROY subs in SeqIO modules

Bio::SeqIO::PIR

Updated SeqIO/Fasta.pm to deal with superfamily numbers (only if requested with the -superfamily tag set to something embodying truth. Added ScoringMatrix.pm and associated matrix files. Yee haw!

Removed extraneous DESTROY subs in SeqIO modules

Bio::SeqIO::Raw

Removed extraneous DESTROY subs in SeqIO modules

Bio::SeqIO::SCF

SeqIO handler to handle chromatogram SCF files.

Added binmode $fh for Win32/Mac compatability

Removed extraneous DESTROY subs in SeqIO modules

Bio::SimpleAlign

A few new methods

Bug fix concerning addition of duplicate sequences

Bio::Tools::Blast

No longer throwing an exception for hitless reports, even if a -signif criteria was used when parsing.

Fixed the -best parsing switch as reported in PR#45

Bio::UnivAln

Edits on univaln

Makefile.PL

Added generic package handler to makefile.PL

Bumping up the require to 5.004. Bumped up release version to 0.05.1. Added note in README about which modules are 5.003 incompatible.