This commit was generated by cvs2svn to compensate for changes in r2,
which included commits to RCS files with non-trunk default branches.

svn path=/bioperl-live/trunk/; revision=775
 Added example script standaloneblast.pl. Also some mods to StandAloneBlast.pm and BPpsilite.pm

svn path=/bioperl-live/trunk/; revision=1629
migrated test data files to dir t/data

svn path=/bioperl-live/trunk/; revision=2324
tests for dba

svn path=/bioperl-live/trunk/; revision=4034
moving to bioperl-run

svn path=/bioperl-live/trunk/; revision=4307
initial commit of FeatureIO subsystem

svn path=/bioperl-live/trunk/; revision=8220
basic support for gff i/o

svn path=/bioperl-live/trunk/; revision=8222
this class tries to be clean of *_tag_* calls, opting to use
Bio::AnnotationCollectionI as a replacement.  we should be able to map
most of the *_tag_* calls to Bio::AnnotationCollectionI calls, but i haven't
done it yet.  currently throwing an error on *_tag_* calls.

svn path=/bioperl-live/trunk/; revision=8223
doc fix

svn path=/bioperl-live/trunk/; revision=8224
gff parser wasn't initializing IO properly

svn path=/bioperl-live/trunk/; revision=8227
added support for more canonical gff attributes.  these are represented
using Bio::Annotation::SimpleValue objects

svn path=/bioperl-live/trunk/; revision=8228
added handling of more gff3 attributes.  added test gff3 file to t/data.
will add unit tests soon.

svn path=/bioperl-live/trunk/; revision=8244
adding BED module.  write-only, and not yet tested.

http://www.genome.ucsc.edu/goldenPath/help/customTrack.html#BED

svn path=/bioperl-live/trunk/; revision=8276
added header functionality to BED writer.

svn path=/bioperl-live/trunk/; revision=8277
now writes GFF v2.5 (GTF)

svn path=/bioperl-live/trunk/; revision=8288
typo

svn path=/bioperl-live/trunk/; revision=8313
added a source() method to Bio::SeqFeature::Annotated.  updated warning
messages to state that tag* methods are deprecated

svn path=/bioperl-live/trunk/; revision=8328
added a shortcut get_Annotations() method to feature to bypass ->annotation->
middleman call.  also added nice list->scalar autoconverstion

svn path=/bioperl-live/trunk/; revision=8329
two things:
  * adding SOFA as an available ontology to DocumentRegistry.pm
  * modifying FeatureIO::gff to use SOFA to validate, and to parse Ontology_term

svn path=/bioperl-live/trunk/; revision=8336
modifications to allow url fetch of gene ontology.  this was not easy
b/c of the multiple .ontology files for each aspect.

Bio::SeqFeature::Annotated objects now instantiate Ontology_term tags
as Bio::Annotation::OntologyTerm objects, not Bio::Annotation::SimpleValue
objects (Scott!)

svn path=/bioperl-live/trunk/; revision=8381