[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Allen Day allenday at ucla.edu
Fri Nov 19 17:50:33 EST 2004

For those of you not on the guts list and interested in the reorganization 
of Bio::SeqFeatureI and Bio::AnnotationCollectionI that is happening, here 
are the CVS commit notes from today.

updated Bio::AnnotationCollection to implement *_tag_* methods with
deprecation warning.  these were taken from Bio::SeqFeatureI and
Bio::SeqFeature::Generic.  *_tag_* methods in Bio::SeqFeature::Annotated
are now implemented by explicit pasthru to the conttained
Bio::Annotation::Collection instance.
changes to Bio::AnnotationCollectionI and Bio::SeqFeatureI.

* Bio::SeqFeatureI now ISA Bio::AnnotationCollectionI
* All Bio::SeqFeatureI *_tag_* methods have been moved to
  Bio::AnnotationCollectionI, marked as deprecated, and mapped to their
  analogous and mostly pre-existing Bio::AnnotationCollectionI methods.

  Methods which were not in Bio::AnnotationCollectionI, but were i
  Bio::Annotation::Collection and were necessary for *_tag_* method 
  remapping were created in Bio::AnnotationCollecitonI.

* Bio::RangeI and Bio::AnnotationCollectionI method documentation removed
  from Bio::SeqFeatureI, and replaced with a link to the interface class
  inherited from.  This reduces documentation maintenance overhead.


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