Module:Bio::SeqFeature::Annotated
From BioPerl
| Pdoc documentation: Bio::SeqFeature::Annotated | CPAN documentation: Bio::SeqFeature::Annotated |
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A Bio::SeqFeature::TypedSeqFeatureI experimental implementation which is strongly type-checked against the latest Sequence Ontology. All added data are stored as Bio::AnnotationI in a Bio::Annotation::Collection, as Bio::SeqFeature::Annotated in subfeatures, or in a Bio::LocationI (which is accessible through the Bio::RangeI interface).
There are several problems with the current implementation which should be addressed by the next BioPerl release:
- Rectify Bio::SeqFeature::TypedSeqFeatureI interface methods, possibly add several other helper methods. See this post.
- Ensure all methods comply with Bio::SeqFeatureI interface, in that methods specified in the interface which accept and return scalar values do not return other things (objects).
- Adding typed tag data as Bio::AnnotationI will require using the Bio::AnnotatableI and Bio::AnnotationCollectionI interfaces.
- Do we want optional checking of type? This has been requested...
As a separate question: do we want alternative, lightweight Bio::SeqFeature::TypedSeqFeatureI implementations? This implementation has been suggested as being being unnecessarily heavy (with everything as an object); alternative suggestions have included using Data::Stag or an XML-like tagging system.
