- Bio::DB::Das::ChadoIterator in lib/Bio/DB/Das/Chado.pm
Changes for version 0.24
- made the srcfeature method always return something; it no longer depends on the call to the constructor to set it.
- Made using organism information more robust; now checks abbreviation and "genus species", and if it fails at everything, throws an error.
- Added an option to the Chado constructor called -reference_class that allows the user to specify what feature type_id to use as the srcfeature. For example, if you have motifs mapped to a polypeptide and that polypeptide mapped to a region, you can speicify either "region" or "polypeptide" for the reference_class. Note that this does not automatically turn on recursive mapping, so by default, the motifs wouldn't be visible on the region. I honestly don't know for sure if recursive mapping still works--I haven't tested it in a long time.
- Fixed a bug that sometimes prevented GBrowse from finding the subfeatures of features (like mRNAs of genes couldn't be found).