GitLab

<ensembl-dev@ebi.ac.uk> to <dev@ensembl.org>.

Formatting of SYNOPSIS code.

Passes unit tests.

In all the feature adaptors, use either _create_feature() or
_create_feature_fast() from BaseFeatureAdaptor in _objs_from_sth() to
create features.

added order as an optional argument to list_dbIDs, mosy useful for genes and transcripts so caching is maximised

Handles a karyotype containing non-existant chromosomes.  Warns, returns no bands for non-existant chr, but no longer dies deep in BaseFeatureAdaptor

-Removed cruft file Range.pm
-Renamed Chromosome chromosome_id() method to dbID()

The only modelue with any significant changes other than that is Transcript where moltype
has been changed to alphabet due to another change in Bioperl 1.0

Changed var name for chromosome in Karyotype adaptor, which caused perl syntax error, somebody have a look, strange nobody picked it up? the variable does not get used anyway...

OK, now band caching really _does_ work on a per-chromosome basis.  Note to self - single quotes do not interpolate variables.  Oook.

Band caching now works on a per-chromosome basis, so that karyotypes are more interesting than merely being 24 copies of chromosome 1...