Patch for release 85 adding a confident_relationship flag to the clos…

Configuration to allow alignments to be exported to GFF

Allow feature boundaries to be retrieved for DNA and protein alignments (this bit of code only appears to be called when handling circular chromosomes)

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Super-tidying commit. Eliminate unnamed statement handle, don't pass fruitless object types, add some comments, change some others, collapse some code into neater forms

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Old xref connections should not be typed by the new master xref. Generate type mappings for both sets explicitly.

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Put all object types of ensembl IDs needed for a process_dependents() call into a hash. Query that every time a type is required, instead of trusting the calling code type.

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Introduce ensembl type for new xrefs, such that the new ensembl ids object_xrefs are not required to share object type with the original master xref

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Add lookup for current xref object type for each iteration. Also syntax fixes, cleanup, and commenting.

At7 84/minor updates deprecation

 added MKG in location validation

nasty way to make versions unique

See https://github.com/Ensembl/ensembl/pull/117

Import deprecate method

Update DBEntryAdaptor.pm