GitLab

Refactored PredictionTranscriptAdaptor to inherit from BaseAlignFeature (and fixed some bugs)
Altered RepeatFeatureAdaptor slightly for changed BaseAlignFeature implementation

StickyExon now handles negative strand slices (forgot to add this before), renamed StickyExon::each_component_Exon to get_all_component_Exons

fixed genes calls - and added deprecated warnings, change get KBs calls to get_all_KBs, minor fixes to DAS code

     $str = substr($str, $start -1, $end -1);
to
     $str = substr($str, $start -1, $end - $start + 1);

add_supporting_features - before supporting features are added a check is made whether they are from the same contig.

RepeatFeatureAdaptor - only one match returned.  (I think I stomped on Arne's fix here
all ok now)

Exon - checks phase is defined before comparison
PredictionTranscript - checks phase is defined.  Commented out LOG print statements
TranscriptFactory - start_exon end_exon same old thang
ExonAdaptor - hmm.

Updates so slices can handle negative strand, not finished yet, and not tested

method name changes and list to listref stuff

Removed an annoying ! from Slice
Removed duplicate declaration in Geneadaptor

Translation and TranslationAdaptor start_exon and end_exon to start_Exon and end_Exon

DBEntryAdaptor check to see if gene has a stable id before trying to used it to get info

Mapper - whitespace
Slice  - whitespace
Transcript - fetch_by_transcript to fetch_by_Transcript
AssemblyMapperAdaptor - debug line
CloneAdaptor - $clone->get_all_Contigs to @{$cone->get_all_Contigs}
DBEntryAdaptor = fetch_by_object_type  - id to $contig->dbID
ExonAdaptor - reformatting and array to arrayref for supporting_features
GeneAdaptor - fetches latest version out - need to talk with G and A about this
              each_DBLink to @$get_all_DBLinks
              get_all_Exons to array ref
              get_all_Transcripts to array ref
RawContigAdaptor - fetch_all_names
SupportingFeatureAdaptor - reformat
TranscriptAdaptor - lots of arrays to array refs