GitLab

fixes RepeatFeatureAdaptor::fetch_by_dbID

where all my transcripts were disappearing to.

I'm assuming it still works for slices.  I don't have slice tests yet.

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

PredictionTranscriptAdaptor was creating RawContigs without going through adaptor creating unnecessary db accesses (object identity was not maintained).  SeqFeature was retrieving contig attributes from the database when they weren't needed

    fetch_by_contig_id(int) -> fetch_by_Contig(RawContig)
  store(int, list of Features) -> store(list of Features with attached contigs)

un-deprecated GeneAdaptor->get_description which should not have been deprecated in first place (oops).
Added more PODs

AnalysisAdaptor - logic_name must be unique so fetch_by_logic_name now only returns one analysis object
DnaAlignFeatureAdaptor - formatting print statements etc
ProteinAlignFeatureAdaptor - Now follows the same format as DnaAlignFeatureAdaptor, has methods to fetch by contig, slice and assembly location and when constrainted by score
or percent id all methods can take an optional type which is logic name
RepeatFeatureAdaptor
PredictionTranscriptAdaptor all have methods which fetch by slice, contig_id and assembly location and each method has optional type which should be logic_name
SimpleFeatureAdaptor

minor bug fixes and addition of method to get things by logic name in case Fgenesh is being run at teh same time as genscan

Not much gain to see so far, all alignments look ungapped.
Probably still buggy.

Adaptor to store in db and retrieve.