GitLab

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

and in Slice to make more consistant.

Sped up general feature creation a bit more

-Sped up general feature retrieval a little bit

-'Flatening' FeaturePair object so that it no longer contains 2 SeqFeatures; It is now isa SeqFeature with some additional Hit attributes (object still bhaves as if it contained two features
-Adding 'fast' constructors to DnaDnaAlignFeatures and PepDnaAlignFeatures
-Some other minor tweaks such as using bind columns instead of fetchrow_hashref

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

more POD writing for ChromosomeAdaptor and BaseFeatureAdaptor\ deprecated landmark_MarkerFeature methods in ChromosomeAdaptor, Slice should be used instead

BaseFeatureAdaptor was returning list when it should have been returning scalar - fixed.  Added dbID to SimpleFeature, dbID of DnaDnaAlignFeatures and PepDnaAlignFeatures now set by their respective feature adaptors upon retrieval from the database

DBAdaptor now allows for attached EST database

Moved generic FeatureAdaptor functions from BaseAlignFeatureAdaptor to BaseFeatureAdaptor, SimpleFeatureAdaptor and AlignFeatureAdaptor now extend BaseFeatureAdaptor

updated ProteinAlignFeatureAdaptor DnaAlignFeatureAdaptor to extend new BaseAlignFeatureAdaptor thereby eliminating quite a few lines of duplicated code