GitLab

Formatting of SYNOPSIS code.

Passes unit tests.

  - Use defined() in if-statements.
  - Properly quote the $hit_name in the SQL.

argument $pid is not defined, even though it isn't and even though $pid
is optional.  Fixed.

that does not exist.  Fixed.

   Arg [1]    : Bio::EnsEMBL::Slice $slice
                The slice from which to obtain align features.
   Arg [2]    : String $external_db_name
                Name of the external DB to which the align features
                should be restricted.
   Arg [3]    : (optional) string $logic_name
                The logic name of the type of features to obtain.
   Example    : @feats =
                 $adaptor->fetch_all_by_Slice_and_external_db( $slice, 'EMBL' );
   Description: Returns a listref of features created from the
                database which are on the Slice $slice and associated
                with external DB $external_db_name.  If logic name
                is defined, only features with an analysis of type
                $logic_name will be returned.
   Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
                in Slice coordinates
   Exceptions : thrown if $external_db_name is not defined or if
                the subclass does not return a table alias for the
                external_db table from _tables()
   Caller     : general
   Status     : At Risk


Also change one occurance of the word "PepAlignFeatureAdaptor" to
"ProteinAlignFeatureAdaptor".

Formatting of method documentation.

modified execute calls to make compatible with other databases. Need to use bind_param first, with the type of the parameter, and execute later

fixes RepeatFeatureAdaptor::fetch_by_dbID

and in Slice to make more consistant.

-'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)

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