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  • Andreas Kusalananda Kähäri's avatar
    Add the method fetch_all_by_Slice_and_external_db(): · 1da5d7e7
    Andreas Kusalananda Kähäri authored
       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