=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut

package XrefMapper::anopheles_gambiae;

use  XrefMapper::BasicMapper;
use  XrefMapper::VBCoordinateMapper;

use vars '@ISA';

@ISA = qw{ XrefMapper::BasicMapper };



sub set_methods{
 
  my $default_method = 'ExonerateGappedBest1_55_perc_id';
  my %override_method_for_source = (  
	   ExonerateGappedBest5_55_perc_id => ['RefSeq_mRNA','RefSeq_mRNA_predicted', 'RefSeq_ncRNA', 'RefSeq_ncRNA_predicted' ],
         );

  return $default_method, \%override_method_for_source;
}



# transcript, gene display_xrefs can use defaults
# since anopheles_symbol is "before" Uniprot

# If there is an Anopheles_symbol xref, use its description

# mh4 says Anopheles_symbol doesn't get chosen over UniP
# (but they do get chosen in other cases)

sub gene_description_sources {

  return ("VB_Community_Annotation",
	  "Uniprot/SWISSPROT",
	  "VB_RNA_Description",
          );
}

sub transcript_display_xref_sources {

  my @list = qw(
		VB_Community_Annotation
		Uniprot/SWISSPROT
		VB_RNA_Description
	       );

  my %ignore;
  return [\@list,\%ignore];

}

# regexps to match any descriptons we want to filter out
sub gene_description_filter_regexps {

  return ();

}

1;