anopheles_gambiae.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
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;