=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


=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

=cut

=head1 NAME

Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric - default Ensembl
InternalIdMapper implementation for genes

=head1 SYNOPSIS

=head1 DESCRIPTION

=head1 METHODS

=cut

package Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric;

use strict;
use warnings;
no warnings 'uninitialized';

use Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper;
our @ISA = qw(Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper);

use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);


#
# basic mapping
#
sub init_basic {
  my $self = shift;
  my $num = shift;
  my $gsb = shift;
  my $mappings = shift;
  my $gene_scores = shift;

  $self->logger->info("Basic gene mapping...\n", 0, 'stamped');

  $mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
  $num++;
  my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $mappings,
    "gene_matrix$num");

  return ($new_scores, $mappings);
}


#
# build the synteny from unambiguous mappings
#
sub synteny {
  my $self = shift;
  my $num = shift;
  my $gsb = shift;
  my $mappings = shift;
  my $gene_scores = shift;

  unless ($gene_scores->loaded) {
    $self->logger->info("Synteny Framework building...\n", 0, 'stamped');
    my $dump_path = path_append($self->conf->param('basedir'), 'mapping');
    my $sf = Bio::EnsEMBL::IdMapping::SyntenyFramework->new(
      -DUMP_PATH    => $dump_path,
      -CACHE_FILE   => 'synteny_framework.ser',
      -LOGGER       => $self->logger,
      -CONF         => $self->conf,
      -CACHE        => $self->cache,
    );
    $sf->build_synteny($mappings);

    # use it to rescore the genes
    $self->logger->info("\nSynteny assisted mapping...\n", 0, 'stamped');
    $gene_scores = $sf->rescore_gene_matrix_lsf($gene_scores);

    # checkpoint
    $gene_scores->write_to_file;
  }

  my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
  $num++;
  my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
    "gene_matrix$num");

  return ($new_scores, $new_mappings); 
}


#
# rescore with simple scoring function and try again
#
sub best_transcript {
  my $self = shift;
  my $num = shift;
  my $gsb = shift;
  my $mappings = shift;
  my $gene_scores = shift;
  my $transcript_scores = shift;

  $self->logger->info("Retry with simple best transcript score...\n", 0, 'stamped');
  
  unless ($gene_scores->loaded) {
    $gsb->simple_gene_rescore($gene_scores, $transcript_scores);
    $gene_scores->write_to_file;
  }
  
  my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
  $num++;
  my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
    "gene_matrix$num");

  return ($new_scores, $new_mappings); 
}


#
# rescore by penalising scores between genes with different biotypes  
#
sub biotype {
  my $self = shift;
  my $num = shift;
  my $gsb = shift;
  my $mappings = shift;
  my $gene_scores = shift;

  $self->logger->info("Retry with biotype disambiguation...\n", 0, 'stamped');
  
  unless ($gene_scores->loaded) {
    $gsb->biotype_gene_rescore($gene_scores);
    $gene_scores->write_to_file;
  }

  my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
  $num++;
  my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
    "gene_matrix$num");

  return ($new_scores, $new_mappings); 
}

sub location {
  my $self = shift;
  my $num = shift;
  my $gsb = shift;
  my $mappings = shift;
  my $gene_scores = shift;

  $self->logger->info("Retry with location disambiguation...\n", 0, 'stamped');

  unless ($gene_scores->loaded) {
    $gsb->location_gene_rescore($gene_scores);
    $gene_scores->write_to_file;
  }

  my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
  $num++;
  my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
    "gene_matrix$num");

  return ($new_scores, $new_mappings);

}


#
# selectively rescore by penalising scores between genes with different
# internalIDs  
#
sub internal_id {
  my $self = shift;
  my $num = shift;
  my $gsb = shift;
  my $mappings = shift;
  my $gene_scores = shift;

  $self->logger->info("Retry with internalID disambiguation...\n", 0, 'stamped');
  
  unless ($gene_scores->loaded) {
    $gsb->internal_id_rescore($gene_scores);
    $gene_scores->write_to_file;
  }

  my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
  $num++;
  my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
    "gene_matrix$num");

  return ($new_scores, $new_mappings); 
}


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