Raw content of Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 METHODS
=cut
package Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric;
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);
#
# basic mapping
#
sub init_basic {
my $self = shift;
my $num = shift;
my $esb = shift;
my $mappings = shift;
my $exon_scores = shift;
$self->logger->info("Basic exon mapping...\n", 0, 'stamped');
$mappings = $self->basic_mapping($exon_scores, "exon_mappings$num");
$num++;
my $new_scores = $esb->create_shrinked_matrix($exon_scores, $mappings,
"exon_matrix$num");
return ($new_scores, $mappings);
}
#
# reduce score for mappings of exons which do not belong to mapped
# transcripts
#
sub mapped_transcript {
my $self = shift;
my $num = shift;
my $esb = shift;
my $mappings = shift;
my $exon_scores = shift;
$self->logger->info("Exons in mapped transcript...\n", 0, 'stamped');
unless ($exon_scores->loaded) {
$esb->non_mapped_transcript_rescore($exon_scores, $mappings);
$exon_scores->write_to_file;
}
$mappings = $self->basic_mapping($exon_scores, "exon_mappings$num");
$num++;
my $new_scores = $esb->create_shrinked_matrix($exon_scores, $mappings,
"exon_matrix$num");
return ($new_scores, $mappings);
}
1;
]]>