Raw content of Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric =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;