Bio::EnsEMBL::IdMapping::InternalIdMapper EnsemblExonGeneric
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Summary
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper
Synopsis
Description
Methods
init_basic
No description
Code
mapped_transcript
No description
Code
Methods description
None available.
Methods code
init_basicdescriptionprevnextTop
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
#
}
mapped_transcriptdescriptionprevnextTop
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;
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.