my $self = shift;
  my $matrix = shift;
  my $exon_matrix = shift;

  unless ($matrix and
          $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a transcript Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }
  
  unless ($exon_matrix and
          $exon_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a exon Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }

  # first find out which source and target transcripts have scoring exons and
  # build a "flag" matrix for these transcripts (all scores are 1)
  $self->flag_matrix_from_exon_scores($matrix, $exon_matrix);

  # now calculate the actual scores for the transcripts in the flag matrix
  my $final_matrix =
    $self->score_matrix_from_flag_matrix($matrix, $exon_matrix);
  
  return $final_matrix;

  my $self = shift;
  my $matrix = shift;

  unless ($matrix and
          $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }

  my $i = 0;

  foreach my $entry (sort { $b->score <=> $a->score }
                      @{ $matrix->get_all_Entries }) {

    # we only do this for perfect matches, i.e. transcript score == 1
    last if ($entry->score < 1);

    my $source_tl = $self->cache->get_by_key('transcripts_by_id',
      'source', $entry->source)->translation;
    my $target_tl = $self->cache->get_by_key('transcripts_by_id',
      'target', $entry->target)->translation;

    # no penalty if both transcripts have no translation
    next if (!$source_tl and !$target_tl);

    if (!$source_tl or !$target_tl or
        ($source_tl->seq ne $target_tl->seq)) {
      # set score to a value less than 1
      $matrix->set_score($entry->source, $entry->target, 0.98);
      $i++;
    }
    
  }

  $self->logger->debug("Non-perfect translations on perfect transcripts: $i\n", 1);

  my $self = shift;
  my $matrix = shift;
  my $exon_matrix = shift;

  # initialise progress logger
  my $i;
  my $num_transcripts =
    scalar(keys %{ $self->cache->get_by_name('transcripts_by_id', 'source') });
  my $progress_id = $self->logger->init_progress($num_transcripts, 100);

  $self->logger->info("Creating flag matrix...\n", 1);

  # loop over source transcripts
  foreach my $source_transcript (values %{ $self->cache->get_by_name('transcripts_by_id', 'source') }) {
    
    # log progress
    $self->logger->log_progress($progress_id, ++$i, 1);

    # get all exons for the source transcript
    foreach my $source_exon (@{ $source_transcript->get_all_Exons }) {

      # get target exons for this source exon from scoring matrix
      foreach my $target_exon_id (@{ $exon_matrix->get_targets_for_source($source_exon->id) }) {

        # get target transcripts that contain this exon
        foreach my $target_transcript (@{ $self->cache->get_by_key('transcripts_by_exon_id', 'target', $target_exon_id) }) {
          
          # add scoring flag for these two transcripts
          $matrix->add_score($source_transcript->id, $target_transcript->id, 1);
          
        }
      }
    }
  }

  $self->logger->info("\n");

  return $matrix;

  my $self = shift;
  my $matrix = shift;
  my $gene_mappings = shift;

  # argument checks
  unless ($matrix and
      $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a transcript Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }

  unless ($gene_mappings and
          $gene_mappings->isa('Bio::EnsEMBL::IdMapping::MappingList')) {
    throw('Need a gene Bio::EnsEMBL::IdMapping::MappingList.');
  }

  # create of lookup hash of mapped source genes to target genes
  my %gene_lookup = map { $_->source => $_->target }
    @{ $gene_mappings->get_all_Entries };

  my $i = 0;

  foreach my $entry (@{ $matrix->get_all_Entries }) {

    my $source_gene = $self->cache->get_by_key('genes_by_transcript_id',
      'source', $entry->source);
    my $target_gene = $self->cache->get_by_key('genes_by_transcript_id',
      'target', $entry->target);

    my $mapped_target = $gene_lookup{$source_gene->id};

    if (!$mapped_target or ($mapped_target != $target_gene->id)) {
      $matrix->set_score($entry->source, $entry->target, ($entry->score * 0.8));
      $i++;
    }
  }

  $self->logger->debug("Scored transcripts in non-mapped genes: $i\n", 1);
}

  
1;

  my $self = shift;
  my $flag_matrix = shift;
  my $exon_matrix = shift;

  unless ($flag_matrix and
          $flag_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a transcript Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }
  
  unless ($exon_matrix and
          $exon_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need an exon Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }

  my $transcript_score_threshold =
    $self->conf->param('transcript_score_threshold') || 0;

  # create a new scoring matrix which will replace the flag matrix
  my $matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
    -DUMP_PATH   => $flag_matrix->dump_path,
    -CACHE_FILE  => $flag_matrix->cache_file_name,
  );

  # initialise progress logger
  my $i;
  my $num_transcripts =
    scalar(keys %{ $self->cache->get_by_name('transcripts_by_id', 'source') });
  my $progress_id = $self->logger->init_progress($num_transcripts, 100);

  $self->logger->info("Creating score matrix from flag matrix...\n", 1);

  # debug
  my $fmt_d1 = "%-14s%-15s%-14s%-14s%-14s\n";
  my $fmt_d2 = "%.6f";
  
  # loop over source transcripts
  foreach my $source_transcript (values %{ $self->cache->get_by_name('transcripts_by_id', 'source') }) {
    
    # log progress
    $self->logger->log_progress($progress_id, ++$i, 1);

    # We are only interested in scoring with exons that are in the target
    # transcript. The ScoredMappingMatrix may contain scores for exons that
    # aren't in this transcript so create a hash of the target transcript's
    # exons
    my %source_exons = map { $_->id => 1 }
      @{ $source_transcript->get_all_Exons };

    my $source_transcript_length = $source_transcript->length;

    # get all corresponding target transcripts from the flag matrix
    foreach my $target_transcript_id (@{ $flag_matrix->get_targets_for_source($source_transcript->id) }) {
      
      my $target_transcript = $self->cache->get_by_key('transcripts_by_id', 'target', $target_transcript_id);

      my $source_transcript_score = 0;
      my $target_transcript_score = 0;
      my $target_transcript_length = $target_transcript->length;

      my %target_exons = map { $_->id => 1 }
        @{ $target_transcript->get_all_Exons };

      # now loop over source exons and find the highest scoring target exon
      # belonging to the target transcript
      
      foreach my $source_exon (@{ $source_transcript->get_all_Exons }) {

        my $max_source_score = -1;
        
        foreach my $target_exon_id (@{ $exon_matrix->get_targets_for_source($source_exon->id) }) {

          next unless ($target_exons{$target_exon_id});

          my $score = $exon_matrix->get_score($source_exon->id,
            $target_exon_id);
          $max_source_score = $score if ($score > $max_source_score);
        }

        if ($max_source_score > 0) {
          $source_transcript_score += ($max_source_score * $source_exon->length);

        }
      }

      # now do the same for target exons
      
      foreach my $target_exon (@{ $target_transcript->get_all_Exons }) {

        my $max_target_score = -1;
        
        foreach my $source_exon_id (@{ $exon_matrix->get_sources_for_target($target_exon->id) }) {

          next unless ($source_exons{$source_exon_id});

          my $score = $exon_matrix->get_score(
            $source_exon_id, $target_exon->id);
          $max_target_score = $score if ($score > $max_target_score);
        }

        if ($max_target_score > 0) {
          $target_transcript_score += ($max_target_score * $target_exon->length);

        }
      }

      #
      # calculate transcript score and add to scoring matrix
      #
      if (($source_transcript_length + $target_transcript_length) > 0) {

        # sanity check
        if (($source_transcript_score > $source_transcript_length) or
            ($target_transcript_score > $target_transcript_length)) {

          $self->logger->warning("Score > length for source ($source_transcript_score <> $source_transcript_length) or target ($target_transcript_score <> $target_transcript_length).\n", 1);

        } else {

  my $self = shift;
  my $exon_matrix = shift;

  unless ($exon_matrix and
          $exon_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }

  $self->logger->info("-- Scoring transcripts...\n\n", 0, 'stamped');

  # build scores based on exon scores
  my $matrix = $self->scores_from_exon_scores($exon_matrix);

  # debug logging
  if ($self->logger->loglevel eq 'debug') {
    $matrix->log('transcript', $self->conf->param('basedir'));
  }

  # log stats of combined matrix
  my $fmt = "%-40s%10.0f\n";

  $self->logger->info("Scoring matrix:\n");

  $self->logger->info(sprintf($fmt, "Total source transcripts:",
    $self->cache->get_count_by_name('transcripts_by_id', 'source')), 1);

  $self->logger->info(sprintf($fmt, "Total target transcripts:",
    $self->cache->get_count_by_name('transcripts_by_id', 'target')), 1);

  $self->log_matrix_stats($matrix);
  
  $self->logger->info("\nDone with transcript scoring.\n\n");

  return $matrix;

  my $self = shift;
  my $exon_matrix = shift;

  unless ($exon_matrix and
          $exon_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }
  
  my $dump_path = path_append($self->conf->param('basedir'), 'matrix');
  
  my $matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
    -DUMP_PATH   => $dump_path,
    -CACHE_FILE  => 'transcript_matrix.ser',
  );

  my $transcript_cache = $matrix->cache_file;

  if (-s $transcript_cache) {
    
    # read from file
    $self->logger->info("Reading transcript scoring matrix from file...\n", 0, 'stamped');
    $self->logger->debug("Cache file $transcript_cache.\n", 1);
    $matrix->read_from_file;
    $self->logger->info("Done.\n\n", 0, 'stamped');
    
  } else {
    
    # build scoring matrix
    $self->logger->info("No transcript scoring matrix found. Will build new one.\n");

    $self->logger->info("Transcript scoring...\n", 0, 'stamped');
    $matrix = $self->build_scores($matrix, $exon_matrix);
    $self->logger->info("Done.\n\n", 0, 'stamped');

    # write scoring matrix to file
    $matrix->write_to_file;

  }

  return $matrix;

  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

  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>.