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 (@{ $matrix->get_all_Entries }) {

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

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

    if ($source_gene->biotype ne $target_gene->biotype) {
      #$self->logger->debug("biotype ".$entry->to_string."\n");
      $matrix->set_score($entry->source, $entry->target, ($entry->score * 0.8));
      $i++;
    }
  }
  
  $self->logger->debug("Scored genes with biotype mismatch: $i\n", 1);
}


1;

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

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

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

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

  my $self = shift;
  my $source_gene = shift;
  my $target_gene = shift;
  my $transcript_matrix = shift;

  my $source_gene_score = 0;
  my $target_gene_score = 0;
  my $source_gene_accum_length = 0; # sum of all transcript lengths
  my $target_gene_accum_length = 0; # sum of all transcript lengths

  # We are only interested in scoring with transcripts that are in the target
  # gene. The scored mapping matrix may contain scores for transcripts that
  # aren't in this gene so create a hash of the target genes's transcripts
  my %target_transcripts = map { $_->id => 1 }
    @{ $target_gene->get_all_Transcripts };
    
  # loop over source transcripts
  foreach my $source_transcript (@{ $source_gene->get_all_Transcripts }) {

    # now loop over target transcripts and find the highest scoring target
    # transcript belonging to the target gene
    my $max_source_score = -1;
    
    foreach my $target_transcript_id (@{ $transcript_matrix->get_targets_for_source($source_transcript->id) }) {

      next unless ($target_transcripts{$target_transcript_id});

      my $score = $transcript_matrix->get_score(
        $source_transcript->id, $target_transcript_id);
      $max_source_score = $score if ($score > $max_source_score);
    }

    if ($max_source_score > 0) {
      $source_gene_score += ($max_source_score * $source_transcript->length);
    }

    $source_gene_accum_length += $source_transcript->length;
  }
    
  # now do the same for target genes
  my %source_transcripts = map { $_->id => 1 }
    @{ $source_gene->get_all_Transcripts };
    
  # loop over target transcripts
  foreach my $target_transcript (@{ $target_gene->get_all_Transcripts }) {

    # now loop over source transcripts and find the highest scoring source
    # transcript belonging to the source gene
    my $max_target_score = -1;
    
    foreach my $source_transcript_id (@{ $transcript_matrix->get_sources_for_target($target_transcript->id) }) {

      next unless ($source_transcripts{$source_transcript_id});

      my $score = $transcript_matrix->get_score(
        $source_transcript_id, $target_transcript->id);
      $max_target_score = $score if ($score > $max_target_score);
    }

    if ($max_target_score > 0) {
      $target_gene_score += ($max_target_score * $target_transcript->length);
    }

    $target_gene_accum_length += $target_transcript->length;
  }

  # calculate overall score for this gene
  my $gene_score = 0;

  if (($source_gene_accum_length + $target_gene_accum_length) > 0) {

    $gene_score = ($source_gene_score + $target_gene_score) /
                  ($source_gene_accum_length + $target_gene_accum_length);

  } else {
  
    $self->logger->warning("Combined transcript length of source (".$source_gene->id.") and target (".$target_gene->id.") gene is zero!\n", 1);
  
  }

  if ($gene_score > 1) {
    $self->logger->warning("Illegal gene score: $gene_score (".
      join("|", $source_gene_score, $target_gene_score,
           $source_gene_accum_length, $target_gene_accum_length).")\n", 1);
  }

  return $gene_score;
}


#
# Simplified scoring for genes. Score is best scoring transcript pair.
# This is used when the more elaborate gene representing score does not
# distinguish very well.
#

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

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

  # initialise progress logger
  my $i;
  my $num_entries = $transcript_matrix->get_entry_count;
  my $progress_id = $self->logger->init_progress($num_entries, 100);
  
  $self->logger->info("Creating flag matrix...\n", 1);

  # for every transcript scoring matrix entry, make an entry in the gene flag
  # matrix.
  foreach my $entry (@{ $transcript_matrix->get_all_Entries }) {

    $self->logger->log_progress($progress_id, ++$i, 1);

    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);

    $matrix->add_score($source_gene->id, $target_gene->id, 1);
  }

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

  return $matrix;

  my $self = shift;
  my $transcript_matrix = shift;

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

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

  # build scores based on transcript scores
  my $matrix = $self->scores_from_transcript_scores($transcript_matrix);

  # debug logging
  if ($self->logger->loglevel eq 'debug') {
    $matrix->log('gene', $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 genes:",
    $self->cache->get_count_by_name('genes_by_id', 'source')), 1);

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

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

  return $matrix;

  my $self = shift;
  my $flag_matrix = shift;
  my $transcript_matrix = shift;
  my $simple_scoring = shift;

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

  # 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_entries = $flag_matrix->get_entry_count;
  my $progress_id = $self->logger->init_progress($num_entries, 100);
  
  $self->logger->info("Creating score matrix from flag matrix...\n", 1);

  # loop over flag matrix and do proper scoring for each entry
  foreach my $entry (@{ $flag_matrix->get_all_Entries }) {
    
    $self->logger->log_progress($progress_id, ++$i, 1);

    my $score = 0;
    my $source_gene = $self->cache->get_by_key('genes_by_id', 'source',
      $entry->source);
    my $target_gene = $self->cache->get_by_key('genes_by_id', 'target',
      $entry->target);

    if ($simple_scoring) {
    
      # simple scoring (used for rescoring purposes)
      $score = $self->simple_gene_gene_score($source_gene, $target_gene,
        $transcript_matrix);
    
    } else {

      # full scoring
      $score = $self->complex_gene_gene_score($source_gene, $target_gene,
        $transcript_matrix);
    }

    $matrix->add_score($entry->source, $entry->target, $score);
  }

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

  return $matrix;

  my $self = shift;
  my $transcript_matrix = shift;

  unless ($transcript_matrix and
          $transcript_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  => 'gene_matrix.ser',
  );

  my $gene_cache = $matrix->cache_file;

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

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

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

  }

  return $matrix;

  my $self = shift;
  my $source_gene = shift;
  my $target_gene = shift;
  my $transcript_matrix = shift;

  my $gene_score = 0;

  foreach my $source_transcript (@{ $source_gene->get_all_Transcripts }) {
    foreach my $target_transcript (@{ $target_gene->get_all_Transcripts }) {
      
      my $score = $transcript_matrix->get_score($source_transcript->id,
        $target_transcript->id);

      $gene_score = $score if ($score > $gene_score);
    }
  }

  return $gene_score;

  my $self = shift;
  my $gene_matrix = shift;
  my $transcript_matrix = shift;

  $gene_matrix = $self->score_matrix_from_flag_matrix($gene_matrix,
    $transcript_matrix, 1);
}

#
# penalise scores between genes with different biotypes.
# entries are modified in place
#

  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>.