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lib/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm  view on Meta::CPAN

  my $sub_matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
    -DUMP_PATH   => $self->dump_path,
    -CACHE_FILE  => $self->cache_file_name,
  );
  my $i = 0;

  foreach my $key (sort keys %{ $self->{'cache'}->{'matrix'} }) {
    $i++;
    next if ($i < $start);
    last if ($i > $end);

    my ($source, $target) = split(/:/, $key);
    $sub_matrix->add_score($source, $target,
      $self->{'cache'}->{'matrix'}->{$key});
  }

  return $sub_matrix;
}


=head2 add_Entry

  Arg[1]      : Bio::EnsEMBL::IdMapping::Entry $entry - Entry to add
  Example     : $gene_scores->add_Entry($entry);
  Description : Adds an Entry to the scoring matrix.
  Return type : Float - the Entry's score
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

=cut

sub add_Entry {
  my $self = shift;
  my $entry = shift;

  unless ($entry and $entry->isa('Bio::EnsEMBL::IdMapping::Entry')) {
    throw("Need a Bio::EnsEMBL::IdMapping::Entry");
  }

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


=head2 update_Entry

  Arg[1]      : Bio::EnsEMBL::IdMapping::Entry $entry - Entry to update
  Example     : $gene_scores->update_Entry($entry);
  Description : Updates an Entry (or rather its score) in the scoring matrix.
                Actually delegates to add_Entry(), only there as an intuitively
                named wrapper.
  Return type : Float - the Entry's score
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

=cut

sub update_Entry {
  return $_[0]->add_Entry($_[1]);
}


#
# not needed in the current application, so not implemented
#
sub remove_Entry {
  warning('Method ScoredMappingMatrix->remove_Entry not implemented (yet).');
}


=head2 add_score

  Arg[1]      : Int $source - source object's internal Id ("dbID")
  Arg[2]      : Int $target - target object's internal Id ("dbID")
  Arg[3]      : Float $score - score for source/target pair
  Example     : $gene_scores->add_score(1234, 5678, 0.997);
  Description : Adds a score for a source/target pair to the scoring matrix.
                This is a low-level version of add_Entry().
  Return type : Float - the score
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

=cut

sub add_score {
  my $self = shift;
  my $source = shift;
  my $target = shift;
  my $score = shift;
  
  # make sure you don't put duplicates on the source and target lists
  unless (exists($self->{'cache'}->{'matrix'}->{"$source:$target"})) {
    push @{ $self->{'cache'}->{'source_list'}->{$source} }, $target;
    push @{ $self->{'cache'}->{'target_list'}->{$target} }, $source;
  }

  $self->{'cache'}->{'matrix'}->{"$source:$target"} = $score;
}


=head2 set_score

  Arg[1]      : Int $source - source object's internal Id ("dbID")
  Arg[2]      : Int $target - target object's internal Id ("dbID")
  Arg[3]      : Float $score - score for source/target pair
  Example     : $gene_scores->set_score(1234, 5678, 0.997);
  Description : Sets the score for a source/target pair in the scoring matrix.
                This method is similar to add_score, but assumes that the Entry
                has been added before, so won't update the sources and target
                lists.
  Return type : Float - the score
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development