Other packages in the module: Bio::EnsEMBL::Analysis::RunnableDB::WGA2Genes

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Methods code

sub _get_all_transcript_cds_features {

  my ($self) = @_;

  my (@orig_cds_feats, @merged_cds_feats);

  foreach my $tran (@{$self->source_transcripts}) {
    foreach my $exon (@{$tran->get_all_translateable_Exons}) {
      push @orig_cds_feats, Bio::EnsEMBL::Feature->
          new(-start  => $exon->start,
              -end    => $exon->end,
              -slice  => $exon->slice);
    }
  }

  foreach my $feat (sort {$a->start <=> $b->start} @orig_cds_feats) {
    if (not @merged_cds_feats or 
        $feat->start > $merged_cds_feats[-1]->end) {
      push @merged_cds_feats, $feat;
    } else {
      if ($feat->end > $merged_cds_feats[-1]->end) {
        $merged_cds_feats[-1]->end($feat->end);
      }
    }
  }

  $self->transcript_cds_feats(\@merged_cds_feats);
}

##################
# get/sets
#################

}

sub clone {

  my ($self) = @_;

  my $new_one = Bio::EnsEMBL::Analysis::RunnableDB::WGA2Genes::GeneRecord
      ->new(-source_transcripts => $self->source_transcripts,
            -gene               => $self->gene);

  return $new_one;
}



#################################################################
# FUNCTION   : get_all_transcript_cds_features
#
# Description : 
#    Returns a list of Bio::EnsEMBL::Features representing the 
#    projection of the coding regions of the given transcripts 
#    onto the query 
#################################################################

}

sub gene {

  my ($self, $val) = @_;

  if (defined $val) {
    $self->{_gene} = $val;
  }

  return $self->{_gene};

}

sub good_source_transcripts {

  my ($self, $val) = @_;

  if (defined $val) {
    $self->{_good_source_transcripts} = $val;
  }

  return $self->{_good_source_transcripts};

}

sub name {

  my ($self, $val) = @_;

  if (defined $val) {
    $self->{_name} = $val;
  }

  return $self->{_name};

}

sub new {

  my ($class, @args) = @_;

  my $self = bless {}, $class;

  my ($name, $gene, $source_trans) = rearrange
    (['NAME', 'GENE', 'SOURCE_TRANSCRIPTS'], @args);

  $self->name($name) if defined $name;
  $self->gene($gene) if defined $gene;
  $self->source_transcripts($source_trans) if defined $source_trans;

  $self->good_source_transcripts([]);
  $self->projected_transcripts([]);

  return $self;

}

sub projected_transcripts {

  my ($self, $val) = @_;

  if (defined $val) {
    $self->{_projected_transcripts} = $val;
  }

  return $self->{_projected_transcripts};
}


1;

}

sub source_transcripts {

  my ($self, $val) = @_;

  if (defined $val) {
    $self->{_source_transcripts} = $val;

    $self->_get_all_transcript_cds_features;
  }

  return $self->{_source_transcripts};

}

sub transcript_cds_feats {

  my ($self, $val) = @_;

  if (defined $val) {
    $self->{_transcript_cds} = $val;
  }

  return $self->{_transcript_cds};

}

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