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lib/Bio/DOOP/SequenceFeature.pm  view on Meta::CPAN

Returns the length of the feature.

=cut

sub length {
  my $self                 = shift;
  return($self->{END} - $self->{START} + 1);
}

=head2 get_seq

Returns the sequence of the feature.

=cut

sub get_seq {
  my $self                 = shift;
  return($self->{SEQ});
}

=head2 get_type

Returns the type of the feature. (con, ssr, tfbs, rep, cpg, tss).

con  : evolutionary conserved non-coding region
ssr  : simple sequence repeat
tfbs : transcription factor binding site
rep  : repeat
cpg  : cpg island
tss  : transcription start site

=cut

sub get_type {
  my $self                 = shift;
  return($self->{TYPE});
}

=head2 get_motifid

Returns the motif primary ID, if the feature type is "con".

=cut

sub get_motifid {
  my $self                 = shift;
  return($self->{MOTIFID});
}

=head2 get_tfbsid

Returns the tfbs primary ID, if the feature type is "tfbs".

=cut

sub get_tfbsid {
  my $self                 = shift;
  return($self->{TFBSID});
}

=head2 get_cpgid

Returns the cpg primary ID, if the feature type is "cpg".

=cut

sub get_cpgid {
  my $self                 = shift;
  return($self->{CPGID});
}

=head2 get_repeatid

Returns the repeat primary ID, if the feature type is "rep".

=cut

sub get_repeatid {
  my $self                 = shift;
  return($self->{REPEATID});
}

=head2 get_ssrid

Returns the ssr primary ID, if the feature type is "ssr".

=cut

sub get_ssrid {
  my $self                 = shift;
  return($self->{SSRID});
}

=head2 get_tssid

Returns the tss primary ID, if the feature type is "tss".

=cut

sub get_tssid {
  my $self                 = shift;
  return($self->{TSSID});
}

=head2 get_seqid

Returns the primary ID of the sequence containing this feature.

=cut

sub get_seqid {
  my $self                 = shift;
  return($self->{SEQ_ID});
}

=head2 get_subsetid

Returns the subset primary ID of the feature, if the feature type is "con".

=cut

sub get_subsetid {
  my $self                 = shift;
  return($self->{SUBSET_ID});
}

=head2 get_motif