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lib/Bio/SeqFeature/Annotated.pm  view on Meta::CPAN

           an exception if not.

           If EXPAND is used, the parent''s start/end/strand will
           be adjusted so that it grows to accommodate the new
           subFeature
 Example :
 Returns : nothing
 Args    : a Bio::SeqFeatureI object

=cut

sub add_SeqFeature {
  my ($self,$val, $expand) = @_;

  return unless $val;

  if ((!ref($val)) || !$val->isa('Bio::SeqFeatureI') ) {
      $self->throw((ref($val) ? ref($val) : $val)
                   ." does not implement Bio::SeqFeatureI.");
  }

  if($expand && ($expand eq 'EXPAND')) {
      $self->_expand_region($val);
  } else {
      if ( !$self->contains($val) ) {
	  $self->warn("$val is not contained within parent feature, and expansion is not valid, ignoring.");
	  return;
      }
  }

  push(@{$self->{'sub_array'}},$val);
}

=head2 remove_SeqFeatures()

 Usage   : $obj->remove_SeqFeatures
 Function: Removes all sub SeqFeatures.  If you want to remove only a subset,
           remove that subset from the returned array, and add back the rest.
 Returns : The array of Bio::SeqFeatureI implementing sub-features that was
           deleted from this feature.
 Args    : none

=cut

sub remove_SeqFeatures {
  my ($self) = @_;

  my @subfeats = @{$self->{'sub_array'} || []};
  $self->{'sub_array'} = []; # zap the array.
  return @subfeats;
}

############################################################

=head1 INTERFACE METHODS FOR Bio::AnnotatableI

=cut

=head2 annotation()

 Usage   : $obj->annotation($annot_obj)
 Function: Get/set the annotation collection object for annotating this
           feature.
 Returns : A Bio::AnnotationCollectionI object
 Args    : newvalue (optional)

=cut

sub annotation {
    my ($obj,$value) = @_;

    # we are smart if someone references the object and there hasn't been
    # one set yet
    if(defined $value || ! defined $obj->{'annotation'} ) {
        $value = Bio::Annotation::Collection->new() unless ( defined $value );
        $obj->{'annotation'} = $value;
    }
    return $obj->{'annotation'};
}

############################################################

=head2 location()

 Usage   : my $location = $seqfeature->location()
 Function: returns a location object suitable for identifying location 
           of feature on sequence or parent feature  
 Returns : Bio::LocationI object
 Args    : [optional] Bio::LocationI object to set the value to.

=cut

sub location {
  my($self, $value ) = @_;

  if (defined($value)) {
    unless (ref($value) and $value->isa('Bio::LocationI')) {
      $self->throw("object $value pretends to be a location but ".
                   "does not implement Bio::LocationI");
    }
    $self->{'location'} = $value;
  }
  elsif (! $self->{'location'}) {
    # guarantees a real location object is returned every time
    $self->{'location'} = Bio::Location::Simple->new();
  }
  return $self->{'location'};
}

=head2 add_target()

 Usage   : $seqfeature->add_target(Bio::LocatableSeq->new(...));
 Function: adds a target location on another reference sequence for this feature
 Returns : true on success
 Args    : a Bio::LocatableSeq object

=cut

sub add_target {
  my ($self,$seq) = @_;
  $self->throw("$seq is not a Bio::LocatableSeq, bailing out") unless ref($seq) and seq->isa('Bio::LocatableSeq');