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Bio/DB/SeqFeature/NormalizedFeature.pm  view on Meta::CPAN

  }

  if (my $store = $self->object_store) {
    return Bio::PrimarySeq->new(-seq => $store->fetch_sequence($self->seq_id,$start,$end) || '',
				-id  => $self->display_name);
  } else {
      return $self->SUPER::seq($self->seq_id,$start,$end);
  }
}

sub subseq {
  my $self = shift;
  my ($newstart,$newstop) = @_;
  my $store = $self->object_store or return;
  my ($start,$stop) = ($self->start+$newstart-1,$self->end+$newstop-1);
  if ($self->strand < 0) {
    ($start,$stop) = ($stop,$start);
  }
  my $seq = $store->fetch_sequence($self->seq_id,$start,$stop);
  return Bio::PrimarySeq->new($seq);
}

=head2 add_SeqFeature

 Title   : add_SeqFeature
 Usage   : $flag = $feature->add_SeqFeature(@features)
 Function: Add subfeatures to the feature
 Returns : true if successful
 Args    : list of Bio::SeqFeatureI objects
 Status  : public

Add one or more subfeatures to the feature. For best results,
subfeatures should be of the same class as the parent feature
(i.e. don't try mixing Bio::DB::SeqFeature::NormalizedFeature with
other feature types).

An alias for this method is add_segment().

=cut

sub add_SeqFeature {
  my $self = shift;
  $self->_add_segment(1,@_);
}

=head2 update

 Title   : update
 Usage   : $flag = $feature->update()
 Function: Update feature in the database
 Returns : true if successful
 Args    : none
 Status  : public

After changing any fields in the feature, call update() to write it to
the database. This is not needed for add_SeqFeature() as update() is
invoked automatically.

=cut

sub update {
  my $self = shift;
  my $store = $self->object_store or return;
  $store->store($self);
}

=head2 get_SeqFeatures

 Title   : get_SeqFeature
 Usage   : @subfeatures = $feature->get_SeqFeatures([@types])
 Function: return subfeatures of this feature
 Returns : list of subfeatures
 Args    : list of subfeature primary_tags (optional)
 Status  : public

This method extends the Bio::SeqFeatureI get_SeqFeatures() slightly by
allowing you to pass a list of primary_tags, in which case only
subfeatures whose primary_tag is contained on the list will be
returned. Without any types passed all subfeatures are returned.

=cut


# segments can be either normalized IDs or ordinary feature objects
sub get_SeqFeatures {
  my $self = shift;
  my @types        = @_;

  my $s     = $self->{segments} or return;
  my $store = $self->object_store;
  my (@ordinary,@ids);
  for (@$s) {
    if (ref ($_)) {
      push @ordinary,$_;
    } else {
      push @ids,$_;
    }
  }
  my @r = grep {$_->type_match(@types)} (@ordinary,$store->fetch_many(\@ids));
  for my $r (@r) {
    eval {$r->object_store($store) };
  }
  return @r;
}

=head2 object_store

 Title   : object_store
 Usage   : $store = $feature->object_store([$new_store])
 Function: get or set the database handle
 Returns : current database handle
 Args    : new database handle (optional)
 Status  : public

This method will get or set the Bio::DB::SeqFeature::Store object that
is associated with the feature. After changing the store, you should
probably unset the feature's primary_id() and call update() to ensure
that the object is written into the database as a new feature.

=cut