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lib/FAST/Bio/Location/Split.pm  view on Meta::CPAN

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

    if( defined $value ) {
	$self->throw("Trying to set the minimum starting point of a split ".
				 "location, that is not possible, try manipulating the sub Locations");
    }
    my @locs = $self->sub_Location(1);
    return $locs[0]->min_start() if @locs; 
    return;
}

=head2 max_start

  Title   : max_start
  Usage   : my $maxstart = $location->max_start();
  Function: Get maximum starting location of feature startpoint  
  Returns : integer or undef if no maximum starting point.
  Args    : none

=cut

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

    if( defined $value ) {
	$self->throw("Trying to set the maximum starting point of a split ".
				 "location, that is not possible, try manipulating the sub Locations");
    }
    my @locs = $self->sub_Location(1);
    return $locs[0]->max_start() if @locs; 
    return;
}

=head2 start_pos_type

  Title   : start_pos_type
  Usage   : my $start_pos_type = $location->start_pos_type();
  Function: Get start position type (ie <,>, ^) 
  Returns : type of position coded as text 
            ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
  Args    : none

=cut

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

    if( defined $value ) {
	$self->throw("Trying to set the start_pos_type of a split location, ".
				 "that is not possible, try manipulating the sub Locations");
    }
    my @locs = $self->sub_Location();
    return ( @locs ) ? $locs[0]->start_pos_type() : undef;    
}

=head2 min_end

  Title   : min_end
  Usage   : my $minend = $location->min_end();
  Function: Get minimum ending location of feature endpoint 
  Returns : integer or undef if no minimum ending point.
  Args    : none

=cut

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

    if( defined $value ) {
	$self->throw("Trying to set the minimum end point of a split location, ".
				 "that is not possible, try manipulating the sub Locations");
    }
    # reverse sort locations by largest ending to smallest ending
    my @locs = $self->sub_Location(-1);
    return $locs[0]->min_end() if @locs; 
    return;
}

=head2 max_end

  Title   : max_end
  Usage   : my $maxend = $location->max_end();
  Function: Get maximum ending location of feature endpoint 
  Returns : integer or undef if no maximum ending point.
  Args    : none

=cut

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

    if( defined $value ) {
	$self->throw("Trying to set the maximum end point of a split location, ".
				 "that is not possible, try manipulating the sub Locations");
    }
    # reverse sort locations by largest ending to smallest ending
    my @locs = $self->sub_Location(-1);
    return $locs[0]->max_end() if @locs; 
    return;
}

=head2 end_pos_type

  Title   : end_pos_type
  Usage   : my $end_pos_type = $location->end_pos_type();
  Function: Get end position type (ie <,>, ^) 
  Returns : type of position coded as text 
            ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
  Args    : none

=cut

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

    if( defined $value ) {
	$self->throw("Trying to set end_pos_type of a split location, ".
				 "that is not possible, try manipulating the sub Locations");
    }
    my @locs = $self->sub_Location();
    return ( @locs ) ? $locs[0]->end_pos_type() : undef;    
}


=head2 seq_id

  Title   : seq_id
  Usage   : my $seqid = $location->seq_id();
  Function: Get/Set seq_id that location refers to

            We override this here in order to propagate to all sublocations
            which are not remote (provided this root is not remote either)
  Returns : seq_id
  Args    : [optional] seq_id value to set


=cut

sub seq_id {
    my $self = shift;

    if(@_ && !$self->is_remote()) {
	foreach my $subloc ($self->sub_Location(0)) {