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Bio/Location/Atomic.pm  view on Meta::CPAN

=head2 min_start

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

=cut

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

    if(defined($value)) {
	$self->{'_start'} = $value;
    }
    return $self->{'_start'};
}

=head2 max_start

  Title   : max_start
  Usage   : my $maxstart = $location->max_start();
  Function: Get maximum starting location of feature startpoint.

            In this implementation this is exactly the same as min_start().

  Returns : integer or undef if no maximum starting point.
  Args    : none

=cut

sub max_start {
    my ($self,@args) = @_;
    return $self->min_start(@args);
}

=head2 start_pos_type

  Title   : start_pos_type
  Usage   : my $start_pos_type = $location->start_pos_type();
  Function: Get start position type (ie <,>, ^).

            In this implementation this will always be 'EXACT'.

  Returns : type of position coded as text 
            ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
  Args    : none

=cut

sub start_pos_type {
    my($self) = @_;
    return 'EXACT';
}

=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->{'_end'} = $value;
    }
    return $self->{'_end'};
}

=head2 max_end

  Title   : max_end
  Usage   : my $maxend = $location->max_end();
  Function: Get maximum ending location of feature endpoint 

            In this implementation this is exactly the same as min_end().

  Returns : integer or undef if no maximum ending point.
  Args    : none

=cut

sub max_end {
    my($self,@args) = @_;
    return $self->min_end(@args);
}

=head2 end_pos_type

  Title   : end_pos_type
  Usage   : my $end_pos_type = $location->end_pos_type();
  Function: Get end position type (ie <,>, ^) 

            In this implementation this will always be 'EXACT'.

  Returns : type of position coded as text 
            ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
  Args    : none

=cut

sub end_pos_type {
    my($self) = @_;
    return 'EXACT';
}

=head2 location_type

  Title   : location_type
  Usage   : my $location_type = $location->location_type();
  Function: Get location type encoded as text
  Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
  Args    : none

=cut

sub location_type {
    my ($self) = @_;
    return 'EXACT';
}

=head2 is_remote

 Title   : is_remote
 Usage   : $is_remote_loc = $loc->is_remote()
 Function: Whether or not a location is a remote location.

           A location is said to be remote if it is on a different
           'object' than the object which 'has' this
           location. Typically, features on a sequence will sometimes
           have a remote location, which means that the location of
           the feature is on a different sequence than the one that is
           attached to the feature. In such a case, $loc->seq_id will
           be different from $feat->seq_id (usually they will be the



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