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

use strict;

use base qw(Bio::LocationI);

=head1 LocationI methods

=head2 location_type

  Title   : loc_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) = @_;
    $self->throw_not_implemented();
}

=head1 Bio::LocationI methods

Bio::LocationI methods follow

=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 maximum starting point.
  Args    : none

=cut

=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

=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

=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

=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

=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

=head2 seq_id

  Title   : seq_id
  Usage   : my $seqid = $location->seq_id();
  Function: Get/Set seq_id that location refers to
  Returns : seq_id
  Args    : [optional] seq_id value to set

=cut

=head2 coordinate_policy

  Title   : coordinate_policy
  Usage   : $policy = $location->coordinate_policy();
            $location->coordinate_policy($mypolicy); # set may not be possible
  Function: Get the coordinate computing policy employed by this object.

            See Bio::Location::CoordinatePolicyI for documentation about
            the policy object and its use.

            The interface *does not* require implementing classes to accept
            setting of a different policy. The implementation provided here
            does, however, allow one to do so.

            Implementors of this interface are expected to initialize every
            new instance with a CoordinatePolicyI object. The implementation
            provided here will return a default policy object if none has
            been set yet. To change this default policy object call this
            method as a class method with an appropriate argument. Note that
            in this case only subsequently created Location objects will be
            affected.

  Returns : A Bio::Location::CoordinatePolicyI implementing object.
  Args    : On set, a Bio::Location::CoordinatePolicyI implementing object.

=cut

=head2 to_FTstring

  Title   : to_FTstring
  Usage   : my $locstr = $location->to_FTstring()
  Function: returns the FeatureTable string of this location
  Returns : string
  Args    : none