comparison variant_effect_predictor/Bio/Location/FuzzyLocationI.pm @ 0:1f6dce3d34e0

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# $Id: FuzzyLocationI.pm,v 1.17 2002/12/01 00:05:20 jason Exp $
#
# BioPerl module for Bio::Location::FuzzyLocationI
# Cared for by Jason Stajich <[e-mail]>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code

=head1 NAME

Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence
which has unclear start/end location

=head1 SYNOPSIS

    # Get a FuzzyLocationI object somehow
    print "Fuzzy FT location string is ", $location->to_FTstring();
    print "location is of the type ", $location->loc_type, "\n";

=head1 DESCRIPTION

This interface encapsulates the necessary methods for representing a
Fuzzy Location, one that does not have clear start and/or end points.
This will initially serve to handle features from Genbank/EMBL feature
tables that are written as 1^100 meaning between bases 1 and 100 or
E<lt>100..300 meaning it starts somewhere before 100.  Advanced
implementations of this interface may be able to handle the necessary
logic of overlaps/intersection/contains/union.  It was constructed to
handle fuzzy locations that can be represented in Genbank/EMBL.

=head1 FEEDBACK

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.

  [e-mail]             - General discussion
  http://bio.perl.org/MailList.html - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via email
or the web:

  [e-mail]
  http://bugzilla.bioperl.org/

=head1 AUTHOR - Jason Stajich

Email [e-mail]

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

=cut

# Let the code begin...


package Bio::Location::FuzzyLocationI;
use vars qw(@ISA);
use strict;

use Bio::LocationI;
use Carp;

@ISA = 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', '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 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

=cut

1;