Raw content of Bio::Map::MarkerI
<![CDATA[# $Id: MarkerI.pm,v 1.9 2002/10/22 07:45:15 lapp Exp $
#
# BioPerl module for Bio::Map::MarkerI
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# 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::Map::MarkerI - Interface for basic marker functionality
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the interface here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
Describe contact details here
=head1 CONTRIBUTORS
Heikki Lehvaslaiho heikki@ebi.ac.uk
Lincoln Stein lstein@cshl.org
Jason Stajich jason@bioperl.org
Chad Matsalla bioinformatics1@dieselwurks.com
=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::Map::MarkerI;
use vars qw(@ISA);
use strict;
use Bio::Map::MappableI;
@ISA = qw(Bio::Map::MappableI);
=head2 name($new_name)
Title : name($new_name)
Usage : my $name = $o_usat->name($new_name) _or_
my $name = $o_usat->name()
Function: Get/Set the name for this Marker
Returns : A scalar representing the current name of this Marker
Args : If provided, the current name of this Marker
will be set to $new_name.
=cut
sub name {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 add_position
Title : add_position
Usage : $position->add_position($map,'100')
Function: Add a numeric or string position to the PositionI container
Returns : none
Args : Map - Reference to Bio::Map::MapI
String or Numeric coding for a position on a map
=cut
sub add_position{
my ($self,$map,$value) = @_;
$self->throw_not_implemented();
}
=head2 each_position
Title : positions
Usage : my @positions = $position->each_position_value('mapname');
Function: Retrieve a list of positions coded as strings or ints
Returns : Array of position values
Args : none
=cut
sub each_position {
my ($self,$mapname) = @_;
$self->throw_not_implemented();
}
=head2 purge_positions
Title : purge_positions
Usage : $position->purge_positions
Function: Remove all the position values stored for a Marker
Returns : none
Args : [optional] only purge values for a given map
=cut
sub purge_position_values{
my ($self, $map) = @_;
$self->throw_not_implemented();
}
=head2 known_maps
Title : known_maps
Usage : my @maps = $marker->known_maps
Function: Returns the list of maps that this position has values for
Returns : list of Bio::Map::MapI unique ids
Args : none
=cut
sub known_maps{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 in_map
Title : in_map
Usage : if ( $position->in_map($map) ) {}
Function: Tests if a position has values in a specific map
Returns : boolean
Args : a map unique id OR Bio::Map::MapI
=cut
sub in_map{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 get_position_object
Title : get_position_class
Usage : my $pos = $marker->get_position_object();
Function: To get an object of the default Position class
for this Marker. Subclasses should redefine this method.
The Position needs to be L<Bio::Map::PositionI>.
Returns : L<Bio::Map::PositionI>
Args : none
=cut
sub get_position_object {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 tuple
Title : tuple
Usage : ($me, $you) = $self->_tuple($compare)
Function: Utility method to extract numbers and test for missing values.
Makes writing subsequent tests easier.
Returns : a tuple of values or ranges
Args : Bio::Map::MappableI or Bio::Map::PositionI
=cut
sub tuple {
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 Bio::Map::MappableI methods
=cut
=head2 position
Title : position
Usage : my position_string = $position->position('mapname');
Function: Get/Set method for single value positions.
Gives a simplified interface when only one map and
one position per marker is used.
Returns : a position value
Args : optional:
Map - Reference to Bio::Map::MapI
String or Numeric coding for a position on a map
=cut
sub position{
my ($self,$map, $value) = @_;
$self->throw_not_implemented();
}
=head2 equals
Title : equals
Usage : if( $mappable->equals($mapable2)) ...
Function: Test if a position is equal to another position
Returns : boolean
Args : Bio::Map::MappableI
=head2 less_than
Title : less_than
Usage : if( $mappable->less_than($m2) ) ...
Function: Tests if a position is less than another position
Returns : boolean
Args : Bio::Map::MappableI
=head2 greater_than
Title : greater_than
Usage : if( $mappable->greater_than($m2) ) ...
Function: Tests if position is greater than another position
Returns : boolean
Args : Bio::Map::MappableI
=cut
1;
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