Raw content of Bio::Map::MappableI
<![CDATA[# $Id: MappableI.pm,v 1.9 2002/10/22 07:45:15 lapp Exp $
#
# BioPerl module for Bio::Map::MappableI
#
# 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::MappableI - An object that can be placed in a map
=head1 SYNOPSIS
# get a Bio::Map::MappableI somehow
my $position = $element->map_position();
# these methods will be important for building sorted lists
if( $position->equals($p2) ) {
# do something
} elsif( $position->less_tha($p2) ) {}
elsif( $position->greater_than($p2) ) { }
=head1 DESCRIPTION
This object handles the generic notion of an element placed on a
(linear) Map. Elements can have multiple positions in a map such as
is the case of Restriction enzyme cut sites on a sequence map. For
exact information about an element's position in a map one must query
the associate PositionI object which is accessible through the
position() method.
=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
=head1 CONTRIBUTORS
Heikki Lehvaslaiho heikki@ebi.ac.uk
Lincoln Stein lstein@cshl.org
=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::MappableI;
use vars qw(@ISA);
use strict;
use Bio::Root::RootI;
use Carp;
@ISA = qw(Bio::Root::RootI);
=head2 position
Title : position
Usage : my $position = $mappable->position();
Function: Get/Set the Bio::Map::PositionI for a mappable element
Returns : Bio::Map::PositionI
Args : (optional) Bio::Map::PositionI
=cut
sub position{
my ($self,@args) = @_;
$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 or Bio::Map::PositionI
=cut
sub equals{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=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 or Bio::Map::PositionI
=cut
sub less_than{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=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 or Bio::Map::PositionI
=cut
sub greater_than{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
1;
]]>