Raw content of Bio::Coordinate::MapperI
<![CDATA[# $Id: MapperI.pm,v 1.5 2002/11/08 09:28:24 heikki Exp $
#
# bioperl module for Bio::Coordinate::MapperI
#
# Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Coordinate::MapperI - Interface describing coordinate mappers
=head1 SYNOPSIS
# not to be used directly
=head1 DESCRIPTION
MapperI defines methods for classes capable for mapping locations
between coordinate systems.
=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 lists Your participation is much appreciated.
bioperl-l@bioperl.org - 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:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk
Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
=head1 CONTRIBUTORS
Additional contributors names and emails here
=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::Coordinate::MapperI;
use vars qw(@ISA );
use strict;
# Object preamble - inherits from Bio::Root::RootI
use Bio::Root::RootI;
@ISA = qw(Bio::Root::RootI);
=head2 in
Title : in
Usage : $obj->in('peptide');
Function: Set and read the input coordinate system.
Example :
Returns : value of input system
Args : new value (optional), Bio::LocationI
=cut
sub in {
my ($self,$value) = @_;
$self->throw_not_implemented();
}
=head2 out
Title : out
Usage : $obj->out('peptide');
Function: Set and read the output coordinate system.
Example :
Returns : value of output system
Args : new value (optional), Bio::LocationI
=cut
sub out {
my ($self,$value) = @_;
$self->throw_not_implemented();
}
=head2 swap
Title : swap
Usage : $obj->swap;
Function: Swap the direction of mapping: input <-> output)
Example :
Returns : 1
Args :
=cut
sub swap {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 test
Title : test
Usage : $obj->test;
Function: test that both components are of same length
Example :
Returns : ( 1 | undef )
Args :
=cut
sub test {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 map
Title : map
Usage : $newpos = $obj->map($loc);
Function: Map the location from the input coordinate system
to a new value in the output coordinate system.
Example :
Returns : new value in the output coordiante system
Args : Bio::LocationI
=cut
sub map {
my ($self,$value) = @_;
$self->throw_not_implemented();
}
=head2 return_match
Title : return_match
Usage : $obj->return_match(1);
Function: A flag to turn on the simplified mode of
returning only one joined Match object or undef
Example :
Returns : boolean
Args : boolean (optional)
=cut
sub return_match {
my ($self,$value) = @_;
if( defined $value) {
$value ? ( $self->{'_return_match'} = 1 ) :
( $self->{'_return_match'} = 0 );
}
return $self->{'_return_match'} || 0 ;
}
1;
]]>