Raw content of Bio::Coordinate::MapperI # $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;