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# $Id: MapperI.pm,v 1.10.4.1 2006/10/02 23:10:14 sendu Exp $
#
# bioperl module for Bio::Coordinate::MapperI
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
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=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://bioperl.org/wiki/Mailing_lists  - 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 the
web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Heikki Lehvaslaiho
Email:  heikki-at-bioperl-dot-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::Coordinate::MapperI;
use strict;
# Object preamble - inherits from Bio::Root::RootI
use base qw(Bio::Root::RootI);
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=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();
}
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=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();
}
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=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();
}
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=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();
}
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=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();
}
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=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;