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package Bio::Coordinate::MapperI;
our $AUTHORITY = 'cpan:BIOPERLML';
$Bio::Coordinate::MapperI::VERSION = '1.007001';
use utf8;
use strict;
use warnings;
use parent qw(Bio::Root::RootI);
# ABSTRACT: Interface describing coordinate mappers.
# AUTHOR: Heikki Lehvaslaiho <heikki@bioperl.org>
# OWNER: Heikki Lehvaslaiho
# LICENSE: Perl_5
sub in {
my ($self,$value) = @_;
$self->throw_not_implemented();
}
sub out {
my ($self,$value) = @_;
$self->throw_not_implemented();
}
sub swap {
my ($self) = @_;
$self->throw_not_implemented();
}
sub test {
my ($self) = @_;
$self->throw_not_implemented();
}
sub map {
my ($self,$value) = @_;
$self->throw_not_implemented();
}
sub return_match {
my ($self,$value) = @_;
if( defined $value) {
$value ? ( $self->{'_return_match'} = 1 ) :
( $self->{'_return_match'} = 0 );
}
return $self->{'_return_match'} || 0 ;
}
1;
__END__
=pod
=encoding utf-8
=head1 NAME
Bio::Coordinate::MapperI - Interface describing coordinate mappers.
=head1 VERSION
version 1.007001
=head1 SYNOPSIS
# not to be used directly
=head1 DESCRIPTION
MapperI defines methods for classes capable for mapping locations
between coordinate systems.
=head1 METHODS
=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
=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
=head2 swap
Title : swap
Usage : $obj->swap;
Function: Swap the direction of mapping: input <-> output)
Example :
Returns : 1
Args :
=head2 test
Title : test
Usage : $obj->test;
Function: test that both components are of same length
Example :
Returns : ( 1 | undef )
Args :
=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
=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)
=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/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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 the
web:
https://github.com/bioperl/%%7Bdist%7D
=head1 AUTHOR
Heikki Lehvaslaiho <heikki@bioperl.org>
=head1 COPYRIGHT
This software is copyright (c) by Heikki Lehvaslaiho.
This software is available under the same terms as the perl 5 programming language system itself.
=cut
|
