NAME

Bio::Coordinate::Pair - Continuous match between two coordinate sets

SYNOPSIS

use Bio::Location::Simple;
use Bio::Coordinate::Pair;

my $match1 = Bio::Location::Simple->new 
    (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
my $match2 = Bio::Location::Simple->new
    (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
my $pair = Bio::Coordinate::Pair->new(-in => $match1,
					-out => $match2
                                      );
# location to match
$pos = Bio::Location::Simple->new 
    (-start => 25, -end => 25, -strand=> -1 );

# results are in a Bio::Coordinate::Result
# they can be Matches and Gaps; are  Bio::LocationIs
$res = $pair->map($pos);
$res->isa('Bio::Coordinate::Result');
$res->each_match == 1;
$res->each_gap == 0;
$res->each_Location == 1;
$res->match->start == 5;
$res->match->end == 5;
$res->match->strand == -1;
$res->match->seq_id eq 'peptide';

DESCRIPTION

This class represents a one continuous match between two coordinate systems represented by Bio::Location::Simple objects. The relationship is directed and reversible. It implements methods to ensure internal consistency, and map continuous and split locations from one coordinate system to another.

The map() method returns Bio::Coordinate::Results with Bio::Coordinate::Result::Gaps. The calling code have to deal (process or ignore) them.

FEEDBACK

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

Support

Please direct usage questions or support issues to the mailing list:

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.

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:

https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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

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

swap

Title   : swap
Usage   : $obj->swap;
Function: Swap the direction of mapping; input <-> output
Example :
Returns : 1
Args    : 

strand

Title   : strand
Usage   : $obj->strand;
Function: Get strand value for the pair
Example :
Returns : ( 1 | 0 | -1 )
Args    :

test

Title   : test
Usage   : $obj->test;
Function: test that both components are of the same length
Example :
Returns : ( 1 | undef )
Args    :

map

Title   : map
Usage   : $newpos = $obj->map($pos);
Function: Map the location from the input coordinate system
          to a new value in the output coordinate system.
Example :
Returns : new Bio::LocationI in the output coordinate system or undef
Args    : Bio::LocationI object

_map

Title   : _map
Usage   : $newpos = $obj->_map($simpleloc);
Function: Internal method that does the actual mapping. Called
          multiple times by map() if the location to be mapped is a
          split location
Example :
Returns : new location in the output coordinate system or undef
Args    : Bio::Location::Simple

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq