Bio::Coordinate::Pair(3pm) User Contributed Perl Documentation Bio::Coordinate::Pair(3pm)
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
perl v5.14.2 2012-03-02 Bio::Coordinate::Pair(3pm)