Bio::Coordinate::ExtrapolatingPair(3pm) User Contributed Perl Documentation Bio::Coordinate::ExtrapolatingPair(3pm)
NAME
Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets
SYNOPSIS
use Bio::Location::Simple;
use Bio::Coordinate::ExtrapolatingPair;
$match1 = Bio::Location::Simple->new
(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
$match2 = Bio::Location::Simple->new
(-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
$pair = Bio::Coordinate::ExtrapolatingPair->
new(-in => $match1,
-out => $match2,
-strict => 1
);
$pos = Bio::Location::Simple->new
(-start => 40, -end => 60, -strand=> 1 );
$res = $pair->map($pos);
$res->start eq 20;
$res->end eq 20;
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.
This class is an elaboration of Bio::Coordinate::Pair. The map function returns only matches which is the mode needed most of tehtime. By
default the matching regions between coordinate systems are boundless, so that you can say e.g. that gene starts from here in the
chromosomal coordinate system and extends indefinetely in both directions. If you want to define the matching regions exactly, you can do
that and set strict() to true.
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 _
strict
Title : strict
Usage : $obj->strict(1);
Function: Set and read the strictness of the coordinate system.
Example :
Returns : value of input system
Args : boolean
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.
In extrapolating coodinate system there is no location zero.
Locations are...
Example :
Returns : new location in the output coordinate system or undef
Args : Bio::Location::Simple
_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::ExtrapolatingPair(3pm)