Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


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


   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->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';


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.


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.                  - General discussion  - About the mailing lists


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

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:

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org


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


  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


  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


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


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


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


  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


  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