Bio::Coordinate::Pair.3pm

Langue: en

Version: 2009-02-27 (fedora - 06/07/09)

Section: 3 (Bibliothèques de fonctions)

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
 
 

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:

   http://bugzilla.open-bio.org/
 
 

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