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