Christopher Fields > BioPerl > Bio::Coordinate::Pair

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BioPerl-1.6.924.tar.gz

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Module Version: 1.006924   Source  

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.

new

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
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