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->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';
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.
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Email: heikki@ebi.ac.uk Address:
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Wellcome Trust Genome Campus, Hinxton
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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