Provided by: libbio-perl-perl_1.6.923-1_all
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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AUTHOR - Heikki Lehvaslaiho
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