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.

Mailing Lists
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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom Additional contributors names and emails here 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