Provided by: libbio-coordinate-perl_1.7.1-3_all
Bio::Coordinate::Result - Results from coordinate transformation.
use Bio::Coordinate::Result; #get results from a Bio::Coordinate::MapperI $matched = $result->each_match;
The results from Bio::Coordinate::MapperI are kept in an object which itself is a split location, See Bio::Location::Split. The results are either Matches or Gaps. See Bio::Coordinate::Result::Match and Bio::Coordinate::Result::Gap. If only one Match is returned, there is a convenience method of retrieving it or accessing its methods. Same holds true for a Gap.
seq_id Title : seq_id Usage : my $seqid = $location->seq_id(); Function: Get/Set seq_id that location refers to We override this here in order to propagate to all sublocations which are not remote (provided this root is not remote either) Returns : seq_id Args : [optional] seq_id value to set each_gap Title : each_gap Usage : $obj->each_gap(); Function: Returns a list of Bio::Coordianate::Result::Gap objects. Returns : list of gaps Args : none each_match Title : each_match Usage : $obj->each_match(); Function: Returns a list of Bio::Coordinate::Result::Match objects. Returns : list of Matchs Args : none
add_location Title : add_sub_Location Usage : $obj->add_sub_Location($variant) Function: Pushes one Bio::LocationI into the list of variants. Example : Returns : 1 when succeeds Args : Location object add_result Title : add_result Usage : $obj->add_result($result) Function: Adds the contents of one Bio::Coordinate::Result Example : Returns : 1 when succeeds Args : Result object match Title : match Usage : $match_object = $obj->match(); #or $gstart = $obj->gap->start; Function: Read only method for retrieving or accessing the match object. Returns : one Bio::Coordinate::Result::Match Args : gap Title : gap Usage : $gap_object = $obj->gap(); #or $gstart = $obj->gap->start; Function: Read only method for retrieving or accessing the gap object. Returns : one Bio::Coordinate::Result::Gap Args : purge_gaps Title : purge_gaps Usage : $gap_count = $obj->purge_gaps; Function: remove all gaps from the Result Returns : count of removed gaps Args :
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Heikki Lehvaslaiho <email@example.com>
This software is copyright (c) by Heikki Lehvaslaiho. This software is available under the same terms as the perl 5 programming language system itself.