#get results from a Bio::Coordinate::MapperI
$matched = $result->each_match;
DESCRIPTIONThe 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.
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AUTHOR - Heikki LehvaslaihoEmail: heikki-at-bioperl-dot-org
APPENDIXThe rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
Convenience methodsThese methods are shortcuts to Match and Gap locations.
Title : each_gap Usage : $obj->each_gap(); Function: Returns a list of Bio::Coordianate::Result::Gap objects. Returns : list of gaps Args : none
Title : each_match Usage : $obj->each_match(); Function: Returns a list of Bio::Coordinate::Result::Match objects. Returns : list of Matchs Args : none
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 :
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 :
Title : purge_gaps Usage : $gap_count = $obj->purge_gaps; Function: remove all gaps from the Result Returns : count of removed gaps Args :