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::Match. If only one Match is returned, there is a convenience method of retrieving it or accessing its methods. Same holds true for a Gap.

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists

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 _

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

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

Convenience methods
These methods are shortcuts to Match and Gap locations.

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

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 :