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 the Bio::Location::Split manpage. The results are either Matches or Gaps. See the Bio::Coordinate::Result::Match manpage and the Bio::Coordinate::Result::Match manpage.
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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The 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
These 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 :