SYNOPSIS¶
use Bio::Coordinate::Result;
#get results from a Bio::Coordinate::MapperI
$matched = $result->each_match;
DESCRIPTION¶
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.
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
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 :