| Bio::Coordinate::Result(3pm) | User Contributed Perl Documentation | Bio::Coordinate::Result(3pm) |
Bio::Coordinate::Result - Results from coordinate transformation.
version 1.007001
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.
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
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 : 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 : 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 :
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 list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/%%7Bdist%7D
Heikki Lehvaslaiho <heikki@bioperl.org>
This software is copyright (c) by Heikki Lehvaslaiho.
This software is available under the same terms as the perl 5 programming language system itself.
| 2020-11-24 | perl v5.32.0 |