/ 
BioPerl-1.6.920
River stage two • 61 direct dependents • 66 total dependents
/ Bio::Coordinate::Result

NAME

Bio::Coordinate::Result - Results from coordinate transformation

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.

FEEDBACK

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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.

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 the web:

https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

APPENDIX

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    :