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Bio::Coordinate::Result.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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    :