Reference

Bio::Coordinate::Result(3pm)

Results from coordinate transformation.

NAME

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

VERSION

version 1.007001

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.

ATTRIBUTES

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

METHODS

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

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    :

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 list. Your participation is much appreciated.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: [email protected]

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 of the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/%%7Bdist%7D

AUTHOR

Heikki Lehvaslaiho <[email protected]>

COPYRIGHT

This software is copyright (c) by Heikki Lehvaslaiho.

This software is available under the same terms as the perl 5 programming language system itself.

History