bio::coordinate::result(3pm) [debian man page]

Bio::Coordinate::Result(3pm)				User Contributed Perl Documentation			      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:

	 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	:

perl v5.14.2							    2012-03-02					      Bio::Coordinate::Result(3pm)