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Bio::Coordinate::ResulUser Contributed Perl DocumentBio::Coordinate::Result(3)

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.

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

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

AUTHOR
       Heikki Lehvaslaiho <heikki@bioperl.org>

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.

perl v5.24.1			  2016-12-15	    Bio::Coordinate::Result(3)

NAME | VERSION | SYNOPSIS | DESCRIPTION | ATTRIBUTES | METHODS | FEEDBACK | AUTHOR | COPYRIGHT

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