Bio::Coordinate::ResulUser Contributed Perl DocumentBio::Coordinate::Result(3)NAMEBio::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 :
perl v5.14.1 2011-07-22 Bio::Coordinate::Result(3)
