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 :