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.\" ========================================================================
.\"
.IX Title "Bio::Coordinate::Result 3pm"
.TH Bio::Coordinate::Result 3pm "2014-07-13" "perl v5.18.2" "User Contributed Perl Documentation"
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.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::Coordinate::Result;
\&
\&  #get results from a Bio::Coordinate::MapperI
\&  $matched = $result\->each_match;
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
If only one Match is returned, there is a convenience method of
retrieving it or accessing its methods. Same holds true for a Gap.
.SS "add_location"
.IX Subsection "add_location"
.Vb 3
\& 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
.Ve
.SS "add_result"
.IX Subsection "add_result"
.Vb 6
\& 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
.Ve
.SS "seq_id"
.IX Subsection "seq_id"
.Vb 3
\&  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
.Ve
.SS "each_gap"
.IX Subsection "each_gap"
.Vb 3
\& Title   : each_gap
\& Usage   : $obj\->each_gap();
\& Function:
\&
\&            Returns a list of Bio::Coordianate::Result::Gap objects.
\&
\& Returns : list of gaps
\& Args    : none
.Ve
.SS "each_match"
.IX Subsection "each_match"
.Vb 3
\& Title   : each_match
\& Usage   : $obj\->each_match();
\& Function:
\&
\&            Returns a list of Bio::Coordinate::Result::Match objects.
\&
\& Returns : list of Matchs
\& Args    : none
.Ve
.SS "match"
.IX Subsection "match"
.Vb 6
\& 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    :
.Ve
.SS "gap"
.IX Subsection "gap"
.Vb 6
\& 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    :
.Ve
.SS "purge_gaps"
.IX Subsection "purge_gaps"
.Vb 5
\& Title   : purge_gaps
\& Usage   : $gap_count = $obj\->purge_gaps;
\& Function: remove all gaps from the Result
\& Returns : count of removed gaps
\& Args    :
.Ve