Christopher Fields > BioPerl > Bio::Coordinate::Result

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Module Version: 1.006924   Source  

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.

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

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    :
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