Bio::Coordinate Result
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Coordinate::Result - Results from coordinate transformation
Package variables
No package variables defined.
Inherit
Bio::Coordinate::ResultI Bio::Location::Split
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.
Methods
add_sub_Location
No description
Code
add_resultDescriptionCode
seq_idDescriptionCode
each_gapDescriptionCode
each_matchDescriptionCode
matchDescriptionCode
gapDescriptionCode
purge_gapsDescriptionCode
Methods description
add_resultcode    nextTop
 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_idcodeprevnextTop
  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_gapcodeprevnextTop
 Title   : each_gap
Usage : $obj->each_gap();
Function:
Returns a list of Bio::Coordianate::Result::Gap objects. Returns : list of gaps Args : none
each_matchcodeprevnextTop
 Title   : each_match
Usage : $obj->each_match();
Function:
Returns a list of Bio::Coordinate::Result::Match objects. Returns : list of Matchs Args : none
matchcodeprevnextTop
 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 :
gapcodeprevnextTop
 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_gapscodeprevnextTop
 Title   : purge_gaps
Usage : $gap_count = $obj->purge_gaps;
Function: remove all gaps from the Result
Returns : count of removed gaps
Args :
Methods code
add_sub_LocationdescriptionprevnextTop
sub add_sub_Location {
  my ($self,$value) = @_;
  if( ! $value ) {
      $self->warn("provding an empty value for location\n");
      return;
  }
  $self->throw("Is not a Bio::LocationI but [$value]")
      unless $value->isa('Bio::LocationI');

  $self->{'_match'} = $value
      if $value->isa('Bio::Coordinate::Result::Match');

  $self->{'_gap'} = $value
      if $value->isa('Bio::Coordinate::Result::Gap');

  $self->SUPER::add_sub_Location($value);
}
add_resultdescriptionprevnextTop
sub add_result {
  my ($self,$value) = @_;

  $self->throw("Is not a Bio::Coordinate::Result but [$value]")
      unless $value->isa('Bio::Coordinate::Result');

  map { $self->add_sub_Location($_) } $value->each_Location;
}
seq_iddescriptionprevnextTop
sub seq_id {
    my ($self, $seqid) = @_;

    my @ls = $self->each_Location;
    if (@ls) {
	return $ls[0]->seq_id;
    } else {
	return;
    }
}
each_gapdescriptionprevnextTop
sub each_gap {
   my ($self) = @_;

   my @gaps;
   foreach my $gap ($self->each_Location) {
       push @gaps, $gap if $gap->isa('Bio::Coordinate::Result::Gap');
   }
   return @gaps;
}
each_matchdescriptionprevnextTop
sub each_match {
   my ($self) = @_;

   my @matches;
   foreach my $match ($self->each_Location) {
       push @matches, $match if $match->isa('Bio::Coordinate::Result::Match');
   }
   return @matches;
}
matchdescriptionprevnextTop
sub match {
   my ($self) = @_;

   $self->warn("More than one match in results")
       if $self->each_match > 1 and $self->verbose > 0;
   unless (defined $self->{'_match'} ) {
       my @m = $self->each_match;
       $self->{'_match'} = $m[-1];
   }
   return $self->{'_match'};
}
gapdescriptionprevnextTop
sub gap {
   my ($self) = @_;

   $self->warn("More than one gap in results")
       if $self->each_gap > 1 and $self->verbose > 0;
   unless (defined $self->{'_gap'} ) {
       my @m = $self->each_gap;
       $self->{'_gap'} = $m[-1];
   }
   return $self->{'_gap'};
}
purge_gapsdescriptionprevnextTop
sub purge_gaps {
    my ($self) = @_;
    my @matches;
    my $count = 0;

    foreach my $loc ($self->each_Location) {
        if ($loc->isa('Bio::Coordinate::Result::Match')) {
            push @matches, $loc;
        } else {
            $count++
        }
    }
    @{$self->{'_sublocations'}} = ();
    delete $self->{'_gap'} ;
    push @{$self->{'_sublocations'}}, @matches;
    return $count;
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
add_locationTop
 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
Convenience methodsTop
These methods are shortcuts to Match and Gap locations.