Bio::Coordinate Result
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Summary
Bio::Coordinate::Result - Results from coordinate transformation
Package variables
No package variables defined.
Included modules
Bio::Coordinate::ResultI
Bio::Location::Split
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::Match.
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_resultDescriptionCode
add_sub_Location
No description
Code
each_gapDescriptionCode
each_matchDescriptionCode
gapDescriptionCode
matchDescriptionCode
purge_gapsDescriptionCode
seq_idDescriptionCode
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
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
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    :
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    :
purge_gapscodeprevnextTop
 Title   : purge_gaps
 Usage   : $gap_count = $obj->purge_gaps;
 Function: remove all gaps from the Result
 Returns : count of removed gaps
 Args    :
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
Methods code
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 {  $self->add_sub_Location($_);} $value->each_Location;
}
add_sub_LocationdescriptionprevnextTop
sub add_sub_Location {
  my ($self,$value) = @_;
  $self->throw("Is not a Bio::LocationI but [$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);
}
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 $match->isa('Bio::Coordinate::Result::Match');
   }
   return @matches;
}
gapdescriptionprevnextTop
sub gap {
   my ($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 $self->{'_gap'};
}
matchdescriptionprevnextTop
sub match {
   my ($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 $self->{'_match'};
}
purge_gapsdescriptionprevnextTop
sub purge_gaps {
    my ($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;
}
seq_iddescriptionprevnextTop
sub seq_id {
    my ($self, $seqid) = @_;

    my @ls = $self->each_Location;
    if (@ls) {
	return $ls[0]->seq_id;
    } else {
	return undef;
    }
}
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://bio.perl.org/MailList.html             - About the mailing lists
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
email or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
AUTHOR - Heikki LehvaslaihoTop
Email: heikki@ebi.ac.uk
Address:
     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom
CONTRIBUTORSTop
Additional contributors names and emails here
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.