Raw content of Bio::Coordinate::Result # $Id: Result.pm,v 2003/02/20 05:11:45 heikki Exp $ # # bioperl module for Bio::Coordinate::Result # # Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk> # # Copyright Heikki Lehvaslaiho # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Coordinate::Result - Results from coordinate transformation =head1 SYNOPSIS use Bio::Coordinate::Result; #get results from a Bio::Coordinate::MapperI $matched = $result->each_match; =head1 DESCRIPTION The results from Bio::Coordinate::MapperI are kept in an object which itself is a split location, See L<Bio::Location::Split>. The results are either Matches or Gaps. See L<Bio::Coordinate::Result::Match> and L<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. =head1 FEEDBACK =head2 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://bio.perl.org/MailList.html - About the mailing lists =head2 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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Heikki Lehvaslaiho Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Coordinate::Result; use vars qw(@ISA ); use strict; use Bio::Location::Split; use Bio::Coordinate::ResultI; @ISA = qw(Bio::Location::Split Bio::Coordinate::ResultI); =head2 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 =cut 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); } =head2 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 =cut 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; } =head2 seq_id Title : seq_id Usage : my $seqid = $location->seq_id(); Function: Get/Set seq_id that location refers to We override this here in order to propagate to all sublocations which are not remote (provided this root is not remote either) Returns : seq_id Args : [optional] seq_id value to set =cut sub seq_id { my ($self, $seqid) = @_; my @ls = $self->each_Location; if (@ls) { return $ls[0]->seq_id; } else { return undef; } } =head2 Convenience methods These methods are shortcuts to Match and Gap locations. =cut =head2 each_gap Title : each_gap Usage : $obj->each_gap(); Function: Returns a list of Bio::Coordianate::Result::Gap objects. Returns : list of gaps Args : none =cut sub each_gap{ my ($self) = @_; my @gaps; foreach my $gap ($self->each_Location) { push @gaps, $gap if $gap->isa('Bio::Coordinate::Result::Gap'); } return @gaps; } =head2 each_match Title : each_match Usage : $obj->each_match(); Function: Returns a list of Bio::Coordinate::Result::Match objects. Returns : list of Matchs Args : none =cut sub each_match { my ($self) = @_; my @matches; foreach my $match ($self->each_Location) { push @matches, $match if $match->isa('Bio::Coordinate::Result::Match'); } return @matches; } =head2 match Title : match Usage : $match_object = $obj->match(); #or $gstart = $obj->gap->start; Function: Read only method for retrieving or accessing the match object. Returns : one Bio::Coordinate::Result::Match Args : =cut sub match { my ($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'}; } =head2 gap Title : gap Usage : $gap_object = $obj->gap(); #or $gstart = $obj->gap->start; Function: Read only method for retrieving or accessing the gap object. Returns : one Bio::Coordinate::Result::Gap Args : =cut sub gap { my ($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'}; } =head2 purge_gaps Title : purge_gaps Usage : $gap_count = $obj->purge_gaps; Function: remove all gaps from the Result Returns : count of removed gaps Args : =cut sub purge_gaps { my ($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;