Raw content of Bio::Coordinate::Result
<![CDATA[# $Id: Result.pm,v 1.5.2.1 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;
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