Raw content of Bio::EnsEMBL::SNP
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::SNP
=head1 SYNOPSIS
$snp = new Bio::EnsEMBL::SNP(
-start => 10,
-end => 10,
-strand => 1,
-source => 'The SNP Consortium',
-score => 99, # new meaning
-status => 'suspected', # new
-alleles => 't|c' # new
);
# add it to an annotated sequence
$annseq->add_SeqFeature($feat);
=head1 DESCRIPTION
This class was written because the EnsEMBL::ExternalData::Variation
object is way too slow. There was simply too much chaining to bioperl
methods many, many layers deep. This object behaves like a Variation
but has a much faster constructor, and faster accessors for the relevant
methods needed by the web.
=head1 METHODS
=cut
package Bio::EnsEMBL::SNP;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::ExternalData::Variation;
@ISA = qw( Bio::EnsEMBL::ExternalData::Variation );
sub new_fast {
my $class = shift;
my $hashref = shift;
return bless $hashref, $class;
}
sub dbID {
my $self = shift;
if(@_) {
$self->{'dbID'} = shift;
}
return $self->{'dbID'};
}
sub position {
my ($self, $arg) = @_;
if(defined $arg) {
$self->{_gsf_start} = $arg;
$self->{_gsf_end} = $arg;
}
return $self->{_gsf_start};
}
sub start {
my ($self, $arg) = @_;
if(defined $arg) {
$self->{_gsf_start} = $arg;
}
return $self->{_gsf_start};
}
sub end {
my ($self, $arg) = @_;
if(defined $arg) {
$self->{_gsf_end} = $arg;
}
return $self->{_gsf_end};
}
sub source {
my ($self, $arg) = @_;
if(defined $arg) {
$self->{_source} = $arg;
}
return $self->{_source};
}
sub score {
my ($self, $arg) = @_;
if(defined $arg) {
$self->{_gsf_score} = $arg;
}
return $self->{_gsf_score};
}
sub source_tag {
my ($self, $arg) = @_;
if(defined $arg) {
$self->{_source_tag} = $arg;
}
return $self->{_source_tag};
}
sub source_version {
my ($self, $arg) = @_;
if(defined $arg) {
$self->{_source_version} = $arg;
}
return $self->{_source_version};
}
=head2 display_name
Arg [1] : none
Example : print $snp->display_name();
Description: This method returns a string that is considered to be
the 'display' identifier. For snps this is the
returns the same thing as the id method.
Returntype : string
Exceptions : none
Caller : web drawing code
=cut
sub display_name {
my $self = shift;
return $self->id();
}
1;
]]>