diff variant_effect_predictor/Bio/EnsEMBL/SNP.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/SNP.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,177 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 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
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=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;
+use Scalar::Util qw(weaken isweak);
+
+@ISA = qw( Bio::EnsEMBL::ExternalData::Variation );
+
+
+sub new_fast {
+  my $class = shift;
+  my $hashref = shift;
+  my $self = bless $hashref, $class;
+  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
+  return $self;
+}
+
+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;