Bio::EnsEMBL SNP
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvsRaw content
Summary
Bio::EnsEMBL::SNP
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::ExternalData::Variation
Inherit
Bio::EnsEMBL::ExternalData::Variation
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);
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.
Methods
dbID
No description
Code
display_nameDescriptionCode
end
No description
Code
new_fast
No description
Code
position
No description
Code
score
No description
Code
source
No description
Code
source_tag
No description
Code
source_version
No description
Code
start
No description
Code
Methods description
display_namecode    nextTop
  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
Methods code
dbIDdescriptionprevnextTop
sub dbID {
  my $self = shift;
  
  if(@_) {
    $self->{'dbID'} = shift;
  }

  return $self->{'dbID'};
}
display_namedescriptionprevnextTop
sub display_name {
  my $self = shift;
  return $self->id();
}



1;
}
enddescriptionprevnextTop
sub end {
  my ($self, $arg) = @_;

  if(defined $arg) {
    $self->{_gsf_end} = $arg;
  }

  return $self->{_gsf_end};
}
new_fastdescriptionprevnextTop
sub new_fast {
  my $class = shift;
  my $hashref = shift;

  return bless $hashref, $class;
}
positiondescriptionprevnextTop
sub position {
  my ($self, $arg) = @_;

  if(defined $arg) {
    $self->{_gsf_start} = $arg;
    $self->{_gsf_end}   = $arg;
  }

  return $self->{_gsf_start};
}
scoredescriptionprevnextTop
sub score {
  my ($self, $arg) = @_;

  if(defined $arg) {
    $self->{_gsf_score} = $arg;
  }

  return $self->{_gsf_score};
}
sourcedescriptionprevnextTop
sub source {
   my ($self, $arg) = @_;

   if(defined $arg) {
     $self->{_source} = $arg;
   }

   return $self->{_source};
}
source_tagdescriptionprevnextTop
sub source_tag {
  my ($self, $arg) = @_;

  if(defined $arg) {
    $self->{_source_tag} = $arg;
  }

  return $self->{_source_tag};
}
source_versiondescriptionprevnextTop
sub source_version {
  my ($self, $arg) = @_;

  if(defined $arg) {
    $self->{_source_version} = $arg;
  }

  return $self->{_source_version};
}
startdescriptionprevnextTop
sub start {
  my ($self, $arg) = @_;

  if(defined $arg) {
    $self->{_gsf_start} = $arg;
  }
  
  return $self->{_gsf_start};
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.