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Summary

Bio::EnsEMBL::Variation::IndividualGenotype- Module representing the genotype
of a single individual at a single position

Package variables

Included modules

Inherit

Bio::EnsEMBL::Feature Bio::EnsEMBL::Variation::Genotype

Synopsis

    print $genotype->variation()->name(), "\n";
    print $genotype->allele1(), '/', $genotype->allele2(), "\n";
    print $genotype->individual()->name(), "\n";

Description

This is a class representing the genotype of a single diploid individual at
a specific position

Methods

Methods description

  Arg [1]    : (optional) Bio::EnsEMBL::Variation::Individual $ind
  Example    : $ind = $ind_genotype->individual();
  Description: Getter/Setter for the individual associated with this genotype
  Returntype : Bio::EnsEMBL::Variation::Individual
  Exceptions : throw on bad argument
  Caller     : general
  Status     : At Risk

  Arg [-adaptor] :
    Bio::EnsEMBL::Variation::DBSQL::IndividualAdaptor
  Arg [-START] :
    see superclass constructor
  Arg [-END] :
    see superclass constructor
  Arg [-STRAND] :
    see superclass constructor
  Arg [-SLICE] :
    see superclass constructor
  Arg [-allele1] :
    string - One of the two alleles defining this genotype
  Arg [-allele2] :
    string - One of the two alleles defining this genotype
  Arg [-variation] :
    Bio::EnsEMBL::Variation::Variation - The variation associated with this
    genotype
  Arg [-individual] :
    Bio::EnsEMBL::Individual - The individual this genotype is for.
  Example    : $ind_genotype = Bio:EnsEMBL::Variation::IndividualGenotype->new
                   (-start   => 100,
		    -end     => 100,
		    -strand  => 1,
		    -slice   => $slice,
		    -allele1 => 'A',
                    -allele2 => 'T',
                    -variation => $variation,
                    -individual => $ind);
  Description: Constructor.  Instantiates an IndividualGenotype object.
  Returntype : Bio::EnsEMBL::Variation::IndividualGenotype
  Exceptions : throw on bad argument
  Caller     : general
  Status     : At Risk

  Arg [1]    : (optional) Bio::EnsEMBL::Variation::Variation $var
  Example    : $var = $genotype->variation();
  Description: Getter/Setter for the Variation as
  Returntype : Bio::EnsEMBL::Variation::Variation
  Exceptions : throw on bad argument
  Caller     : general
  Status     : At Risk

Methods code

sub individual {

  my $self = shift;
  if(@_) {
    my $ind = shift;
    if(defined($ind) &&
       (!ref($ind) || !$ind->isa('Bio::EnsEMBL::Variation::Individual'))) {
      throw('Bio::EnsEMBL::Variation::Individual argument expected');
    }
    return $self->{'individual'} = $ind;
  }
  return $self->{'individual'};

}

sub new {

    my $caller = shift;
    my $class = ref($caller) || $caller;

  my $self = $class->SUPER::new(@_);

  my ($adaptor, $allele1, $allele2, $var, $ind) =
    rearrange([qw(adaptor allele1 allele2 variation individual)],@_);

  if(defined($var) &&
     (!ref($var) || !$var->isa('Bio::EnsEMBL::Variation::Variation'))) {
    throw("Bio::EnsEMBL::Variation::Variation argument expected");
  }

  if(defined($ind) &&
     (!ref($ind) || !$ind->isa('Bio::EnsEMBL::Variation::Individual'))) {
    throw("Bio::EnsEMBL::Variation::Individual argument expected");
  }

    $self->{'adaptor'} = $adaptor;
    $self->{'allele1'} = $allele1;
    $self->{'allele2'} = $allele2;
    $self->{'individual'} = $ind;
    $self->{'variation'} = $var;
    
    return $self;

}

sub new_fast {

  my $class = shift;
  my $hashref = shift;
  return bless $hashref, $class;

}

sub variation {

  my $self = shift;

  if(@_) {
      #Setter: check wether it is a variation and return it
      my $v = shift;
      if(defined($v) &&
	 (!ref($v) || !$v->isa('Bio::EnsEMBL::Variation::Variation'))) {
	  throw('Bio::EnsEMBL::Variation::Variation argument expected.');
      }
      $self->{'variation'} = $v;
  }
  else{
      if(!defined($self->{'variation'}) && $self->{'adaptor'})    {
	  #lazy-load from database on demand
	  my $vfa = $self->{'adaptor'}->db()->get_VariationFeatureAdaptor();
	  %{$vfa->{'_slice_feature_cache'}} = (); #this is ugly, but I have no clue why the cache is not being properly stored...
	  my $vf = shift @{$vfa->fetch_all_by_Slice($self->feature_Slice())};
	  $self->{'variation'} = $vf->variation;
      }
  }
  return $self->{'variation'};
}

1;

}

General documentation

Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk