Bio::EnsEMBL::Variation Allele
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Summary
Bio::EnsEMBL::Variation::Allele - A single allele of a nucleotide variation.
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Storable
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Inherit
Bio::EnsEMBL::Storable
Synopsis
    $allele = Bio::EnsEMBL::Variation::Allele->new
       (-allele => 'A',
        -frequency => 0.85,
        -population => $population);

    $delete = Bio::EnsEMBL::Variation::Allele->new
       (-allele => '-',
        -frequency => 0.15,
        -population => $population);

    ...

    $astr = $a->allele();
    $pop  = $a->population();
    $freq = $a->frequency();

    print $a->allele();
    if($a->populaton) {
       print " found in population ", $allele->population->name();
    }
    if(defined($a->frequency())) {
      print " with frequency ", $a->frequency();
    }
    print "\n";
Description
This is a class representing a single allele of a variation. In addition to
the nucleotide(s) (or absence of) that representing the allele frequency
and population information may be present.
Methods
alleleDescriptionCode
frequencyDescriptionCode
newDescriptionCode
populationDescriptionCode
Methods description
allelecode    nextTop
  Arg [1]    : string $newval (optional) 
               The new value to set the allele attribute to
  Example    : print $a->allele();
               $a1->allele('A');
               $a2->allele('-');
  Description: Getter/Setter for the allele attribute.  The allele is a string
               of nucleotide sequence, or a '-' representing the absence of
               sequence (deletion).
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : At Risk
frequencycodeprevnextTop
  Arg [1]    : float $newval (optional) 
               The new value to set the frequency attribute to
  Example    : $frequency = $a->frequency();
  Description: Getter/Setter for the frequency attribute. The frequency is
               the frequency of the occurance of the allele. If the population
               attribute it is the frequency of the allele within that
               population.
  Returntype : float
  Exceptions : none
  Caller     : general
  Status     : At Risk
newcodeprevnextTop
  Arg [-dbID]: int - unique internal identifier for the Allele
  Arg [-ADAPTOR]: Bio::EnsEMBL::Variation::DBSQL::AlleleAdaptor
  Arg [-ALLELE]: string - the nucleotide string representing the allele
  Arg [-FREQUENCY]: float - the frequency of the allele
  Arg [-POPULATION]: Bio::EnsEMBL::Variation::Population - the population
                     in which the allele was recorded
  Example    :     $allele = Bio::EnsEMBL::Variation::Allele->new
                      (-allele => 'A',
                       -frequency => 0.85,
                       -population => $pop);

  Description: Constructor.  Instantiates a new Allele object.
  Returntype : Bio::EnsEMBL::Variation::Allele
  Exceptions : none
  Caller     : general
  Status     : At Risk
populationcodeprevnextTop
  Arg [1]    : Bio::EnsEMBL::Variation::Population $newval (optional)
               The new value to set the population attribute to
  Example    : $population = $a->population();
  Description: Getter/Setter for the population attribute
  Returntype : Bio::EnsEMBL::Variation::Population
  Exceptions : throw on incorrect argument
  Caller     : general
  Status     : At Risk
Methods code
alleledescriptionprevnextTop
sub allele {
  my $self = shift;
  return $self->{'allele'} = shift if(@_);
  return $self->{'allele'};
}
frequencydescriptionprevnextTop
sub frequency {
  my $self = shift;
  return $self->{'frequency'} = shift if(@_);
  return $self->{'frequency'};
}
newdescriptionprevnextTop
sub new {
  my $caller = shift;
  my $class = ref($caller) || $caller;

  my ($dbID, $adaptor, $allele, $freq, $pop) =
    rearrange(['dbID', 'ADAPTOR', 'ALLELE', 'FREQUENCY', 'POPULATION'], @_);

  return bless {'dbID'    => $dbID,
                'adaptor' => $adaptor,
                'allele'  => $allele,
                'frequency' => $freq,
                'population' => $pop}, $class;
}
populationdescriptionprevnextTop
sub population {
  my $self = shift;

  if(@_) {
    if(!ref($_[0]) || !$_[0]->isa('Bio::EnsEMBL::Variation::Population')) {
      throw('Bio::EnsEMBL::Variation::Population argument expected.');
    }
    $self->{'population'} = shift;
  }

  return $self->{'population'};
}


1;
}
General documentation
CONTACTTop
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