Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Variation::Allele - Sequence object with allele-specific attributes


         $allele1 = Bio::Variation::Allele->new ( -seq => 'A',
                                                  -id  => 'AC00001.1',
                                                  -alphabet => 'dna',
                                                  -is_reference => 1


       List of alleles describe known sequence alternatives in a variable region.  Alleles are
       contained in Bio::Variation::VariantI complying objects.  See Bio::Variation::VariantI for

       Bio::Varation::Alleles are PrimarySeqI complying objects which can contain database cross
       references as specified in Bio::DBLinkContainerI interface, too.

       A lot of the complexity with dealing with Allele objects are caused by null alleles;
       Allele objects that have zero length sequence string.

       In addition describing the allele by its sequence , it possible to give describe repeat
       structure within the sequence. This done using methods repeat_unit (e.g. 'ca') and
       repeat_count (e.g. 7).


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AUTHOR - Heikki Lehvaslaiho

       Email:  heikki-at-bioperl-dot-org


       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        Title   : is_reference
        Usage   : $obj->is_reference()
        Function: sets and returns boolean values.
                  Unset values return false.
        Example : $obj->is_reference()
        Returns : boolean
        Args    : optional true of false value

        Title   : add_DBLink
        Usage   : $self->add_DBLink($ref)
        Function: adds a link object
        Example :
        Returns :
        Args    :

        Title   : each_DBLink
        Usage   : foreach $ref ( $self->each_DBlink() )
        Function: gets an array of DBlink of objects
        Example :
        Returns :
        Args    :

        Title   : repeat_unit
        Usage   : $obj->repeat_unit('ca');

                   Sets and returns the sequence of the repeat_unit the
                   allele is composed of.

        Example :
        Returns : string
        Args    : string

        Title   : repeat_count
        Usage   : $obj->repeat_count();

                   Sets and returns the number of repeat units in the allele.

        Example :
        Returns : string
        Args    : string

        Title   : count
        Usage   : $obj->count();

                   Sets and returns the number of times this allele was observed.

        Example :
        Returns : string
        Args    : string

        Title   : frequency
        Usage   : $obj->frequency();

                   Sets and returns the frequency of the allele in the observed

        Example :
        Returns : string
        Args    : string