Provided by: libbio-perl-perl_1.6.901-2_all bug


       Bio::PopGen::Genotype - An implementation of GenotypeI which is just an allele container


         use Bio::PopGen::Genotype;
         my $genotype = Bio::PopGen::Genotype->new(-marker_name   => $name,
                                                  -individual_id => $indid,
                                                  -alleles       => \@alleles);


       This object will contain alleles for a given marker for a given individual.

       The class variable BlankAlleles (accessible through $Bio::PopGen::Genotype::BlankAlleles =
       'somepattern') can be set to a regexp pattern for identifying blank alleles which should
       no be counted (they are effectively missing data).  By default it set to match white
       space, '-', 'N' or 'n', and '?' as blank alleles which are skipped.


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AUTHOR - Jason Stajich



       Matthew Hahn,


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

        Title   : new
        Usage   : my $obj = Bio::PopGen::Genotype->new();
        Function: Builds a new Bio::PopGen::Genotype object
        Returns : an instance of Bio::PopGen::Genotype
        Args    : -marker_name   => string representing name of the marker
                  -individual_id => string representing individual id (optional)
                  -alleles       => arrayref with each item in the array being an allele

        Title   : marker_name
        Usage   : my $name = $genotype->marker_name();
        Function: Get the marker name for a genotype result
        Returns : string
        Args    : [optional] marker name value to store

        Title   : individual_id
        Usage   : my $indid = $genotype->individual_id();
        Function: Gets the individual id associated with a genotype
                  This is effectively a back reference since we will typically
                  associate a genotype with an individual with an
                  individual HAS-A genotype relationship.
        Returns : unique id string for an individual
        Args    : none

        Title   : get_Alleles
        Usage   : my @alleles = $genotype->get_Alleles();
        Function: Get the alleles for a given marker and individual
        Returns : array of alleles (strings in this implementation)
        Args    : $showblank - boolean flag to indicate return ALL alleles not
                               skipping the coded EMPTY alleles

        Note    : Uses the class variable $BlankAlleles to test if alleles
                  should be skipped or not.

        Title   : add_Allele
        Usage   : $genotype->add_Allele(@alleles);
        Function: Add alleles to the genotype, at this point there is no
                  verification to insure that haploid individuals only have 1
                  allele or that diploids only have 2 - we assume that is
                  done by the user creating these objects
        Returns : count of the number of alleles in genotype
        Args    : Array of alleles to store

        Title   : reset_Alleles
        Usage   : $genotype->reset_Alleles;
        Function: Resets the stored alleles so the list is empty
        Returns : None
        Args    : None