NAME

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

SYNOPSIS

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

DESCRIPTION

       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.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

       Email jason-at-bioperl.org

CONTRIBUTORS

       Matthew Hahn, matthew.hahn-at-duke.edu

APPENDIX

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

   new
        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

   marker_name
        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

   marker_type
        Title   : marker_type
        Usage   : my $name = $genotype->marker_type();
        Function: Get the marker type for a genotype result
        Returns : M (microsatellite, or other multi-allelic
                  locus) or S (biallelic/SNP locus)
        Args    : [optional] marker type value to store

   individual_id
        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

   get_Alleles
        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.

   add_Allele
        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

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