NAME

       Bio::PopGen::MarkerI - A Population Genetic conceptual marker

SYNOPSIS

       # Get a Bio::PopGen::MarkerI somehow - like using a Bio::PopGen::Marker

         my $name = $marker->name();            # marker name
         my $description = $marker->description(); # description
         my $type = $marker->type();            # coded type of the marker
         my $unique_id = $marker->unique_id;    # optional unique ID

         my @alleles = $marker->get_Alleles();  # the known alleles
         my %allele_freqs = $marker->get_Allele_Frequencies(); # keys are marker names
                                                # vals are frequencies
                                                # may change to handle multiple populations

DESCRIPTION

       This is the basic interface for Markers which one can associate alleles with for
       calculating Theta and Pi.

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 email or 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 _

   name
        Title   : name
        Usage   : my $name = $marker->name();
        Function: Get the name of the marker
        Returns : string representing the name of the marker
        Args    :

   description
        Title   : description
        Usage   : my $desc = $marker->description
        Function: Get the marker description free text
        Returns : string
        Args    : [optional] string

   type
        Title   : type
        Usage   : my $type = $marker->type;
        Function: Get coded string for marker type
        Returns : string
        Args    : [optional] string

   unique_id
        Title   : unique_id
        Usage   : my $id = $marker->unique_id;
        Function: Get the unique marker ID
        Returns : unique ID string
        Args    : [optional ] string

   annotation
        Title   : annotation
        Usage   : $obj->annotation($seq_obj)
        Function: retrieve the attached annotation object
        Returns : Bio::AnnotationCollectionI or none;

       See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information. This
       method comes through extension from Bio::AnnotatableI.

   get_Alleles
        Title   : get_Alleles
        Usage   : my @alleles = $marker->get_Alleles();
        Function: Get the available marker alleles if they are known and stored
        Returns : Array of strings
        Args    : none

   get_Allele_Frequencies
        Title   : get_Allele_Frequencies
        Usage   : my %allele_freqs = $marker->get_Allele_Frequencies;
        Function: Get the alleles and their frequency (set relative to
                  a given population - you may want to create different
                  markers with the same name for different populations
                  with this current implementation
        Returns : Associative array (hash) where keys are the names of the alleles
        Args    : none