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


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


       # 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


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


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

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

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

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

        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.

        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

        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