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.\" ========================================================================
.\"
.IX Title "Bio::PopGen::MarkerI 3pm"
.TH Bio::PopGen::MarkerI 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::PopGen::MarkerI \- A Population Genetic conceptual marker
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
# Get a Bio::PopGen::MarkerI somehow \- like using a Bio::PopGen::Marker
.PP
.Vb 4
\&  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
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is the basic interface for Markers which one can associate
alleles with for calculating Theta and Pi.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason\-at\-bioperl.org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Matthew Hahn, matthew.hahn\-at\-duke.edu
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "name"
.IX Subsection "name"
.Vb 5
\& Title   : name
\& Usage   : my $name = $marker\->name();
\& Function: Get the name of the marker
\& Returns : string representing the name of the marker
\& Args    :
.Ve
.SS "description"
.IX Subsection "description"
.Vb 5
\& Title   : description
\& Usage   : my $desc = $marker\->description
\& Function: Get the marker description free text
\& Returns : string
\& Args    : [optional] string
.Ve
.SS "type"
.IX Subsection "type"
.Vb 5
\& Title   : type
\& Usage   : my $type = $marker\->type;
\& Function: Get coded string for marker type
\& Returns : string
\& Args    : [optional] string
.Ve
.SS "unique_id"
.IX Subsection "unique_id"
.Vb 5
\& Title   : unique_id
\& Usage   : my $id = $marker\->unique_id;
\& Function: Get the unique marker ID
\& Returns : unique ID string
\& Args    : [optional ] string
.Ve
.SS "annotation"
.IX Subsection "annotation"
.Vb 4
\& Title   : annotation
\& Usage   : $obj\->annotation($seq_obj)
\& Function: retrieve the attached annotation object
\& Returns : Bio::AnnotationCollectionI or none;
.Ve
.PP
See Bio::AnnotationCollectionI and Bio::Annotation::Collection
for more information. This method comes through extension from
Bio::AnnotatableI.
.SS "get_Alleles"
.IX Subsection "get_Alleles"
.Vb 5
\& 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
.Ve
.SS "get_Allele_Frequencies"
.IX Subsection "get_Allele_Frequencies"
.Vb 8
\& 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
.Ve