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.\" ========================================================================
.\"
.IX Title "Bio::PopGen::PopulationI 3pm"
.TH Bio::PopGen::PopulationI 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::PopulationI \- Interface for Populations
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  # Get Bio::PopGen::PopulationI object somehow, like
\&  # from Bio::Population::Population
\&
\&  print "name is ", $population\->name(), "\en";
\&  print "source is ", $population\->source(), "\en";
\&  print "description is ", $population\->description(), "\en";
\&
\&  print "For marker $markername:\en";
\&  foreach my $genotype ( $population\->get_Genotypes(\-marker => $markername) ) {
\&      print "Individual ", $genotype\->individual_id, " genotype alleles are ",
\&      join(\*(Aq,\*(Aq, $genotype\->get_Alleles()), "\en";
\&  }
\&  # get a marker with allele frequencies calculated from the population
\&  my $marker = $population\->get_Marker($markername); 
\&  my %af = $marker\->get_Allele_Frequencies;
\&  foreach my $allele ( keys %af ) {
\&      print "$allele $af{$allele}\en";
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This interface describes the basics of a population.  One can use this
object to get the genotypes of specific individuals, only those
individuals which have a certain marker, or create a marker with
allele frequency information.
.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 = $pop\->name
\& Function: Get the population name
\& Returns : string representing population name
\& Args    : [optional] string representing population name
.Ve
.SS "description"
.IX Subsection "description"
.Vb 5
\& Title   : description
\& Usage   : my $description = $pop\->description
\& Function: Get the population description
\& Returns : string representing population description
\& Args    : [optional] string representing population description
.Ve
.SS "source"
.IX Subsection "source"
.Vb 5
\& Title   : source
\& Usage   : my $source = $pop\->source
\& Function: Get the population source
\& Returns : string representing population source
\& Args    : [optional] string representing population source
.Ve
.SS "annotation"
.IX Subsection "annotation"
.Vb 5
\& Title   : annotation
\& Usage   : my $annotation_collection = $pop\->annotation;
\& Function: Get/set a Bio::AnnotationCollectionI for this population
\& Returns : Bio::AnnotationCollectionI object
\& Args    : [optional set] Bio::AnnotationCollectionI object
.Ve
.SS "get_Individuals"
.IX Subsection "get_Individuals"
.Vb 8
\& Title   : get_Individuals
\& Usage   : my @inds = $pop\->get_Individuals();
\& Function: Return the individuals, alternatively restrict by a criteria
\& Returns : Array of L<Bio::PopGen::IndividualI> objects
\& Args    : none if want all the individuals OR,
\&           \-unique_id => To get an individual with a specific id
\&           \-marker    => To only get individuals which have a genotype specific
\&                        for a specific marker name
.Ve
.SS "get_Genotypes"
.IX Subsection "get_Genotypes"
.Vb 6
\& Title   : get_Genotypes
\& Usage   : my @genotypes = $pop\->get_Genotypes(\-marker => $name)
\& Function: Get the genotypes for all the individuals for a specific
\&           marker name
\& Returns : Array of L<Bio::PopGen::GenotypeI> objects
\& Args    : \-marker => name of the marker
.Ve
.SS "get_Marker"
.IX Subsection "get_Marker"
.Vb 5
\& Title   : get_Marker
\& Usage   : my $marker = $population\->get_Marker($name)
\& Function: Get a Bio::PopGen::Marker object based on this population
\& Returns : L<Bio::PopGen::MarkerI> object
\& Args    : name of the marker
.Ve
.SS "get_marker_names"
.IX Subsection "get_marker_names"
.Vb 5
\& Title   : get_marker_names
\& Usage   : my @names = $pop\->get_marker_names;
\& Function: Get the names of the markers
\& Returns : Array of strings
\& Args    : none
.Ve
.SS "get_Markers"
.IX Subsection "get_Markers"
.Vb 7
\& Title   : get_Markers
\& Usage   : my @markers = $pop\->get_Markers();
\& Function: Will retrieve a list of instantiated MarkerI objects 
\&           for a population.  This is a convience method combining
\&           get_marker_names with get_Marker
\& Returns : List of array of Bio::PopGen::MarkerI objects
\& Args    : none
.Ve
.SS "get_number_individuals"
.IX Subsection "get_number_individuals"
.Vb 6
\& Title   : get_number_individuals
\& Usage   : my $count = $pop\->get_number_individuals;
\& Function: Get the count of the number of individuals
\& Returns : integer >= 0
\& Args    : [optional] marker name, will return a count of the number
\&           of individuals which have this marker
.Ve