# $Id: PopulationI.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::PopGen::PopulationI # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::PopulationI - Interface for Populations =head1 SYNOPSIS # Get Bio::PopGen::PopulationI object somehow, like # from Bio::Population::Population print "name is ", $population->name(), "\n"; print "source is ", $population->source(), "\n"; print "description is ", $population->description(), "\n"; print "For marker $markername:\n"; foreach my $genotype ( $population->get_Genotypes(-marker => $markername) ) { print "Individual ", $genotype->individual_id, " genotype alleles are ", join(',', $genotype->get_Alleles()), "\n"; } # 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}\n"; } =head1 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. =head1 FEEDBACK =head2 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 =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =head2 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: http://bugzilla.open-bio.org/ =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, matthew.hahn-at-duke.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::PopulationI; use strict; use Carp; use base qw(Bio::Root::RootI); =head2 name Title : name Usage : my $name = $pop->name Function: Get the population name Returns : string representing population name Args : [optional] string representing population name =cut sub name{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 description Title : description Usage : my $description = $pop->description Function: Get the population description Returns : string representing population description Args : [optional] string representing population description =cut sub description{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 source Title : source Usage : my $source = $pop->source Function: Get the population source Returns : string representing population source Args : [optional] string representing population source =cut sub source{ my ($self,@args) = @_; $self->throw_not_implemented(); } =head2 annotation Title : annotation Usage : my $annotation_collection = $pop->annotation; Function: Get/set a Bio::AnnotationCollectionI for this population Returns : Bio::AnnotationCollectionI object Args : [optional set] Bio::AnnotationCollectionI object =cut sub annotation{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_Individuals Title : get_Individuals Usage : my @inds = $pop->get_Individuals(); Function: Return the individuals, alternatively restrict by a criteria Returns : Array of L 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 =cut sub get_Individuals{ shift->throw_not_implemented(); } =head2 get_Genotypes 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 objects Args : -marker => name of the marker =cut sub get_Genotypes{ shift->throw_not_implemented; } =head2 get_Marker Title : get_Marker Usage : my $marker = $population->get_Marker($name) Function: Get a Bio::PopGen::Marker object based on this population Returns : L object Args : name of the marker =cut sub get_Marker{ shift->throw_not_implemented(); } =head2 get_marker_names Title : get_marker_names Usage : my @names = $pop->get_marker_names; Function: Get the names of the markers Returns : Array of strings Args : none =cut sub get_marker_names{ my ($self) = @_; $self->throw_not_implemented(); } =head2 get_Markers Title : get_Markers Usage : my @markers = $pop->get_Markers(); Function: Will retrieve a list of instantiated MarkerI objects for a population. This is a convience method combining get_marker_names with get_Marker Returns : List of array of Bio::PopGen::MarkerI objects Args : none =cut sub get_Markers{ my ($self) = shift; return map { $self->get_Marker($_) } $self->get_marker_names(); } =head2 get_number_individuals Title : get_number_individuals Usage : my $count = $pop->get_number_individuals; Function: Get the count of the number of individuals Returns : integer >= 0 Args : [optional] marker name, will return a count of the number of individuals which have this marker =cut sub get_number_individuals{ my ($self) = @_; $self->throw_not_implemented(); } 1;