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Bio::PopGen::IndividuaUser Contributed Perl DocumentBio::PopGen::Individual(3)

NAME
       Bio::PopGen::Individual - An implementation of an Individual who	has
       Genotype	or Sequence Results

SYNOPSIS
	 use Bio::PopGen::Individual;

	 my $ind = Bio::PopGen::Individual->new(-unique_id => $id,
					       -genotypes => \@genotypes);

DESCRIPTION
       This object is a	container for genotypes.

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 the
       web:

	 https://github.com/bioperl/bioperl-live/issues

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 _

   new
	Title	: new
	Usage	: my $obj = Bio::PopGen::Individual->new();
	Function: Builds a new Bio::PopGen::Individual object
	Returns	: an instance of Bio::PopGen::Individual
	Args	: -unique_id =>	$id,
		  -genotypes =>	\@genotypes

   unique_id
	Title	: unique_id
	Usage	: my $id = $individual->unique_id
	Function: Unique Identifier
	Returns	: string representing unique identifier
	Args	: string

   num_of_results
	Title	: num_of_results
	Usage	: my $count = $person->num_results;
	Function: returns the count of the number of Results for a person
	Returns	: integer
	Args	: none

   annotation
	Title	: annotation
	Usage	: my $annotation_collection = $ind->annotation;
	Function: Get/set a Bio::AnnotationCollectionI for this	individual
	Returns	: Bio::AnnotationCollectionI object
	Args	: [optional set] Bio::AnnotationCollectionI object

   add_Genotype
	Title	: add_Genotype
	Usage	: $individual->add_Genotype
	Function: add a	genotype value
	Returns	: count	of the number of genotypes associated with this	individual
	Args	: @genotypes - L<Bio::PopGen::GenotypeI> object(s) containing
			       alleles plus a marker name

   reset_Genotypes
	Title	: reset_Genotypes
	Usage	: $individual->reset_Genotypes;
	Function: Reset	the genotypes stored for this individual
	Returns	: none
	Args	: none

   remove_Genotype
	Title	: remove_Genotype
	Usage	: $individual->remove_Genotype(@names)
	Function: Removes the genotypes	for the	requested markers
	Returns	: none
	Args	: Names	of markers

   get_Genotypes
	Title	: get_Genotypes
	Usage	: my @genotypes	= $ind->get_Genotypes(-marker => $markername);
	Function: Get the genotypes for	an individual, based on	a criteria
	Returns	: Array	of genotypes
	Args	: either none (return all genotypes) or
		  -marker => name of marker to return (exact match, case matters)

   has_Marker
	Title	: has_Marker
	Usage	: if( $ind->has_Marker($name) )	{}
	Function: Boolean test to see if an Individual has a genotype
		  for a	specific marker
	Returns	: Boolean (true	or false)
	Args	: String representing a	marker name

   get_marker_names
	Title	: get_marker_names
	Usage	: my @names = $individual->get_marker_names;
	Function: Returns the list of known marker names
	Returns	: List of strings
	Args	: none

perl v5.24.1			  2017-07-08	    Bio::PopGen::Individual(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | CONTRIBUTORS | APPENDIX

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