Bio::PopGen IndividualI
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Summary
Bio::PopGen::IndividualI - An individual who has Genotype or Sequence Results
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
  # Get a Bio::PopGen::IndividualI somehow
  # test if it has alleles/genotypes for a given marker
  if( $ind->has_marker($markername) ) {
  }
  # get the unique id
  print $ind->unique_id, "\n";

  # get the number of results (genotypes)
  print $ind->num_results;
Description
Describe the interface here
Methods
unique_idDescriptionCode
num_genotypesDescriptionCode
num_of_results
No description
Code
annotationDescriptionCode
get_GenotypesDescriptionCode
has_MarkerDescriptionCode
get_marker_namesDescriptionCode
Methods description
unique_idcode    nextTop
 Title   : unique_id
 Usage   : my $id = $individual->unique_id
 Function: Unique Identifier
 Returns : string representing unique identifier
 Args    : string
num_genotypescodeprevnextTop
 Title   : num_genotypes
 Usage   : my $count = $person->num_results;
 Function: returns the count of the number of Results for a person
 Returns : integer
 Args    : none
annotationcodeprevnextTop
 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
get_GenotypescodeprevnextTop
 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_MarkercodeprevnextTop
 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_namescodeprevnextTop
 Title   : get_marker_names
 Usage   : my @names = $individual->get_marker_names;
 Function: Returns the list of known marker names
 Returns : List of strings
 Args    : none
Methods code
unique_iddescriptionprevnextTop
sub unique_id {
   my ($self) = @_;
   $self->throw_not_implemented();
}
num_genotypesdescriptionprevnextTop
sub num_genotypes {
     shift->throw_not_implemented;
}
num_of_resultsdescriptionprevnextTop
sub num_of_results {
    my $self = shift;
    $self->deprecated("num_of_results is deprecated, use num_genotypes instead");
    $self->num_genotypes;
}
annotationdescriptionprevnextTop
sub annotation {
   my ($self, $arg) = @_;
   $self->throw_not_implemented();
}
get_GenotypesdescriptionprevnextTop
sub get_Genotypes {
    my ($self) = @_;
    $self->throw_not_implemented();
}
has_MarkerdescriptionprevnextTop
sub has_Marker {
   my ($self,$name) = @_;
   $self->throw_not_implemented();
}
get_marker_namesdescriptionprevnextTop
sub get_marker_names {
   my ($self) = @_;
   $self->throw_not_implemented();
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _