Bio::PopGen Individual
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::PopGen::Individual - An implementation of an Individual who has
Genotype or Sequence Results
Package variables
No package variables defined.
Inherit
Bio::PopGen::IndividualI Bio::Root::Root
Synopsis
  use Bio::PopGen::Individual;
my $ind = Bio::PopGen::Individual->new(-unique_id => $id, -genotypes => \@genotypes);
Description
This object is a container for genotypes.
Methods
BEGIN Code
newDescriptionCode
unique_idDescriptionCode
num_of_resultsDescriptionCode
annotationDescriptionCode
add_GenotypeDescriptionCode
reset_GenotypesDescriptionCode
remove_GenotypeDescriptionCode
get_GenotypesDescriptionCode
has_MarkerDescriptionCode
get_marker_namesDescriptionCode
Methods description
newcode    nextTop
 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_idcodeprevnextTop
 Title   : unique_id
Usage : my $id = $individual->unique_id
Function: Unique Identifier
Returns : string representing unique identifier
Args : string
num_of_resultscodeprevnextTop
 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
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
add_GenotypecodeprevnextTop
 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 - Bio::PopGen::GenotypeI object(s) containing
alleles plus a marker name
reset_GenotypescodeprevnextTop
 Title   : reset_Genotypes
Usage : $individual->reset_Genotypes;
Function: Reset the genotypes stored for this individual
Returns : none
Args : none
remove_GenotypecodeprevnextTop
 Title   : remove_Genotype
Usage : $individual->remove_Genotype(@names)
Function: Removes the genotypes for the requested markers
Returns : none
Args : Names of markers
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
BEGINTop
BEGIN {
 $UIDCOUNTER = 1
}
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  $self->{'_genotypes'} = {};
  my ($uid,$genotypes) = $self->_rearrange([qw(UNIQUE_ID
					       GENOTYPES)],@args);
  unless( defined $uid ) {
      $uid = $UIDCOUNTER++;
  } 
  $self->unique_id($uid);
  if( defined $genotypes ) {
      if( ref($genotypes) =~ /array/i ) {
	  $self->add_Genotype(@$genotypes);
      } else { 
	  $self->warn("Must provide a valid array reference to set the genotypes value in the contructor");
      }
  }
  return $self;
}
unique_iddescriptionprevnextTop
sub unique_id {
   my ($self) = shift;
   return $self->{'_unique_id'} = shift if @_;
   return $self->{'_unique_id'};
}
num_of_resultsdescriptionprevnextTop
sub num_of_results {
    return scalar keys %{shift->{'_genotypes'}};
}
annotationdescriptionprevnextTop
sub annotation {
   my ($self, $arg) = @_;
   return $self->{_annotation} unless $arg;
   $self->throw("Bio::AnnotationCollectionI required for argument") unless
       ref($arg) && $arg->isa('Bio::AnnotationCollectionI');
   return $self->{_annotation} = $arg;
}
add_GenotypedescriptionprevnextTop
sub add_Genotype {
   my ($self,@genotypes) = @_;
   
   foreach my $g ( @genotypes ) {
       if( !ref($g) || ! $g->isa('Bio::PopGen::GenotypeI') ) {
	   $self->warn("cannot add $g as a genotype skipping");
	   next;
       }
       my $mname = $g->marker_name;
       if( ! defined $mname || ! length($mname) ) { 
         # can't just say ! name b/c '0' wouldn't be valid 
$self->warn("cannot add genotype because marker name is not defined or is an empty string"); next; } if( $self->verbose > 0 && defined $self->{'_genotypes'}->{$mname} ) { # a warning when we have verbosity cranked up
$self->debug("Overwriting the previous value for $mname for this individual"); } # this will force Genotype individual_id to be set to
# the Individual it has been added for
$g->individual_id($self->unique_id); $self->{'_genotypes'}->{$mname} = $g; } return scalar keys %{$self->{'_genotypes'}};
}
reset_GenotypesdescriptionprevnextTop
sub reset_Genotypes {
    shift->{'_genotypes'} = {};
}
remove_GenotypedescriptionprevnextTop
sub remove_Genotype {
   my ($self,@mkrs) = @_;
   foreach my $m ( @mkrs ) {
       delete($self->{'_genotypes'}->{$m});
   }
}
get_GenotypesdescriptionprevnextTop
sub get_Genotypes {
   my ($self,@args) = @_;
   if( @args ) {
       unshift @args, '-marker' if( @args == 1 );  # deal with single args
my ($name) = $self->_rearrange([qw(MARKER)], @args); if( ! defined($name) ) { $self->warn("Only know how to process the -marker field currently"); return(); } my $v = $self->{'_genotypes'}->{$name}; return $v; } return values %{$self->{'_genotypes'} || {}};
}
has_MarkerdescriptionprevnextTop
sub has_Marker {
   my ($self,$name) = @_;
   return 0 if ! defined $name;

   $name = $name->name if ref($name) && $name->isa('Bio::PopGen::MarkerI');
   if( ref($name) ) { 
       $self->warn("Passed in a ".ref($name). " to has_Marker, expecting either a string or a Bio::PopGen::MarkerI");
       return 0;
   }
   return defined $self->{'_genotypes'}->{$name};
}
get_marker_namesdescriptionprevnextTop
sub get_marker_names {
   my ($self) = @_;
   return keys %{$self->{'_genotypes'}};
}


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
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
CONTRIBUTORSTop
Matthew Hahn, matthew.hahn-at-duke.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _