Bio/PopGen/IndividualI.pm

   1 # $Id $
   2 #
   3 # BioPerl module for Bio::PopGen::IndividualI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Jason Stajich <jason-at-bioperl.org>
   8 #
   9 # Copyright Jason Stajich
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::PopGen::IndividualI - An individual who has Genotype or Sequence Results
  18
  19 =head1 SYNOPSIS
  20
  21   # Get a Bio::PopGen::IndividualI somehow
  22   # test if it has alleles/genotypes for a given marker
  23   if( $ind->has_marker($markername) ) {
  24   }
  25   # get the unique id
  26   print $ind->unique_id, "\n";
  27
  28   # get the number of results (genotypes)
  29   print $ind->num_results;
  30
  31 =head1 DESCRIPTION
  32
  33 Describe the interface here
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to
  41 the Bioperl mailing list.  Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 I<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 of the bugs and their resolution. Bug reports can be submitted via
  61 email or the web:
  62
  63   https://github.com/bioperl/bioperl-live/issues
  64
  65 =head1 AUTHOR - Jason Stajich
  66
  67 Email jason-at-bioperl.org
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object methods.
  72 Internal methods are usually preceded with a _
  73
  74 =cut
  75
  76
  77 # Let the code begin...
  78
  79
  80 package Bio::PopGen::IndividualI;
  81 use strict;
  82
  83
  84 use base qw(Bio::Root::RootI);
  85
  86
  87 =head2 unique_id
  88
  89  Title   : unique_id
  90  Usage   : my $id = $individual->unique_id
  91  Function: Unique Identifier
  92  Returns : string representing unique identifier
  93  Args    : string
  94
  95
  96 =cut
  97
  98 sub unique_id{
  99    my ($self) = @_;
 100    $self->throw_not_implemented();
 101 }
 102
 103
 104 =head2 num_genotypes
 105
 106  Title   : num_genotypes
 107  Usage   : my $count = $person->num_results;
 108  Function: returns the count of the number of Results for a person
 109  Returns : integer
 110  Args    : none
 111
 112 =cut
 113
 114 sub num_genotypes {
 115     shift->throw_not_implemented;
 116 }
 117
 118 sub num_of_results{
 119     my $self = shift;
 120     $self->deprecated("num_of_results is deprecated, use num_genotypes instead");
 121     $self->num_genotypes;
 122 }
 123
 124 =head2 annotation
 125
 126  Title   : annotation
 127  Usage   : my $annotation_collection = $ind->annotation;
 128  Function: Get/set a Bio::AnnotationCollectionI for this individual
 129  Returns : Bio::AnnotationCollectionI object
 130  Args    : [optional set] Bio::AnnotationCollectionI object
 131
 132 =cut
 133
 134 sub annotation{
 135    my ($self, $arg) = @_;
 136    $self->throw_not_implemented();
 137 }
 138
 139 =head2 get_Genotypes
 140
 141  Title   : get_Genotypes
 142  Usage   : my @genotypes = $ind->get_Genotypes(-marker => $markername);
 143  Function: Get the genotypes for an individual, based on a criteria
 144  Returns : Array of genotypes
 145  Args    : either none (return all genotypes) or
 146            -marker => name of marker to return (exact match, case matters)
 147
 148
 149 =cut
 150
 151 sub get_Genotypes{
 152     my ($self) = @_;
 153     $self->throw_not_implemented();
 154 }
 155
 156 =head2 has_Marker
 157
 158  Title   : has_Marker
 159  Usage   : if( $ind->has_Marker($name) ) {}
 160  Function: Boolean test to see if an Individual has a genotype
 161            for a specific marker
 162  Returns : Boolean (true or false)
 163  Args    : String representing a marker name
 164
 165
 166 =cut
 167
 168 sub has_Marker{
 169    my ($self,$name) = @_;
 170    $self->throw_not_implemented();
 171 }
 172
 173 =head2 get_marker_names
 174
 175  Title   : get_marker_names
 176  Usage   : my @names = $individual->get_marker_names;
 177  Function: Returns the list of known marker names
 178  Returns : List of strings
 179  Args    : none
 180
 181
 182 =cut
 183
 184 sub get_marker_names{
 185    my ($self) = @_;
 186    $self->throw_not_implemented();
 187 }
 188
 189
 190 1;