File Coverage

Bio/PopGen/IndividualI.pm
Criterion Covered Total %
statement 6 20 30.0
branch n/a
condition n/a
subroutine 2 9 22.2
pod 6 7 85.7
total 14 36 38.8


line stmt bran cond sub pod time code
1             # $Id $
2             #
3             # BioPerl module for Bio::PopGen::IndividualI
4             #
5             # Please direct questions and support issues to
6             #
7             # Cared for by Jason Stajich
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
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 4     4   20 use strict;
  4         4  
  4         105  
82              
83              
84 4     4   14 use base qw(Bio::Root::RootI);
  4         140  
  4         798  
85              
86              
87             =head2 unique_id
88              
89             Title : unique_id
90             Usage : my $id = $individual->unique_id
91             Function: Unique Identifier
92             Returns : string representing unique identifier
93             Args : string
94              
95              
96             =cut
97              
98             sub unique_id{
99 0     0 1   my ($self) = @_;
100 0           $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 0     0 1   shift->throw_not_implemented;
116             }
117              
118             sub num_of_results{
119 0     0 0   my $self = shift;
120 0           $self->deprecated("num_of_results is deprecated, use num_genotypes instead");
121 0           $self->num_genotypes;
122             }
123              
124             =head2 annotation
125              
126             Title : annotation
127             Usage : my $annotation_collection = $ind->annotation;
128             Function: Get/set a Bio::AnnotationCollectionI for this individual
129             Returns : Bio::AnnotationCollectionI object
130             Args : [optional set] Bio::AnnotationCollectionI object
131              
132             =cut
133              
134             sub annotation{
135 0     0 1   my ($self, $arg) = @_;
136 0           $self->throw_not_implemented();
137             }
138              
139             =head2 get_Genotypes
140              
141             Title : get_Genotypes
142             Usage : my @genotypes = $ind->get_Genotypes(-marker => $markername);
143             Function: Get the genotypes for an individual, based on a criteria
144             Returns : Array of genotypes
145             Args : either none (return all genotypes) or
146             -marker => name of marker to return (exact match, case matters)
147              
148              
149             =cut
150              
151             sub get_Genotypes{
152 0     0 1   my ($self) = @_;
153 0           $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 0     0 1   my ($self,$name) = @_;
170 0           $self->throw_not_implemented();
171             }
172              
173             =head2 get_marker_names
174              
175             Title : get_marker_names
176             Usage : my @names = $individual->get_marker_names;
177             Function: Returns the list of known marker names
178             Returns : List of strings
179             Args : none
180              
181              
182             =cut
183              
184             sub get_marker_names{
185 0     0 1   my ($self) = @_;
186 0           $self->throw_not_implemented();
187             }
188              
189              
190             1;