File Coverage

Bio/PopGen/GenotypeI.pm
Criterion Covered Total %
statement 6 14 42.8
branch n/a
condition n/a
subroutine 2 6 33.3
pod 4 4 100.0
total 12 24 50.0


line stmt bran cond sub pod time code
1             # $Id $
2             #
3             # BioPerl module for Bio::PopGen::GenotypeI
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::GenotypeI - A marker and alleles for a specific individual
18              
19             =head1 SYNOPSIS
20              
21             Give standard usage here
22              
23             =head1 DESCRIPTION
24              
25             Describe the interface here
26              
27             =head1 FEEDBACK
28              
29             =head2 Mailing Lists
30              
31             User feedback is an integral part of the evolution of this and other
32             Bioperl modules. Send your comments and suggestions preferably to
33             the Bioperl mailing list. Your participation is much appreciated.
34              
35             bioperl-l@bioperl.org - General discussion
36             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
37              
38             =head2 Support
39              
40             Please direct usage questions or support issues to the mailing list:
41              
42             I
43              
44             rather than to the module maintainer directly. Many experienced and
45             reponsive experts will be able look at the problem and quickly
46             address it. Please include a thorough description of the problem
47             with code and data examples if at all possible.
48              
49             =head2 Reporting Bugs
50              
51             Report bugs to the Bioperl bug tracking system to help us keep track
52             of the bugs and their resolution. Bug reports can be submitted via
53             email or the web:
54              
55             https://github.com/bioperl/bioperl-live/issues
56              
57             =head1 AUTHOR - Jason Stajich
58              
59             Email jason-at-bioperl.org
60              
61             =head1 APPENDIX
62              
63             The rest of the documentation details each of the object methods.
64             Internal methods are usually preceded with a _
65              
66             =cut
67              
68              
69             # Let the code begin...
70              
71              
72             package Bio::PopGen::GenotypeI;
73 5     5   24 use strict;
  5         5  
  5         129  
74              
75              
76 5     5   18 use base qw(Bio::Root::RootI);
  5         7  
  5         644  
77              
78             =head2 marker_name
79              
80             Title : marker_name
81             Usage : my $name = $genotype->marker_name();
82             Function: Get the marker name for a genotype result
83             Returns : string
84             Args : none
85              
86              
87             =cut
88              
89             sub marker_name{
90 0     0 1   my ($self) = @_;
91 0           $self->throw_not_implemented();
92             }
93              
94             =head2 individual_id
95              
96             Title : individual_id
97             Usage : my $indid = $genotype->individual_id();
98             Function: Gets the individual id associated with a genotype
99             This is effectively a back reference since we will typically
100             associate a genotype with an individual with an
101             individual HAS-A genotype relationship.
102             Returns : unique id string for an individual
103             Args : none
104              
105              
106             =cut
107              
108             sub individual_id{
109 0     0 1   my ($self) = @_;
110 0           $self->throw_not_implemented();
111             }
112              
113              
114             =head2 annotation
115              
116             Title : annotation
117             Usage : my $annotation_collection = $genotype->annotation;
118             Function: Get/set a Bio::AnnotationCollectionI for this genotype
119             Returns : Bio::AnnotationCollectionI object
120             Args : [optional set] Bio::AnnotationCollectionI object
121              
122              
123             =cut
124              
125             sub annotation{
126 0     0 1   my ($self) = @_;
127 0           $self->throw_not_implemented();
128             }
129              
130             =head2 get_Alleles
131              
132             Title : get_Alleles
133             Usage : my @alleles = $genotype->get_Alleles();
134             Function: Get the alleles for a given marker and individual
135             Returns : array of alleles (strings in many implementations)
136             Args : none
137              
138              
139             =cut
140              
141             sub get_Alleles{
142 0     0 1   my ($self) = @_;
143 0           $self->throw_not_implemented();
144             }
145             1;