File Coverage

Bio/Ontology/OBOterm.pm
Criterion Covered Total %
statement 15 15 100.0
branch n/a
condition n/a
subroutine 5 5 100.0
pod 1 1 100.0
total 21 21 100.0


line stmt bran cond sub pod time code
1              
2             =head1 NAME
3              
4             Bio::Ontology::OBOterm - representation of OBO terms
5              
6             =head1 SYNOPSIS
7              
8             $term = Bio::Ontology::OBOterm->new
9             ( -identifier => "GO:0005623",
10             -name => "Cell",
11             -definition => "The basic structural and functional unit ...",
12             -is_obsolete => 0,
13             -comment => "" );
14              
15             $term->add_reference( @refs );
16             $term->add_secondary_id( @ids );
17             $term->add_synonym( @synonym );
18              
19             # etc.
20              
21             =head1 DESCRIPTION
22              
23             This is data holder class for OBO terms. It is currently a dummy class since we anticipate that the
24             OBO term will become more richer with more features being added to OBO flat-file format.
25              
26             =head1 FEEDBACK
27              
28             =head2 Mailing Lists
29              
30             User feedback is an integral part of the evolution of this and other
31             Bioperl modules. Send your comments and suggestions preferably to one
32             of the Bioperl mailing lists. Your participation is much appreciated.
33              
34             bioperl-l@bioperl.org - General discussion
35             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
36              
37             =head2 Support
38              
39             Please direct usage questions or support issues to the mailing list:
40              
41             I
42              
43             rather than to the module maintainer directly. Many experienced and
44             reponsive experts will be able look at the problem and quickly
45             address it. Please include a thorough description of the problem
46             with code and data examples if at all possible.
47              
48             =head2 Reporting Bugs
49              
50             Report bugs to the Bioperl bug tracking system to help us keep track
51             the bugs and their resolution. Bug reports can be submitted via the web:
52              
53             https://github.com/bioperl/bioperl-live/issues
54              
55             =head1 AUTHOR
56              
57             Sohel Merchant
58              
59             Email: s-merchant@northwestern.edu
60              
61             Address:
62              
63             Northwestern University
64             Center for Genetic Medicine (CGM), dictyBase
65             Suite 1206,
66             676 St. Clair st
67             Chicago IL 60611
68              
69             =head1 APPENDIX
70              
71             The rest of the documentation details each of the object
72             methods.
73              
74             =cut
75              
76             # Let the code begin...
77              
78             package Bio::Ontology::OBOterm;
79 1     1   6 use strict;
  1         2  
  1         26  
80              
81 1     1   4 use constant TRUE => 1;
  1         1  
  1         53  
82 1     1   4 use constant FALSE => 0;
  1         68  
  1         43  
83              
84 1     1   51 use base qw(Bio::Ontology::Term);
  1         2  
  1         98  
85              
86             =head2 new
87              
88             Title : new
89             Usage : $term = Bio::Ontology::OBOterm->new
90             ( -identifier => "GO:0005623",
91             -name => "Cell",
92             -definition => "The basic structural and functional unit ...",
93             -is_obsolete => 0,
94             -comment => "" );
95              
96             Function: Creates a new Bio::Ontology::OBOterm.
97             Returns : A new Bio::Ontology::OBOterm object.
98             Args : -identifier => the id of this OBO term [GO:nnnnnnn]
99             integer of seven digits)
100             -name => the name of this OBO term [scalar]
101             -definition => the definition of this OBO term [scalar]
102             -ontology => the ontology for this term (a
103             Bio::Ontology::OntologyI compliant object)
104             -version => version information [scalar]
105             -is_obsolete => the obsoleteness of this OBO term [0 or 1]
106             -comment => a comment [scalar]
107              
108             =cut
109              
110             sub new {
111              
112 2252     2252 1 3629 my ( $class, @args ) = @_;
113 2252         4739 my $self = $class->SUPER::new(@args);
114 2252         4171 return $self;
115             } # new
116              
117              
118              
119             1;