annotate variant_effect_predictor/Bio/DescribableI.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.
author devteam <devteam@galaxyproject.org>
date Mon, 13 Jan 2014 10:38:30 -0500
parents 1f6dce3d34e0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
1 # $Id: DescribableI.pm,v 1.6 2002/10/25 01:29:37 lapp Exp $
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
2
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
3 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
4 # This module is licensed under the same terms as Perl itself. You use,
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
5 # modify, and redistribute it under the terms of the Perl Artistic License.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
6 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
7
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
8 =head1 NAME
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
9
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
10 Bio::DescribableI - interface for objects with human readable names and descriptions
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
11
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
12 =head1 SYNOPSIS
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
13
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
14
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
15 # to test this is a describable object
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
16
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
17 $obj->isa("Bio::DescribableI") ||
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
18 $obj->throw("$obj does not implement the Bio::DescribableI interface");
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
19
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
20 # accessors
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
21
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
22 $name = $obj->display_name();
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
23 $desc = $obj->description();
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
24
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
25
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
26
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
27 =head1 DESCRIPTION
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
28
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
29 This interface describes methods expected on describable objects, ie
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
30 ones which have human displayable names and descriptions
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
31
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
32 =head1 FEEDBACK
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
33
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
34 =head2 Mailing Lists
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
35
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
36 User feedback is an integral part of the evolution of this and other
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
37 Bioperl modules. Send your comments and suggestions preferably to one
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
38 of the Bioperl mailing lists. Your participation is much appreciated.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
39
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
40 bioperl-l@bioperl.org - General discussion
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
41 http://bio.perl.org/MailList.html - About the mailing lists
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
42
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
43 =head2 Reporting Bugs
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
44
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
45 Report bugs to the Bioperl bug tracking system to help us keep track
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
46 the bugs and their resolution. Bug reports can be submitted via email
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
47 or the web:
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
48
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
49 bioperl-bugs@bio.perl.org
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
50 http://bugzilla.bioperl.org/
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
51
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
52 =head1 AUTHOR - Ewan Birney
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
53
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
54 Email birney@sanger.ac.uk
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
55
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
56 =cut
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
57
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
58 package Bio::DescribableI;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
59 use vars qw(@ISA );
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
60 use strict;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
61 use Bio::Root::RootI;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
62
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
63
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
64 @ISA = qw(Bio::Root::RootI);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
65
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
66 =head1 Implementation Specific Functions
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
67
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
68 These functions are the ones that a specific implementation must
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
69 define.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
70
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
71 =head2 display_name
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
72
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
73 Title : display_name
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
74 Usage : $string = $obj->display_name()
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
75 Function: A string which is what should be displayed to the user
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
76 the string should have no spaces (ideally, though a cautious
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
77 user of this interface would not assumme this) and should be
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
78 less than thirty characters (though again, double checking
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
79 this is a good idea)
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
80 Returns : A scalar
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
81 Status : Virtual
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
82
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
83 =cut
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
84
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
85 sub display_name {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
86 my ($self) = @_;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
87 $self->throw_not_implemented();
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
88 }
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
89
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
90
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
91 =head2 description
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
92
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
93 Title : description
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
94 Usage : $string = $obj->description()
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
95 Function: A text string suitable for displaying to the user a
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
96 description. This string is likely to have spaces, but
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
97 should not have any newlines or formatting - just plain
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
98 text. The string should not be greater than 255 characters
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
99 and clients can feel justified at truncating strings at 255
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
100 characters for the purposes of display
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
101 Returns : A scalar
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
102 Status : Virtual
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
103
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
104 =cut
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
105
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
106 sub description {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
107 my ($self) = @_;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
108 $self->throw_not_implemented();
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
109 }
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
110
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
111 1;