annotate variant_effect_predictor/Bio/Factory/HitFactoryI.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 #-----------------------------------------------------------------
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
2 # $Id: HitFactoryI.pm,v 1.6 2002/10/22 07:38:32 lapp Exp $
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
3 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
4 # BioPerl module for Bio::Factory::HitFactoryI
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
5 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
6 # Cared for by Steve Chervitz <sac@bioperl.org>
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
7 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
8 # You may distribute this module under the same terms as perl itself
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
9 #-----------------------------------------------------------------
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
10
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
11 # POD documentation - main docs before the code
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
12
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
13 =head1 NAME
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
14
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
15 Bio::Factory::HitFactoryI - Interface for an object that builds Bio::Search::Hit::HitI objects
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
16
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
17 =head1 SYNOPSIS
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
18
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
19 To be completed.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
20
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
21 =head1 DESCRIPTION
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
22
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
23 To be completed.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
24
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
25 =head1 FEEDBACK
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
26
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
27 =head2 Mailing Lists
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
28
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
29 User feedback is an integral part of the evolution of this
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
30 and other Bioperl modules. Send your comments and suggestions preferably
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
31 to one of the Bioperl mailing lists.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
32 Your participation is much appreciated.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
33
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
34 bioperl-l@bioperl.org - General discussion
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
35 http://bio.perl.org/MailList.html - About the mailing lists
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
36
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
37 =head2 Reporting Bugs
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
38
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
39 Report bugs to the Bioperl bug tracking system to help us keep track
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
40 the bugs and their resolution. Bug reports can be submitted via email
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
41 or the web:
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
42
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
43 bioperl-bugs@bio.perl.org
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
44 http://bugzilla.bioperl.org/
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
45
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
46 =head1 AUTHOR
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
47
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
48 Steve Chervitz E<lt>sac@bioperl.orgE<gt>
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
49
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
50 See L<the FEEDBACK section | FEEDBACK> for where to send bug reports and comments.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
51
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
52 =head1 COPYRIGHT
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
53
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
54 Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
55
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
56 =head1 DISCLAIMER
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
57
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
58 This software is provided "as is" without warranty of any kind.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
59
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
60 =head1 APPENDIX
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
61
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
62 The rest of the documentation details each of the object methods.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
63
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
64 =cut
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
65
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
66 #'
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
67
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
68 package Bio::Factory::HitFactoryI;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
69
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
70 use strict;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
71 use Bio::Root::RootI;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
72
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
73 use vars qw(@ISA);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
74
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
75 @ISA = qw(Bio::Root::RootI);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
76
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
77 =head2 create_hit
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
78
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
79 Title : create_hit
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
80 Usage : $hit = $factory->create_hit( %params );
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
81 Function: Creates a new Bio::Search::Hit::HitI object.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
82 Returns : An object that implements the Bio::Search::Hit::HitI interface
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
83 Args : Named parameters (to be defined)
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
84
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
85 =cut
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
86
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
87 sub create_hit {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
88 my ($self, @args) = @_;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
89 $self->throw_not_implemented;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
90 }
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
91
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
92
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
93 1;