annotate variant_effect_predictor/Bio/Coordinate/Result/Match.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: Match.pm,v 1.2.2.1 2003/02/20 05:11:45 heikki Exp $
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
2 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
3 # BioPerl module for Bio::Coordinate::Result::Match
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
4 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
5 # Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
6 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
7 # Copywright Heikki Lehvaslaiho
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
8 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
9 # You may distribute this module under the same terms as perl itself
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
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
14 =head1 NAME
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
15
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
16 Bio::Coordinate::Result::Match - An other name for Bio::Location::Simple
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
17
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
18 =head1 SYNOPSIS
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
19
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
20 $loc = new Bio::Coordinate::Result::Match(-start=>10,
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
21 -end=>30,
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
22 -strand=>+1);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
23
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
24 =head1 DESCRIPTION
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
25
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
26 This is a location class for coordinate mapping results.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
27
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
28 =head1 FEEDBACK
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
29
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
30 =head2 Mailing Lists
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
31
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
32 User feedback is an integral part of the evolution of this and other
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
33 Bioperl modules. Send your comments and suggestions preferably to one
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
34 of the Bioperl mailing lists. Your participation is much appreciated.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
35
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
36 bioperl-l@bioperl.org - General discussion
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
37 http://bio.perl.org/MailList.html - About the mailing lists
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
38
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
39 =head2 Reporting Bugs
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
40
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
41 Report bugs to the Bioperl bug tracking system to help us keep track
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
42 the bugs and their resolution. Bug reports can be submitted via email
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
43 or the web:
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
44
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
45 bioperl-bugs@bio.perl.org
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
46 http://bugzilla.bioperl.org/
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
47
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
48 =head1 AUTHOR - Heikki Lehvaslaiho
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
49
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
50 Email heikki@ebi.ac.uk
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
51
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
52 =head1 CONTRIBUTORS
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
53
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
54 Additional contributors names and emails here
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
55
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
56 =head1 APPENDIX
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
57
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
58 The rest of the documentation details each of the object
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
59 methods. Internal methods are usually preceded with a _
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
60
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
61 =cut
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
62
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
63 package Bio::Coordinate::Result::Match;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
64 use vars qw(@ISA);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
65 use strict;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
66
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
67 use Bio::Location::Simple;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
68 use Bio::Coordinate::ResultI;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
69
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
70 @ISA = qw(Bio::Location::Simple Bio::Coordinate::ResultI);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
71
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
72
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
73 1;