ViewVC Help
View File | Revision Log | Show Annotations | Root Listing
root/PrimerMatch/alignment_code.h
Revision: 1.2
Committed: Wed May 4 18:03:44 2005 UTC (11 years, 1 month ago) by nje01
Branch: MAIN
CVS Tags: HEAD
Changes since 1.1: +13 -3 lines
Log Message:
Small bug fixes, plus codon based edit distance for peptide searching.

Line File contents
1 /**************************************************************************
2 * This code is part of the supporting infrastructure for ATA Mapper.
3 * Copyright (C) 2002,2003,2004 Applera Corporation. All rights reserved.
4 * Author: Nathan Edwards
5 *
6 * This program is free software; you can redistribute it and/or modify
7 * it under the terms of the GNU General Public License as published by
8 * the Free Software Foundation; either version 2 of the License, or
9 * (at your option) any later version.
10 *
11 * This program is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received (LICENSE.txt) a copy of the GNU General Public
17 * License along with this program; if not, write to the Free Software
18 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
19 *************************************************************************/
20
21
22 #ifndef _IBPEP_alignment_code_h
23 #define _IBPEP_alignment_code_h
24
25 # define alignment_codes 13
26 enum alignment_code {
27 alignment_none=0,
28 alignment_equal=1,
29 alignment_wildcard_equal=2,
30 alignment_substitution=3,
31 alignment_insertion=4,
32 alignment_deletion=5,
33 alignment_constraint_violation=6,
34 alignment_end = 7,
35 alignment_substitution_1=8,
36 alignment_substitution_2=9,
37 alignment_substitution_3=10,
38 alignment_insertion_3=11,
39 alignment_deletion_3=12
40 };
41
42 enum alignment_masks {
43 alignment_mask_none = 1,
44 alignment_mask_equal = 2,
45 alignment_mask_wildcard_equal = 4,
46 alignment_mask_substitution = 8,
47 alignment_mask_insertion = 16,
48 alignment_mask_deletion = 32,
49 alignment_mask_constraint_violation = 64,
50 alignment_mask_alignment_end = 128,
51 alignment_mask_substitution_1 = 256,
52 alignment_mask_substitution_2 = 512,
53 alignment_mask_substitution_3 = 1024,
54 alignment_mask_insertion_3 = 2048,
55 alignment_mask_deletion_3 = 4096
56 };
57
58 #endif