1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
|
/*
* The MIT License
*
* Wavefront Alignment Algorithms
* Copyright (c) 2017 by Santiago Marco-Sola <santiagomsola@gmail.com>
*
* This file is part of Wavefront Alignment Algorithms.
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* PROJECT: Wavefront Alignment Algorithms
* AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
* DESCRIPTION: DNA text encoding/decoding utils
*/
#ifndef DNA_TEXT_H_
#define DNA_TEXT_H_
/*
* Range of DNA Nucleotides
*/
#define DNA_RANGE 4
#define DNA_EXTENDED_RANGE 5
#define DNA_RANGE_BITS 2
/*
* DNA Nucleotides
*/
#define DNA_CHAR_A 'A'
#define DNA_CHAR_C 'C'
#define DNA_CHAR_G 'G'
#define DNA_CHAR_T 'T'
#define DNA_CHAR_N 'N'
/*
* Encoded DNA Nucleotides
*/
#define ENC_DNA_CHAR_A 0
#define ENC_DNA_CHAR_C 1
#define ENC_DNA_CHAR_G 2
#define ENC_DNA_CHAR_T 3
#define ENC_DNA_CHAR_N 4
/*
* Translation tables
*/
extern const uint8_t dna_encode_table[256];
extern const char dna_decode_table[DNA_EXTENDED_RANGE];
/*
* Translation functions
*/
#define dna_encode(character) (dna_encode_table[(int)(character)])
#define dna_decode(enc_char) (dna_decode_table[(int)(enc_char)])
#endif /* DNA_TEXT_H_ */
|
