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
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
|
/*
DNACount.h DNA Count
This module contains DNA occurrence counting functions. The DNA must be
in word-packed format.
Copyright (C) 2004, Wong Chi Kwong.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#ifndef __DNA_COUNT_H__
#define __DNA_COUNT_H__
#include "TypeNLimit.h"
// DNA
#define DNA_ALPHABET_SIZE 4
#define DNA_CHAR_PER_WORD 16
#define DNA_BIT_PER_CHAR 2
// DNA occurrence count table
#define DNA_OCC_CNT_TABLE_SIZE_IN_WORD 65536
#define DNA_OCC_SUM_EXCEPTION(sum) ((sum & 0xfefefeff) == 0)
// DNA with 'n'
#define DNA_N_ALPHABET_SIZE 5
#define DNA_N_CHAR_PER_WORD 10
#define DNA_N_BIT_PER_CHAR 3
// DNA with 'n' occurrence count table
#define DNA_N_OCC_CNT_TABLE_SIZE_IN_WORD 32786
void GenerateDNAOccCountTable(unsigned int *dnaDecodeTable);
// The following functions can only count up to 255 characters
unsigned int ForwardDNAOccCount(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable);
unsigned int BackwardDNAOccCount(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable);
void ForwardDNAAllOccCount(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable);
void BackwardDNAAllOccCount(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable);
unsigned int Forward1OccCount(const unsigned int* bitVector, const unsigned int index, const unsigned int* dnaDecodeTable); // Count number of 1 bit
unsigned int Backward1OccCount(const unsigned int* bitVector, const unsigned int index, const unsigned int* dnaDecodeTable); // Count number of 1 bit
// The following functions have no limit on the number of characters
unsigned int ForwardDNAOccCountNoLimit(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable);
unsigned int BackwardDNAOccCountNoLimit(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable);
void ForwardDNAAllOccCountNoLimit(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable);
void BackwardDNAAllOccCountNoLimit(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable);
void GenerateDNA_NOccCountTable(unsigned int *dnaDecodeTable);
// The following functions have no limit on the number of characters
unsigned int ForwardDNA_NOccCount(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable);
unsigned int BackwardDNA_NOccCount(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable);
void ForwardDNA_NAllOccCount(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable);
void BackwardDNA_NAllOccCount(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable);
// The following functions have no limit on the number of characters
unsigned int ForwardDNAnOccCountNoLimit(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable);
unsigned int BackwardDNA_NOccCountNoLimit(const unsigned int* dna, const unsigned int index, const unsigned int character, const unsigned int* dnaDecodeTable);
void ForwardDNA_NAllOccCountNoLimit(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable);
void BackwardDNA_NAllOccCountNoLimit(const unsigned int* dna, const unsigned int index, unsigned int* __restrict occCount, const unsigned int* dnaDecodeTable);
// The first character from startAddr is indexed as 1
// DNA_NAllOccCount only count occurrence from character 0 to 3
// The following functions work for any word packed text
unsigned int ForwardOccCount(const unsigned int* packed, const unsigned int index, const unsigned int character, const unsigned int alphabetSize);
unsigned int BackwardOccCount(const unsigned int* packed, const unsigned int index, const unsigned int character, const unsigned int alphabetSize);
void ForwardAllOccCount(const unsigned int* packed, const unsigned int index, const unsigned int alphabetSize, unsigned int* occCount);
void BackwardAllOccCount(const unsigned int* packed, const unsigned int index, const unsigned int alphabetSize, unsigned int* occCount);
#endif
|
