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
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
|
/*
HSP.h BWTBlastn functions
This module contains miscellaneous BWTBlastn functions.
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 __HSP_H__
#define __HSP_H__
#include "TypeNLimit.h"
#include "MemManager.h"
#include "TextConverter.h"
#define ALPHABET_SIZE 4
#define BIT_PER_CHAR 2
#define CHAR_PER_128 64
#define CHAR_PER_WORD 16
#define CHAR_PER_BYTE 4
#define MAX_ALIGNMENT_LENGTH 131072
#define SHORTEST 70
typedef struct _ChrBlock{
int chrID;
unsigned int blockStart;
unsigned int blockEnd;
unsigned int ori;
}ChrBlock;
typedef struct _NewAnnotation{
char chrName[MAX_SEQ_NAME_LENGTH];
int nameLen;
unsigned int chrStart;
unsigned int chrEnd;
int blockNum;
ChrBlock *blockInChr;
}NewAnnotation;
typedef struct Annotation {
int gi;
char text[MAX_SEQ_NAME_LENGTH+1];
} Annotation;
typedef struct HSP {
unsigned int* packedDNA;
int chrNum;
char **chrName;
int numOfBlock;
ChrBlock *blockList;
unsigned int dnaLength;
}HSP;
#define MAX_SEQ_NAME_LENGTH 256
#define MAX_HISTO_SIZE 256
#define INVALID_CHAR_INDEX 15
#define ALIGN_MATCH 0
#define ALIGN_MISMATCH_AMBIGUITY 1
#define ALIGN_INSERT 2
#define ALIGN_DELETE 3
#define ALIGN_PER_WORD 16
#define ALIGN_BIT 2
#define AUX_TEXT_PER_WORD 8
#define AUX_TEXT_BIT 4
static const char lowercaseDnaCharIndex = 14; // Seems that BLAST treat masked characters as 'N' (still have 1/4 chance of matching)
static const char nonMatchDnaCharIndex = 15;
static const char dnaChar[16] = {'A', 'C', 'G', 'T', 'M', 'R', 'S', 'V', 'W', 'Y', 'H', 'K', 'D', 'B', 'N', 'L'};
static const char dnaComplement[16] = {'T', 'G', 'C', 'A', 'K', 'Y', 'S', 'B', 'W', 'R', 'D', 'M', 'H', 'V', 'N', 'L'};
static const char ambiguityCount[16] = { 1 , 1 , 1 , 1 , 2 , 2 , 2 , 3 , 2 , 2 , 3 , 2 , 3 , 3 , 4 , 0 };
static const char ambiguityMatch[16][4] = {{0, 0, 0, 0},
{1, 0, 0, 0},
{2, 0, 0, 0},
{3, 0, 0, 0},
{0, 1, 0, 0},
{0, 2, 0, 0},
{1, 2, 0, 0},
{0, 1, 2, 0},
{0, 3, 0, 0},
{1, 3, 0, 0},
{0, 1, 3, 0},
{2, 3, 0, 0},
{0, 2, 3, 0},
{1, 2, 3, 0},
{0, 1, 2, 3},
{0, 0, 0, 0}
};
// Map must be allocated with char[256]
void HSPFillCharMap(unsigned char *charMap);
void HSPFillComplementMap(unsigned char *complementMap);
HSP *HSPLoad(MMPool *mmPool, const char *PackedDNAFileName, const char *AnnotationFileName);
HSP *HSPConvertFromText(MMPool *mmPool, const unsigned char *text, const unsigned int textLength,
const unsigned int FASTARandomSeed, const int maskLowerCase,
const int gi, const char *seqName);
void HSPFree(MMPool *mmPool, HSP *hsp);
unsigned int HSPParseFASTAToPacked(const char* FASTAFileName, const char* annotationFileName, const char* packedDNAFileName, const char* ambiguityFileName,
const unsigned int FASTARandomSeed, const int maskLowerCase);
unsigned int HSPPackedToFASTA(const char* FASTAFileName, const char* annotationFileName, const char* packedDNAFileName, const char* ambiguityFileName);
#endif
|
