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
|
#ifndef _ALIGN_H
#define _ALIGN_H
#include "os.h"
#include "misc.h"
/*
#ifdef __alpha
typedef long FastInt;
#else
typedef int FastInt;
#endif
*/
typedef int FastInt;
typedef FastInt align_int;
#define MAX_SCORE_MATRIX 30
/* Basic job number */
#define ALIGN_J_MASK 0x0F
#define ALIGN_J_SS 0
#define ALIGN_J_SV 1
#define ALIGN_J_BSV 2
#define ALIGN_J_SSH 3
/* How to expand the sequence up */
#define ALIGN_J_PADS 0x10
/* Which ends to penalise gaps for. Only applies to ALIGN_J_SSH */
#define ALIGN_GAP_S1 0x020
#define ALIGN_GAP_E1 0x040
#define ALIGN_GAP_S2 0x080
#define ALIGN_GAP_E2 0x100
/*
* Initialise 128x128 weight matrix from our score matrix
*/
extern void init_W128(int **matrix,
char *order, int unknown);
extern int calign(void *seq1, void *seq2, int len1, int len2,
void *rseq1, void *rseq2, int *rlen1, int *rlen2,
int low_band, int high_band, int gap_open, int gap_extend,
int job, int is_protein, align_int *res);
extern void cdisplay(void *seq1, void *seq2, int len1, int len2, int job,
align_int *results, int pos1, int pos2);
extern void cexpand(void *seq1, void *seq2, int len1, int len2,
void *rseq1, void *rseq2, int *rlen1, int *rlen2,
int job, align_int *results);
extern int_f align_(void *seq1, int_f *len1, void *seq2, int_f *len2,
void *rseq1, int_f *rlen1, void *rseq2, int_f *rlen2,
int_f *low_band, int_f *high_band,
int_f *gap_open, int_f *gap_extend,
int_f *job, int_f *is_protein, int_fl seq1_l,
int_fl seq2_l, int_fl rseq1_l, int_fl rseq2_l);
extern FastInt align_ss(char *A, char *B, FastInt M, FastInt N,
FastInt low, FastInt up, FastInt W[][128],
FastInt G, FastInt H, FastInt *S,
FastInt s1, FastInt s2, FastInt e1, FastInt e2);
extern FastInt align_ss2(char *A, char *B, FastInt M, FastInt N,
FastInt low, FastInt up, FastInt W[][128],
FastInt G, FastInt H, FastInt *S,
FastInt s1, FastInt s2, FastInt e1, FastInt e2);
extern FastInt align_sv(char *A, FastInt (*B)[6], FastInt M,
FastInt N, FastInt low, FastInt up,
FastInt W[][128], FastInt G, FastInt H, FastInt *S,
FastInt s1, FastInt s2, FastInt e1, FastInt e2);
extern FastInt balign_sv(char *A, FastInt (*B)[6], FastInt M,
FastInt N, FastInt low, FastInt up,
FastInt W[][128], FastInt G, FastInt H, FastInt *S,
FastInt s1, FastInt s2, FastInt e1, FastInt e2);
extern void display_ss(char *A, char *B, FastInt M, FastInt N,
FastInt *S, FastInt AP, FastInt BP);
extern void display_ss2(char *A, char *B, FastInt M, FastInt N,
FastInt *S, FastInt AP, FastInt BP);
extern void display_sv(char *A, FastInt (*B)[6], FastInt M, FastInt N,
FastInt *S, FastInt AP, FastInt BP);
#include "align_lib_old.h"
#endif /* _ALIGN_H */
|
