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
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
|
#ifndef SIM4_H
#define SIM4_H
/* $Id: sim4.h,v 1.21 2002/01/24 00:56:23 schwartz Exp $ */
#define DEFAULT_NUM_I 3
#define DIST_CUTOFF 3
#define DEFAULT_MIN_COV (.8)
#define MININT (-99999)
#define MIN_INTRON 30
#define MAX_INTRON 20000
#define MAX_GRINIT 500
#define MAX_INTERNAL_GAP 50 /* 50 */
#define LL 60
#define DEFAULT_DRANGE 10
#define DEFAULT_WEIGHT 100
#define DEFAULT_RELINK_H 500
#define DEFAULT_W 12
#define DEFAULT_X 12
#define DEFAULT_K 16
#define DEFAULT_C 12
#define LINK 0
#define RELINK 1
#define P (.2)
#define min(x,y) ((x>y) ? (y):(x))
#define max(x,y) ((x<y) ? (y):(x))
#define START_SIG ((G_score >= abs(C_score)) ? "GT" : "CT")
#define END_SIG ((G_score >= abs(C_score)) ? "AG" : "AC")
#define MATCH 1
#define MISMATCH (-5)
#define L 8
#define DELETE 1
#define INSERT 2
#define SUBSTITUTE 3
#define INTRON 4
#define O_INTRON 5
#undef TRUE
#undef FALSE
enum { FALSE = 0, TRUE = 1};
enum { INIT = 0, PERM = 1, TEMP = 2};
enum { EST_GEN = 1, GEN_EST = 2 };
enum { FWD = 0, BWD = 1, BOTH = 2 };
enum { OK = 0, FREE_START = 1, FREE_END = 2, FREE_BOTH_ENDS = 3};
/* data structures */
/* used in select_path() */
typedef struct msp {
int len, pos1, pos2;
int score;
int Score;
int prev;
struct msp *next_msp;
} *Msp_ptr;
typedef struct exon {
int from1, from2, to1, to2;
int min_diag, max_diag;
int match;
char ori;
int length;
int flag;
int ematches;
int nmatches;
int edist;
int alen;
Msp_ptr msps;
struct exon *next_exon;
} *Exon_ptr;
typedef struct intron {
int from1, from2, to1, to2;
int length;
char orientation;
struct intron *next_intron;
} *Intron_ptr, Intron;
typedef struct exon Exon;
typedef struct coordinates {
int pos1;
int pos2;
} coords;
/* used only in the alignment stage */
typedef struct edit_script {
char op_type; /* SUB, INS, or DEL */
int num; /* Number of operations */
struct edit_script *next;
} edit_script;
typedef struct edit_script_list {
int offset1, offset2;
int len1, len2;
int score;
struct edit_script *script;
struct edit_script_list *next_script;
} edit_script_list;
struct edit {
struct edit *link; /* previous edit instruction */
char type[2];
int accumulation;
char op; /* INSERT, DELETE or INTRON */
int line1; /* line number in file1 */
int line2; /* line number in file2 */
};
typedef void *Pointer;
typedef struct ValNode {
Pointer data;
struct ValNode *next;
} *ValNodePtr;
typedef int signal_t[5][5];
typedef struct spliced {
int xs, xe, ys, ye, score;
char type;
struct spliced *next;
} splice_t;
typedef struct sim4_stats {
int internal, icoverage, mult, nmatches;
double fcoverage, marginals;
} sim4_stats_t;
typedef struct sim4_args {
int ali_flag, poly_flag, acc_flag, reverse, DRANGE, weight, cutoff;
int set_K, set_C, set_H;
int W, K, C, X, B, CDS_from, CDS_to;
char *S;
} sim4_args_t;
#endif
|
