RNAlib-2.2.9

- Main Page
- Related Pages
- Modules
- Data Structures
- Files

- File List
- Globals

pair_mat.h
1 #include <ctype.h>
2 #include <ViennaRNA/utils.h>
3 #include <ViennaRNA/fold_vars.h>
4
5 #define NBASES 8
6 /*@notnull@*/
7
8 static const char Law_and_Order[] = "_ACGUTXKI";
9 static int BP_pair[NBASES][NBASES]=
10 /* _ A C G U X K I */
11 {{ 0, 0, 0, 0, 0, 0, 0, 0},
12 { 0, 0, 0, 0, 5, 0, 0, 5},
13 { 0, 0, 0, 1, 0, 0, 0, 0},
14 { 0, 0, 2, 0, 3, 0, 0, 0},
15 { 0, 6, 0, 4, 0, 0, 0, 6},
16 { 0, 0, 0, 0, 0, 0, 2, 0},
17 { 0, 0, 0, 0, 0, 1, 0, 0},
18 { 0, 6, 0, 0, 5, 0, 0, 0}};
19
20 #define MAXALPHA 20 /* maximal length of alphabet */
21
22 static short alias[MAXALPHA+1];
23 static int pair[MAXALPHA+1][MAXALPHA+1];
24 /* rtype[pair[i][j]]:=pair[j][i] */
25 static int rtype[8] = {0, 2, 1, 4, 3, 6, 5, 7};
26
27 #ifdef _OPENMP
28 #pragma omp threadprivate(Law_and_Order, BP_pair, alias, pair, rtype)
29 #endif
30
31 /* for backward compatibility */
32 #define ENCODE(c) encode_char(c)
33
34 static int encode_char(char c) {
35 /* return numerical representation of base used e.g. in pair[][] */
36 int code;
37 if (energy_set>0) code = (int) (c-'A')+1;
38 else {
39 const char *pos;
40 pos = strchr(Law_and_Order, c);
41 if (pos==NULL) code=0;
42 else code = (int) (pos-Law_and_Order);
43 if (code>5) code = 0;
44 if (code>4) code--; /* make T and U equivalent */
45 }
46 return code;
47 }
48
49 /*@+boolint +charint@*/
50 /*@null@*/
51 extern char *nonstandards;
52
53 static void make_pair_matrix(void)
54 {
55 int i,j;
56
57 if (energy_set==0) {
58 for (i=0; i<5; i++) alias[i] = (short) i;
59 alias[5] = 3; /* X <-> G */
60 alias[6] = 2; /* K <-> C */
61 alias[7] = 0; /* I <-> default base '@' */
62 for (i=0; i<NBASES; i++) {
63 for (j=0; j<NBASES; j++)
64 pair[i][j] = BP_pair[i][j];
65 }
66 if (noGU) pair[3][4] = pair[4][3] =0;
67 if (nonstandards!=NULL) { /* allow nonstandard bp's */
68 for (i=0; i<(int)strlen(nonstandards); i+=2)
69 pair[encode_char(nonstandards[i])]
70 [encode_char(nonstandards[i+1])]=7;
71 }
72 for (i=0; i<NBASES; i++) {
73 for (j=0; j<NBASES; j++)
74 rtype[pair[i][j]] = pair[j][i];
75 }
76 } else {
77 for (i=0; i<=MAXALPHA; i++) {
78 for (j=0; j<=MAXALPHA; j++)
79 pair[i][j] = 0;
80 }
81 if (energy_set==1) {
82 for (i=1; i<MAXALPHA;) {
83 alias[i++] = 3; /* A <-> G */
84 alias[i++] = 2; /* B <-> C */
85 }
86 for (i=1; i<MAXALPHA; i++) {
87 pair[i][i+1] = 2; /* AB <-> GC */
88 i++;
89 pair[i][i-1] = 1; /* BA <-> CG */
90 }
91 }
92 else if (energy_set==2) {
93 for (i=1; i<MAXALPHA;) {
94 alias[i++] = 1; /* A <-> A*/
95 alias[i++] = 4; /* B <-> U */
96 }
97 for (i=1; i<MAXALPHA; i++) {
98 pair[i][i+1] = 5; /* AB <-> AU */
99 i++;
100 pair[i][i-1] = 6; /* BA <-> UA */
101 }
102 }
103 else if (energy_set==3) {
104 for (i=1; i<MAXALPHA-2; ) {
105 alias[i++] = 3; /* A <-> G */
106 alias[i++] = 2; /* B <-> C */
107 alias[i++] = 1; /* C <-> A */
108 alias[i++] = 4; /* D <-> U */
109 }
110 for (i=1; i<MAXALPHA-2; i++) {
111 pair[i][i+1] = 2; /* AB <-> GC */
112 i++;
113 pair[i][i-1] = 1; /* BA <-> CG */
114 i++;
115 pair[i][i+1] = 5; /* CD <-> AU */
116 i++;
117 pair[i][i-1] = 6; /* DC <-> UA */
118 }
119 }
120 else vrna_message_error("What energy_set are YOU using??");
121 for (i=0; i<=MAXALPHA; i++) {
122 for (j=0; j<=MAXALPHA; j++)
123 rtype[pair[i][j]] = pair[j][i];
124 }
125 }
126 }
127
128 static short *encode_sequence(const char *sequence, short how){
129 unsigned int i,l = (unsigned int)strlen(sequence);
130 short *S = (short *) vrna_alloc(sizeof(short)*(l+2));
131
132 switch(how){
133 /* standard encoding as always used for S */
134 case 0: for(i=1; i<=l; i++) /* make numerical encoding of sequence */
135 S[i]= (short) encode_char(toupper(sequence[i-1]));
136 S[l+1] = S[1];
137 S[0] = (short) l;
138 break;
139 /* encoding for mismatches of nostandard bases (normally used for S1) */
140 case 1: for(i=1; i<=l; i++)
141 S[i] = alias[(short) encode_char(toupper(sequence[i-1]))];
142 S[l+1] = S[1];
143 S[0] = S[l];
144 break;
145 }
146
147 return S;
148 }
vrna_alloc
void * vrna_alloc(unsigned size)
Allocate space safely.
energy_set
int energy_set
0 = BP; 1=any mit GC; 2=any mit AU-parameter
noGU
int noGU
Global switch to forbid/allow GU base pairs at all.
nonstandards
char * nonstandards
contains allowed non standard base pairs
utils.h
General utility- and helper-functions used throughout the ViennaRNA Package.
MAXALPHA
#define MAXALPHA
Maximal length of alphabet.
Definition: model.h:174
fold_vars.h
Here all all declarations of the global variables used throughout RNAlib.
vrna_message_error
void vrna_message_error(const char message[])
Die with an error message.