pair_mat.h
#include <ctype.h>
#include <ViennaRNA/utils.h>
#include <ViennaRNA/fold_vars.h>
#define NBASES 8
/*@notnull@*/
static const char Law_and_Order[] = "_ACGUTXKI";
static int BP_pair[NBASES][NBASES]=
/* _ A C G U X K I */
{{ 0, 0, 0, 0, 0, 0, 0, 0},
{ 0, 0, 0, 0, 5, 0, 0, 5},
{ 0, 0, 0, 1, 0, 0, 0, 0},
{ 0, 0, 2, 0, 3, 0, 0, 0},
{ 0, 6, 0, 4, 0, 0, 0, 6},
{ 0, 0, 0, 0, 0, 0, 2, 0},
{ 0, 0, 0, 0, 0, 1, 0, 0},
{ 0, 6, 0, 0, 5, 0, 0, 0}};
#define MAXALPHA 20 /* maximal length of alphabet */
static short alias[MAXALPHA+1];
static int pair[MAXALPHA+1][MAXALPHA+1];
/* rtype[pair[i][j]]:=pair[j][i] */
static int rtype[8] = {0, 2, 1, 4, 3, 6, 5, 7};
#ifdef _OPENMP
#pragma omp threadprivate(Law_and_Order, BP_pair, alias, pair, rtype)
#endif
/* for backward compatibility */
#define ENCODE(c) encode_char(c)
static int encode_char(char c) {
/* return numerical representation of base used e.g. in pair[][] */
int code;
if (energy_set>0) code = (int) (c-'A')+1;
else {
const char *pos;
pos = strchr(Law_and_Order, c);
if (pos==NULL) code=0;
else code = (int) (pos-Law_and_Order);
if (code>5) code = 0;
if (code>4) code--; /* make T and U equivalent */
}
return code;
}
/*@+boolint +charint@*/
/*@null@*/
extern char *nonstandards;
static void make_pair_matrix(void)
{
int i,j;
if (energy_set==0) {
for (i=0; i<5; i++) alias[i] = (short) i;
alias[5] = 3; /* X <-> G */
alias[6] = 2; /* K <-> C */
alias[7] = 0; /* I <-> default base '@' */
for (i=0; i<NBASES; i++) {
for (j=0; j<NBASES; j++)
pair[i][j] = BP_pair[i][j];
}
if (noGU) pair[3][4] = pair[4][3] =0;
if (nonstandards!=NULL) { /* allow nonstandard bp's */
for (i=0; i<(int)strlen(nonstandards); i+=2)
pair[encode_char(nonstandards[i])]
[encode_char(nonstandards[i+1])]=7;
}
for (i=0; i<NBASES; i++) {
for (j=0; j<NBASES; j++)
rtype[pair[i][j]] = pair[j][i];
}
} else {
for (i=0; i<=MAXALPHA; i++) {
for (j=0; j<=MAXALPHA; j++)
pair[i][j] = 0;
}
if (energy_set==1) {
for (i=1; i<MAXALPHA;) {
alias[i++] = 3; /* A <-> G */
alias[i++] = 2; /* B <-> C */
}
for (i=1; i<MAXALPHA; i++) {
pair[i][i+1] = 2; /* AB <-> GC */
i++;
pair[i][i-1] = 1; /* BA <-> CG */
}
}
else if (energy_set==2) {
for (i=1; i<MAXALPHA;) {
alias[i++] = 1; /* A <-> A*/
alias[i++] = 4; /* B <-> U */
}
for (i=1; i<MAXALPHA; i++) {
pair[i][i+1] = 5; /* AB <-> AU */
i++;
pair[i][i-1] = 6; /* BA <-> UA */
}
}
else if (energy_set==3) {
for (i=1; i<MAXALPHA-2; ) {
alias[i++] = 3; /* A <-> G */
alias[i++] = 2; /* B <-> C */
alias[i++] = 1; /* C <-> A */
alias[i++] = 4; /* D <-> U */
}
for (i=1; i<MAXALPHA-2; i++) {
pair[i][i+1] = 2; /* AB <-> GC */
i++;
pair[i][i-1] = 1; /* BA <-> CG */
i++;
pair[i][i+1] = 5; /* CD <-> AU */
i++;
pair[i][i-1] = 6; /* DC <-> UA */
}
}
else vrna_message_error("What energy_set are YOU using??");
for (i=0; i<=MAXALPHA; i++) {
for (j=0; j<=MAXALPHA; j++)
rtype[pair[i][j]] = pair[j][i];
}
}
}
static short *encode_sequence(const char *sequence, short how){
unsigned int i,l = (unsigned int)strlen(sequence);
short *S = (short *) vrna_alloc(sizeof(short)*(l+2));
switch(how){
/* standard encoding as always used for S */
case 0: for(i=1; i<=l; i++) /* make numerical encoding of sequence */
S[i]= (short) encode_char(toupper(sequence[i-1]));
S[l+1] = S[1];
S[0] = (short) l;
break;
/* encoding for mismatches of nostandard bases (normally used for S1) */
case 1: for(i=1; i<=l; i++)
S[i] = alias[(short) encode_char(toupper(sequence[i-1]))];
S[l+1] = S[1];
S[0] = S[l];
break;
}
return S;
}
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.