WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / H / pair_mat.h

diff --git a/binaries/src/ViennaRNA/H/pair_mat.h b/binaries/src/ViennaRNA/H/pair_mat.h
new file mode 100644 (file)
index 0000000..867862d
--- /dev/null
+++ b/binaries/src/ViennaRNA/H/pair_mat.h
@@ -0,0 +1,148 @@
+#include <ctype.h>
+#include "utils.h"
+#include "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;
+extern void   nrerror(const char message[]);
+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 nrerror("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 *) space(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;
+}