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

[jabaws.git] / binaries / src / ViennaRNA / Utils / b2ct.c

diff --git a/binaries/src/ViennaRNA/Utils/b2ct.c b/binaries/src/ViennaRNA/Utils/b2ct.c
new file mode 100644 (file)
index 0000000..5b0dc4b
--- /dev/null
+++ b/binaries/src/ViennaRNA/Utils/b2ct.c
@@ -0,0 +1,152 @@
+/* Last Changed Time-stamp: <2001-09-07 10:17:47 ivo> */
+/* This program converts the bracket notation for RNA secondary structures
+   produced by RNAfold to .ct files used by Michael Zukers Program.
+   To compile enter:
+                    cc -o b2ct b2ct.c
+   And use as
+                    b2ct < structure_file > ct_file.ct
+   or
+                    RNAfold < sequence_file | b2ct > ct_file.ct
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#define MAXLENGTH 30000
+
+void write_ct_file(char *fname, char *sequence, char *structure, char *name,
+                  float energy);
+short *make_pair_table(const char *structure);
+void *space(unsigned size);
+void nrerror(char *message);
+
+int main(void)
+{
+   char line[MAXLENGTH+1];
+   char *string=NULL, *structure=NULL, *name=NULL;
+   float energy;
+   int n=0;
+   
+   while (fgets(line, MAXLENGTH, stdin)!=NULL) {
+       if (strcmp(line,"@")==0) break;
+      
+       switch (line[0]) {
+       case '>': name = (char *) space(strlen(line));
+        sscanf(line,"> %s", name);
+        break;
+       case '.':
+       case '(':
+       case ')': structure = (char *) space(strlen(line));
+        if (sscanf(line,"%s (%f)", structure, &energy)!=2) {
+          free(structure); structure=NULL; break;
+        }
+        n++;
+        break;
+       default: string = (char *) space(strlen(line)+1);
+        sscanf(line, "%s", string);
+       }
+       if (structure!=NULL) {
+        if (name==NULL) {
+          name = (char *) space(10);
+          sprintf(name,"%d",n);
+        }
+        write_ct_file("-", string, structure, name, energy);
+        free(string); 
+        free(structure); 
+        free(name);
+        string = structure = name = NULL;
+       }
+   }
+   return 0;
+}
+
+void write_ct_file(char *fname, char *sequence, char *structure, char *name,
+                  float energy)
+{
+   int i, length;
+   short *table;
+   FILE *ct;
+
+   length = strlen(structure);
+   if ((table = make_pair_table(structure))==NULL) {
+     return;
+   }
+   if (length!=strlen(sequence))
+     nrerror("sequence and structure have unequal length");
+   
+   if (strcmp(fname,"-")==0) 
+     ct = stdout;
+   else {
+     ct = fopen(fname, "a");
+     if (ct==NULL) nrerror("can't open .ct file");
+   }
+
+   fprintf(ct, "%5d ENERGY = %7.1f    %s\n", length, energy, name);
+   for (i=1; i<=length; i++) 
+     fprintf(ct, "%5d %c   %5d %4d %4d %4d\n",
+            i, sequence[i-1], i-1, (i+1)%(length+1), table[i], i);
+   if (strcmp(fname,"-"))
+     fclose(ct);
+   else fflush(ct);
+}
+
+short *make_pair_table(const char *structure)
+{
+    /* returns array representation of structure.
+       table[i] is 0 if unpaired or j if (i.j) pair.  */
+   int i,j,hx;
+   int length;
+   short *stack;
+   short *table;
+   
+   length = strlen(structure);
+   stack = (short *) space(sizeof(short)*(length+1));
+   table = (short *) space(sizeof(short)*(length+2));
+   table[0] = length;
+   
+   for (hx=0, i=1; i<=length; i++) {
+      switch (structure[i-1]) {
+       case '(': 
+         stack[hx++]=i;
+         break;
+       case ')':
+         j = stack[--hx];
+         if (hx<0) {
+            fprintf(stderr, "unbalanced brackets in %s\n", structure);
+           free(stack); free(table); return NULL;
+         }
+         table[i]=j;
+         table[j]=i;
+         break;
+       default:   /* unpaired base, usually '.' */
+         table[i]= 0;
+         break;
+      }
+   }
+   free(stack);
+   if (hx!=0) {
+      fprintf(stderr, "unbalanced brackets %s\n", structure);
+      free(table);
+      return NULL;
+   }
+   return(table);
+}
+
+void *space(unsigned size)
+{
+    void *pointer;
+    
+    if ( (pointer = (void *) calloc(1, size)) == NULL) {
+       fprintf(stderr,"SPACE: requested size: %d\n", size);
+       nrerror("SPACE allocation failure -> no memory");
+    }
+    return  pointer;
+}
+
+
+void nrerror(char *message)       /* output message upon error */
+{
+    fprintf(stderr, "\n%s\n", message);
+    exit(0);
+}
+