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

[jabaws.git] / binaries / src / ViennaRNA / RNAforester / src / utils.h

diff --git a/binaries/src/ViennaRNA/RNAforester/src/utils.h b/binaries/src/ViennaRNA/RNAforester/src/utils.h
new file mode 100644 (file)
index 0000000..402380e
--- /dev/null
+++ b/binaries/src/ViennaRNA/RNAforester/src/utils.h
@@ -0,0 +1,52 @@
+#ifndef _UTILS_H_
+#define _UTILS_H_
+
+// matthias : added naview_xy_coordinates to header
+//            removed extern's
+//            added ifndef
+//            added ectern "C"
+//            removed unsigned short xsubi[3]; from this file
+
+/* Header file for utils.c */
+
+#if defined(__cplusplus)
+extern "C"
+{
+#endif
+
+int   naview_xy_coordinates(short *pair_table, float *X, float *Y);
+void  *space(unsigned size);           /* allocate space safely */
+
+/*@exits@*/
+void   nrerror(const char message[]);  /* die with error message */
+void   init_rand(void);                /* make random number seeds */
+  //unsigned short xsubi[3];               /* current 48bit random number */
+double urn(void);                      /* random number from [0..1] */
+int    int_urn(int from, int to);      /* random integer */
+void   filecopy(FILE *from, FILE *to); /* inefficient `cp' */
+/*@observer@*/
+char  *time_stamp(void);               /* current date in a string */
+char  *random_string(int l, const char symbols[]);
+/* random string of length l using characters from symbols[] */
+int    hamming(const char *s1, const char *s2);
+/* calculate hamming distance */
+char  *get_line(FILE *fp); /* read one (arbitrary length) line from fp */
+
+
+char *pack_structure(const char *struc);
+/* pack secondary secondary structure, 5:1 compression using base 3 encoding */
+char *unpack_structure(const char *packed);
+/* unpack sec structure packed with pack_structure() */
+short *make_pair_table(const char *structure);
+/* returns a newly allocated table, such that:  table[i]=j if (i.j) pair or
+   0 if i is unpaired, table[0] contains the length of the structure. */
+
+int bp_distance(const char *str1, const char *str2);
+/* dist = {number of base pairs in one structure but not in the other} 
+   same as edit distance with open-pair close-pair as move-set */
+
+#if defined(__cplusplus)
+}
+#endif
+
+#endif