JPRED-2 Add sources of all binaries (except alscript) to Git

[jpred.git] / sources / oc / gjutil.h

diff --git a/sources/oc/gjutil.h b/sources/oc/gjutil.h
new file mode 100644 (file)
index 0000000..f81c2d0
--- /dev/null
+++ b/sources/oc/gjutil.h
@@ -0,0 +1,135 @@
+#ifndef GJ_UTIL_H
+#define GJ_UTIL_H
+
+/*
+$Id: gjutil.h,v 1.1 2002/08/04 19:06:18 geoff Exp $
+*/
+
+#include <stdio.h>
+
+
+typedef int GJ_LIM;              /* type for limits - e.g. max buffer length */
+typedef int GJ_PEN;              /* type for gap penalties */
+typedef int GJ_FLG;              /* Flag type - usually just 1 or 0 */
+typedef float GJ_FLOAT;          /* Single precision floating point type */
+typedef double GJ_DBL;           /* a double precision floating point type */
+typedef int GJ_S_COUNT;          /* small counter */
+typedef long GJ_L_COUNT;         /* long counter */
+
+typedef struct {                    /* structure to hold a filename and */
+  char *name;                    /* associated handle */
+  FILE *handle;
+} GJFILE;
+
+struct tokens {                  /* structure to hold tokens parsed from */
+  int ntok;                      /* string with strtok */
+  char **tok;
+};
+
+typedef struct {
+  int min;
+  int max;
+} IRANGE;
+
+typedef struct {
+  char *val;
+  int i;
+} CWORK;
+
+int Sworkcomp(const void *left, const void *right);
+void GJindexxS(char **arrin,int n,int *indx);
+
+#define STD_FILES extern FILE *std_in,*std_out,*std_err
+
+/* utility.h function definitions */
+
+void *GJmalloc(size_t);
+void *GJrealloc(void *,size_t);
+void *GJmallocNQ(size_t);
+void *GJreallocNQ(void *,size_t);
+void GJfree(void *);
+void GJerror(const char *);
+char *GJstrdup(const char *);
+char *GJstoupper(const char *);
+char *GJstolower(const char *);
+char *GJstoup(char *);
+char *GJstolo(char *);
+
+FILE *GJfopen(const char *, const char *,int);
+int  GJfclose(FILE *,int);
+GJFILE *GJfilemake(const char *name,const char *type,int action);
+GJFILE *GJfilerename(GJFILE *ret_val, const char *name);
+GJFILE *GJfileclose(GJFILE *ret_val,int action);
+GJFILE *GJfileopen(GJFILE *ret_val,const char *type,int action);
+GJFILE *GJfileclean(GJFILE *fval,int action);
+void GJinitfile(void);
+
+char *GJfnonnull(char *);
+char *GJstrappend(char *,char *);
+char *GJremovechar(char *,char);
+char *GJremovechar2(char *string,char c);
+char *GJstrcreate(size_t, char *);
+char *GJstrlocate(char *,char *);
+char *GJsubchar(char *,char,char);
+char *GJstrtok(char *,const char *);
+void error(const char *, int);
+unsigned char **uchararr(int,int);
+void ucharfree(unsigned char **array,int i);
+signed   char **chararr(int,int);
+void GJCinit(signed char **,int ,int ,char );
+void mcheck(void *, char *);
+char *GJstrblank(char *, int);
+void GJUCinit(unsigned char **,int ,int ,unsigned char );
+char *GJcat(int N,...);
+struct tokens *GJgettokens(const char *delims, char *buff);
+void GJfreetokens(struct tokens *tok);
+char * GJtoktostr(struct tokens *tok, char delim, int s, int e);
+void GJ_start_clock(void);
+void GJ_stop_clock(FILE *fp);
+char *GJstrrename(char *old,const char *new);
+void GJindexx(int *arrin,int n,int *indx);
+void GJindexxD(double *arrin,int n,int *indx);
+void GJindexxS(char **arrin,int n,int *indx);
+int GJbsearchINXS(char **cod, int n, char *query);
+int GJbsearchINX_IS(char **cod, int *inx, int n, char *query);
+
+void GJpline(FILE *fp,char c,int n);
+char *GJlocaltime(void);
+void GJpstring(FILE *fp,char *s,int n);
+
+IRANGE *irange(int *ivec, int n);
+
+/*
+$Log: gjutil.h,v $
+Revision 1.1  2002/08/04 19:06:18  geoff
+Add the gjutil programs to oc archive
+
+Revision 1.1.1.1  2002/06/25 22:30:32  geoff
+Import of gjnoc routines
+
+
+Revision 1.7  2000/12/21 17:25:44  geoff
+Add the option to output the sequence fragments from the multiple alignment
+output option in fasta or pir format.  Unlike the block file output, these
+fragments contain the complete sequence between the start and end points, including
+any parts deleted in the alignment process.
+Add appropriate commands to scanps_alias.dat, getpars and getcmd.
+
+Revision 1.6  1999/11/17 21:06:47  geoff
+Add setup_caleb and other changes to swpp2 and so on.
+
+Revision 1.5  1997/06/27 07:17:32  gjb
+Added rlic.c linfo.h and
+changes to gjutil.c to give better support for
+token manipulation
+
+Revision 1.4  1997/05/12 11:10:54  gjb
+Re-added gjutil.c and gjutil.h to repository
+after deleting them
+
+Revision 1.2  1997/05/12 10:47:52  gjb
+Modified CVS header and log position
+
+*/
+#endif  /* GJ_UTIL_H */
+