+++ /dev/null
-#ifndef GJ_UTIL_H
-#define GJ_UTIL_H
-
-/*
-$Id: gjutil.h,v 1.8 2002/08/09 12:30:31 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);
-double **GJdarr(int i,int j);
-void GJdarrfree(double **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 1.8 2002/08/09 12:30:31 geoff
-Experiment with different weighting schemes.
-Changes to build_profile to accommodate new schemes
-pwf 3 Complex clustering to get sequence weights at each position
-pwf 4 Dirichlet mixture alone
-pwf 5 Dirichlet mixture + psiblast windowing + blosum weights
-pwf 6 local blosum matrix calculation + HH sequence weights + blosum
-
-Also add wander_check opton
-Also add option to turn off sw7 bug work around.
-Add option to suppress multiple alignment output
-Add gjnoc2 to distribution
-
-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 */
-
git://source.jalview.org / jabaws.git / blobdiff