+++ /dev/null
-
-/****************************************************************************
-
-gjutil.c: Various utility routines - error checking malloc and
-free, string functions etc...
-
-Copyright: Geoffrey J. Barton (1992, 1993, 1995, 1997)
-email: geoff@ebi.ac.uk
-
-This software is made available for educational and non-commercial research
-purposes.
-
-For commercial use, a commercial licence is required - contact the author
-at the above address for details.
-
-
-******************************************************************************/
-#include <stdio.h>
-#include <stdarg.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-#include <errno.h>
-#include <time.h>
-
-#include <gjutil.h>
-
-/* define pointers for standard streams to allow redefinition to files */
-
-FILE *std_err;
-FILE *std_in;
-FILE *std_out;
-
-/* clock externs */
-clock_t start_time, end_time,initial_time,final_time;
-
-void *GJmalloc(size_t size)
-/* malloc with simple error check */
-/* G. J. Barton 1992 */
-{
- void *ptr;
- ptr = (void *) malloc(size);
- if(ptr == NULL){
- GJerror("malloc error");
- exit(0);
- }
- return ptr;
-}
-
-void *GJrealloc(void *ptr,size_t size)
-/* realloc with error check */
-/* G. J. Barton 1992 */
-{
- ptr = (void *) realloc(ptr,size);
- if(ptr == NULL){
- GJerror("realloc error");
- exit(0);
- }
- return ptr;
-}
-void *GJmallocNQ(size_t size)
-/* as for GJmalloc, but returns NULL on error*/
-/* G. J. Barton 1992 */
-{
- void *ptr;
- ptr = (void *) malloc(size);
- if(ptr == NULL){
- GJerror("malloc error");
- return NULL;
- }
- return ptr;
-}
-
-void *GJreallocNQ(void *ptr,size_t size)
-/* as for GJrealloc with error check but returns NULL on error*/
-/* G. J. Barton 1992 */
-{
- ptr = (void *) realloc(ptr,size);
- if(ptr == NULL){
- GJerror("realloc error");
- return NULL;
- }
- return ptr;
-}
-void GJfree(void *ptr)
-/* free with error check */
-/* G. J. Barton 1992 */
-{
- if(ptr == NULL){
- GJerror("Attempt to free NULL pointer");
- exit(0);
- }
- free(ptr);
-}
-
-void GJerror(const char *prefix)
-/* writes error message contained in prefix and contents of errno
- to std_err.
-*/
-/* G. J. Barton 1992 */
-{
- if(prefix != NULL){
- if(*prefix != '\0'){
- fprintf(std_err,"%s: ",prefix);
- }
- }
- fprintf(std_err,"%s\n",strerror(errno));
-}
-
-/*
-error: calls GJerror
-*/
-void error(const char *str,int flag)
-{
- GJerror(str);
- if(flag)exit(0);
-}
-
-
-char *GJstoupper(const char *s)
-/* return a copy of s in upper case */
-/* G. J. Barton 1992 */
-{
- char *temp;
- int i;
- temp = GJstrdup(s);
- i=0;
- while(temp[i] != '\0'){
- temp[i] = toupper(temp[i]);
- ++i;
- }
- return temp;
-}
-char *GJstolower(const char *s)
-/* return a copy of s in lower case */
-/* G. J. Barton 1992 */
-{
- char *temp;
- int i;
- temp = GJstrdup(s);
- i=0;
- while(temp[i] != '\0'){
- temp[i] = tolower(temp[i]);
- ++i;
- }
- return temp;
-}
-char *GJstoup(char *s)
-/* return s in upper case */
-/* G. J. Barton 1992 */
-{
- int i;
- i=0;
- while(s[i] != '\0'){
- s[i] = toupper(s[i]);
- ++i;
- }
- return s;
-}
-char *GJstolo(char *s)
-/* return s in lower case */
-/* G. J. Barton 1992 */
-{
- int i;
- i=0;
- while(s[i] != '\0'){
- s[i] = tolower(s[i]);
- ++i;
- }
- return s;
-}
-
-char *GJstrdup(const char *s)
-/* returns a pointer to a copy of string s */
-/* G. J. Barton 1992 */
-
-{
- char *temp;
- temp = (char *) GJmalloc(sizeof(char) * (strlen(s)+1));
- temp = strcpy(temp,s);
- return temp;
-}
-
-char *GJstrrename(char *old,const char *new)
-/* takes old which is a pointer to a string, then replaces the contents
- of the string with new, reallocating to the correct size
-*/
-{
- int nlen;
- nlen = strlen(new);
- old = (char *) GJrealloc(old,sizeof(char) * (nlen + 1));
- old = strcpy(old,new);
- return old;
-}
-
-
-
-FILE *GJfopen(const char *fname,const char *type,int action)
-/* a file open function with error checking. The third argument
-is set to 0 if we want a failed open to return, or 1 if we
-want a failed open to exit the program.
-*/
-/* G. J. Barton 1992 */
-/* modified July 1995 - error message only printed if action is 1 */
-{
- FILE *ret_val;
- ret_val = fopen(fname,type);
- if(ret_val == NULL){
- /* GJerror(strcat("Cannot Open File: ",fname));*/
- if(action == 1){
- GJerror(strcat("Cannot Open File: ",fname));
- exit(1);
- }
- }
- return ret_val;
-}
-
-int GJfclose(FILE *fp,int action)
-/* a file close function with error checking. The second argument
-is set to 0 if we want a failed close to return, or 1 if we
-want a failed close to exit the program.
-*/
-/* G. J. Barton 1992 */
-{
- int ret_val;
- ret_val = fclose(fp);
- if(ret_val != 0){
- if(action == 1){
- GJerror("Error closing File");
- exit(1);
- }
- }
- return ret_val;
-}
-
-
-GJFILE *GJfilemake(const char *name,const char *type,int action)
-/* If action = 1 then
-Tries to open the file with the given name. If successful returns
-a pointer to a struct file structure with the name and filehandle. If
-the open fails, or action= 0 then returns a struct file structure
-with the name and a NULL filehandle */
-/* G. J. Barton 1995 */
-{
- GJFILE *ret_val;
- ret_val = (GJFILE *) GJmalloc(sizeof(GJFILE));
- ret_val->name = GJstrdup(name);
- if(action == 1) {
- ret_val->handle = GJfopen(ret_val->name,type,0);
- }else if(action == 0){
- ret_val->handle = NULL;
- }
- return ret_val;
-}
-
-GJFILE *GJfilerename(GJFILE *ret_val, const char *name)
-/* When passed the fval structure - renames the name part of the
-file structure to name, if the handle is non null it tries to close
-the file, then sets the file handle to NULL. */
-/* G. J. Barton 1995 */
-{
- if(ret_val->name != NULL) {
- GJfree(ret_val->name);
- ret_val->name = GJstrdup(name);
- }
- if(ret_val->handle != NULL) {
- GJfclose(ret_val->handle,0);
- ret_val->handle = NULL;
- }
- return ret_val;
-}
-
-GJFILE *GJfileclose(GJFILE *ret_val,int action)
-/* Closes a file named in the struct file structure returns the struct
- file structure */
-
-/* G. J. Barton July 1995 */
-{
- STD_FILES;
-
- if(GJfclose(ret_val->handle,0) == 0){
- return ret_val;
- }else {
- if(action == 1){
- GJerror("Error closing File");
- fprintf(std_err,"%s\n",ret_val->name);
- exit(-1);
- }
- }
- return ret_val;
-}
-
-GJFILE *GJfileopen(GJFILE *ret_val,const char *type,int action)
-/* Opens a file named in the struct file structure */
-
-/* G. J. Barton October 1995 */
-{
- STD_FILES;
-
- ret_val->handle = GJfopen(ret_val->name,type,0);
- if(ret_val->handle == NULL){
- if(action == 1){
- GJerror("Error opening File");
- fprintf(std_err,"%s\n",ret_val->name);
- exit(-1);
- }
- }
- return ret_val;
-}
-
-GJFILE *GJfileclean(GJFILE *ret_val,int action)
-/* Closes the file then sets the file pointer to NULL, then
- frees the filename string */
-
-/* G. J. Barton July 1995 */
-{
- if(GJfclose(ret_val->handle,0) == 0) {
- ret_val->handle = NULL;
- GJfree(ret_val->name);
- return ret_val;
- }else {
- if(action == 1){
- GJerror("Error closing File");
- fprintf(std_err,"%s\n",ret_val->name);
- exit(-1);
- }
- }
- return ret_val;
-}
-
-void GJinitfile(void)
-/* just set the standard streams */
-{
- std_err = stderr;
- std_in = stdin;
- std_out = stdout;
-}
-
-char *GJfnonnull(char *string)
-/* return pointer to first non null character in the string */
-/* this could cause problems if the string is not null terminated */
-{
- while(*string != '\0'){
- ++string;
- }
- return ++string;
-}
-
-char *GJstrappend(char *string1, char *string2)
-/* appends string2 to the end of string2. Any newline characters are removed
-from string1, then the first character of string2 overwrites the null at the
-end of string1.
-string1 and string2 must have been allocated with malloc.
-*/
-/* G. J. Barton July 1992 */
-{
- char *ret_val;
- ret_val = GJremovechar(string1,'\n');
- ret_val = (char *) GJrealloc(ret_val,
- sizeof(char) * (strlen(ret_val) + strlen(string2) + 1));
- ret_val = strcat(ret_val,string2);
- return ret_val;
-}
-
-char *GJremovechar(char *string,char c)
-/* removes all instances of character c from string
- returns a pointer to the reduced, null terminated string
- 11/8/1996: couple of bugs found in this routine.
- the length of the string returned was too short by 2 bytes.
- This is a dodgy routine since string is freed.
-*/
-/* G. J. Barton (July 1992) */
-{
- char *temp;
- int j,i,nchar;
- nchar = 0;
- i=0;
- while(string[i] != '\0'){
- if(string[i] == c){
- ++nchar;
- }
- ++i;
- }
- if(nchar == 0){
- return string;
- }else{
- temp = (char *) GJmalloc(sizeof(char) * (strlen(string)-nchar + 1));
- j=0;
- i=0;
- while(string[i] != '\0'){
- if(string[i] != c){
- temp[j] = string[i];
- ++j;
- }
- ++i;
- }
- temp[j] = '\0';
- GJfree(string);
- return temp;
- }
-}
-
-char *GJremovechar2(char *string,char c)
-/* removes all instances of character c from string
- returns a pointer to the reduced, null terminated string
-*/
-/* G. J. Barton (July 1992) */
-{
- char *temp;
- int i,k,len;
- k=0;
- len=strlen(string);
- temp = (char *) GJmalloc(sizeof(char) * (len+1));
- for(i=0;i<(len+1);++i){
- if(string[i] != c){
- temp[k] = string[i];
- ++k;
- }
- }
- for(i=0;i<(strlen(temp)+1);++i){
- string[i] = temp[i];
- }
- GJfree(temp);
- return string;
-}
-
-
-char *GJsubchar(char *string,char c2,char c1)
-/* substitutes c1 for c2 in string
-*/
-/* G. J. Barton (July 1992) */
-{
- int i;
-
- i=0;
- while(string[i] != '\0'){
- if(string[i] == c1){
- string[i] = c2;
- }
- ++i;
- }
- return string;
-}
-
-/* create a string and if fchar != NULL fill with characters */
-/* always set the len-1 character to '\0' */
-
-char *GJstrcreate(size_t len,char *fchar)
-{
- char *ret_val;
- ret_val = (char *) GJmalloc(sizeof(char) * len);
- --len;
- ret_val[len] = '\0';
- if(fchar != NULL){
- while(len > -1){
- ret_val[len] = *fchar;
- --len;
- }
- }
- return ret_val;
-}
-
-/* searches for string s2 in string s1 and returns pointer to first instance
-of s2 in s1 or NULL if no instance found. s1 and s2 must be null terminated
-*/
-char *GJstrlocate(char *s1, char *s2)
-{
- int i=0;
- int j=0;
- int k;
- if(strlen(s1) == 0 || strlen(s2) == 0) return NULL;
- while(i < strlen(s1)){
- j=0;
- k=i;
- while(j < strlen(s2) && s1[k] == s2[j]){
- ++k;
- ++j;
- }
- if(j == strlen(s2)) return &s1[i];
- ++i;
- }
- return NULL;
-}
-#include <stdlib.h>
-#include <string.h>
-
-
-/* GJstrtok()
-
-This version of strtok places the work pointer at the location of the first
-character in the next token, rather than just after the last character of the
-current token. This is useful for extracting quoted strings
-*/
-
-char *GJstrtok(char *input_string,const char *token_list)
-{
- static char *work;
- char *return_ptr;
-
- if(input_string != NULL){
- /* first call */
- work = input_string;
- }
-
- /* search for next non-token character */
- while(strchr(token_list,*work)!=NULL){
- ++work;
- }
-
- if(*work == '\0'){
- /* if we've reached the end of string, then return NULL */
- return NULL;
- }else{
- return_ptr = (char *) work;
- while(strchr(token_list,*work) == NULL){
- if(*work == '\0'){
- /* end of the string */
- return return_ptr;
- }else{
- ++work;
- }
- }
- *work = '\0';
- ++work;
- /* now increment work until we find the next non-delimiter character */
- while(strchr(token_list,*work) != NULL){
- if(*work == '\0'){
- break;
- }else{
- ++work;
- }
- }
- return return_ptr;
- }
-}
-/**************************************************************************
-return a pointer to space for a rectangular unsigned character array
-Version 2.0 ANSI and uses GJmallocNQ
---------------------------------------------------------------------------*/
-
-unsigned char **uchararr(int i,int j)
-{
- unsigned char **temp;
- int k, rowsiz;
-
- temp = (unsigned char **) GJmallocNQ(sizeof(unsigned char *) * i);
- if(temp == NULL) return NULL;
-
- rowsiz = sizeof(unsigned char) * j;
-
- for (k = 0; k < i; ++k){
- temp[k] = (unsigned char *) GJmallocNQ(rowsiz);
- if(temp[k] == NULL) return NULL;
- }
- return temp;
-}
-
-/**************************************************************************
-free up space pointed to by rectangular unsigned character array
--------------------------------------------------------------------------*/
-void ucharfree(unsigned char **array,int i)
-
-{
- int k;
-
- for (k = 0; k < i; ++k){
- GJfree((char *) array[k]);
- }
- GJfree((char *) array);
-
-}
-/**************************************************************************
-return a pointer to space for a rectangular double array
---------------------------------------------------------------------------*/
-
-double **GJdarr(int i,int j)
-{
- double **temp;
- int k, rowsiz;
-
- temp = (double **) GJmallocNQ(sizeof(double *) * i);
- if(temp == NULL) return NULL;
-
- rowsiz = sizeof(double) * j;
-
- for (k = 0; k < i; ++k){
- temp[k] = (double *) GJmallocNQ(rowsiz);
- if(temp[k] == NULL) return NULL;
- }
- return temp;
-}
-void GJdarrfree(double **array,int i)
-
-{
- int k;
-
- for (k = 0; k < i; ++k){
- GJfree((char *) array[k]);
- }
- GJfree((char *) array);
-
-}
-
-/**************************************************************************
-return a pointer to space for a rectangular signed character array
-Version 2.0 ANSI
---------------------------------------------------------------------------*/
-signed char **chararr(int i,int j)
-
-{
- signed char **temp;
- int k, rowsiz;
-
- temp = (signed char **) GJmallocNQ(sizeof(char *) * i);
-
- if(temp == NULL) return NULL;
-
- rowsiz = sizeof(char) * j;
-
- for (k = 0; k < i; ++k){
- temp[k] = (signed char *) GJmallocNQ(rowsiz);
- if(temp[k] == NULL) return NULL;
- }
- return temp;
-}
-
-
-/* mcheck - check a call to malloc - if the call has failed, print the
-error message and exit the program */
-/* ANSI Version - also uses GJerror routine and ptr is declared void*/
-
-void mcheck(void *ptr,char *msg)
-
-{
- if(ptr == NULL){
- GJerror("malloc/realloc error");
- exit(0);
- }
-}
-
-/* set a string to blanks and add terminating nul */
-char *GJstrblank(char *string,int len)
-
-{
- --len;
- string[len] = '\0';
- --len;
- while(len > -1){
- string[len] = ' ';
- --len;
- }
- return string;
-}
-
-/* Initialise an unsigned char array */
-void GJUCinit(unsigned char **array,int i,int j,unsigned char val)
-{
- int k,l;
-
- for(k=0;k<i;++k){
- for(l=0;l<j;++l){
- array[k][l] = val;
- }
- }
-}
-/*Initialise a signed char array */
-
-void GJCinit(signed char **array,int i,int j,char val)
-
-{
- int k,l;
-
- for(k=0;k<i;++k){
- for(l=0;l<j;++l){
- array[k][l] = val;
- }
- }
-}
-
-/* Initialise an integer vector */
-void GJIinit(int *array,int i,int val)
-{
- int k;
-
- for(k=0;k<i;++k){
- array[k] = val;
- }
-}
-
-/******************************************************************
-GJcat: concatenate N NULL terminated strings into a single string.
-The source strings are not altered
-Author: G. J. Barton (Feb 1993)
-------------------------------------------------------------------*/
-char *GJcat(int N,...)
-{
- va_list parminfo;
- int i,j,k;
- char **values; /*input strings */
- int *value_len; /*lengths of input strings */
- int ret_len; /*length of returned string */
- char *ret_val; /*returned string */
-
- ret_len = 0;
- values = (char **) GJmalloc(sizeof(char *) * N);
- value_len = (int *) GJmalloc(sizeof(int *) * N);
-
- va_start(parminfo,N);
-
- /* Get pointers and lengths for the N arguments */
- for(i=0;i<N;++i){
- values[i] = va_arg(parminfo,char *);
- value_len[i] = strlen(values[i]);
- ret_len += value_len[i];
- }
-
- ret_val = (char *) GJmalloc(sizeof(char) * (ret_len+1));
-
- /* Transfer input strings to output string */
- k=0;
- for(i=0;i<N;++i){
- for(j=0;j<value_len[i];++j){
- ret_val[k] = values[i][j];
- ++k;
- }
- }
- ret_val[k] = '\0';
- GJfree(values);
- GJfree(value_len);
-
- va_end(parminfo);
-
- return ret_val;
-}
-
-/************************************************************************
-
-GJGetToken:
-
-The aim of this routine is to emulate the strtok() function, but reading
-from a file. The functionality may differ slightly...
-
-Characters are read from the file until a character that is found in
-delim is encountered. When this occurs, token is returned. If the
-file consists entirely of delimiters, then token is freed
-and NULL is returned. Similarly, if end of file is encountered.
-
-------------------------------------------------------------------------*/
-
-
-char *GJGetToken(FILE *in, const char *delim)
-
-{
- int i;
- int c;
- char *token;
-
- i=0;
-
- token = GJmalloc(sizeof(char));
-
- while((c=fgetc(in)) != EOF){
- if(strchr(delim,c) == NULL){
- /* not a delimiter */
- token[i++] = c;
- token = GJrealloc(token,sizeof(char) * (i+1));
- }else if(i>0){
- token[i] = '\0';
- return token;
- }
- }
-/* GJerror("End of File Encountered");*/
- GJfree(token);
- return NULL;
-}
-
-struct tokens *GJgettokens(const char *delims, char *buff)
-/* This splits a buffer into tokens at each position defined by delims.*/
-/* The structure returned contains the number of tokens and the */
-/* tokens themselves as a char ** array */
-{
- char *token;
- struct tokens *tok;
-
- token = strtok(buff,delims);
- if(token == NULL) return NULL;
-
- tok = (struct tokens *) GJmalloc(sizeof(struct tokens));
- tok->ntok = 0;
- tok->tok = (char **) GJmalloc(sizeof(char *));
- tok->tok[0] = GJstrdup(token);
- ++tok->ntok;
- while((token = strtok(NULL,delims)) != NULL) {
- tok->tok = (char **) GJrealloc(tok->tok,sizeof(char *) * (tok->ntok+1));
- tok->tok[tok->ntok] = GJstrdup(token);
- ++tok->ntok;
- }
-
- return tok;
-}
-
-void GJfreetokens(struct tokens *tok)
-/* frees a tokens structure */
-
-{
- int i;
- for(i=0;i<tok->ntok;++i) {
- GJfree(tok->tok[i]);
- }
- GJfree(tok->tok);
- GJfree(tok);
- tok = NULL; /* add this to avoid odd pointer 27/6/1997*/
-}
-
-char * GJtoktostr(struct tokens *tok,char delim,int s, int e)
-
-/*
- returns a string with the tokens between s and e inclusive written to
- it separated by delim
- the tok structure is unmodified.
-*/
-
-{
- int n, i, j,k;
- char *ret_val;
-
- n = 0;
-
-
- if(s < 0 || s >= tok->ntok) s = 0;
- if(e < 0 || e >= tok->ntok) e = tok->ntok - 1;
-
- for(i=s;i<=e;++i){
- n += strlen(tok->tok[i]);
- ++n;
- }
-
- ret_val = (char *) GJmalloc(sizeof(char) * n);
- j = 0;
- for(i=s;i<=e;++i){
- for(k=0;k<strlen(tok->tok[i]);++k){
- ret_val[j] = tok->tok[i][k];
- ++j;
- }
- ret_val[j++] = delim;
- }
- ret_val[n-1] = '\0';
- return ret_val;
-}
-
-
-void GJindexx(int *arrin,int n,int *indx)
- /* indexed heap sort - adapted from the NR routine indexx.
- inarr is an integer array to sort,
- indx is the returned index array
- */
-{
- int l,j,ir,indxt,i;
-/* SMJS
- float q;
-*/
- int q;
-
- for (j=1;j<=n;j++) indx[j]=j;
- l=(n >> 1) + 1;
- ir=n;
- for (;;) {
- if (l > 1)
- q=arrin[(indxt=indx[--l])];
- else {
- q=arrin[(indxt=indx[ir])];
- indx[ir]=indx[1];
- if (--ir == 1) {
- indx[1]=indxt;
- return;
- }
- }
- i=l;
- j=l << 1;
- while (j <= ir) {
- if (j < ir && arrin[indx[j]] < arrin[indx[j+1]]) j++;
- if (q < arrin[indx[j]]) {
- indx[i]=indx[j];
- j += (i=j);
- }
- else j=ir+1;
- }
- indx[i]=indxt;
- }
-}
-
-void GJindexxD(double *arrin,int n,int *indx)
- /* indexed heap sort - adapted from the NR routine indexx.
- arrin is a double array to sort,
- indx is the returned index array
- */
-{
- int l,j,ir,indxt,i;
-/*
- float q;
-*/
- double q;
-
- for (j=1;j<=n;j++) indx[j]=j;
- l=(n >> 1) + 1;
- ir=n;
- for (;;) {
- if (l > 1)
- q=arrin[(indxt=indx[--l])];
- else {
- q=arrin[(indxt=indx[ir])];
- indx[ir]=indx[1];
- if (--ir == 1) {
- indx[1]=indxt;
- return;
- }
- }
- i=l;
- j=l << 1;
- while (j <= ir) {
- if (j < ir && arrin[indx[j]] < arrin[indx[j+1]]) j++;
- if (q < arrin[indx[j]]) {
- indx[i]=indx[j];
- j += (i=j);
- }
- else j=ir+1;
- }
- indx[i]=indxt;
- }
-}
-
-void GJindexxS1(char **arrin,int n,int *indx)
- /*indexed sort of a character array - this uses qsort rather than the
- heapsort in GJindexxS. indx runs from 0..(n-1) rather than 1..n as in
- GJindexxS.
- */
-{
- int i;
- CWORK *ret;
-
- ret = (CWORK *) GJmalloc(sizeof(CWORK) * n);
-
- for(i=0;i<n;++i){
- ret[i].val = arrin[i];
- ret[i].i = i;
- }
- qsort(ret, n, sizeof(CWORK), Sworkcomp);
-
- for(i=0;i<n;++i){
- indx[i] = ret[i].i;
- }
- GJfree(ret);
-}
-
-int Sworkcomp(const void *left, const void *right)
-{
- CWORK *a = (CWORK *) left;
- CWORK *b = (CWORK *) right;
-
- return strcmp(a->val,b->val);
-}
-
-
-void GJindexxS(char **arrin,int n,int *indx)
- /* indexed heap sort - adapted from the NR routine indexx.
- arrin is a character string array to sort
- indx is the returned index array
- */
-{
- int l,j,ir,indxt,i;
-/*
- float q;
-*/
- char *q;
-
- for (j=1;j<=n;j++) indx[j]=j;
- l=(n >> 1) + 1;
- ir=n;
- for (;;) {
- if (l > 1)
- q=arrin[(indxt=indx[--l])];
- else {
- q=arrin[(indxt=indx[ir])];
- indx[ir]=indx[1];
- if (--ir == 1) {
- indx[1]=indxt;
- return;
- }
- }
- i=l;
- j=l << 1;
- while (j <= ir) {
- if (j < ir && (strcmp(arrin[indx[j]],arrin[indx[j+1]]) < 0) ) j++;
- if (strcmp(q,arrin[indx[j]])<0) {
- indx[i]=indx[j];
- j += (i=j);
- }
- else j=ir+1;
- }
- indx[i]=indxt;
- }
-}
-
-
-
-void GJpline(FILE *fp,char c,int n)
-/* print n copies of c to fp terminated by newline */
-{
- int i;
- for(i=0;i<n;++i){
- fprintf(fp,"%c",c);
- }
- fprintf(fp,"\n");
-}
-
-char *GJlocaltime(void)
-{
- time_t t;
- char *ret_val;
- t = time(NULL);
- ret_val=asctime(localtime(&t));
- return ret_val;
-}
-
-void GJpstring(FILE *fp,char *s,int n)
-/* print a string so that it occupies n characters */
-/* strings are left-justified and either truncated or padded on output */
-{
- int i,l;
-
-
- l = strlen(s);
-
- if(l > n){
- for(i=0;i<n;++i){
- fprintf(fp,"%c",s[i]);
- }
- }else{
- for(i=0;i<l;++i){
- fprintf(fp,"%c",s[i]);
- }
- for(i=l;i<n;++i){
- fprintf(fp," ");
- }
- }
-}
-
-/* return min and max of an integer vector */
-IRANGE *irange(int *ivec,int n)
-{
- int i;
- int imin,imax;
- IRANGE *ret_val;
-
- imin = imax = ivec[0];
-
- for(i=1;i<n;++i){
- if(ivec[i] > imax) imax = ivec[i];
- if(ivec[i] < imin) imin = ivec[i];
- }
-
- ret_val = (IRANGE *) GJmalloc(sizeof(IRANGE));
- ret_val->min = imin;
- ret_val->max = imax;
-
- return ret_val;
-}
-
-#define BLIM 5
-int GJbsearchINXS(char **cod, int n, char *query)
-
-/* binary search for query in table cod. If query is found, return index of query in cod.*/
-/* if it is not found, return -1 */
-
-{
- int r; /* right limit */
- int l; /* left limit */
- int cv; /* centre value */
-
- r = n-1;
- l = 0;
-
- for(;;){
- if((r-l) > BLIM){
- cv = (r+l)/2;
- if(strcmp(query,cod[cv]) == 0){
- return cv;
- }else if(strcmp(query,cod[cv]) > 0){
- l = cv;
- }else if(strcmp(query,cod[cv]) < 0){
- r = cv;
- }
- }else{
- for(cv=l;cv<(r+1);++cv){
- if(strcmp(query,cod[cv]) == 0){
- return cv;
- }
- }
- return (int) -1;
- }
- }
-}
-
-int GJbsearchINX_IS(char **cod, int *inx, int n, char *query)
-
-/* binary search for query in table cod. inx is the index into the table that specifies
- the sorted order of the table cod.
- If query is found, return index of query in inx that can be used to recover the value of
- cod .*/
-/* if it is not found, return -1 */
-
-{
- int r; /* right limit */
- int l; /* left limit */
- int cv; /* centre value */
-
- r = n-1;
- l = 0;
-
- for(;;){
- if((r-l) > BLIM){
- cv = (r+l)/2;
- if(strcmp(query,cod[inx[cv]]) == 0){
- return cv;
- }else if(strcmp(query,cod[inx[cv]]) > 0){
- l = cv;
- }else if(strcmp(query,cod[inx[cv]]) < 0){
- r = cv;
- }
- }else{
- for(cv=l;cv<(r+1);++cv){
- if(strcmp(query,cod[inx[cv]]) == 0){
- return cv;
- }
- }
- return (int) -1;
- }
- }
-}
-
-/*
-
-$Id: gjutil.c,v 1.13 2002/08/09 12:30:31 geoff Exp $
-
-$Log: gjutil.c,v $
-Revision 1.13 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 1.12 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 1.11 2000/07/04 11:01:37 searle
-Changes for MMX
-
-Revision 1.10 1999/11/17 21:06:47 geoff
-Add setup_caleb and other changes to swpp2 and so on.
-
-Revision 1.9 1999/07/09 13:34:10 geoff
-modified these as a test
-
-Revision 1.8 1998/08/11 15:38:50 geoff
-Modified the copyright notice to reflect the new
-ownership of this software.
-
-Revision 1.7 1997/06/29 00:43:57 gjb
-Changes to add sysinfo calls and test of license reading routines
-
-Revision 1.6 1997/06/27 16:42:41 gjb
-Add trlic.c test.lic and clean up gjutil.c
-
-Revision 1.5 1997/06/27 07:17:31 gjb
-Added rlic.c linfo.h and
-changes to gjutil.c to give better support for
-token manipulation
-
-Revision 1.4 1997/05/12 11:10:53 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
-
-*/
-
-
-
-
git://source.jalview.org / jabaws.git / blobdiff