#include <stdlib.h>#include <stdio.h>#include <string.h>#include <errno.h>#include <stdarg.h>#include <ctype.h>#include "clustalw.h"extern char **seq_array;extern sint  *seqlen_array;extern char **names,**titles;extern sint *output_index;extern sint *seq_weight;extern double **tmat;/**	ckalloc()**	Tries to allocate "bytes" bytes of memory. Exits program if failed.*	Return value:*		Generic pointer to the newly allocated memory.*/void *ckalloc(size_t bytes){	register void *ret;		if( (ret = calloc(bytes, sizeof(char))) == NULL)/*	if( (ret = malloc(bytes)) == NULL)*/		fatal("Out of memory\n");	else		return ret;		return ret;	}/**	ckrealloc()**	Tries to reallocate "bytes" bytes of memory. Exits program if failed.*	Return value:*		Generic pointer to the re-allocated memory.*/void *ckrealloc(void *ptr, size_t bytes){	register void *ret=NULL;	if (ptr == NULL)			fatal("Bad call to ckrealloc\n");	else if( (ret = realloc(ptr, bytes)) == NULL)		fatal("Out of memory\n");	else		return ret;		return ret;	}/**	ckfree()**	Tries to free memory allocated by ckalloc.*	Return value:*		None.*/void *ckfree(void *ptr){	if (ptr == NULL)		warning("Bad call to ckfree\n");	else {	 	free(ptr);		ptr = NULL;	}	return ptr;}/**	rtrim()**	Removes trailing blanks from a string**	Return values:*		Pointer to the processed string*/char * rtrim(char *str){	register int p;	p = strlen(str) - 1;		while ( isspace(str[p]) )		p--;			str[p + 1] = EOS;		return str;}/**	blank_to_()**	Replace blanks in a string with underscores**       Also replaces , ; : ( or ) with _**	Return value:*		Pointer to the processed string*/char * blank_to_(char *str){	int i,p;	p = strlen(str) - 1;		for(i=0;i<=p;i++) 		if(                     (str[i]==' ') ||                     (str[i]==';') ||                     (str[i]==',') ||                     (str[i]=='(') ||                     (str[i]==')') ||                     (str[i]==':')                   )                      str[i] = '_';		return str;}/**	upstr()**	Converts string str to uppercase.*	Return values:*		Pointer to the converted string.*/char * upstr(char *str){	register char *s = str;		while( (*s = toupper(*s)) )		s++;			return str;}/**	lowstr()**	Converts string str to lower case.*	Return values:*		Pointer to the converted string.*/char * lowstr(char *str){	register char *s = str;		while( (*s = tolower(*s)) )		s++;			return str;}void getstr(char *instr,char *outstr){		fprintf(stdout,"%s: ",instr);	gets(outstr);}double getreal(char *instr,double minx,double maxx,double def){	int status;	float ret;	char line[MAXLINE];			while(TRUE) {		fprintf(stdout,"%s (%.1f-%.1f)   [%.1f]: ",instr,minx,maxx,def);		gets(line);		status=sscanf(line,"%f",&ret);		if(status == EOF) return def;		if(ret>maxx) {			fprintf(stdout,"ERROR: Max. value=%.1f\n\n",maxx);			continue;		}		if(ret<minx) {			fprintf(stdout,"ERROR: Min. value=%.1f\n\n",minx);			continue;		}		break;	}	return (double)ret;}int getint(char *instr,int minx,int maxx, int def){	int ret,status;	char line[MAXLINE];		while(TRUE) {		fprintf(stdout,"%s (%d..%d)    [%d]: ",		instr,(pint)minx,(pint)maxx,(pint)def);		gets(line);		status=sscanf(line,"%d",&ret);		if(status == EOF) return def;		if(ret>maxx) {			fprintf(stdout,"ERROR: Max. value=%d\n\n",(pint)maxx);			continue;		}		if(ret<minx) {			fprintf(stdout,"ERROR: Min. value=%d\n\n",(pint)minx);			continue;		}		break;	}	return ret;}void do_system(void){	char line[MAXLINE];		getstr("\n\nEnter system command",line);	if(*line != EOS)		system(line);	fprintf(stdout,"\n\n");}Boolean linetype(char *line,char *code){	return( strncmp(line,code,strlen(code)) == 0 );}Boolean keyword(char *line,char *code){	int i;	char key[MAXLINE];	for(i=0;!isspace(line[i]) && line[i]!=EOS;i++)		key[i]=line[i];	key[i]=EOS;	return( strcmp(key,code) == 0 );}Boolean blankline(char *line){	int i;	for(i=0;line[i]!='\n' && line[i]!=EOS;i++) {		if( isdigit(line[i]) ||		    isspace(line[i]) ||		    (line[i] == '*') ||		    (line[i] == ':') ||                    (line[i] == '.')) 			;		else			return FALSE;	}	return TRUE;}void get_path(char *str,char *path){	register int i;		strcpy(path,str);	for(i=strlen(path)-1;i>-1;--i) {		if(str[i]==DIRDELIM) {			i = -1;			break;		}		if(str[i]=='.') break;	}	if(i<0)		strcat(path,".");	else		path[i+1]=EOS;}void alloc_aln(sint nseqs){	sint i,j;        seqlen_array = (sint *)ckalloc( (nseqs+1) * sizeof (sint));        seq_array = (char **)ckalloc( (nseqs + 1) * sizeof (char *) );	for(i=0;i<nseqs+1;i++)		seq_array[i]=NULL;        names = (char **)ckalloc( (nseqs+1) * sizeof (char *) );        for(i=1;i<=nseqs;i++)                names[i] = (char *)ckalloc((MAXNAMES+1) * sizeof (char));        titles = (char **)ckalloc( (nseqs+1) * sizeof (char *) );        for(i=1;i<=nseqs;i++)                titles[i] = (char *)ckalloc((MAXTITLES+1) * sizeof (char));        output_index = (sint *)ckalloc( (nseqs+1) * sizeof (sint));        tmat = (double **) ckalloc( (nseqs+1) * sizeof (double *) );        for(i=1;i<=nseqs;i++)                tmat[i] = (double *)ckalloc( (nseqs+1) * sizeof (double) );        for(i=1;i<=nseqs;i++)        	for(j=1;j<=nseqs;j++)			tmat[i][j]=0.0;        seq_weight = (sint *)ckalloc( (nseqs+1) * sizeof (sint));        for(i=1;i<=nseqs;i++)		seq_weight[i]=100;}void realloc_aln(sint first_seq,sint nseqs){	sint i,j;        seqlen_array = (sint *)ckrealloc(seqlen_array, (first_seq+nseqs+1) * sizeof (sint));        seq_array = (char **)ckrealloc(seq_array, (first_seq+nseqs+1) * sizeof (char *) );	for(i=first_seq;i<first_seq+nseqs+1;i++)		seq_array[i]=NULL;        names = (char **)ckrealloc(names, (first_seq+nseqs+1) * sizeof (char *) );        for(i=first_seq;i<first_seq+nseqs;i++)                names[i] = (char *)ckalloc((MAXNAMES+1) * sizeof (char));        titles = (char **)ckrealloc(titles, (first_seq+nseqs+1) * sizeof (char *) );        for(i=first_seq;i<first_seq+nseqs;i++)                titles[i] = (char *)ckalloc((MAXTITLES+1) * sizeof (char));        output_index = (sint *)ckrealloc(output_index, (first_seq+nseqs+1) * sizeof (sint));        seq_weight = (sint *)ckrealloc(seq_weight, (first_seq+nseqs+1) * sizeof (sint));        for(i=first_seq;i<first_seq+nseqs;i++)		seq_weight[i]=100;        tmat = (double **) ckrealloc(tmat, (first_seq+nseqs+1) * sizeof (double *) );        for(i=1;i<first_seq;i++)                tmat[i] = (double *)ckrealloc(tmat[i], (first_seq+nseqs+1) * sizeof (double) );        for(i=first_seq;i<first_seq+nseqs;i++)                tmat[i] = (double *)ckalloc( (first_seq+nseqs+1) * sizeof (double) );        for(i=1;i<first_seq;i++)        	for(j=first_seq;j<first_seq+nseqs;j++)		{			tmat[i][j]=0.0;			tmat[j][i]=0.0;		}}void free_aln(sint nseqs){	sint i;	if(nseqs<=0) return;	seqlen_array = ckfree(seqlen_array);        for(i=1;i<=nseqs;i++)		seq_array[i] = ckfree(seq_array[i]);	seq_array = ckfree(seq_array);	for(i=1;i<=nseqs;i++)		names[i] = ckfree(names[i]);	names = ckfree(names);	for(i=1;i<=nseqs;i++)		titles[i] = ckfree(titles[i]);	titles = ckfree(titles);	output_index = ckfree(output_index);	seq_weight = ckfree(seq_weight);        for(i=1;i<=nseqs;i++)		tmat[i] = ckfree(tmat[i]);	tmat = ckfree(tmat);}void alloc_seq(sint seq_no,sint length){	seq_array[seq_no] = (char *)ckalloc((length+2) * sizeof (char));}void realloc_seq(sint seq_no,sint length){	seq_array[seq_no] = (char *)realloc(seq_array[seq_no], (length+2) * sizeof (char));}void free_seq(sint seq_no){	seq_array[seq_no]=ckfree(seq_array[seq_no]);}