source: tags/arb-6.0.2/GDE/CLUSTALW/util.c

#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]);
}