/* cluster.c

   Compile with: gcc -g cluster.c -lm -o cluster
   Example run:  cluster hs2.l4.list > hs2.l4.c

   Clusters regions reported by kkno/kunk/(infocon/phylogen/agree).
*/

#include <stdio.h>
#include <stdlib.h>
#include <strings.h>
#include <ctype.h>

#define Usage "%s <filename>\n" 
#define LARGE_NUMBER 99999999
#define DEFAULT_MAX_GAP 0 

void fatalf(char *msg, char *val);
FILE *ckopen(char *name, char *mode);
void *ckalloc(size_t amount);

int main(int argc, char *argv[]) {

 char  buffer[1000];
 int   cFrom[10000], cTo[10000], MAX_GAP;
 int   k, i, from, to; 
 FILE *fp;

 if ((argc!=2) && (argc!=3)) fatalf(Usage,argv[0]); 

 if ((argc==3) && !strncmp(argv[2],"G=",2))
     MAX_GAP = atoi(argv[2]+2);
 else MAX_GAP = DEFAULT_MAX_GAP;

 fp = ckopen(argv[1],"r");
  
 k = -1;
 cFrom[0] = cTo[0] = LARGE_NUMBER;
 while (fgets(buffer,1000,fp)!=NULL) {
    if (!isdigit(buffer[0]))
        continue;
    sscanf(buffer, "%d %d", &from, &to);
    if ((k>=0) && (from<=cTo[k]+1+MAX_GAP))  
         /* overlap -- extend cluster */ 
         cTo[k] = to;
    else {  
         /* new cluster */
         cFrom[++k] = from;
         cTo[k] = to;
    }
 }          
 printf("#clusters: %d\n#========================\n",++k);
 for (i=0; i<k; i++)
      printf("%d %d\n",cFrom[i],cTo[i]); 
      
 fclose(fp);
 return 0;
}


void fatal(char *msg)
{
        (void)fprintf(stderr, "%s\n", msg); 
        exit(1);
}               

void fatalf(char *msg, char *val)
{
        (void)fprintf(stderr, msg, val);
        (void)putc('\n', stderr);
        exit(1);
}


FILE *ckopen(char *name, char *mode)
{
        FILE *fp; 
 
        if ((fp = fopen(name, mode)) == NULL)
                fatalf("Cannot open %s.", name);
        return fp;
}           


void *ckalloc(size_t amount)
{
        void *p;
        
        if ((p = malloc(amount)) == NULL)
                fatal("Ran out of memory.");
        return p;
}