/*
 Program From Progressive Alignment of Amino Acid
 Sequences and Construction of Phylogenetic Trees
 from Them, by D. F. Feng and R. F. Doolittle,
 Methods of Enzymology, v266, p368 (1996)
				2/7/1996
 Read "readme.doc" before using.
*/

#include <stdio.h>
#define MAX 60000

char seqt[100],code[8];
char seq[MAX];
int len;

main(ac,av)
int ac;
char *av[];
{
	FILE *fd1, *fopen();
	int i,sp,ep;

	if(ac<3)
		{
		fprintf(stderr,"\nPurpose: Cut Sequence to Order.\n");
		fprintf(stderr,"Usage: ");
		fprintf(stderr,"%s rf St [Ed] [>wf]\n",av[0]);
		fprintf(stderr,"\trf: Sequence.\n");
		fprintf(stderr,"\tSt: Starting point.\n");
		fprintf(stderr,"\tEd: Ending point(default=end of ");
		fprintf(stderr,"sequence).\n");
		fprintf(stderr,"\twf: Cropped sequence.\n");
		fprintf(stderr,"Note: Sequence in rf must be in");
		fprintf(stderr," Old Atlas format.\n\n");
		exit();
		}

   /* Open fd1 */
	if( (fd1 = fopen( av[1],"r" )) == NULL )   /*error check*/
		exit(fprintf(stderr,"%s: can't open %s\n",av[1]) );

	sp=atoi(av[2]);
	Read_seq(fd1);
	if((ep=atoi(av[3]))==0)
		ep=len;
	Rite_seq(sp,ep);
}

Read_seq(fd)
FILE *fd;
{
	int i;
	char s;

   /* Enter sequences */

	fgetc(fd);
	fgets(code,6L,fd); /*Get the 1st 5 letters as code*/
	while((s=fgetc(fd))==' ')
		;
	ungetc(s,fd);
	fgets(seqt, sizeof seqt, fd);  /*Get sequence title*/

       	fseek(fd,11,1); /*Skip 11 characters*/
       	for(i=0; (s=fgetc(fd)) && (s != '*'); ++i)
		{
		if(s=='\n')
			{
			--i;
			fseek(fd,11,1);
			}
		else if(s==' ')
			--i;
		else
			seq[i]=s;
       		}
	fgetc(fd);
	if(i > MAX-1)
		{
		printf("%s length exceeded %d,",MAX);
		printf(" execution terminated!\n");
		exit(0);
		}
	seq[i]='\0';
	len=strlen(seq);
}

Rite_seq(sp,ep)
int sp,ep;
{
	int j,k,l;

	j = k = 0;
	l=ep-sp+1;
	printf("T%s   (%d->%d=%d)%s",code,sp,ep,l,seqt);
	printf("P%s %3d",code,j+1);
	while(sp<=ep)
		{
		printf("%2c",seq[sp-1]);
		sp++;
		j++;
		k++;
		if(k==30)
			{
			printf("\nP%s%4d",code,j+1);
			k = 0;
			}
		}
	printf("%2c\n",'*');
}