/*
 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>

main(ac,av)
int ac;
char *av[];
{
	FILE *fd,*fopen();
	char code[6],seqt[110];
	int i,c,ct,flag;

   /* Check for correct command line */
	if(ac<2)
		{
		fprintf(stderr,"\nPurpose: Convert Sequences to \"Old Atlas\"");
		fprintf(stderr," format.\n");
		fprintf(stderr,"Usage: ");
		fprintf(stderr,"%s rf [>wf]\n",av[0]);
		fprintf(stderr,"\trf: Sequence-any format.\n");
		fprintf(stderr,"\twf: Sequence-Old Atlas format.\n\n");
		exit();
		}

	if( (fd = fopen( av[1],"r" )) == NULL )
		exit(fprintf(stderr,"%s: can't open %s\n",av[1]) );

	fprintf(stderr,"\tD(NA) or P(rotein)? ");
	c = getchar();
	if( c== 'D' || c == 'd' )
		ct = 0;
	else
		ct = 1;
	getchar();

	fprintf(stderr,"\tType a title for the sequence (<101 characters)\n");
	i = 0;
	while((c=getchar())!='\n')
		{
		if( c >= 'a' && c <= 'z' )
			seqt[i++] = c + 'A' - 'a';
		else
			seqt[i++] = c;
	       	}
	seqt[i++] = '\n';
	seqt[i] = '\0';

	fprintf(stderr,"\tType a 4-letter code for the sequence\n");
	i = 0;
	while((c=getchar())!='\n')
		{
		if( c >= 'a' && c <= 'z' )
			code[i++] = c + 'A' - 'a';
		else
			code[i++] = c;
		if(i==4)
			break;
	       	}
	if(i==3)
		code[i++] = ' ';
	code[i] = '\0';

	printf("T%s  %s",code,seqt);
	if(ct==0)
		printf("D%s    1",code);
	else
		printf("P%s    1",code);
	
	flag = 0;
	for(i=0; (c=fgetc(fd))!=EOF; )
		{
		if( c >= 'A' && c <= 'Z')
			{
			i++;
			flag = 1;
			printf("%2c",c);
			}
		else if( c >= 'a' && c <= 'z' )
			{
			c = c + 'A' - 'a';
			i++;
			flag = 1;
			printf("%2c",c);
			}
		if(i%30==0 && flag==1)
			{
			if(ct==0)
				printf("\nD%s%5d",code,i+1);
			else
				printf("\nP%s%5d",code,i+1);
			flag = 0;
			}
		}
	printf(" *\n");
}