/*
 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.
*/

#define MAXS 700
#define nseq 40

#include <stdio.h>
int NSEQ, nax;
char seq[nseq][MAXS];

main(ac,av)
int ac;
char *av[];
{
	FILE *fd;	
	int c, flag, i, ii, j, k, m, n, nline;

 	char stitle[nseq][100], code[nseq][12];
	
	if(ac<2)
		{
		fprintf(stderr,"\nPurpose: Change Aligned Sequences");
		fprintf(stderr," to Compact Format.\n");
		fprintf(stderr,"usage: %s rf [Nr] [>wf]\n",av[0]);
		fprintf(stderr,"\trf: Progressive aligned sequences.\n");
		fprintf(stderr,"\twf: Formatted sequences.\n");
		fprintf(stderr,"\tNr: Number of residues per line");
		fprintf(stderr," (default=65).\n");
		fprintf(stderr,"Current limitations: NSEQ=<%d, length=<%d\n\n",
				nseq,MAXS);
		exit(0);
		}

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

	nline = 0;
	NSEQ=0;
	for(i=0; ; ++i)
		{
		if((c=getc(fd))==EOF)
			break;
		ungetc(c,fd);
		NSEQ++;
		while((c=getc(fd))==' ')
			;
		ungetc(c,fd);
		fgets(stitle[i],sizeof stitle[i],fd);
		fgetc(fd);
		fgets(code[i],5,fd);
		for(ii=4; ii<10; ii++)
			code[i][ii] = ' ';
		code[i][ii] = '\0';
		fseek(fd,6,1);
	       	for(j=0;(c=getc(fd)) && c != '*'; ++j)
			{
			if(c=='\n')
				{
				fseek(fd,11,1);	
				--j;
				continue;
				}
			if(c==' ')
				{
				--j;
				continue;
				}
			seq[i][j]=c;
		       }
		seq[i][j]='*';
		seq[i][j+1]='\0';
		getc(fd);
		}

	if(av[2] == NULL)
		nax=65;
	else
		nax = atoi(av[2]);

	fprintf(stderr,"If you want to use the Old_Codes, hit <CR>, otherwise\n");
	fprintf(stderr,"enter a New_Code with no more than 10 characters.\n\n");
	
	for(i=0; i<NSEQ; ++i)
		{
		j=0;
		fprintf(stderr,"Seq (%2d), Old_Code (%c%c%c%c), New_Code:",
			i+1,code[i][0],code[i][1],code[i][2],code[i][3]);
		while((c=getchar())!='\n')
			code[i][j++]=c;
		if(j>0)
			{
			while(j<10)
				code[i][j++]=' ';
			code[i][j]='\0';
			}
		}
	
	for(i=0; seq[0][i]!='\0'; ++i)
		{
		flag=0;
		for(j=0; j<NSEQ; ++j)
			if(seq[j][i]!='X')
				flag=1;
		if(flag==0)
			{
			for(n=0; n<NSEQ; ++n)
				{
				for(m=i; seq[n][m]!='\0'; ++m)
					seq[n][m]=seq[n][m+1];
				seq[n][m]='\0';
				}
			i--;
			}
		}
	nline=i-1;
	if(nline%nax)
		nline=nline/nax+1;
	else 
		nline=nline/nax;

	for(i=0; i<nline; ++i)
		{
		printf("\n\n            ");
		for(k=i*nax; k<(nax+i*nax) && (seq[0][k]!='*'); ++k)
				{
				if(match(0,k)==NSEQ)
					printf("*");
				else
					printf(" ");
				j++;
				}
		for(j=0; j<NSEQ; ++j)
			{
			printf("\n");
				printf("%s  ",code[j]);
			for(k=i*nax; k<(nax+i*nax) && (seq[j][k]!='*'); ++k)
				{
				if(seq[j][k]=='X' || seq[j][k]=='J')
					printf("%c",' ');
				else if( (match(j,k)>=NSEQ)&&(seq[j][k]=='C') )
					printf("%c",seq[j][k]+'a'-'A');
				else 
					printf("%c",seq[j][k]); 
				}
			}
		}
	printf("\n");
}


match(j,k)
int j,k;
{
	int i, mtch;

	mtch=0;
	for(i=0; i<NSEQ; ++i)
		{
		if((seq[j][k]==seq[i][k])&&(seq[j][k]!='X'))
			mtch++;
		}
	return(mtch);
}