/**********************************************************
File: rmsd.c
Author: Scot Cunningham

Usage: rmsd [infile]

This file calculates an Root Mean Square Differentiation (RMSD)
between two identical sized vectors.  The input is two vectors
that have been pasted together.  For example, to compare the 
vector {1,3,5,9} with {2,4,6,8}, the input would be the following:
1	2
3	4
5	6
7	8

A tab should separate each element.

If a filename is not specified, input is obtained from stdin.

Compile with -lm option to get math libraries

**********************************************************/

#include <math.h>
#include <stdio.h>
#include <string.h>

int rmsd (FILE *fp)
{
	char s[256];
	char *token;
	char *search = "	"; /* tab is the delimiter */
	int i;
	int numvalues=0;
	int a,b;
	int diff;
	int sumdiff=0;

	/* This loop is the meat of the algorithm */
	while (fgets(s,256,fp))
	{
		token = strtok(s, search);	
		a=atoi(token);

		token = strtok(NULL, search);	
		b=atoi(token);
		diff = a - b;
		sumdiff += diff * diff;
		++numvalues;
	}

	return sqrt(sumdiff/numvalues);
}

int main(int argc, char** argv)
{
	float dist;
	FILE *fp;
	
	/* See if a filename is specified */
	if (argc < 2){
		fp = stdin;
	}else{
		if ((fp = fopen(argv[1],"r")) == NULL)
		{
			fprintf(stderr, "Unable to open file %s\n",argv[1]);
			exit(1);
		}
	}

	/* Calculate the distance */
	dist = rmsd(fp);

	if (argc > 0)
		fclose(fp);

	/* Output the distance to stdout */
	printf("%d\n", (int)dist);

	return dist;
}