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


#include "cl.h"

typedef struct {
  int nrow, ncol;
  char **data;
  double *y;
  char **cname;
  char **rname;
} DATA_MATRIX;


DATA_MATRIX *ReadData( char *infile );

int main( int argc, char **argv ) {
  char infile1[256];
  char infile2[256];
  DATA_MATRIX *d1=NULL;
  int n, m, i;

  getarg( "-chr1", infile1, argc, argv);

  d1 = ReadData( infile1 );

  for(m=0;m<d1->nrow;m++) {
    char *g1 = d1->data[m];
    for(n=0;n<m;n++) {
      int ibs = 0;
      int nibs=0;
      char *g2 = d1->data[n];
      for(i=0;i<d1->ncol;i++) {
	if ( g1[i]>0 & g2[i]>0 ) {
	  ibs += abs(g1[i]-g2[i]);
	  nibs++;
	}
      }
      printf( "%s %s %d %d %.5f\n", d1->rname[m], d1->rname[n], ibs, nibs, ibs/(double)(nibs ? nibs : 1) );
    }
  }
}


DATA_MATRIX *ReadData( char *infile ) {
  FILE *fp;
  int nrow, ncol;
  char **data = NULL;
  char *buffer;
  char name[256];
  int n, m;
  double x;
  double *y;
  DATA_MATRIX *d = NULL;


  if ( fp = fopen( infile, "r" ) ) {

    if ( fscanf( fp, "%d %d", &nrow, &ncol ) ==2 ) {
      int i;
      char tmp[256];
      char **cname = (char**)calloc(ncol,sizeof(char*));
      char **rname = (char**)calloc(nrow,sizeof(char*));
      for(i=0;i<ncol;i++) {
	fscanf(fp, "%s", tmp );
      	cname[i] = strdup(tmp);
	/*	printf( "names[%d] = %s\n", i, names[i]); */
      }
      nrow++;
      data = (char**)malloc(nrow*sizeof(char*));
      buffer = (char*)malloc( (ncol+100) * sizeof(char));
      y = (double*)calloc(nrow, sizeof(double));
      n = 0;
      
      while( n <nrow && fscanf( fp, "%s %lf %s", tmp, &x, buffer ) == 3  ) {
	rname[n] = (char*)strdup(tmp);
	y[n] = x;
	data[n] = (char*)strdup(buffer);
	ncol = strlen(buffer);
	for(m=0;m<ncol;m++) 
	  data[n][m] -= '0';
	
	n++;
	/*	printf( "%d %d %s\n", n, strlen(buffer), data[n-1]); */
      }
      d = (DATA_MATRIX*)calloc( 1, sizeof(DATA_MATRIX));
      d->nrow = n;
      d->ncol = ncol;
      d->data = data;
      d->y = y;
      d->cname = cname;
      d->rname = rname;
    }
  }

  return d;
}