[BHCluster]

Hi all
I need a bit of help here I have wore a program do take in a declared array as shown bellow but my problem is how to convert this program to read the numbers which I have in the array in the main from a file so it calculate them automatically and outputs them back into new file.

Code:

import java.io.*;
import static java.lang.Math.*;

class numbers
	{
public static void Manhattan(double[][] a,double[][] b,int n,int n2)
  {
    int q=n2;
    int c=n;
    for(int m=0;m<q;m++)
    {
      for(int h=0;h<q;h++)
      {
        double d=0;
        double d2=0;
        for(int j=0;j<c;j++)
        {
          d2=a[m][j]-a[h][j];
          if(d2<0)
          d2=d2*-1;
          d=d+d2;
          }
        b[m][h]=d;

      }
    }

  }


public static double Euclidean(double[] array1, double[] array2)
{
	//Store the numbers of the both arrays
	double x1= array1[0];
	double y1=array2[0];
	double x2= array1[1];
    double y2= array2[1];
    double x3=array1[2];
    double y3=array2[2];

	//Compute the minus part of the formula
	double minusResult1 = y1-x1;
	double minusResult2 = y2-x2;
	double minusResult3 = y3-x3;

	//Square the answers
	double square1 = pow(minusResult1, 2);
 	double square2 = pow(minusResult2, 2);
    double square3 = pow(minusResult3, 2);

	//Sum the squares
	double sumOfSquares = square1+square2+square3;

	//Get the square root of the sumOfSquares
	double finalResult = sqrt(sumOfSquares);

	return finalResult;
}

public static double Manhattan(double[] array1, double[] array2)
		{

//Store the numbers of the both arrays
double x1= array1[0];
	double y1=array2[0];
	double x2= array1[1];
    double y2= array2[1];
    double x3=array1[2];
    double y3=array2[2];

	//Compute the minus part of the formula
	double minusResult1 = y1-x1;
	double minusResult2 = y2-x2;
	double minusResult3 = y3-x3;
     //Square the answers
	double abs1 = abs(minusResult1 );
 	double abs2 = abs(minusResult2);
    double abs3 = abs(minusResult3 );

	//Sum the squares
	double sumOfAbs = abs1+abs2+abs3;

	//Get the square root of the sumOfAbs
	double finalResult = sqrt(sumOfAbs);

	return finalResult;
}

public static double Pearson(double[] array1, double[] array2)
{
	//Store the numbers of the both arrays
	double x1= array1[0];
	double y1=array2[0];
	double x2= array1[1];
	double y2= array2[1];
    double x3=array1[2];
    double y3=array2[2];

	//Compute the minus part of the formula
	double mean1 = (x1 + x2 + x3)/3;
	double mean2 = (y1 + y2 + y3)/3;

	double t = (x1 - mean1)*(y1 - mean2) + (x2 - mean1)*(y2 - mean2) + (x3 - mean1)*(y3 - mean2);


	//Square the answers
	double square1 = sqrt((x1 - mean1)*(x1 - mean1) + (x2 - mean1)*(x2 - mean1) + (x3 - mean1)*(x3 - mean1));
	double square2 = sqrt((y1 - mean2)*(y1 - mean2) + (y2 - mean2)*(y2 - mean2) + (y3 - mean2)*(y3 - mean2));


	//Get the square root of the sumOfSquares
	double finalResult = t/(square1*square2);

	return finalResult;
}
public static void main(String[] args)
	{


	double[] gene={-9.30, 5.65, -5.02};
	double[] gene1={-4.10, 5.68, 0.56};
	double EuclideanDist = Euclidean(gene, gene1);
	System.out.println("Euclidean distance = " + EuclideanDist);

	double ManhattanDist = Manhattan(gene, gene1);
	System.out.println("Manhattan = " + ManhattanDist);

	double PearsonDist = Pearson(gene, gene1);
	System.out.println("Pearson = " + PearsonDist);

	}

}

file looks like this

Code:

-9.30		5.65		-5.02
-4.10		5.68		0.56
4.75		0.11		2.86
-1.54		-10.01		-1.99
-6.29		5.62		-2.78
-13.02		1.31		1.61
-5.85		3.79		-6.56
-12.71		-0.45		0.62
-3.05		-12.65		-5.07
2.18		-5.82		-9.73
1.74		-0.99		-3.66
-7.88		0.93		-8.33
-6.34		-1.85		-4.00
-0.71		-2.64		-5.64

If somebody know the way to do this please help.
Thank you.