As the topic name said I have a Algorithms and data from a File Problem. To be more precise I can read and display the contents of the file on the screen shown bellow:

experiment.java
Java Code:
package get.set; // packaged for reuse

 public class experiment
 {
 private double experiment1;
 private double experiment2;
 private double experiment3;

 // no-argument constructor calls other constructor with default values
 public experiment()
 {
 this ( 0.0, 0.0, 0.0 ); // call four-argument constructor
 } // end no-argument AccountRecord constructor

 // initialize a record
 public experiment( double exp1, double exp2, double exp3 )
 {
 setExperiment1( exp1 );
 setExperiment2( exp2 );
 setExperiment3( exp3 );
 } // end three-argument experiment constructor

 // set experiment1
 public void setExperiment1( double exp1 )
 {
 experiment1 = exp1;
 } // end method setExperiment1

 // get account number
 public double getExperiment1()
 {
 return experiment1;
 } // end method getExperiment1

 // set experiment2
 public void setExperiment2( double exp2 )
 {
 experiment2 = exp2;
 } // end method setExperiment2

 // get first name
 public double getExperiment2()
 {
 return experiment2;
 } // end method getExperiment2

 // set set experiment3
 public void setExperiment3( double exp3 )
 {
 experiment3 = exp3;
 } // end method setExperiment3

 // get experiment3
 public double getExperiment3()
 {
 return experiment3;
 } // end method getExperiment3
 } // end class experiment
readFile.java
Java Code:
 
import java.io.File;
 import java.io.FileNotFoundException;
 import java.lang.IllegalStateException;
 import java.util.NoSuchElementException;
 import java.util.Scanner;

 import get.set.experiment;

 public class readFile
 {
 private Scanner input;

 // enable user to open file
 public void openFile()
 {
 try
 {
 input = new Scanner( new File("Data_Set_1.txt") );
 } // end try
 catch ( FileNotFoundException fileNotFoundException )
 {
 System.err.println( "Error opening file." );
 System.exit( 1 );
 } // end catch
 } // end method openFile

 // read record from file
 public void readRecords()
 {
 // object to be written to screen
 experiment record = new experiment();

 System.out.printf( "%10s%15s%15s\n", "Experiment 1",
 " Experiment 2", " Experiment 3" );

 try // read records from file using Scanner object
 {
 while ( input.hasNext() )
 {
 record.setExperiment1(  input.nextDouble() ); // read experiment1
 record.setExperiment2(  input.nextDouble() ); // read experiment2
 record.setExperiment3(  input.nextDouble() ); // read experiment3


 // display record contents
 System.out.printf( "%10f%15f%15f\n",
 record.getExperiment1(), record.getExperiment2(),record.getExperiment3());
 } // end while
 } // end try
 catch ( NoSuchElementException elementException )
 {
 System.err.println( "File improperly formed." );
 input.close();
 System.exit( 1 );
 } // end catch
 catch ( IllegalStateException stateException )
 {
 System.err.println( "Error reading from file." );
 System.exit( 1 );
 } // end catch
 } // end method readRecords

 // close file and terminate application
 public void closeFile()
 {
 if ( input != null )
 input.close(); // close file
 } // end method closeFile
 } // end class readFile
runReadFileTest.java
Java Code:
public class runReadFileTest
 {
 public static void main( String args[] )
 {
 readFile application = new readFile();

 application.openFile();
 application.readRecords();
 application.closeFile();
 } // end main
 } // end class runReadFileTest
Now my issue is that I can not implement the algorithms which I wrote for the simpler version of this program (which works as well).

numbers.java
Java Code:
import java.io.*;
import static java.lang.Math.*;

class numbers2
	{
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);

	}

}
If anybody know how to implement those three algorithms (Euclidean, Manhattan, Pearson) into the the program above please help. I greatly appreciate any help.