Problem in file implementation

[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.

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

-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.

[Eranga]

Read the file line by line and get substring from there. It's easy because there is a space between two number of each line. You got it?

[Eranga]

Is there two tab spaces between two values in a single line?

[BHCluster]

Thanks for taking interest, and to answer your question the space between columns is not important, what is important is that there are three columns.

[BHCluster]

I have added this so it reads the files one by one:

Get Set methods

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

Read file class

 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

Test Class

public class runReadFileTest
 {
 public static void main( String args[] )
 {
 readFile application = new readFile();

 application.openFile();
 application.readRecords();
 application.closeFile();
 } // end main
 } // end class runReadFileTest

Ok my next question is how to use algorithms from above to combine with these classes so they do waht they are suppose to do. Your help is greatly appreciated

[Eranga]

Thanks for taking interest, and to answer your question the space between columns is not important, what is important is that there are three columns.

Have a reason to ask that question. After reading a line of a file, easily use the StringTokenizer class to get those three columns. So simple it is :)

[Eranga]

I'm not sure how and why you going to use algorithms for this. In simple way you can read the file and get the numbers of each columns. As i said earlier, space in between two numbers of a each line is important for my application. I assumed that the space is two tabs.

        FileInputStream fis = null;
        try {
            fis = new FileInputStream("files/ReadFileByLines.txt");
            InputStreamReader isr = new InputStreamReader(fis);
            LineNumberReader lnr = new LineNumberReader(isr);
            
            String line = null;
            while((line = lnr.readLine()) != null){
                
                StringTokenizer st1 = new StringTokenizer(line, "\t\t");
                
                String s1 = st1.nextToken();
                String s2 = st1.nextToken();
                String s3 = st1.nextToken();
                
                System.out.println(s1 + "\t" + s2 + "\t" + s3);
            }
            System.out.println("Total number of lines on the file " +
                    "is " + lnr.getLineNumber());
        } 
        catch (IOException ex) {
            System.out.println(ex.getMessage());
        }        
        finally {
            try {
                fis.close();
            } 
            catch (IOException ex) {
                System.out.println(ex.getMessage());
            }
        }