[BHCluster]

Finally after few posts and few attempts I have managed to read text file and out put it on the screen. The file has 60 lines of data in three columns. Every thing works until I try to read 1 row of three doubles for calculation. So when I had this:

Code:

double[] gene={-9.30, 5.65, -5.02};
double[] gene1={-5.30, 3.65, -2.02};

it worked perfect but when I have tryed to read gen1 from the file with the use of errors I get this error:

Code:

G:\Read File\csv.java:145: parseDouble(java.lang.String) in java.lang.Double cannot be applied to (java.lang.String[])
	double ii = Double.parseDouble(myarray);
	                  ^
1 error

Tool completed with exit code 1

If anybody know what the problem is please help me cos I am running out of ideas. Here is the full program:

Code:

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileInputStream;
import java.io.FileWriter;
import java.io.InputStreamReader;
import java.io.Writer;
import static java.lang.Math.*;

public class csv {

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) throws Exception {


	// Set file name & path
	String filepath = "Data_Set_1.txt";
	//String output = "Output_Data_Set_1.txt";

	// Read in file
	FileInputStream in = new FileInputStream(filepath);
	BufferedReader br = new BufferedReader(new InputStreamReader(in));
	String strLine;

	//Write file
	//FileOutputStream out = new FileOutputStream(output);
	//BufferedWriter wr = new BufferedWriter(new OutputStreamWriter(out));

	// Declare Array which will hold 61 lines
	String[] myarray;
	myarray = new String[61];


	double ii = Double.parseDouble(myarray);



	// Read each line into the array
	for (int i = 0; i < myarray.length; i++){
		myarray[i] = br.readLine();
	}

	in.close();



	// Print out array info in desired order. Delete " characters
	for (int i = 1; i < myarray.length; i++){
		System.out.println(myarray[i].replace("\"", ""));

	}

		double[] gene={-9.30, 5.65, -5.02};
		double[] gene1={ii};

	for (int i = 1; i < myarray.length; i++){
		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);
	}

  }
}

Text 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

Thank you!