"Created a new dir tarantula with all the classes neccessary for using the...

package TarantulaCalculator;

import java.util.ArrayList;

import java.util.List;

import org.junit.runner.JUnitCore;

import org.junit.runner.Result;

import org.junit.runner.notification.Failure;

public class Runner {

	/**Holds a list of all the tests numbers that fail **/

    private ArrayList<Integer> failCases;

    /**Holds the results from the test program**/

    Result result;

    public Runner(){}

    @SuppressWarnings("rawtypes")

    /**Initialize a Runner object**/

    public Runner(Class testClass){

        failCases = new ArrayList<Integer>();

        result = JUnitCore.runClasses(testClass);

    }

    /**Loops through all the failures in result and gets the test header

     * pre: all the test headers must in the format: test# e.g: test1, test 10 

     * post: adds the test header integer segment to the failCases **/

    public void determineFailCases(){

        for (Failure failure : result.getFailures()) {

            String header = failure.getTestHeader();

            String header_segment = header.substring(0, header.indexOf("("));

            String test_case_num = header.substring(4, header_segment.length());

            failCases.add(Integer.parseInt(test_case_num));

        }

    }   

    /**Return the list of the fail cases**/

    public ArrayList<Integer> getFailCases(){

        return failCases;

    }

}

package TarantulaCalculator;

import java.util.Arrays;

import java.io.File;

import java.util.ArrayList;

public class TarantulaMain {

	    public static void main(String[] args) throws ClassNotFoundException {

	        // create the Matrix Reader to get Test -- Stmt information

	        File f = new File(args[0]/*"/homes/iws/kevinb22/Downloads/triangle-mvn-compact-cov-matrix.json"*/);

	        covMatrixReader reader = new covMatrixReader(f);

	        Long testCountLong = reader.getTestCount();

	        String testCountString = testCountLong.toString();

	        int testCountInt = Integer.parseInt(testCountString);

	        // create Runner class to get the failing cases from JUnit tests

	        Class testClass = Class.forName(args[1]/*"TarantulaCalculator.TriangleTest"*/);

	        Runner r = new Runner(testClass);

	        r.determineFailCases();

	        ArrayList<Integer> fails = r.getFailCases();

	        // set coverage matrix -- [test] [stmt]

	        boolean[][] M = reader.getM();

	        TarantulaSuspiciousnessCalculation calc = new TarantulaSuspiciousnessCalculation(M);

	        // set coverable statements -- [stmt]

	        boolean[] C = reader.getC();

	        calc.setC(C);

	        // set failing test cases -- [test]

	        boolean[] F =new boolean[testCountInt];

	        Arrays.fill(F, false);

	        for(Integer i : fails) {

	            F[i - 1] = true;

	        }

	        calc.setF(F);

	        // set live test cases -- [test]

	        boolean[] L = new boolean[testCountInt];

	        Arrays.fill(L, true);

	        calc.setL(L);

	        calc.compute();

	        System.out.println("For program: " + reader.getFullName());

	        displayConf(calc.getConfidence(), reader.getFirstLine());

	        System.out.println("------------------------------------------------------------------");

	        displaySusp(calc.getSuspiciousness(), reader.getFirstLine());

	    }

	    public static void displayConf(double[] a, Long firstLine){

	        System.out.println("Confidence Array");

	        for(int i = 0; i < a.length; i++) {

	            System.out.println("line " + (i+firstLine) + ": " + a[i]);

	        }

	    }

	    public static void displaySusp(double[] a, Long firstLine){

	        System.out.println("Suspicion Array");

	        for(int i = 0; i < a.length; i++) {

	            System.out.println("line " + (i+firstLine) + ": " + a[i]);

	        }

	    }

}