package bicat.run_machine;

import javax.swing.JOptionPane;

import bicat.gui.BicatGui;

/**
 * <p>
 * Title: cHawk for BicAT Tool
 * </p>
 * 
 * 
 * @author Waseem Ahmad (wahmad at acm dor org)
 * 
 * 
 * Run Machine for cHawk algorithm (2007).
 * 
 * For its execution, a shared library is needed (lib/linux/libcHawk.so for Linux).
 * 
 */

public class RunMachine_cHawk extends RunMachine {

	// ===========================================================================

	public RunMachine_cHawk(BicatGui o) {
		owner = o;
	}

	// ===========================================================================
	public native void run_cHawk(double[] data, int total_gs, int total_cs,
	// String[] g_names, String[] c_names,
			int algo, double delta, int iter, double p_rand_1,
			double p_rand_2, double p_rand_3, int logarithm, int randomize,
			int n, String out_file);


	static {
		System.loadLibrary("cHawk");
		System.out.println("cHawk library loaded");
	}

	public synchronized void runBiclustering(final ArgumentscHawk cca) {


		final SwingWorker worker = new SwingWorker() {

			public Object construct() {
				// new RunMachineCC(null).runCC();
				if (BicatGui.debug)System.out.println("gene number: "+ cca.getGeneNumber() +" Chip number: "+  cca.getChipNumber());
				run_cHawk(cca.getData(), cca.getGeneNumber(), cca.getChipNumber(),
						cca.getAlgorithm(), cca.getDelta(), cca.getIter(), cca
								.getPR1(), cca.getPR2(), cca.getPR3(), cca
								.getLogarithm(), cca.getRandomize(),
						cca.getN(), cca.getOutputFile());

				if (owner.debug) {
					System.out.println("Started cHawk in a new thread!\n");
				}

				return null;
			}

			public void finished() {

				System.out.println("Getting results from cHawk... "
						+ owner.currentDirectoryPath + "/output.cHawk");

				computedBiclusters = getOutputBiclusters(owner.currentDirectoryPath
						+ "/output.cHawk");
								
				outputBiclusters = computedBiclusters; // is a LinkedList of
				// BitSet
				// representated-BCs
				// (bicat.runMachine.Bicluster_bitset)
				
				transferList();

				owner.finishUpRun(cca.getDatasetIdx(), outputBiclusters, cca
						.getPreprocessOptions(), "cHawk");
				JOptionPane
						.showMessageDialog(
								null,
								"Calculations finished.\nThe results can be found in the bicluster results section of the current dataset.");

			}
		};
		worker.start();
	}
}