Launcher.java

/*******************************************************************************
 * GenPlay, Einstein Genome Analyzer
 * Copyright (C) 2009, 2014 Albert Einstein College of Medicine
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 * Authors: Julien Lajugie <julien.lajugie@einstein.yu.edu>
 *          Nicolas Fourel <nicolas.fourel@einstein.yu.edu>
 *          Eric Bouhassira <eric.bouhassira@einstein.yu.edu>
 * 
 * Website: <http://genplay.einstein.yu.edu>
 ******************************************************************************/
package edu.yu.einstein.genplay.gui.launcher;

import java.awt.EventQueue;
import java.io.File;
import java.io.InputStream;
import java.util.concurrent.CountDownLatch;

import javax.swing.JOptionPane;
import javax.swing.ToolTipManager;

import edu.yu.einstein.genplay.core.manager.application.ConfigurationManager;
import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.dataStructure.chromosome.Chromosome;
import edu.yu.einstein.genplay.dataStructure.genome.Assembly;
import edu.yu.einstein.genplay.dataStructure.genome.Clade;
import edu.yu.einstein.genplay.dataStructure.genome.Genome;
import edu.yu.einstein.genplay.dataStructure.genomeWindow.SimpleGenomeWindow;
import edu.yu.einstein.genplay.exception.ExceptionManager;
import edu.yu.einstein.genplay.gui.OSIntegration.OSXIntegrator;
import edu.yu.einstein.genplay.gui.OSIntegration.X11Integrator;
import edu.yu.einstein.genplay.gui.action.multiGenome.synchronization.MGASynchronizing;
import edu.yu.einstein.genplay.gui.action.project.PAInitMGManager;
import edu.yu.einstein.genplay.gui.action.project.PAInitManagers;
import edu.yu.einstein.genplay.gui.action.project.PALoadProject;
import edu.yu.einstein.genplay.gui.dialog.quickViewDialog.QuickViewDialog;
import edu.yu.einstein.genplay.gui.fileFilter.GenPlayTrackFilter;
import edu.yu.einstein.genplay.gui.mainFrame.MainFrame;
import edu.yu.einstein.genplay.gui.projectFrame.ProjectFrame;
import edu.yu.einstein.genplay.util.Utils;


/**
 * This class loads GenPlay with a welcome screen.
 * Then, the main frame is loaded.
 * @author Nicolas Fourel
 * @author Julien Lajugie
 */
public class Launcher {

	/**
	 * This class loads the rest of the project (multigenome manager and the tracks).
	 * The loading of the Multi Genome manager has to be done before the loading of the tracks.
	 * This is why both processes are within a same thread managing a waiting time between them.
	 *
	 * @author Nicolas Fourel
	 */
	private static class LoadingThread extends Thread {

		@Override
		public void run() {
			PAInitMGManager initMGAction = new PAInitMGManager();
			CountDownLatch latch = new CountDownLatch(1);
			initMGAction.setLatch(latch);
			initMGAction.actionPerformed(null);
			try {
				latch.await();
			} catch (InterruptedException e) {
				ExceptionManager.getInstance().caughtException(e);
			}
			PALoadProject load = new PALoadProject();
			load.setSkipFileSelection(true);
			load.actionPerformed(null);
		}
	}


	/**
	 * Tooltip dismissal delay value for the entire program
	 */
	private static final int TOOLTIP_DISMISS_DELAY = Integer.MAX_VALUE;


	/**
	 * Tooltip initial delay value for the entire program
	 */
	private static final int TOOLTIP_INITIAL_DELAY = 500;


	/**
	 * This constant can be set to a project file path in the resource folder of the jar.
	 * In this case this project will be directly loaded when GenPlay starts.
	 */
	private static final String DEMO_PROJECT_PATH = null;


	/**
	 * Initialize the exception manager
	 */
	private static void initializeExceptionManagement () {
		// Set the uncaught exception handler for GenPlay
		Thread.setDefaultUncaughtExceptionHandler(ExceptionManager.getInstance());

		// Set the exception manager options
		ExceptionManager.getInstance().enablePrintReport(false);
		ExceptionManager.getInstance().enablePrintStackTrace(true);
	}


	/**
	 * This method is used by the ProjectFrame after closing
	 * to initiate a new project.
	 */
	public static void initiateNewProject() {
		ProjectFrame projectFrame = ProjectFrame.getInstance();
		Clade clade = projectFrame.getSelectedClade();
		Genome genome = projectFrame.getSelectedGenome();
		Assembly assembly = projectFrame.getSelectedAssembly();
		assembly.setChromosomeList(projectFrame.getSelectedChromosomes());
		ProjectManager projectManager = ProjectManager.getInstance();
		projectManager.setProjectName(projectFrame.getProjectName());
		projectManager.setProjectScorePrecision(projectFrame.getProjectScorePrecision());
		projectManager.setCladeName(clade.getName());
		projectManager.setGenomeName(genome.getName());
		projectManager.setAssembly(assembly);
		projectManager.updateChromosomeList();
		projectFrame.setVisible(false);

		// Initializes the genome window manager
		Chromosome currentChromosome = ProjectManager.getInstance().getProjectChromosomes().get(0);
		SimpleGenomeWindow genomeWindow = new SimpleGenomeWindow(currentChromosome, 1, currentChromosome.getLength() + 1);
		ProjectManager.getInstance().getProjectWindow().setGenomeWindow(genomeWindow);

		// Set the project as a multi genome project before any call of the MainFrame (some graphical elements check it out in order to be displayed)
		if (!projectFrame.isSingleProject()) {
			ProjectManager.getInstance().setMultiGenomeProject(true);
		}

		// reinit the MainFrame if needed (in the case where the user chose the new project option from the mainframe)
		MainFrame.reinit();

		// starts the main frame of the application
		MainFrame.getInstance().setVisible(true);
		MainFrame.getInstance().initStatusBarForFirstUse();

		// generate the multi-genome manager if the user starts a multi-genome project
		if (!projectFrame.isSingleProject()) {
			MGASynchronizing multiGenome = new MGASynchronizing();
			multiGenome.setGenomeFileAssociation(projectFrame.getGenomeFileAssociation());
			multiGenome.actionPerformed(null);
		} else {
			projectManager.setMultiGenomeProject(false);
		}
	}


	/**
	 * Loads a file using a file object.
	 * First initializes the managers and then load the file.
	 * @param file the file
	 */
	private static void loadFile (File file) {
		PAInitManagers init = new PAInitManagers();
		init.setFile(file);

		loadProject(init);
	}


	/**
	 * Loads a file using an input stream.
	 * First initializes the managers and then load the file.
	 * @param is the input strean
	 */
	private static void loadFile (InputStream is) {
		PAInitManagers init = new PAInitManagers();
		init.setInputStream(is);

		loadProject(init);
	}


	/**
	 * Loads a project.
	 */
	private static void loadProject (PAInitManagers initAction) {
		initAction.setLoadingFromWelcomeScreen(true);
		initAction.actionPerformed(null);

		if (initAction.hasBeenInitialized()) {
			MainFrame.getInstance().setVisible(true);
			LoadingThread thread = new LoadingThread();
			thread.start();
		} else {
			JOptionPane.showMessageDialog(null, initAction.getErrorMessage(), "The project has not been initialized", JOptionPane.WARNING_MESSAGE);
			ProjectFrame.getInstance().setVisible(true);
		}
	}


	/**
	 * Starts the application
	 * @param args a project file path can be specified. In this case the project
	 * screen will be skipped and the project file will be directly loaded
	 */
	public static void main(final String[] args) {
		if (Utils.isMacOS()) {
			// Handle mac-specific events (if we're running under OS X).
			OSXIntegrator.integrateApplication();
		} else if (!Utils.isWindowsOS()) {
			// set the WM_CLASS property for X11
			X11Integrator.setWMClassName();
		}
		// load the application settings
		try {
			ConfigurationManager.getInstance().loadConfiguration();
		} catch (Exception e) {}
		// Initialize the exception manager
		initializeExceptionManagement();
		// set the tooltip properties
		ToolTipManager.sharedInstance().setDismissDelay(TOOLTIP_DISMISS_DELAY);
		ToolTipManager.sharedInstance().setInitialDelay(TOOLTIP_INITIAL_DELAY);
		//SwingUtilities.invokeLater(new Runnable() {
		/*
		 * Fix for the exception that starts like:
		 * Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
		 * at javax.swing.plaf.basic.BasicProgressBarUI.updateSizes(Unknown Source)
		 * at javax.swing.plaf.basic.BasicProgressBarUI.getBox(Unknown Source)
		 * at javax.swing.plaf.basic.BasicProgressBarUI.paintString(Unknown Source)
		 * at javax.swing.plaf.basic.BasicProgressBarUI.paintDeterminate(Unknown Source)
		 * at javax.swing.plaf.metal.MetalProgressBarUI.paintDeterminate(Unknown Source)
		 * at javax.swing.plaf.basic.BasicProgressBarUI.paint(Unknown Source)
		 *
		 * Found on several website:
		 * You are probably here, because you searched for the line above in a search engine.
		 * If you are a Java-Programmer and you get this problem, here is the solution:
		 * The problem is, that Swing is not thread-safe. You have probably tried to call a method on a Swing-Component from another thread (than the AWT-EventQueue-Thread). You should not do that!
		 * Methods of Swing-Components should always be called from the EventQueue.
		 */
		EventQueue.invokeLater(new Runnable() {
			@Override
			public void run() {
				// if the DEMO_PROJECT_PATH constant has been set it means that we're starting a demo project
				boolean isDemo = (DEMO_PROJECT_PATH != null);
				// mac only
				if (Utils.isMacOS() && (OSXIntegrator.getInstance().getFileToOpen() != null)) {
					startProjectFromFile(OSXIntegrator.getInstance().getFileToOpen());
				} else if (isDemo) {
					startDemoProject();
				} else if (args.length == 1) { // if a project file path has been specified to the main method we load this file
					File file = new File(args[0]);
					startProjectFromFile(file);
				} else { // normal execution of the software
					startProjectFrame();
				}
			}
		});
	}


	/**
	 * This method starts a demo project.  The project file needs to be in the resource folder and
	 * the path to this file must be specified in the DEMO_PROJECT_PATH constant
	 */
	private static void startDemoProject() {
		InputStream is = ProjectFrame.getInstance().getClass().getClassLoader().getResourceAsStream(DEMO_PROJECT_PATH);
		try {
			loadFile(is);
		} catch (Exception e) {
			ExceptionManager.getInstance().caughtException(e);
		}
	}


	/**
	 * Displays the project screen manager which is the first screen of GenPlay.
	 */
	private static void startProjectFrame() {
		//Welcome screen initialization
		ProjectFrame projectFrame = ProjectFrame.getInstance();
		//Create a new thread to display the welcome screen
		projectFrame.initScreen();
	}


	/**
	 * This method starts a project from a file.
	 * @param file project file to load
	 */
	public static void startProjectFromFile(File file) {
		try {
			if (Utils.getExtension(file).equals(GenPlayTrackFilter.EXTENSIONS[0])) {
				QuickViewDialog.showDialog(file);
			} else {
				loadFile(file);
			}
		} catch (Exception e) {
			ExceptionManager.getInstance().caughtException(e);
			System.out.println("Invalid Project File: The specifed file is not a valid project file");
			System.out.println(file.getPath());
		}
	}
}