MGASynchronizing.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.action.multiGenome.synchronization;

import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;

import javax.swing.ActionMap;

import edu.yu.einstein.genplay.core.manager.project.MultiGenomeProject;
import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFFile.VCFFile;
import edu.yu.einstein.genplay.exception.ExceptionManager;
import edu.yu.einstein.genplay.gui.action.TrackListActionWorker;
import edu.yu.einstein.genplay.gui.mainFrame.MainFrame;
import edu.yu.einstein.genplay.gui.track.Track;


/**
 * This class performs the multi-genome synchronization algorithm.
 * There is two ways to perform the synchronization:
 * - At the creation of the project when the synchronization is initiated for the first time (must provide parameters).
 * - To update the synchronization in case of low memory mode (every time user changes current chromosome) (DO NOT provide parameters).
 * 
 * In order to initiate the synchronization for the first time, please set parameters:
 * - fileReaders
 * - genomeFileAssociation
 * 
 * In a project, before using the {@link MGASynchronizing} action for the first time,
 * please set the multi-genome project boolean presents in {@link ProjectManager} to true.
 * 
 * @author Nicolas Fourel
 * @author Julien Lajugie
 * @version 0.1
 */
public class MGASynchronizing extends TrackListActionWorker<Track[]> {

	private static final long serialVersionUID = 6498078428524511709L;	// generated ID
	private static final String 	DESCRIPTION =
			"Performs the multi genome algorithm"; 										// tooltip
	private static final int 				MNEMONIC = KeyEvent.VK_M; 				// mnemonic key
	private static		 String 			ACTION_NAME = "Multi-genome loading";	// action name
	private final MultiGenomeProject 					multiGenomeProject;							// instance of the multi genome
	private Map<String, List<VCFFile>> 	genomeFileAssociation;					// Mapping between genome names and their readers.


	/**
	 * key of the action in the {@link ActionMap}
	 */
	public static final String ACTION_KEY = "Multi Genome";


	/**
	 * Creates an instance of {@link MGASynchronizing}.
	 */
	public MGASynchronizing() {
		super();
		putValue(NAME, ACTION_NAME);
		putValue(ACTION_COMMAND_KEY, ACTION_KEY);
		putValue(SHORT_DESCRIPTION, DESCRIPTION);
		putValue(MNEMONIC_KEY, MNEMONIC);
		multiGenomeProject = ProjectManager.getInstance().getMultiGenomeProject();
	}


	@Override
	protected void doAtTheEnd(Track[] actionResult) {
		multiGenomeProject.updateChromosomeList();

		MainFrame.getInstance().getControlPanel().reinitChromosomePanel();
		MainFrame.getInstance().getControlPanel().resetGenomeNames(multiGenomeProject.getGenomeNames());

		// Unlocks the main frame
		MainFrame.getInstance().unlock();

		//multiGenomeProject.show();
	}


	private List<String> getRequiredGenomeNames () {
		List<String> genomes = null;
		if (genomeFileAssociation != null) {
			genomes = new ArrayList<String>(genomeFileAssociation.keySet());
		}
		return genomes;
	}


	/**
	 * Checks if file readers and genome file association parameters are null,
	 * if they are not, it sets the genome synchronizer using them.
	 * Then, it checks if genome synchronizer has been initialized.
	 * @return true if genome synchronizer has been initialized, false if not.
	 */
	private boolean hasBeenInitialized () {
		boolean valid = false;

		// If parameter have been given,
		// sets the genome synchronizer.
		if (genomeFileAssociation != null) {
			multiGenomeProject.setGenomeFileAssociation(genomeFileAssociation);
		}

		// Checks if genome synchronizer has been initialized
		if (multiGenomeProject.getGenomeFileAssociation() != null) {
			valid = true;
		}

		return valid;
	}


	@Override
	protected Track[] processAction() throws Exception {
		ProjectManager projectManager = ProjectManager.getInstance();

		// Checks if the project is multi-genome
		if (projectManager.isMultiGenomeProject()) {

			// Checks if parameters have been set
			if (hasBeenInitialized()) {

				// Notifies the action
				notifyActionStart(ACTION_NAME, 1, false);

				// Locks the main frame
				MainFrame.getInstance().lock();

				// Initializes the genome synchronization
				multiGenomeProject.initializeSynchronization (genomeFileAssociation);

				// Insert synchronization data into the data structure
				multiGenomeProject.getMultiGenomeSynchronizer().processFiles(getRequiredGenomeNames(), null, null);

				// Sort lists of position for every chromosome of every genome
				multiGenomeProject.getMultiGenome().sort();

				// Remove the duplicate from the reference genome lists of position
				multiGenomeProject.getMultiGenome().getReferenceGenome().removeDuplicate();

				// Performs the synchronization in order to get all genome positions and their offset with the meta genome
				multiGenomeProject.getMultiGenomeSynchronizer().performPositionSynchronization();

				// Compacts the offset lists in order to optimize the memory usage
				multiGenomeProject.getMultiGenome().compactLists();

				// Loads the current variants into the memory
				multiGenomeProject.getFileContentManager().updateCurrentVariants();

			} else {
				// Generates error when parameters have not been set
				ExceptionManager.getInstance().caughtException(Thread.currentThread(), new Throwable(), "Multi-genome synchronization cannot be performed because the file readers and/or the genome file association parameters have not been set.");
			}
		} else {
			// Generates error if the project is not multi-genome
			ExceptionManager.getInstance().caughtException(Thread.currentThread(), new Throwable(), "Multi-genome synchronization cannot be performed because the project does not seem to be multi-genome.");
		}
		return null;
	}



	/**
	 * This method must be used when multi-genome synchronization is performed for the first time in a project.
	 * @param genomeFileAssociation the genomeFileAssociation to set
	 */
	public void setGenomeFileAssociation(Map<String, List<VCFFile>> genomeFileAssociation) {
		this.genomeFileAssociation = genomeFileAssociation;
	}
}