LAConvert.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.layer;

import javax.swing.ActionMap;

import edu.yu.einstein.genplay.core.operation.Operation;
import edu.yu.einstein.genplay.core.operation.converter.ConverterFactory;
import edu.yu.einstein.genplay.dataStructure.enums.ScoreOperation;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.GenomicListView;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.SCWList;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.binList.BinList;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.geneList.GeneList;
import edu.yu.einstein.genplay.gui.action.TrackListActionOperationWorker;
import edu.yu.einstein.genplay.gui.dialog.ConvertDialog;
import edu.yu.einstein.genplay.gui.track.Track;
import edu.yu.einstein.genplay.gui.track.layer.BinLayer;
import edu.yu.einstein.genplay.gui.track.layer.GeneLayer;
import edu.yu.einstein.genplay.gui.track.layer.Layer;
import edu.yu.einstein.genplay.gui.track.layer.LayerType;
import edu.yu.einstein.genplay.gui.track.layer.MaskLayer;
import edu.yu.einstein.genplay.gui.track.layer.SimpleSCWLayer;
import edu.yu.einstein.genplay.gui.track.layer.VersionedLayer;
import edu.yu.einstein.genplay.util.colors.Colors;


/**
 * Converts the selected {@link Layer} into another type of {@link Layer}
 * @author Nicolas Fourel
 * @param <T> type of the list returned by the converter
 */
public class LAConvert<T extends GenomicListView<?>> extends TrackListActionOperationWorker<T> {

	private static final long serialVersionUID = 4027173438789911860L; 	// generated ID
	private static final String 	ACTION_NAME = "Convert Layer";// action name
	private static final String 	DESCRIPTION = "Convert the current layer into another type of layer";			// tooltip
	private Layer<?> 				selectedLayer;					// The selected layer.
	private Track					resultTrack;					// The result track.
	private Operation<T>			converter;						// The track converter.

	private GenomicListView<?> 		data;
	private LayerType 				layerType;
	private String 					layerName;
	private int 					binSize;
	private ScoreOperation 			method;


	/**
	 * key of the action in the {@link ActionMap}
	 */
	public static final String ACTION_KEY = LAConvert.class.getName();


	/**
	 * Creates an instance of {@link LAConvert}
	 */
	public LAConvert() {
		super();
		putValue(NAME, ACTION_NAME);
		putValue(ACTION_COMMAND_KEY, ACTION_KEY);
		putValue(SHORT_DESCRIPTION, DESCRIPTION);

		resultTrack = null;
		data = null;
		layerType = null;
		layerName = "";
		binSize = 0;
		method = null;
	}


	@Override
	protected void doAtTheEnd(T actionResult) {
		if (actionResult != null) {
			Layer<?> newLayer = null;
			if (layerType == LayerType.GENE_LAYER) {
				newLayer = new GeneLayer(resultTrack, (GeneList) actionResult, layerName);
			} else if (layerType == LayerType.BIN_LAYER) {
				newLayer = new BinLayer(resultTrack, (BinList) actionResult, layerName);
			} else if (layerType == LayerType.SIMPLE_SCW_LAYER) {
				newLayer = new SimpleSCWLayer(resultTrack, (SCWList) actionResult, layerName);
			} else if (layerType == LayerType.MASK_LAYER) {
				newLayer = new MaskLayer(resultTrack, (SCWList) actionResult, layerName);
			}
			if (newLayer != null) {
				((VersionedLayer<?>) newLayer).getHistory().add(layerType + " generated from " + selectedLayer.getType() + " \"" + selectedLayer.getName()+ "\"", Colors.GREY);
				resultTrack.getLayers().add(newLayer);
				resultTrack.setActiveLayer(newLayer);
			} else {
				System.err.println("The track could not be converted");
			}
		}
	}


	@Override
	public Operation<T> initializeOperation() throws Exception {
		selectedLayer = (Layer<?>) getValue("Layer");
		ConvertDialog dialog = new ConvertDialog(selectedLayer);
		if (dialog.showDialog(getRootPane()) == ConvertDialog.APPROVE_OPTION) {
			layerType = dialog.getOutputLayerType();
			if (layerType == LayerType.BIN_LAYER) {
				binSize = dialog.getBinSize();
				method = dialog.getBinScoreCalculationMethod();
			} else if (layerType == LayerType.SIMPLE_SCW_LAYER) {
				method = dialog.getSCWScoreCalculationMethod();
			}
			resultTrack = dialog.getOutputTrack();
			layerName = dialog.getOutputLayerName();
			data = (GenomicListView<?>) selectedLayer.getData();

			if (data != null) {
				converter = ConverterFactory.createConverter(data, layerType, binSize, method);
			}

			if (converter != null) {
				return converter;
			} else {
				System.err.println("No converter found");
			}
		}
		return null;
	}

}