/*******************************************************************************
* 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.geneLayer;
import javax.swing.ActionMap;
import javax.swing.JOptionPane;
import edu.yu.einstein.genplay.core.operation.Operation;
import edu.yu.einstein.genplay.core.operation.geneList.GLOCountAllGenes;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.geneList.GeneList;
import edu.yu.einstein.genplay.gui.action.TrackListActionOperationWorker;
import edu.yu.einstein.genplay.gui.track.layer.GeneLayer;
import edu.yu.einstein.genplay.util.NumberFormats;
import edu.yu.einstein.genplay.util.Utils;
/**
* Counts the number of genes of the selected {@link GeneLayer}
* @author Julien Lajugie
* @author Nicolas Fourel
*/
public final class GLACountAllGenes extends TrackListActionOperationWorker<Long> {
private static final long serialVersionUID = -7198642565173540167L; // generated ID
private static final String ACTION_NAME = "Count Genes"; // action name
private static final String DESCRIPTION = "Count the number of genes" + HELP_TOOLTIP_SUFFIX; // tooltip
private static final String HELP_URL = "http://genplay.einstein.yu.edu/wiki/index.php/Documentation#Count_Genes";
/**
* key of the action in the {@link ActionMap}
*/
public static final String ACTION_KEY = GLACountAllGenes.class.getName();
/**
* Creates an instance of {@link GLACountAllGenes}
*/
public GLACountAllGenes() {
super();
putValue(NAME, ACTION_NAME);
putValue(ACTION_COMMAND_KEY, ACTION_KEY);
putValue(SHORT_DESCRIPTION, DESCRIPTION);
putValue(HELP_URL_KEY, HELP_URL);
}
@Override
protected void doAtTheEnd(Long actionResult) {
if (actionResult != null) {
JOptionPane.showMessageDialog(getRootPane(), "Number of genes: \n" + NumberFormats.getScoreFormat().format(actionResult), "Count Genes", JOptionPane.INFORMATION_MESSAGE);
}
}
@Override
public Operation<Long> initializeOperation() {
GeneLayer selectedLayer = (GeneLayer) getValue("Layer");
if (selectedLayer != null) {
boolean[] selectedChromo = Utils.chooseChromosomes(getRootPane());
if (selectedChromo != null) {
GeneList binList = selectedLayer.getData();
Operation<Long> operation = new GLOCountAllGenes(binList, selectedChromo);
return operation;
}
}
return null;
}
}