/******************************************************************************* * 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.binlayer; import javax.swing.ActionMap; import edu.yu.einstein.genplay.core.operation.Operation; import edu.yu.einstein.genplay.core.operation.binList.BLODensity; import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.binList.BinList; import edu.yu.einstein.genplay.gui.action.TrackListActionOperationWorker; import edu.yu.einstein.genplay.gui.dialog.NumberOptionPane; import edu.yu.einstein.genplay.gui.dialog.trackChooser.TrackChooser; import edu.yu.einstein.genplay.gui.track.Track; import edu.yu.einstein.genplay.gui.track.layer.BinLayer; import edu.yu.einstein.genplay.util.colors.Colors; /** * Computes the densities of none null bins of the selected {@link BinLayer} * @author Julien Lajugie */ public class BLADensity extends TrackListActionOperationWorker<BinList> { private static final long serialVersionUID = 8669677084318132021L; // generated ID private static final String ACTION_NAME = "Density"; // action name private static final String DESCRIPTION = "Computes the densities of none null bins of the selected layer" + HELP_TOOLTIP_SUFFIX;// tooltip private static final String HELP_URL = "http://genplay.einstein.yu.edu/wiki/index.php/Documentation#Density"; private BinLayer selectedLayer; // selected layer private Track resultTrack; // result track private Number halfWidth; // half width /** * key of the action in the {@link ActionMap} */ public static final String ACTION_KEY = BLADensity.class.getName(); /** * Creates an instance of {@link BLADensity} */ public BLADensity() { 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(BinList actionResult) { if (actionResult != null) { BinLayer newLayer = new BinLayer(resultTrack, actionResult, "Densities of " + selectedLayer.getName()); // add info to the history newLayer.getHistory().add("Result of the density calculation of " + selectedLayer.getName() + ", Half Width = " + halfWidth); newLayer.getHistory().add("Window Size = " + actionResult.getBinSize() + "bp", Colors.GREY); resultTrack.getLayers().add(newLayer); } } @Override public Operation<BinList> initializeOperation() { selectedLayer = (BinLayer) getValue("Layer"); if (selectedLayer != null) { BinList binList = selectedLayer.getData(); halfWidth = NumberOptionPane.getValue(getRootPane(), "Enter Value", "<html>Enter the half width<br><center>(in number of bins)</center></html>", 1, Integer.MAX_VALUE, 5); if(halfWidth != null) { resultTrack = TrackChooser.getTracks(getRootPane(), "Choose A Track", "Generate the result on track:", getTrackListPanel().getModel().getTracks()); if (resultTrack != null) { Operation<BinList> operation = new BLODensity(binList, halfWidth.intValue()); return operation; } } } return null; } }