/*******************************************************************************
* 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.sequenceLayer;
import java.util.List;
import javax.swing.ActionMap;
import edu.yu.einstein.genplay.core.operation.Operation;
import edu.yu.einstein.genplay.core.operation.nucleotideList.NLOCompare2NucleotideLists;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.SCWList;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.nucleotideList.NucleotideList;
import edu.yu.einstein.genplay.gui.action.TrackListActionOperationWorker;
import edu.yu.einstein.genplay.gui.dialog.layerChooser.LayerChooserDialog;
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.AbstractSCWLayer;
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.NucleotideLayer;
import edu.yu.einstein.genplay.gui.track.layer.SimpleSCWLayer;
import edu.yu.einstein.genplay.util.Utils;
import edu.yu.einstein.genplay.util.colors.Colors;
/**
* Creates a {@link SCWList} showing the differences between to {@link NucleotideList}
* @author Julien Lajugie
*/
public class NLACompare2NucleotideLists extends TrackListActionOperationWorker<SCWList> {
private static final long serialVersionUID = -7322522489324602187L; // generated ID
private static final String ACTION_NAME = "Compare Sequences"; // action name
private static final String DESCRIPTION =
"Creates a track showing the differences between 2 sequence layers" + HELP_TOOLTIP_SUFFIX; // tooltip
private static final String HELP_URL = "http://genplay.einstein.yu.edu/wiki/index.php/Documentation#Compare_Sequences";
private NucleotideLayer selectedLayer; // selected layer
private NucleotideLayer otherLayer; // other layer
private Track resultTrack; // track where to add the result
/**
* key of the action in the {@link ActionMap}
*/
public static final String ACTION_KEY = NLACompare2NucleotideLists.class.getName();
/**
* Creates an instance of {@link NLACompare2NucleotideLists}
*/
public NLACompare2NucleotideLists() {
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(SCWList actionResult) {
if (actionResult != null) {
AbstractSCWLayer<SCWList> resultLayer = new SimpleSCWLayer(resultTrack, actionResult, selectedLayer.getName() + " and " + otherLayer.getName() + " diff");
// add info to the history
resultLayer.getHistory().add("Differences between " + selectedLayer.getName() + " and " + otherLayer.getName(), Colors.GREY);
resultTrack.getLayers().add(resultLayer);
resultTrack.setActiveLayer(resultLayer);
}
}
@Override
public Operation<SCWList> initializeOperation() throws Exception {
selectedLayer = (NucleotideLayer) getValue("Layer");
if (selectedLayer != null) {
LayerChooserDialog layerChooserDialog = new LayerChooserDialog();
List<Layer<?>> sequenceLayer = Utils.getLayers(getTrackListPanel().getModel().getAllLayers(), new LayerType[] {LayerType.NUCLEOTIDE_LAYER});
layerChooserDialog.setLayers(sequenceLayer);
layerChooserDialog.setSelectableLayerTypes(new LayerType[] {LayerType.NUCLEOTIDE_LAYER});
layerChooserDialog.setMultiselectable(false);
if (layerChooserDialog.showDialog(getRootPane(), "Select 2nd Sequence Layer") == LayerChooserDialog.APPROVE_OPTION) {
otherLayer = (NucleotideLayer) layerChooserDialog.getSelectedLayer();
if (otherLayer != null) {
resultTrack = TrackChooser.getTracks(getRootPane(), "Choose A Track", "Generate the result on track:", getTrackListPanel().getModel().getTracks());
if (resultTrack != null) {
operation = new NLOCompare2NucleotideLists(selectedLayer.getData(), otherLayer.getData());
return operation;
}
}
}
}
return null;
}
}