/*******************************************************************************
* 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 edu.yu.einstein.genplay.core.operation.Operation;
import edu.yu.einstein.genplay.core.operation.geneList.GLOExtractExons;
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.ExtractExonsDialog;
import edu.yu.einstein.genplay.gui.dialog.ExtractGeneIntervalsDialog;
import edu.yu.einstein.genplay.gui.track.layer.GeneLayer;
/**
* Extract Exons
* @author Chirag Gorasia
*/
public class GLAExtractExons extends TrackListActionOperationWorker<GeneList> {
private static final long serialVersionUID = 4450568171298987897L;
private static final String ACTION_NAME = "Extract Exons"; // action name
private static final String DESCRIPTION = "Extract Exons " +
"defined relative to genes" + HELP_TOOLTIP_SUFFIX; // tooltip
private static final String HELP_URL = "http://genplay.einstein.yu.edu/wiki/index.php/Documentation#Extract_Exons";
private GeneLayer selectedLayer; // selected layer
/**
* key of the action in the {@link ActionMap}
*/
public static final String ACTION_KEY = GLAExtractExons.class.getName();
/**
* Creates an instance of {@link GLAExtractExons}
*/
public GLAExtractExons() {
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(GeneList actionResult) {
if (actionResult != null) {
selectedLayer.setData(actionResult, operation.getDescription());
}
}
@Override
public Operation<GeneList> initializeOperation() throws Exception {
selectedLayer = (GeneLayer) getValue("Layer");
if (selectedLayer != null) {
GeneList geneList = selectedLayer.getData();
ExtractExonsDialog dialog = new ExtractExonsDialog();
if (dialog.showDialog(getRootPane()) == ExtractGeneIntervalsDialog.APPROVE_OPTION) {
operation = new GLOExtractExons(geneList, dialog.getSelectedExonOption());
return operation;
}
}
return null;
}
}