/*******************************************************************************
* 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.dataStructure.list.chromosomeWideList.SCWListView.mask;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.util.List;
import edu.yu.einstein.genplay.dataStructure.list.listView.AbstractListView;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListView;
import edu.yu.einstein.genplay.dataStructure.scoredChromosomeWindow.AbstractScoredChromosomeWindow;
import edu.yu.einstein.genplay.dataStructure.scoredChromosomeWindow.ScoredChromosomeWindow;
/**
* {@link ListView} of masks {@link ScoredChromosomeWindow}. Masks always have a score of 1.
* {@link MaskListView} objects are immutable.
* @author Julien Lajugie
*/
public final class MaskListView extends AbstractListView<ScoredChromosomeWindow> implements ListView<ScoredChromosomeWindow> {
/**
* Implementation of the {@link ScoredChromosomeWindow} interface for windows retrieved from a {@link ListView}
* @author Julien Lajugie
*/
private class SCWFromListView extends AbstractScoredChromosomeWindow implements ScoredChromosomeWindow {
/** Generated serial ID */
private static final long serialVersionUID = -6957465234746429275L;
/** Index of the window in the parent {@link ListView} */
private final int windowIndex;
/**
* Creates an instance of {@link SCWFromListView}
* @param windowIndex index of the window in the parent {@link ListView}
*/
private SCWFromListView(int windowIndex) {
this.windowIndex = windowIndex;
}
@Override
public float getScore() {
return 1f;
}
@Override
public int getStart() {
return maskStarts.get(windowIndex);
}
@Override
public int getStop() {
return maskStops.get(windowIndex);
}
}
/** Generated serial ID */
private static final long serialVersionUID = -2065237090366294538L;
/** Version number of the class */
private static final transient int CLASS_VERSION_NUMBER = 0;
/** List of the start positions of the masks */
private final List<Integer> maskStarts;
/** List of the stop positions of the masks */
private final List<Integer> maskStops;
/**
* Creates an instance of {@link MaskListView}
* @param maskStarts list of the start positions of the masks
* @param maskStops list of the stop positions of the masks
*/
MaskListView(List<Integer> maskStarts, List<Integer> maskStops) {
super();
this.maskStarts = maskStarts;
this.maskStops = maskStops;
}
@Override
public ScoredChromosomeWindow get(int elementIndex) {
return new SCWFromListView(elementIndex);
}
/**
* Method used for deserialization
* @param in
* @throws IOException
* @throws ClassNotFoundException
*/
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
// read the version number of the object
in.readInt();
// read the final fields
in.defaultReadObject();
}
@Override
public int size() {
return maskStarts.size();
}
/**
* Method used for serialization
* @param out
* @throws IOException
*/
private void writeObject(ObjectOutputStream out) throws IOException {
// write the format version number of the object
out.writeInt(CLASS_VERSION_NUMBER);
// write the final fields
out.defaultWriteObject();
}
}