/*******************************************************************************
* 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.bin;
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;
/**
* A memory efficient {@link ListView} of bins with a fix size
* {@link BinListView} objects are immutable.
* @author Julien Lajugie
*/
public final class BinListView 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 = -4636772386393755263L;
/** 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 binScores.get(windowIndex);
}
@Override
public int getStart() {
return (windowIndex * binSize) + 1;
}
@Override
public int getStop() {
return ((windowIndex + 1) * binSize) + 1;
}
}
/** Generated serial ID */
private static final long serialVersionUID = 304172516803341537L;
/** Version number of the class */
private static final transient int CLASS_VERSION_NUMBER = 0;
/** Size of the bins of the list */
private final int binSize;
/** List of the score values of the bins */
private final List<Float> binScores;
/**
* Creates an instance of {@link BinListView}
* @param binSize size of the bins of the list
* @param windowScore list of the score values of the bins
*/
BinListView(int binSize, List<Float> binScores) {
super();
this.binSize = binSize;
this.binScores = binScores;
}
@Override
public ScoredChromosomeWindow get(int elementIndex) {
return new SCWFromListView(elementIndex);
}
/**
* @return the size of the bins of the {@link ListView}
*/
public int getBinSize() {
return binSize;
}
/**
* 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 binScores.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();
}
}