/*******************************************************************************
* 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.primitiveList;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.AbstractList;
import java.util.ArrayList;
import java.util.List;
import java.util.RandomAccess;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
import edu.yu.einstein.genplay.dataStructure.compressible.CompressibleList;
import edu.yu.einstein.genplay.dataStructure.enums.ScorePrecision;
import edu.yu.einstein.genplay.exception.ExceptionManager;
import edu.yu.einstein.genplay.exception.exceptions.CompressionException;
import edu.yu.einstein.genplay.exception.exceptions.InvalidPrimitiveArrayGenericParameterException;
/**
* Abstract class defining the common methods and properties for the different of
* primitive list wrappers implementing the {@link List} interface
* @param <T> type of the data of the list
* @author Julien Lajugie
*/
public class PrimitiveList<T> extends AbstractList<T> implements Cloneable, Serializable, List<T>, RandomAccess, CompressibleList<T> {
/** Generated serial ID */
private static final long serialVersionUID = -3250259696514106453L;
/** Version number of the class */
private static final transient int CLASS_VERSION_NUMBER = 0;
/** Size of the sub arrays */
private static final int DEFAULT_SUBARRAY_SIZE = 5000;
/** Precision of the data of the project */
private transient static ScorePrecision scorePrecision = ScorePrecision.PRECISION_32BIT;
/**
* Sets the score precision of the project
* @param scorePrecision
*/
public static void setScorePrecision(ScorePrecision scorePrecision) {
PrimitiveList.scorePrecision = scorePrecision;
}
/** We need to store the type of the element of the list because java
* generics are not reified */
private final Class<T> elementClass;
/** Size of the subarrays of the list */
private final int subarraySize;
/** List compressed as a ByteArrayOutputStream */
private transient ByteArrayOutputStream compressedData = null;
/** Size of the list */
private transient int size = 0;
/** Data of the list */
private transient List<PrimitiveArrayWrapper<T>> elementData;
/** True if the list is compressed */
private transient boolean isCompressed = false;
/**
* Creates an instance of {@link PrimitiveList} with default initial capacity.
* @param elementClass class of the elements of the list
*/
public PrimitiveList(Class<T> elementClass) {
this(elementClass, DEFAULT_SUBARRAY_SIZE);
}
/**
* Constructs an empty list with the specified initial capacity.
* @param elementClass class of the elements of the list
* @param subarraySize size of the subarrays constituting the list
* @throws IllegalArgumentException If the specified initial capacity is negative
*/
public PrimitiveList(Class<T> elementClass, int subarraySize) {
super();
if (subarraySize < 0) {
throw new IllegalArgumentException("Illegal Subarray Size: " + subarraySize);
}
this.elementClass = elementClass;
this.subarraySize = subarraySize;
elementData = new ArrayList<PrimitiveArrayWrapper<T>>();
}
@Override
public boolean add(T e) {
int subarrayIndex = getSubarrayIndex(size);
int indexWithinSubarray = getIndexWithinSubarray(size);
ensureCapacity(++size);
elementData.get(subarrayIndex).set(indexWithinSubarray, e);
return true;
}
@Override
public void compress() throws CompressionException {
try {
if ((!isCompressed) && (elementData != null)) {
compressedData = new ByteArrayOutputStream();
GZIPOutputStream gz = new GZIPOutputStream(compressedData);
ObjectOutputStream oos = new ObjectOutputStream(gz);
oos.writeObject(elementData);
oos.flush();
oos.close();
gz.flush();
gz.close();
elementData = null;
isCompressed = true;
}
} catch (IOException e) {
throw new CompressionException("An error occure during the data compression");
}
}
/**
* Increases the capacity of this PrimitiveList instance, if
* necessary, to ensure that it can hold at least the number of elements
* specified by the minimum capacity argument.
* @param minCapacity the desired minimum capacity
*/
public void ensureCapacity(int minCapacity) {
modCount++;
int oldCapacity = elementData.size() * subarraySize;
while (minCapacity > oldCapacity) {
@SuppressWarnings("unchecked")
PrimitiveArrayWrapper<T> newSubarray = (PrimitiveArrayWrapper<T>) generateEmptyPrimitiveArrayWrapper(subarraySize);
elementData.add(newSubarray);
oldCapacity += subarraySize;
}
}
/**
* @param capacity
* @return an empty {@link PrimitiveArrayWrapper} list and with the specified capacity
* @throws InvalidPrimitiveArrayGenericParameterException If the generic paramter of the instance is not valid
*/
private PrimitiveArrayWrapper<?> generateEmptyPrimitiveArrayWrapper(int capacity) throws InvalidPrimitiveArrayGenericParameterException {
if (elementClass == Integer.class) {
return new IntArrayWrapper(capacity);
} else if (elementClass == Float.class) {
if (scorePrecision == ScorePrecision.PRECISION_16BIT) {
return new HalfArrayWrapper(capacity);
} else if (scorePrecision == ScorePrecision.PRECISION_32BIT) {
return new FloatArrayWrapper(capacity);
}
} else if (elementClass == Byte.class) {
return new ByteArrayWrapper(capacity);
} else if (elementClass == Boolean.class) {
return new BooleanArrayWrapper(capacity);
}
throw new InvalidPrimitiveArrayGenericParameterException(elementClass);
}
@Override
public T get(int index) {
rangeCheck(index);
int subarrayIndex = getSubarrayIndex(index);
int indexWithinSubarray = getIndexWithinSubarray(index);
return elementData.get(subarrayIndex).get(indexWithinSubarray);
}
/**
* @param index an index
* @return the index within the subarray containing the specified index
*/
private int getIndexWithinSubarray(int index) {
return index % subarraySize;
}
/**
* @param index an index
* @return the index of the subarray containing the specified index
*/
private int getSubarrayIndex(int index) {
return index / subarraySize;
}
@Override
public boolean isCompressed() throws CompressionException {
return isCompressed;
}
@Override
public boolean isEmpty() {
return size == 0;
}
/**
* @param index
* @return A message specifying what was the index and what was the size of the list
*/
private String outOfBoundsMsg(int index) {
return "Index: " + index + ", Size: " + size();
}
/**
* Checks if the given index is in range. If not, throws an appropriate
* runtime exception. This method does *not* check if the index is
* negative: It is always used immediately prior to an array access,
* which throws an ArrayIndexOutOfBoundsException if index is negative.
* @param index an index
*/
private void rangeCheck(int index) {
if (index >= size) {
throw new IndexOutOfBoundsException(outOfBoundsMsg(index));
}
}
/**
* Method used for deserialization
* @param in
* @throws IOException
* @throws ClassNotFoundException
*/
@SuppressWarnings("unchecked")
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
// read the class version number
in.readInt();
// read non transient fields
in.defaultReadObject();
// read other fields
size = in.readInt();
elementData = (List<PrimitiveArrayWrapper<T>>) in.readObject();
isCompressed = in.readBoolean();
// compress the list if it was compressed when serialized
if (isCompressed) {
compress();
}
}
@Override
public T set(int index, T element) {
rangeCheck(index);
int subarrayIndex = getSubarrayIndex(index);
int indexWithinSubarray = getIndexWithinSubarray(index);
return elementData.get(subarrayIndex).set(indexWithinSubarray, element);
}
@Override
public int size() {
return this.size;
}
/**
* Trims the capacity of this <tt>ArrayList</tt> instance to be the
* list's current size. An application can use this operation to minimize
* the storage of an <tt>ArrayList</tt> instance.
*/
public void trimToSize() {
modCount++;
int oldCapacity = elementData.size() * subarraySize;
if (size < oldCapacity) {
PrimitiveArrayWrapper<T> lastSubarray = elementData.get(elementData.size() - 1);
int lastSubarraySize = getIndexWithinSubarray(size);
lastSubarray.trimToSize(lastSubarraySize);
}
}
@SuppressWarnings("unchecked")
@Override
public void uncompress() throws CompressionException {
try {
if ((isCompressed) && (compressedData != null)) {
ByteArrayInputStream bais = new ByteArrayInputStream(compressedData.toByteArray());
GZIPInputStream gz = new GZIPInputStream(bais);
ObjectInputStream ois = new ObjectInputStream(gz);
elementData = (List<PrimitiveArrayWrapper<T>>) ois.readObject();
compressedData = null;
isCompressed = false;
}
} catch (IOException e) {
throw new CompressionException("An error occure during the data uncompression");
} catch (ClassNotFoundException e) {
throw new CompressionException("An error occure during the data uncompression");
}
}
/**
* Method used for serialization
* @param out
* @throws IOException
*/
private void writeObject(ObjectOutputStream out) throws IOException {
// write the class version number
out.writeInt(CLASS_VERSION_NUMBER);
// write non transient fields
out.defaultWriteObject();
// write the other fields
out.writeInt(size);
/* Makes sure that the list is uncompressed before serialization.
Recompresses the list is the list has been uncompressed. */
if (isCompressed()) {
try {
uncompress();
out.writeObject(elementData);
compress();
} catch (CompressionException e) {
ExceptionManager.getInstance().caughtException(e);
}
} else {
out.writeObject(elementData);
}
out.writeBoolean(isCompressed);
}
}