Author: ruschein
Date: 2010-02-02 08:40:30 -0800 (Tue, 02 Feb 2010)
New Revision: 19118
Modified:
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/IntCompressor.java
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/RLEIntCompressor.java
Log:
First feature-complete implementation.
Modified:
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/IntCompressor.java
===================================================================
---
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/IntCompressor.java
2010-02-02 16:18:45 UTC (rev 19117)
+++
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/IntCompressor.java
2010-02-02 16:40:30 UTC (rev 19118)
@@ -3,5 +3,5 @@
interface IntCompressor {
int[] compress(final int[] uncompressedData);
- int[] expand(final int[] compressedData);
+ int[] expand(final int[] compressedData) throws IllegalStateException;
}
Modified:
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/RLEIntCompressor.java
===================================================================
---
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/RLEIntCompressor.java
2010-02-02 16:18:45 UTC (rev 19117)
+++
csplugins/trunk/util.compression/src/org/cytoscape/util/compression/RLEIntCompressor.java
2010-02-02 16:40:30 UTC (rev 19118)
@@ -1,11 +1,18 @@
package org.cytoscape.util.compression;
+/**
+ * Class to maintain a dynamically growing int array.
+ */
class DynamicIntArray {
private static final int DEFAULT_INITIAL_CAPACITY = 1000;
private int[] array;
private int nextIndex = 0;
+ DynamicIntArray() {
+ this(0);
+ }
+
DynamicIntArray(final int initialCapacity) {
if (initialCapacity > 0)
array = new int[initialCapacity];
@@ -20,6 +27,20 @@
array[nextIndex++] = newValue;
}
+ /**
+ * @return An array of the exact size of the data.
+ */
+ int[] toArray() {
+ final int[] retval = new int[nextIndex];
+ System.arraycopy(array, 0, retval, 0, nextIndex);
+
+ return retval;
+ }
+
+ /**
+ * Used to grow our internal array. This is done by capacity doubling
which implies that the
+ * amortised asymptotic complexity of append() is O(1) which is the
best we can hope for!
+ */
private void resize() {
final int[] newArray = new int[array.length << 1];
System.arraycopy(array, 0, newArray, 0, array.length);
@@ -28,10 +49,58 @@
}
+/**
+ * Class that implements run-length encoding of int arrays.
+ */
public class RLEIntCompressor {
public int[] compress(final int[] uncompressedData) {
+ int runLength = 0;
+ int currentValue = uncompressedData[0];
+
+ final DynamicIntArray dynArray = new
DynamicIntArray(uncompressedData.length);
+
+ for (final int value : uncompressedData) {
+ if (value == currentValue) {
+ ++runLength;
+ if (runLength == Integer.MAX_VALUE) { // Yes, I
am *that* paranoid! ;)
+ dynArray.append(runLength);
+ dynArray.append(currentValue);
+ runLength = 0;
+ }
+ }
+ else {
+ dynArray.append(runLength);
+ dynArray.append(currentValue);
+ runLength = 1;
+ currentValue = value;
+ }
+ }
+
+ // Unfinished business?
+ if (runLength > 0) {
+ dynArray.append(runLength);
+ dynArray.append(currentValue);
+ }
+
+ return dynArray.toArray();
}
- public int[] expand(final int[] compressedData) {
+ public int[] expand(final int[] compressedData) throws
IllegalStateException {
+ final DynamicIntArray dynArray = new
DynamicIntArray(compressedData.length << 2);
+
+ try {
+ int i = 0;
+ while (i < compressedData.length) {
+ final int runLength = compressedData[i++];
+ final int value = compressedData[i++];
+
+ for (int k = 0; k < runLength; ++k)
+ dynArray.append(value);
+ }
+ } catch (final ArrayIndexOutOfBoundsException e) {
+ throw new IllegalStateException("garbled compressed
data!");
+ }
+
+ return dynArray.toArray();
}
}
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