Author: mes
Date: 2012-04-19 13:44:54 -0700 (Thu, 19 Apr 2012)
New Revision: 28889
Removed:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/LongTHash.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/internal/LongTHashTest.java
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/SimpleNetwork.java
core3/impl/trunk/model-impl/pom.xml
Log:
changed from LongTHash to parallel colt OpenLongObjectHashMap
Deleted:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/LongTHash.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/LongTHash.java
2012-04-19 20:17:16 UTC (rev 28888)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/LongTHash.java
2012-04-19 20:44:54 UTC (rev 28889)
@@ -1,270 +0,0 @@
-
-/*
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library 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. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
-
-package org.cytoscape.model.internal;
-
-import java.util.NoSuchElementException;
-
-
-/**
- * An insert-only hashtable that has non-negative 32 bit integer keys and
- * non-null object values.<p>
- * In the underlying implementation, this hashtable increases in size to adapt
- * to key/value pairs being added (the underlying size of the hashtable is
- * invisible to the programmer). In the underlying implementation, this
- * hashtable never decreases in size. As a hashtable increases in size,
- * it takes at most four times as much memory as it would take
- * to store the hashtable's keys and values in perfectly-sized arrays.
- * Underlying size expansions are implemented such that the operation of
- * expanding in size is amortized over the contstant time complexity needed to
- * insert new elements.<p>
- * An instance of this class is serializable; however, serialized instances of
- * this class should not be stored in a persistent manner because the
- * serialization implemented in this class makes no attempt at handling
- * class versioning. For an instance of this class to be properly
- * serialized, all object values stored in that instance must be
- * serializable.
- */
-public final class LongTHash<T> {
- private final static long serialVersionUID = 121374594955439L;
- private static final int[] PRIMES = {
- 11, 23, 53, 113, 251, 509,
1019, 2039, 4079, 8179,
- 16369, 32749, 65521, 131063,
262133, 524269, 1048571,
- 2097143, 4194287, 8388587,
16777183, 33554393, 67108837,
- 134217689, 268435399,
536870879, 1073741789, 2147483647
- };
- private static final int INITIAL_SIZE = PRIMES[0];
- private static final double THRESHOLD_FACTOR = 0.77;
- private long[] m_keys;
- private Object[] m_vals;
- private int m_elements;
- private int m_thresholdSize;
-
- // These are caching variables. The idea is that programmers will
- // frequently first do a get(), and based on that result, will perform
- // some other operations and then maybe do a put() operation with the
same
- // key as the previous get() operation.
- private long m_prevKey;
- private int m_prevInx;
-
- private final Class<T> clazz;
-
- private static final int REUSABLE = -1;
- private static final int UNSET = -2;
- private static final int FIRST_AVAILABLE = 0;
-
- /**
- * Creates a new hashtable.
- */
- public LongTHash(Class<T> clazz) {
- this.clazz = clazz;
- m_keys = new long[INITIAL_SIZE];
- m_vals = new Object[INITIAL_SIZE];
- m_elements = 0;
- m_thresholdSize = (int) (THRESHOLD_FACTOR * (double)
m_keys.length);
-
- for (int i = 0; i < m_keys.length; i++)
- m_keys[i] = UNSET;
-
- m_prevKey = UNSET;
- m_prevInx = UNSET;
- }
-
- /**
- * Puts a new key/value pair into this hashtable, potentially
overwriting
- * an existing value whose key is the same as the one specified.
- * Returns the old value associated with the specified key or null if no
- * value is associated with specified key at the time of this call.<p>
- * Insertions into the hashtable are performed in [amortized] time
- * complexity O(1).
- * @exception IllegalArgumentException if key is negative.
- * @exception NullPointerException if value is null.
- */
- public final T put(final long key, final T value) {
- if (key < 0)
- throw new IllegalArgumentException("key is negative");
-
- //System.err.println("put " + key + " -> " + value);
-
- if (key != m_prevKey) {
- calcPrevInx(key,FIRST_AVAILABLE);
- m_prevKey = key;
- }
-
- final Object returnVal = m_vals[m_prevInx];
- //System.err.println("put m_prevInx:" + m_prevInx + " val: " +
returnVal);
-
- if (returnVal == null) {
- //System.err.println(" entering null");
- if (m_elements == m_thresholdSize) {
- incrSize();
-
- return put(key, value);
- }
-
- m_elements++;
- }
-
- m_vals[m_prevInx] = value;
- if ( value == null )
- m_keys[m_prevInx] = REUSABLE;
- else
- m_keys[m_prevInx] = key;
-
- //dump("put");
-
- return clazz.cast(returnVal);
- }
-
- private void dump(String s) {
- System.err.println(s + " m_prevInx: " + m_prevInx);
- System.err.println(s + " m_keys: " +
java.util.Arrays.toString(m_keys));
- System.err.println(s + " m_vals: " +
java.util.Arrays.toString(m_vals));
- }
-
- /**
- * Returns the value bound to the specified key or null if no value is
- * currently bound to the specified key.<p>
- * Searches in this hashtable are performed in [amortized] time
- * complexity O(1).
- * @exception IllegalArgumentException if key is negative.
- */
- public final T get(final long key) {
- if (key < 0)
- return null;
- //System.err.println("get " + key );
-
- if (key != m_prevKey) {
- if (!calcPrevInx(key,REUSABLE)) {
- return null;
- }
- m_prevKey = key;
- }
-
- //dump("get");
- return clazz.cast(m_vals[m_prevInx]);
- }
-
- public final T remove(final long key) {
- //System.err.println("remove " + key );
- Object ret = get(key);
- if (ret == null) {
- return null;
- }
-
- put(key,null);
- m_elements--;
- //dump("remove");
- return clazz.cast(ret);
- }
-
- // for unit testing
- int size() {
- return m_elements;
- }
-
- // The threshold value determines when to stop searching for an index.
- // If threshold is set to 0, it will stop at the first unset entry (used
- // for putting new values into the hash). If the threshold is set to
-1,
- // then it will search all available indices (used for getting values
from
- // the hash).
- private boolean calcPrevInx(long key, int threshold) {
- int incr = 0;
-
- int initialIndex = m_prevInx;
-
- for (m_prevInx = (int)(key % (long)m_keys.length);
- (m_keys[m_prevInx] >= threshold) && (m_keys[m_prevInx] !=
key);
- m_prevInx = (m_prevInx + incr) % m_keys.length) {
- if (initialIndex == m_prevInx) {
- return false;
- }
- //System.err.println(" m_prevInx: " + m_prevInx);
- if (incr == 0) {
- incr = 1 + (int)(key % ((long)m_keys.length -
1));
- }
- }
- return true;
- }
-
- private final void incrSize() {
- final int newSize;
-
- try {
- int primesInx = 0;
-
- while (m_keys.length != PRIMES[primesInx++])
- ;
-
- newSize = PRIMES[primesInx];
- } catch (ArrayIndexOutOfBoundsException e) {
- throw new IllegalStateException("too many elements in
this hashtable");
- }
-
- final long[] newKeys = new long[newSize];
- final Object[] newVals = new Object[newSize];
-
- for (int i = 0; i < newKeys.length; i++)
- newKeys[i] = UNSET;
-
- m_thresholdSize = (int) (THRESHOLD_FACTOR * (double)
newKeys.length);
-
- int incr;
- int newIndex;
- int oldIndex = -1;
-
- for (int i = 0; i < m_elements; i++) {
- while (m_keys[++oldIndex] < 0);
-
- incr = 0;
-
- for (newIndex = (int)(m_keys[oldIndex] %
(long)newKeys.length);
- newKeys[newIndex] >= 0;
- newIndex = (newIndex + incr) % newKeys.length)
- if (incr == 0)
- incr = 1 + ((int)(m_keys[oldIndex] %
(long)(newKeys.length - 1)));
-
- newKeys[newIndex] = m_keys[oldIndex];
- newVals[newIndex] = m_vals[oldIndex];
- }
-
- m_keys = newKeys;
- m_vals = newVals;
- m_prevKey = UNSET;
- m_prevInx = UNSET;
- //dump("incrSize");
- }
-}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/SimpleNetwork.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/SimpleNetwork.java
2012-04-19 20:17:16 UTC (rev 28888)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/SimpleNetwork.java
2012-04-19 20:44:54 UTC (rev 28889)
@@ -36,6 +36,8 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNode;
+
+import cern.colt.map.tobject.OpenLongObjectHashMap;
/**
@@ -49,13 +51,13 @@
// Unique ID for this
private final Long suid;
- // We use LongTHash here because we really don't want to
+ // We use OpenLongObjectHashMap here because we really don't want to
// constantly convert the int node/edge index to an Interger
// object necessary for a Map<Integer,NodePointer>. That
// allocates a bunch of otherwise unused Integer objects
// which also takes extra time.
- private final LongTHash<NodePointer> nodePointers;
- private final LongTHash<EdgePointer> edgePointers;
+ private final OpenLongObjectHashMap nodePointers;
+ private final OpenLongObjectHashMap edgePointers;
private int nodeCount;
private int edgeCount;
@@ -67,8 +69,8 @@
nodeCount = 0;
edgeCount = 0;
firstNode = null;
- nodePointers = new LongTHash<NodePointer>(NodePointer.class);
- edgePointers = new LongTHash<EdgePointer>(EdgePointer.class);
+ nodePointers = new OpenLongObjectHashMap();
+ edgePointers = new OpenLongObjectHashMap();
}
public Long getSUID() {
@@ -84,7 +86,7 @@
}
public synchronized CyEdge getEdge(final long e) {
- final EdgePointer ep = edgePointers.get(e);
+ final EdgePointer ep = (EdgePointer)edgePointers.get(e);
if ( ep != null )
return ep.cyEdge;
else
@@ -92,7 +94,7 @@
}
public synchronized CyNode getNode(final long n) {
- final NodePointer np = nodePointers.get(n);
+ final NodePointer np = (NodePointer)nodePointers.get(n);
if ( np != null )
return np.cyNode;
else
@@ -242,7 +244,8 @@
// remove adjacent edges from network
removeEdgesInternal(getAdjacentEdgeList(n,
CyEdge.Type.ANY));
- final NodePointer node =
nodePointers.remove(n.getSUID());
+ final NodePointer node =
(NodePointer)nodePointers.get(n.getSUID());
+ nodePointers.removeKey(n.getSUID());
firstNode = node.remove(firstNode);
nodeCount--;
@@ -291,7 +294,8 @@
if (!containsEdge(edge))
return false;
- final EdgePointer e =
edgePointers.remove(edge.getSUID());
+ final EdgePointer e =
(EdgePointer)edgePointers.get(edge.getSUID());
+ edgePointers.removeKey(edge.getSUID());
e.remove();
@@ -309,7 +313,7 @@
final NodePointer thisNode;
synchronized (this) {
- thisNode = nodePointers.get(node.getSUID());
+ thisNode =
(NodePointer)nodePointers.get(node.getSUID());
}
if ( thisNode == null )
@@ -325,7 +329,7 @@
final EdgePointer thisEdge;
synchronized (this) {
- thisEdge = edgePointers.get(edge.getSUID());
+ thisEdge =
(EdgePointer)edgePointers.get(edge.getSUID());
}
if ( thisEdge == null )
@@ -448,7 +452,7 @@
}
numRemaining--;
- return edgePointers.get(returnIndex);
+ return
(EdgePointer)edgePointers.get(returnIndex);
}
};
}
@@ -512,7 +516,7 @@
final long returnIndex = nextIndex;
nextIndex = -1;
- return edgePointers.get(returnIndex);
+ return
(EdgePointer)edgePointers.get(returnIndex);
}
};
}
@@ -565,7 +569,7 @@
private NodePointer getNodePointer(final CyNode node) {
assert(node != null);
- return nodePointers.get(node.getSUID());
+ return (NodePointer)nodePointers.get(node.getSUID());
}
Deleted:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/internal/LongTHashTest.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/internal/LongTHashTest.java
2012-04-19 20:17:16 UTC (rev 28888)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/internal/LongTHashTest.java
2012-04-19 20:44:54 UTC (rev 28889)
@@ -1,132 +0,0 @@
-
-package org.cytoscape.model.internal;
-
-import java.lang.Thread.State;
-
-import org.junit.Before;
-import org.junit.Test;
-import static org.junit.Assert.*;
-
-public class LongTHashTest {
-
- @Test
- public void testBasicPutGet() {
- LongTHash<String> ith = new LongTHash<String>(String.class);
- ith.put(1L,"homer");
- ith.put(2L,"marge");
- ith.put(3L,"lisa");
- assertEquals( "homer", ith.get(1L) );
- assertEquals( "marge", ith.get(2L) );
- assertEquals( "lisa", ith.get(3L) );
- }
-
- @Test
- public void testSize() {
- LongTHash<String> ith = new LongTHash<String>(String.class);
- ith.put(1,"homer");
- ith.put(2,"marge");
- ith.put(3,"lisa");
- assertEquals( 3, ith.size() );
- }
-
- @Test
- public void testRemove() {
- LongTHash<String> ith = new LongTHash<String>(String.class);
- ith.put(1L,"homer");
- ith.put(2L,"marge");
- ith.put(3L,"lisa");
-
- assertEquals( 3, ith.size() );
-
- ith.remove(3L);
- assertEquals( 2, ith.size() );
- assertNull( ith.get(3L) );
-
- ith.remove(2L);
- assertEquals( 1, ith.size() );
- assertNull( ith.get(2L) );
-
- ith.remove(1L);
- assertEquals( 0, ith.size() );
- assertNull( ith.get(1L) );
- }
-
- @Test
- public void testAddRemove() {
- LongTHash<String> ith = new LongTHash<String>(String.class);
- ith.put(1L,"homer");
- ith.put(2L,"marge");
- ith.put(3L,"lisa");
- ith.put(4L,"bart");
- ith.put(5L,"maggie");
- ith.put(6L,"smithers");
- ith.put(7L,"burns");
-
- ith.remove(1L);
- ith.remove(2L);
- ith.remove(3L);
-
- ith.put(1L,"homer");
- ith.put(2L,"marge");
- ith.put(3L,"lisa");
-
- ith.remove(4L);
- ith.remove(5L);
- ith.remove(6L);
-
- ith.put(4L,"bart");
- ith.put(5L,"maggie");
- ith.put(6L,"smithers");
- }
-
- @Test
- public void testTicket849() {
- LongTHash<String> hash = new LongTHash<String>(String.class);
- hash.put(3476L, "A");
- hash.put(3477L, "B");
- hash.put(3478L, "C");
- hash.put(3479L, "D");
- hash.put(3490L, "E");
- hash.put(3491L, "F");
-
- hash.remove(3490L);
- assertEquals("F", hash.get(3491L));
- }
-
- @Test
- public void testForceResize() {
- LongTHash<String> hash = new LongTHash<String>(String.class);
- hash.put(0L, "A");
- hash.put(1L, "A");
- hash.put(2L, "A");
- hash.put(3L, "A");
- hash.put(4L, "A");
- hash.put(5L, "A");
- hash.put(6L, "A");
- hash.put(7L, "A");
- hash.put(8L, "A");
- hash.put(9L, "A");
- hash.put(10L, "A");
- hash.put(11L, "A");
- }
-
- @Test
- public void testTicket853() throws InterruptedException {
- Thread thread = new Thread(new Runnable() {
- @Override
- public void run() {
- int size = 6;
- LongTHash<Integer> hash = new
LongTHash<Integer>(Integer.class);
- for (int i = 0; i < size; i++) {
- hash.put((long) i, i);
- }
- for (int i = size; i < (size * 2); i++) {
- hash.remove((long) i);
- }
- }
- });
- thread.start();
- thread.join(2000);
- assertEquals(State.TERMINATED, thread.getState());
- }
-}
Modified: core3/impl/trunk/model-impl/pom.xml
===================================================================
--- core3/impl/trunk/model-impl/pom.xml 2012-04-19 20:17:16 UTC (rev 28888)
+++ core3/impl/trunk/model-impl/pom.xml 2012-04-19 20:44:54 UTC (rev 28889)
@@ -126,6 +126,11 @@
<artifactId>guava-osgi</artifactId>
<version>9.0.0</version>
</dependency>
+ <dependency>
+ <groupId>cytoscape-temp</groupId>
+ <artifactId>parallelcolt</artifactId>
+ <version>0.9.4</version>
+ </dependency>
</dependencies>
</project>
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