Author: mes
Date: 2012-01-24 15:30:26 -0800 (Tue, 24 Jan 2012)
New Revision: 28095
Added:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/WeakMapList.java
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableFactoryImpl.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NameSetListener.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
Log:
now avoiding a lot of service registration when adding subnetworks
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2012-01-24 23:00:09 UTC (rev 28094)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2012-01-24 23:30:26 UTC (rev 28095)
@@ -48,6 +48,8 @@
import org.cytoscape.model.SUIDFactory;
import org.cytoscape.model.events.ColumnCreatedListener;
import org.cytoscape.model.events.RowsSetListener;
+import org.cytoscape.model.events.NetworkAddedListener;
+import org.cytoscape.model.events.NetworkAddedEvent;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.model.subnetwork.CySubNetwork;
import org.cytoscape.service.util.CyServiceRegistrar;
@@ -91,16 +93,19 @@
private final CyTableManagerImpl tableMgr;
private final CyNetworkTableManagerImpl networkTableMgr;
private final CyTableFactory tableFactory;
- private final CyServiceRegistrar serviceRegistrar;
private final boolean publicTables;
+ private final VirtualColumnAdder columnAdder;
+ private final NameSetListener nameSetListener;
+ private final NetworkAddedListenerDelegator
networkAddedListenerDelegator;
+
/**
* Creates a new ArrayGraph object.
* @param eh The CyEventHelper used for firing events.
*/
public ArrayGraph(final CyEventHelper eh, final CyTableManagerImpl
tableMgr,
- final CyNetworkTableManagerImpl
networkTableMgr,
- final CyTableFactory tableFactory,
+ final CyNetworkTableManagerImpl networkTableMgr,
+ final CyTableFactory tableFactory,
final CyServiceRegistrar serviceRegistrar, final
boolean publicTables)
{
this.eventHelper = eh;
@@ -108,7 +113,6 @@
this.networkTableMgr = networkTableMgr;
this.tableFactory = tableFactory;
this.publicTables = publicTables;
- this.serviceRegistrar = serviceRegistrar;
suid = SUIDFactory.getNextSUID();
numSubNetworks = 0;
nodeCount = 0;
@@ -117,14 +121,21 @@
nodePointers = new ArrayList<NodePointer>();
edgePointers = new ArrayList<EdgePointer>();
+ columnAdder = new VirtualColumnAdder();
+ serviceRegistrar.registerService(columnAdder,
ColumnCreatedListener.class, new Properties());
+ nameSetListener = new NameSetListener();
+ serviceRegistrar.registerService(nameSetListener,
RowsSetListener.class, new Properties());
+ networkAddedListenerDelegator = new
NetworkAddedListenerDelegator();
+ serviceRegistrar.registerService(networkAddedListenerDelegator,
NetworkAddedListener.class, new Properties());
+
netTables = createNetworkTables(suid);
getCyRow().set(CyTableEntry.NAME, "");
nodeTables = createNodeTables(suid);
edgeTables = createEdgeTables(suid);
- networkTableMgr.setTableMap(CyNetwork.class, this, netTables);
- networkTableMgr.setTableMap(CyNode.class, this, nodeTables);
- networkTableMgr.setTableMap(CyEdge.class, this, edgeTables);
+ networkTableMgr.setTableMap(CyNetwork.class, this, netTables);
+ networkTableMgr.setTableMap(CyNode.class, this, nodeTables);
+ networkTableMgr.setTableMap(CyEdge.class, this, edgeTables);
subNetworks = new ArrayList<CySubNetwork>();
@@ -200,12 +211,10 @@
// Now add a listener for column created events to add
// virtual columns to any subsequent source columns added.
- serviceRegistrar.registerService(new
VirtualColumnAdder(srcTable,tgtTable),
- ColumnCreatedListener.class,
new Properties());
+ columnAdder.addInterestedTables(srcTable,tgtTable);
// Another listener tracks changes to the NAME column in local
tables
- serviceRegistrar.registerService(new
NameSetListener(srcTable,tgtTable),
- RowsSetListener.class, new
Properties());
+ nameSetListener.addInterestedTables(srcTable,tgtTable);
}
/**
@@ -944,7 +953,7 @@
final Map<String,CyTable> newNodeTable =
createNodeTables(newSUID);
final Map<String,CyTable> newEdgeTable =
createEdgeTables(newSUID);
final ArraySubGraph sub = new
ArraySubGraph(this,newSUID,newId,eventHelper,newNetTable,newNodeTable,newEdgeTable,tableMgr);
- serviceRegistrar.registerAllServices(sub, new Properties());
+ networkAddedListenerDelegator.addListener(sub);
subNetworks.add(sub);
networkTableMgr.setTableMap(CyNetwork.class, sub, newNetTable);
networkTableMgr.setTableMap(CyNode.class, sub, newNodeTable);
@@ -1072,4 +1081,17 @@
public CyRow getRow(CyTableEntry t) {
return getRow(t,CyNetwork.DEFAULT_ATTRS);
}
+
+ private class NetworkAddedListenerDelegator implements
NetworkAddedListener {
+ List<NetworkAddedListener> listeners = new
ArrayList<NetworkAddedListener>();
+ public void addListener(NetworkAddedListener l) {
+ listeners.add(l);
+ }
+ public void handleEvent(NetworkAddedEvent e) {
+ for (NetworkAddedListener l : listeners)
+ l.handleEvent(e);
+ }
+ }
+
}
+
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableFactoryImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableFactoryImpl.java
2012-01-24 23:00:09 UTC (rev 28094)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyTableFactoryImpl.java
2012-01-24 23:30:26 UTC (rev 28095)
@@ -33,10 +33,13 @@
import java.util.Map;
import java.util.HashMap;
import java.util.Properties;
+import java.lang.ref.WeakReference;
import org.cytoscape.model.CyTable;
import org.cytoscape.model.CyTable.SavePolicy;
import org.cytoscape.model.CyTableFactory;
+import org.cytoscape.model.events.TableAddedListener;
+import org.cytoscape.model.events.TableAddedEvent;
import org.cytoscape.equations.Interpreter;
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.service.util.CyServiceRegistrar;
@@ -51,6 +54,7 @@
private final CyEventHelper help;
private final Interpreter interpreter;
private final CyServiceRegistrar serviceRegistrar;
+ private final WeakEventDelegator eventDelegator;
public CyTableFactoryImpl(final CyEventHelper help, final Interpreter
interpreter,
final CyServiceRegistrar serviceRegistrar)
@@ -58,14 +62,32 @@
this.help = help;
this.interpreter = interpreter;
this.serviceRegistrar = serviceRegistrar;
+ this.eventDelegator = new WeakEventDelegator();
+ this.serviceRegistrar.registerService(eventDelegator,
TableAddedListener.class, new Properties());
}
public CyTable createTable(final String name, final String primaryKey,
final Class<?> primaryKeyType,
final boolean pub, final boolean isMutable)
{
- final CyTable table = new CyTableImpl(name, primaryKey,
primaryKeyType, pub, isMutable,
+ final CyTableImpl table = new CyTableImpl(name, primaryKey,
primaryKeyType, pub, isMutable,
SavePolicy.SESSION_FILE,
help, interpreter);
- serviceRegistrar.registerAllServices(table, new Properties());
+ eventDelegator.addListener(table);
return table;
}
+
+ private class WeakEventDelegator implements TableAddedListener {
+ List<WeakReference<TableAddedListener>> tables = new
ArrayList<WeakReference<TableAddedListener>>();
+
+ public void addListener(TableAddedListener t) {
+ tables.add(new WeakReference<TableAddedListener>(t));
+ }
+
+ public void handleEvent(TableAddedEvent e) {
+ for ( WeakReference<TableAddedListener> ref : tables ) {
+ TableAddedListener l = ref.get();
+ if ( l != null )
+ l.handleEvent(e);
+ }
+ }
+ }
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NameSetListener.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NameSetListener.java
2012-01-24 23:00:09 UTC (rev 28094)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NameSetListener.java
2012-01-24 23:30:26 UTC (rev 28095)
@@ -38,6 +38,9 @@
import org.cytoscape.model.events.RowsSetEvent;
import org.cytoscape.model.events.RowSetRecord;
+import java.util.List;
+import java.util.ArrayList;
+
/**
* Any time that the CyTableEntry.NAME column is set
* in a local table, update the shared table with the
@@ -45,32 +48,37 @@
*/
class NameSetListener implements RowsSetListener {
- private final CyTable shared;
- private final CyTable local;
+ private final WeakMapList<CyTable,CyTable> tables;
- NameSetListener(CyTable shared, CyTable local) {
+ NameSetListener() {
+ tables = new WeakMapList<CyTable,CyTable>();
+ }
+
+ public void handleEvent(RowsSetEvent e) {
+ CyTable local = e.getSource();
+ List<CyTable> sharedList = tables.get(local);
+ for ( CyTable shared : sharedList ) {
+ for ( RowSetRecord record : e.getPayloadCollection() ) {
+ // assume payload collection is for same column
+ if (
!record.getColumn().equals(CyTableEntry.NAME) )
+ continue;
+ CyRow r = shared.getRow( record.getRow().get(
CyTableEntry.SUID, Long.class ) );
+ if ( r != null )
+ r.set(CyRootNetwork.SHARED_NAME,
record.getValue());
+ }
+ }
+ }
+
+ public void addInterestedTables(CyTable local, CyTable shared) {
if ( shared == null )
throw new NullPointerException("source table is null");
if ( local == null )
throw new NullPointerException("target table is null");
if ( shared == local )
throw new IllegalArgumentException("source and target
tables cannot be the same!");
- this.shared = shared;
- this.local = local;
- }
- public void handleEvent(RowsSetEvent e) {
- if ( e.getSource() != local )
- return;
- for ( RowSetRecord record : e.getPayloadCollection() ) {
- // assume payload collection is for same column
- if ( !record.getColumn().equals(CyTableEntry.NAME) )
- return;
+ tables.put(local,shared);
+ }
- CyRow r = shared.getRow( record.getRow().get(
CyTableEntry.SUID, Long.class ) );
- if ( r != null )
- r.set(CyRootNetwork.SHARED_NAME,
record.getValue());
- }
- }
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
2012-01-24 23:00:09 UTC (rev 28094)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/VirtualColumnAdder.java
2012-01-24 23:30:26 UTC (rev 28095)
@@ -35,34 +35,38 @@
import org.cytoscape.model.events.ColumnCreatedEvent;
import org.cytoscape.model.events.ColumnCreatedListener;
+import java.util.List;
+import java.util.ArrayList;
/**
* Any time that the source table adds a column, the
* target table add it as a virtual column.
*/
class VirtualColumnAdder implements ColumnCreatedListener {
- private final CyTable src;
- private final CyTable tgt;
+ private final WeakMapList<CyTable,CyTable> tables;
- VirtualColumnAdder(CyTable src, CyTable tgt) {
+ VirtualColumnAdder() {
+ tables = new WeakMapList<CyTable,CyTable>();
+ }
+
+ public void handleEvent(ColumnCreatedEvent e) {
+ CyTable src = e.getSource();
+ List<CyTable> targets = tables.get( src );
+ String srcName = e.getColumnName();
+ CyColumn srcCol = src.getColumn(srcName);
+
+ for ( CyTable tgt : targets )
+
tgt.addVirtualColumn(srcName,srcName,src,CyTableEntry.SUID,srcCol.isImmutable());
+ }
+
+ public void addInterestedTables(CyTable src, CyTable tgt) {
if ( src == null )
throw new NullPointerException("source table is null");
if ( tgt == null )
throw new NullPointerException("target table is null");
if ( src == tgt )
throw new IllegalArgumentException("source and target
tables cannot be the same!");
- this.src = src;
- this.tgt = tgt;
+ tables.put(src,tgt);
}
-
- public void handleEvent(ColumnCreatedEvent e) {
- if ( e.getSource() != src )
- return;
- String srcName = e.getColumnName();
- if ( tgt.getColumn(srcName) != null )
- return;
- CyColumn srcCol = src.getColumn(srcName);
-
tgt.addVirtualColumn(srcName,srcName,src,CyTableEntry.SUID,srcCol.isImmutable());
- }
}
Added:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/WeakMapList.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/WeakMapList.java
(rev 0)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/WeakMapList.java
2012-01-24 23:30:26 UTC (rev 28095)
@@ -0,0 +1,74 @@
+
+/*
+ Copyright (c) 2008, 2010-2011, The Cytoscape Consortium (www.cytoscape.org)
+
+ 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 org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.model.events.ColumnCreatedEvent;
+import org.cytoscape.model.events.ColumnCreatedListener;
+
+import java.util.List;
+import java.util.ArrayList;
+import java.util.WeakHashMap;
+
+import java.lang.ref.WeakReference;
+
+/**
+ * A WeakHashMap where the keys point to lists of WeakReferences.
+ */
+class WeakMapList<S,T> {
+
+ WeakHashMap<S,List<WeakReference<T>>> data = new
WeakHashMap<S,List<WeakReference<T>>>();
+
+ public List<T> get(S src) {
+ List<WeakReference<T>> list = data.get(src);
+ List<T> ret = new ArrayList<T>();
+ if ( list == null )
+ return ret;
+ for (WeakReference<T> ref : list) {
+ T t = ref.get();
+ if ( t != null )
+ ret.add(t);
+ }
+ return ret;
+ }
+
+
+ public void put(S src, T tgt) {
+ List<WeakReference<T>> refs = data.get(src);
+ if ( refs == null ) {
+ refs = new ArrayList<WeakReference<T>>();
+ data.put(src,refs);
+ }
+ refs.add( new WeakReference<T>( tgt ) );
+ }
+}
+
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
