Author: mes
Date: 2010-08-10 13:02:33 -0700 (Tue, 10 Aug 2010)
New Revision: 21286
Added:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/TableManager.java
core3/model-impl/trunk/src/test/java/org/cytoscape/model/CyTableManagerTest.java
Modified:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
core3/model-impl/trunk/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
Log:
changed how CyDataTables are managed for networks
Modified:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
===================================================================
---
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2010-08-10 20:01:56 UTC (rev 21285)
+++
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArrayGraph.java
2010-08-10 20:02:33 UTC (rev 21286)
@@ -44,6 +44,7 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyDataTable;
+import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
@@ -99,14 +100,16 @@
private final List<CySubNetwork> subNets;
private final List<CyMetaNode> metaNodes;
private CySubNetwork base;
+
+ private CyTableManager tableMgr;
- private final Map<String, Map<String, CyDataTable>> dataTableMap;
/**
* Creates a new ArrayGraph object.
* @param eh The CyEventHelper used for firing events.
*/
- public ArrayGraph(final CyEventHelper eh) {
+ public ArrayGraph(final CyEventHelper eh, final CyTableManager
tableMgr) {
+ this.tableMgr = tableMgr;
suid = SUIDFactory.getNextSUID();
numSubNetworks = 0;
nodeCount = 0;
@@ -121,6 +124,8 @@
netAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn("name",String.class,false);
attrs().set("name","");
+ // potential leak since "this" isn't yet fully constructed
+ tableMgr.setTableMap("NETWORK", this, netAttrMgr);
nodeAttrMgr = new HashMap<String, CyDataTable>();
nodeAttrMgr.put(CyNetwork.DEFAULT_ATTRS, new
CyDataTableImpl(null, suid + " node", true,eh));
@@ -128,6 +133,7 @@
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn("name",String.class,false);
nodeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn("selected",Boolean.class,false);
+ tableMgr.setTableMap("NODE", this, nodeAttrMgr);
edgeAttrMgr = new HashMap<String, CyDataTable>();
edgeAttrMgr.put(CyNetwork.DEFAULT_ATTRS, new
CyDataTableImpl(null, suid + " edge", true,eh));
@@ -136,12 +142,8 @@
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn("name",String.class,false);
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn("selected",Boolean.class,false);
edgeAttrMgr.get(CyNetwork.DEFAULT_ATTRS).createColumn("interaction",String.class,false);
+ tableMgr.setTableMap("EDGE", this, edgeAttrMgr);
- dataTableMap = new HashMap<String, Map<String, CyDataTable>>();
- dataTableMap.put(NODE, nodeAttrMgr);
- dataTableMap.put(EDGE, edgeAttrMgr);
- dataTableMap.put(NETWORK, netAttrMgr);
-
eventHelper = eh;
subNets = new ArrayList<CySubNetwork>();
@@ -582,31 +584,6 @@
return getCyRow(CyNetwork.DEFAULT_ATTRS);
}
- /**
- * {...@inheritdoc}
- */
- public Map<String, CyDataTable> getNetworkCyDataTables() {
- return netAttrMgr;
- }
-
- /**
- * {...@inheritdoc}
- */
- public Map<String, CyDataTable> getNodeCyDataTables() {
- return nodeAttrMgr;
- }
-
- /**
- * {...@inheritdoc}
- */
- public Map<String, CyDataTable> getEdgeCyDataTables() {
- return edgeAttrMgr;
- }
-
- public Map<String, CyDataTable> getCyDataTables(String graphObjectType)
{
- return dataTableMap.get(graphObjectType);
- }
-
private Iterator<EdgePointer> edgesAdjacent(final NodePointer n, final
CyEdge.Type edgeType, final int inId) {
assert(n!=null);
Modified:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
===================================================================
---
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
2010-08-10 20:01:56 UTC (rev 21285)
+++
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/ArraySubGraph.java
2010-08-10 20:02:33 UTC (rev 21286)
@@ -232,31 +232,6 @@
/**
* {...@inheritdoc}
*/
- public Map<String,CyDataTable> getNetworkCyDataTables() {
- return parent.getNetworkCyDataTables();
- }
-
- /**
- * {...@inheritdoc}
- */
- public Map<String,CyDataTable> getNodeCyDataTables() {
- return parent.getNodeCyDataTables();
- }
-
- /**
- * {...@inheritdoc}
- */
- public Map<String,CyDataTable> getEdgeCyDataTables() {
- return parent.getEdgeCyDataTables();
- }
-
- public Map<String, CyDataTable> getCyDataTables(String graphObjectType)
{
- return parent.getCyDataTables(graphObjectType);
- }
-
- /**
- * {...@inheritdoc}
- */
public CyRow getCyRow(final String namespace) {
return parent.getCyRow(namespace);
}
Modified:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
===================================================================
---
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
2010-08-10 20:01:56 UTC (rev 21285)
+++
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
2010-08-10 20:02:33 UTC (rev 21286)
@@ -38,6 +38,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyTableManager;
/**
@@ -46,17 +47,22 @@
public class CyNetworkFactoryImpl implements CyNetworkFactory {
private final CyEventHelper help;
+ private final CyTableManager mgr;
/**
* Creates a new CyNetworkFactoryImpl object.
*
* @param help An instance of CyEventHelper.
*/
- public CyNetworkFactoryImpl(final CyEventHelper help) {
+ public CyNetworkFactoryImpl(final CyEventHelper help, final
CyTableManager mgr) {
if (help == null)
throw new NullPointerException("CyEventHelper is null");
+ if (mgr == null)
+ throw new NullPointerException("CyTableManager is
null");
+
this.help = help;
+ this.mgr = mgr;
}
/**
@@ -64,7 +70,7 @@
*/
public CyNetwork getInstance() {
//return new MGraph(help);
- ArrayGraph net = new ArrayGraph(help);
+ ArrayGraph net = new ArrayGraph(help,mgr);
return net.getBaseNetwork();
}
}
Added:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/TableManager.java
===================================================================
---
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/TableManager.java
(rev 0)
+++
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/TableManager.java
2010-08-10 20:02:33 UTC (rev 21286)
@@ -0,0 +1,93 @@
+
+/*
+ Copyright (c) 2010, 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.List;
+import java.util.ArrayList;
+import java.util.Map;
+import java.util.HashMap;
+
+import org.cytoscape.model.CyDataTable;
+import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.CyNetwork;
+
+/**
+ * An interface describing a factory used for managing
+ * {...@link CyDataTable} objects. This class will be
+ * provided as a service through Spring/OSGi.
+ */
+public class TableManager implements CyTableManager {
+
+ private final Map<String, Map<CyNetwork, Map<String,CyDataTable>>> map;
+
+ public TableManager() {
+ map = new HashMap<String, Map<CyNetwork,
Map<String,CyDataTable>>>();
+ map.put( "NETWORK", new HashMap<CyNetwork,
Map<String,CyDataTable>>() );
+ map.put( "NODE", new HashMap<CyNetwork,
Map<String,CyDataTable>>() );
+ map.put( "EDGE", new HashMap<CyNetwork,
Map<String,CyDataTable>>() );
+ }
+
+ public Map<String,CyDataTable> getTableMap(String type, CyNetwork o) {
+ if ( o == null || type == null )
+ return null;
+
+ Map<CyNetwork, Map<String,CyDataTable>> tmap = map.get(type);
+
+ if ( tmap == null )
+ throw new IllegalArgumentException("no data tables of
type: " + type + " exist");
+
+ return map.get(type).get(o);
+ }
+
+ public void setTableMap(String type, CyNetwork net,
Map<String,CyDataTable> tm) {
+ if ( net == null )
+ throw new NullPointerException("CyNetwork is null");
+ if ( type == null )
+ throw new NullPointerException("Type is null");
+
+ if ( !map.containsKey(type) )
+ map.put(type, new HashMap<CyNetwork,
Map<String,CyDataTable>>());
+
+ Map<CyNetwork, Map<String,CyDataTable>> tmap = map.get(type);
+
+ if ( tm == null )
+ tmap.remove(net);
+ else
+ tmap.put(net,tm);
+ }
+
+}
Modified:
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-08-10 20:01:56 UTC (rev 21285)
+++
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-08-10 20:02:33 UTC (rev 21286)
@@ -9,30 +9,21 @@
<!-- Individual Service -->
<osgi:service id="cyNetworkFactoryService"
ref="cyNetworkFactory"
interface="org.cytoscape.model.CyNetworkFactory">
- <osgi:service-properties>
- <entry key="service.type" value="factory" />
- </osgi:service-properties>
</osgi:service>
<osgi:service id="cyDataTableFactoryService"
ref="cyDataTableFactory"
interface="org.cytoscape.model.CyDataTableFactory">
- <osgi:service-properties>
- <entry key="service.type" value="factory" />
- </osgi:service-properties>
</osgi:service>
<osgi:service id="cyRootNetworkFactoryService"
ref="cyRootNetworkFactory"
interface="org.cytoscape.model.subnetwork.CyRootNetworkFactory">
- <osgi:service-properties>
- <entry key="service.type" value="factory" />
- </osgi:service-properties>
</osgi:service>
<osgi:service id="cyEventHelperService"
ref="cyEventHelper"
interface="org.cytoscape.event.CyEventHelper">
- <osgi:service-properties>
- <entry key="service.type" value="helper" />
- </osgi:service-properties>
</osgi:service>
+ <osgi:service id="cyTableManagerService"
+ ref="cyTableManager"
interface="org.cytoscape.model.CyTableManager">
+ </osgi:service>
</beans>
Modified:
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2010-08-10 20:01:56 UTC (rev 21285)
+++
core3/model-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2010-08-10 20:02:33 UTC (rev 21286)
@@ -15,8 +15,12 @@
<context:annotation-config/>
+ <bean id="cyTableManager"
class="org.cytoscape.model.internal.TableManager">
+ </bean>
+
<bean id="cyNetworkFactory"
class="org.cytoscape.model.internal.CyNetworkFactoryImpl">
<constructor-arg ref="cyEventHelper" />
+ <constructor-arg ref="cyTableManager" />
</bean>
<bean id="cyDataTableFactory"
class="org.cytoscape.model.internal.CyDataTableFactoryImpl">
Added:
core3/model-impl/trunk/src/test/java/org/cytoscape/model/CyTableManagerTest.java
===================================================================
---
core3/model-impl/trunk/src/test/java/org/cytoscape/model/CyTableManagerTest.java
(rev 0)
+++
core3/model-impl/trunk/src/test/java/org/cytoscape/model/CyTableManagerTest.java
2010-08-10 20:02:33 UTC (rev 21286)
@@ -0,0 +1,59 @@
+/*
+ Copyright (c) 2008, 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;
+
+import org.cytoscape.model.internal.TableManager;
+
+/**
+ * DOCUMENT ME!
+ */
+public class CyTableManagerTest extends AbstractCyTableManagerTest {
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void setUp() {
+ super.setUp();
+ mgr = new TableManager();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void tearDown() {
+ mgr = null;
+ }
+}
Modified:
core3/model-impl/trunk/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
===================================================================
---
core3/model-impl/trunk/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
2010-08-10 20:01:56 UTC (rev 21285)
+++
core3/model-impl/trunk/src/test/java/org/cytoscape/model/TestCyNetworkFactory.java
2010-08-10 20:02:33 UTC (rev 21286)
@@ -40,6 +40,7 @@
//import org.cytoscape.model.internal.CyNetworkImpl;
//import org.cytoscape.model.internal.MGraph;
import org.cytoscape.model.internal.ArrayGraph;
+import org.cytoscape.model.internal.TableManager;
import org.cytoscape.event.DummyCyEventHelper;
import org.cytoscape.model.subnetwork.CyRootNetwork;
@@ -51,11 +52,11 @@
public static CyNetwork getInstance() {
//return new CyNetworkImpl(new DummyCyEventHelper());
//return new MGraph(new DummyCyEventHelper());
- return new ArrayGraph(new DummyCyEventHelper());
+ return new ArrayGraph(new DummyCyEventHelper(), new
TableManager());
}
public static CyRootNetwork getRootInstance() {
- return new ArrayGraph(new DummyCyEventHelper());
+ return new ArrayGraph(new DummyCyEventHelper(), new
TableManager());
}
}
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