Author: scooter
Date: 2012-01-26 10:27:23 -0800 (Thu, 26 Jan 2012)
New Revision: 28115
Added:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/CollapseGroupTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodeContextTaskFactory.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTaskFactory.java
core3/impl/trunk/group-view-impl/
core3/impl/trunk/group-view-impl/pom.xml
core3/impl/trunk/group-view-impl/src/
core3/impl/trunk/group-view-impl/src/main/
core3/impl/trunk/group-view-impl/src/main/java/
core3/impl/trunk/group-view-impl/src/main/java/org/
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/group/
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/group/view/
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/group/view/internal/
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/group/view/internal/CyActivator.java
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/group/view/internal/GroupViewCollapseHandler.java
Modified:
core3/impl/trunk/core-task-impl/pom.xml
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
core3/impl/trunk/group-impl/src/main/java/org/cytoscape/group/internal/CyGroupImpl.java
core3/impl/trunk/group-impl/src/test/java/org/cytoscape/group/TestCyGroupFactory.java
Log:
Next round of group changes. Not ready for prime-time, yet.
Modified: core3/impl/trunk/core-task-impl/pom.xml
===================================================================
--- core3/impl/trunk/core-task-impl/pom.xml 2012-01-26 18:27:21 UTC (rev
28114)
+++ core3/impl/trunk/core-task-impl/pom.xml 2012-01-26 18:27:23 UTC (rev
28115)
@@ -90,6 +90,10 @@
<groupId>org.cytoscape</groupId>
<artifactId>io-api</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>group-api</artifactId>
+ </dependency>
<dependency>
<groupId>org.cytoscape</groupId>
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2012-01-26 18:27:21 UTC (rev 28114)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2012-01-26 18:27:23 UTC (rev 28115)
@@ -7,6 +7,8 @@
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.datasource.DataSourceManager;
import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.group.CyGroupFactory;
+import org.cytoscape.group.CyGroupManager;
import org.cytoscape.io.read.CyNetworkReaderManager;
import org.cytoscape.io.read.CySessionReaderManager;
import org.cytoscape.io.read.CyTableReaderManager;
@@ -51,6 +53,8 @@
import org.cytoscape.task.internal.export.table.ExportEdgeTableTaskFactory;
import org.cytoscape.task.internal.export.table.ExportNodeTableTaskFactory;
import org.cytoscape.task.internal.export.vizmap.ExportVizmapTaskFactory;
+import org.cytoscape.task.internal.group.GroupNodesTaskFactory;
+import org.cytoscape.task.internal.group.GroupNodeContextTaskFactory;
import org.cytoscape.task.internal.hide.HideSelectedEdgesTaskFactory;
import org.cytoscape.task.internal.hide.HideSelectedNodesTaskFactory;
import org.cytoscape.task.internal.hide.HideSelectedTaskFactory;
@@ -156,6 +160,9 @@
LoadAttributesFileTaskFactoryImpl loadAttrsFileTaskFactory =
new LoadAttributesFileTaskFactoryImpl(cyDataTableReaderManagerServiceRef);
LoadAttributesURLTaskFactoryImpl loadAttrsURLTaskFactory = new
LoadAttributesURLTaskFactoryImpl(cyDataTableReaderManagerServiceRef);
+
+ CyGroupManager cyGroupManager = getService(bc,
CyGroupManager.class);
+ CyGroupFactory cyGroupFactory = getService(bc,
CyGroupFactory.class);
LoadVizmapFileTaskFactoryImpl loadVizmapFileTaskFactory = new
LoadVizmapFileTaskFactoryImpl(vizmapReaderManagerServiceRef,visualMappingManagerServiceRef,synchronousTaskManagerServiceRef);
@@ -221,6 +228,10 @@
BioGridPreprocessor bioGridPreprocessor = new
BioGridPreprocessor(cyPropertyServiceRef,cyApplicationConfigurationServiceRef);
ConnectSelectedNodesTaskFactory connectSelectedNodesTaskFactory
= new
ConnectSelectedNodesTaskFactory(undoSupportServiceRef,cyApplicationManagerServiceRef,cyEventHelperRef);
+
+ GroupNodesTaskFactory groupNodesTaskFactory = new
GroupNodesTaskFactory(cyGroupManager, cyGroupFactory);
+ GroupNodeContextTaskFactory collapseGroupTaskFactory = new
GroupNodeContextTaskFactory(cyGroupManager, true);
+ GroupNodeContextTaskFactory expandGroupTaskFactory = new
GroupNodeContextTaskFactory(cyGroupManager, false);
Properties loadNetworkFileTaskFactoryProps = new Properties();
@@ -690,6 +701,25 @@
registerServiceListener(bc,subnetworkBuilderUtil,"addProcessor","removeProcessor",InteractionFilePreprocessor.class);
registerServiceListener(bc,subnetworkBuilderUtil,"addFactory","removeFactory",VisualMappingFunctionFactory.class);
+
+ Properties groupNodesTaskFactoryProps = new Properties();
+ groupNodesTaskFactoryProps.setProperty("title","Group Nodes");
+ groupNodesTaskFactoryProps.setProperty("tooltip","Group
Selected Nodes Together");
+ groupNodesTaskFactoryProps.setProperty("preferredAction",
"NEW");
+
registerService(bc,groupNodesTaskFactory,NetworkViewTaskFactory.class,
groupNodesTaskFactoryProps);
+
+ Properties collapseGroupTaskFactoryProps = new Properties();
+ collapseGroupTaskFactoryProps.setProperty("title","Collapse
Group");
+ collapseGroupTaskFactoryProps.setProperty("tooltip","Collapse
Grouped Nodes");
+ collapseGroupTaskFactoryProps.setProperty("preferredAction",
"NEW");
+
registerService(bc,collapseGroupTaskFactory,NodeViewTaskFactory.class,
collapseGroupTaskFactoryProps);
+
+ Properties expandGroupTaskFactoryProps = new Properties();
+ expandGroupTaskFactoryProps.setProperty("title","Expand Group");
+ expandGroupTaskFactoryProps.setProperty("tooltip","Expand
Group");
+ expandGroupTaskFactoryProps.setProperty("preferredAction",
"NEW");
+
registerService(bc,expandGroupTaskFactory,NodeViewTaskFactory.class,
expandGroupTaskFactoryProps);
+
//ShowWelcomeScreenTask ws = new ShowWelcomeScreenTask();
//registerAllServices(bc, ws, new Properties());
Added:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/CollapseGroupTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/CollapseGroupTask.java
(rev 0)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/CollapseGroupTask.java
2012-01-26 18:27:23 UTC (rev 28115)
@@ -0,0 +1,72 @@
+/*
+ File: SelectFirstNeighborsNodeViewTask.java
+
+ Copyright (c) 2006, 2010, 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.task.internal.group;
+
+import java.util.List;
+
+import org.cytoscape.group.CyGroup;
+import org.cytoscape.group.CyGroupFactory;
+import org.cytoscape.group.CyGroupManager;
+
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTableUtil;
+
+import org.cytoscape.view.model.CyNetworkView;
+
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+
+public class CollapseGroupTask extends AbstractTask {
+ private CyNetwork net;
+ private CyGroupManager mgr;
+ private CyGroup group;
+ private boolean collapse;
+
+ public CollapseGroupTask(CyNetwork net, CyGroup group, CyGroupManager
manager, boolean collapse) {
+ if (net == null)
+ throw new NullPointerException("network is null");
+ if (group == null)
+ throw new NullPointerException("group is null");
+ this.net = net;
+ this.mgr = manager;
+ this.group = group;
+ this.collapse = collapse;
+ }
+
+ public void run(TaskMonitor tm) throws Exception {
+ tm.setProgress(0.0);
+ if (collapse)
+ group.collapse(net);
+ else
+ group.expand(net);
+ tm.setProgress(1.0d);
+ }
+}
Added:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodeContextTaskFactory.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodeContextTaskFactory.java
(rev 0)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodeContextTaskFactory.java
2012-01-26 18:27:23 UTC (rev 28115)
@@ -0,0 +1,87 @@
+/*
+ File: SelectFirstNeighborsNodeViewTaskFactory.java
+
+ Copyright (c) 2006, 2010, 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.task.internal.group;
+
+import org.cytoscape.group.CyGroupManager;
+import org.cytoscape.group.CyGroup;
+import org.cytoscape.task.AbstractNodeViewTaskFactory;
+import org.cytoscape.work.TaskFactoryPredicate;
+import org.cytoscape.work.TaskIterator;
+
+import java.util.List;
+
+public class GroupNodeContextTaskFactory extends AbstractNodeViewTaskFactory
implements TaskFactoryPredicate {
+ private CyGroupManager mgr;
+ private boolean collapse;
+
+ public GroupNodeContextTaskFactory(CyGroupManager mgr, boolean
collapse) {
+ super();
+ this.mgr = mgr;
+ this.collapse = collapse;
+ }
+
+ public boolean isReady() {
+ if (collapse) {
+ // We're ready to collapse if the node view is in a
group
+ if (getExpandedGroupForNode() != null)
+ return true;
+ } else {
+ // We're ready to expand if the node view is a group
+ CyGroup group = mgr.getGroup(nodeView.getModel(),
netView.getModel());
+ if (group != null &&
group.isCollapsed(netView.getModel()))
+ return true;
+ }
+ return false;
+ }
+
+ public TaskIterator createTaskIterator() {
+ CyGroup group;
+ if (collapse)
+ group = getExpandedGroupForNode();
+ else
+ group = mgr.getGroup(nodeView.getModel(),
netView.getModel());
+
+ return new TaskIterator(new
CollapseGroupTask(netView.getModel(), group, mgr, collapse));
+ }
+
+ private CyGroup getExpandedGroupForNode() {
+ List<CyGroup> groups =
mgr.getGroupsForNode(nodeView.getModel());
+ if (groups == null || groups.size() == 0)
+ return null;
+
+ // Return the first uncollapsed group in this network
+ for (CyGroup group: groups) {
+ if (group.isInNetwork(netView.getModel()) &&
+ !group.isCollapsed(netView.getModel()))
+ return group;
+ }
+ return null;
+ }
+}
Added:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTask.java
(rev 0)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTask.java
2012-01-26 18:27:23 UTC (rev 28115)
@@ -0,0 +1,71 @@
+/*
+ File: SelectFirstNeighborsNodeViewTask.java
+
+ Copyright (c) 2006, 2010, 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.task.internal.group;
+
+import java.util.List;
+
+import org.cytoscape.group.CyGroup;
+import org.cytoscape.group.CyGroupFactory;
+import org.cytoscape.group.CyGroupManager;
+
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTableUtil;
+
+import org.cytoscape.view.model.CyNetworkView;
+
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+
+public class GroupNodesTask extends AbstractTask {
+ private CyNetwork net;
+ private CyGroupManager mgr;
+ private CyGroupFactory factory;
+
+ public GroupNodesTask(CyNetworkView netView, CyGroupManager mgr,
CyGroupFactory factory) {
+ if (netView == null)
+ throw new NullPointerException("network view is null");
+ this.net = netView.getModel();
+ this.mgr = mgr;
+ this.factory = factory;
+ }
+
+ public void run(TaskMonitor tm) throws Exception {
+ tm.setProgress(0.0);
+
+ // Get all of the selected nodes
+ final List<CyNode> selNodes = CyTableUtil.getNodesInState(net,
CyNetwork.SELECTED, true);
+
+ // At some point, we'll want to seriously think about only
adding those edges that are also
+ // selected, but for now....
+ CyGroup group = factory.createGroup(net, selNodes, null);
+ tm.setProgress(1.0d);
+ }
+}
Added:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTaskFactory.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTaskFactory.java
(rev 0)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTaskFactory.java
2012-01-26 18:27:23 UTC (rev 28115)
@@ -0,0 +1,50 @@
+/*
+ File: SelectFirstNeighborsNodeViewTaskFactory.java
+
+ Copyright (c) 2006, 2010, 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.task.internal.group;
+
+import org.cytoscape.group.CyGroupFactory;
+import org.cytoscape.group.CyGroupManager;
+import org.cytoscape.task.AbstractNetworkViewTaskFactory;
+import org.cytoscape.work.TaskIterator;
+
+public class GroupNodesTaskFactory extends AbstractNetworkViewTaskFactory {
+ private CyGroupManager mgr;
+ private CyGroupFactory groupFactory;
+
+ public GroupNodesTaskFactory(CyGroupManager mgr, CyGroupFactory
groupFactory) {
+ super();
+ this.mgr = mgr;
+ this.groupFactory = groupFactory;
+ }
+
+ public TaskIterator createTaskIterator() {
+ return new TaskIterator(new GroupNodesTask(view, mgr,
groupFactory));
+ }
+}
Modified:
core3/impl/trunk/group-impl/src/main/java/org/cytoscape/group/internal/CyGroupImpl.java
===================================================================
---
core3/impl/trunk/group-impl/src/main/java/org/cytoscape/group/internal/CyGroupImpl.java
2012-01-26 18:27:21 UTC (rev 28114)
+++
core3/impl/trunk/group-impl/src/main/java/org/cytoscape/group/internal/CyGroupImpl.java
2012-01-26 18:27:23 UTC (rev 28115)
@@ -33,6 +33,7 @@
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
+import java.util.ListIterator;
import java.util.Map;
import java.util.Set;
@@ -43,16 +44,25 @@
import org.cytoscape.group.events.GroupAddedToNetworkEvent;
import org.cytoscape.group.events.GroupChangedEvent;
import org.cytoscape.group.events.GroupCollapsedEvent;
+import org.cytoscape.group.events.GroupAboutToCollapseEvent;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.subnetwork.CyRootNetwork;
import org.cytoscape.model.subnetwork.CySubNetwork;
+// TODO: Update attributes
+
class CyGroupImpl implements CyGroup {
+ final private static String CHILDREN_ATTR = "NumChildren";
+ final private static String DESCENDENTS_ATTR = "NumDescendents";
+ final private static String GROUP_STATE_ATTR = "__groupState";
+ final private static String ISMETA_EDGE_ATTR = "__isMetaEdge";
+
final private CyEventHelper cyEventHelper;
final private CyGroupManager mgr;
@@ -119,14 +129,6 @@
// This is an external edge,
which means that we need to create
// a corresponding meta-edge
externalEdges.add(e);
- CyNode source = e.getSource();
- CyNode target = e.getTarget();
- boolean directed =
e.isDirected();
- if (nodeMap.contains(source))
- source = groupNode;
- else
- target = groupNode;
-
metaEdges.add(rootNetwork.addEdge(source, target, directed));
}
}
}
@@ -134,6 +136,13 @@
// Create the subnetwork
groupNet = rootNetwork.addSubNetwork(nodes, edges);
+
+ // Update our meta-edges
+ updateMetaEdges(true);
+
+ // Initialize our attributes
+ // TODO: updateCountAttributes();
+ // TODO: setGroupStateAttribute(false);
}
/**
@@ -153,18 +162,18 @@
}
/**
- * @see org.cytoscape.group.CyGroup#getContainedEdgeList()
+ * @see org.cytoscape.group.CyGroup#getInternalEdgeList()
*/
@Override
- public List<CyEdge> getInteriorEdgeList() {
+ public List<CyEdge> getInternalEdgeList() {
return groupNet.getEdgeList();
}
/**
- * @see org.cytoscape.group.CyGroup#getExteriorEdgeList()
+ * @see org.cytoscape.group.CyGroup#getExternalEdgeList()
*/
@Override
- public Set<CyEdge> getExteriorEdgeList() {
+ public Set<CyEdge> getExternalEdgeList() {
return externalEdges;
}
@@ -184,7 +193,12 @@
if (!rootNetwork.containsNode(node))
throwIllegalArgumentException("Can only add a node in
the same network tree");
groupNet.addNode(node);
- cyEventHelper.fireEvent(new GroupChangedEvent(CyGroupImpl.this,
node, GroupChangedEvent.ChangeType.NODE_ADDED));
+
+ if (!batchUpdate) {
+ updateMetaEdges(false);
+ // TODO: updateCountAttributes();
+ cyEventHelper.fireEvent(new
GroupChangedEvent(CyGroupImpl.this, node,
GroupChangedEvent.ChangeType.NODE_ADDED));
+ }
}
/**
@@ -234,6 +248,8 @@
addExternalEdge(e);
}
}
+ updateMetaEdges(false);
+ // TODO: updateCountAttributes();
batchUpdate = false;
cyEventHelper.fireEvent(new GroupChangedEvent(CyGroupImpl.this,
nodes, GroupChangedEvent.ChangeType.NODES_ADDED));
}
@@ -277,6 +293,8 @@
groupNet.removeEdges(netEdges);
groupNet.removeNodes(nodes);
batchUpdate = false;
+ updateMetaEdges(false);
+ // TODO: updateCountAttributes();
cyEventHelper.fireEvent(new GroupChangedEvent(CyGroupImpl.this,
nodes, GroupChangedEvent.ChangeType.NODES_REMOVED));
}
@@ -361,28 +379,38 @@
if (!networkSet.contains(net))
return; // We're not in that network
+ System.out.println("Collapsing -- firing");
+ cyEventHelper.fireEvent(new
GroupAboutToCollapseEvent(CyGroupImpl.this, net, true));
+
CySubNetwork subnet = (CySubNetwork) net;
// Collapse it.
// Remove all of the nodes from the target network
+ System.out.println("Collapsing -- removing
"+getNodeList().size()+" nodes from "+subnet);
subnet.removeNodes(getNodeList());
+ System.out.println("Collapsing -- adding group node");
subnet.addNode(groupNode);
// Add the group node and it's edges
List<CyEdge> groupNodeEdges =
rootNetwork.getAdjacentEdgeList(groupNode, CyEdge.Type.ANY);
+ System.out.println("Collapsing -- adding
"+groupNodeEdges.size()+" edges");
for (CyEdge e: groupNodeEdges)
subnet.addEdge(e);
Set<CyNode> memberNodes = new HashSet<CyNode>(getNodeList());
+ System.out.println("Collapsing -- adding
"+getMetaEdgeList().size()+" MetaEdges");
// Add the meta-edges
for (CyEdge e: getMetaEdgeList()) {
subnet.addEdge(e);
}
collapseSet.add(net);
+ System.out.println("Collapsed -- firing");
cyEventHelper.fireEvent(new
GroupCollapsedEvent(CyGroupImpl.this, net, true));
+ // Update attributes?
+ // TODO: setGroupStateAttribute(net, true);
}
/**
@@ -396,6 +424,8 @@
if (!networkSet.contains(net))
return; // We're not in that network
+ cyEventHelper.fireEvent(new
GroupAboutToCollapseEvent(CyGroupImpl.this, net, false));
+
CySubNetwork subnet = (CySubNetwork) net;
// Expand it.
@@ -407,11 +437,11 @@
subnet.addNode(n);
// Add all of the interior edges in
- for (CyEdge e: getInteriorEdgeList())
+ for (CyEdge e: getInternalEdgeList())
subnet.addEdge(e);
// Add all of the exterior edges in
- for (CyEdge e: getExteriorEdgeList()) {
+ for (CyEdge e: getExternalEdgeList()) {
// We need to be careful to only add the edge in
// if both the edge and the target are available
// since the target node might have been part of a
@@ -422,6 +452,8 @@
collapseSet.remove(net);
cyEventHelper.fireEvent(new
GroupCollapsedEvent(CyGroupImpl.this, net, false));
+ // Update attributes?
+ // TODO: setGroupStateAttribute(net, false);
}
/**
@@ -487,4 +519,188 @@
batchUpdate = false;
throw new IllegalArgumentException(message);
}
+
+ /**
+ * This method is the central method for the creation and maintenance
of a
+ * meta-node. Essentially, it is responsible for creating all of the
meta-edges
+ * that connect this meta-node to external nodes.
+ *
+ * Basic approach:
+ * for each external edge:
+ * add a meta-edge to the parter
+ * if the partner is a group and the group is in our network:
+ * add ourselves to the group's outer edges list (recursively)
+ * add ourselves to the partner's meta edge list
+ * if the partner is in a group:
+ * add ourselves to the group's meta edge list
+ */
+ private void updateMetaEdges(boolean ignoreMetaEdges) {
+ metaEdges = new HashSet<CyEdge>();
+
+ // We need to use a list iterator because we might need to add
new
+ // edges to our outer edge list and we want to add them to the
+ // iterator to re-examine them
+ ListIterator<CyEdge> iterator = (new
ArrayList<CyEdge>(externalEdges)).listIterator();
+ while (iterator.hasNext()) {
+ CyEdge edge = iterator.next();
+ CyNode node = getPartner(edge);
+
+ if (ignoreMetaEdges && isMeta(edge)) {
+ this.addMetaEdge(edge);
+ continue;
+ }
+
+ // If the edge is already on our group node, don't
create a metaedge for it
+ if (edge.getSource() == groupNode || edge.getTarget()
== groupNode)
+ continue;
+
+ // Create the meta-edge to the external node, but
maintain the directionality
+ // of the original edge
+ CyEdge metaEdge = createMetaEdge(edge, node, groupNode);
+
+ for (CyNetwork net: networkSet) {
+ CyGroup metaPartner = mgr.getGroup(node, net);
+ if (metaPartner != null) {
+ // Recursively add links to the
appropriate children
+ addPartnerEdges(metaPartner, net);
+
((CyGroupImpl)metaPartner).addMetaEdge(metaEdge);
+ }
+
+ // Now, handle the case where the partner is a
member of one or more groups
+ List<CyGroup> nodeGroups =
mgr.getGroupsForNode(node);
+ if (nodeGroups != null && nodeGroups.size() >
0) {
+ addPartnerMetaEdges(net, edge, node,
metaEdge);
+ }
+ }
+ }
+ }
+
+ protected int getDescendents(CyNetwork net) {
+ int nDescendents = groupNet.getNodeCount();
+ for (CyNode node: groupNet.getNodeList()) {
+ CyGroup group = mgr.getGroup(node, net);
+ if (group != null)
+ nDescendents +=
((CyGroupImpl)group).getDescendents(net);
+ }
+ return nDescendents;
+ }
+
+ // Find the edge in our partner that links to us
+ protected void addPartnerEdges(CyGroup metaPartner, CyNetwork net) {
+ Set<CyEdge> partnerEdges = metaPartner.getExternalEdgeList();
+ Set<CyEdge> newEdges = new HashSet<CyEdge>();
+ for (CyEdge edge: partnerEdges) {
+ CyNode source = edge.getSource();
+ CyNode target = edge.getTarget();
+ CyNode partner = null;
+ boolean directed = edge.isDirected();
+ if (groupNet.containsNode(target)) {
+ source = groupNode;
+ partner = target;
+ } else if (groupNet.containsNode(source)) {
+ target = groupNode;
+ partner = source;
+ } else {
+ continue;
+ }
+
+ // Create a new edge
+ CyEdge newEdge = rootNetwork.addEdge(source, target,
directed);
+ newEdges.add(newEdge);
+
+ externalEdges.add(edge);
+
+ CyGroup partnerMeta = mgr.getGroup(partner, net);
+ if (partnerMeta != null)
+ addPartnerEdges(partnerMeta, net);
+
+ metaEdges.add(newEdge);
+ }
+
+ for (CyEdge edge: newEdges) {
metaPartner.addExternalEdge(edge); }
+ }
+
+ private CyEdge createMetaEdge(CyEdge edge, CyNode node, CyNode
groupNode) {
+ CyEdge metaEdge = null;
+ if (isIncoming(edge))
+ metaEdge = rootNetwork.addEdge(node, groupNode,
edge.isDirected());
+ else
+ metaEdge = rootNetwork.addEdge(groupNode, node,
edge.isDirected());
+
+ // Add the name and mark this as a meta-edge
+ String edgeName = rootNetwork.getRow(edge).get(CyNetwork.NAME,
String.class);
+ rootNetwork.getRow(metaEdge).set(CyNetwork.NAME,
"meta-"+edgeName);
+ createIfNecessary(metaEdge, CyNetwork.HIDDEN_ATTRS,
ISMETA_EDGE_ATTR, Boolean.class);
+ rootNetwork.getRow(metaEdge,
CyNetwork.HIDDEN_ATTRS).set(ISMETA_EDGE_ATTR, Boolean.TRUE);
+
+ return metaEdge;
+ }
+
+ private void addPartnerMetaEdges(CyNetwork net, CyEdge connectingEdge,
+ CyNode partnerNode, CyEdge metaEdge) {
+ for (CyGroup partnerGroup: mgr.getGroupsForNode(partnerNode)) {
+ // Are we partners in this network?
+ if (!partnerGroup.getNetworkSet().contains(net))
+ continue;
+
+ CyEdge metaMetaEdge = null;
+ CyGroupImpl partner = (CyGroupImpl)partnerGroup;
+ if (isIncoming(connectingEdge)) {
+ metaMetaEdge = createMetaEdge(connectingEdge,
partnerGroup.getGroupNode(), this.groupNode);
+ } else {
+ metaMetaEdge = createMetaEdge(connectingEdge,
this.groupNode, partnerGroup.getGroupNode());
+ }
+
+ partner.addMetaEdge(metaMetaEdge);
+ partner.addMetaEdge(metaEdge);
+
+ // Now, get our partner's metaEdges and add any that
point to our children
+ for (CyEdge outerEdge: partner.getMetaEdgeList()) {
+ if (isConnectingEdge(outerEdge))
+ addExternalEdge(outerEdge);
+ }
+
+ }
+ }
+
+ private boolean isMeta(CyEdge edge) {
+ Boolean meta = rootNetwork.getRow(edge, CyNetwork.HIDDEN_ATTRS).
+ get(ISMETA_EDGE_ATTR, Boolean.class,
Boolean.FALSE);
+
+ return meta.booleanValue();
+ }
+
+ private boolean isConnectingEdge(CyEdge edge) {
+ CyNode source = edge.getSource();
+ CyNode target = edge.getTarget();
+ if (groupNet.containsNode(source) ||
groupNet.containsNode(target))
+ return true;
+ return false;
+ }
+
+ private boolean isIncoming(CyEdge edge) {
+ CyNode source = edge.getSource();
+ CyNode target = edge.getTarget();
+ if (source.equals(groupNode) || groupNet.containsNode(source))
+ return false;
+ return true;
+ }
+
+ private CyNode getPartner(CyEdge edge) {
+ CyNode source = edge.getSource();
+ CyNode target = edge.getTarget();
+ if (source.equals(groupNode) || groupNet.containsNode(source))
+ return target;
+ return source;
+ }
+
+ private void createIfNecessary(CyTableEntry entry, String tableName,
+ String attribute, Class type) {
+ CyTable table = rootNetwork.getRow(entry, tableName).getTable();
+ if (table.getColumn(attribute) == null)
+ table.createColumn(attribute, type, false);
+
+ return;
+ }
+
}
Modified:
core3/impl/trunk/group-impl/src/test/java/org/cytoscape/group/TestCyGroupFactory.java
===================================================================
---
core3/impl/trunk/group-impl/src/test/java/org/cytoscape/group/TestCyGroupFactory.java
2012-01-26 18:27:21 UTC (rev 28114)
+++
core3/impl/trunk/group-impl/src/test/java/org/cytoscape/group/TestCyGroupFactory.java
2012-01-26 18:27:23 UTC (rev 28115)
@@ -93,18 +93,18 @@
CyGroup group1 = factory.createGroup(network, groupNodes, null);
assertNotNull(group1);
assertTrue("group1 node count = 3", group1.getNodeList().size()
== 3);
- assertTrue("group1 internal edge count = 2",
group1.getInteriorEdgeList().size() == 2);
- assertTrue("group1 external edge count = 3",
group1.getExteriorEdgeList().size() == 3);
+ assertTrue("group1 internal edge count = 2",
group1.getInternalEdgeList().size() == 2);
+ assertTrue("group1 external edge count = 3",
group1.getExternalEdgeList().size() == 3);
CyGroup group2 = factory.createGroup(network, groupNodes, new
ArrayList<CyEdge>());
assertNotNull(group2);
assertTrue("group2 node count = 3", group2.getNodeList().size()
== 3);
- assertTrue("group2 internal edge count = 0",
group2.getInteriorEdgeList().size() == 0);
- assertTrue("group2 external edge count = 0",
group2.getExteriorEdgeList().size() == 0);
+ assertTrue("group2 internal edge count = 0",
group2.getInternalEdgeList().size() == 0);
+ assertTrue("group2 external edge count = 0",
group2.getExternalEdgeList().size() == 0);
CyGroup group3 = factory.createGroup(network, groupNodes,
groupEdges);
assertNotNull(group3);
assertTrue("group3 node count = 3", group3.getNodeList().size()
== 3);
- assertTrue("group3 internal edge count = 2",
group3.getInteriorEdgeList().size() == 2);
- assertTrue("group3 external edge count = 2",
group3.getExteriorEdgeList().size() == 2);
+ assertTrue("group3 internal edge count = 2",
group3.getInternalEdgeList().size() == 2);
+ assertTrue("group3 external edge count = 2",
group3.getExternalEdgeList().size() == 2);
}
}
Added: core3/impl/trunk/group-view-impl/pom.xml
===================================================================
--- core3/impl/trunk/group-view-impl/pom.xml (rev 0)
+++ core3/impl/trunk/group-view-impl/pom.xml 2012-01-26 18:27:23 UTC (rev
28115)
@@ -0,0 +1,138 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";>
+ <parent>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>impl-parent</artifactId>
+ <version>3.0.0-alpha8-SNAPSHOT</version>
+ </parent>
+
+ <properties>
+ <bundle.symbolicName>org.cytoscape.group-view-impl</bundle.symbolicName>
+ <bundle.namespace>org.cytoscape.group.view.internal</bundle.namespace>
+ </properties>
+
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>group-view-impl</artifactId>
+
+ <name>${bundle.symbolicName} [${bundle.namespace}]</name>
+
+ <packaging>bundle</packaging>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>${maven-surefire-plugin.version}</version>
+ <configuration>
+ <redirectTestOutputToFile>true</redirectTestOutputToFile>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+ <version>${maven-bundle-plugin.version}</version>
+ <extensions>true</extensions>
+ <configuration>
+ <instructions>
+ <Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
+ <Bundle-Version>${project.version}</Bundle-Version>
+ <Export-Package>!${bundle.namespace}.*</Export-Package>
+
<Private-Package>${bundle.namespace}.*</Private-Package>
+
<Bundle-Activator>${bundle.namespace}.CyActivator</Bundle-Activator>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+
<url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+
<url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>group-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>group-api</artifactId>
+ <scope>test</scope>
+ <type>test-jar</type>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>model-impl</artifactId>
+ <scope>test</scope>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>model-impl</artifactId>
+ <scope>test</scope>
+ <type>test-jar</type>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>event-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>model-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>viewmodel-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>presentation-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>vizmap-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>service-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>com.googlecode.guava-osgi</groupId>
+ <artifactId>guava-osgi</artifactId>
+ <version>9.0.0</version>
+ </dependency>
+ </dependencies>
+</project>
+
Added:
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/group/view/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/group/view/internal/CyActivator.java
(rev 0)
+++
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/group/view/internal/CyActivator.java
2012-01-26 18:27:23 UTC (rev 28115)
@@ -0,0 +1,40 @@
+
+package org.cytoscape.group.view.internal;
+
+import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.service.util.CyServiceRegistrar;
+
+import org.osgi.framework.BundleContext;
+
+import org.cytoscape.group.CyGroupManager;
+import org.cytoscape.group.events.GroupAboutToCollapseListener;
+import org.cytoscape.group.events.GroupCollapsedListener;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+
+
+import org.cytoscape.service.util.AbstractCyActivator;
+
+import java.util.Properties;
+
+
+public class CyActivator extends AbstractCyActivator {
+ public CyActivator() {
+ super();
+ }
+
+ public void start(BundleContext bc) {
+ CyEventHelper cyEventHelperServiceRef =
getService(bc,CyEventHelper.class);
+ CyServiceRegistrar cyServiceRegistrarServiceRef =
getService(bc,CyServiceRegistrar.class);
+ CyGroupManager cyGroupManager =
getService(bc,CyGroupManager.class);
+ CyNetworkViewManager cyNetworkViewManager =
getService(bc,CyNetworkViewManager.class);
+ VisualMappingManager styleManager =
getService(bc,VisualMappingManager.class);
+
+ GroupViewCollapseHandler gvcHandler =
+ new GroupViewCollapseHandler(cyGroupManager,
cyNetworkViewManager, styleManager);
+
+
registerService(bc,gvcHandler,GroupAboutToCollapseListener.class, new
Properties());
+ registerService(bc,gvcHandler,GroupCollapsedListener.class, new
Properties());
+ }
+}
+
Added:
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/group/view/internal/GroupViewCollapseHandler.java
===================================================================
---
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/group/view/internal/GroupViewCollapseHandler.java
(rev 0)
+++
core3/impl/trunk/group-view-impl/src/main/java/org/cytoscape/group/view/internal/GroupViewCollapseHandler.java
2012-01-26 18:27:23 UTC (rev 28115)
@@ -0,0 +1,227 @@
+/*
+ File: GroupViewCollapseHandler.java
+
+ Copyright (c) 2006, 2010, 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.group.view.internal;
+
+import java.awt.Dimension;
+import java.util.List;
+
+import org.cytoscape.group.CyGroup;
+import org.cytoscape.group.CyGroupManager;
+import org.cytoscape.group.events.GroupAboutToCollapseEvent;
+import org.cytoscape.group.events.GroupAboutToCollapseListener;
+import org.cytoscape.group.events.GroupCollapsedEvent;
+import org.cytoscape.group.events.GroupCollapsedListener;
+
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.model.VisualProperty;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyle;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Handle the view portion of group collapse/expand
+ */
+public class GroupViewCollapseHandler implements GroupAboutToCollapseListener,
+ GroupCollapsedListener
+{
+
+ private final CyGroupManager cyGroupManager;
+ private final CyNetworkViewManager cyNetworkViewManager;
+ private final VisualMappingManager cyStyleManager;
+ private static final Logger logger =
LoggerFactory.getLogger(GroupViewCollapseHandler.class);
+ private static final VisualProperty<Double> xLoc =
MinimalVisualLexicon.NODE_X_LOCATION;
+ private static final VisualProperty<Double> yLoc =
MinimalVisualLexicon.NODE_Y_LOCATION;
+
+ private static final String X_OFFSET_ATTR = "__xOffset";
+ private static final String Y_OFFSET_ATTR = "__yOffset";
+ private static final String X_LOCATION_ATTR = "__xLocation";
+ private static final String Y_LOCATION_ATTR = "__yLocation";
+
+ /**
+ *
+ * @param cyEventHelper
+ */
+ public GroupViewCollapseHandler(final CyGroupManager groupManager,
+ final CyNetworkViewManager viewManager,
+ final VisualMappingManager
styleManager) {
+ this.cyGroupManager = groupManager;
+ this.cyNetworkViewManager = viewManager;
+ this.cyStyleManager = styleManager;
+ }
+
+ public void handleEvent(GroupAboutToCollapseEvent e) {
+ CyNetwork network = e.getNetwork();
+ CyGroup group = e.getSource();
+ CyRootNetwork rootNetwork = group.getRootNetwork();
+ CyNetworkView view =
cyNetworkViewManager.getNetworkView(network);
+
+ if (e.collapsing()) {
+ System.out.println("Collapsing");
+ // Calculate the center position of all of the
+ // member nodes
+ Dimension center = calculateCenter(view,
group.getNodeList());
+
+ System.out.println("Center: "+center);
+
+ // Save it in the groupNode attribute
+ updateGroupLocation(rootNetwork, group.getGroupNode(),
center);
+
+ // For each member node,
+ // calculate the offset for each member node from
the center
+ // save it in the node's attribute
+ for (CyNode node: group.getNodeList()) {
+ Dimension offset = calculateOffset(center,
view, node);
+ updateNodeOffset(rootNetwork, node, offset);
+ }
+ } else {
+ System.out.println("Expanding");
+ // Get the current position of the groupNode
+ View<CyNode>nView =
view.getNodeView(group.getGroupNode());
+ double x = nView.getVisualProperty(xLoc);
+ double y = nView.getVisualProperty(yLoc);
+ // Save it in the groupNode attribute
+ updateGroupLocation(rootNetwork, group.getGroupNode(),
getDim(x,y));
+ }
+ }
+
+ public void handleEvent(GroupCollapsedEvent e) {
+ CyNetwork network = e.getNetwork();
+ CyGroup group = e.getSource();
+ CyNetworkView view =
cyNetworkViewManager.getNetworkView(network);
+ CyRootNetwork rootNetwork = group.getRootNetwork();
+ VisualStyle viewStyle = cyStyleManager.getVisualStyle(view);
+
+ if (e.collapsed()) {
+ System.out.println("Collapsed");
+ // Get the location to move the group node to
+ Dimension d = getLocation(rootNetwork,
group.getGroupNode());
+ // Move it.
+ moveNode(view, group.getGroupNode(), d);
+ System.out.println("Done");
+ } else {
+ System.out.println("Expanded");
+ // Get the location of the group node before it went
away
+ Dimension center = getLocation(rootNetwork,
group.getGroupNode());
+ // Now, get the offsets for each of the member nodes
and move them
+ for (CyNode node: group.getNodeList()) {
+ Dimension location =
getOffsetLocation(rootNetwork, node, center);
+ moveNode(view, node, location);
+ }
+ System.out.println("Done");
+ }
+ // viewStyle.apply(view);
+ }
+
+ private Dimension calculateCenter(CyNetworkView view, List<CyNode>
nodeList) {
+ double xCenter = 0.0d;
+ double yCenter = 0.0d;
+
+ for (CyNode node: nodeList) {
+ View<CyNode>nView = view.getNodeView(node);
+ xCenter += (nView.getVisualProperty(xLoc)) /
nodeList.size();
+ yCenter += (nView.getVisualProperty(yLoc)) /
nodeList.size();
+ }
+ return getDim(xCenter, yCenter);
+ }
+
+ private Dimension calculateOffset(Dimension center, CyNetworkView view,
CyNode node) {
+ View<CyNode>nView = view.getNodeView(node);
+ double xOffset = nView.getVisualProperty(xLoc) -
center.getWidth();
+ double yOffset = nView.getVisualProperty(yLoc) -
center.getHeight();
+ return getDim(xOffset, yOffset);
+ }
+
+ private Dimension getLocation(CyNetwork network, CyNode node) {
+ CyRow nodeRow = network.getRow(node, CyNetwork.HIDDEN_ATTRS);
+ double x = nodeRow.get(X_LOCATION_ATTR, Double.class);
+ double y = nodeRow.get(Y_LOCATION_ATTR, Double.class);
+ return getDim(x,y);
+ }
+
+ private Dimension getOffsetLocation(CyNetwork network, CyNode node,
Dimension center) {
+ CyRow nodeRow = network.getRow(node, CyNetwork.HIDDEN_ATTRS);
+ double xLocation = nodeRow.get(X_OFFSET_ATTR, Double.class) +
center.getWidth();
+ double yLocation = nodeRow.get(Y_OFFSET_ATTR, Double.class) +
center.getHeight();
+ return getDim(xLocation, yLocation);
+ }
+
+ private void updateNodeOffset(CyNetwork network, CyNode node, Dimension
offset) {
+ CyRow nodeRow = network.getRow(node, CyNetwork.HIDDEN_ATTRS);
+ createColumnIfNeeded(nodeRow.getTable(), X_OFFSET_ATTR,
Double.class);
+ createColumnIfNeeded(nodeRow.getTable(), Y_OFFSET_ATTR,
Double.class);
+ nodeRow.set(X_OFFSET_ATTR, new Double(offset.getWidth()));
+ nodeRow.set(Y_OFFSET_ATTR, new Double(offset.getHeight()));
+ System.out.println("Location for "+node+" is "+
+ nodeRow.get(X_OFFSET_ATTR, Double.class)+","+
+ nodeRow.get(Y_OFFSET_ATTR, Double.class));
+ }
+
+ private void updateGroupLocation(CyNetwork network, CyNode node,
Dimension offset) {
+ CyRow nodeRow = network.getRow(node, CyNetwork.HIDDEN_ATTRS);
+ createColumnIfNeeded(nodeRow.getTable(), X_LOCATION_ATTR,
Double.class);
+ createColumnIfNeeded(nodeRow.getTable(), Y_LOCATION_ATTR,
Double.class);
+ nodeRow.set(X_LOCATION_ATTR, new Double(offset.getWidth()));
+ nodeRow.set(Y_LOCATION_ATTR, new Double(offset.getHeight()));
+ System.out.println("Location for "+node+" is "+
+ nodeRow.get(X_LOCATION_ATTR,
Double.class)+","+
+ nodeRow.get(Y_LOCATION_ATTR, Double.class));
+ }
+
+ private void moveNode(CyNetworkView view, CyNode node, Dimension
location) {
+ View<CyNode>nView = view.getNodeView(node);
+ nView.setVisualProperty(xLoc, location.getWidth());
+ nView.setVisualProperty(yLoc, location.getHeight());
+ System.out.println("Moving node "+node+" to "+
+ location.getWidth()+","+
+ location.getHeight());
+ }
+
+ private void createColumnIfNeeded(CyTable table, String name, Class
type) {
+ if (table.getColumn(name) == null)
+ table.createColumn(name, type, false);
+ }
+
+ private Dimension getDim(double x, double y) {
+ Dimension d = new Dimension();
+ d.setSize(x, y);
+ return d;
+ }
+}
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