Author: scooter
Date: 2012-07-30 17:28:17 -0700 (Mon, 30 Jul 2012)
New Revision: 30047
Added:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupEdit.java
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/group/CollapseGroupTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodeContextTaskFactoryImpl.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/GroupNodesTaskFactoryImpl.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/UnGroupNodesTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/UnGroupNodesTaskFactoryImpl.java
Log:
Add undo support for grouping and ungrouping nodes
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
2012-07-30 23:45:09 UTC (rev 30046)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2012-07-31 00:28:17 UTC (rev 30047)
@@ -971,7 +971,7 @@
connectSelectedNodesTaskFactoryProps);
GroupNodesTaskFactoryImpl groupNodesTaskFactory =
- new GroupNodesTaskFactoryImpl(cyGroupManager,
cyGroupFactory);
+ new GroupNodesTaskFactoryImpl(cyGroupManager,
cyGroupFactory, undoSupportServiceRef);
Properties groupNodesTaskFactoryProps = new Properties();
groupNodesTaskFactoryProps.setProperty(PREFERRED_MENU,NETWORK_GROUP_MENU);
groupNodesTaskFactoryProps.setProperty(TITLE,"Group Selected
Nodes");
@@ -998,7 +998,7 @@
registerService(bc,groupNodesTaskFactory,NodeViewTaskFactory.class,
groupNodeViewTaskFactoryProps);
UnGroupNodesTaskFactoryImpl unGroupTaskFactory =
- new UnGroupNodesTaskFactoryImpl(cyGroupManager);
+ new UnGroupNodesTaskFactoryImpl(cyGroupManager,
cyGroupFactory, undoSupportServiceRef);
Properties unGroupNodesTaskFactoryProps = new Properties();
unGroupNodesTaskFactoryProps.setProperty(PREFERRED_MENU,NETWORK_GROUP_MENU);
unGroupNodesTaskFactoryProps.setProperty(TITLE,"Ungroup
Selected Nodes");
Modified:
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
2012-07-30 23:45:09 UTC (rev 30046)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/CollapseGroupTask.java
2012-07-31 00:28:17 UTC (rev 30047)
@@ -1,7 +1,7 @@
/*
- File: SelectFirstNeighborsNodeViewTask.java
+ File: CollapseGroupTask.java
- Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2012, 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
Added:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupEdit.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupEdit.java
(rev 0)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupEdit.java
2012-07-31 00:28:17 UTC (rev 30047)
@@ -0,0 +1,164 @@
+/*
+ File: GroupEdit.java
+
+ Copyright (c) 2012, 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.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.cytoscape.group.CyGroup;
+import org.cytoscape.group.CyGroupFactory;
+import org.cytoscape.group.CyGroupManager;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.work.undo.AbstractCyEdit;
+
+public class GroupEdit extends AbstractCyEdit {
+ private CyNetwork net;
+ private CyGroupManager mgr;
+ private CyGroupFactory factory;
+ private CyGroup group;
+ private Set<CyGroup> groupSet;
+
+ private Map<CyGroup, List<CyNode>> nodeMap;
+ private Map<CyGroup, List<CyEdge>> edgesMap;
+ private Map<CyGroup, List<CyNetwork>> networkMap;
+ private Map<CyGroup, List<CyNetwork>> collapseMap;
+
+ public GroupEdit(CyNetwork net, CyGroupManager mgr, CyGroupFactory
factory, CyGroup group) {
+ super("Group Nodes");
+ this.net = net;
+ this.mgr = mgr;
+ this.factory = factory;
+ this.group = group;
+ this.groupSet = null;
+ initMaps();
+ createShadowGroup(group);
+ }
+
+ public GroupEdit(CyNetwork net, CyGroupManager mgr, CyGroupFactory
factory, Set <CyGroup> groupSet) {
+ super("Ungroup Nodes");
+ this.net = net;
+ this.mgr = mgr;
+ this.factory = factory;
+ this.group = null;
+ this.groupSet = groupSet;
+ initMaps();
+ for (CyGroup group: groupSet)
+ createShadowGroup(group);
+ }
+
+ public void undo() {
+ if (group != null) {
+ // Undo group nodes
+ mgr.destroyGroup(group);
+ } else if (groupSet != null) {
+ Set<CyGroup>newGroups = new HashSet<CyGroup>();
+
+ // Undo ungroup nodes
+ for (CyGroup group: groupSet) {
+ newGroups.add(reGroup(group));
+ }
+
+ // Now recreate our maps in case we redo
+ initMaps();
+ groupSet = newGroups;
+ for (CyGroup group: groupSet)
+ createShadowGroup(group);
+ }
+ }
+
+ public void redo() {
+ if (group != null) {
+ // This is sort of a pain. We need to reconfigure the
+ // group from scratch...
+ this.group = reGroup(group);
+ initMaps();
+ createShadowGroup(group);
+ } else if (groupSet != null) {
+ for (CyGroup group: groupSet) {
+ mgr.destroyGroup(group);
+ }
+ }
+ }
+
+ private CyGroup reGroup(CyGroup group) {
+ List<CyNetwork> netList = networkMap.get(group);
+
+ // network 0 is always the root network
+ CyNetwork firstNet = netList.get(1);
+ CyGroup newGroup = factory.createGroup(firstNet,
nodeMap.get(group), edgesMap.get(group), true);
+
+ // It should be at least 2 (rootNetwork + initial network)
+ if (netList.size() > 2) {
+ for (int i = 2; i < netList.size(); i++) {
+ newGroup.addGroupToNetwork(netList.get(i));
+ }
+ }
+
+ for (CyNetwork net: collapseMap.get(group)) {
+ newGroup.collapse(net);
+ }
+ return newGroup;
+ }
+
+ private void initMaps() {
+ nodeMap = new HashMap<CyGroup, List<CyNode>>();
+ edgesMap = new HashMap<CyGroup, List<CyEdge>>();
+ networkMap = new HashMap<CyGroup, List<CyNetwork>>();
+ collapseMap = new HashMap<CyGroup, List<CyNetwork>>();
+ }
+
+ private void createShadowGroup(CyGroup group) {
+ // Get the nodes, edges, and external edges
+ nodeMap.put(group, group.getNodeList());
+ List<CyEdge> edgesList = new
ArrayList<CyEdge>(group.getInternalEdgeList());
+ edgesList.addAll(group.getExternalEdgeList());
+ edgesMap.put(group, edgesList);
+
+ // Get the networks
+ networkMap.put(group, new
ArrayList<CyNetwork>(group.getNetworkSet()));
+
+ // Get the collapse set
+ List<CyNetwork> collapseList = new ArrayList<CyNetwork>();
+ for (CyNetwork net: group.getNetworkSet()) {
+ if (group.isCollapsed(net)) {
+ collapseList.add(net);
+ }
+ }
+ collapseMap.put(group, collapseList);
+ }
+
+}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodeContextTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodeContextTaskFactoryImpl.java
2012-07-30 23:45:09 UTC (rev 30046)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodeContextTaskFactoryImpl.java
2012-07-31 00:28:17 UTC (rev 30047)
@@ -1,7 +1,7 @@
/*
- File: SelectFirstNeighborsNodeViewTaskFactory.java
+ File: GroupNodeContextTaskFactoryImpl.java
- Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2012, 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
Modified:
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
2012-07-30 23:45:09 UTC (rev 30046)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTask.java
2012-07-31 00:28:17 UTC (rev 30047)
@@ -1,7 +1,7 @@
/*
- File: SelectFirstNeighborsNodeViewTask.java
+ File: GroupNodesTask.java
- Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2012, 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
@@ -43,18 +43,21 @@
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.undo.UndoSupport;
public class GroupNodesTask extends AbstractTask {
private CyNetwork net;
private CyGroupManager mgr;
private CyGroupFactory factory;
+ private UndoSupport undoSupport;
- public GroupNodesTask(CyNetworkView netView, CyGroupManager mgr,
CyGroupFactory factory) {
+ public GroupNodesTask(UndoSupport undoSupport, 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;
+ this.undoSupport = undoSupport;
}
public void run(TaskMonitor tm) throws Exception {
@@ -66,6 +69,7 @@
// 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, true);
+ undoSupport.postEdit(new GroupEdit(net, mgr, factory, group));
// mgr.addGroup(group);
tm.setProgress(1.0d);
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTaskFactoryImpl.java
2012-07-30 23:45:09 UTC (rev 30046)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/GroupNodesTaskFactoryImpl.java
2012-07-31 00:28:17 UTC (rev 30047)
@@ -1,7 +1,7 @@
/*
- File: SelectFirstNeighborsNodeViewTaskFactory.java
+ File: GroupNodesTaskFactoryImpl.java
- Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2012, 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
@@ -42,24 +42,27 @@
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.undo.UndoSupport;
public class GroupNodesTaskFactoryImpl extends AbstractNetworkViewTaskFactory
implements NodeViewTaskFactory,
GroupNodesTaskFactory {
private CyGroupManager mgr;
private CyGroupFactory groupFactory;
+ private UndoSupport undoSupport;
- public GroupNodesTaskFactoryImpl(CyGroupManager mgr, CyGroupFactory
groupFactory) {
+ public GroupNodesTaskFactoryImpl(CyGroupManager mgr, CyGroupFactory
groupFactory, UndoSupport undoSupport) {
super();
this.mgr = mgr;
this.groupFactory = groupFactory;
+ this.undoSupport = undoSupport;
}
public TaskIterator createTaskIterator(CyNetworkView view) {
- return new TaskIterator(new GroupNodesTask(view, mgr,
groupFactory));
+ return new TaskIterator(new GroupNodesTask(undoSupport, view,
mgr, groupFactory));
}
public TaskIterator createTaskIterator(View<CyNode> nodeView,
CyNetworkView view) {
- return new TaskIterator(new GroupNodesTask(view, mgr,
groupFactory));
+ return new TaskIterator(new GroupNodesTask(undoSupport, view,
mgr, groupFactory));
}
public boolean isReady(CyNetworkView netView) {
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/UnGroupNodesTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/UnGroupNodesTask.java
2012-07-30 23:45:09 UTC (rev 30046)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/UnGroupNodesTask.java
2012-07-31 00:28:17 UTC (rev 30047)
@@ -1,7 +1,7 @@
/*
- File: SelectFirstNeighborsNodeViewTask.java
+ File: UnGroupNodesTask.java
- Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2012, 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
@@ -33,6 +33,7 @@
import java.util.Set;
import org.cytoscape.group.CyGroup;
+import org.cytoscape.group.CyGroupFactory;
import org.cytoscape.group.CyGroupManager;
import org.cytoscape.model.CyNetwork;
@@ -40,27 +41,35 @@
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.undo.UndoSupport;
public class UnGroupNodesTask extends AbstractTask {
private CyNetwork net;
private CyGroupManager mgr;
+ private CyGroupFactory factory;
private Set<CyGroup>groupSet = null;
+ private UndoSupport undoSupport;
- public UnGroupNodesTask(CyNetwork net, Set<CyGroup>groups,
CyGroupManager mgr) {
+ public UnGroupNodesTask(UndoSupport undoSupport, CyNetwork net,
CyGroupFactory factory,
+ Set<CyGroup>groups, CyGroupManager mgr) {
if (net == null)
throw new NullPointerException("network is null");
this.net = net;
this.mgr = mgr;
+ this.factory = factory;
this.groupSet = groups;
+ this.undoSupport = undoSupport;
}
public void run(TaskMonitor tm) throws Exception {
tm.setProgress(0.0);
+ GroupEdit edit = new GroupEdit(net, mgr, factory, groupSet);
for (CyGroup group: groupSet) {
mgr.destroyGroup(group);
tm.setProgress(1.0d/(double)groupSet.size());
}
+ undoSupport.postEdit(edit);
tm.setProgress(1.0d);
}
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/UnGroupNodesTaskFactoryImpl.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/UnGroupNodesTaskFactoryImpl.java
2012-07-30 23:45:09 UTC (rev 30046)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/group/UnGroupNodesTaskFactoryImpl.java
2012-07-31 00:28:17 UTC (rev 30047)
@@ -1,7 +1,7 @@
/*
- File: SelectFirstNeighborsNodeViewTaskFactory.java
+ File: UnGroupNodesTaskFactoryImpl.java
- Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2012, 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
@@ -35,6 +35,7 @@
import java.util.Set;
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;
@@ -46,14 +47,19 @@
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.undo.UndoSupport;
public class UnGroupNodesTaskFactoryImpl implements NetworkViewTaskFactory,
UnGroupTaskFactory,
UnGroupNodesTaskFactory {
+ private CyGroupFactory factory;
private CyGroupManager mgr;
+ private UndoSupport undoSupport;
- public UnGroupNodesTaskFactoryImpl(CyGroupManager mgr) {
+ public UnGroupNodesTaskFactoryImpl(CyGroupManager mgr, CyGroupFactory
factory, UndoSupport undoSupport) {
this.mgr = mgr;
+ this.undoSupport = undoSupport;
+ this.factory = factory;
}
public boolean isReady(View<CyNode> nodeView, CyNetworkView netView) {
@@ -91,14 +97,14 @@
CyNetwork net = netView.getModel();
Set<CyGroup> groups = getGroups(net, nodeList);
- return new TaskIterator(new UnGroupNodesTask(net, groups, mgr));
+ return new TaskIterator(new UnGroupNodesTask(undoSupport, net,
factory, groups, mgr));
}
public TaskIterator createTaskIterator(CyNetworkView netView) {
CyNetwork net = netView.getModel();
final List<CyNode> selNodes = CyTableUtil.getNodesInState(net,
CyNetwork.SELECTED, true);
Set<CyGroup> groups = getGroups(net, selNodes);
- return new TaskIterator(new
UnGroupNodesTask(netView.getModel(), groups, mgr));
+ return new TaskIterator(new UnGroupNodesTask(undoSupport,
netView.getModel(), factory, groups, mgr));
}
private Set<CyGroup>getGroups(CyNetwork net, List<CyNode>nodeList) {
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