Author: scooter
Date: 2010-08-18 20:32:26 -0700 (Wed, 18 Aug 2010)
New Revision: 21465
Added:
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/commands/
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/commands/NamedSelectionCommandHandler.java
Modified:
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/NamedSelection.java
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupPanel.java
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupTreeModel.java
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupTreeUtils.java
Log:
Added extra layer to support multiple viewers. Also added commands to
simplify interaction with other viewers.
Modified:
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/NamedSelection.java
===================================================================
---
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/NamedSelection.java
2010-08-18 23:49:14 UTC (rev 21464)
+++
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/NamedSelection.java
2010-08-19 03:32:26 UTC (rev 21465)
@@ -63,6 +63,7 @@
import cytoscape.groups.CyGroupViewer;
// our imports
+import namedSelection.commands.NamedSelectionCommandHandler;
import namedSelection.ui.GroupPanel;
import namedSelection.ui.NamedSelectionMenuListener;
@@ -131,6 +132,9 @@
CyGroupManager.registerGroupViewer(groupViewer);
groupPanel.addViewer(groupViewer);
+ // Finally, register our commands (which are pretty sparse...)
+ new NamedSelectionCommandHandler("namedselection", myLogger,
groupPanel);
+
myLogger.info("namedSelectionPlugin "+VERSION+" initialized");
}
Added:
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/commands/NamedSelectionCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/commands/NamedSelectionCommandHandler.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/commands/NamedSelectionCommandHandler.java
2010-08-19 03:32:26 UTC (rev 21465)
@@ -0,0 +1,128 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2010 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+
+package namedSelection.commands;
+
+import namedSelection.NamedSelection;
+import namedSelection.ui.GroupPanel;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import cytoscape.command.AbstractCommandHandler;
+import cytoscape.command.CyCommandException;
+import cytoscape.command.CyCommandManager;
+import cytoscape.command.CyCommandResult;
+import cytoscape.groups.CyGroup;
+import cytoscape.groups.CyGroupManager;
+import cytoscape.groups.CyGroupViewer;
+import cytoscape.layout.Tunable;
+import cytoscape.logger.CyLogger;
+
+public class NamedSelectionCommandHandler extends AbstractCommandHandler {
+ CyLogger logger;
+ GroupPanel groupPanel;
+
+ private static String ADDVIEWER = "add viewer";
+ private static String DESELECT = "deselect";
+ private static String GROUPNAME = "group";
+ private static String UPDATE = "update";
+ private static String SELECT = "select";
+ private static String VIEWERNAME = "viewer";
+
+ public NamedSelectionCommandHandler(String namespace, CyLogger logger,
GroupPanel groupPanel) {
+ super(CyCommandManager.reserveNamespace(namespace));
+
+ this.logger = logger;
+ this.groupPanel = groupPanel;
+
+ addDescription(ADDVIEWER, "Add an additional viewer to the
group panel");
+ addArgument(ADDVIEWER, VIEWERNAME);
+
+ addDescription(DESELECT, "Deselect a group");
+ addArgument(DESELECT, GROUPNAME);
+
+ addDescription(UPDATE, "Update the group panel");
+ addArgument(UPDATE);
+
+ addDescription(SELECT, "Select a group");
+ addArgument(SELECT, GROUPNAME);
+ }
+
+ public CyCommandResult execute(String command, Collection<Tunable>args)
throws CyCommandException {
+ return execute(command, createKVMap(args));
+ }
+
+ public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ // System.out.println("namedselection command: "+command);
+ if (ADDVIEWER.equals(command)) {
+ String viewerName = getArg(command, VIEWERNAME, args);
+ if (viewerName == null)
+ throw new CyCommandException("The name of a
group viewer must be specified");
+ CyGroupViewer groupViewer =
CyGroupManager.getGroupViewer(viewerName);
+ if (groupViewer == null)
+ throw new CyCommandException("Group viewer
"+viewerName+" isn't registered");
+ groupPanel.addViewer(groupViewer);
+ result.addMessage("Added viewer "+viewerName+" to the
group panel");
+
+ } else if (UPDATE.equals(command)) {
+ groupPanel.reload();
+ result.addMessage("Updated the group panel");
+
+ } else if (SELECT.equals(command) || DESELECT.equals(command)) {
+ String groupName = getArg(command, GROUPNAME, args);
+ if (groupName == null)
+ throw new CyCommandException("The name of a
group must be specified");
+ CyGroup group = CyGroupManager.findGroup(groupName);
+ if (group == null)
+ throw new CyCommandException("Can't find group:
"+groupName);
+ // Make sure we're the viewer for this group
+ if
(!group.getViewer().equals(NamedSelection.viewerName))
+ throw new CyCommandException("Group
"+groupName+" is not a named selection");
+
+ // OK, now do what we're told
+ if (SELECT.equals(command)) {
+ group.setState(NamedSelection.SELECTED);
+ result.addMessage("Selected
"+group.getNodes().size()+" nodes in group "+groupName);
+ } else {
+ group.setState(NamedSelection.UNSELECTED);
+ result.addMessage("Deselected group
"+groupName);
+ }
+ }
+ return result;
+ }
+}
+
Modified:
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupPanel.java
===================================================================
---
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupPanel.java
2010-08-18 23:49:14 UTC (rev 21464)
+++
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupPanel.java
2010-08-19 03:32:26 UTC (rev 21465)
@@ -166,6 +166,8 @@
viewerList.add(viewer);
navTree.setViewerList(viewerList);
+ System.out.println("Added new viewer: "+viewer.getViewerName());
+
// Do a reload so we can get the new groups
reload();
}
Modified:
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupTreeModel.java
===================================================================
---
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupTreeModel.java
2010-08-18 23:49:14 UTC (rev 21464)
+++
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupTreeModel.java
2010-08-19 03:32:26 UTC (rev 21465)
@@ -135,6 +135,7 @@
if (nodeMap.containsKey((CyNode)node)) {
List<TreePath> pathList =
nodeMap.get((CyNode)node);
for (TreePath path: pathList) {
+ // System.out.println("Selecting path:
"+path);
GroupTreeUtils.selectTreeNode(navTree,
path, select);
}
}
@@ -201,7 +202,18 @@
maxDepth = 1;
for (CyGroupViewer viewer: viewerList) {
+ DefaultMutableTreeNode viewerNode = rootNode;
+ TreePath viewerPath = rootPath;
+ int depth = 2;
+ if (viewerList.size() > 1) {
+ // Add our viewer as a node in the tree
+ viewerNode = new
DefaultMutableTreeNode(viewer.getViewerName()+"s");
+ rootNode.add(viewerNode);
+ viewerPath =
rootPath.pathByAddingChild(viewerNode);
+ depth = 3;
+ }
+
List<CyGroup> groupList =
CyGroupManager.getGroupList(viewer);
if (groupList == null || groupList.size() == 0) {
continue;
@@ -213,7 +225,7 @@
for (CyNetwork network:
(List<CyNetwork>)GroupTreeUtils.sortNetworkList(netList)) {
// System.out.println("Adding network:
"+network.getTitle());
List<CyGroup> netGroupList =
groupMap.get(network);
- rootNode.add(addNetworkToTree(network,
netGroupList, viewer, rootNode, rootPath, 2));
+ viewerNode.add(addNetworkToTree(network,
netGroupList, viewer, viewerNode, viewerPath, depth));
}
}
return rootNode;
Modified:
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupTreeUtils.java
===================================================================
---
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupTreeUtils.java
2010-08-18 23:49:14 UTC (rev 21464)
+++
csplugins/trunk/ucsf/scooter/namedSelection/src/namedSelection/ui/GroupTreeUtils.java
2010-08-19 03:32:26 UTC (rev 21465)
@@ -79,6 +79,9 @@
*/
public static void handlePromotion(GroupTree navTree,
DefaultMutableTreeNode groupTreeNode,
TreePath path, boolean selected) {
+ if (!(groupTreeNode.getUserObject() instanceof CyGroup))
+ return;
+
CyGroup group = (CyGroup) groupTreeNode.getUserObject();
// Now, see if we need to promote (or demote) the selection
if (checkForPromotion(navTree, groupTreeNode, selected)) {
--
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