Author: scooter
Date: 2011-09-17 21:12:16 -0700 (Sat, 17 Sep 2011)
New Revision: 26857
Added:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CustomGraphicsUtil.java
Log:
Added support for node selection listeners to select associated residues.
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
2011-09-18 01:31:08 UTC (rev 26856)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
2011-09-18 04:12:16 UTC (rev 26857)
@@ -61,6 +61,7 @@
// structureViz imports
import structureViz.commands.StructureVizCommandHandler;
import structureViz.ui.StructureVizMenuListener;
+import structureViz.ui.GraphObjectSelectionListener;
/**
* The StructureViz class provides the primary interface to the
@@ -82,12 +83,15 @@
public static final int GETIMAGE = 9;
private CyLogger logger = null;
+ private GraphObjectSelectionListener gvcListener = null;
/**
* Create our action and add it to the plugins menu
*/
public StructureViz() {
logger = CyLogger.getLogger(StructureViz.class);
+ gvcListener = new GraphObjectSelectionListener(logger);
+
try {
// Set ourselves up to listen for new networks
@@ -96,6 +100,7 @@
// Add ourselves to the current network context menu
((DGraphView)Cytoscape.getCurrentNetworkView()).addNodeContextMenuListener(this);
+
Cytoscape.getCurrentNetworkView().addGraphViewChangeListener(gvcListener);
} catch (ClassCastException e) {
logger.error(e.getMessage());
}
@@ -119,8 +124,12 @@
*/
public void propertyChange(PropertyChangeEvent evt) {
if (evt.getPropertyName() ==
CytoscapeDesktop.NETWORK_VIEW_CREATED) {
+ CyNetworkView view = (CyNetworkView)evt.getNewValue();
// Add menu to the context dialog
-
((CyNetworkView)evt.getNewValue()).addNodeContextMenuListener(this);
+ view.addNodeContextMenuListener(this);
+ // Add our graph view change listener
+ view.removeGraphViewChangeListener(gvcListener);
+ view.addGraphViewChangeListener(gvcListener);
}
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
2011-09-18 01:31:08 UTC (rev 26856)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
2011-09-18 04:12:16 UTC (rev 26857)
@@ -81,6 +81,7 @@
private static Map<String, Structure> smilesStructureMap = null;
private static CyAttributes cyAttributes;
private static CyLogger logger = null;
+ private static boolean enableNodeSelection = true;
static List<GraphObject> selectedList = null;
@@ -363,6 +364,8 @@
if (selectedList == null) selectedList = new
ArrayList<GraphObject>();
+ enableNodeSelection = false;
+
// We need to do this in two passes since some parts of a
structure might be
// selected and some might not. Our selection model
(unfortunately) only tells
// us that something has changed, not what...
@@ -417,6 +420,7 @@
*/
networkView.updateView();
+ enableNodeSelection = true;
}
/**
@@ -460,6 +464,14 @@
return structure;
}
+ public static boolean selectionEnabled() {
+ return enableNodeSelection;
+ }
+
+ public static void setSelectionEnabled(boolean enable) {
+ enableNodeSelection = enable;
+ }
+
private static List<Structure> getStructures(CyNode node,
List<Structure>
structureList,
String matchName) {
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CustomGraphicsUtil.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CustomGraphicsUtil.java
2011-09-18 01:31:08 UTC (rev 26856)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CustomGraphicsUtil.java
2011-09-18 04:12:16 UTC (rev 26857)
@@ -129,7 +129,7 @@
// Now, delete the temp file we created
tmpFile.delete();
- Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
+ Cytoscape.getCurrentNetworkView().updateView();
}
}
Added:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
2011-09-18 04:12:16 UTC (rev 26857)
@@ -0,0 +1,119 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 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 structureViz.ui;
+
+import structureViz.actions.Chimera;
+import structureViz.actions.CyChimera;
+import structureViz.model.Structure;
+
+import java.util.List;
+
+import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
+
+import giny.model.GraphObject;
+import giny.view.GraphView;
+import giny.view.GraphViewChangeEvent;
+import giny.view.GraphViewChangeListener;
+
+/**
+ * This class is used to implement the listener for the
+ * context menu on the ModelNavigatorDialog
+ */
+public class GraphObjectSelectionListener implements GraphViewChangeListener {
+ private CyLogger logger;
+
+ public GraphObjectSelectionListener(CyLogger logger) {
+ this.logger = logger;
+ }
+
+ public void graphViewChanged(GraphViewChangeEvent event) {
+ if (!CyChimera.selectionEnabled())
+ return;
+ CyChimera.setSelectionEnabled(false);
+ GraphView view = (GraphView)event.getSource();
+ if (event.isEdgesSelectedType()) {
+ setSelection(view, event.getSelectedEdges(), true);
+ } else if (event.isEdgesUnselectedType()) {
+ setSelection(view, event.getSelectedEdges(), false);
+ } else if (event.isNodesSelectedType()) {
+ setSelection(view, event.getSelectedNodes(), true);
+ } else if (event.isNodesUnselectedType()) {
+ setSelection(view, event.getSelectedNodes(), false);
+ }
+ CyChimera.setSelectionEnabled(true);
+ }
+
+ private void setSelection(GraphView view, GraphObject[] goArray,
boolean selected) {
+ if (goArray == null || goArray.length == 0) return;
+
+ // Get the chimera instance for this view
+ Chimera chimera =
Chimera.GetChimeraInstance((CyNetworkView)view, logger);
+
+ // Get all of the open structures
+ List<Structure> structureList = chimera.getOpenStructs();
+
+ // For each graph object, see if the selection has changed
+ for (Structure structure: structureList) {
+ List<GraphObject> objList =
structure.getGraphObjectList();
+ for (int index = 0; index < goArray.length; index++ ) {
+ GraphObject object = goArray[index];
+ if (objList.contains(object) &&
structure.getResidueList(object) != null) {
+ setResidueSelection(chimera, structure,
object, selected);
+ }
+ }
+ }
+ chimera.modelChanged();
+ }
+
+ private void setResidueSelection(Chimera chimera, Structure structure,
+ GraphObject object, boolean selected) {
+ String command = "select ";
+ if (!selected)
+ command = "~select ";
+
+ List<String> residueList = structure.getResidueList(object);
+ if (residueList == null || residueList.size() == 0) return;
+
+ int model = structure.modelNumber();
+ if (chimera.getChimeraModel(model) == null) return;
+
+ String residues = "";
+ for (String residue: residueList) {
+ residues = residues.concat(residue+",");
+ }
+ residues = residues.substring(0,residues.length()-1);
+ command = command.concat("
#"+structure.modelNumber()+":"+residues);
+ chimera.select(command);
+ }
+}
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