Author: scooter
Date: 2011-09-17 18:22:15 -0700 (Sat, 17 Sep 2011)
New Revision: 26855
Added:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CustomGraphicsUtil.java
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuListener.java
Log:
Added "Paint image onto node"
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
2011-09-17 01:41:38 UTC (rev 26854)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/StructureViz.java
2011-09-18 01:22:15 UTC (rev 26855)
@@ -79,6 +79,7 @@
public static final int SALIGN = 6;
public static final int SELECTRES = 7;
public static final int FINDMODELS = 8;
+ public static final int GETIMAGE = 9;
private CyLogger logger = null;
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
2011-09-17 01:41:38 UTC (rev 26854)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
2011-09-18 01:22:15 UTC (rev 26855)
@@ -498,6 +498,23 @@
return listener.getResponse(command);
}
+
+ public void chimeraSendNoReply(String command) {
+ if (chimera == null)
+ return;
+
+ // System.out.println("To Chimera --> "+command);
+ listener.clearResponse(command);
+ String text = command.concat("\n");
+ try {
+ // send the command
+ chimera.getOutputStream().write(text.getBytes());
+ chimera.getOutputStream().flush();
+ } catch (IOException e) {
+ CyLogger.getLogger(Chimera.class).warning("Unable to
execute command: "+text);
+ }
+ return;
+ }
/**
* Terminate the running Chimera process
Added:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CustomGraphicsUtil.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CustomGraphicsUtil.java
(rev 0)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/CustomGraphicsUtil.java
2011-09-18 01:22:15 UTC (rev 26855)
@@ -0,0 +1,129 @@
+/* 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;
+
+// System imports
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+import java.net.MalformedURLException;
+
+// Cytoscape imports
+import cytoscape.Cytoscape;
+import cytoscape.CyNode;
+import cytoscape.data.CyAttributes;
+import cytoscape.logger.CyLogger;
+
+import cytoscape.visual.CalculatorCatalog;
+import cytoscape.visual.NodeAppearanceCalculator;
+import cytoscape.visual.VisualMappingManager;
+import cytoscape.visual.VisualPropertyType;
+import cytoscape.visual.VisualStyle;
+import cytoscape.visual.calculators.Calculator;
+import cytoscape.visual.calculators.GenericNodeCustomGraphicCalculator;
+import cytoscape.visual.customgraphic.CustomGraphicsManager;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.customgraphic.ImageUtil;
+import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+import cytoscape.visual.mappings.DiscreteMapping;
+import cytoscape.visual.mappings.ObjectMapping;
+
+import giny.model.GraphObject;
+
+// structureViz imports
+import structureViz.StructureViz;
+import structureViz.actions.Chimera;
+
+/**
+ * The StructureViz class provides the primary interface to the
+ * Cytoscape plugin mechanism
+ */
+public class CustomGraphicsUtil {
+
+ static void applyImage(CyLogger logger, Chimera chimera,
+ GraphObject context) {
+ VisualMappingManager vmm = Cytoscape.getVisualMappingManager();
+ CalculatorCatalog catalog = vmm.getCalculatorCatalog();
+ String path = null;
+ CyCustomGraphics cg = null;
+ try {
+ File tmpFile = File.createTempFile("structureViz",
".png");
+ path = tmpFile.getAbsolutePath();
+ // Not really a select command, but it does cause us to
wait....
+ chimera.select("copy file "+path+" png ");
+ // Create the custom graphics
+ URL imageURL = tmpFile.toURI().toURL();
+ CustomGraphicsManager cgm =
vmm.getCustomGraphicsManager();
+ cg = new URLImageCustomGraphics(imageURL.toString());
+ cgm.addGraphics(cg, imageURL);
+ } catch (MalformedURLException mue) {
+ logger.warning("Unable to get a URL from "+path+":
"+mue.getMessage());
+ return;
+ } catch (IOException ioe) {
+ logger.warning("IO exception reading "+path+":
"+ioe.getMessage());
+ return;
+ }
+
+ // We need to create an attribute we can map to...
+ String value = context.getIdentifier()+": "+path;
+ CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
+ nodeAttributes.setAttribute(context.getIdentifier(),
"ChimeraImage", value);
+
+ // Now, add it to the visual style
+ VisualStyle style = vmm.getVisualStyle(); // Get the visual
style
+ // We need to create a calculator
+ NodeAppearanceCalculator nac =
style.getNodeAppearanceCalculator();
+ Calculator cgcalc =
+
nac.getCalculator(VisualPropertyType.NODE_CUSTOM_GRAPHICS_1);
+
+ // Do we already have a discrete map?
+ if (cgcalc != null && (cgcalc.getMapping(0) instanceof
DiscreteMapping)) {
+ // Yes, add to it
+ ObjectMapping mapping = cgcalc.getMapping(0);
+ DiscreteMapping disMapping = (DiscreteMapping)mapping;
+ disMapping.putMapValue(value, cg);
+ } else {
+ // No, create a new one
+ DiscreteMapping dm =
+ new DiscreteMapping(CyCustomGraphics.class,
"ChimeraImage");
+ dm.putMapValue(value, cg);
+
+ cgcalc =
+ new
GenericNodeCustomGraphicCalculator("ChimeraImage", dm,
+
VisualPropertyType.NODE_CUSTOM_GRAPHICS_1);
+ catalog.addCalculator(cgcalc);
+ }
+ nac.setCalculator(cgcalc);
+ vmm.applyNodeAppearances();
+ }
+}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
2011-09-17 01:41:38 UTC (rev 26854)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
2011-09-18 01:22:15 UTC (rev 26855)
@@ -40,6 +40,7 @@
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.IOException;
+import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.ListIterator;
@@ -56,6 +57,10 @@
import cytoscape.view.CytoscapeDesktop;
import cytoscape.view.CyNetworkView;
+import cytoscape.visual.customgraphic.CyCustomGraphics;
+import cytoscape.visual.customgraphic.ImageUtil;
+import cytoscape.visual.customgraphic.impl.bitmap.URLImageCustomGraphics;
+
import giny.model.GraphObject;
// structureViz imports
@@ -119,6 +124,8 @@
seqAlignAction(label);
} else if (command == StructureViz.COMPARE) {
seqCompareAction(label);
+ } else if (command == StructureViz.GETIMAGE) {
+ CustomGraphicsUtil.applyImage(logger, chimera, context);
}
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuListener.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuListener.java
2011-09-17 01:41:38 UTC (rev 26854)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuListener.java
2011-09-18 01:22:15 UTC (rev 26855)
@@ -112,6 +112,15 @@
m.add(item);
}
{
+ if (overNode != null) {
+ JMenuItem item = new JMenuItem("Find modelled
structures");
+ StructureVizMenuHandler l =
+ new
StructureVizMenuHandler(StructureViz.FINDMODELS, (CyNode)overNode.getNode(),
logger);
+ item.addActionListener(l);
+ m.add(item);
+ }
+ }
+ {
JMenuItem item = new JMenuItem("Align structures");
List<Structure> structures =
CyChimera.getSelectedStructures(overNode, false);
StructureVizMenuHandler l = new
StructureVizMenuHandler(StructureViz.ALIGN, structures, logger);
@@ -140,12 +149,14 @@
}
}
{
- if (overNode != null) {
- JMenuItem item = new JMenuItem("Find modelled
structures");
+ if (overNode != null && chimera.isLaunched()) {
+ JMenuItem item = new JMenuItem("Paint Chimera image
onto node");
StructureVizMenuHandler l =
- new
StructureVizMenuHandler(StructureViz.FINDMODELS, (CyNode)overNode.getNode(),
logger);
- item.addActionListener(l);
- m.add(item);
+ new
StructureVizMenuHandler(StructureViz.GETIMAGE,
+ null,
(CyNode)overNode.getNode(),
+ logger);
+ item.addActionListener(l);
+ m.add(item);
}
}
{
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