Author: scooter
Date: 2011-10-07 18:33:24 -0700 (Fri, 07 Oct 2011)
New Revision: 27098
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/OpenTask.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
Log:
Fixes for various problems discovered while preparing for the Advisory
Committee Meeting.
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
2011-10-08 00:08:57 UTC (rev 27097)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/Chimera.java
2011-10-08 01:33:24 UTC (rev 27098)
@@ -40,7 +40,6 @@
import java.util.Map;
import java.util.Set;
import java.io.*;
-import javax.swing.JOptionPane;
import java.awt.Color;
import cytoscape.Cytoscape;
@@ -456,6 +455,7 @@
chimeraSend("listen stop models; listen stop select;
close #"+model+"."+subModel);
}
chimeraSend("listen start models; listen start select");
+ Structure.close(structure);
return;
}
@@ -498,6 +498,10 @@
chimera.getOutputStream().flush();
} catch (IOException e) {
CyLogger.getLogger(Chimera.class).warning("Unable to
execute command: "+text);
+ CyLogger.getLogger(Chimera.class).warning("Exiting...");
+ chimera = null;
+ if (mnDialog != null)
+ mnDialog.lostChimera();
}
return listener.getResponse(command);
@@ -516,6 +520,10 @@
chimera.getOutputStream().flush();
} catch (IOException e) {
CyLogger.getLogger(Chimera.class).warning("Unable to
execute command: "+text);
+ CyLogger.getLogger(Chimera.class).warning("Exiting...");
+ chimera = null;
+ if (mnDialog != null)
+ mnDialog.lostChimera();
}
return;
}
@@ -538,6 +546,8 @@
if (mnDialog != null)
mnDialog.setVisible(false);
+
+ Structure.closeAll();
}
/**
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
2011-10-08 00:08:57 UTC (rev 27097)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/CyChimera.java
2011-10-08 01:33:24 UTC (rev 27098)
@@ -528,7 +528,7 @@
boolean state) {
for (GraphObject obj: goList) {
if (obj instanceof Node) {
- // Handle secondary paint??
+ // TODO: Handle secondary paint??
NodeView nv = view.getNodeView((Node)obj);
if (nv != null)
nv.setSelected(state);
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/OpenTask.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/OpenTask.java
2011-10-08 00:08:57 UTC (rev 27097)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/OpenTask.java
2011-10-08 01:33:24 UTC (rev 27098)
@@ -66,7 +66,7 @@
// See if this structure is already open somewhere
Structure s = CyChimera.findStructureForModel(null,
structureName, false);
if (s != null) {
- // System.out.println("Found existing
structure: "+s.toString());
+ // System.out.println("Found existing
structure: "+s.toString()+", model = "+s.modelNumber());
s.addStructure(structure);
structure = s;
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2011-10-08 00:08:57 UTC (rev 27097)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/model/Structure.java
2011-10-08 01:33:24 UTC (rev 27098)
@@ -62,10 +62,25 @@
/**
* Get the next available model number
*
+ * TODO: This really should be a table of models based
+ * on what the Chimera module tells us.
+ *
* @return the next model number
*/
public static int getNextModel() {return nextModel++;}
+ public static void closeAll() {
+ nextModel = 0;
+ structureMap.clear();
+ }
+
+ public static void close(Structure structure) {
+ if (structureMap.containsKey(structure.name()))
+ structureMap.remove(structure.name());
+
+ if (structureMap.size() == 0) nextModel = 0;
+ }
+
public static Structure getStructure(String name, CyNode node,
StructureType type) {
// System.out.println("Getting structure for "+name);
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
2011-10-08 00:08:57 UTC (rev 27097)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/GraphObjectSelectionListener.java
2011-10-08 01:33:24 UTC (rev 27098)
@@ -114,7 +114,7 @@
}
// System.out.println("SelectionMap has "+selectionMap.size()+
" values");
setResidueSelection(chimera, selectionMap.values());
- chimera.modelChanged();
+ // chimera.modelChanged();
}
private String getSelectionString(Chimera chimera, Structure structure,
@@ -147,6 +147,6 @@
}
}
// System.out.println("Selection command: "+command);
- chimera.selectNoReply(command);
+ chimera.chimeraSendNoReply(command);
}
}
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-10-08 00:08:57 UTC (rev 27097)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-10-08 01:33:24 UTC (rev 27098)
@@ -120,6 +120,7 @@
return mnDialog;
}
+
/**
* Create a new ModelNavigatorDialog.
*
@@ -136,6 +137,17 @@
}
/**
+ * We lost our connection to Chimera! Tell the user and exit.
+ */
+ public void lostChimera() {
+ JOptionPane.showMessageDialog(this,
+ "Lost connection to Chimera!
structureViz must exit",
+ "Lost connection",
+ JOptionPane.ERROR_MESSAGE);
+ chimeraObject.exit();
+ }
+
+ /**
* Call this method when something significant has changed in the model
* such as a new model opened or closed
*/
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