JAL-3818 process Jmol callbacks in AWT thread

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 8accd0d..b0a7b0c 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,24 +20,6 @@
  */
 package jalview.ext.jmol;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.IProgressIndicator;
-import jalview.io.DataSourceType;
-import jalview.io.StructureFile;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-
 import java.awt.Color;
 import java.awt.Container;
 import java.awt.event.ComponentEvent;
@@ -52,6 +34,8 @@ import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
+import javax.swing.SwingUtilities;
+
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolSelectionListener;
@@ -61,6 +45,27 @@ import org.jmol.c.CBK;
 import org.jmol.script.T;
 import org.jmol.viewer.Viewer;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.SequenceRenderer;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AppJmol;
+import jalview.gui.IProgressIndicator;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
+
 public abstract class JalviewJmolBinding extends AAStructureBindingModel
         implements JmolStatusListener, JmolSelectionListener,
         ComponentListener
@@ -479,6 +484,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   Thread colourby = null;
+
   /**
    * Sends a set of colour commands to the structure viewer
    * 
@@ -845,6 +851,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             pdbfilename);
     if (label != null)
     {
+      // change comma to pipe separator (newline token for Jmol)
+      label = label.replace(',', '|');
       StringTokenizer toks = new StringTokenizer(strInfo, " ");
       StringBuilder sb = new StringBuilder();
       sb.append("select ").append(String.valueOf(pdbResNum)).append(":")
@@ -935,6 +943,28 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   @Override
   public void notifyCallback(CBK type, Object[] data)
   {
+    /*
+     * ensure processed in AWT thread to avoid risk of deadlocks
+     */
+    SwingUtilities.invokeLater(new Runnable()
+    {
+
+      @Override
+      public void run()
+      {
+        processCallback(type, data);
+      }
+    });
+  }
+
+  /**
+   * Processes one callback notification from Jmol
+   * 
+   * @param type
+   * @param data
+   */
+  protected void processCallback(CBK type, Object[] data)
+  {
     try
     {
       switch (type)
@@ -1101,8 +1131,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           // see JAL-623 - need method of matching pasted data up
           {
             pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
-                    pdbfile, DataSourceType.PASTE,
-                    getIProgressIndicator());
+                    pdbfile, DataSourceType.PASTE, getIProgressIndicator());
             getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
             matches = true;
             foundEntry = true;
@@ -1188,7 +1217,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       FeatureRenderer fr = getFeatureRenderer(null);
       if (fr != null)
       {
-        fr.featuresAdded();
+        FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
+        ((AppJmol) getViewer()).getAlignmentPanel().av
+                .applyFeaturesStyle(colours);
       }
       refreshGUI();
       loadNotifiesHandled++;