JAL-1957 deleted stale comment

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index b648bea..eee8bca 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -20,18 +20,6 @@
  */
 package jalview.ext.rbvi.chimera;
 
-import java.awt.Color;
-import java.net.BindException;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
@@ -49,6 +37,18 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.net.BindException;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+
 public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 {
   // Chimera clause to exclude alternate locations in atom selection
@@ -608,6 +608,11 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public void sendChimeraCommand(final String command, boolean logResponse)
   {
+    if (viewer == null)
+    {
+      // ? thread running after viewer shut down
+      return;
+    }
     viewerCommandHistory(false);
     if (lastCommand == null || !lastCommand.equals(command))
     {
@@ -826,6 +831,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
     StringBuilder atomSpecs = new StringBuilder();
     boolean first = true;
+
     for (AtomSpec atom : atoms)
     {
       int pdbResNum = atom.getPdbResNum();
@@ -834,13 +840,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
       if (cms != null && !cms.isEmpty())
       {
-        /*
-         * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we
-         * concatenate multiple 'show' commands
-         */
-        atomSpecs.append(first ? "" : ";show ");
+        atomSpecs.append(first ? "" : ",");
         first = false;
-        atomSpecs.append("#" + cms.get(0).getModelNumber());
+        atomSpecs.append(cms.get(0).getModelNumber());
         atomSpecs.append(":" + pdbResNum);
         if (!chain.equals(" "))
         {
@@ -862,7 +864,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     viewerCommandHistory(false);
     if (atomSpec.length() > 0)
     {
-      command.append("show ").append(atomSpec);
+      command.append("show #").append(atomSpec);
       viewer.sendChimeraCommand(command.toString(), false);
     }
     viewerCommandHistory(true);
@@ -989,6 +991,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public abstract void refreshGUI();
 
+  @Override
   public void setLoadingFromArchive(boolean loadingFromArchive)
   {
     this.loadingFromArchive = loadingFromArchive;
@@ -999,6 +1002,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @return true if Chimeral is still restoring state or loading is still going
    *         on (see setFinsihedLoadingFromArchive)
    */
+  @Override
   public boolean isLoadingFromArchive()
   {
     return loadingFromArchive && !loadingFinished;
@@ -1010,6 +1014,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * 
    * @param finishedLoading
    */
+  @Override
   public void setFinishedLoadingFromArchive(boolean finishedLoading)
   {
     loadingFinished = finishedLoading;