From 3916d19d9be0e912ddc0a3fd6241f387aec72f76 Mon Sep 17 00:00:00 2001
From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Tue, 16 Apr 2019 16:06:36 -0500
Subject: [PATCH 1/1] localizes Thread colourby so that it does not cause
 ThreadStateException in Java

---
 src/jalview/ext/jmol/JalviewJmolBinding.java |   43 ++++++++++++++------------
 1 file changed, 24 insertions(+), 19 deletions(-)

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 2cabefa..fa31fd9 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -167,7 +167,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     // remove listeners for all structures in viewer
     getSsm().removeStructureViewerListener(this, this.getStructureFiles());
     if (viewer != null)
+    {
       viewer.dispose();
+    }
     lastCommand = null;
     viewer = null;
     releaseUIResources();
@@ -480,6 +482,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   Thread colourby = null;
+
   /**
    * Sends a set of colour commands to the structure viewer
    * 
@@ -494,7 +497,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       colourby.interrupt();
       colourby = null;
     }
-    colourby = new Thread(new Runnable()
+    Thread colourby = new Thread(new Runnable()
     {
       @Override
       public void run()
@@ -509,6 +512,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
     });
     colourby.start();
+    this.colourby = colourby;
   }
 
   /**
@@ -1154,8 +1158,7 @@ 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;
@@ -1331,8 +1334,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public void showHelp()
   {
     showUrl("http://wiki.jmol.org"
-    	// BH 2018	"http://jmol.sourceforge.net/docs/JmolUserGuide/"
-    			, "jmolHelp");
+    // BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/"
+            , "jmolHelp");
   }
 
   /**
@@ -1356,7 +1359,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   public abstract void showConsole(boolean show);
 
-  
   public static Viewer getJmolData(JmolParser jmolParser)
   {
     return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null,
@@ -1404,9 +1406,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           String commandOptions, final Container consolePanel,
           String buttonsToShow)
   {
-    
+
     System.err.println("Allocating Jmol Viewer: " + commandOptions);
-    
+
     if (commandOptions == null)
     {
       commandOptions = "";
@@ -1418,10 +1420,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
     viewer.setJmolStatusListener(this); // extends JmolCallbackListener
 
-    try {
+    try
+    {
       console = createJmolConsole(consolePanel, buttonsToShow);
-    } catch (Throwable e) {
-      System.err.println("Could not create Jmol application console. " + e.getMessage());
+    } catch (Throwable e)
+    {
+      System.err.println("Could not create Jmol application console. "
+              + e.getMessage());
       e.printStackTrace();
     }
     if (consolePanel != null)
@@ -1435,8 +1440,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   protected abstract JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow);
 
-  // BH 2018 -- Jmol console is not working due to problems with styled documents.
-  
+  // BH 2018 -- Jmol console is not working due to problems with styled
+  // documents.
 
   protected org.jmol.api.JmolAppConsoleInterface console = null;
 
@@ -1444,20 +1449,20 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public void setBackgroundColour(java.awt.Color col)
   {
     jmolHistory(false);
-    jmolScript("background [" + col.getRed() + ","
-            + col.getGreen() + "," + col.getBlue() + "];");
+    jmolScript("background [" + col.getRed() + "," + col.getGreen() + ","
+            + col.getBlue() + "];");
     jmolHistory(true);
   }
 
   private String jmolScript(String script)
   {
-    
+
     System.err.println(">>Jmol>> " + script);
-    
+
     String s = viewer.scriptWait(script);
-    
+
     System.err.println("<<Jmol<< " + s);
-    
+
     return s;
   }
 
-- 
1.7.10.2