Merge branch 'develop' into trialMerge

[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 2cabefa..4698e4d 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -44,7 +44,6 @@ import java.awt.event.ComponentEvent;
 import java.awt.event.ComponentListener;
 import java.io.File;
 import java.net.URL;
-import java.security.AccessControlException;
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.Hashtable;
@@ -167,7 +166,9 @@ 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 +481,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   Thread colourby = null;
+
   /**
    * Sends a set of colour commands to the structure viewer
    * 
@@ -494,7 +496,7 @@ 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 +511,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
     });
     colourby.start();
+    this.colourby = colourby;
   }
 
   /**
@@ -615,74 +618,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   private int _modelFileNameMap[];
 
-  // ////////////////////////////////
-  // /StructureListener
-  // @Override
-  public synchronized String[] getPdbFilex()
-  {
-    if (viewer == null)
-    {
-      return new String[0];
-    }
-    if (modelFileNames == null)
-    {
-      List<String> mset = new ArrayList<>();
-      _modelFileNameMap = new int[viewer.ms.mc];
-      String m = viewer.ms.getModelFileName(0);
-      if (m != null)
-      {
-        String filePath = m;
-        try
-        {
-          filePath = new File(m).getAbsolutePath();
-        } catch (AccessControlException x)
-        {
-          // usually not allowed to do this in applet
-          System.err.println(
-                  "jmolBinding: Using local file string from Jmol: " + m);
-        }
-        if (filePath.indexOf("/file:") != -1)
-        {
-          // applet path with docroot - discard as format won't match pdbfile
-          filePath = m;
-        }
-        mset.add(filePath);
-        _modelFileNameMap[0] = 0; // filename index for first model is always 0.
-      }
-      int j = 1;
-      for (int i = 1; i < viewer.ms.mc; i++)
-      {
-        m = viewer.ms.getModelFileName(i);
-        String filePath = m;
-        if (m != null)
-        {
-          try
-          {
-            filePath = new File(m).getAbsolutePath();
-          } catch (AccessControlException x)
-          {
-            // usually not allowed to do this in applet, so keep raw handle
-            // System.err.println("jmolBinding: Using local file string from
-            // Jmol: "+m);
-          }
-        }
-
-        /*
-         * add this model unless it is read from a structure file we have
-         * already seen (example: 2MJW is an NMR structure with 10 models)
-         */
-        if (!mset.contains(filePath))
-        {
-          mset.add(filePath);
-          _modelFileNameMap[j] = i; // record the model index for the filename
-          j++;
-        }
-      }
-      modelFileNames = mset.toArray(new String[mset.size()]);
-    }
-    return modelFileNames;
-  }
-
   @Override
   public synchronized String[] getStructureFiles()
   {
@@ -877,7 +812,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       try
       {
         // recover PDB filename for the model hovered over.
-        int mnumber = new Integer(mdlId).intValue() - 1;
+        int mnumber = Integer.valueOf(mdlId).intValue() - 1;
         if (_modelFileNameMap != null)
         {
           int _mp = _modelFileNameMap.length - 1;
@@ -1154,8 +1089,7 @@ 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 +1265,8 @@ 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 +1290,6 @@ 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 +1337,9 @@ 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 +1351,13 @@ 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 +1371,8 @@ 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 +1380,20 @@ 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;
   }