refactored to remove App reference in Applet (JAL-638)

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 8e72380..31f91ee 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -376,7 +376,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
       }
     }
     String[] selcom = new String[files.length];
-    int nmatched=0;
+    int nmatched = 0;
     // generate select statements to select regions to superimpose structures
     {
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
@@ -390,7 +390,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
         {
           if (matched[r])
           {
-            if (pdbfnum==0) {
+            if (pdbfnum == 0)
+            {
               nmatched++;
             }
             if (lpos != commonrpositions[pdbfnum][r] - 1)
@@ -439,8 +440,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
         }
       }
     }
-    // TODO: consider bailing if nmatched less than 4 because superposition not well defined.
-    // TODO: refactor superposable position search (above) from jmol selection construction (below)
+    // TODO: consider bailing if nmatched less than 4 because superposition not
+    // well defined.
+    // TODO: refactor superposable position search (above) from jmol selection
+    // construction (below)
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       if (pdbfnum == refStructure)
@@ -689,7 +692,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
   // /StructureListener
   public synchronized String[] getPdbFile()
   {
-    if (viewer==null)
+    if (viewer == null)
     {
       return new String[0];
     }
@@ -705,8 +708,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
         mset[j] = viewer.getModelFileName(i);
         _modelFileNameMap[j] = i; // record the model index for the filename
         // skip any additional models in the same file (NMR structures)
-        if ((mset[j] == null ? mset[j] != mset[j - 1] : (mset[j - 1] == null
-                || !mset[j].equals(mset[j - 1]))))
+        if ((mset[j] == null ? mset[j] != mset[j - 1]
+                : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
         {
           j++;
         }
@@ -1019,12 +1022,16 @@ public abstract class JalviewJmolBinding implements StructureListener,
     return false;
   }
 
-  // incremented every time a load notification is successfully handled - lightweight mechanism for other threads to detect when they can start referrring to new structures. 
-  private long loadNotifiesHandled=0;
+  // incremented every time a load notification is successfully handled -
+  // lightweight mechanism for other threads to detect when they can start
+  // referrring to new structures.
+  private long loadNotifiesHandled = 0;
+
   public long getLoadNotifiesHandled()
   {
     return loadNotifiesHandled;
   }
+
   public void notifyFileLoaded(String fullPathName, String fileName2,
           String modelName, String errorMsg, int modelParts)
   {
@@ -1093,9 +1100,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
       if (loadedInline)
       {
         // calculate essential attributes for the pdb data imported inline.
-        // prolly need to resolve modelnumber properly - for now just use our 'best guess'
-        pdbfile = viewer.getData(""+(1+_modelFileNameMap[modelnum])+".0",
-                "PDB");
+        // prolly need to resolve modelnumber properly - for now just use our
+        // 'best guess'
+        pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+                + ".0", "PDB");
         pdbfhash = "" + pdbfile.hashCode();
       }
       if (pdbentry != null)
@@ -1107,8 +1115,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
           boolean matches = false;
           if (fileName == null)
           {
-            if (false) 
-              // see JAL-623 - need method of matching pasted data up
+            if (false)
+            // see JAL-623 - need method of matching pasted data up
             {
               pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile,
                       AppletFormatAdapter.PASTE);
@@ -1144,7 +1152,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
               pdb = ssm.setMapping(sequence[pe], chains[pe],
                       pdbentry[pe].getFile(), protocol);
 
-
             }
           }
           if (matches)
@@ -1162,19 +1169,19 @@ public abstract class JalviewJmolBinding implements StructureListener,
       }
       if (!foundEntry && associateNewStructs)
       {
-          // this is a foreign pdb file that jalview doesn't know about - add
-          // it to the dataset and try to find a home - either on a matching
-          // sequence or as a new sequence.
-          String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
-                  "PDB");
-          // parse pdb file into a chain, etc.
-          // locate best match for pdb in associated views and add mapping to
-          // ssm
-          // if properly registered then
-          notifyLoaded = true;
+        // this is a foreign pdb file that jalview doesn't know about - add
+        // it to the dataset and try to find a home - either on a matching
+        // sequence or as a new sequence.
+        String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
+                "PDB");
+        // parse pdb file into a chain, etc.
+        // locate best match for pdb in associated views and add mapping to
+        // ssm
+        // if properly registered then
+        notifyLoaded = true;
 
-        }
       }
+    }
     // FILE LOADED OK
     // so finally, update the jmol bits and pieces
     if (jmolpopup != null)
@@ -1292,9 +1299,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   /**
    * called to show or hide the associated console window container.
+   * 
    * @param show
    */
   public abstract void showConsole(boolean show);
+
   /**
    * @param renderPanel
    * @param jmolfileio
@@ -1309,8 +1318,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
           String htmlName, URL documentBase, URL codeBase,
           String commandOptions)
   {
-    allocateViewer(renderPanel, jmolfileio, htmlName, documentBase, codeBase, commandOptions, null,null);
+    allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
+            codeBase, commandOptions, null, null);
   }
+
   /**
    * 
    * @param renderPanel
@@ -1321,22 +1332,26 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * @param documentBase
    * @param codeBase
    * @param commandOptions
-   * @param consolePanel - panel to contain Jmol console
-   * @param buttonsToShow - buttons to show on the console, in ordr
+   * @param consolePanel
+   *          - panel to contain Jmol console
+   * @param buttonsToShow
+   *          - buttons to show on the console, in ordr
    */
-    public void allocateViewer(Component renderPanel, boolean jmolfileio,
-            String htmlName, URL documentBase, URL codeBase,
-            String commandOptions, final Container consolePanel, String buttonsToShow)
-    {
-      viewer = JmolViewer.allocateViewer(renderPanel,
+  public void allocateViewer(Component renderPanel, boolean jmolfileio,
+          String htmlName, URL documentBase, URL codeBase,
+          String commandOptions, final Container consolePanel,
+          String buttonsToShow)
+  {
+    viewer = JmolViewer.allocateViewer(renderPanel,
             (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
                     + ((Object) this).toString(), documentBase, codeBase,
             commandOptions, this);
-      
-      console = createJmolConsole(viewer, consolePanel,
-              buttonsToShow);
-      
-      viewer.setConsole(new JmolAppConsoleInterface() {
+
+    console = createJmolConsole(viewer, consolePanel, buttonsToShow);
+    if (console != null)
+    {
+      viewer.setConsole(new JmolAppConsoleInterface()
+      {
 
         @Override
         public JmolScriptEditorInterface getScriptEditor()
@@ -1372,7 +1387,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
         public void sendConsoleEcho(String strEcho)
         {
           console.sendConsoleEcho(strEcho);
-          
+
         }
 
         @Override
@@ -1392,15 +1407,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
         {
           console.dispose();
         }
-        
-        
+
       });
-      
-      
+    }
+
   }
-    
-    protected abstract JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
-             Container consolePanel, String buttonsToShow);
+
+  protected abstract JmolAppConsoleInterface createJmolConsole(
+          JmolViewer viewer2, Container consolePanel, String buttonsToShow);
 
   protected org.jmol.api.JmolAppConsoleInterface console = null;