From e1a2bb8c2129346c0c1307604a4d3c2a604bf3b8 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 25 Aug 2010 14:13:22 +0000
Subject: [PATCH] excluded methods related to broken Jmol applet binding
 mechanism (JAL-621)

---
 src/jalview/bin/JalviewLite.java |  101 +++++++++++++++++++++++++-------------
 1 file changed, 67 insertions(+), 34 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 90092b6..0e77f02 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -17,18 +17,35 @@
  */
 package jalview.bin;
 
-import java.applet.*;
-
-import java.awt.*;
-import java.awt.event.*;
+import jalview.api.SequenceStructureBinding;
+import jalview.appletgui.AlignFrame;
+import jalview.appletgui.EmbmenuFrame;
+import jalview.appletgui.FeatureSettings;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FileParse;
+import jalview.io.IdentifyFile;
+import jalview.io.JnetAnnotationMaker;
+
+import java.applet.Applet;
+import java.awt.Button;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
 import java.io.BufferedReader;
 import java.io.InputStreamReader;
-import java.util.*;
-
-import jalview.api.SequenceStructureBinding;
-import jalview.appletgui.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+import java.lang.reflect.Method;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
 /**
  * Jalview Applet. Runs in Java 1.18 runtime
@@ -956,7 +973,7 @@ public class JalviewLite extends Applet
               // the local pdb file was identified in the class loader
               protocol = AppletFormatAdapter.URL; // this is probably NOT
               // CORRECT!
-              param = addProtocol(param); // 
+              param = addProtocol(param); //
             }
 
             pdb.setFile(param);
@@ -982,8 +999,9 @@ public class JalviewLite extends Applet
                 }
               }
 
-              newAlignFrame.newStructureView(applet, pdb, seqs, chains, protocol);
-              
+              newAlignFrame.newStructureView(applet, pdb, seqs, chains,
+                      protocol);
+
             }
           }
 
@@ -1284,38 +1302,53 @@ public class JalviewLite extends Applet
     }
     return false;
   }
+
   /**
-   * bind a pdb file to a sequence in the given alignFrame.  
-   * @param alFrame - null or specific alignFrame. This specifies the dataset that will be searched for a seuqence called sequenceId
-   * @param sequenceId - sequenceId within the dataset.
-   * @param pdbEntryString - the short name for the PDB file
-   * @param pdbFile - pdb file - either a URL or a valid PDB file.
-   * @return true if binding was as success
-   * TODO: consider making an exception structure for indicating when PDB parsing or seqeunceId location fails.
+   * bind a pdb file to a sequence in the given alignFrame.
+   * 
+   * @param alFrame
+   *          - null or specific alignFrame. This specifies the dataset that
+   *          will be searched for a seuqence called sequenceId
+   * @param sequenceId
+   *          - sequenceId within the dataset.
+   * @param pdbEntryString
+   *          - the short name for the PDB file
+   * @param pdbFile
+   *          - pdb file - either a URL or a valid PDB file.
+   * @return true if binding was as success TODO: consider making an exception
+   *         structure for indicating when PDB parsing or seqeunceId location
+   *         fails.
    */
-  public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile)
+  public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+          String pdbEntryString, String pdbFile)
   {
     return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
   }
+
+
   /**
-   * bind structures in a viewer to any matching sequences in an alignFrame (use sequenceIds to limit scope of search to specific sequences)
+   * bind structures in a viewer to any matching sequences in an alignFrame (use
+   * sequenceIds to limit scope of search to specific sequences)
+   * 
    * @param alFrame
    * @param viewer
    * @param sequenceIds
-   * @return
-   * TODO: consider making an exception structure for indicating when binding fails
-   */
-  public SequenceStructureBinding addStructureViewInstance(AlignFrame alFrame, Object viewer, String sequenceIds) 
+   * @return TODO: consider making an exception structure for indicating when
+   *         binding fails
+  public SequenceStructureBinding addStructureViewInstance(
+          AlignFrame alFrame, Object viewer, String sequenceIds)
   {
-    if (viewer!=null)
+
+    if (sequenceIds != null && sequenceIds.length() > 0)
     {
-      if (sequenceIds!=null && sequenceIds.length()>0)
-      {
-        return alFrame.addStructureViewInstance(viewer, separatorListToArray(sequenceIds));
-      } else {
-        return alFrame.addStructureViewInstance(viewer, null);
-      }
+      return alFrame.addStructureViewInstance(viewer,
+              separatorListToArray(sequenceIds));
     }
-    return null;
+    else
+    {
+      return alFrame.addStructureViewInstance(viewer, null);
+    }
+    // return null;
   }
+   */
 }
-- 
1.7.10.2