From 9adeaab28df6873e67ebe42e1ccd3a87cf6507af Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 20 Aug 2010 11:55:01 +0000
Subject: [PATCH] improved debug output when Jmol viewer creation fails

---
 src/jalview/appletgui/AppletJmol.java |  100 ++++++++++++++-------------------
 1 file changed, 43 insertions(+), 57 deletions(-)

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index fb15c82..afbc83c 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -33,7 +33,7 @@ import org.jmol.viewer.JmolConstants;
 
 import jalview.schemes.*;
 
-public class AppletJmol extends EmbmenuFrame implements 
+public class AppletJmol extends EmbmenuFrame implements
 // StructureListener,
         KeyListener, ActionListener, ItemListener, SequenceStructureBinding
 
@@ -178,9 +178,22 @@ public class AppletJmol extends EmbmenuFrame implements
     renderPanel = new RenderPanel();
     embedMenuIfNeeded(renderPanel);
     this.add(renderPanel, BorderLayout.CENTER);
-    jmb.allocateViewer(renderPanel, 
-            "jalviewJmol", ap.av.applet.getDocumentBase(), ap.av.applet
-                    .getCodeBase(), "");
+    try
+    {
+      jmb.allocateViewer(renderPanel, "jalviewJmol",
+              ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(),
+              "");
+    } catch (Exception e)
+    {
+      System.err
+              .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase="
+                      + ap.av.applet.getDocumentBase()
+                      + "\nCodebase="
+                      + ap.av.applet.getCodeBase());
+      e.printStackTrace();
+      dispose();
+      return;
+    }
     jmb.newJmolPopup(true, "Jmol", true);
 
     this.addWindowListener(new WindowAdapter()
@@ -244,7 +257,8 @@ public class AppletJmol extends EmbmenuFrame implements
             throw new Exception(
                     "Invalid datasource. Could not obtain Reader.");
           }
-          jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader);
+          jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
+                  freader);
         } catch (Exception e)
         {
           // give up!
@@ -259,24 +273,6 @@ public class AppletJmol extends EmbmenuFrame implements
     jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
   }
 
-  /**
-   * create a new binding between structures in an existing jmol viewer instance
-   * and an alignpanel with sequences that have existing PDBFile entries. Note,
-   * this does not open a new Jmol window, or modify the display of the
-   * structures in the original jmol window.
-   * 
-   * @param viewer2
-   * @param alignPanel
-   * @param seqs
-   *          - sequences to search for associations
-   */
-  public AppletJmol(JmolViewer viewer2, AlignmentPanel alignPanel,
-          SequenceI[] seqs)
-  {
-
-    // TODO Auto-generated constructor stub
-  }
-
   public void loadInline(String string)
   {
     loadedInline = true;
@@ -427,13 +423,15 @@ public class AppletJmol extends EmbmenuFrame implements
   }
 
   /**
-   * tick or untick the seqColour menu entry depending upon if it was selected or not.
+   * tick or untick the seqColour menu entry depending upon if it was selected
+   * or not.
+   * 
    * @param itm
    */
   private void setEnabled(MenuItem itm)
   {
-    seqColour.setState(itm==seqColour);
-    jmb.setColourBySequence(itm==seqColour);
+    seqColour.setState(itm == seqColour);
+    jmb.setColourBySequence(itm == seqColour);
   }
 
   public void itemStateChanged(ItemEvent evt)
@@ -441,9 +439,7 @@ public class AppletJmol extends EmbmenuFrame implements
     if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb
-              .colourBySequence(ap.av.getShowSequenceFeatures(),
-                      ap.av.alignment);
+      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
     }
     else if (!allChainsSelected)
       centerViewer();
@@ -555,35 +551,25 @@ public class AppletJmol extends EmbmenuFrame implements
       }
     }
   }
-/*
-  @Override
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbId)
-  {
-    return jmb.getColour(atomIndex, pdbResNum, chain, pdbId);
-  }
 
-  @Override
-  public String[] getPdbFile()
-  {
-    return jmb.getPdbFile();
-  }
-
-  @Override
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbId)
-  {
-    jmb.highlightAtom(atomIndex, pdbResNum, chain, pdbId);
-
-  }
-
-  @Override
-  public void mouseOverStructure(int atomIndex, String strInfo)
-  {
-    jmb.mouseOverStructure(atomIndex, strInfo);
-
-  }
-*/
+  /*
+   * @Override public Color getColour(int atomIndex, int pdbResNum, String
+   * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain,
+   * pdbId); }
+   * 
+   * @Override public String[] getPdbFile() { return jmb.getPdbFile(); }
+   * 
+   * @Override public void highlightAtom(int atomIndex, int pdbResNum, String
+   * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain,
+   * pdbId);
+   * 
+   * }
+   * 
+   * @Override public void mouseOverStructure(int atomIndex, String strInfo) {
+   * jmb.mouseOverStructure(atomIndex, strInfo);
+   * 
+   * }
+   */
   public void setJalviewColourScheme(UserColourScheme ucs)
   {
     jmb.setJalviewColourScheme(ucs);
-- 
1.7.10.2