patch to fix occasional arrayoutofbounds exception when working with hidden columns...

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 393476d..9a09df4 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -305,6 +305,7 @@ public class JalviewLite extends Applet
   boolean embedded = false;
 
   private boolean checkForJmol = true;
+  private boolean checkedForJmol = false; // ensure we don't check for jmol every time the app is re-inited
 
   public boolean jmolAvailable = false;
 
@@ -327,7 +328,7 @@ public class JalviewLite extends Applet
      * if true disable the check for jmol
      */
     String chkforJmol = getParameter("nojmol");
-    if (chkforJmol!=null)
+    if (chkforJmol != null)
     {
       checkForJmol = !chkforJmol.equals("true");
     }
@@ -397,9 +398,6 @@ public class JalviewLite extends Applet
       }
     }
 
-    LoadJmolThread jmolAvailable = new LoadJmolThread();
-    jmolAvailable.start();
-
     final JalviewLite applet = this;
     if (getParameter("embedded") != null
             && getParameter("embedded").equalsIgnoreCase("true"))
@@ -540,8 +538,14 @@ public class JalviewLite extends Applet
 
   class LoadJmolThread extends Thread
   {
+    private boolean running=false;
+
     public void run()
     {
+      if (running || checkedForJmol) {
+        return;
+      }
+      running=true;
       if (checkForJmol)
       {
         try
@@ -559,13 +563,23 @@ public class JalviewLite extends Applet
         } catch (java.lang.ClassNotFoundException ex)
         {
         }
-      } else {
-        jmolAvailable=false;
+      }
+      else
+      {
+        jmolAvailable = false;
         if (debug)
         {
-          System.err.println("Skipping Jmol check. Will use MCView (probably)");
+          System.err
+                  .println("Skipping Jmol check. Will use MCView (probably)");
         }
       }
+      checkedForJmol=true;
+      running=false;
+    }
+
+    public boolean notFinished()
+    {
+      return running || !checkedForJmol;
     }
   }
 
@@ -585,9 +599,8 @@ public class JalviewLite extends Applet
      * State variable: format of file source
      */
     String format;
-
+    String _file;
     JalviewLite applet;
-
     private void dbgMsg(String msg)
     {
       if (applet.debug)
@@ -622,24 +635,32 @@ public class JalviewLite extends Applet
       dbgMsg("Protocol identified as '" + protocol + "'");
       return file;
     }
-
+    
     public LoadingThread(String _file, JalviewLite _applet)
     {
-      dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
-      file = setProtocolState(_file);
-
-      format = new jalview.io.IdentifyFile().Identify(file, protocol);
-      dbgMsg("File identified as '" + format + "'");
+      this._file=_file;
       applet = _applet;
     }
 
     public void run()
     {
+      LoadJmolThread jmolchecker = new LoadJmolThread();
+      jmolchecker.start();
+      while (jmolchecker.notFinished())
+      {
+        // wait around until the Jmol check is complete.
+        try { Thread.sleep(2); } catch (Exception e) {};
+      }
       startLoading();
     }
 
     private void startLoading()
     {
+      dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
+      file = setProtocolState(_file);
+
+      format = new jalview.io.IdentifyFile().Identify(file, protocol);
+      dbgMsg("File identified as '" + format + "'");
       dbgMsg("Loading started.");
       Alignment al = null;
       try
@@ -747,13 +768,13 @@ public class JalviewLite extends Applet
                     param, protocol);
             JnetAnnotationMaker.add_annotation(predictions,
                     currentAlignFrame.viewport.getAlignment(), 0, false); // false==do
-                                                                          // not
-                                                                          // add
-                                                                          // sequence
-                                                                          // profile
-                                                                          // from
-                                                                          // concise
-                                                                          // output
+            // not
+            // add
+            // sequence
+            // profile
+            // from
+            // concise
+            // output
             currentAlignFrame.alignPanel.fontChanged();
             currentAlignFrame.alignPanel.setScrollValues(0, 0);
           } catch (Exception ex)
@@ -829,14 +850,16 @@ public class JalviewLite extends Applet
             }
             param = setProtocolState(param);
 
-            if (!jmolAvailable
-                    && protocol == AppletFormatAdapter.CLASSLOADER)
+            if (// !jmolAvailable
+            // &&
+            protocol == AppletFormatAdapter.CLASSLOADER)
             {
-              // TODO: pass PDB file in classloader on to Jmol
+              // TODO: verify this Re:
+              // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
               // This exception preserves the current behaviour where, even if
               // the local pdb file was identified in the class loader
               protocol = AppletFormatAdapter.URL; // this is probably NOT
-                                                  // CORRECT!
+              // CORRECT!
               param = addProtocol(param); // 
             }
 
@@ -971,7 +994,8 @@ public class JalviewLite extends Applet
    * separator used for separatorList
    */
   protected String separator = "|"; // this is a safe(ish) separator - tabs
-                                    // don't work for firefox
+
+  // don't work for firefox
 
   /**
    * parse the string into a list
@@ -1119,7 +1143,7 @@ public class JalviewLite extends Applet
           boolean state)
   {
     boolean st = state;// !(state==null || state.equals("") ||
-                        // state.toLowerCase().equals("false"));
+    // state.toLowerCase().equals("false"));
     alf.setFeatureGroupState(separatorListToArray(groups), st);
   }