merge from 2_4_Release branch

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

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 393476d..cb8f4f7 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
@@ -327,7 +327,7 @@ 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");
     }
@@ -559,11 +559,14 @@ 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)");
         }
       }
     }
@@ -747,13 +750,13 @@ 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 +832,16 @@ 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 +976,8 @@ 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 +1125,7 @@ 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);
   }