loadingFromArchive flag added

diff --git a/src/jalview/gui/AppJMol.java b/src/jalview/gui/AppJMol.java
index 575c6ec..2f9fadc 100644 (file)
--- a/src/jalview/gui/AppJMol.java
+++ b/src/jalview/gui/AppJMol.java
@@ -55,6 +55,7 @@ public class AppJMol
   AlignmentPanel ap;\r
   String fileLoadingError;\r
   boolean colourBySequence = true;\r
+  boolean loadingFromArchive = false;\r
 \r
   public AppJMol(String file, String id,\r
                  SequenceI[] seq,\r
@@ -62,6 +63,7 @@ public class AppJMol
                  String loadStatus,\r
                  Rectangle bounds)\r
   {\r
+    loadingFromArchive = true;\r
     pdbentry = new PDBEntry();\r
     pdbentry.setFile(file);\r
     pdbentry.setId(id);\r
@@ -477,6 +479,15 @@ public class AppJMol
   }\r
 \r
 \r
+  public void jmolHelp_actionPerformed(ActionEvent actionEvent)\r
+  {\r
+       try{\r
+         jalview.util.BrowserLauncher.openURL(\r
+             "http://jmol.sourceforge.net/docs/JmolUserGuide/");\r
+       }catch(Exception ex){}\r
+   }\r
+\r
+\r
   //////////////////////////////////\r
   ///StructureListener\r
   public String getPdbFile()\r
@@ -553,6 +564,7 @@ public class AppJMol
     colourBySequence( (AlignmentPanel) source);\r
   }\r
 \r
+\r
 //End StructureListener\r
 ////////////////////////////\r
 \r
@@ -707,10 +719,16 @@ public class AppJMol
       setChainMenuItems(chains);\r
 \r
       jmolpopup.updateComputedMenus();\r
-      viewer.evalStringQuiet(\r
-          "select backbone;restrict;cartoon;wireframe off;spacefill off");\r
 \r
-      colourBySequence(ap);\r
+      if(!loadingFromArchive)\r
+      {\r
+        viewer.evalStringQuiet(\r
+             "select backbone;restrict;cartoon;wireframe off;spacefill off");\r
+\r
+        colourBySequence(ap);\r
+      }\r
+\r
+      loadingFromArchive = false;\r
     }\r
     else\r
       return;\r