From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 23 Mar 2007 10:47:10 +0000 (+0000)
Subject: loadingFromArchive flag added
X-Git-Tag: Release_2_3~310
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b1b09b4b6438b2cbde31369115d961f524111549;p=jalview.git

loadingFromArchive flag added
---

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