X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=955ad7be3313eea63ca8ba721b74107deaa4ff95;hb=bb3f28791ddb1a4f55e78a3bcd2ff4a591ebe95d;hp=5c5e3e8503919925d5c349e0ab836e392e6a6f92;hpb=7178ab15790c2e7bffcead037f99dca883846073;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 5c5e3e8..955ad7b 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -236,7 +236,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
    * @param ap
    */
   public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
-          AlignmentPanel ap)
+          final AlignmentPanel ap)
   {
     progressBar = ap.alignFrame;
     // ////////////////////////////////
@@ -271,7 +271,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
         {
           if (frames[i] instanceof AppJmol)
           {
-            AppJmol topJmol = ((AppJmol) frames[i]);
+            final AppJmol topJmol = ((AppJmol) frames[i]);
             // JBPNOTE: this looks like a binding routine, rather than a gui
             // routine
             for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
@@ -280,7 +280,10 @@ public class AppJmol extends GStructureViewer implements Runnable,
               {
                 topJmol.jmb.addSequence(pe, seq);
                 topJmol.addAlignmentPanel(ap);
+                // add it to the set used for colouring
+                topJmol.useAlignmentPanelForColourbyseq(ap);
                 topJmol.buildJmolActionMenu();
+                ap.getStructureSelectionManager().sequenceColoursChanged(ap);
                 break;
               }
             }
@@ -1053,7 +1056,12 @@ public class AppJmol extends GStructureViewer implements Runnable,
     buriedColour.setSelected(true);
     jmb.setJalviewColourScheme(new BuriedColourScheme());
   }
-
+  
+  public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+  {
+    setJalviewColourScheme(new PurinePyrimidineColourScheme());
+  }
+  
   public void userColour_actionPerformed(ActionEvent actionEvent)
   {
     userColour.setSelected(true);