JAL-766 JAL-733 - new alignment->jmol associations are automatically used to colour...

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 5c5e3e8..e500240 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -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;
               }
             }