Make sure sequence is in mouse over alignment

[jalview.git] / src / jalview / appletgui / AppletJmol.java

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index b7e67c1..4951516 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -461,6 +461,14 @@ public class AppletJmol extends Frame
 //End StructureListener
 ////////////////////////////
 
+  public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  {
+    if (!pdbfile.equals(pdbentry.getFile()))
+      return null;
+
+    return new Color(viewer.getAtomArgb(atomIndex));
+  }
+
   FeatureRenderer fr;
   public void colourBySequence(AlignmentPanel ap)
   {
@@ -494,7 +502,8 @@ public class AppletJmol extends Frame
     {
       for (int m = 0; m < mapping.length; m++)
       {
-        if (mapping[m].getSequence() == sequence[s])
+        if (mapping[m].getSequence() == sequence[s]
+            && ap.av.alignment.findIndex(sequence[s])>-1)
         {
           for (int r = 0; r < sequence[s].getLength(); r++)
           {