Get colour from structure added

diff --git a/src/jalview/gui/AppJMol.java b/src/jalview/gui/AppJMol.java
index da94e4c..e3aa9ea 100644 (file)
--- a/src/jalview/gui/AppJMol.java
+++ b/src/jalview/gui/AppJMol.java
@@ -195,8 +195,6 @@ public synchronized void addSequence(SequenceI [] seq)
     jmolpopup = JmolPopup.newJmolPopup(viewer);
 
     viewer.evalStringQuiet(command);
-
-    colourBySequence = true;
   }
 
 
@@ -582,6 +580,14 @@ public synchronized void addSequence(SequenceI [] seq)
 
   }
 
+  public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  {
+    if (!pdbfile.equals(pdbentry.getFile()))
+      return null;
+
+    return new Color(viewer.getAtomArgb(atomIndex));
+  }
+
   public void updateColours(Object source)
   {
     colourBySequence( (AlignmentPanel) source);