JAL-2430 colour columns hidden in alignment gray on structure

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index f21f630..82e188f 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.jmol;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
@@ -499,16 +500,16 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * @param files
    * @param sr
    * @param fr
-   * @param alignment
+   * @param viewport
    * @return
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
           String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          AlignViewportI viewport)
   {
     return JmolCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, fr, alignment);
+            getSequence(), sr, fr, viewport);
   }
 
   /**