JAL-3148 show/hide features on structure independent of alignment

[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 7a8bc9c..eb13c30 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -175,7 +175,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   @Override
   public void colourByChain()
   {
-       super.colourByChain();
+    super.colourByChain();
     // TODO: colour by chain should colour each chain distinctly across all
     // visible models
     // TODO: http://issues.jalview.org/browse/JAL-628
@@ -518,10 +518,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRendererI sr, AlignmentViewPanel viewPanel)
+          String[] files, SequenceRendererI sr, AlignmentViewPanel viewPanel, boolean showFeatures)
   {
     return JmolCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, viewPanel);
+            getSequence(), sr, viewPanel, showFeatures);
   }
 
   /**