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

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

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index b2aeee4..f3de86b 100644 (file)
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -49,6 +49,7 @@ public class JmolCommands
   /**
    * Jmol utility which constructs the commands to colour chains by the given
    * alignment
+ * @param showFeatures 
    * 
    * @returns Object[] { Object[] { <model being coloured>,
    * 
@@ -56,10 +57,10 @@ public class JmolCommands
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRendererI sr,
-          AlignmentViewPanel viewPanel)
+          AlignmentViewPanel viewPanel, boolean showFeatures)
   {
     FeatureRenderer fr = viewPanel.getFeatureRenderer();
-    FeatureColourFinder finder = new FeatureColourFinder(fr);
+    FeatureColourFinder finder = showFeatures ? new FeatureColourFinder(fr) : null;
     AlignViewportI viewport = viewPanel.getAlignViewport();
     HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
     AlignmentI al = viewport.getAlignment();