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

[jalview.git] / src / jalview / ext / rbvi / chimera / ChimeraCommands.java

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index dad8511..ba8f4b8 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -23,7 +23,7 @@ package jalview.ext.rbvi.chimera;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
+import jalview.api.SequenceRendererI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceFeature;
@@ -66,11 +66,11 @@ public class ChimeraCommands
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr,
-          AlignmentViewPanel viewPanel)
+          SequenceI[][] sequence, SequenceRendererI sr,
+          AlignmentViewPanel viewPanel, boolean showFeatures)
   {
     Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
-            sequence, sr, viewPanel);
+            sequence, sr, viewPanel, showFeatures);
 
     List<String> colourCommands = buildColourCommands(colourMap);
 
@@ -188,11 +188,11 @@ public class ChimeraCommands
    */
   protected static Map<Object, AtomSpecModel> buildColoursMap(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr,
-          AlignmentViewPanel viewPanel)
+          SequenceI[][] sequence, SequenceRendererI sr,
+          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();