JAL-2430 colour columns hidden in alignment gray on structure

[jalview.git] / src / jalview / structures / models / AAStructureBindingModel.java

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index bb9ee85..7d57886 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -20,6 +20,7 @@
  */
 package jalview.structures.models;
 
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
@@ -724,7 +725,7 @@ public abstract class AAStructureBindingModel extends
 
   protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
           String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment);
+          AlignViewportI alignViewportI);
 
   /**
    * returns the current featureRenderer that should be used to colour the
@@ -760,8 +761,6 @@ public abstract class AAStructureBindingModel extends
    */
   public void colourBySequence(AlignmentViewPanel alignmentv)
   {
-    boolean showFeatures = alignmentv.getAlignViewport()
-            .isShowSequenceFeatures();
     if (!colourBySequence || !isLoadingFinished())
     {
       return;
@@ -775,14 +774,15 @@ public abstract class AAStructureBindingModel extends
     SequenceRenderer sr = getSequenceRenderer(alignmentv);
   
     FeatureRenderer fr = null;
+    boolean showFeatures = alignmentv.getAlignViewport()
+            .isShowSequenceFeatures();
     if (showFeatures)
     {
       fr = getFeatureRenderer(alignmentv);
     }
-    AlignmentI alignment = alignmentv.getAlignment();
   
     StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
-            files, sr, fr, alignment);
+            files, sr, fr, alignmentv.getAlignViewport());
     colourBySequence(colourBySequenceCommands);
   }