X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.java;h=795cd3681e4ea9a059604ee6cf58462c41e64c69;hb=cf64def09a8b741483854ddd8c034d0aefff15b4;hp=1f47da3421c039c2f9f15950421709927a2004bc;hpb=a2f6cd5b735ce1a8adf4dd5cd4d71b6d0a477587;p=jalview.git

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 1f47da3..795cd36 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -304,14 +304,19 @@ public class FeatureRenderer extends FeatureRendererModel
       List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
               visiblePositions.getBegin(), visiblePositions.getEnd(), type);
 
-      filterFeaturesForDisplay(overlaps, fc);
+      if (fc.isSimpleColour())
+      {
+        filterFeaturesForDisplay(overlaps);
+      }
 
       for (SequenceFeature sf : overlaps)
       {
-        Color featureColour = fc.getColor(sf);
+        Color featureColour = getColor(sf, fc);
         if (featureColour == null)
         {
-          // score feature outwith threshold for colouring
+          /*
+           * feature excluded by visibility settings, filters, or colour threshold
+           */
           continue;
         }