Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / schemes / FeatureColour.java

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index a40a690..54d1c6c 100644 (file)
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -550,16 +550,27 @@ public class FeatureColour implements FeatureColourI
       return getColour();
     }
 
-    // todo should we check for above/below threshold here?
-    if (range == 0.0)
-    {
-      return getMaxColour();
-    }
+    /*
+     * graduated colour case, optionally with threshold
+     * Float.NaN is assigned minimum visible score colour
+     */
     float scr = feature.getScore();
     if (Float.isNaN(scr))
     {
       return getMinColour();
     }
+    if (isAboveThreshold() && scr <= threshold)
+    {
+      return null;
+    }
+    if (isBelowThreshold() && scr >= threshold)
+    {
+      return null;
+    }
+    if (range == 0.0)
+    {
+      return getMaxColour();
+    }
     float scl = (scr - base) / range;
     if (isHighToLow)
     {
@@ -601,44 +612,6 @@ public class FeatureColour implements FeatureColourI
     return (isHighToLow) ? (base + range) : base;
   }
 
-  /**
-   * Answers true if the feature has a simple colour, or is coloured by label,
-   * or has a graduated colour and the score of this feature instance is within
-   * the range to render (if any), i.e. does not lie below or above any
-   * threshold set.
-   * 
-   * @param feature
-   * @return
-   */
-  @Override
-  public boolean isColored(SequenceFeature feature)
-  {
-    if (isColourByLabel() || !isGraduatedColour())
-    {
-      return true;
-    }
-
-    float val = feature.getScore();
-    if (Float.isNaN(val))
-    {
-      return true;
-    }
-    if (Float.isNaN(this.threshold))
-    {
-      return true;
-    }
-
-    if (isAboveThreshold() && val <= threshold)
-    {
-      return false;
-    }
-    if (isBelowThreshold() && val >= threshold)
-    {
-      return false;
-    }
-    return true;
-  }
-
   @Override
   public boolean isSimpleColour()
   {