From e584930ae4941e8508c9073c6f08eb484a914bdf Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Sat, 22 Jul 2017 16:38:54 +0100
Subject: [PATCH] JAL-2624 check feature colour threshold when colouring
 structure

---
 .../renderer/seqfeatures/FeatureRenderer.java      |    8 ++-
 .../seqfeatures/FeatureRendererModel.java          |   10 ++-
 .../seqfeatures/FeatureColourFinderTest.java       |   65 ++++++++++++++++++++
 3 files changed, 81 insertions(+), 2 deletions(-)

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 98f5bff..759101d 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -335,6 +335,12 @@ public class FeatureRenderer extends FeatureRendererModel
         }
 
         Color featureColour = getColour(sequenceFeature);
+        if (featureColour == null)
+        {
+          // score feature outwith threshold for colouring
+          continue;
+        }
+
         boolean isContactFeature = sequenceFeature.isContactFeature();
 
         if (isContactFeature)
@@ -352,7 +358,7 @@ public class FeatureRenderer extends FeatureRendererModel
             drawnColour = featureColour;
           }
         }
-        else if (showFeature(sequenceFeature))
+        else
         {
           if (av.isShowSequenceFeaturesHeight()
                   && !Float.isNaN(sequenceFeature.score))
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index f6addb8..40f38b6 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -575,9 +575,17 @@ public abstract class FeatureRendererModel implements
   public Color getColour(SequenceFeature feature)
   {
     FeatureColourI fc = getFeatureStyle(feature.getType());
-    return fc.getColor(feature);
+    return fc.isColored(feature) ? fc.getColor(feature) : null;
   }
 
+  /**
+   * Answers true unless the feature has a score value which lies outside a
+   * minimum or maximum threshold configured for colouring. This method does not
+   * check feature type or group visibility.
+   * 
+   * @param sequenceFeature
+   * @return
+   */
   protected boolean showFeature(SequenceFeature sequenceFeature)
   {
     FeatureColourI fc = getFeatureStyle(sequenceFeature.type);
diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 9b68b43..4fc079e 100644
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -450,4 +450,69 @@ public class FeatureColourFinderTest
     FeatureColourFinder finder2 = new FeatureColourFinder(null);
     assertTrue(finder2.noFeaturesDisplayed());
   }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_graduatedWithThreshold()
+  {
+    seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2,
+            2, 0f, "KdGroup"));
+    seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4,
+            4, 5f, "KdGroup"));
+    seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7,
+            7, 10f, "KdGroup"));
+  
+    /*
+     * graduated colour from 0 to 10
+     * above threshold value of 5
+     */
+    Color min = new Color(100, 50, 150);
+    Color max = new Color(200, 0, 100);
+    FeatureColourI fc = new FeatureColour(min, max, 0, 10);
+    fc.setAboveThreshold(true);
+    fc.setThreshold(5f);
+    fr.setColour("kd", fc);
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+  
+    /*
+     * position 2, column 1, score 0 - below threshold - default colour
+     */
+    Color c = finder.findFeatureColour(Color.blue, seq, 1);
+    assertEquals(c, Color.blue);
+
+    /*
+     * position 4, column 3, score 5 - at threshold - default colour
+     */
+    c = finder.findFeatureColour(Color.blue, seq, 3);
+    assertEquals(c, Color.blue);
+  
+    /*
+     * position 7, column 9, score 10 - maximum colour in range
+     */
+    c = finder.findFeatureColour(Color.blue, seq, 9);
+    assertEquals(c, max);
+
+    /*
+     * now colour below threshold of 5
+     */
+    fc.setBelowThreshold(true);
+
+    /*
+     * position 2, column 1, score 0 - min colour
+     */
+    c = finder.findFeatureColour(Color.blue, seq, 1);
+    assertEquals(c, min);
+
+    /*
+     * position 4, column 3, score 5 - at threshold - default colour
+     */
+    c = finder.findFeatureColour(Color.blue, seq, 3);
+    assertEquals(c, Color.blue);
+
+    /*
+     * position 7, column 9, score 10 - above threshold - default colour
+     */
+    c = finder.findFeatureColour(Color.blue, seq, 9);
+    assertEquals(c, Color.blue);
+  }
 }
-- 
1.7.10.2