From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Sun, 23 Jul 2017 08:37:51 +0000 (+0100)
Subject: JAL-2481 JAL-2624 test for render feature below score feature outwith
X-Git-Tag: Release_2_10_3b1~173
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ef7ded229ddd70a406c37a7aac160b832736eb76;p=jalview.git

JAL-2481 JAL-2624 test for render feature below score feature outwith
threshold
---

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index d661915..8feee1f 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -416,7 +416,8 @@ public class FeatureRenderer extends FeatureRendererModel
    * Returns the sequence feature colour rendered at the given column position,
    * or null if none found. The feature of highest render order (i.e. on top) is
    * found, subject to both feature type and feature group being visible, and
-   * its colour returned.
+   * its colour returned. This method is suitable when no feature transparency
+   * applied (only the topmost visible feature colour is rendered).
    * <p>
    * Note this method does not check for a gap in the column so would return the
    * colour for features enclosing a gapped column. Check for gap before calling
diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index ecabfca..7fd7abc 100644
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -452,15 +452,19 @@ public class FeatureColourFinderTest
   @Test(groups = "Functional")
   public void testFindFeatureColour_graduatedWithThreshold()
   {
-    seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2,
+    String kdFeature = "kd";
+    String metalFeature = "Metal";
+    seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 2,
             2, 0f, "KdGroup"));
-    seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4,
+    seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 4,
             4, 5f, "KdGroup"));
-    seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7,
+    seq.addSequenceFeature(new SequenceFeature(metalFeature, "Fe", 4, 4,
+            5f, "MetalGroup"));
+    seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 7,
             7, 10f, "KdGroup"));
   
     /*
-     * graduated colour from 0 to 10
+     * kd feature has graduated colour from 0 to 10
      * above threshold value of 5
      */
     Color min = new Color(100, 50, 150);
@@ -468,8 +472,19 @@ public class FeatureColourFinderTest
     FeatureColourI fc = new FeatureColour(min, max, 0, 10);
     fc.setAboveThreshold(true);
     fc.setThreshold(5f);
-    fr.setColour("kd", fc);
+    fr.setColour(kdFeature, fc);
+    FeatureColour green = new FeatureColour(Color.green);
+    fr.setColour(metalFeature, green);
     fr.featuresAdded();
+
+    /*
+     * render order is kd above Metal
+     */
+    Object[][] data = new Object[2][];
+    data[0] = new Object[] { kdFeature, fc, true };
+    data[1] = new Object[] { metalFeature, green, true };
+    fr.setFeaturePriority(data);
+
     av.setShowSequenceFeatures(true);
   
     /*
@@ -479,10 +494,11 @@ public class FeatureColourFinderTest
     assertEquals(c, Color.blue);
 
     /*
-     * position 4, column 3, score 5 - at threshold - default colour
+     * position 4, column 3, score 5 - at threshold
+     * should return Green (colour of Metal feature)
      */
     c = finder.findFeatureColour(Color.blue, seq, 3);
-    assertEquals(c, Color.blue);
+    assertEquals(c, Color.green);
   
     /*
      * position 7, column 9, score 10 - maximum colour in range
@@ -502,10 +518,11 @@ public class FeatureColourFinderTest
     assertEquals(c, min);
 
     /*
-     * position 4, column 3, score 5 - at threshold - default colour
+     * position 4, column 3, score 5 - at threshold
+     * should return Green (colour of Metal feature)
      */
     c = finder.findFeatureColour(Color.blue, seq, 3);
-    assertEquals(c, Color.blue);
+    assertEquals(c, Color.green);
 
     /*
      * position 7, column 9, score 10 - above threshold - default colour