X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureColourFinderTest.java;h=4fc079ec119e7e3f4a898cbc748754b7d9a597a6;hb=b4d2b6a2ed131265ed599db27de9b82aaf010400;hp=127b6c2da20a2b517f0581bd4ffa0cc9fafac33c;hpb=846f3f1ad573cad309d41356af68887a4a3348eb;p=jalview.git

diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 127b6c2..4fc079e 100644
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -1,6 +1,9 @@
 package jalview.renderer.seqfeatures;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
 
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
@@ -14,8 +17,8 @@ import jalview.schemes.FeatureColour;
 
 import java.awt.Color;
 
-import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
 
 /**
@@ -47,7 +50,7 @@ public class FeatureColourFinderTest
 
   private FeatureRenderer fr;
 
-  @BeforeClass(alwaysRun = true)
+  @BeforeTest(alwaysRun = true)
   public void setUp()
   {
     // aligned column 8 is sequence position 6
@@ -61,7 +64,8 @@ public class FeatureColourFinderTest
   }
 
   /**
-   * Clear down any sequence features before each test
+   * Clear down any sequence features before each test (not as easy as it
+   * sounds...)
    */
   @BeforeMethod(alwaysRun = true)
   public void setUpBeforeTest()
@@ -83,6 +87,9 @@ public class FeatureColourFinderTest
     {
       fr.setGroupVisibility(group, true);
     }
+
+    fr.clearRenderOrder();
+    av.setShowSequenceFeatures(true);
   }
 
   @Test(groups = "Functional")
@@ -120,6 +127,10 @@ public class FeatureColourFinderTest
     assertEquals(c, Color.red);
   }
 
+  /**
+   * feature colour at a gap is null (not white) - a user defined colour scheme
+   * can then provide a bespoke gap colour if configured to do so
+   */
   @Test(groups = "Functional")
   public void testFindFeatureColour_gapPosition()
   {
@@ -129,7 +140,7 @@ public class FeatureColourFinderTest
     fr.featuresAdded();
     av.setShowSequenceFeatures(true);
     Color c = finder.findFeatureColour(null, seq, 6);
-    assertEquals(c, Color.white);
+    assertNull(c);
   }
 
   @Test(groups = "Functional")
@@ -384,4 +395,124 @@ public class FeatureColourFinderTest
     c = finder.findFeatureColour(Color.pink, seq, 10);
     assertEquals(c, new Color(102, 223, 70));
   }
+
+  @Test(groups = "Functional")
+  public void testNoFeaturesDisplayed()
+  {
+    /*
+     * no features on alignment to render
+     */
+    assertTrue(finder.noFeaturesDisplayed());
+
+    /*
+     * add a feature
+     * it will be automatically set visible but we leave
+     * the viewport configured not to show features
+     */
+    av.setShowSequenceFeatures(false);
+    seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
+            Float.NaN, "MetalGroup"));
+    FeatureColour red = new FeatureColour(Color.red);
+    fr.setColour("Metal", red);
+    fr.featuresAdded();
+    assertTrue(finder.noFeaturesDisplayed());
+
+    /*
+     * turn on feature display
+     */
+    av.setShowSequenceFeatures(true);
+    assertFalse(finder.noFeaturesDisplayed());
+
+    /*
+     * turn off display of Metal
+     */
+    Object[][] data = new Object[1][];
+    data[0] = new Object[] { "Metal", red, false };
+    fr.setFeaturePriority(data);
+    assertTrue(finder.noFeaturesDisplayed());
+
+    /*
+     * turn display of Metal back on
+     */
+    fr.setVisible("Metal");
+    assertFalse(finder.noFeaturesDisplayed());
+
+    /*
+     * turn off MetalGroup - has no effect here since the group of a
+     * sequence feature instance is independent of its type
+     */
+    fr.setGroupVisibility("MetalGroup", false);
+    assertFalse(finder.noFeaturesDisplayed());
+
+    /*
+     * a finder with no feature renderer
+     */
+    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);
+  }
 }