JAL-2876 some Checkstyle and other review comments addressed

[jalview.git] / test / jalview / schemes / FeatureColourTest.java

diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java
index 1beca80..85c3f8b 100644 (file)
--- a/test/jalview/schemes/FeatureColourTest.java
+++ b/test/jalview/schemes/FeatureColourTest.java
@@ -22,6 +22,7 @@ package jalview.schemes;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 
@@ -84,82 +85,26 @@ public class FeatureColourTest
   }
 
   @Test(groups = { "Functional" })
-  public void testIsColored_simpleColour()
-  {
-    FeatureColour fc = new FeatureColour(Color.RED);
-    assertTrue(fc
-            .isColored(new SequenceFeature("Cath", "", 1, 2, 0f, null)));
-  }
-
-  @Test(groups = { "Functional" })
-  public void testIsColored_colourByLabel()
-  {
-    FeatureColour fc = new FeatureColour();
-    fc.setColourByLabel(true);
-    assertTrue(fc
-            .isColored(new SequenceFeature("Cath", "", 1, 2, 0f, null)));
-  }
-
-  @Test(groups = { "Functional" })
-  public void testIsColored_aboveThreshold()
-  {
-    // graduated colour range from score 20 to 100
-    FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 20f,
-            100f);
-
-    // score 0 is adjusted to bottom of range
-    SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 0f,
-            null);
-    assertTrue(fc.isColored(sf));
-    assertEquals(Color.WHITE, fc.getColor(sf));
-
-    // score 120 is adjusted to top of range
-    sf = new SequenceFeature(sf, sf.getBegin(), sf.getEnd(),
-            sf.getFeatureGroup(), 120f);
-    assertEquals(Color.BLACK, fc.getColor(sf));
-
-    // value below threshold is still rendered
-    // setting threshold has no effect yet...
-    fc.setThreshold(60f);
-    sf = new SequenceFeature(sf, sf.getBegin(), sf.getEnd(),
-            sf.getFeatureGroup(), 36f);
-    assertTrue(fc.isColored(sf));
-    assertEquals(new Color(204, 204, 204), fc.getColor(sf));
-
-    // now apply threshold:
-    fc.setAboveThreshold(true);
-    assertFalse(fc.isColored(sf));
-    // colour is still returned though ?!?
-    assertEquals(new Color(204, 204, 204), fc.getColor(sf));
-
-    sf = new SequenceFeature(sf, sf.getBegin(), sf.getEnd(),
-            sf.getFeatureGroup(), 84f);
-    // above threshold now
-    assertTrue(fc.isColored(sf));
-    assertEquals(new Color(51, 51, 51), fc.getColor(sf));
-  }
-
-  @Test(groups = { "Functional" })
-  public void testGetColor_simpleColour()
+  public void testGetColour_simpleColour()
   {
     FeatureColour fc = new FeatureColour(Color.RED);
     assertEquals(Color.RED,
-            fc.getColor(new SequenceFeature("Cath", "", 1, 2, 0f, null)));
+            fc.getColour(new SequenceFeature("Cath", "", 1, 2, 0f, null)));
   }
 
   @Test(groups = { "Functional" })
-  public void testGetColor_colourByLabel()
+  public void testGetColour_colourByLabel()
   {
     FeatureColour fc = new FeatureColour();
     fc.setColourByLabel(true);
     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
             null);
     Color expected = ColorUtils.createColourFromName("desc");
-    assertEquals(expected, fc.getColor(sf));
+    assertEquals(expected, fc.getColour(sf));
   }
 
   @Test(groups = { "Functional" })
-  public void testGetColor_Graduated()
+  public void testGetColour_Graduated()
   {
     // graduated colour from score 0 to 100, gray(128, 128, 128) to red(255, 0,
     // 0)
@@ -172,24 +117,39 @@ public class FeatureColourTest
     float green = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
     float blue = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
     Color expected = new Color(red, green, blue);
-    assertEquals(expected, fc.getColor(sf));
+    assertEquals(expected, fc.getColour(sf));
   }
 
   @Test(groups = { "Functional" })
-  public void testGetColor_belowThreshold()
+  public void testGetColour_aboveBelowThreshold()
   {
     // gradient from [50, 150] from WHITE(255, 255, 255) to BLACK(0, 0, 0)
     FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 50f,
             150f);
     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 70f,
             null);
+
+    /*
+     * feature with score of Float.NaN is always assigned minimum colour
+     */
+    SequenceFeature sf2 = new SequenceFeature("type", "desc", 0, 20,
+            Float.NaN, null);
+
     fc.setThreshold(100f); // ignore for now
-    assertTrue(fc.isColored(sf));
-    assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+    assertEquals(new Color(204, 204, 204), fc.getColour(sf));
+    assertEquals(Color.white, fc.getColour(sf2));
 
     fc.setAboveThreshold(true); // feature lies below threshold
-    assertFalse(fc.isColored(sf));
-    assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+    assertNull(fc.getColour(sf));
+    assertEquals(Color.white, fc.getColour(sf2));
+
+    fc.setBelowThreshold(true);
+    fc.setThreshold(70f);
+    assertNull(fc.getColour(sf)); // feature score == threshold - hidden
+    assertEquals(Color.white, fc.getColour(sf2));
+    fc.setThreshold(69f);
+    assertNull(fc.getColour(sf)); // feature score > threshold - hidden
+    assertEquals(Color.white, fc.getColour(sf2));
   }
 
   /**
@@ -380,4 +340,33 @@ public class FeatureColourTest
     fc = FeatureColour.parseJalviewFeatureColour(descriptor);
     assertTrue(fc.isGraduatedColour());
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetColour_colourByLabel_withThreshold()
+  {
+    FeatureColour fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
+            null);
+    fc.setThreshold(0);
+    Color expected = ColorUtils.createColourFromName("desc");
+    assertEquals(expected, fc.getColour(sf));
+
+    // score (1f) is above threshold
+    fc.setAboveThreshold(true);
+    assertEquals(expected, fc.getColour(sf));
+
+    // score is not above threshold
+    fc.setThreshold(2f);
+    assertNull(fc.getColour(sf));
+
+    // score is not below threshold
+    fc.setThreshold(0f);
+    fc.setBelowThreshold(true);
+    assertNull(fc.getColour(sf));
+
+    // score is below threshold
+    fc.setThreshold(3f);
+    assertEquals(expected, fc.getColour(sf));
+  }
 }