JAL-2286 javadoc, refactor, unit tests for threshold and conservation

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

diff --git a/test/jalview/schemes/ResidueColourSchemeTest.java b/test/jalview/schemes/ResidueColourSchemeTest.java
new file mode 100644 (file)
index 0000000..8173dd1
--- /dev/null
+++ b/test/jalview/schemes/ResidueColourSchemeTest.java
@@ -0,0 +1,147 @@
+package jalview.schemes;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.analysis.Profile;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class ResidueColourSchemeTest
+{
+  @Test(groups = "Functional")
+  public void testAboveThreshold()
+  {
+    /*
+     * make up profiles for this alignment:
+     * AR-Q
+     * AR--
+     * SR-T
+     * SR-T
+     */
+    Profile[] profiles = new Profile[4]; 
+    profiles[0] = new Profile(4, 0, 2, "AS");
+    profiles[1] = new Profile(4, 0, 4, "R");
+    profiles[2] = new Profile(4, 4, 0, "");
+    profiles[3] = new Profile(4, 1, 2, "T");
+    ResidueColourScheme rcs = new ResidueColourScheme();
+    rcs.setConsensus(profiles);
+    
+    /*
+     * no threshold
+     */
+    rcs.setThreshold(0, true);
+    assertTrue(rcs.aboveThreshold('a', 0));
+    assertTrue(rcs.aboveThreshold('S', 0));
+    assertFalse(rcs.aboveThreshold('W', 0));
+    assertTrue(rcs.aboveThreshold('R', 1));
+    assertFalse(rcs.aboveThreshold('W', 2));
+    assertTrue(rcs.aboveThreshold('t', 3));
+    assertFalse(rcs.aboveThreshold('Q', 3));
+
+    /*
+     * with threshold, include gaps
+     */
+    rcs.setThreshold(60, false);
+    assertFalse(rcs.aboveThreshold('a', 0));
+    assertFalse(rcs.aboveThreshold('S', 0));
+    assertTrue(rcs.aboveThreshold('R', 1));
+    assertFalse(rcs.aboveThreshold('W', 2));
+    assertFalse(rcs.aboveThreshold('t', 3)); // 50% < 60%
+
+    /*
+     * with threshold, ignore gaps
+     */
+    rcs.setThreshold(60, true);
+    assertFalse(rcs.aboveThreshold('a', 0));
+    assertFalse(rcs.aboveThreshold('S', 0));
+    assertTrue(rcs.aboveThreshold('R', 1));
+    assertFalse(rcs.aboveThreshold('W', 2));
+    assertTrue(rcs.aboveThreshold('t', 3)); // 67% > 60%
+  }
+
+  /**
+   * Test colour bleaching based on conservation score and conservation slider.
+   * Scores of 10 or 11 should leave colours unchanged. Gap is always white.
+   */
+  @Test(groups = "Functional")
+  public void testApplyConservation()
+  {
+    ResidueColourScheme rcs = new ResidueColourScheme();
+
+    // no conservation present - no fading
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 12));
+    
+    // cheat by setting conservation sequence directly
+    // rather than calculating it - good enough for this test
+    String consensus = "0123456789+*-";
+    rcs.conservation = consensus.toCharArray();
+
+    // column out of range:
+    assertEquals(Color.RED,
+            rcs.applyConservation(Color.RED, consensus.length()));
+
+    /*
+     * with 100% threshold, 'fade factor' is 
+     * (11-score)/10 * 100/20 = (11-score)/2
+     * which is >= 1 for all scores i.e. all fade to white except +, *
+     */
+    rcs.setConservationInc(100);
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 0));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 1));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 2));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 3));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 4));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 5));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 6));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 7));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 8));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 9));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12));
+
+    /*
+     * with 0% threshold, there should be no fading
+     */
+    rcs.setConservationInc(0);
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 0));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 1));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 2));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 3));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 4));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 5));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 6));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 7));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 8));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 9));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
+    assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
+    assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12)); // gap
+
+    /*
+     * with 40% threshold, 'fade factor' is 
+     * (11-score)/10 * 40/20 = (11-score)/5
+     * which is {>1, >1, >1, >1, >1, >1, 1, 0.8, 0.6, 0.4} for score 0-9
+     * e.g. score 7 colour fades 80% of the way to white (255, 255, 255)
+     */
+    rcs.setConservationInc(40);
+    Color colour = new Color(155, 105, 55);
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 0));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 1));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 2));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 3));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 4));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 5));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 6));
+    assertEquals(new Color(235, 225, 215), rcs.applyConservation(colour, 7));
+    assertEquals(new Color(215, 195, 175), rcs.applyConservation(colour, 8));
+    assertEquals(new Color(195, 165, 135), rcs.applyConservation(colour, 9));
+    assertEquals(colour, rcs.applyConservation(colour, 10));
+    assertEquals(colour, rcs.applyConservation(colour, 11));
+    assertEquals(Color.WHITE, rcs.applyConservation(colour, 12));
+  }
+}