JAL-2069 update spike branch with latest

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

diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java
index 7a72c15..3f60152 100644 (file)
--- a/test/jalview/schemes/FeatureColourTest.java
+++ b/test/jalview/schemes/FeatureColourTest.java
@@ -33,6 +33,8 @@ import jalview.util.Format;
 
 import java.awt.Color;
 
+import junit.extensions.PA;
+
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -57,6 +59,8 @@ public class FeatureColourTest
     assertTrue(fc1.getColour().equals(Color.RED));
     assertFalse(fc1.isGraduatedColour());
     assertFalse(fc1.isColourByLabel());
+    assertFalse(fc1.isColourByAttribute());
+    assertNull(fc1.getAttributeName());
 
     /*
      * min-max colour
@@ -68,9 +72,31 @@ public class FeatureColourTest
     assertTrue(fc1.isGraduatedColour());
     assertFalse(fc1.isColourByLabel());
     assertTrue(fc1.isAboveThreshold());
+    assertFalse(fc1.isColourByAttribute());
+    assertNull(fc1.getAttributeName());
     assertEquals(12f, fc1.getThreshold());
     assertEquals(Color.gray, fc1.getMinColour());
     assertEquals(Color.black, fc1.getMaxColour());
+    assertEquals(Color.gray, fc1.getNoColour());
+    assertEquals(10f, fc1.getMin());
+    assertEquals(20f, fc1.getMax());
+
+    /*
+     * min-max-noValue colour
+     */
+    fc = new FeatureColour(Color.gray, Color.black, Color.green, 10f, 20f);
+    fc.setAboveThreshold(true);
+    fc.setThreshold(12f);
+    fc1 = new FeatureColour(fc);
+    assertTrue(fc1.isGraduatedColour());
+    assertFalse(fc1.isColourByLabel());
+    assertFalse(fc1.isColourByAttribute());
+    assertNull(fc1.getAttributeName());
+    assertTrue(fc1.isAboveThreshold());
+    assertEquals(12f, fc1.getThreshold());
+    assertEquals(Color.gray, fc1.getMinColour());
+    assertEquals(Color.black, fc1.getMaxColour());
+    assertEquals(Color.green, fc1.getNoColour());
     assertEquals(10f, fc1.getMin());
     assertEquals(20f, fc1.getMax());
 
@@ -82,6 +108,102 @@ public class FeatureColourTest
     fc1 = new FeatureColour(fc);
     assertTrue(fc1.isColourByLabel());
     assertFalse(fc1.isGraduatedColour());
+    assertFalse(fc1.isColourByAttribute());
+    assertNull(fc1.getAttributeName());
+
+    /*
+     * colour by attribute (label)
+     */
+    fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    fc.setAttributeName("AF");
+    fc1 = new FeatureColour(fc);
+    assertTrue(fc1.isColourByLabel());
+    assertFalse(fc1.isGraduatedColour());
+    assertTrue(fc1.isColourByAttribute());
+    assertEquals("AF", fc1.getAttributeName());
+
+    /*
+     * colour by attribute (value)
+     */
+    fc = new FeatureColour(Color.gray, Color.black, Color.green, 10f, 20f);
+    fc.setAboveThreshold(true);
+    fc.setThreshold(12f);
+    fc.setAttributeName("AF");
+    fc1 = new FeatureColour(fc);
+    assertTrue(fc1.isGraduatedColour());
+    assertFalse(fc1.isColourByLabel());
+    assertTrue(fc1.isColourByAttribute());
+    assertEquals("AF", fc1.getAttributeName());
+    assertTrue(fc1.isAboveThreshold());
+    assertEquals(12f, fc1.getThreshold());
+    assertEquals(Color.gray, fc1.getMinColour());
+    assertEquals(Color.black, fc1.getMaxColour());
+    assertEquals(Color.green, fc1.getNoColour());
+    assertEquals(10f, fc1.getMin());
+    assertEquals(20f, fc1.getMax());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testCopyConstructor_minMax()
+  {
+    /*
+     * graduated colour
+     */
+    FeatureColour fc = new FeatureColour(Color.BLUE, Color.RED, 1f, 5f);
+    assertTrue(fc.isGraduatedColour());
+    assertFalse(fc.isColourByLabel());
+    assertFalse(fc.isColourByAttribute());
+    assertNull(fc.getAttributeName());
+    assertEquals(1f, fc.getMin());
+    assertEquals(5f, fc.getMax());
+
+    /*
+     * update min-max bounds
+     */
+    FeatureColour fc1 = new FeatureColour(fc, 2f, 6f);
+    assertTrue(fc1.isGraduatedColour());
+    assertFalse(fc1.isColourByLabel());
+    assertFalse(fc1.isColourByAttribute());
+    assertNull(fc1.getAttributeName());
+    assertEquals(2f, fc1.getMin());
+    assertEquals(6f, fc1.getMax());
+    assertFalse((boolean) PA.getValue(fc1, "isHighToLow"));
+
+    /*
+     * update min-max bounds - high to low
+     */
+    fc1 = new FeatureColour(fc, 23f, 16f);
+    assertTrue(fc1.isGraduatedColour());
+    assertFalse(fc1.isColourByLabel());
+    assertFalse(fc1.isColourByAttribute());
+    assertNull(fc1.getAttributeName());
+    assertEquals(23f, fc1.getMin());
+    assertEquals(16f, fc1.getMax());
+    assertTrue((boolean) PA.getValue(fc1, "isHighToLow"));
+
+    /*
+     * colour by label
+     */
+    fc = new FeatureColour(Color.BLUE, Color.RED, 1f, 5f);
+    fc.setColourByLabel(true);
+    assertFalse(fc.isGraduatedColour());
+    assertTrue(fc.isColourByLabel());
+    assertFalse(fc.isColourByAttribute());
+    assertNull(fc.getAttributeName());
+    assertEquals(1f, fc.getMin());
+    assertEquals(5f, fc.getMax());
+
+    /*
+     * update min-max bounds - converts to graduated colour
+     */
+    fc1 = new FeatureColour(fc, 2f, 6f);
+    assertTrue(fc1.isGraduatedColour());
+    assertFalse(fc1.isColourByLabel());
+    assertFalse(fc1.isColourByAttribute());
+    assertNull(fc1.getAttributeName());
+    assertEquals(2f, fc1.getMin());
+    assertEquals(6f, fc1.getMax());
   }
 
   @Test(groups = { "Functional" })
@@ -106,8 +228,11 @@ public class FeatureColourTest
   @Test(groups = { "Functional" })
   public void testGetColor_Graduated()
   {
-    // graduated colour from score 0 to 100, gray(128, 128, 128) to red(255, 0,
-    // 0)
+    /*
+     * graduated colour from 
+     * score 0 to 100
+     * gray(128, 128, 128) to red(255, 0, 0)
+     */
     FeatureColour fc = new FeatureColour(Color.GRAY, Color.RED, 0f, 100f);
     // feature score is 75 which is 3/4 of the way from GRAY to RED
     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
@@ -340,4 +465,59 @@ public class FeatureColourTest
     fc = FeatureColour.parseJalviewFeatureColour(descriptor);
     assertTrue(fc.isGraduatedColour());
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetColor_colourByAttributeText()
+  {
+    FeatureColour fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    fc.setAttributeName("consequence");
+    SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
+            null);
+
+    /*
+     * if feature has no such attribute, use 'no value' colour
+     */
+    assertEquals(FeatureColour.DEFAULT_NO_COLOUR, fc.getColor(sf));
+
+    /*
+     * if feature has attribute, generate colour from value
+     */
+    sf.setValue("consequence", "benign");
+    Color expected = ColorUtils.createColourFromName("benign");
+    assertEquals(expected, fc.getColor(sf));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetColor_GraduatedByAttributeValue()
+  {
+    /*
+     * graduated colour based on attribute value for AF
+     * given a min-max range of 0-100
+     */
+    FeatureColour fc = new FeatureColour(new Color(50, 100, 150),
+            new Color(150, 200, 250), Color.yellow, 0f, 100f);
+    String attName = "AF";
+    fc.setAttributeName(attName);
+
+    /*
+     * first case: feature lacks the attribute - use 'no value' colour
+     */
+    SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
+            null);
+    assertEquals(Color.yellow, fc.getColor(sf));
+
+    /*
+     * second case: attribute present but not numeric - treat as if absent
+     */
+    sf.setValue(attName, "twelve");
+    assertEquals(Color.yellow, fc.getColor(sf));
+
+    /*
+     * third case: valid attribute value
+     */
+    sf.setValue(attName, "20.0");
+    Color expected = new Color(70, 120, 170);
+    assertEquals(expected, fc.getColor(sf));
+  }
 }