JAL-3597 additional references nulled, bug in test corrected

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

diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java
index 1a6a5f3..dae70f7 100644 (file)
--- a/test/jalview/schemes/FeatureColourTest.java
+++ b/test/jalview/schemes/FeatureColourTest.java
@@ -173,6 +173,13 @@ public class FeatureColourTest
     assertEquals(Color.yellow, fc1.getColour());
     assertEquals(10f, fc1.getMin());
     assertEquals(20f, fc1.getMax());
+
+    /*
+     * modify original attribute label and check that copy doesn't change
+     */
+    fc.setAttributeName("MAF", "AF");
+    assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
+
   }
 
   @Test(groups = { "Functional" })
@@ -469,11 +476,60 @@ public class FeatureColourTest
     assertFalse(fc.hasThreshold());
     assertEquals(Color.RED, fc.getMinColour());
     assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(Color.RED, fc.getNoColour());
     assertEquals(10f, fc.getMin());
     assertEquals(20f, fc.getMax());
     assertTrue(fc.isAutoScaled());
 
     /*
+     * the same, with 'no value colour' specified as max
+     */
+    fc = FeatureColour
+            .parseJalviewFeatureColour("red|green|novaluemax|10.0|20.0");
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(Color.GREEN, fc.getNoColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+
+    /*
+     * the same, with 'no value colour' specified as min
+     */
+    fc = FeatureColour
+            .parseJalviewFeatureColour("red|green|novalueMin|10.0|20.0");
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(Color.RED, fc.getNoColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+
+    /*
+     * the same, with 'no value colour' specified as none
+     */
+    fc = FeatureColour
+            .parseJalviewFeatureColour("red|green|novaluenone|10.0|20.0");
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertNull(fc.getNoColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+
+    /*
+     * the same, with invalid 'no value colour'
+     */
+    try
+    {
+      fc = FeatureColour
+              .parseJalviewFeatureColour("red|green|blue|10.0|20.0");
+      fail("expected exception");
+    } catch (IllegalArgumentException e)
+    {
+      assertEquals(
+              "Couldn't parse the minimum value for graduated colour ('blue')",
+              e.getMessage());
+    }
+
+    /*
      * graduated colour (explicitly by 'score') (no threshold)
      */
     fc = FeatureColour
@@ -610,4 +666,142 @@ public class FeatureColourTest
     Color expected = new Color(70, 120, 170);
     assertEquals(expected, fc.getColor(sf));
   }
+
+  @Test(groups = { "Functional" })
+  public void testIsOutwithThreshold()
+  {
+    FeatureColourI fc = new FeatureColour(Color.red);
+    SequenceFeature sf = new SequenceFeature("METAL", "desc", 10, 12, 1.2f, "grp");
+    assertFalse(fc.isOutwithThreshold(null));
+    assertFalse(fc.isOutwithThreshold(sf));
+
+    fc = new FeatureColour(null, Color.white, Color.black, Color.green, 0f,
+            10f);
+    assertFalse(fc.isOutwithThreshold(sf)); // no threshold
+
+    fc.setAboveThreshold(true);
+    fc.setThreshold(1f);
+    assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is above 1
+
+    fc.setThreshold(2f);
+    assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not above 2
+
+    fc.setBelowThreshold(true);
+    assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is below 2
+
+    fc.setThreshold(1f);
+    assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not below 1
+
+    /*
+     * with attribute value threshold
+     */
+    fc.setAttributeName("AC");
+    assertFalse(fc.isOutwithThreshold(sf)); // missing attribute AC is ignored
+
+    sf.setValue("AC", "-1");
+    assertFalse(fc.isOutwithThreshold(sf)); // value -1 is below 1
+
+    sf.setValue("AC", "1");
+    assertTrue(fc.isOutwithThreshold(sf)); // value 1 is not below 1
+
+    sf.setValue("AC", "junk");
+    assertFalse(fc.isOutwithThreshold(sf)); // bad value is ignored
+  }
+
+  /**
+   * Test description of feature colour suitable for a tooltip
+   */
+  @Test(groups = { "Functional" })
+  public void testGetDescription()
+  {
+    /*
+     * plain colour
+     */
+    FeatureColour fc = new FeatureColour(Color.RED);
+    assertEquals(
+            String.format("r=%d,g=%d,b=%d", Color.RED.getRed(),
+                    Color.red.getGreen(), Color.red.getBlue()),
+            fc.getDescription());
+  
+    /*
+     * colour by label (no threshold)
+     */
+    fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    assertEquals("By Label", fc.getDescription());
+  
+    /*
+     * colour by attribute text (no threshold)
+     */
+    fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    fc.setAttributeName("CLIN_SIG");
+    assertEquals("By CLIN_SIG", fc.getDescription());
+  
+    /*
+     * colour by label (above score threshold) 
+     */
+    fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    fc.setAutoScaled(false);
+    fc.setThreshold(12.5f);
+    fc.setAboveThreshold(true);
+    assertEquals("By Label (Score > 12.5)",
+            fc.getDescription());
+  
+    /*
+     * colour by label (below score threshold)
+     */
+    fc.setBelowThreshold(true);
+    assertEquals("By Label (Score < 12.5)",
+            fc.getDescription());
+  
+    /*
+     * colour by attributes text (below score threshold)
+     */
+    fc.setBelowThreshold(true);
+    fc.setAttributeName("CSQ", "Consequence");
+    assertEquals(
+            "By CSQ:Consequence (Score < 12.5)",
+            fc.getDescription());
+  
+    /*
+     * graduated colour by score, no threshold
+     */
+    fc = new FeatureColour(null, Color.GREEN, Color.RED, null, 12f, 25f);
+    assertEquals("By Score", fc.getDescription());
+  
+    /*
+     * graduated colour by score, below threshold
+     */
+    fc.setThreshold(12.5f);
+    fc.setBelowThreshold(true);
+    assertEquals("By Score (< 12.5)",
+            fc.getDescription());
+  
+    /*
+     * graduated colour by score, above threshold
+     */
+    fc.setThreshold(12.5f);
+    fc.setAboveThreshold(true);
+    fc.setAutoScaled(false);
+    assertEquals("By Score (> 12.5)",
+            fc.getDescription());
+
+    /*
+     * graduated colour by attribute, no threshold
+     */
+    fc.setAttributeName("CSQ", "AF");
+    fc.setAboveThreshold(false);
+    fc.setAutoScaled(false);
+    assertEquals("By CSQ:AF", fc.getDescription());
+  
+    /*
+     * graduated colour by attribute, above threshold
+     */
+    fc.setAboveThreshold(true);
+    fc.setAutoScaled(false);
+    assertEquals("By CSQ:AF (> 12.5)",
+            fc.getDescription());
+  }
 }