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;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
import jalview.datamodel.SequenceFeature;
import jalview.gui.JvOptionPane;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
public class FeatureColourTest
{
assertTrue(fc1.getColour().equals(Color.RED));
assertFalse(fc1.isGraduatedColour());
assertFalse(fc1.isColourByLabel());
+ assertFalse(fc1.isColourByAttribute());
+ assertNull(fc1.getAttributeName());
/*
* min-max colour
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());
fc1 = new FeatureColour(fc);
assertTrue(fc1.isColourByLabel());
assertFalse(fc1.isGraduatedColour());
- }
+ assertFalse(fc1.isColourByAttribute());
+ assertNull(fc1.getAttributeName());
- @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();
+ /*
+ * colour by attribute (label)
+ */
+ fc = new FeatureColour();
fc.setColourByLabel(true);
- assertTrue(fc
- .isColored(new SequenceFeature("Cath", "", 1, 2, 0f, null)));
+ fc.setAttributeName("AF");
+ fc1 = new FeatureColour(fc);
+ assertTrue(fc1.isColourByLabel());
+ assertFalse(fc1.isGraduatedColour());
+ assertTrue(fc1.isColourByAttribute());
+ assertArrayEquals(new String[] { "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());
+ assertArrayEquals(new String[] { "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 testIsColored_aboveThreshold()
+ public void testCopyConstructor_minMax()
{
- // graduated colour range from score 20 to 100
- FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 20f,
- 100f);
+ /*
+ * 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());
- // 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));
+ /*
+ * 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"));
- // now apply threshold:
- fc.setAboveThreshold(true);
- assertFalse(fc.isColored(sf));
- // colour is still returned though ?!?
- assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+ /*
+ * 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"));
- 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));
+ /*
+ * graduated colour by attribute
+ */
+ fc1.setAttributeName("AF");
+ fc1 = new FeatureColour(fc1, 13f, 36f);
+ assertTrue(fc1.isGraduatedColour());
+ assertFalse(fc1.isColourByLabel());
+ assertTrue(fc1.isColourByAttribute());
+ assertEquals(new String[] { "AF" }, fc1.getAttributeName());
+ assertEquals(13f, fc1.getMin());
+ assertEquals(36f, fc1.getMax());
+ assertFalse((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
+ */
+ fc1 = new FeatureColour(fc, 2f, 6f);
+ assertFalse(fc1.isGraduatedColour());
+ assertTrue(fc1.isColourByLabel());
+ assertFalse(fc1.isColourByAttribute());
+ assertNull(fc1.getAttributeName());
+ assertEquals(2f, fc1.getMin());
+ assertEquals(6f, fc1.getMax());
+
+ /*
+ * colour by attribute text
+ */
+ fc1.setAttributeName("AC");
+ fc1 = new FeatureColour(fc1, 13f, 36f);
+ assertFalse(fc1.isGraduatedColour());
+ assertTrue(fc1.isColourByLabel());
+ assertTrue(fc1.isColourByAttribute());
+ assertEquals("AC", fc1.getAttributeName());
+ assertEquals(13f, fc1.getMin());
+ assertEquals(36f, fc1.getMax());
}
@Test(groups = { "Functional" })
@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,
}
@Test(groups = { "Functional" })
- public void testGetColor_belowThreshold()
+ public void testGetColor_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(Color.white, fc.getColor(sf2));
fc.setAboveThreshold(true); // feature lies below threshold
- assertFalse(fc.isColored(sf));
- assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+ assertNull(fc.getColor(sf));
+ assertEquals(Color.white, fc.getColor(sf2));
+
+ fc.setBelowThreshold(true);
+ fc.setThreshold(70f);
+ assertNull(fc.getColor(sf)); // feature score == threshold - hidden
+ assertEquals(Color.white, fc.getColor(sf2));
+ fc.setThreshold(69f);
+ assertNull(fc.getColor(sf)); // feature score > threshold - hidden
+ assertEquals(Color.white, fc.getColor(sf2));
}
/**
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));
+ }
}
git://source.jalview.org / jalview.git / blobdiff