import static org.testng.Assert.assertEquals;
-import java.awt.Color;
-
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.GraphLine;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
{
final static int WIDTH = 11;
- final static int THRESHOLD = 5;
+ final static int THRESHOLD_FIVE = 5;
private AlignmentAnnotation ann;
+ private SequenceI seq;
+
+ private AlignmentI al;
+
Color minColour = new Color(50, 200, 150);
Color maxColour = new Color(150, 100, 250);
+ /**
+ * Setup creates an annotation over 11 columns with values 0-10 and threshold
+ * 5
+ */
@BeforeClass
public void setUp()
{
Annotation[] anns = new Annotation[WIDTH];
/*
- * set annotations with values 0-10
+ * set annotations with values 0-10, graded colours
*/
for (int col = 0; col < WIDTH; col++)
{
- anns[col] = new Annotation("a", "a", 'a', col);
+ int hue = col * 20;
+ Color colour = new Color(hue, hue, hue);
+ anns[col] = new Annotation("a", "a", 'a', col, colour);
}
+ seq = new Sequence("", "");
+ al = new Alignment(new SequenceI[]{ seq});
+
/*
* AlignmentAnnotation constructor works out min-max range
*/
ann = new AlignmentAnnotation("", "", anns);
- ann.setThreshold(new GraphLine(THRESHOLD, "", Color.RED));
+ ann.setThreshold(new GraphLine(THRESHOLD_FIVE, "", Color.RED));
+ seq.addAlignmentAnnotation(ann);
}
@Test(groups = "Functional")
Color result = testee.shadeCalculation(ann, col);
/*
* colour is derived regardless of the threshold value
- * (the renderer that will suppress colouring if
- * above/below threshold)
+ * (the renderer will suppress colouring if above/below threshold)
*/
Color expected = new Color(50 + 10 * col, 200 - 10 * col,
150 + 10 * col);
* (annotation value == column number in this test)
*/
testee.setThresholdIsMinMax(true);
- for (int col = 0; col < THRESHOLD; col++)
+ for (int col = 0; col < THRESHOLD_FIVE; col++)
{
/*
* colours below the threshold are computed as before
Color result = testee.shadeCalculation(ann, col);
assertEquals(result, expected, "for column " + col);
}
- for (int col = THRESHOLD; col < WIDTH; col++)
+ for (int col = THRESHOLD_FIVE; col < WIDTH; col++)
{
/*
* colours for values >= threshold are graduated
* range is 6-10 so steps of 100/5 = 20
*/
- int factor = col - THRESHOLD;
+ int factor = col - THRESHOLD_FIVE;
Color expected = new Color(50 + 20 * factor, 200 - 20 * factor,
150 + 20 * factor);
Color result = testee.shadeCalculation(ann, col);
@Test(groups = "Functional")
public void testShadeCalculation_belowThreshold()
{
- /*
- * change threshold to 5 so we have an easy calculation of
- * the min-max range 0-5
- */
- int threshold = 5;
- ann.setThreshold(new GraphLine(threshold, "", Color.RED));
AnnotationColourGradient testee = new AnnotationColourGradient(ann,
minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
Color result = testee.shadeCalculation(ann, col);
/*
* colour is derived regardless of the threshold value
- * (the renderer that will suppress colouring if
- * above/below threshold)
+ * (the renderer will suppress colouring if above/below threshold)
*/
Color expected = new Color(50 + 10 * col, 200 - 10 * col,
150 + 10 * col);
* (annotation value == column number in this test)
*/
testee.setThresholdIsMinMax(true);
- for (int col = threshold + 1; col < WIDTH; col++)
+ for (int col = THRESHOLD_FIVE + 1; col < WIDTH; col++)
{
/*
* colours above the threshold are computed as before
assertEquals(result, expected, "for column " + col);
}
- for (int col = 0; col <= threshold; col++)
+ for (int col = 0; col <= THRESHOLD_FIVE; col++)
{
/*
* colours for values <= threshold are graduated
assertEquals(result, expected, "for column " + col);
}
}
+
+ /**
+ * Test the 'colour above threshold' case
+ */
+ @Test(groups = "Functional")
+ public void testFindColour_aboveThreshold()
+ {
+ AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+ minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
+ testee = (AnnotationColourGradient) testee.getInstance(al, null);
+
+ for (int col = 0; col < WIDTH; col++)
+ {
+ Color result = testee.findColour('a', col, seq);
+ /*
+ * expect white below threshold of 5
+ */
+ Color expected = col < 5 ? Color.white : new Color(50 + 10 * col,
+ 200 - 10 * col,
+ 150 + 10 * col);
+ assertEquals(result, expected, "for column " + col);
+ }
+
+ /*
+ * now make 6-10 the span of the colour range
+ * (annotation value == column number in this test)
+ */
+ testee.setThresholdIsMinMax(true);
+ for (int col = 0; col < WIDTH; col++)
+ {
+ /*
+ * colours for values >= threshold are graduated
+ * range is 6-10 so steps of 100/5 = 20
+ */
+ int factor = col - THRESHOLD_FIVE;
+ Color expected = col < 5 ? Color.white : new Color(50 + 20 * factor,
+ 200 - 20 * factor,
+ 150 + 20 * factor);
+ Color result = testee.findColour('a', col, seq);
+ assertEquals(result, expected, "for column " + col);
+ }
+ }
+
+ /**
+ * Test the 'colour below threshold' case
+ */
+ @Test(groups = "Functional")
+ public void testFindColour_belowThreshold()
+ {
+ AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+ minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
+ testee = (AnnotationColourGradient) testee.getInstance(al, null);
+
+ for (int col = 0; col < WIDTH; col++)
+ {
+ Color result = testee.findColour('a', col, seq);
+ Color expected = col > 5 ? Color.white : new Color(50 + 10 * col,
+ 200 - 10 * col, 150 + 10 * col);
+ assertEquals(result, expected, "for column " + col);
+ }
+
+ /*
+ * now make 0-5 the span of the colour range
+ * (annotation value == column number in this test)
+ */
+ testee.setThresholdIsMinMax(true);
+ for (int col = 0; col < WIDTH; col++)
+ {
+ /*
+ * colours for values <= threshold are graduated
+ * range is 0-5 so steps of 100/5 = 20
+ */
+ Color expected = col > 5 ? Color.white : new Color(50 + 20 * col,
+ 200 - 20 * col, 150 + 20 * col);
+ Color result = testee.findColour('a', col, seq);
+ assertEquals(result, expected, "for column " + col);
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testFindColour_noThreshold()
+ {
+ AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+ minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
+ testee = (AnnotationColourGradient) testee.getInstance(al, null);
+
+ for (int col = 0; col < WIDTH; col++)
+ {
+ Color result = testee.findColour('a', col, seq);
+ /*
+ * column <n> is n/10 of the way from minCol to maxCol
+ */
+ Color expected = new Color(50 + 10 * col, 200 - 10 * col,
+ 150 + 10 * col);
+ assertEquals(result, expected, "for column " + col);
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testFindColour_originalColours()
+ {
+ AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+ minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
+ testee = (AnnotationColourGradient) testee.getInstance(al, null);
+
+ /*
+ * flag corresponding to 'use original colours' checkbox
+ * - just use the individual annotation colours
+ */
+ testee.setPredefinedColours(true);
+
+ /*
+ * the annotation colour is returned, except for column 0 where it is
+ * black - in this case the colour scheme colour overrides it
+ */
+ for (int col = 0; col < WIDTH; col++)
+ {
+ int hue = col * 20;
+ Color c = col == 0 ? minColour : new Color(hue, hue, hue);
+ assertEquals(testee.findColour('a', col, seq), c, "for column " + col);
+ }
+ }
}
git://source.jalview.org / jalview.git / commitdiff