+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
+import static org.testng.Assert.assertEquals;
+
+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;
public class AnnotationColourGradientTest
{
+ final static int WIDTH = 11;
+
+ 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(alwaysRun = true)
+ public void setUp()
+ {
+ Annotation[] anns = new Annotation[WIDTH];
+ /*
+ * set annotations with values 0-10, graded colours
+ */
+ for (int col = 0; col < WIDTH; col++)
+ {
+ int hue = col * 20;
+ Color colour = new Color(hue, hue, hue);
+ anns[col] = new Annotation("a", "a", 'a', col, colour);
+ }
+
+ seq = new Sequence("Seq", "");
+ al = new Alignment(new SequenceI[] { seq });
+
+ /*
+ * AlignmentAnnotation constructor works out min-max range
+ */
+ ann = new AlignmentAnnotation("", "", anns);
+ ann.setThreshold(new GraphLine(THRESHOLD_FIVE, "", Color.RED));
+ seq.addAlignmentAnnotation(ann);
+ }
+
@Test(groups = "Functional")
- public void testShadeCalculation()
+ public void testShadeCalculation_noThreshold()
{
+ AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+ minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
+ for (int col = 0; col < WIDTH; col++)
+ {
+ Color result = testee.shadeCalculation(ann, col);
+ /*
+ * 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 the 'colour above threshold' case
+ */
+ @Test(groups = "Functional")
+ public void testShadeCalculation_aboveThreshold()
+ {
+ AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+ minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
+ for (int col = 0; col < WIDTH; col++)
+ {
+ Color result = testee.shadeCalculation(ann, col);
+ /*
+ * colour is derived regardless of the threshold value
+ * (the renderer will suppress colouring if above/below threshold)
+ */
+ Color expected = 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 < THRESHOLD_FIVE; col++)
+ {
+ /*
+ * colours below the threshold are computed as before
+ */
+ Color expected = new Color(50 + 10 * col, 200 - 10 * col,
+ 150 + 10 * col);
+ Color result = testee.shadeCalculation(ann, col);
+ assertEquals(result, expected, "for column " + 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_FIVE;
+ Color expected = new Color(50 + 20 * factor, 200 - 20 * factor,
+ 150 + 20 * factor);
+ Color result = testee.shadeCalculation(ann, col);
+ assertEquals(result, expected, "for column " + col);
+ }
+
+ /*
+ * test for boundary case threshold == graphMax (JAL-3206)
+ */
+ float thresh = ann.threshold.value;
+ ann.threshold.value = ann.graphMax;
+ Color result = testee.shadeCalculation(ann, WIDTH - 1);
+ assertEquals(result, maxColour);
+ testee.setThresholdIsMinMax(false);
+ result = testee.shadeCalculation(ann, WIDTH - 1);
+ assertEquals(result, maxColour);
+ ann.threshold.value = thresh; // reset
+ }
+
+ /**
+ * Test the 'colour below threshold' case
+ */
+ @Test(groups = "Functional")
+ public void testShadeCalculation_belowThreshold()
+ {
+ AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+ minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
+
+ for (int col = 0; col < WIDTH; col++)
+ {
+ Color result = testee.shadeCalculation(ann, col);
+ /*
+ * colour is derived regardless of the threshold value
+ * (the renderer will suppress colouring if above/below threshold)
+ */
+ Color expected = 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 = THRESHOLD_FIVE + 1; col < WIDTH; col++)
+ {
+ /*
+ * colours above the threshold are computed as before
+ */
+ Color expected = new Color(50 + 10 * col, 200 - 10 * col,
+ 150 + 10 * col);
+ Color result = testee.shadeCalculation(ann, col);
+ assertEquals(result, expected, "for column " + col);
+ }
+
+ for (int col = 0; col <= THRESHOLD_FIVE; col++)
+ {
+ /*
+ * colours for values <= threshold are graduated
+ * range is 0-5 so steps of 100/5 = 20
+ */
+ Color expected = new Color(50 + 20 * col, 200 - 20 * col,
+ 150 + 20 * col);
+ Color result = testee.shadeCalculation(ann, col);
+ assertEquals(result, expected, "for column " + col);
+ }
+
+ /*
+ * test for boundary case threshold == graphMin (JAL-3206)
+ */
+ float thresh = ann.threshold.value;
+ ann.threshold.value = ann.graphMin;
+ Color result = testee.shadeCalculation(ann, 0);
+ assertEquals(result, minColour);
+ testee.setThresholdIsMinMax(false);
+ result = testee.shadeCalculation(ann, 0);
+ assertEquals(result, minColour);
+ ann.threshold.value = thresh; // reset
+ }
+
+ /**
+ * 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(null, al);
+
+ for (int col = 0; col < WIDTH; col++)
+ {
+ Color result = testee.findColour('a', col, seq);
+ /*
+ * expect white at or 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(null, al);
+
+ 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(null, al);
+
+ 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(null, al);
+
+ /*
+ * 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 / blobdiff