X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FAnnotationColourGradientTest.java;h=35e3c2fd14b7797cc6abbfa7f20f13122d3ae10c;hb=a3f8f05c73d08184254a8751c99824cfd126c4be;hp=42e3eb4b0cdddc54127228faeb002da42b27324b;hpb=2963965a346b42b6b9a2d0878ee076220be7077b;p=jalview.git diff --git a/test/jalview/schemes/AnnotationColourGradientTest.java b/test/jalview/schemes/AnnotationColourGradientTest.java index 42e3eb4..35e3c2f 100644 --- a/test/jalview/schemes/AnnotationColourGradientTest.java +++ b/test/jalview/schemes/AnnotationColourGradientTest.java @@ -1,12 +1,36 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.schemes; 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; @@ -15,31 +39,45 @@ public class AnnotationColourGradientTest { 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); - @BeforeClass + /** + * 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 + * 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("Seq", ""); + 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") @@ -72,8 +110,7 @@ public class AnnotationColourGradientTest 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); @@ -85,7 +122,7 @@ public class AnnotationColourGradientTest * (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 @@ -95,18 +132,30 @@ public class AnnotationColourGradientTest 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); 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 } /** @@ -115,12 +164,6 @@ public class AnnotationColourGradientTest @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); @@ -129,8 +172,7 @@ public class AnnotationColourGradientTest 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); @@ -142,7 +184,7 @@ public class AnnotationColourGradientTest * (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 @@ -153,7 +195,7 @@ public class AnnotationColourGradientTest 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 @@ -164,5 +206,139 @@ public class AnnotationColourGradientTest 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 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); + } } }