/* * 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.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; import jalview.datamodel.Profile; import jalview.datamodel.ProfileI; import jalview.datamodel.Profiles; import jalview.gui.JvOptionPane; import java.awt.Color; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class ResidueColourSchemeTest { @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } @Test(groups = "Functional") public void testAboveThreshold() { /* * make up profiles for this alignment: * AR-Q * AR-- * SR-T * SR-T */ ProfileI[] profiles = new ProfileI[4]; profiles[0] = new Profile(4, 0, 2, "AS"); profiles[1] = new Profile(4, 0, 4, "R"); profiles[2] = new Profile(4, 4, 0, ""); profiles[3] = new Profile(4, 1, 2, "T"); ResidueColourScheme rcs = new ResidueColourScheme(); rcs.setConsensus(new Profiles(profiles)); /* * no threshold */ rcs.setThreshold(0, true); assertTrue(rcs.aboveThreshold('a', 0)); assertTrue(rcs.aboveThreshold('S', 0)); assertFalse(rcs.aboveThreshold('W', 0)); assertTrue(rcs.aboveThreshold('R', 1)); assertFalse(rcs.aboveThreshold('W', 2)); assertTrue(rcs.aboveThreshold('t', 3)); assertFalse(rcs.aboveThreshold('Q', 3)); /* * with threshold, include gaps */ rcs.setThreshold(60, false); assertFalse(rcs.aboveThreshold('a', 0)); assertFalse(rcs.aboveThreshold('S', 0)); assertTrue(rcs.aboveThreshold('R', 1)); assertFalse(rcs.aboveThreshold('W', 2)); assertFalse(rcs.aboveThreshold('t', 3)); // 50% < 60% /* * with threshold, ignore gaps */ rcs.setThreshold(60, true); assertFalse(rcs.aboveThreshold('a', 0)); assertFalse(rcs.aboveThreshold('S', 0)); assertTrue(rcs.aboveThreshold('R', 1)); assertFalse(rcs.aboveThreshold('W', 2)); assertTrue(rcs.aboveThreshold('t', 3)); // 67% > 60% } /** * Test colour bleaching based on conservation score and conservation slider. * Scores of 10 or 11 should leave colours unchanged. Gap is always white. */ @Test(groups = "Functional") public void testApplyConservation() { ResidueColourScheme rcs = new ResidueColourScheme(); // no conservation present - no fading assertEquals(Color.RED, rcs.applyConservation(Color.RED, 12)); // cheat by setting conservation sequence directly // rather than calculating it - good enough for this test String consensus = "0123456789+*-"; rcs.conservation = consensus.toCharArray(); // column out of range: assertEquals(Color.RED, rcs.applyConservation(Color.RED, consensus.length())); /* * with 100% threshold, 'fade factor' is * (11-score)/10 * 100/20 = (11-score)/2 * which is >= 1 for all scores i.e. all fade to white except +, * */ rcs.setConservationInc(100); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 0)); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 1)); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 2)); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 3)); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 4)); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 5)); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 6)); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 7)); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 8)); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 9)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11)); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12)); /* * with 0% threshold, there should be no fading */ rcs.setConservationInc(0); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 0)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 1)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 2)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 3)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 4)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 5)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 6)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 7)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 8)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 9)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10)); assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11)); assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12)); // gap /* * with 40% threshold, 'fade factor' is * (11-score)/10 * 40/20 = (11-score)/5 * which is {>1, >1, >1, >1, >1, >1, 1, 0.8, 0.6, 0.4} for score 0-9 * e.g. score 7 colour fades 80% of the way to white (255, 255, 255) */ rcs.setConservationInc(40); Color colour = new Color(155, 105, 55); assertEquals(Color.WHITE, rcs.applyConservation(colour, 0)); assertEquals(Color.WHITE, rcs.applyConservation(colour, 1)); assertEquals(Color.WHITE, rcs.applyConservation(colour, 2)); assertEquals(Color.WHITE, rcs.applyConservation(colour, 3)); assertEquals(Color.WHITE, rcs.applyConservation(colour, 4)); assertEquals(Color.WHITE, rcs.applyConservation(colour, 5)); assertEquals(Color.WHITE, rcs.applyConservation(colour, 6)); assertEquals(new Color(235, 225, 215), rcs.applyConservation(colour, 7)); assertEquals(new Color(215, 195, 175), rcs.applyConservation(colour, 8)); assertEquals(new Color(195, 165, 135), rcs.applyConservation(colour, 9)); assertEquals(colour, rcs.applyConservation(colour, 10)); assertEquals(colour, rcs.applyConservation(colour, 11)); assertEquals(Color.WHITE, rcs.applyConservation(colour, 12)); } }