2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.schemes;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertTrue;
27 import jalview.datamodel.Profile;
28 import jalview.datamodel.ProfileI;
29 import jalview.datamodel.Profiles;
30 import jalview.gui.JvOptionPane;
32 import java.awt.Color;
34 import org.testng.annotations.BeforeClass;
35 import org.testng.annotations.Test;
37 public class ResidueColourSchemeTest
40 @BeforeClass(alwaysRun = true)
41 public void setUpJvOptionPane()
43 JvOptionPane.setInteractiveMode(false);
44 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
47 @Test(groups = "Functional")
48 public void testAboveThreshold()
51 * make up profiles for this alignment:
57 ProfileI[] profiles = new ProfileI[4];
58 profiles[0] = new Profile(4, 0, 2, "AS");
59 profiles[1] = new Profile(4, 0, 4, "R");
60 profiles[2] = new Profile(4, 4, 0, "");
61 profiles[3] = new Profile(4, 1, 2, "T");
62 ResidueColourScheme rcs = new ResidueColourScheme();
63 rcs.setConsensus(new Profiles(profiles));
68 rcs.setThreshold(0, true);
69 assertTrue(rcs.aboveThreshold('a', 0));
70 assertTrue(rcs.aboveThreshold('S', 0));
71 assertFalse(rcs.aboveThreshold('W', 0));
72 assertTrue(rcs.aboveThreshold('R', 1));
73 assertFalse(rcs.aboveThreshold('W', 2));
74 assertTrue(rcs.aboveThreshold('t', 3));
75 assertFalse(rcs.aboveThreshold('Q', 3));
78 * with threshold, include gaps
80 rcs.setThreshold(60, false);
81 assertFalse(rcs.aboveThreshold('a', 0));
82 assertFalse(rcs.aboveThreshold('S', 0));
83 assertTrue(rcs.aboveThreshold('R', 1));
84 assertFalse(rcs.aboveThreshold('W', 2));
85 assertFalse(rcs.aboveThreshold('t', 3)); // 50% < 60%
88 * with threshold, ignore gaps
90 rcs.setThreshold(60, true);
91 assertFalse(rcs.aboveThreshold('a', 0));
92 assertFalse(rcs.aboveThreshold('S', 0));
93 assertTrue(rcs.aboveThreshold('R', 1));
94 assertFalse(rcs.aboveThreshold('W', 2));
95 assertTrue(rcs.aboveThreshold('t', 3)); // 67% > 60%
99 * Test colour bleaching based on conservation score and conservation slider.
100 * Scores of 10 or 11 should leave colours unchanged. Gap is always white.
102 @Test(groups = "Functional")
103 public void testApplyConservation()
105 ResidueColourScheme rcs = new ResidueColourScheme();
107 // no conservation present - no fading
108 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 12));
110 // cheat by setting conservation sequence directly
111 // rather than calculating it - good enough for this test
112 String consensus = "0123456789+*-";
113 rcs.conservation = consensus.toCharArray();
115 // column out of range:
116 assertEquals(Color.RED,
117 rcs.applyConservation(Color.RED, consensus.length()));
120 * with 100% threshold, 'fade factor' is
121 * (11-score)/10 * 100/20 = (11-score)/2
122 * which is >= 1 for all scores i.e. all fade to white except +, *
124 rcs.setConservationInc(100);
125 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 0));
126 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 1));
127 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 2));
128 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 3));
129 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 4));
130 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 5));
131 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 6));
132 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 7));
133 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 8));
134 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 9));
135 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
136 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
137 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12));
140 * with 0% threshold, there should be no fading
142 rcs.setConservationInc(0);
143 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 0));
144 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 1));
145 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 2));
146 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 3));
147 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 4));
148 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 5));
149 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 6));
150 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 7));
151 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 8));
152 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 9));
153 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
154 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
155 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12)); // gap
158 * with 40% threshold, 'fade factor' is
159 * (11-score)/10 * 40/20 = (11-score)/5
160 * which is {>1, >1, >1, >1, >1, >1, 1, 0.8, 0.6, 0.4} for score 0-9
161 * e.g. score 7 colour fades 80% of the way to white (255, 255, 255)
163 rcs.setConservationInc(40);
164 Color colour = new Color(155, 105, 55);
165 assertEquals(Color.WHITE, rcs.applyConservation(colour, 0));
166 assertEquals(Color.WHITE, rcs.applyConservation(colour, 1));
167 assertEquals(Color.WHITE, rcs.applyConservation(colour, 2));
168 assertEquals(Color.WHITE, rcs.applyConservation(colour, 3));
169 assertEquals(Color.WHITE, rcs.applyConservation(colour, 4));
170 assertEquals(Color.WHITE, rcs.applyConservation(colour, 5));
171 assertEquals(Color.WHITE, rcs.applyConservation(colour, 6));
172 assertEquals(new Color(235, 225, 215), rcs.applyConservation(colour, 7));
173 assertEquals(new Color(215, 195, 175), rcs.applyConservation(colour, 8));
174 assertEquals(new Color(195, 165, 135), rcs.applyConservation(colour, 9));
175 assertEquals(colour, rcs.applyConservation(colour, 10));
176 assertEquals(colour, rcs.applyConservation(colour, 11));
177 assertEquals(Color.WHITE, rcs.applyConservation(colour, 12));