1 package jalview.schemes;
3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertFalse;
5 import static org.testng.AssertJUnit.assertTrue;
7 import jalview.datamodel.Profile;
8 import jalview.datamodel.ProfileI;
9 import jalview.datamodel.Profiles;
10 import jalview.gui.JvOptionPane;
12 import java.awt.Color;
14 import org.testng.annotations.BeforeClass;
15 import org.testng.annotations.Test;
17 public class ResidueColourSchemeTest
20 @BeforeClass(alwaysRun = true)
21 public void setUpJvOptionPane()
23 JvOptionPane.setInteractiveMode(false);
24 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
27 @Test(groups = "Functional")
28 public void testAboveThreshold()
31 * make up profiles for this alignment:
37 ProfileI[] profiles = new ProfileI[4];
38 profiles[0] = new Profile(4, 0, 2, "AS");
39 profiles[1] = new Profile(4, 0, 4, "R");
40 profiles[2] = new Profile(4, 4, 0, "");
41 profiles[3] = new Profile(4, 1, 2, "T");
42 ResidueColourScheme rcs = new ResidueColourScheme();
43 rcs.setConsensus(new Profiles(profiles));
48 rcs.setThreshold(0, true);
49 assertTrue(rcs.aboveThreshold('a', 0));
50 assertTrue(rcs.aboveThreshold('S', 0));
51 assertFalse(rcs.aboveThreshold('W', 0));
52 assertTrue(rcs.aboveThreshold('R', 1));
53 assertFalse(rcs.aboveThreshold('W', 2));
54 assertTrue(rcs.aboveThreshold('t', 3));
55 assertFalse(rcs.aboveThreshold('Q', 3));
58 * with threshold, include gaps
60 rcs.setThreshold(60, false);
61 assertFalse(rcs.aboveThreshold('a', 0));
62 assertFalse(rcs.aboveThreshold('S', 0));
63 assertTrue(rcs.aboveThreshold('R', 1));
64 assertFalse(rcs.aboveThreshold('W', 2));
65 assertFalse(rcs.aboveThreshold('t', 3)); // 50% < 60%
68 * with threshold, ignore gaps
70 rcs.setThreshold(60, true);
71 assertFalse(rcs.aboveThreshold('a', 0));
72 assertFalse(rcs.aboveThreshold('S', 0));
73 assertTrue(rcs.aboveThreshold('R', 1));
74 assertFalse(rcs.aboveThreshold('W', 2));
75 assertTrue(rcs.aboveThreshold('t', 3)); // 67% > 60%
79 * Test colour bleaching based on conservation score and conservation slider.
80 * Scores of 10 or 11 should leave colours unchanged. Gap is always white.
82 @Test(groups = "Functional")
83 public void testApplyConservation()
85 ResidueColourScheme rcs = new ResidueColourScheme();
87 // no conservation present - no fading
88 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 12));
90 // cheat by setting conservation sequence directly
91 // rather than calculating it - good enough for this test
92 String consensus = "0123456789+*-";
93 rcs.conservation = consensus.toCharArray();
95 // column out of range:
96 assertEquals(Color.RED,
97 rcs.applyConservation(Color.RED, consensus.length()));
100 * with 100% threshold, 'fade factor' is
101 * (11-score)/10 * 100/20 = (11-score)/2
102 * which is >= 1 for all scores i.e. all fade to white except +, *
104 rcs.setConservationInc(100);
105 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 0));
106 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 1));
107 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 2));
108 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 3));
109 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 4));
110 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 5));
111 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 6));
112 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 7));
113 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 8));
114 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 9));
115 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
116 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
117 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12));
120 * with 0% threshold, there should be no fading
122 rcs.setConservationInc(0);
123 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 0));
124 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 1));
125 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 2));
126 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 3));
127 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 4));
128 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 5));
129 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 6));
130 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 7));
131 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 8));
132 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 9));
133 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
134 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
135 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12)); // gap
138 * with 40% threshold, 'fade factor' is
139 * (11-score)/10 * 40/20 = (11-score)/5
140 * which is {>1, >1, >1, >1, >1, >1, 1, 0.8, 0.6, 0.4} for score 0-9
141 * e.g. score 7 colour fades 80% of the way to white (255, 255, 255)
143 rcs.setConservationInc(40);
144 Color colour = new Color(155, 105, 55);
145 assertEquals(Color.WHITE, rcs.applyConservation(colour, 0));
146 assertEquals(Color.WHITE, rcs.applyConservation(colour, 1));
147 assertEquals(Color.WHITE, rcs.applyConservation(colour, 2));
148 assertEquals(Color.WHITE, rcs.applyConservation(colour, 3));
149 assertEquals(Color.WHITE, rcs.applyConservation(colour, 4));
150 assertEquals(Color.WHITE, rcs.applyConservation(colour, 5));
151 assertEquals(Color.WHITE, rcs.applyConservation(colour, 6));
152 assertEquals(new Color(235, 225, 215), rcs.applyConservation(colour, 7));
153 assertEquals(new Color(215, 195, 175), rcs.applyConservation(colour, 8));
154 assertEquals(new Color(195, 165, 135), rcs.applyConservation(colour, 9));
155 assertEquals(colour, rcs.applyConservation(colour, 10));
156 assertEquals(colour, rcs.applyConservation(colour, 11));
157 assertEquals(Color.WHITE, rcs.applyConservation(colour, 12));