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.analysis.Profile;
11 import org.testng.annotations.Test;
13 public class ResidueColourSchemeTest
15 @Test(groups = "Functional")
16 public void testAboveThreshold()
19 * make up profiles for this alignment:
25 Profile[] profiles = new Profile[4];
26 profiles[0] = new Profile(4, 0, 2, "AS");
27 profiles[1] = new Profile(4, 0, 4, "R");
28 profiles[2] = new Profile(4, 4, 0, "");
29 profiles[3] = new Profile(4, 1, 2, "T");
30 ResidueColourScheme rcs = new ResidueColourScheme();
31 rcs.setConsensus(profiles);
36 rcs.setThreshold(0, true);
37 assertTrue(rcs.aboveThreshold('a', 0));
38 assertTrue(rcs.aboveThreshold('S', 0));
39 assertFalse(rcs.aboveThreshold('W', 0));
40 assertTrue(rcs.aboveThreshold('R', 1));
41 assertFalse(rcs.aboveThreshold('W', 2));
42 assertTrue(rcs.aboveThreshold('t', 3));
43 assertFalse(rcs.aboveThreshold('Q', 3));
46 * with threshold, include gaps
48 rcs.setThreshold(60, false);
49 assertFalse(rcs.aboveThreshold('a', 0));
50 assertFalse(rcs.aboveThreshold('S', 0));
51 assertTrue(rcs.aboveThreshold('R', 1));
52 assertFalse(rcs.aboveThreshold('W', 2));
53 assertFalse(rcs.aboveThreshold('t', 3)); // 50% < 60%
56 * with threshold, ignore gaps
58 rcs.setThreshold(60, true);
59 assertFalse(rcs.aboveThreshold('a', 0));
60 assertFalse(rcs.aboveThreshold('S', 0));
61 assertTrue(rcs.aboveThreshold('R', 1));
62 assertFalse(rcs.aboveThreshold('W', 2));
63 assertTrue(rcs.aboveThreshold('t', 3)); // 67% > 60%
67 * Test colour bleaching based on conservation score and conservation slider.
68 * Scores of 10 or 11 should leave colours unchanged. Gap is always white.
70 @Test(groups = "Functional")
71 public void testApplyConservation()
73 ResidueColourScheme rcs = new ResidueColourScheme();
75 // no conservation present - no fading
76 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 12));
78 // cheat by setting conservation sequence directly
79 // rather than calculating it - good enough for this test
80 String consensus = "0123456789+*-";
81 rcs.conservation = consensus.toCharArray();
83 // column out of range:
84 assertEquals(Color.RED,
85 rcs.applyConservation(Color.RED, consensus.length()));
88 * with 100% threshold, 'fade factor' is
89 * (11-score)/10 * 100/20 = (11-score)/2
90 * which is >= 1 for all scores i.e. all fade to white except +, *
92 rcs.setConservationInc(100);
93 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 0));
94 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 1));
95 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 2));
96 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 3));
97 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 4));
98 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 5));
99 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 6));
100 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 7));
101 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 8));
102 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 9));
103 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
104 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
105 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12));
108 * with 0% threshold, there should be no fading
110 rcs.setConservationInc(0);
111 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 0));
112 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 1));
113 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 2));
114 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 3));
115 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 4));
116 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 5));
117 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 6));
118 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 7));
119 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 8));
120 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 9));
121 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 10));
122 assertEquals(Color.RED, rcs.applyConservation(Color.RED, 11));
123 assertEquals(Color.WHITE, rcs.applyConservation(Color.RED, 12)); // gap
126 * with 40% threshold, 'fade factor' is
127 * (11-score)/10 * 40/20 = (11-score)/5
128 * which is {>1, >1, >1, >1, >1, >1, 1, 0.8, 0.6, 0.4} for score 0-9
129 * e.g. score 7 colour fades 80% of the way to white (255, 255, 255)
131 rcs.setConservationInc(40);
132 Color colour = new Color(155, 105, 55);
133 assertEquals(Color.WHITE, rcs.applyConservation(colour, 0));
134 assertEquals(Color.WHITE, rcs.applyConservation(colour, 1));
135 assertEquals(Color.WHITE, rcs.applyConservation(colour, 2));
136 assertEquals(Color.WHITE, rcs.applyConservation(colour, 3));
137 assertEquals(Color.WHITE, rcs.applyConservation(colour, 4));
138 assertEquals(Color.WHITE, rcs.applyConservation(colour, 5));
139 assertEquals(Color.WHITE, rcs.applyConservation(colour, 6));
140 assertEquals(new Color(235, 225, 215), rcs.applyConservation(colour, 7));
141 assertEquals(new Color(215, 195, 175), rcs.applyConservation(colour, 8));
142 assertEquals(new Color(195, 165, 135), rcs.applyConservation(colour, 9));
143 assertEquals(colour, rcs.applyConservation(colour, 10));
144 assertEquals(colour, rcs.applyConservation(colour, 11));
145 assertEquals(Color.WHITE, rcs.applyConservation(colour, 12));