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