1 package jalview.analysis;
3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertNull;
6 import jalview.datamodel.Sequence;
7 import jalview.datamodel.SequenceI;
9 import java.util.Hashtable;
11 import org.testng.annotations.Test;
13 public class AAFrequencyTest
15 private static final String C = AAFrequency.MAXCOUNT;
17 private static final String R = AAFrequency.MAXRESIDUE;
19 private static final String G = AAFrequency.PID_GAPS;
21 private static final String N = AAFrequency.PID_NOGAPS;
23 private static final String P = AAFrequency.PROFILE;
25 @Test(groups = { "Functional" })
26 public void testCalculate_noProfile()
28 SequenceI seq1 = new Sequence("Seq1", "CAGT");
29 SequenceI seq2 = new Sequence("Seq2", "CACT");
30 SequenceI seq3 = new Sequence("Seq3", "C--G");
31 SequenceI seq4 = new Sequence("Seq4", "CA-t");
32 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
33 Hashtable[] result = new Hashtable[seq1.getLength()];
35 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
38 Hashtable col = result[0];
39 assertEquals(100f, (Float) col.get(G), 0.0001f);
40 assertEquals(100f, (Float) col.get(N), 0.0001f);
41 assertEquals(4, col.get(C));
42 assertEquals("C", col.get(R));
43 assertNull(col.get(P));
47 assertEquals(75f, (Float) col.get(G), 0.0001f);
48 assertEquals(100f, (Float) col.get(N), 0.0001f);
49 assertEquals(3, col.get(C));
50 assertEquals("A", col.get(R));
52 // col 2 is 50% G 50% C or 25/25 counting gaps
54 assertEquals(25f, (Float) col.get(G), 0.0001f);
55 assertEquals(50f, (Float) col.get(N), 0.0001f);
56 assertEquals(1, col.get(C));
57 assertEquals("CG", col.get(R));
59 // col 3 is 75% T 25% G
61 assertEquals(75f, (Float) col.get(G), 0.0001f);
62 assertEquals(75f, (Float) col.get(N), 0.0001f);
63 assertEquals(3, col.get(C));
64 assertEquals("T", col.get(R));
67 @Test(groups = { "Functional" })
68 public void testCalculate_withProfile()
70 SequenceI seq1 = new Sequence("Seq1", "CAGT");
71 SequenceI seq2 = new Sequence("Seq2", "CACT");
72 SequenceI seq3 = new Sequence("Seq3", "C--G");
73 SequenceI seq4 = new Sequence("Seq4", "CA-t");
74 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
75 Hashtable[] result = new Hashtable[seq1.getLength()];
77 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
78 int[][] profile = (int[][]) result[0].get(P);
79 assertEquals(4, profile[0]['C']);
80 assertEquals(4, profile[1][0]); // no of seqs
81 assertEquals(4, profile[1][1]); // nongapped in column
83 profile = (int[][]) result[1].get(P);
84 assertEquals(3, profile[0]['A']);
85 assertEquals(4, profile[1][0]);
86 assertEquals(3, profile[1][1]);
88 profile = (int[][]) result[2].get(P);
89 assertEquals(1, profile[0]['G']);
90 assertEquals(1, profile[0]['C']);
91 assertEquals(4, profile[1][0]);
92 assertEquals(2, profile[1][1]);
94 profile = (int[][]) result[3].get(P);
95 assertEquals(3, profile[0]['T']);
96 assertEquals(1, profile[0]['G']);
97 assertEquals(4, profile[1][0]);
98 assertEquals(4, profile[1][1]);
101 @Test(groups = { "Functional" })
102 public void testCalculate_withProfileTiming()
104 SequenceI seq1 = new Sequence("Seq1", "CAGT");
105 SequenceI seq2 = new Sequence("Seq2", "CACT");
106 SequenceI seq3 = new Sequence("Seq3", "C--G");
107 SequenceI seq4 = new Sequence("Seq4", "CA-t");
108 SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
109 Hashtable[] result = new Hashtable[seq1.getLength()];
111 // ensure class loaded and initialized
112 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
114 long start = System.currentTimeMillis();
115 for (int i = 0; i < reps; i++)
117 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
119 System.out.println(System.currentTimeMillis() - start);
122 @Test(groups = { "Functional" })
123 public void testGetPercentageFormat()
125 assertNull(AAFrequency.getPercentageFormat(0));
126 assertNull(AAFrequency.getPercentageFormat(99));
127 assertEquals("%3.1f", AAFrequency.getPercentageFormat(100).toString());
128 assertEquals("%3.1f", AAFrequency.getPercentageFormat(999).toString());
129 assertEquals("%3.2f", AAFrequency.getPercentageFormat(1000).toString());
130 assertEquals("%3.2f", AAFrequency.getPercentageFormat(9999).toString());