2 package jalview.analysis;
3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertNull;
5 import org.testng.annotations.Test;
6 import jalview.datamodel.Sequence;
7 import jalview.datamodel.SequenceI;
9 import java.util.Hashtable;
11 public class AAFrequencyTest
13 private static final String C = AAFrequency.MAXCOUNT;
15 private static final String R = AAFrequency.MAXRESIDUE;
17 private static final String G = AAFrequency.PID_GAPS;
19 private static final String N = AAFrequency.PID_NOGAPS;
21 private static final String P = AAFrequency.PROFILE;
24 public void testCalculate_noProfile()
26 SequenceI seq1 = new Sequence("Seq1", "CAGT");
27 SequenceI seq2 = new Sequence("Seq2", "CACT");
28 SequenceI seq3 = new Sequence("Seq3", "C--G");
29 SequenceI seq4 = new Sequence("Seq4", "CA-t");
30 SequenceI[] seqs = new SequenceI[]
31 { seq1, seq2, seq3, seq4 };
32 Hashtable[] result = new Hashtable[seq1.getLength()];
34 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
37 Hashtable col = result[0];
38 assertEquals(100f, (Float) col.get(G), 0.0001f);
39 assertEquals(100f, (Float) col.get(N), 0.0001f);
40 assertEquals(4, col.get(C));
41 assertEquals("C", col.get(R));
42 assertNull(col.get(P));
46 assertEquals(75f, (Float) col.get(G), 0.0001f);
47 assertEquals(100f, (Float) col.get(N), 0.0001f);
48 assertEquals(3, col.get(C));
49 assertEquals("A", col.get(R));
51 // col 2 is 50% G 50% C or 25/25 counting gaps
53 assertEquals(25f, (Float) col.get(G), 0.0001f);
54 assertEquals(50f, (Float) col.get(N), 0.0001f);
55 assertEquals(1, col.get(C));
56 assertEquals("CG", col.get(R));
58 // col 3 is 75% T 25% G
60 assertEquals(75f, (Float) col.get(G), 0.0001f);
61 assertEquals(75f, (Float) col.get(N), 0.0001f);
62 assertEquals(3, col.get(C));
63 assertEquals("T", col.get(R));
67 public void testCalculate_withProfile()
69 SequenceI seq1 = new Sequence("Seq1", "CAGT");
70 SequenceI seq2 = new Sequence("Seq2", "CACT");
71 SequenceI seq3 = new Sequence("Seq3", "C--G");
72 SequenceI seq4 = new Sequence("Seq4", "CA-t");
73 SequenceI[] seqs = new SequenceI[]
74 { 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]);
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[]
109 { seq1, seq2, seq3, seq4 };
110 Hashtable[] result = new Hashtable[seq1.getLength()];
112 // ensure class loaded and initialized
113 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
115 long start = System.currentTimeMillis();
116 for (int i = 0; i < reps; i++)
118 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
120 System.out.println(System.currentTimeMillis() - start);
124 public void testGetPercentageFormat()
126 assertNull(AAFrequency.getPercentageFormat(0));
127 assertNull(AAFrequency.getPercentageFormat(99));
128 assertEquals("%3.1f", AAFrequency.getPercentageFormat(100).toString());
129 assertEquals("%3.1f", AAFrequency.getPercentageFormat(999).toString());
130 assertEquals("%3.2f", AAFrequency.getPercentageFormat(1000).toString());
131 assertEquals("%3.2f", AAFrequency.getPercentageFormat(9999).toString());