2 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;
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[]
33 { seq1, seq2, seq3, seq4 };
34 Hashtable[] result = new Hashtable[seq1.getLength()];
36 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
39 Hashtable col = result[0];
40 assertEquals(100f, (Float) col.get(G), 0.0001f);
41 assertEquals(100f, (Float) col.get(N), 0.0001f);
42 assertEquals(4, col.get(C));
43 assertEquals("C", col.get(R));
44 assertNull(col.get(P));
48 assertEquals(75f, (Float) col.get(G), 0.0001f);
49 assertEquals(100f, (Float) col.get(N), 0.0001f);
50 assertEquals(3, col.get(C));
51 assertEquals("A", col.get(R));
53 // col 2 is 50% G 50% C or 25/25 counting gaps
55 assertEquals(25f, (Float) col.get(G), 0.0001f);
56 assertEquals(50f, (Float) col.get(N), 0.0001f);
57 assertEquals(1, col.get(C));
58 assertEquals("CG", col.get(R));
60 // col 3 is 75% T 25% G
62 assertEquals(75f, (Float) col.get(G), 0.0001f);
63 assertEquals(75f, (Float) col.get(N), 0.0001f);
64 assertEquals(3, col.get(C));
65 assertEquals("T", col.get(R));
69 public void testCalculate_withProfile()
71 SequenceI seq1 = new Sequence("Seq1", "CAGT");
72 SequenceI seq2 = new Sequence("Seq2", "CACT");
73 SequenceI seq3 = new Sequence("Seq3", "C--G");
74 SequenceI seq4 = new Sequence("Seq4", "CA-t");
75 SequenceI[] seqs = new SequenceI[]
76 { seq1, seq2, seq3, seq4 };
77 Hashtable[] result = new Hashtable[seq1.getLength()];
79 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
80 int[][] profile = (int[][]) result[0].get(P);
81 assertEquals(4, profile[0]['C']);
82 assertEquals(4, profile[1][0]); // no of seqs
83 assertEquals(4, profile[1][1]); // nongapped in column
85 profile = (int[][]) result[1].get(P);
86 assertEquals(3, profile[0]['A']);
87 assertEquals(4, profile[1][0]);
88 assertEquals(3, profile[1][1]);
90 profile = (int[][]) result[2].get(P);
91 assertEquals(1, profile[0]['G']);
92 assertEquals(1, profile[0]['C']);
93 assertEquals(4, profile[1][0]);
94 assertEquals(2, profile[1][1]);
96 profile = (int[][]) result[3].get(P);
97 assertEquals(3, profile[0]['T']);
98 assertEquals(1, profile[0]['G']);
99 assertEquals(4, profile[1][0]);
100 assertEquals(4, profile[1][1]);
104 public void testCalculate_withProfileTiming()
106 SequenceI seq1 = new Sequence("Seq1", "CAGT");
107 SequenceI seq2 = new Sequence("Seq2", "CACT");
108 SequenceI seq3 = new Sequence("Seq3", "C--G");
109 SequenceI seq4 = new Sequence("Seq4", "CA-t");
110 SequenceI[] seqs = new SequenceI[]
111 { seq1, seq2, seq3, seq4 };
112 Hashtable[] result = new Hashtable[seq1.getLength()];
114 // ensure class loaded and initialized
115 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
117 long start = System.currentTimeMillis();
118 for (int i = 0; i < reps; i++)
120 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
122 System.out.println(System.currentTimeMillis() - start);
126 public void testGetPercentageFormat()
128 assertNull(AAFrequency.getPercentageFormat(0));
129 assertNull(AAFrequency.getPercentageFormat(99));
130 assertEquals("%3.1f", AAFrequency.getPercentageFormat(100).toString());
131 assertEquals("%3.1f", AAFrequency.getPercentageFormat(999).toString());
132 assertEquals("%3.2f", AAFrequency.getPercentageFormat(1000).toString());
133 assertEquals("%3.2f", AAFrequency.getPercentageFormat(9999).toString());