2 package jalview.analysis;
3 import static org.junit.Assert.assertEquals;
4 import static org.junit.Assert.assertNull;
5 import jalview.datamodel.Sequence;
6 import jalview.datamodel.SequenceI;
8 import java.util.Hashtable;
10 import org.junit.Test;
12 public class AAFrequencyTest
14 private static final String C = AAFrequency.MAXCOUNT;
16 private static final String R = AAFrequency.MAXRESIDUE;
18 private static final String G = AAFrequency.PID_GAPS;
20 private static final String N = AAFrequency.PID_NOGAPS;
22 private static final String P = AAFrequency.PROFILE;
25 public void testCalculate_noProfile()
27 SequenceI seq1 = new Sequence("Seq1", "CAGT");
28 SequenceI seq2 = new Sequence("Seq2", "CACT");
29 SequenceI seq3 = new Sequence("Seq3", "C--G");
30 SequenceI seq4 = new Sequence("Seq4", "CA-t");
31 SequenceI[] seqs = new SequenceI[]
32 { 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));
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[]
75 { seq1, seq2, seq3, seq4 };
76 Hashtable[] result = new Hashtable[seq1.getLength()];
78 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
79 int[][] profile = (int[][]) result[0].get(P);
80 assertEquals(4, profile[0]['C']);
81 assertEquals(4, profile[1][0]); // no of seqs
82 assertEquals(4, profile[1][1]); // nongapped in column
84 profile = (int[][]) result[1].get(P);
85 assertEquals(3, profile[0]['A']);
86 assertEquals(4, profile[1][0]);
87 assertEquals(3, profile[1][1]);
89 profile = (int[][]) result[2].get(P);
90 assertEquals(1, profile[0]['G']);
91 assertEquals(1, profile[0]['C']);
92 assertEquals(4, profile[1][0]);
93 assertEquals(2, profile[1][1]);
95 profile = (int[][]) result[3].get(P);
96 assertEquals(3, profile[0]['T']);
97 assertEquals(1, profile[0]['G']);
98 assertEquals(4, profile[1][0]);
99 assertEquals(4, profile[1][1]);
103 public void testCalculate_withProfileTiming()
105 SequenceI seq1 = new Sequence("Seq1", "CAGT");
106 SequenceI seq2 = new Sequence("Seq2", "CACT");
107 SequenceI seq3 = new Sequence("Seq3", "C--G");
108 SequenceI seq4 = new Sequence("Seq4", "CA-t");
109 SequenceI[] seqs = new SequenceI[]
110 { seq1, seq2, seq3, seq4 };
111 Hashtable[] result = new Hashtable[seq1.getLength()];
113 // ensure class loaded and initialized
114 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
116 long start = System.currentTimeMillis();
117 for (int i = 0; i < reps; i++)
119 AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
121 System.out.println(System.currentTimeMillis() - start);
125 public void testGetPercentageFormat()
127 assertNull(AAFrequency.getPercentageFormat(0));
128 assertNull(AAFrequency.getPercentageFormat(99));
129 assertEquals("%3.1f", AAFrequency.getPercentageFormat(100).toString());
130 assertEquals("%3.1f", AAFrequency.getPercentageFormat(999).toString());
131 assertEquals("%3.2f", AAFrequency.getPercentageFormat(1000).toString());
132 assertEquals("%3.2f", AAFrequency.getPercentageFormat(9999).toString());