Merge branch 'features/JAL-845splitPaneMergeDevelop' into develop

[jalview.git] / test / jalview / analysis / AAFrequencyTest.java

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
new file mode 100644 (file)
index 0000000..1c30c79
--- /dev/null
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -0,0 +1,115 @@
+package jalview.analysis;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.util.Hashtable;
+
+import org.junit.Test;
+
+public class AAFrequencyTest
+{
+  private static final String C = AAFrequency.MAXCOUNT;
+
+  private static final String R = AAFrequency.MAXRESIDUE;
+
+  private static final String G = AAFrequency.PID_GAPS;
+
+  private static final String N = AAFrequency.PID_NOGAPS;
+
+  private static final String P = AAFrequency.PROFILE;
+
+  @Test
+  public void testCalculate_noProfile()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "CAGT");
+    SequenceI seq2 = new Sequence("Seq2", "CACT");
+    SequenceI seq3 = new Sequence("Seq3", "C--G");
+    SequenceI seq4 = new Sequence("Seq4", "CA-t");
+    SequenceI[] seqs = new SequenceI[]
+    { seq1, seq2, seq3, seq4 };
+    Hashtable[] result = new Hashtable[seq1.getLength()];
+    
+    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
+    Hashtable col = result[0];
+    assertEquals(100f, (Float) col.get(G), 0.0001f);
+    assertEquals(100f, (Float) col.get(N), 0.0001f);
+    assertEquals(4, col.get(C));
+    assertEquals("C", col.get(R));
+    assertNull(col.get(P));
+    col = result[1];
+    assertEquals(75f, (Float) col.get(G), 0.0001f);
+    assertEquals(100f, (Float) col.get(N), 0.0001f);
+    assertEquals(3, col.get(C));
+    assertEquals("A", col.get(R));
+    col = result[2];
+    assertEquals(0f, (Float) col.get(G), 0.0001f);
+    assertEquals(0f, (Float) col.get(N), 0.0001f);
+    assertEquals(0, col.get(C));
+    assertEquals("-", col.get(R));
+    col = result[3];
+    assertEquals(75f, (Float) col.get(G), 0.0001f);
+    assertEquals(75f, (Float) col.get(N), 0.0001f);
+    assertEquals(3, col.get(C));
+    assertEquals("T", col.get(R));
+  }
+
+  @Test
+  public void testCalculate_withProfile()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "CAGT");
+    SequenceI seq2 = new Sequence("Seq2", "CACT");
+    SequenceI seq3 = new Sequence("Seq3", "C--G");
+    SequenceI seq4 = new Sequence("Seq4", "CA-t");
+    SequenceI[] seqs = new SequenceI[]
+    { seq1, seq2, seq3, seq4 };
+    Hashtable[] result = new Hashtable[seq1.getLength()];
+
+    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
+    int[][] profile = (int[][]) result[0].get(P);
+    assertEquals(4, profile[0]['C']);
+    assertEquals(4, profile[1][0]); // no of seqs
+    assertEquals(4, profile[1][1]); // nongapped in column
+
+    profile = (int[][]) result[1].get(P);
+    assertEquals(3, profile[0]['A']);
+    assertEquals(4, profile[1][0]);
+    assertEquals(3, profile[1][1]);
+
+    profile = (int[][]) result[2].get(P);
+    assertEquals(1, profile[0]['G']);
+    assertEquals(1, profile[0]['C']);
+    assertEquals(4, profile[1][0]);
+    assertEquals(2, profile[1][1]);
+
+    profile = (int[][]) result[3].get(P);
+    assertEquals(3, profile[0]['T']);
+    assertEquals(1, profile[0]['G']);
+    assertEquals(4, profile[1][0]);
+    assertEquals(4, profile[1][1]);
+  }
+
+  @Test
+  public void testCalculate_withProfileTiming()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "CAGT");
+    SequenceI seq2 = new Sequence("Seq2", "CACT");
+    SequenceI seq3 = new Sequence("Seq3", "C--G");
+    SequenceI seq4 = new Sequence("Seq4", "CA-t");
+    SequenceI[] seqs = new SequenceI[]
+    { seq1, seq2, seq3, seq4 };
+    Hashtable[] result = new Hashtable[seq1.getLength()];
+
+    // ensure class loaded and initialized
+    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
+    int reps = 100000;
+    long start = System.currentTimeMillis();
+    for (int i = 0; i < reps; i++)
+    {
+      AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
+    }
+    System.out.println(System.currentTimeMillis() - start);
+  }
+}