JAL-98 use Profile to store consensus, ResidueCount for fast compact

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

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index eff6bbf..ecddad1 100644 (file)
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -26,8 +26,6 @@ import static org.testng.AssertJUnit.assertNull;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
-import java.util.Hashtable;
-
 import org.testng.annotations.Test;
 
 public class AAFrequencyTest
@@ -50,38 +48,38 @@ public class AAFrequencyTest
     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()];
+    Profile[] result = new Profile[seq1.getLength()];
 
     AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
 
     // col 0 is 100% C
-    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));
+    Profile col = result[0];
+    assertEquals(100f, col.getPercentageIdentity(false));
+    assertEquals(100f, col.getPercentageIdentity(true));
+    assertEquals(4, col.getMaxCount());
+    assertEquals("C", col.getModalResidue());
+    assertNull(col.getCounts());
 
     // col 1 is 75% A
     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));
+    assertEquals(75f, col.getPercentageIdentity(false));
+    assertEquals(100f, col.getPercentageIdentity(true));
+    assertEquals(3, col.getMaxCount());
+    assertEquals("A", col.getModalResidue());
 
     // col 2 is 50% G 50% C or 25/25 counting gaps
     col = result[2];
-    assertEquals(25f, (Float) col.get(G), 0.0001f);
-    assertEquals(50f, (Float) col.get(N), 0.0001f);
-    assertEquals(1, col.get(C));
-    assertEquals("CG", col.get(R));
+    assertEquals(25f, col.getPercentageIdentity(false));
+    assertEquals(50f, col.getPercentageIdentity(true));
+    assertEquals(1, col.getMaxCount());
+    assertEquals("CG", col.getModalResidue());
 
     // col 3 is 75% T 25% G
     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));
+    assertEquals(75f, col.getPercentageIdentity(false));
+    assertEquals(75f, col.getPercentageIdentity(true));
+    assertEquals(3, col.getMaxCount());
+    assertEquals("T", col.getModalResidue());
   }
 
   @Test(groups = { "Functional" })
@@ -92,30 +90,30 @@ public class AAFrequencyTest
     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()];
+    Profile[] result = new Profile[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]);
+    Profile profile = result[0];
+    assertEquals(4, profile.getCounts().getCount('C'));
+    assertEquals(4, profile.getHeight());
+    assertEquals(4, profile.getNonGapped());
+
+    profile = result[1];
+    assertEquals(3, profile.getCounts().getCount('A'));
+    assertEquals(4, profile.getHeight());
+    assertEquals(3, profile.getNonGapped());
+
+    profile = result[2];
+    assertEquals(1, profile.getCounts().getCount('C'));
+    assertEquals(1, profile.getCounts().getCount('G'));
+    assertEquals(4, profile.getHeight());
+    assertEquals(2, profile.getNonGapped());
+
+    profile = result[3];
+    assertEquals(3, profile.getCounts().getCount('T'));
+    assertEquals(1, profile.getCounts().getCount('G'));
+    assertEquals(4, profile.getHeight());
+    assertEquals(4, profile.getNonGapped());
   }
 
   @Test(groups = { "Functional" })
@@ -126,7 +124,7 @@ public class AAFrequencyTest
     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()];
+    Profile[] result = new Profile[seq1.getLength()];
 
     // ensure class loaded and initialized
     AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
@@ -138,15 +136,4 @@ public class AAFrequencyTest
     }
     System.out.println(System.currentTimeMillis() - start);
   }
-
-  @Test(groups = { "Functional" })
-  public void testGetPercentageFormat()
-  {
-    assertNull(AAFrequency.getPercentageFormat(0));
-    assertNull(AAFrequency.getPercentageFormat(99));
-    assertEquals("%3.1f", AAFrequency.getPercentageFormat(100).toString());
-    assertEquals("%3.1f", AAFrequency.getPercentageFormat(999).toString());
-    assertEquals("%3.2f", AAFrequency.getPercentageFormat(1000).toString());
-    assertEquals("%3.2f", AAFrequency.getPercentageFormat(9999).toString());
-  }
 }