test HMM annotaTION

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

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index 1c04b8e..646412f 100644 (file)
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -25,14 +25,32 @@ import static org.testng.AssertJUnit.assertNull;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.ProfileI;
+import jalview.datamodel.ProfilesI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
 
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class AAFrequencyTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Functional" })
   public void testCalculate_noProfile()
   {
@@ -41,12 +59,12 @@ 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 };
-    ProfileI[] result = new ProfileI[seq1.getLength()];
-
-    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, false);
+    int width = seq1.getLength();
+    ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
+            false);
 
     // col 0 is 100% C
-    ProfileI col = result[0];
+    ProfileI col = result.get(0);
     assertEquals(100f, col.getPercentageIdentity(false));
     assertEquals(100f, col.getPercentageIdentity(true));
     assertEquals(4, col.getMaxCount());
@@ -54,28 +72,28 @@ public class AAFrequencyTest
     assertNull(col.getCounts());
 
     // col 1 is 75% A
-    col = result[1];
+    col = result.get(1);
     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];
+    col = result.get(2);
     assertEquals(25f, col.getPercentageIdentity(false));
     assertEquals(50f, col.getPercentageIdentity(true));
     assertEquals(1, col.getMaxCount());
     assertEquals("CG", col.getModalResidue());
 
     // col 3 is all gaps
-    col = result[3];
+    col = result.get(3);
     assertEquals(0f, col.getPercentageIdentity(false));
     assertEquals(0f, col.getPercentageIdentity(true));
     assertEquals(0, col.getMaxCount());
     assertEquals("", col.getModalResidue());
 
     // col 4 is 75% T 25% G
-    col = result[4];
+    col = result.get(4);
     assertEquals(75f, col.getPercentageIdentity(false));
     assertEquals(75f, col.getPercentageIdentity(true));
     assertEquals(3, col.getMaxCount());
@@ -90,26 +108,27 @@ 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 };
-    ProfileI[] result = new ProfileI[seq1.getLength()];
+    int width = seq1.getLength();
+    ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
+            true);
 
-    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
-    ProfileI profile = result[0];
+    ProfileI profile = result.get(0);
     assertEquals(4, profile.getCounts().getCount('C'));
     assertEquals(4, profile.getHeight());
     assertEquals(4, profile.getNonGapped());
 
-    profile = result[1];
+    profile = result.get(1);
     assertEquals(3, profile.getCounts().getCount('A'));
     assertEquals(4, profile.getHeight());
     assertEquals(3, profile.getNonGapped());
 
-    profile = result[2];
+    profile = result.get(2);
     assertEquals(1, profile.getCounts().getCount('C'));
     assertEquals(1, profile.getCounts().getCount('G'));
     assertEquals(4, profile.getHeight());
     assertEquals(2, profile.getNonGapped());
 
-    profile = result[3];
+    profile = result.get(3);
     assertEquals(3, profile.getCounts().getCount('T'));
     assertEquals(1, profile.getCounts().getCount('G'));
     assertEquals(4, profile.getHeight());
@@ -124,15 +143,16 @@ 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 };
-    ProfileI[] result = new ProfileI[seq1.getLength()];
 
-    // ensure class loaded and initialized
-    AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
+    // ensure class loaded and initialised
+    int width = seq1.getLength();
+    AAFrequency.calculate(seqs, width, 0, width, true);
+
     int reps = 100000;
     long start = System.currentTimeMillis();
     for (int i = 0; i < reps; i++)
     {
-      AAFrequency.calculate(seqs, 0, seq1.getLength(), result, true);
+      AAFrequency.calculate(seqs, width, 0, width, true);
     }
     System.out.println(System.currentTimeMillis() - start);
   }
@@ -154,11 +174,11 @@ 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 };
-    ProfileI[] profiles = new ProfileI[seq1.getLength()];
-    AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
+    int width = seq1.getLength();
+    ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true);
 
     AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
-            "PID", new Annotation[seq1.getLength()]);
+            "PID", new Annotation[width]);
     AAFrequency
             .completeConsensus(consensus, profiles, 0, 5, false, true, 4);
 
@@ -195,11 +215,11 @@ 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 };
-    ProfileI[] profiles = new ProfileI[seq1.getLength()];
-    AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
+    int width = seq1.getLength();
+    ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true);
   
     AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
-            "PID", new Annotation[seq1.getLength()]);
+            "PID", new Annotation[width]);
     AAFrequency
             .completeConsensus(consensus, profiles, 0, 5, true, false, 4);
   
@@ -219,4 +239,45 @@ public class AAFrequencyTest
     assertEquals("T 75%", ann.description);
     assertEquals("T", ann.displayCharacter);
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetHMMProfileFor()
+          throws MalformedURLException, IOException
+  {
+
+    HMMFile hmmFile = new HMMFile(new FileParse(
+            "test/jalview/io/test_MADE1_hmm.txt", DataSourceType.FILE));
+    hmmFile.parse();
+    HiddenMarkovModel hmm = hmmFile.getHMM();
+    AlignmentAnnotation aa = hmm.createAnnotation(80);
+    aa.setHMM(hmm);
+
+    int[] expected = { 0, 4, 100, 'T', 71, 'C', 12, 'G', 9, 'A', 9 };
+    int[] actual = AAFrequency.getHMMProfileFor(aa, 17, false);
+    for (int i = 0; i < actual.length; i++)
+    {
+      if (i == 2)
+      {
+        assertEquals(actual[i], expected[i], 5);
+      }
+      else
+      {
+        assertEquals(actual[i], expected[i], 1);
+      }
+    }
+
+    int[] expected2 = { 0, 4, 85, 'A', 85, 'C', 0, 'G', 0, 'T', 0 };
+    int[] actual2 = AAFrequency.getHMMProfileFor(aa, 2, true);
+    for (int i = 0; i < actual.length; i++)
+    {
+      if (i == 2)
+      {
+        assertEquals(actual[i], expected[i], 5);
+      }
+      else
+      {
+        assertEquals(actual[i], expected[i], 1);
+      }
+    }
+  }
 }