JAL-98 minor fixes to / tests for annotation derivation

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

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index ecddad1..0ddbddc 100644 (file)
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -23,6 +23,8 @@ package jalview.analysis;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
@@ -30,23 +32,13 @@ import org.testng.annotations.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(groups = { "Functional" })
   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 seq1 = new Sequence("Seq1", "CAG-T");
+    SequenceI seq2 = new Sequence("Seq2", "CAC-T");
+    SequenceI seq3 = new Sequence("Seq3", "C---G");
+    SequenceI seq4 = new Sequence("Seq4", "CA--t");
     SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
     Profile[] result = new Profile[seq1.getLength()];
 
@@ -74,8 +66,15 @@ public class AAFrequencyTest
     assertEquals(1, col.getMaxCount());
     assertEquals("CG", col.getModalResidue());
 
-    // col 3 is 75% T 25% G
+    // col 3 is all gaps
     col = result[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];
     assertEquals(75f, col.getPercentageIdentity(false));
     assertEquals(75f, col.getPercentageIdentity(true));
     assertEquals(3, col.getMaxCount());
@@ -116,7 +115,7 @@ public class AAFrequencyTest
     assertEquals(4, profile.getNonGapped());
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional" }, enabled = false)
   public void testCalculate_withProfileTiming()
   {
     SequenceI seq1 = new Sequence("Seq1", "CAGT");
@@ -136,4 +135,87 @@ public class AAFrequencyTest
     }
     System.out.println(System.currentTimeMillis() - start);
   }
+
+  /**
+   * Test generation of consensus annotation with options 'include gaps'
+   * (profile percentages are of all sequences, whether gapped or not), and
+   * 'show logo' (the full profile with all residue percentages is reported in
+   * the description for the tooltip)
+   */
+  @Test(groups = { "Functional" })
+  public void testCompleteConsensus_includeGaps_showLogo()
+  {
+    /*
+     * first compute the profiles
+     */
+    SequenceI seq1 = new Sequence("Seq1", "CAG-T");
+    SequenceI seq2 = new Sequence("Seq2", "CAC-T");
+    SequenceI seq3 = new Sequence("Seq3", "C---G");
+    SequenceI seq4 = new Sequence("Seq4", "CA--t");
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
+    Profile[] profiles = new Profile[seq1.getLength()];
+    AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
+
+    AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
+            "PID", new Annotation[seq1.getLength()]);
+    AAFrequency
+            .completeConsensus(consensus, profiles, 0, 5, false, true, 4);
+
+    Annotation ann = consensus.annotations[0];
+    assertEquals("C 100%", ann.description);
+    assertEquals("C", ann.displayCharacter);
+    ann = consensus.annotations[1];
+    assertEquals("A 75%", ann.description);
+    assertEquals("A", ann.displayCharacter);
+    ann = consensus.annotations[2];
+    assertEquals("C 25%; G 25%", ann.description);
+    assertEquals("+", ann.displayCharacter);
+    ann = consensus.annotations[3];
+    assertEquals("", ann.description);
+    assertEquals("-", ann.displayCharacter);
+    ann = consensus.annotations[4];
+    assertEquals("T 75%; G 25%", ann.description);
+    assertEquals("T", ann.displayCharacter);
+  }
+
+  /**
+   * Test generation of consensus annotation with options 'ignore gaps' (profile
+   * percentages are of the non-gapped sequences) and 'no logo' (only the modal
+   * residue[s] percentage is reported in the description for the tooltip)
+   */
+  @Test(groups = { "Functional" })
+  public void testCompleteConsensus_ignoreGaps_noLogo()
+  {
+    /*
+     * first compute the profiles
+     */
+    SequenceI seq1 = new Sequence("Seq1", "CAG-T");
+    SequenceI seq2 = new Sequence("Seq2", "CAC-T");
+    SequenceI seq3 = new Sequence("Seq3", "C---G");
+    SequenceI seq4 = new Sequence("Seq4", "CA--t");
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
+    Profile[] profiles = new Profile[seq1.getLength()];
+    AAFrequency.calculate(seqs, 0, seq1.getLength(), profiles, true);
+  
+    AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
+            "PID", new Annotation[seq1.getLength()]);
+    AAFrequency
+            .completeConsensus(consensus, profiles, 0, 5, true, false, 4);
+  
+    Annotation ann = consensus.annotations[0];
+    assertEquals("C 100%", ann.description);
+    assertEquals("C", ann.displayCharacter);
+    ann = consensus.annotations[1];
+    assertEquals("A 100%", ann.description);
+    assertEquals("A", ann.displayCharacter);
+    ann = consensus.annotations[2];
+    assertEquals("[CG] 50%", ann.description);
+    assertEquals("+", ann.displayCharacter);
+    ann = consensus.annotations[3];
+    assertEquals("", ann.description);
+    assertEquals("-", ann.displayCharacter);
+    ann = consensus.annotations[4];
+    assertEquals("T 75%", ann.description);
+    assertEquals("T", ann.displayCharacter);
+  }
 }