JAL-98 minor fixes to / tests for annotation derivation

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 569b036..61e11c4 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -47,18 +47,8 @@ import java.util.List;
  */
 public class AAFrequency
 {
-  public static final String MAXCOUNT = "C";
-
-  public static final String MAXRESIDUE = "R";
-
-  public static final String PID_GAPS = "G";
-
-  public static final String PID_NOGAPS = "N";
-
   public static final String PROFILE = "P";
 
-  public static final String ENCODED_CHARS = "E";
-
   /*
    * Quick look-up of String value of char 'A' to 'Z'
    */
@@ -275,7 +265,16 @@ public class AAFrequency
       String description = getTooltip(profile, value, showSequenceLogo,
               ignoreGaps, dp);
 
-      consensus.annotations[i] = new Annotation(profile.getModalResidue(),
+      String modalResidue = profile.getModalResidue();
+      if ("".equals(modalResidue))
+      {
+        modalResidue = "-";
+      }
+      else if (modalResidue.length() > 1)
+      {
+        modalResidue = "+";
+      }
+      consensus.annotations[i] = new Annotation(modalResidue,
               description, ' ', value);
     }
     // long elapsed = System.currentTimeMillis() - now;
@@ -318,15 +317,18 @@ public class AAFrequency
       String maxRes = profile.getModalResidue();
       if (maxRes.length() > 1)
       {
-        sb.append("[").append(maxRes).append("] ");
-        maxRes = "+";
+        sb.append("[").append(maxRes).append("]");
       }
       else
       {
-        sb.append(maxRes).append(" ");
+        sb.append(maxRes);
+      }
+      if (maxRes.length() > 0)
+      {
+        sb.append(" ");
+        Format.appendPercentage(sb, pid, dp);
+        sb.append("%");
       }
-      Format.appendPercentage(sb, pid, dp);
-      sb.append("%");
       description = sb.toString();
     }
     return description;

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);
+  }
 }