JAL-3760 fix tests for changed behaviour

[jalview.git] / test / jalview / util / ComparisonTest.java

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index f955879..2e646f5 100644 (file)
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -85,15 +85,15 @@ public class ComparisonTest
     seq = new Sequence("DNA", "ACTugGCCAG");
     SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
     /*
-     * 90% DNA:
+     * 90% DNA but one protein sequence - expect false
      */
-    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
         seq, seq, seq, seq, seq, seq, seq2 }));
-    assertTrue(Comparison.isNucleotide(new SequenceI[][] {
+    assertFalse(Comparison.isNucleotide(new SequenceI[][] {
         new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
         new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
     /*
-     * 80% DNA:
+     * 80% DNA but one protein sequence - Expect false
      */
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
         seq, seq, seq, seq, seq, seq2, seq2 }));
@@ -115,7 +115,7 @@ public class ComparisonTest
   @Test(groups = { "Functional" })
   public void testPID_includingGaps()
   {
-    String seq1 = "ABCDEF";
+    String seq1 = "ABCDEFG"; // extra length here is ignored
     String seq2 = "abcdef";
     assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
 
@@ -129,12 +129,14 @@ public class ComparisonTest
     int length = seq1.length();
 
     // match gap-residue, match gap-gap: 9/10 identical
+    // TODO should gap-gap be included in a PID score? JAL-791
     assertEquals(90f, Comparison.PID(seq1, seq2, 0, length, true, false),
             0.001f);
     // overloaded version of the method signature above:
     assertEquals(90f, Comparison.PID(seq1, seq2), 0.001f);
 
     // don't match gap-residue, match gap-gap: 7/10 identical
+    // TODO should gap-gap be included in a PID score?
     assertEquals(70f, Comparison.PID(seq1, seq2, 0, length, false, false),
             0.001f);
   }
@@ -163,7 +165,8 @@ public class ComparisonTest
   public void testPID_ungappedOnly()
   {
     // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
-    String seq1 = "a--b-cdefh";
+    // the extra length of seq1 is ignored
+    String seq1 = "a--b-cdefhr";
     String seq2 = "a---bcdefg";
     int length = seq1.length();