X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FComparisonTest.java;h=cef9ffc1d94806d0103546cc2da6f6b425d9a42e;hb=5221c772a071266446c5c959f34ec89c8e874201;hp=ec1779bbe5f35d437ca03cb29326d5078ddb1f5e;hpb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;p=jalview.git

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index ec1779b..cef9ffc 100644
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -62,8 +62,9 @@ public class ComparisonTest
   {
     SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
-    assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
-    { seq } }));
+    assertFalse(
+            Comparison.isNucleotide(new SequenceI[][]
+            { new SequenceI[] { seq } }));
 
     seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
@@ -85,21 +86,27 @@ 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,
-        seq, seq, seq, seq, seq, seq, seq2 }));
-    assertTrue(Comparison.isNucleotide(new SequenceI[][] {
-        new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
-        new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
+    assertFalse(
+            Comparison.isNucleotide(new SequenceI[]
+            { seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 }));
+    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 }));
-    assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
-    { seq }, new SequenceI[] { seq, seq, seq },
-        new SequenceI[] { seq, seq, seq, seq, seq2, seq2, null } }));
+    assertFalse(
+            Comparison.isNucleotide(new SequenceI[]
+            { seq, seq, seq, seq, seq, seq, seq, seq, seq2, seq2 }));
+    assertFalse(
+            Comparison.isNucleotide(new SequenceI[][]
+            { new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
+                new SequenceI[]
+                { seq, seq, seq, seq, seq2, seq2, null } }));
 
     seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
     // 12/14 = 85.7%
@@ -115,7 +122,7 @@ 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);
 
@@ -165,7 +172,8 @@ 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();