develop merge

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

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index 0c2c998..9aab66c 100644 (file)
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -49,7 +49,7 @@ public class ComparisonTest
    * AGCTU. Test is not case-sensitive and ignores gaps.
    */
   @Test(groups = { "Functional" })
-  public void testIsNucleotide()
+  public void testIsNucleotide_sequences()
   {
     SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
@@ -130,6 +130,23 @@ public class ComparisonTest
             0.001f);
   }
 
+  @Test(groups = { "Functional" })
+  public void testIsNucleotide()
+  {
+    assertTrue(Comparison.isNucleotide('a'));
+    assertTrue(Comparison.isNucleotide('A'));
+    assertTrue(Comparison.isNucleotide('c'));
+    assertTrue(Comparison.isNucleotide('C'));
+    assertTrue(Comparison.isNucleotide('g'));
+    assertTrue(Comparison.isNucleotide('G'));
+    assertTrue(Comparison.isNucleotide('t'));
+    assertTrue(Comparison.isNucleotide('T'));
+    assertTrue(Comparison.isNucleotide('u'));
+    assertTrue(Comparison.isNucleotide('U'));
+    assertFalse(Comparison.isNucleotide('-'));
+    assertFalse(Comparison.isNucleotide('P'));
+  }
+
   /**
    * Test the percentage identity calculation for two sequences
    */
@@ -158,4 +175,17 @@ public class ComparisonTest
     assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, false, true),
             0.001f);
   }
+
+  @Test(groups = { "Functional" })
+  public void testIsNucleotideSequence()
+  {
+    assertFalse(Comparison.isNucleotideSequence(null, true));
+    assertTrue(Comparison.isNucleotideSequence("", true));
+    assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", true));
+    assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", false));
+    assertFalse(Comparison.isNucleotideSequence("xAgGcCtTuU", false));
+    assertFalse(Comparison.isNucleotideSequence("aAgGcCtTuUx", false));
+    assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true));
+    assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false));
+  }
 }