develop merge

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

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 8f878f0..9a4c357 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -457,4 +457,58 @@ public class DnaTest
     assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
     assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
   }
+
+  /**
+   * Test dna complementing
+   */
+  @Test(groups = "Functional")
+  public void testGetComplement()
+  {
+    assertEquals('t', Dna.getComplement('a'));
+    assertEquals('T', Dna.getComplement('A'));
+    assertEquals('a', Dna.getComplement('t'));
+    assertEquals('A', Dna.getComplement('T'));
+    assertEquals('c', Dna.getComplement('g'));
+    assertEquals('C', Dna.getComplement('G'));
+    assertEquals('g', Dna.getComplement('c'));
+    assertEquals('G', Dna.getComplement('C'));
+    // note uU --> aA but not vice versa
+    assertEquals('a', Dna.getComplement('u'));
+    assertEquals('A', Dna.getComplement('U'));
+    // ambiguity codes, see http://www.bioinformatics.org/sms/iupac.html
+    assertEquals('r', Dna.getComplement('y'));
+    assertEquals('R', Dna.getComplement('Y'));
+    assertEquals('y', Dna.getComplement('r'));
+    assertEquals('Y', Dna.getComplement('R'));
+    assertEquals('k', Dna.getComplement('m'));
+    assertEquals('K', Dna.getComplement('M'));
+    assertEquals('m', Dna.getComplement('k'));
+    assertEquals('M', Dna.getComplement('K'));
+    assertEquals('b', Dna.getComplement('v'));
+    assertEquals('B', Dna.getComplement('V'));
+    assertEquals('v', Dna.getComplement('b'));
+    assertEquals('V', Dna.getComplement('B'));
+    assertEquals('d', Dna.getComplement('h'));
+    assertEquals('D', Dna.getComplement('H'));
+    assertEquals('h', Dna.getComplement('d'));
+    assertEquals('H', Dna.getComplement('D'));
+    assertEquals('Q', Dna.getComplement('Q'));
+  }
+
+  @Test(groups = "Functional")
+  public void testReverseSequence()
+  {
+    String seq = "AcGtUrYkMbVdHNX";
+
+    // reverse:
+    SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
+    assertEquals(new StringBuilder(seq).reverse()
+            .toString(), reversed.getSequenceAsString());
+    assertEquals("Seq1|rev", reversed.getName());
+
+    // reverse complement:
+    SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
+    assertEquals("XNDhBvKmRyAaCgT", revcomp.getSequenceAsString());
+    assertEquals("Seq1|revcomp", revcomp.getName());
+  }
 }