JAL-3794 new test for recognition of protein or DNA with ambiguity characters, includ...

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index e549978..6d07113 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -110,6 +110,23 @@ public class SequenceTest
     assertTrue(sq.isProtein());
   }
 
+  @Test(groups = ("Functional"))
+  public void testIsProteinWithXorNAmbiguityCodes()
+  {
+    // test Protein with N - poly asparagine 
+    assertTrue(new Sequence("prot", "ASDFASDFASDFNNNNNNNNN").isProtein());
+    assertTrue(new Sequence("prot", "NNNNNNNNNNNNNNNNNNNNN").isProtein());
+    // test Protein with X
+    assertTrue(new Sequence("prot", "ASDFASDFASDFXXXXXXXXX").isProtein());
+    // test DNA with X
+    assertFalse(new Sequence("prot", "ACGTACGTACGTXXXXXXXX").isProtein());
+    // test DNA with N
+    assertFalse(new Sequence("prot", "ACGTACGTACGTNNNNNNNN").isProtein());
+    // test RNA with X
+    assertFalse(new Sequence("prot", "ACGUACGUACGUXXXXXXXXX").isProtein());
+    assertFalse(new Sequence("prot", "ACGUACGUACGUNNNNNNNNN").isProtein());
+  }
+
   @Test(groups = { "Functional" })
   public void testGetAnnotation()
   {