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 5ae7dd9..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()
   {
@@ -2181,9 +2198,19 @@ public class SequenceTest
     Sequence toSeq = new Sequence("MYSEQ","THISISASEQ");
     origSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, true));
     toSeq.transferAnnotation(origSeq, null);
-    assertTrue(toSeq.getDBRefs().size()>0);
+    assertTrue(toSeq.getDBRefs().size()==1);
     
     assertTrue(toSeq.getDBRefs().get(0).isCanonical());
     
+    // check for promotion of non-canonical 
+    // to canonical (e.g. fetch-db-refs on a jalview project pre 2.11.2)
+    toSeq.setDBRefs(null);
+    toSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, false));
+    toSeq.transferAnnotation(origSeq, null);
+    assertTrue(toSeq.getDBRefs().size()==1);
+    
+    assertTrue("Promotion of non-canonical DBRefEntry failed",toSeq.getDBRefs().get(0).isCanonical());
+    
+    
   }
 }