From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 8 Jan 2021 16:05:39 +0000 (+0000)
Subject: JAL-3794 new test for recognition of protein or DNA with ambiguity characters, includ... 
X-Git-Tag: Release_2_11_2_0~34^2~15
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0bf5983f8a17fdfecb2cac649e3650763a8973ce;p=jalview.git

JAL-3794 new test for recognition of protein or DNA with ambiguity characters, including the ‘all N’ case (that should be protein..).
---

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index e549978..6d07113 100644
--- 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()
   {