JAL-1636 translate stop codon as '*', mouseover * as STOP

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

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 693c912..765ec2b 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -3,7 +3,7 @@ package jalview.analysis;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
+
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.Alignment;
@@ -15,6 +15,8 @@ import jalview.io.FormatAdapter;
 
 import java.io.IOException;
 
+import org.testng.annotations.Test;
+
 public class DnaTest
 {
   // @formatter:off
@@ -92,7 +94,7 @@ public class DnaTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testTranslateCdna_withUntranslatableCodons()
           throws IOException
   {
@@ -114,7 +116,7 @@ public class DnaTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns()
           throws IOException
   {
@@ -146,11 +148,11 @@ public class DnaTest
   }
 
   /**
-   * Test simple translation to Amino Acids (with STOP codons translated to X).
+   * Test simple translation to Amino Acids (with STOP codons translated to *).
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testTranslateCdna_simple() throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(fasta,
@@ -162,7 +164,7 @@ public class DnaTest
     AlignmentI translated = dna.translateCdna();
     String aa = translated.getSequenceAt(0).getSequenceAsString();
     assertEquals(
-            "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYYXXX",
+            "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
             aa);
   }
 
@@ -171,7 +173,7 @@ public class DnaTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testTranslateCdna_hiddenColumns() throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(fasta,
@@ -191,7 +193,7 @@ public class DnaTest
   /**
    * Use this test to help debug into any cases of interest.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testCompareCodonPos_oneOnly()
   {
     assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
@@ -200,7 +202,7 @@ public class DnaTest
   /**
    * Tests for method that compares 'alignment' of two codon position triplets.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testCompareCodonPos()
   {
     /*
@@ -257,7 +259,7 @@ public class DnaTest
    * reorders the cDNA and retranslates, and verifies that the translations are
    * the same (apart from ordering).
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testTranslateCdna_sequenceOrderIndependent()
   {
     /*
@@ -311,7 +313,7 @@ public class DnaTest
    * Test that all the cases in testCompareCodonPos have a 'symmetric'
    * comparison (without checking the actual comparison result).
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testCompareCodonPos_isSymmetric()
   {
     assertSymmetric("AAA", "GGG");
@@ -434,7 +436,7 @@ public class DnaTest
   /**
    * Weirdly, maybe worth a test to prove the helper method of this test class.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testConvertCodon()
   {
     assertEquals("[0, 1, 2]", convertCodon("AAA").toString());