JAL-1759 merge from develop

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

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index a503460..61b2487 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
@@ -95,7 +96,7 @@ public class AlignmentUtilsTests
   public static Sequence ts = new Sequence("short",
           "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testExpandContext()
   {
     AlignmentI al = new Alignment(new Sequence[] {});
@@ -149,7 +150,7 @@ public class AlignmentUtilsTests
   /**
    * Test that annotations are correctly adjusted by expandContext
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testExpandContext_annotation()
   {
     AlignmentI al = new Alignment(new Sequence[]
@@ -239,7 +240,7 @@ public class AlignmentUtilsTests
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetSequencesByName() throws IOException
   {
     final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
@@ -264,7 +265,7 @@ public class AlignmentUtilsTests
    */
   protected AlignmentI loadAlignment(final String data, String format) throws IOException
   {
-    Alignment a = new FormatAdapter().readFile(data,
+    AlignmentI a = new FormatAdapter().readFile(data,
             AppletFormatAdapter.PASTE, format);
     a.setDataset(null);
     return a;
@@ -277,7 +278,7 @@ public class AlignmentUtilsTests
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapProteinToCdna_noXrefs() throws IOException
   {
     List<SequenceI> protseqs = new ArrayList<SequenceI>();
@@ -340,7 +341,7 @@ public class AlignmentUtilsTests
   /**
    * Test for the alignSequenceAs method that takes two sequences and a mapping.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignSequenceAs_withMapping_noIntrons()
   {
     MapList map = new MapList(new int[]
@@ -386,7 +387,7 @@ public class AlignmentUtilsTests
   /**
    * Test for the alignSequenceAs method that takes two sequences and a mapping.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignSequenceAs_withMapping_withIntrons()
   {
     /*
@@ -436,7 +437,7 @@ public class AlignmentUtilsTests
   /**
    * Test for the case where not all of the protein sequence is mapped to cDNA.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignSequenceAs_withMapping_withUnmappedProtein()
   {
     
@@ -486,7 +487,7 @@ public class AlignmentUtilsTests
   /**
    * Test for the alignSequenceAs method where we preserve gaps in introns only.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignSequenceAs_keepIntronGapsOnly()
   {
 
@@ -505,7 +506,7 @@ public class AlignmentUtilsTests
    * Test for the method that generates an aligned translated sequence from one
    * mapping.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetAlignedTranslation_dnaLikeProtein()
   {
     // dna alignment will be replaced
@@ -529,7 +530,7 @@ public class AlignmentUtilsTests
   /**
    * Test the method that realigns protein to match mapped codon alignment.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignProteinAsDna()
   {
     // seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
@@ -573,7 +574,7 @@ public class AlignmentUtilsTests
    * Test the method that tests whether a CDNA sequence translates to a protein
    * sequence
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testTranslatesAs()
   {
     assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
@@ -612,7 +613,7 @@ public class AlignmentUtilsTests
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapProteinToCdna_withStartAndStopCodons()
           throws IOException
   {
@@ -705,7 +706,7 @@ public class AlignmentUtilsTests
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapProteinToCdna_withXrefs() throws IOException
   {
     List<SequenceI> protseqs = new ArrayList<SequenceI>();
@@ -781,7 +782,7 @@ public class AlignmentUtilsTests
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapProteinToCdna_prioritiseXrefs() throws IOException
   {
     List<SequenceI> protseqs = new ArrayList<SequenceI>();
@@ -831,7 +832,7 @@ public class AlignmentUtilsTests
    * Test the method that shows or hides sequence annotations by type(s) and
    * selection group.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testShowOrHideSequenceAnnotations()
   {
     SequenceI seq1 = new Sequence("Seq1", "AAA");
@@ -939,7 +940,7 @@ public class AlignmentUtilsTests
   /**
    * Tests for the method that checks if one sequence cross-references another
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testHasCrossRef()
   {
     assertFalse(AlignmentUtils.hasCrossRef(null, null));
@@ -968,7 +969,7 @@ public class AlignmentUtilsTests
    * Tests for the method that checks if either sequence cross-references the
    * other
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testHaveCrossRef()
   {
     assertFalse(AlignmentUtils.hasCrossRef(null, null));
@@ -998,7 +999,7 @@ public class AlignmentUtilsTests
   /**
    * Test the method that extracts the exon-only part of a dna alignment.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeExonAlignment()
   {
     SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
@@ -1093,7 +1094,7 @@ public class AlignmentUtilsTests
    * already has a protein product (Uniprot translation) which in turn has an
    * x-ref to the EMBLCDS record.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeExonSequences()
   {
     SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
@@ -1135,7 +1136,7 @@ public class AlignmentUtilsTests
    * its product mappings, for the case where there are multiple exon mappings
    * to different protein products.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMakeExonAlignment_multipleProteins()
   {
     SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");