X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=2c0045b2f54a64a04c279d92df1004355f442981;hb=4e4cd7954b978bfe1ba652e44be2510626efa177;hp=ec9ace4b29dd7514033c8e8ac4867619b20ee00d;hpb=f2f654875a6eb5f4e90b2c5c545bfed3a70f2b5f;p=jalview.git

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index ec9ace4..2c0045b 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -1,22 +1,12 @@
 package jalview.util;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
 
-import java.awt.Color;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.junit.Test;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SearchResults;
@@ -28,6 +18,16 @@ import jalview.gui.AlignViewport;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FormatAdapter;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.Test;
+
 public class MappingUtilsTest
 {
   private AlignViewportI dnaView;
@@ -36,7 +36,7 @@ public class MappingUtilsTest
   /**
    * Simple test of mapping with no intron involved.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testBuildSearchResults()
   {
     final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
@@ -89,7 +89,7 @@ public class MappingUtilsTest
   /**
    * Simple test of mapping with introns involved.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testBuildSearchResults_withIntron()
   {
     final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT");
@@ -166,7 +166,7 @@ public class MappingUtilsTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapSequenceGroup_sequences() throws IOException
   {
     /*
@@ -248,7 +248,7 @@ public class MappingUtilsTest
   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;
@@ -259,7 +259,7 @@ public class MappingUtilsTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapColumnSelection_proteinToDna() throws IOException
   {
     setupMappedAlignments();
@@ -357,7 +357,7 @@ public class MappingUtilsTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapColumnSelection_dnaToProtein() throws IOException
   {
     setupMappedAlignments();
@@ -384,7 +384,7 @@ public class MappingUtilsTest
     assertEquals("[0, 1, 3]", cs.getSelected().toString());
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapColumnSelection_null() throws IOException
   {
     setupMappedAlignments();
@@ -397,7 +397,7 @@ public class MappingUtilsTest
    * Tests for the method that converts a series of [start, end] ranges to
    * single positions
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testFlattenRanges()
   {
     assertEquals("[1, 2, 3, 4]",
@@ -423,7 +423,7 @@ public class MappingUtilsTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapSequenceGroup_columns() throws IOException
   {
     /*
@@ -506,7 +506,7 @@ public class MappingUtilsTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testMapSequenceGroup_region() throws IOException
   {
     /*
@@ -600,7 +600,7 @@ public class MappingUtilsTest
     assertEquals(4, mappedGroup.getEndRes());
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testFindMappingsForSequence()
   {
     SequenceI seq1 = new Sequence("Seq1", "ABC");