JAL-1759 merge from develop

[jalview.git] / test / jalview / datamodel / AlignmentTest.java

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index fc73307..e885733 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -3,8 +3,7 @@ package jalview.datamodel;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
+
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FormatAdapter;
 import jalview.util.MapList;
@@ -12,6 +11,9 @@ import jalview.util.MapList;
 import java.io.IOException;
 import java.util.Iterator;
 
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 /**
  * Unit tests for Alignment datamodel.
  * 
@@ -67,7 +69,7 @@ public class AlignmentTest
   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;
@@ -92,7 +94,7 @@ public class AlignmentTest
   /**
    * Test method that returns annotations that match on calcId.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testFindAnnotation_byCalcId()
   {
     Iterable<AlignmentAnnotation> anns = al
@@ -104,7 +106,7 @@ public class AlignmentTest
     assertFalse(iter.hasNext());
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testDeleteAllAnnotations_includingAutocalculated()
   {
     AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
@@ -118,7 +120,7 @@ public class AlignmentTest
     assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testDeleteAllAnnotations_excludingAutocalculated()
   {
     AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
@@ -142,7 +144,7 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignAs_dnaAsDna() throws IOException
   {
     // aligned cDNA:
@@ -174,7 +176,7 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignAs_proteinAsCdna() throws IOException
   {
     // see also AlignmentUtilsTests
@@ -198,7 +200,7 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignAs_cdnaAsProtein() throws IOException
   {
     /*
@@ -230,7 +232,7 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAlignAs_dnaAsProtein_withIntrons() throws IOException
   {
     /*