JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / test / jalview / io / AnnotationFileIOTest.java

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 3d911e0..c9b5f4a 100644 (file)
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -23,21 +23,20 @@ package jalview.io;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.io.AnnotationFile.ViewDef;
+
 import java.io.File;
 import java.util.Hashtable;
 
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.io.AnnotationFile.ViewDef;
-
 public class AnnotationFileIOTest
 {
 
-  static String TestFiles[][] =
-  {
+  static String TestFiles[][] = {
       { "Test example annotation import/export", "examples/uniref50.fa",
           "examples/testdata/example_annot_file.jva" },
       { "Test multiple combine annotation statements import/export",
@@ -52,7 +51,7 @@ public class AnnotationFileIOTest
       { "Test hiding/showing of insertions on sequence_ref",
           "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
 
-  @Test
+  @Test(groups = { "Functional" })
   public void exampleAnnotationFileIO() throws Exception
   {
     for (String[] testPair : TestFiles)
@@ -71,13 +70,12 @@ public class AnnotationFileIOTest
       FormatAdapter rf = new FormatAdapter();
 
       AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
-              new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+              new IdentifyFile().identify(ff, AppletFormatAdapter.FILE));
 
       // make sure dataset is initialised ? not sure about this
       for (int i = 0; i < al.getSequencesArray().length; ++i)
       {
-        al.getSequenceAt(i).setDatasetSequence(
-                al.getSequenceAt(i).createDatasetSequence());
+        al.getSequenceAt(i).createDatasetSequence();
       }
       assertNotNull("Couldn't read supplied alignment data.", al);
       return al;
@@ -100,7 +98,7 @@ public class AnnotationFileIOTest
    *          f
    */
 
-  // @Test
+  // @Test(groups ={ "Functional" })
   public static void testAnnotationFileIO(String testname, File f,
           File annotFile)
   {