X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FPhylipFileTests.java;h=9c95486dcce25b7c299dfa1021af85578d55875d;hb=8bbcfb93404decd6d660ca32b69a29f8a1f34e82;hp=70e3f2c153b93eaf477fed7066630f088b721368;hpb=77abb3fac2965a8966410cd77cd749c7c1dc6453;p=jalview.git

diff --git a/test/jalview/io/PhylipFileTests.java b/test/jalview/io/PhylipFileTests.java
index 70e3f2c..9c95486 100644
--- a/test/jalview/io/PhylipFileTests.java
+++ b/test/jalview/io/PhylipFileTests.java
@@ -1,15 +1,16 @@
 package jalview.io;
 
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import jalview.datamodel.Alignment;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;
 
-import org.junit.Test;
+import org.testng.annotations.Test;
 
 /**
  * Test file for {@link PhylipFile}.
@@ -78,7 +79,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSequentialDataExtraction() throws Exception
   {
     testDataExtraction(sequentialFile);
@@ -90,7 +91,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testInterleavedDataExtraction() throws Exception
   {
     testDataExtraction(interleavedFile);
@@ -105,7 +106,7 @@ public class PhylipFileTests
   private void testDataExtraction(String file) throws IOException
   {
     AppletFormatAdapter rf = new AppletFormatAdapter();
-    Alignment al = rf.readFile(file, AppletFormatAdapter.FILE,
+    AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
             PhylipFile.FILE_DESC);
     assertNotNull("Couldn't read supplied alignment data.", al);
 
@@ -123,7 +124,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSequentialIO() throws Exception
   {
     testIO(sequentialFile);
@@ -135,7 +136,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testInterleavedIO() throws Exception
   {
     testIO(interleavedFile);
@@ -150,17 +151,17 @@ public class PhylipFileTests
   public void testIO(String file) throws IOException
   {
     AppletFormatAdapter rf = new AppletFormatAdapter();
-    Alignment al = rf.readFile(file, AppletFormatAdapter.FILE,
+    AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
             PhylipFile.FILE_DESC);
     assertNotNull("Couldn't read supplied alignment data.", al);
 
     String outputfile = rf.formatSequences(PhylipFile.FILE_DESC, al, true);
 
-    Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+    AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
             AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
     assertNotNull("Couldn't parse reimported alignment data.", al_input);
 
-    StockholmFileTest.testAlignmentEquivalence(al, al_input);
+    StockholmFileTest.testAlignmentEquivalence(al, al_input, false);
 
   }
 }
\ No newline at end of file