X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fio%2FPhylipFileTests.java;h=9c95486dcce25b7c299dfa1021af85578d55875d;hb=8bbcfb93404decd6d660ca32b69a29f8a1f34e82;hp=2fd8e209e42cda94f2bb7d2db32a515864adc9d2;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git

diff --git a/test/jalview/io/PhylipFileTests.java b/test/jalview/io/PhylipFileTests.java
index 2fd8e20..9c95486 100644
--- a/test/jalview/io/PhylipFileTests.java
+++ b/test/jalview/io/PhylipFileTests.java
@@ -3,15 +3,15 @@ package jalview.io;
 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.testng.annotations.Test;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.SequenceI;
-
 /**
  * Test file for {@link PhylipFile}.
  *
@@ -79,7 +79,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSequentialDataExtraction() throws Exception
   {
     testDataExtraction(sequentialFile);
@@ -91,7 +91,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testInterleavedDataExtraction() throws Exception
   {
     testDataExtraction(interleavedFile);
@@ -106,7 +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);
 
@@ -124,7 +124,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSequentialIO() throws Exception
   {
     testIO(sequentialFile);
@@ -136,7 +136,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testInterleavedIO() throws Exception
   {
     testIO(interleavedFile);
@@ -151,13 +151,13 @@ 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);