X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FPhylipFileTests.java;h=8c5838243d9eee952ca88dec5ef4d2aa6fe1da65;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=2fd8e209e42cda94f2bb7d2db32a515864adc9d2;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git

diff --git a/test/jalview/io/PhylipFileTests.java b/test/jalview/io/PhylipFileTests.java
index 2fd8e20..8c58382 100644
--- a/test/jalview/io/PhylipFileTests.java
+++ b/test/jalview/io/PhylipFileTests.java
@@ -1,17 +1,37 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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 +99,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testSequentialDataExtraction() throws Exception
   {
     testDataExtraction(sequentialFile);
@@ -91,7 +111,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testInterleavedDataExtraction() throws Exception
   {
     testDataExtraction(interleavedFile);
@@ -106,7 +126,7 @@ 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 +144,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testSequentialIO() throws Exception
   {
     testIO(sequentialFile);
@@ -136,7 +156,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testInterleavedIO() throws Exception
   {
     testIO(interleavedFile);
@@ -151,17 +171,17 @@ 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, false);
 
   }
-}
\ No newline at end of file
+}