JAL-2446 merged to spike branch

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

diff --git a/test/jalview/io/PhylipFileTests.java b/test/jalview/io/PhylipFileTests.java
index e411272..d853350 100644 (file)
--- a/test/jalview/io/PhylipFileTests.java
+++ b/test/jalview/io/PhylipFileTests.java
@@ -1,15 +1,38 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.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 jalview.gui.JvOptionPane;
 
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;
 
-import org.junit.Test;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 /**
  * Test file for {@link PhylipFile}.
@@ -24,6 +47,13 @@ import org.junit.Test;
 public class PhylipFileTests
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   // interleaved file from
   // http://www.molecularevolution.org/molevolfiles/fileformats/dna.phy.dat
   // sequential file is the interleave file converted into sequential format
@@ -78,7 +108,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testSequentialDataExtraction() throws Exception
   {
     testDataExtraction(sequentialFile);
@@ -90,7 +120,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testInterleavedDataExtraction() throws Exception
   {
     testDataExtraction(interleavedFile);
@@ -105,8 +135,8 @@ public class PhylipFileTests
   private void testDataExtraction(String file) throws IOException
   {
     AppletFormatAdapter rf = new AppletFormatAdapter();
-    Alignment al = rf.readFile(file, AppletFormatAdapter.FILE,
-            PhylipFile.FILE_DESC);
+    AlignmentI al = rf.readFile(file, DataSourceType.FILE,
+            FileFormat.Phylip);
     assertNotNull("Couldn't read supplied alignment data.", al);
 
     Map<String, String> data = PhylipFileTests.getTestData();
@@ -123,7 +153,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testSequentialIO() throws Exception
   {
     testIO(sequentialFile);
@@ -135,7 +165,7 @@ public class PhylipFileTests
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testInterleavedIO() throws Exception
   {
     testIO(interleavedFile);
@@ -150,17 +180,18 @@ public class PhylipFileTests
   public void testIO(String file) throws IOException
   {
     AppletFormatAdapter rf = new AppletFormatAdapter();
-    Alignment al = rf.readFile(file, AppletFormatAdapter.FILE,
-            PhylipFile.FILE_DESC);
+    AlignmentI al = rf.readFile(file, DataSourceType.FILE,
+            FileFormat.Phylip);
     assertNotNull("Couldn't read supplied alignment data.", al);
 
-    String outputfile = rf.formatSequences(PhylipFile.FILE_DESC, al, true);
+    String outputfile = rf.formatSequences(FileFormat.Phylip, al, true);
 
-    Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
-            AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
+    AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
+            DataSourceType.PASTE, FileFormat.Phylip);
     assertNotNull("Couldn't parse reimported alignment data.", al_input);
 
-    StockholmFileTest.testAlignmentEquivalence(al, al_input, false);
+    StockholmFileTest.testAlignmentEquivalence(al, al_input, false, false,
+            false);
 
   }
-}
\ No newline at end of file
+}