X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FPhylipFileTests.java;h=d85335027c59fcd5fdde7bc6f3b3724a88d5ad4a;hb=049cfa5fc078e6daac6158f25cea7d9a60b48969;hp=ec222fb96895f390f54eba4805fcd7388a905faa;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/io/PhylipFileTests.java b/test/jalview/io/PhylipFileTests.java
index ec222fb..d853350 100644
--- a/test/jalview/io/PhylipFileTests.java
+++ b/test/jalview/io/PhylipFileTests.java
@@ -135,8 +135,8 @@ public class PhylipFileTests
   private void testDataExtraction(String file) throws IOException
   {
     AppletFormatAdapter rf = new AppletFormatAdapter();
-    AlignmentI 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();
@@ -180,17 +180,18 @@ public class PhylipFileTests
   public void testIO(String file) throws IOException
   {
     AppletFormatAdapter rf = new AppletFormatAdapter();
-    AlignmentI 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);
 
     AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
-            AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
+            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);
 
   }
 }