X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=885c6736752b47ee51da89ad735855c90f04de0a;hb=717215fa552eba980616292d76cd0032c548e459;hp=bcaa7b1982dd04681130405ed5c51f6abf65ca28;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index bcaa7b1..885c673 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -70,7 +70,7 @@ public class AnnotationFileIOTest
     }
   }
 
-  public static AlignmentI readAlignmentFile(File f)
+  AlignmentI readAlignmentFile(File f)
   {
     System.out.println("Reading file: " + f);
     String ff = f.getPath();
@@ -78,8 +78,8 @@ public class AnnotationFileIOTest
     {
       FormatAdapter rf = new FormatAdapter();
 
-      AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
-              new IdentifyFile().identify(ff, AppletFormatAdapter.FILE));
+      AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
+              new IdentifyFile().identify(ff, DataSourceType.FILE));
 
       // make sure dataset is initialised ? not sure about this
       for (int i = 0; i < al.getSequencesArray().length; ++i)
@@ -106,9 +106,7 @@ public class AnnotationFileIOTest
    *          - label for IO class used to write and read back in the data from
    *          f
    */
-
-  // @Test(groups ={ "Functional" })
-  public static void testAnnotationFileIO(String testname, File f,
+  void testAnnotationFileIO(String testname, File f,
           File annotFile)
   {
     System.out.println("Test: " + testname + "\nReading annotation file '"
@@ -123,7 +121,7 @@ public class AnnotationFileIOTest
                       + testname
                       + "\nAlignment was not annotated - annotation file not imported.",
               new AnnotationFile().readAnnotationFile(al, cs, af,
-                      FormatAdapter.FILE));
+                      DataSourceType.FILE));
 
       AnnotationFile aff = new AnnotationFile();
       ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
@@ -151,7 +149,7 @@ public class AnnotationFileIOTest
                       + testname
                       + "\nregenerated annotation file did not annotate alignment.",
               new AnnotationFile().readAnnotationFile(al_new, anfileout,
-                      FormatAdapter.PASTE));
+                      DataSourceType.PASTE));
 
       // test for consistency in io
       StockholmFileTest.testAlignmentEquivalence(al, al_new, false);