X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=c39cc4a6da848ba8a8d3b4145d27571f51beef52;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=a63923af60ca5cce0188bfb7b5d5a797648a1a82;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index a63923a..c39cc4a 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -36,8 +36,7 @@ import org.testng.annotations.Test;
 public class AnnotationFileIOTest
 {
 
-  static String TestFiles[][] =
-  {
+  static String TestFiles[][] = {
       { "Test example annotation import/export", "examples/uniref50.fa",
           "examples/testdata/example_annot_file.jva" },
       { "Test multiple combine annotation statements import/export",
@@ -52,7 +51,7 @@ public class AnnotationFileIOTest
       { "Test hiding/showing of insertions on sequence_ref",
           "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void exampleAnnotationFileIO() throws Exception
   {
     for (String[] testPair : TestFiles)
@@ -70,8 +69,8 @@ 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)
@@ -116,7 +115,7 @@ 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,
@@ -144,7 +143,7 @@ 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);