X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=885c6736752b47ee51da89ad735855c90f04de0a;hb=b0832234b2a89510d715951d94ae213e449ca6b2;hp=a63923af60ca5cce0188bfb7b5d5a797648a1a82;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index a63923a..885c673 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -25,19 +25,27 @@ import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.gui.JvOptionPane;
 import jalview.io.AnnotationFile.ViewDef;
 
 import java.io.File;
 import java.util.Hashtable;
 
 import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class AnnotationFileIOTest
 {
 
-  static String TestFiles[][] =
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
   {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  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 +60,7 @@ 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)
@@ -62,7 +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();
@@ -70,14 +78,13 @@ 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)
       {
-        al.getSequenceAt(i).setDatasetSequence(
-                al.getSequenceAt(i).createDatasetSequence());
+        al.getSequenceAt(i).createDatasetSequence();
       }
       assertNotNull("Couldn't read supplied alignment data.", al);
       return al;
@@ -99,9 +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 '"
@@ -116,7 +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,
@@ -144,7 +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);