X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FJpredJabaStructExportImport.java;h=d5b6ed118f621d6324ee3e7e7948f72cd0bf2b08;hb=dfa39e09cf3ffa44cc1e764bfa72900bab96136d;hp=25fb190d4e55c95361edc448efc02aba415e4d66;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index 25fb190..d5b6ed1 100644
--- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
 import jalview.io.AnnotationFile;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -55,6 +56,14 @@ import compbio.metadata.WrongParameterException;
 
 public class JpredJabaStructExportImport
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   public static String testseqs = "examples/uniref50.fa";
 
   public static Jws2Discoverer disc;
@@ -179,8 +188,8 @@ public class JpredJabaStructExportImport
     try
     {
       // what format would be appropriate for RNAalifold annotations?
-      String aligfileout = new FormatAdapter().formatSequences("PFAM",
-              al.getSequencesArray());
+      String aligfileout = FileFormat.Pfam.getWriter(null).print(
+              al.getSequencesArray(), true);
 
       String anfileout = new AnnotationFile()
               .printAnnotationsForAlignment(al);