X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FJpredJabaStructExportImport.java;h=b8fe0a32b087f9fa8a4b795380a97b5268d65401;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=9398d1857b5105aa6b307d8b65ae24e3acd41972;hpb=cbc07eab0291f023f89b2554c488ae9e4587ae2a;p=jalview.git

diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index 9398d18..b8fe0a3 100644
--- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@ -23,9 +23,13 @@ package jalview.ws.jabaws;
 import static org.testng.AssertJUnit.assertNotNull;
 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;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
 import jalview.ws.jws2.JPred301Client;
@@ -52,6 +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;
@@ -65,8 +77,8 @@ public class JpredJabaStructExportImport
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-
-    jalview.bin.Cache.initLogger();
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.initLogger();
     disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
 
     for (Jws2Instance svc : disc.getServices())
@@ -80,7 +92,7 @@ public class JpredJabaStructExportImport
     System.out.println("State of jpredws: " + jpredws);
     Assert.assertNotNull(jpredws, "jpredws is null!");
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
-    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
   }
 
@@ -176,8 +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.getAlignmentFile().print(
+              al.getSequencesArray(), true);
 
       String anfileout = new AnnotationFile()
               .printAnnotationsForAlignment(al);
@@ -197,13 +209,13 @@ public class JpredJabaStructExportImport
 
       // again what format would be appropriate?
       AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
-              FormatAdapter.PASTE, "PFAM");
+              DataSourceType.PASTE, FileFormat.Fasta);
       assertTrue(
               "Test "
                       + 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);