X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fws%2Fjabaws%2FJpredJabaStructExportImport.java;h=dc157e222a8712f56a21edabe004445fb3ece7ff;hb=cd126a7085c5ebcfc8c05378c71bd862abc4fd91;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..dc157e2 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;
@@ -48,6 +49,7 @@ import javax.swing.JMenuItem;
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeGroups;
 import org.testng.annotations.Test;
 
 import compbio.metadata.Argument;
@@ -55,6 +57,14 @@ 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;
@@ -65,7 +75,7 @@ public class JpredJabaStructExportImport
 
   public static jalview.gui.AlignFrame af = null;
 
-  @BeforeClass(alwaysRun = true)
+  @BeforeGroups(groups = { "Network" })
   public static void setUpBeforeClass() throws Exception
   {
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
@@ -97,7 +107,7 @@ public class JpredJabaStructExportImport
     }
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" }, enabled = false)
   public void testJPredStructOneSeqOnly()
   {
     af.selectAllSequenceMenuItem_actionPerformed(null);
@@ -149,7 +159,7 @@ public class JpredJabaStructExportImport
 
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" }, enabled = false)
   public void testJPredStructExport()
   {
 
@@ -179,8 +189,8 @@ 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);
@@ -209,7 +219,8 @@ public class JpredJabaStructExportImport
                       DataSourceType.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+              false);
       return;
     } catch (Exception e)
     {
@@ -220,7 +231,7 @@ public class JpredJabaStructExportImport
             + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" }, enabled = false)
   public void testJpredwsSettingsRecovery()
   {
     Assert.fail("not implemnented");