JAL-2314 Re-annotated unit tests using Jws2Discoverer

[jalview.git] / test / jalview / ws / jabaws / RNAStructExportImport.java

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 418e827..6cd32c7 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -29,7 +29,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.gui.Jalview2XML;
 import jalview.gui.JvOptionPane;
 import jalview.io.AnnotationFile;
-import jalview.io.FileLoader;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -54,6 +55,11 @@ import org.testng.annotations.Test;
 import compbio.metadata.Argument;
 import compbio.metadata.WrongParameterException;
 
+/*
+ * All methods in this class are set to the Network group because setUpBeforeClass will fail
+ * if there is no network.
+ */
+@Test(singleThreaded = true)
 public class RNAStructExportImport
 {
 
@@ -99,9 +105,9 @@ public class RNAStructExportImport
       Assert.fail("no web service");
     }
 
-    FileLoader fl = new FileLoader(false);
+    jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
 
-    af = fl.LoadFileWaitTillLoaded(testseqs, FormatAdapter.FILE);
+    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
 
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
 
@@ -138,7 +144,7 @@ public class RNAStructExportImport
     }
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" })
   public void testRNAAliFoldValidStructure()
   {
 
@@ -171,7 +177,7 @@ public class RNAStructExportImport
     }
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" })
   public void testRNAStructExport()
   {
 
@@ -200,8 +206,8 @@ public class RNAStructExportImport
     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);
@@ -221,13 +227,13 @@ public class RNAStructExportImport
 
       // again what format would be appropriate?
       AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
-              FormatAdapter.PASTE, "PFAM");
+              DataSourceType.PASTE, FileFormat.Pfam);
       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);
@@ -241,7 +247,7 @@ public class RNAStructExportImport
             + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" })
   public void testRnaalifoldSettingsRecovery()
   {
     List<Argument> opts = new ArrayList<Argument>();