X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=06c803f8396fb83aac2218d83fa76ede11c94006;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=d526cf490dd7074820ca62f6d98848fbae67dff6;hpb=f859015ce7abf2402b9b77fb01ae944160b0a198;p=jalview.git

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index d526cf4..06c803f 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -23,10 +23,14 @@ package jalview.ws.jabaws;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 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.Jws2Discoverer;
@@ -36,6 +40,7 @@ import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Component;
+import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -47,11 +52,21 @@ import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import compbio.metadata.Argument;
 import compbio.metadata.WrongParameterException;
 
-
 public class RNAStructExportImport
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
+
   public static String testseqs = "examples/RF00031_folded.stk";
 
   public static Jws2Discoverer disc;
@@ -62,11 +77,11 @@ public class RNAStructExportImport
 
   public static jalview.gui.AlignFrame af = null;
 
-  @BeforeClass
+  @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())
@@ -87,7 +102,7 @@ public class RNAStructExportImport
 
     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);
 
@@ -109,17 +124,22 @@ public class RNAStructExportImport
                                                       // public?
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     if (af != null)
     {
       af.setVisible(false);
       af.dispose();
+      File f = new File(JAR_FILE_NAME);
+      if (f.exists())
+      {
+        f.delete();
+      }
     }
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testRNAAliFoldValidStructure()
   {
 
@@ -135,11 +155,10 @@ public class RNAStructExportImport
       } catch (InterruptedException x)
       {
       }
-      ;
     } while (af.getViewport().getCalcManager().isWorking());
 
     AlignmentI orig_alig = af.getViewport().getAlignment();
-    for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation())
+    for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
     {
       if (alifoldClient.involves(aa))
       {
@@ -153,7 +172,7 @@ public class RNAStructExportImport
     }
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testRNAStructExport()
   {
 
@@ -169,7 +188,6 @@ public class RNAStructExportImport
       } catch (InterruptedException x)
       {
       }
-      ;
     } while (af.getViewport().getCalcManager().isWorking());
 
     AlignmentI orig_alig = af.getViewport().getAlignment();
@@ -183,16 +201,16 @@ public class RNAStructExportImport
     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);
-      assertTrue(
+      assertNotNull(
               "Test "
                       + testname
                       + "\nAlignment annotation file was not regenerated. Null string",
-              anfileout != null);
+              anfileout);
       assertTrue(
               "Test "
                       + testname
@@ -204,13 +222,13 @@ 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);
@@ -224,12 +242,12 @@ public class RNAStructExportImport
             + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testRnaalifoldSettingsRecovery()
   {
-    List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
-    for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) rnaalifoldws
-            .getRunnerConfig().getArguments())
+    List<Argument> opts = new ArrayList<Argument>();
+    for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
+            .getArguments())
     {
       if (rg.getDescription().contains("emperature"))
       {
@@ -268,10 +286,10 @@ public class RNAStructExportImport
     // write out parameters
     jalview.gui.AlignFrame nalf = null;
     assertTrue("Couldn't write out the Jar file",
-            new Jalview2XML(false).saveAlignment(af,
-                    "testRnalifold_param.jar", "trial parameter writeout"));
+            new Jalview2XML(false).saveAlignment(af, JAR_FILE_NAME,
+                    "trial parameter writeout"));
     assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
-            false).loadJalviewAlign("testRnalifold_param.jar")) != null);
+            false).loadJalviewAlign(JAR_FILE_NAME)) != null);
     if (nalf != null)
     {
       AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(