JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[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 e74ebe7..745e37d 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,42 +20,39 @@
  */
 package jalview.ws.jabaws;
 
-import static org.junit.Assert.*;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
 
-import java.awt.Component;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-
-import jalview.api.AlignCalcManagerI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
 import jalview.gui.Jalview2XML;
 import jalview.io.AnnotationFile;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.AADisorderClient;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.RNAalifoldClient;
 import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.dm.JabaOption;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.AutoCalcSetting;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import java.awt.Component;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 import compbio.metadata.WrongParameterException;
 
+
 public class RNAStructExportImport
 {
-  public static String testseqs = "examples/unfolded_RF00031.aln";
+  public static String testseqs = "examples/RF00031_folded.stk";
 
   public static Jws2Discoverer disc;
 
@@ -65,7 +62,7 @@ public class RNAStructExportImport
 
   public static jalview.gui.AlignFrame af = null;
 
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
 
@@ -84,7 +81,9 @@ public class RNAStructExportImport
     System.out.println("State of rnaalifoldws: " + rnaalifoldws);
 
     if (rnaalifoldws == null)
-      System.exit(0);
+    {
+      Assert.fail("no web service");
+    }
 
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
 
@@ -92,6 +91,22 @@ public class RNAStructExportImport
 
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
 
+    // remove any existing annotation
+    List<AlignmentAnnotation> aal = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation rna : af.getViewport().getAlignment()
+            .getAlignmentAnnotation())
+    {
+      if (rna.isRNA())
+      {
+        aal.add(rna);
+      }
+    }
+    for (AlignmentAnnotation rna : aal)
+    {
+      af.getViewport().getAlignment().deleteAnnotation(rna);
+    }
+    af.getViewport().alignmentChanged(af.alignPanel); // why is af.alignPanel
+                                                      // public?
   }
 
   @AfterClass
@@ -104,7 +119,41 @@ public class RNAStructExportImport
     }
   }
 
-  @Test
+  @Test(groups = { "Functional" })
+  public void testRNAAliFoldValidStructure()
+  {
+
+    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+
+    af.getViewport().getCalcManager().startWorker(alifoldClient);
+
+    do
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException x)
+      {
+      }
+      ;
+    } while (af.getViewport().getCalcManager().isWorking());
+
+    AlignmentI orig_alig = af.getViewport().getAlignment();
+    for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
+    {
+      if (alifoldClient.involves(aa))
+      {
+        if (aa.isRNA())
+        {
+          assertTrue(
+                  "Did not create valid structure from RNAALiFold prediction",
+                  aa.isValidStruc());
+        }
+      }
+    }
+  }
+
+  @Test(groups = { "Functional" })
   public void testRNAStructExport()
   {
 
@@ -137,9 +186,8 @@ public class RNAStructExportImport
       String aligfileout = new FormatAdapter().formatSequences("PFAM",
               al.getSequencesArray());
 
-      String anfileout = new AnnotationFile().printAnnotations(
-              al.getAlignmentAnnotation(), al.getGroups(),
-              al.getProperties());
+      String anfileout = new AnnotationFile()
+              .printAnnotationsForAlignment(al);
       assertTrue(
               "Test "
                       + testname
@@ -165,18 +213,18 @@ public class RNAStructExportImport
                       FormatAdapter.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
       return;
     } catch (Exception e)
     {
       e.printStackTrace();
     }
-    fail("Test "
+    Assert.fail("Test "
             + testname
             + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testRnaalifoldSettingsRecovery()
   {
     List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
@@ -190,7 +238,7 @@ public class RNAStructExportImport
           rg.setValue("292");
         } catch (WrongParameterException q)
         {
-          fail("Couldn't set the temperature parameter "
+          Assert.fail("Couldn't set the temperature parameter "
                   + q.getStackTrace());
         }
         opts.add(rg);