X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=58bcb44d34f9361bd29d2852ef99ce8572ba5cb8;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=4e407afa775cde17fd46b368b8f14c3207760f77;hpb=a4afd02409c7c45ee4042bf81b310a537d75c73d;p=jalview.git

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 4e407af..58bcb44 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -1,31 +1,58 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.jabaws;
 
-import static org.junit.Assert.*;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Vector;
-
-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.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Component;
+import java.util.ArrayList;
+import java.util.List;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
 
-public class RNAStructExportImport 
+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;
 
@@ -35,33 +62,51 @@ public class RNAStructExportImport
 
   public static jalview.gui.AlignFrame af = null;
 
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-  	
-  	
+
     jalview.bin.Cache.initLogger();
-    disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
-    
+    disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
+
     for (Jws2Instance svc : disc.getServices())
     {
-    	
+
       if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
       {
         rnaalifoldws = svc;
       }
     }
-    
+
     System.out.println("State of rnaalifoldws: " + rnaalifoldws);
-    
-    if (rnaalifoldws == null) System.exit(0);
-    
+
+    if (rnaalifoldws == null)
+    {
+      Assert.fail("no web service");
+    }
+
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
-    
+
     af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
-    
+
     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
@@ -74,16 +119,48 @@ 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()
   {
-  	
-  	
+
     alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
-    
+
     af.getViewport().getCalcManager().startWorker(alifoldClient);
-    
-    
+
     do
     {
       try
@@ -94,10 +171,9 @@ public class RNAStructExportImport
       }
       ;
     } while (af.getViewport().getCalcManager().isWorking());
-    
-    
+
     AlignmentI orig_alig = af.getViewport().getAlignment();
-    
+
     testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
 
   }
@@ -106,14 +182,12 @@ public class RNAStructExportImport
   {
     try
     {
-    	// what format would be appropriate for RNAalifold annotations?
+      // what format would be appropriate for RNAalifold annotations?
       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
@@ -139,15 +213,107 @@ 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(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())
+    {
+      if (rg.getDescription().contains("emperature"))
+      {
+        try
+        {
+          rg.setValue("292");
+        } catch (WrongParameterException q)
+        {
+          Assert.fail("Couldn't set the temperature parameter "
+                  + q.getStackTrace());
+        }
+        opts.add(rg);
+      }
+      if (rg.getDescription().contains("max"))
+      {
+        opts.add(rg);
+      }
+    }
+    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
+
+    af.getViewport().getCalcManager().startWorker(alifoldClient);
+
+    do
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException x)
+      {
+      }
+      ;
+    } while (af.getViewport().getCalcManager().isWorking());
+    AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(
+            alifoldClient.getCalcId());
+    String oldsettings = oldacs.getWsParamFile();
+    // 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"));
+    assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
+            false).loadJalviewAlign("testRnalifold_param.jar")) != null);
+    if (nalf != null)
+    {
+      AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
+              alifoldClient.getCalcId());
+      assertTrue("Calc ID settings not recovered from viewport stash",
+              acs.equals(oldacs));
+      assertTrue(
+              "Serialised Calc ID settings not identical to those recovered from viewport stash",
+              acs.getWsParamFile().equals(oldsettings));
+      JMenu nmenu = new JMenu();
+      new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu,
+              rnaalifoldws, af);
+      assertTrue("Couldn't get menu entry for service",
+              nmenu.getItemCount() > 0);
+      for (Component itm : nmenu.getMenuComponents())
+      {
+        if (itm instanceof JMenuItem)
+        {
+          JMenuItem i = (JMenuItem) itm;
+          if (i.getText().equals(
+                  rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
+          {
+            i.doClick();
+            break;
+          }
+        }
+      }
+      while (af.getViewport().isCalcInProgress())
+      {
+        try
+        {
+          Thread.sleep(200);
+        } catch (Exception x)
+        {
+        }
+        ;
+      }
+      AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(
+              alifoldClient.getCalcId());
+      assertTrue(
+              "Calc ID settings after recalculation has not been recovered.",
+              acs2.getWsParamFile().equals(oldsettings));
+    }
+  }
 }