JAL-3560 from JAL-3563. This commit is expected to be reverted. Just

getting back to a branch that Bamboo is compiling.

diff --git a/.j2s b/.j2s
index ea8e54f..51b5c7d 100644 (file)
--- a/.j2s
+++ b/.j2s
@@ -1,4 +1,4 @@
-j2s.compiler.status=enable
+j2s.compiler.status=disable
 j2s.compiler.java.version=11
 
 #a semicolon-separated list of package-level file paths to be excluded

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ff8d52f..13ac248 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -86,6 +86,7 @@ import java.util.Map;
 import java.util.Vector;
 
 import javax.swing.LookAndFeel;
+import javax.swing.SwingUtilities;
 import javax.swing.UIManager;
 
 import groovy.lang.Binding;
@@ -148,6 +149,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
   private boolean noAnnotation;
 
+  public static final String TERMINATOR_LINE = "Jalview argument parsing complete.";
+
   public boolean getStartCalculations()
   {
     return !noCalculation;
@@ -312,6 +315,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
             || "true".equals(System.getProperty("java.awt.headless")))
     {
       headless = true;
+      setSynchronous(true);
     }
 
     if (isJS)
@@ -346,7 +350,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         System.exit(0);
       }
 
-
       // anything else!
 
       final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
@@ -402,11 +405,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     try
     {
       if (!isJS && Platform.isWin())
-       {
+      {
         UIManager.setLookAndFeel(
                 headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
                         : UIManager.getSystemLookAndFeelClassName());
-//      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+        // UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
       }
     } catch (Exception ex)
     {
@@ -460,7 +463,21 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
     }
 
-    if (!headless)
+    if (headless)
+    {
+      // If this is not tested, then
+
+      if (aparser.contains(ArgsParser.NOUSAGESTATS))
+      {
+        System.err.println("CMD [-nousagestats] executed successfully!");
+      }
+      if (aparser.contains(ArgsParser.NOQUESTIONNAIRE))
+      {
+        System.err.println("CMD [-noquestionnaire] executed successfully!");
+      }
+
+    }
+    else
     {
       desktop = Desktop.getInstance();
       desktop.setInBatchMode(true); // indicate we are starting up
@@ -527,6 +544,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     }
 
     parseArguments(aparser, true);
+    System.err.println(TERMINATOR_LINE);
   }
 
   /**
@@ -2170,5 +2188,84 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     // + " " + status);
   }
 
-}
+  /**
+   * flag to allow selected Runnable and Thread processes to run synchronously
+   * 
+   * JAL-3563
+   * 
+   */
+  private static boolean isSynchronous = false;
+
+  /**
+   * Set Jalview to run selected processes synchronously in test and headless
+   * environments.
+   * 
+   * JAL-3563
+   * 
+   * @param b
+   * @author Bob Hanson
+   */
+  public static void setSynchronous(boolean b)
+  {
+
+    isSynchronous = b;
+
+  }
+
+  /**
+   * Allows optional synchronous running of a Runnable that would otherwise use
+   * SwingUtilities.invokeLater.
+   * 
+   * JAL-3563
+   * 
+   * @param t
+   * @author Bob Hanson
+   */
+  public static boolean isSynchronous()
+  {
+    return isSynchronous;
+  }
+
+  /**
+   * Allows optional synchronous running of a Runnable that would otherwise use
+   * SwingUtilities.invokeLater.
+   * 
+   * JAL-3563
+   * 
+   * @param t
+   * @author Bob Hanson
+   */
+  public static void execRunnable(Runnable r)
+  {
+    if (isSynchronous())
+    {
+      r.run();
+    }
+    else
+    {
+      SwingUtilities.invokeLater(r);
+    }
+  }
+
+  /**
+   * Allows optional synchronous running of a thread that would otherwise be run
+   * using start().
+   * 
+   * JAL-3563
+   * 
+   * @param t
+   * @author Bob Hanson
+   */
+  public static void execThread(Thread t)
+  {
+    if (isSynchronous())
+    {
+      t.run();
+    }
+    else
+    {
+      t.start();
+    }
+  }
 
+}
\ No newline at end of file

diff --git a/src/jalview/bin/JalviewJS2.java b/src/jalview/bin/JalviewJS2.java
index 0bfc930..508ccc7 100644 (file)
--- a/src/jalview/bin/JalviewJS2.java
+++ b/src/jalview/bin/JalviewJS2.java
@@ -34,10 +34,11 @@ public class JalviewJS2
     if (args.length == 0)
     {
       args = new String[] {
-        //  "headless",
+          "headless",
           "open", "examples/uniref50.fa",
           "features",
-          "examples/exampleFeatures.txt"
+          "examples/exampleFeatures.txt", " -eps",
+          "test/jalview/bin/test_uniref50_out.eps"
           // , "noannotation"
           // , "showoverview"
         //  , "png", "test-bh.png"

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2371be3..8d7a600 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4167,6 +4167,10 @@ public class AlignFrame extends GAlignFrame
    */
   public void BuildWebServiceMenu()
   {
+    if (Jalview.isSynchronous())
+    {
+      return;
+    }
     while (buildingMenu)
     {
       try

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 9e0c89b..1e58d1b 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -441,7 +441,7 @@ public class Desktop extends GDesktop
       // it deletes the unneeded Java-only code form the JavaScript version
       // completely (@j2sIgnore), since it will never be used there.
 
-      if (!Platform.isJS())
+      if (!Platform.isJS() && !Jalview.isSynchronous())
       /**
        * Java only
        * 

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index b0315e8..2c93ee5 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -35,6 +35,7 @@ import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -189,7 +190,6 @@ import java.util.jar.JarInputStream;
 import java.util.jar.JarOutputStream;
 
 import javax.swing.JInternalFrame;
-import javax.swing.SwingUtilities;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBElement;
 import javax.xml.bind.Marshaller;
@@ -2784,8 +2784,9 @@ public class Jalview2XML
     {
       try
       {
+
          // BH 2019 -- can't wait
-        SwingUtilities.invokeLater(new Runnable()
+        Jalview.execRunnable(new Runnable()
         {
           @Override
           public void run()
@@ -3354,16 +3355,16 @@ public class Jalview2XML
    *          data source provider
    * @return alignment frame created from view stored in DOM
    */
-  AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
+  private AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
           boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
   {
 
-//    Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK);
+    // Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK);
 
-    SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
+    SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
+            .get(0);
     List<Sequence> vamsasSeqs = vamsasSet.getSequence();
 
-
     // JalviewModelSequence jms = object.getJalviewModelSequence();
 
     // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
@@ -3394,7 +3395,7 @@ public class Jalview2XML
               : view.getId() + uniqueSetSuffix);
     }
 
-//    Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK);
+    // Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK);
     // ////////////////////////////////
     // LOAD SEQUENCES
 
@@ -3480,8 +3481,8 @@ public class Jalview2XML
       }
     }
 
-//    Platform.timeCheck("Jalview2XML.loadFromObject-seq",
-//            Platform.TIME_MARK);
+    // Platform.timeCheck("Jalview2XML.loadFromObject-seq",
+    // Platform.TIME_MARK);
     // /
     // Create the alignment object from the sequence set
     // ///////////////////////////////
@@ -3522,8 +3523,8 @@ public class Jalview2XML
       recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
     }
 
-//    Platform.timeCheck("Jalview2XML.loadFromObject-align",
-//            Platform.TIME_MARK);
+    // Platform.timeCheck("Jalview2XML.loadFromObject-align",
+    // Platform.TIME_MARK);
     if (referenceseqForView != null)
     {
       al.setSeqrep(referenceseqForView);
@@ -3536,8 +3537,8 @@ public class Jalview2XML
       al.setProperty(ssp.getKey(), ssp.getValue());
     }
 
-//    Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop",
-//            Platform.TIME_MARK);
+    // Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop",
+    // Platform.TIME_MARK);
     // ///////////////////////////////
 
     Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
@@ -3551,7 +3552,7 @@ public class Jalview2XML
       // now, for 2.10 projects, this is also done if the xml doc includes
       // dataset sequences not actually present in any particular view.
       //
-//      Platform.timeCheck("J2XML features0", Platform.TIME_RESET);
+      // Platform.timeCheck("J2XML features0", Platform.TIME_RESET);
       for (int i = 0; i < vamsasSeqs.size(); i++)
       {
         JSeq jseq = jseqs.get(i);
@@ -3606,9 +3607,9 @@ public class Jalview2XML
             }
 
             // adds feature to datasequence's feature set (since Jalview 2.10)
-//            Platform.timeCheck(null, Platform.TIME_SET);
+            // Platform.timeCheck(null, Platform.TIME_SET);
             al.getSequenceAt(i).addSequenceFeature(sf);
-//            Platform.timeCheck(null, Platform.TIME_MARK);
+            // Platform.timeCheck(null, Platform.TIME_MARK);
           }
         }
         if (vamsasSeqs.get(i).getDBRef().size() > 0)
@@ -3668,8 +3669,7 @@ public class Jalview2XML
             {
               entry.setProperty(prop.getName(), prop.getValue());
             }
-            Desktop.getStructureSelectionManager()
-                    .registerPDBEntry(entry);
+            Desktop.getStructureSelectionManager().registerPDBEntry(entry);
             // adds PDBEntry to datasequence's set (since Jalview 2.10)
             if (al.getSequenceAt(i).getDatasetSequence() != null)
             {
@@ -3684,9 +3684,9 @@ public class Jalview2XML
 
       }
 
-//      Platform.timeCheck("features done", Platform.TIME_GET);
-//      Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview",
-//              Platform.TIME_MARK);
+      // Platform.timeCheck("features done", Platform.TIME_GET);
+      // Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview",
+      // Platform.TIME_MARK);
     } // end !multipleview
 
     // ///////////////////////////////
@@ -3720,16 +3720,16 @@ public class Jalview2XML
               else
               {
                 // defer to later
-                frefedSequence.add(
-                        newAlcodMapRef(map.getDnasq(), cf, mapping));
+                frefedSequence
+                        .add(newAlcodMapRef(map.getDnasq(), cf, mapping));
               }
             }
           }
           al.addCodonFrame(cf);
         }
       }
-//      Platform.timeCheck("Jalview2XML.loadFromObject-seqmap",
-//              Platform.TIME_MARK);
+      // Platform.timeCheck("Jalview2XML.loadFromObject-seqmap",
+      // Platform.TIME_MARK);
     }
 
     // ////////////////////////////////
@@ -3790,8 +3790,8 @@ public class Jalview2XML
         }
         // Construct new annotation from model.
         List<AnnotationElement> ae = annotation.getAnnotationElement();
-//        System.err.println(
-//                "Jalview2XML processing " + ae.size() + " annotations");
+        // System.err.println(
+        // "Jalview2XML processing " + ae.size() + " annotations");
 
         jalview.datamodel.Annotation[] anot = null;
         java.awt.Color firstColour = null;
@@ -3936,8 +3936,7 @@ public class Jalview2XML
         jaa.setCalcId(annotation.getCalcId());
         if (annotation.getProperty().size() > 0)
         {
-          for (Annotation.Property prop : annotation
-                  .getProperty())
+          for (Annotation.Property prop : annotation.getProperty())
           {
             jaa.setProperty(prop.getName(), prop.getValue());
           }
@@ -3954,8 +3953,8 @@ public class Jalview2XML
           al.addAnnotation(jaa);
         }
       }
-//      Platform.timeCheck("Jalview2XML.loadFromObject-annot",
-//              Platform.TIME_MARK);
+      // Platform.timeCheck("Jalview2XML.loadFromObject-annot",
+      // Platform.TIME_MARK);
     }
     // ///////////////////////
     // LOAD GROUPS
@@ -4020,9 +4019,9 @@ public class Jalview2XML
         sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
         sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
         // attributes with a default in the schema are never null
-          sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
-          sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
-          sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
+        sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
+        sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
+        sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
         sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
         if (jGroup.getConsThreshold() != null
                 && jGroup.getConsThreshold().intValue() != 0)
@@ -4066,12 +4065,13 @@ public class Jalview2XML
         if (addAnnotSchemeGroup)
         {
           // reconstruct the annotation colourscheme
-          sg.setColourScheme(constructAnnotationColour(
-                  jGroup.getAnnotationColours(), null, al, jalviewModel, false));
+          sg.setColourScheme(
+                  constructAnnotationColour(jGroup.getAnnotationColours(),
+                          null, al, jalviewModel, false));
         }
       }
-//      Platform.timeCheck("Jalview2XML.loadFromObject-groups",
-//              Platform.TIME_MARK);
+      // Platform.timeCheck("Jalview2XML.loadFromObject-groups",
+      // Platform.TIME_MARK);
     }
     if (view == null)
     {
@@ -4111,8 +4111,8 @@ public class Jalview2XML
         }
 
       }
-//      Platform.timeCheck("Jalview2XML.loadFromObject-viewport",
-//              Platform.TIME_MARK);
+      // Platform.timeCheck("Jalview2XML.loadFromObject-viewport",
+      // Platform.TIME_MARK);
     }
     /**
      * indicate that annotation colours are applied across all groups (pre
@@ -4165,47 +4165,47 @@ public class Jalview2XML
     final AlignFrame af0 = af;
     final AlignViewport av0 = av;
     final AlignmentPanel ap0 = ap;
-//    Platform.timeCheck("Jalview2XML.loadFromObject-beforetree",
-//            Platform.TIME_MARK);
+    // Platform.timeCheck("Jalview2XML.loadFromObject-beforetree",
+    // Platform.TIME_MARK);
     if (loadTreesAndStructures)
     {
       if (!jalviewModel.getTree().isEmpty())
       {
-        SwingUtilities.invokeLater(new Runnable()
+        Jalview.execRunnable(new Runnable()
         {
           @Override
           public void run()
           {
-//            Platform.timeCheck(null, Platform.TIME_MARK);
+            // Platform.timeCheck(null, Platform.TIME_MARK);
             loadTrees(jalviewModel, view, af0, av0, ap0);
-//            Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK);
+            // Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK);
           }
         });
       }
       if (!jalviewModel.getPcaViewer().isEmpty())
       {
-        SwingUtilities.invokeLater(new Runnable()
+        Jalview.execRunnable(new Runnable()
         {
           @Override
           public void run()
           {
-//            Platform.timeCheck(null, Platform.TIME_MARK);
+            // Platform.timeCheck(null, Platform.TIME_MARK);
             loadPCAViewers(jalviewModel, ap0);
-//            Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK);
+            // Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK);
           }
         });
       }
-      SwingUtilities.invokeLater(new Runnable()
+      Jalview.execRunnable(new Runnable()
       {
         @Override
         public void run()
         {
-//          Platform.timeCheck(null, Platform.TIME_MARK);
+          // Platform.timeCheck(null, Platform.TIME_MARK);
           loadPDBStructures(jprovider, jseqs, af0, ap0);
-//          Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK);
+          // Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK);
         }
       });
-      SwingUtilities.invokeLater(new Runnable()
+      Jalview.execRunnable(new Runnable()
       {
         @Override
         public void run()
@@ -4213,6 +4213,7 @@ public class Jalview2XML
           loadRnaViewers(jprovider, jseqs, ap0);
         }
       });
+
     }
     // and finally return.
     // but do not set holdRepaint true just yet, because this could be the
@@ -4773,7 +4774,7 @@ public class Jalview2XML
             svattrib.getWidth(), svattrib.getHeight());
     // try
     // {
-      javax.swing.SwingUtilities.invokeLater(new Runnable()
+    Jalview.execRunnable(new Runnable()
       {
         @Override
         public void run()
@@ -4799,7 +4800,8 @@ public class Jalview2XML
             }
           }
         }
-      });
+    });
+    // javax.swing.SwingUtilities.invokeLater(r);
     // } catch (InvocationTargetException ex)
     // {
     // warn("Unexpected error when opening Jmol view.", ex);

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 4174f5b..4b99911 100644 (file)
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -365,4 +365,11 @@ public class StructureMapping
 
     return true;
   }
+
+  @Override
+  public String toString()
+  {
+    return "[StructureMapping " + pdbfile + "\n" + mappingDetails + "]";
+  }
+
 }

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index 9a3fc8d..77908b6 100644 (file)
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -190,7 +190,8 @@ public class AlignCalcManager implements AlignCalcManagerI
     {
       Thread tw = new Thread(worker);
       tw.setName(worker.getClass().toString());
-      tw.start();
+      Jalview.execThread(tw); // JAL-3563
+      // tw.start();
     }
   }
 

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 564e57d..4ffc022 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -203,11 +203,21 @@ public class CommandLineOperations
     {
       System.out.println(ln);
       successfulCMDs.add(ln);
+      if (ln.equals(Jalview.TERMINATOR_LINE))
+      {
+        break;
+      }
     }
-    while ((ln = worker.getErrorReader().readLine()) != null)
+    if (worker != null && worker.exit == null)
     {
-      System.err.println(ln);
+      worker.interrupt();
+      Thread.currentThread().interrupt();
+      worker.process.destroy();
     }
+    // while ((ln = worker.getErrorReader().readLine()) != null)
+    // {
+    // System.err.println(ln);
+    // }
 
   }
 
@@ -224,6 +234,11 @@ public class CommandLineOperations
     {
       System.out.println(ln);
       successfulCMDs.add(ln);
+      if (ln.equals(Jalview.TERMINATOR_LINE))
+      {
+        break;
+      }
+
       if (++count > 5)
       {
         break;

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 830a759..3c74b9e 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -32,6 +32,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenSequences;
@@ -68,6 +69,7 @@ import jalview.schemes.RNAHelicesColour;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureMapping;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -96,6 +98,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     JvOptionPane.setInteractiveMode(false);
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+    Jalview.setSynchronous(true);
   }
 
   @Test(groups = { "Functional" })
@@ -104,6 +107,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     String inFile = "examples/RF00031_folded.stk";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
             DataSourceType.FILE);
     assertNotNull(af, "Didn't read input file " + inFile);
@@ -119,7 +123,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(af.isSaveAlignmentSuccessful(),
             "Failed to store as a project.");
     af.closeMenuItem_actionPerformed(true);
-    af = null;
     af = new FileLoader().LoadFileWaitTillLoaded(tfile,
             DataSourceType.FILE);
     assertNotNull(af, "Failed to import new project");
@@ -144,6 +147,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             inAnnot = "examples/uniref50.score_ascii";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
             DataSourceType.FILE);
     assertNotNull(af, "Didn't read input file " + inFile);
@@ -162,7 +166,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(af.isSaveAlignmentSuccessful(),
             "Failed to store as a project.");
     af.closeMenuItem_actionPerformed(true);
-    af = null;
     af = new FileLoader().LoadFileWaitTillLoaded(tfile,
             DataSourceType.FILE);
     assertNotNull(af, "Failed to import new project");
@@ -180,6 +183,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             inAnnot = "examples/testdata/uniref50_iupred.jva";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
             DataSourceType.FILE);
     assertNotNull(af, "Didn't read input file " + inFile);
@@ -268,6 +272,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     int origCount = Desktop.getAlignFrames() == null ? 0
             : Desktop.getAlignFrames().length;
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -286,6 +291,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     StructureImportSettings.setProcessSecondaryStructure(true);
     StructureImportSettings.setVisibleChainAnnotation(true);
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -294,9 +300,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     // count number of PDB mappings the structure selection manager holds -
     String pdbFile = af.getCurrentView().getStructureSelectionManager()
             .findFileForPDBId("1A70");
-    assertEquals(
-            af.getCurrentView().getStructureSelectionManager()
-                    .getMapping(pdbFile).length,
+    StructureMapping[] x = af.getCurrentView()
+            .getStructureSelectionManager()//
+            .getMapping(pdbFile);
+    assertEquals(x.length,
             2, "Expected only two mappings for 1A70");
 
   }
@@ -306,6 +313,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     StructureImportSettings.setProcessSecondaryStructure(true);
     StructureImportSettings.setVisibleChainAnnotation(true);
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -367,6 +375,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testCopyViewSettings() throws Exception
   {
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -406,7 +415,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testStoreAndRecoverExpandedviews() throws Exception
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
-
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     Assert.assertEquals(Desktop.getAlignFrames().length, 1);
@@ -460,6 +469,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -593,6 +603,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testStoreAndRecoverGroupRepSeqs() throws Exception
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -714,6 +725,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
     String exampleFile = "examples/3W5V.pdb";
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
             DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -813,6 +825,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testStoreAndRecoverColourThresholds() throws IOException
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
 
@@ -906,6 +919,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testSaveLoadFeatureColoursAndFilters() throws IOException
   {
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
@@ -1066,6 +1080,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testMergeDatasetsforViews() throws IOException
   {
     // simple project - two views on one alignment
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
             "examples/testdata/projects/twoViews.jvp", DataSourceType.FILE);
     assertNotNull(af);
@@ -1084,6 +1099,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Desktop.getInstance().closeAll_actionPerformed(null);
 
     // complex project - one dataset, several views on several alignments
+    // Jalview.setSynchronous(true);
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
             "examples/testdata/projects/manyViews.jvp",
             DataSourceType.FILE);
@@ -1126,6 +1142,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testPcaViewAssociation() throws IOException
   {
     Desktop.getInstance().closeAll_actionPerformed(null);
+    // Jalview.setSynchronous(true);
     final String PCAVIEWNAME = "With PCA";
     // create a new tempfile
     File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");