JAL-629 null checks for Desktop.instance.closeAll(). Props re-loaded after CommandsTest.

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index 65162f3..c5f8bff 100644 (file)
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -3,6 +3,7 @@ package jalview.bin;
 import java.util.Date;
 
 import org.testng.Assert;
+import org.testng.annotations.AfterClass;
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
@@ -24,6 +25,12 @@ public class CommandsTest
     Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
   }
 
+  @AfterClass(alwaysRun = true)
+  public static void resetProps()
+  {
+    Cache.loadProperties("test/jalview/testProps.jvprops");
+  }
+
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
@@ -34,7 +41,8 @@ public class CommandsTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = "Functional", dataProvider = "cmdLines")

diff --git a/test/jalview/bin/HiDPISettingTest1.java b/test/jalview/bin/HiDPISettingTest1.java
index 4561ff4..49a721f 100644 (file)
--- a/test/jalview/bin/HiDPISettingTest1.java
+++ b/test/jalview/bin/HiDPISettingTest1.java
@@ -85,7 +85,8 @@ public class HiDPISettingTest1
   @AfterClass(alwaysRun = true)
   public void tearDown()
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = { "Functional" })

diff --git a/test/jalview/ext/jmol/JmolViewerTest.java b/test/jalview/ext/jmol/JmolViewerTest.java
index e451ed2..9dec19b 100644 (file)
--- a/test/jalview/ext/jmol/JmolViewerTest.java
+++ b/test/jalview/ext/jmol/JmolViewerTest.java
@@ -24,6 +24,12 @@ import static org.junit.Assert.assertNotNull;
 import static org.testng.Assert.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.lang.reflect.InvocationTargetException;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
@@ -31,6 +37,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.gui.Preferences;
 import jalview.gui.StructureViewer;
@@ -39,12 +46,6 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileLoader;
 
-import java.lang.reflect.InvocationTargetException;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 @Test(singleThreaded = true)
 public class JmolViewerTest
 {
@@ -74,7 +75,8 @@ public class JmolViewerTest
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = { "Functional" })

diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index 7f9aa9b..c8e30a7 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -100,7 +100,8 @@ public class JalviewChimeraView
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @AfterMethod(alwaysRun = true)

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index 2a768ff..ab2a1d0 100644 (file)
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -75,7 +75,8 @@ public class AlignFrameTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
   }
 
   /**

diff --git a/test/jalview/gui/FeatureSettingsTest.java b/test/jalview/gui/FeatureSettingsTest.java
index 98c04b3..1b988ec 100644 (file)
--- a/test/jalview/gui/FeatureSettingsTest.java
+++ b/test/jalview/gui/FeatureSettingsTest.java
@@ -63,7 +63,8 @@ public class FeatureSettingsTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
   }
 
   /**

diff --git a/test/jalview/gui/FreeUpMemoryTest.java b/test/jalview/gui/FreeUpMemoryTest.java
index 81e37d8..a9eca49 100644 (file)
--- a/test/jalview/gui/FreeUpMemoryTest.java
+++ b/test/jalview/gui/FreeUpMemoryTest.java
@@ -137,7 +137,8 @@ public class FreeUpMemoryTest
 
     doStuffInJalview(f);
 
-    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
 
     checkUsedMemory(MAX_RESIDUAL_HEAP);
   }

diff --git a/test/jalview/gui/QuitHandlerTest.java b/test/jalview/gui/QuitHandlerTest.java
index b257088..299b0d1 100644 (file)
--- a/test/jalview/gui/QuitHandlerTest.java
+++ b/test/jalview/gui/QuitHandlerTest.java
@@ -66,7 +66,8 @@ public class QuitHandlerTest
     // reset mock response
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
     // close desktop windows/frames
-    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
     // reset debug delay
     Jalview2XML.setDebugDelaySave(20);
   }
@@ -79,7 +80,8 @@ public class QuitHandlerTest
     // reset mock response
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
     // close desktop windows/frames
-    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
     // reset debug delay
     Cache.setProperty("DEBUG_DELAY_SAVE", "false");
     Jalview2XML.setDebugDelaySave(3);
@@ -126,7 +128,6 @@ public class QuitHandlerTest
     Assert.assertTrue(end - start < 500,
             "Quit-with-no-save-needed took too long (" + (end - start)
                     + "ms)");
-    Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = { "Functional" }, singleThreaded = true, priority = 10)
@@ -154,8 +155,6 @@ public class QuitHandlerTest
     Assert.assertEquals(response, QResponse.QUIT);
     Assert.assertTrue(end - start > 2900,
             "Quit-whilst-saving was too short (" + (end - start) + "ms)");
-
-    Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = { "Functional" }, singleThreaded = true, priority = 9)
@@ -182,7 +181,6 @@ public class QuitHandlerTest
 
     // if not saved this would be CANCEL_QUIT
     Assert.assertEquals(response, QResponse.QUIT);
-    Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = { "Functional" }, singleThreaded = true, priority = 9)
@@ -207,7 +205,6 @@ public class QuitHandlerTest
 
     // if not saved this would be CANCEL_QUIT
     Assert.assertEquals(response, QResponse.QUIT);
-    Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = { "Functional" }, singleThreaded = true, priority = 1)
@@ -227,7 +224,6 @@ public class QuitHandlerTest
     QResponse response = QuitHandler.getQuitResponse(true);
 
     Assert.assertEquals(response, QResponse.CANCEL_QUIT);
-    Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = { "Functional" }, singleThreaded = true, priority = 1)
@@ -255,7 +251,6 @@ public class QuitHandlerTest
     QResponse response = QuitHandler.getQuitResponse(false);
 
     Assert.assertEquals(response, QResponse.QUIT);
-    Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = { "Functional" }, singleThreaded = true, priority = 11)
@@ -298,7 +293,6 @@ public class QuitHandlerTest
             "Force-Quit-whilst-saving was too long (" + (end - start)
                     + "ms)");
 
-    Desktop.instance.closeAll_actionPerformed(null);
   }
 
 }

diff --git a/test/jalview/gui/SeqPanelTest.java b/test/jalview/gui/SeqPanelTest.java
index f905ef2..701431b 100644 (file)
--- a/test/jalview/gui/SeqPanelTest.java
+++ b/test/jalview/gui/SeqPanelTest.java
@@ -250,7 +250,8 @@ public class SeqPanelTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = "Functional")
@@ -920,7 +921,7 @@ public class SeqPanelTest
     }
     assertEquals(dna.length(), 51200);
     AlignFrame alignFrame = new FileLoader()
-            .LoadFileWaitTillLoaded("dna "+dna, DataSourceType.PASTE);
+            .LoadFileWaitTillLoaded("dna " + dna, DataSourceType.PASTE);
     SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
     AlignViewport av = alignFrame.getViewport();
     av.setScaleAboveWrapped(true);

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 689bd59..1b62ce3 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -24,6 +24,15 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.io.File;
+import java.util.List;
+
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -32,19 +41,11 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureImportSettings.StructureParser;
 
-import java.io.File;
-import java.util.List;
-
-import org.junit.Assert;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 public class AnnotatedPDBFileInputTest
 {
 
@@ -207,8 +208,8 @@ public class AnnotatedPDBFileInputTest
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = { "Functional" })

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 3ca6ed8..0189ef2 100644 (file)
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -24,20 +24,6 @@ import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNotNull;
 import static org.testng.Assert.assertTrue;
 
-import jalview.analysis.CrossRef;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentTest;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.CrossRefAction;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.gui.SequenceFetcher;
-import jalview.project.Jalview2XML;
-import jalview.util.DBRefUtils;
-
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -51,6 +37,19 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import jalview.analysis.CrossRef;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentTest;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.CrossRefAction;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.SequenceFetcher;
+import jalview.project.Jalview2XML;
+import jalview.util.DBRefUtils;
 import junit.extensions.PA;
 
 @Test(singleThreaded = true)
@@ -211,7 +210,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
       }
       else
       {
-        Desktop.instance.closeAll_actionPerformed(null);
+        if (Desktop.instance != null)
+          Desktop.instance.closeAll_actionPerformed(null);
         // recover stored project
         af = new FileLoader(false).LoadFileWaitTillLoaded(
                 savedProjects.get(first).toString(), DataSourceType.FILE);
@@ -278,7 +278,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           }
           else
           {
-            Desktop.instance.closeAll_actionPerformed(null);
+            if (Desktop.instance != null)
+              Desktop.instance.closeAll_actionPerformed(null);
             pass3 = 0;
             // recover stored project
             File storedProject = savedProjects.get(nextxref);
@@ -389,7 +390,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                 }
                 else
                 {
-                  Desktop.instance.closeAll_actionPerformed(null);
+                  if (Desktop.instance != null)
+                    Desktop.instance.closeAll_actionPerformed(null);
                   // recover stored project
                   File storedProject = savedProjects.get(nextnextxref);
                   if (storedProject == null)
@@ -416,7 +418,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                     cra_views2.add(af2.getViewport().getAlignPanel());
                     cra_views2.add(((jalview.gui.AlignViewport) af2
                             .getViewport().getCodingComplement())
-                                    .getAlignPanel());
+                            .getAlignPanel());
 
                   }
                   else
@@ -424,7 +426,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                     // bottom view, then top
                     cra_views2.add(((jalview.gui.AlignViewport) af2
                             .getViewport().getCodingComplement())
-                                    .getAlignPanel());
+                            .getAlignPanel());
                     cra_views2.add(af2.getViewport().getAlignPanel());
                   }
                   Assert.assertEquals(cra_views2.size(), 2);

diff --git a/test/jalview/io/Jalview2xmlBase.java b/test/jalview/io/Jalview2xmlBase.java
index dde23e6..a197340 100644 (file)
--- a/test/jalview/io/Jalview2xmlBase.java
+++ b/test/jalview/io/Jalview2xmlBase.java
@@ -20,6 +20,12 @@
  */
 package jalview.io;
 
+import java.util.Date;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeTest;
+
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentAnnotation;
@@ -27,12 +33,6 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 
-import java.util.Date;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeTest;
-
 public class Jalview2xmlBase
 {
 
@@ -71,7 +71,8 @@ public class Jalview2xmlBase
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @BeforeTest(alwaysRun = true)

diff --git a/test/jalview/io/JalviewExportPropertiesTests.java b/test/jalview/io/JalviewExportPropertiesTests.java
index 1d138c0..59c5986 100644 (file)
--- a/test/jalview/io/JalviewExportPropertiesTests.java
+++ b/test/jalview/io/JalviewExportPropertiesTests.java
@@ -22,14 +22,15 @@ package jalview.io;
 
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.datamodel.SequenceGroup;
-import jalview.gui.AlignFrame;
-import jalview.gui.JvOptionPane;
-
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+
 /**
  * tests which verify that properties and preferences are correctly interpreted
  * when exporting/importing data
@@ -64,7 +65,8 @@ public class JalviewExportPropertiesTests
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
 
   }
 

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 510b21d..094e0ea 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -110,6 +110,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
     JvOptionPane.setInteractiveMode(false);
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
@@ -285,6 +287,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     int origCount = Desktop.getAlignFrames() == null ? 0
             : Desktop.getAlignFrames().length;
+    System.out
+            .println("###### Calling FileLoader().LoadFileWaitTillLoaded");
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -1564,10 +1568,12 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     }
     PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
     String content = ContactMatrix.contactToFloatString(dummyMat);
-    Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1
-    float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength());
-    assertEquals(vals[3][4],paevals[3][4]);
-    
+    Assert.assertTrue(content.contains("\t1.")); // at least one element must be
+                                                 // 1
+    float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
+            sq.getLength(), sq.getLength());
+    assertEquals(vals[3][4], paevals[3][4]);
+
     AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
     al.addAnnotation(paeCm);
     File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
@@ -1598,7 +1604,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
         Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j));
       }
     }
-    
+
   }
 
 }

diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index a3d0a7c..f7d8be5 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -27,6 +27,16 @@ import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.analysis.GeneticCodes;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
@@ -46,17 +56,14 @@ import jalview.schemes.FeatureColour;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
 
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.Test;
-
 public class FeatureRendererTest
 {
+  @BeforeMethod(alwaysRun = true)
+  public void closeAll()
+  {
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
+  }
 
   @Test(groups = "Functional")
   public void testFindAllFeatures()
@@ -618,7 +625,7 @@ public class FeatureRendererTest
   {
     Jalview.main(
             new String[]
-            { "-nonews", "-props", "test/jalview/testProps.jvprops" });
+            { "-nonews", "--props", "test/jalview/testProps.jvprops" });
 
     // codons for MCWHSE
     String cdsSeq = ">cds\nATGtgtTGGcacTCAgaa";

diff --git a/test/jalview/schemes/ColourSchemesTest.java b/test/jalview/schemes/ColourSchemesTest.java
index 58e272d..0184f12 100644 (file)
--- a/test/jalview/schemes/ColourSchemesTest.java
+++ b/test/jalview/schemes/ColourSchemesTest.java
@@ -25,6 +25,14 @@ import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import java.awt.Color;
+import java.util.Iterator;
+import java.util.Map;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
@@ -38,14 +46,6 @@ import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.schemes.ClustalxColourScheme.ClustalColour;
 
-import java.awt.Color;
-import java.util.Iterator;
-import java.util.Map;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 public class ColourSchemesTest
 {
   /*
@@ -192,7 +192,8 @@ public class ColourSchemesTest
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = "Functional")

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index ac8235d..624548f 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -204,7 +204,8 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
   {
     // for some reason 'BeforeMethod' (which should be inherited from
     // Jalview2XmlBase isn't always called)...
-    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
     try
     {
       Thread.sleep(200);