X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=644761effc0ad1f7ffd6a31b0c781f7c2f86204f;hb=49db0dff1da16c3355b43a41498c1fc93ef47e91;hp=b72852fbcd85d006e7923d077dca26cbf63569a9;hpb=c794c5033adeee182b03a5ea92c0a7495a29661f;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index b72852f..644761e 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -33,12 +33,14 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 
 import javax.swing.JInternalFrame;
 
 import org.testng.Assert;
 import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -96,6 +98,11 @@ import junit.extensions.PA;
 @Test(singleThreaded = true)
 public class Jalview2xmlTests extends Jalview2xmlBase
 {
+  @AfterMethod(alwaysRun = true)
+  public void tearDown()
+  {
+    Desktop.getInstance().closeAll_actionPerformed(null);
+  }
 
   @Override
   @BeforeClass(alwaysRun = true)
@@ -278,9 +285,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
-    assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
+    assertEquals(Desktop.getAlignFrames().length,
+            1 + origCount,
             "Didn't gather the views in the example file.");
-
   }
 
   /**
@@ -412,7 +419,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" }, enabled = true)
   public void testStoreAndRecoverExpandedviews() throws Exception
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
 
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
@@ -440,7 +447,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.fail("Didn't save the expanded view state", e);
     }
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     if (Desktop.getAlignFrames() != null)
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@@ -466,7 +473,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testStoreAndRecoverReferenceSeqSettings() throws Exception
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -505,7 +512,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.fail("Didn't save the expanded view state", e);
     }
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     if (Desktop.getAlignFrames() != null)
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@@ -599,7 +606,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testStoreAndRecoverGroupRepSeqs() throws Exception
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
@@ -674,7 +681,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.fail("Didn't save the expanded view state", e);
     }
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     if (Desktop.getAlignFrames() != null)
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@@ -719,7 +726,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testStoreAndRecoverPDBEntry() throws Exception
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     String exampleFile = "examples/3W5V.pdb";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
             DataSourceType.FILE);
@@ -768,7 +775,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.fail("Didn't save the state", e);
     }
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     if (Desktop.getAlignFrames() != null)
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@@ -806,6 +813,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
               "Mismatch PDBEntry 'Type'");
       Assert.assertNotNull(recov.getFile(),
               "Recovered PDBEntry should have a non-null file entry");
+      Assert.assertEquals(recov.getFile().toLowerCase(Locale.ENGLISH).lastIndexOf("pdb"),recov.getFile().length()-3, "Recovered PDBEntry file should have PDB suffix");
     }
   }
 
@@ -819,7 +827,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testStoreAndRecoverColourThresholds() throws IOException
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
 
@@ -882,7 +890,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             ".jvp");
     tfile.deleteOnExit();
     new Jalview2XML(false).saveState(tfile);
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
             DataSourceType.FILE);
     Assert.assertNotNull(af, "Failed to reload project");
@@ -1077,7 +1085,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testStoreAndRecoverHmmProfile() throws IOException
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
   
@@ -1107,7 +1115,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             ".jvp");
     tfile.deleteOnExit();
     new Jalview2XML(false).saveState(tfile);
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
             DataSourceType.FILE);
     Assert.assertNotNull(af, "Failed to reload project");
@@ -1144,7 +1152,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testMergeDatasetsforManyViews() throws IOException
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
 
     // complex project - one dataset, several views on several alignments
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
@@ -1188,7 +1196,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = "Functional")
   public void testPcaViewAssociation() throws IOException
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     final String PCAVIEWNAME = "With PCA";
     // create a new tempfile
     File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
@@ -1222,10 +1230,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     }
 
     // load again.
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             tempfile.getCanonicalPath(), DataSourceType.FILE);
-    JInternalFrame[] frames = Desktop.instance.getAllFrames();
+    JInternalFrame[] frames = Desktop.getInstance().getAllFrames();
     // PCA and the tabbed alignment view should be the only two windows on the
     // desktop
     assertEquals(frames.length, 2,
@@ -1255,7 +1263,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testStoreAndRecoverGeneLocus() throws Exception
   {
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
             DataSourceType.PASTE);
@@ -1291,7 +1299,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.fail("Didn't save the state", e);
     }
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
   
     new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
             DataSourceType.FILE);