JAL-1772 non-functional test added. not doing any more work for 2.9 release

[jalview.git] / test / jalview / io / Jalview2xmlTests.java

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index b3e37f4..982be0c 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -22,14 +22,6 @@ package jalview.io;
 
 import static org.testng.AssertJUnit.assertTrue;
 
-import java.io.File;
-
-import org.testng.Assert;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
@@ -38,16 +30,25 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 
+import java.io.File;
+
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 public class Jalview2xmlTests
 {
 
   /**
    * @throws java.lang.Exception
    */
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
     jalview.bin.Jalview.main(new String[]
@@ -83,7 +84,7 @@ public class Jalview2xmlTests
     return numdsann;
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testRNAStructureRecovery() throws Exception
   {
     String inFile = "examples/RF00031_folded.stk";
@@ -118,7 +119,7 @@ public class Jalview2xmlTests
             af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testTCoffeeScores() throws Exception
   {
     String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
@@ -154,7 +155,7 @@ public class Jalview2xmlTests
             .println("T-Coffee score shading successfully recovered from project.");
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testColourByAnnotScores() throws Exception
   {
     String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
@@ -240,7 +241,7 @@ public class Jalview2xmlTests
             .println("Per sequence (Group) colourscheme successfully applied and recovered.");
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void gatherViewsHere() throws Exception
   {
     int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
@@ -253,7 +254,7 @@ public class Jalview2xmlTests
 
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void viewRefPdbAnnotation() throws Exception
   {
     Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
@@ -315,7 +316,7 @@ public class Jalview2xmlTests
     
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testCopyViewSettings() throws Exception
   {
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
@@ -347,4 +348,68 @@ public class Jalview2xmlTests
             .getViewStyle()));
 
   }
+
+  /**
+   * test store and recovery of expanded views - 
+   * currently this is disabled since the 
+   * Desktop.explodeViews method doesn't seem 
+   * to result in the views being expanded to 
+   * distinct align frames when executed programmatically.
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" }, enabled = false)
+  public void testStoreAndRecoverExpandedviews() throws Exception
+  {
+    AlignFrame af = new jalview.io.FileLoader()
+            .LoadFileWaitTillLoaded(
+            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+    assertTrue("Didn't read in the example file correctly.", af != null);
+    String afid = af.getViewport().getSequenceSetId();
+    {
+      final AlignFrame xaf = af;
+      af = null;
+      new Thread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+          Desktop.instance.explodeViews(xaf);
+      }
+      }).start();
+      Thread.sleep(1000);
+    }
+    // int times = 0;
+    // while (++times < 5 && Desktop.getAlignFrames().length < )
+    // {
+    // Thread.sleep(300);
+    // }
+    int oldviews = Desktop.getAlignFrames().length;
+    Assert.assertEquals(
+            Desktop.getAlignFrames().length,
+            Desktop.getAlignmentPanels(afid).length);
+    File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
+    try
+    {
+      new Jalview2XML(false).saveState(tfile);
+    } catch (Error e)
+    {
+      Assert.fail("Didn't save the expanded view state", e);
+    } catch (Exception e)
+    {
+      Assert.fail("Didn't save the expanded view state", e);
+    }
+    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.getAlignFrames() != null)
+    {
+      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+    }
+    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+            tfile.getAbsolutePath(), FormatAdapter.FILE);
+    Assert.assertNotNull(af);
+    Assert.assertEquals(Desktop.getAlignFrames().length,
+            Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
+    Assert.assertEquals(oldviews,
+            Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
+  }
+
 }