merge from develop

[jalview.git] / test / jalview / ext / rbvi / chimera / JalviewChimeraView.java

diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index 0c5d7fa..34e07f2 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -1,10 +1,13 @@
 package jalview.ext.rbvi.chimera;
 
+import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.Preferences;
 import jalview.gui.StructureViewer;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.FormatAdapter;
@@ -13,6 +16,7 @@ import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+@Test(singleThreaded = true)
 public class JalviewChimeraView
 {
 
@@ -23,7 +27,9 @@ public class JalviewChimeraView
   public static void setUpBeforeClass() throws Exception
   {
     jalview.bin.Jalview.main(new String[]
-    { "-noquestionnaire -nonews -props", "test/src/jalview/ext/rbvi/chimera/testProps.jvprops" });
+ {
+        "-noquestionnaire -nonews -props",
+        "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
   }
 
   /**
@@ -32,94 +38,50 @@ public class JalviewChimeraView
   @AfterClass
   public static void tearDownAfterClass() throws Exception
   {
-    try
-    {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-    } catch (Exception e)
-    {
-      // ignore NullPointerException thrown by JMol
-    }
-
-  }
-
-  @Test(groups ={ "Functional" })
-  public void testSingleSeqViewJMol()
-  {
-    String inFile = "examples/1gaq.txt";
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, FormatAdapter.FILE);
-    assertTrue("Didn't read input file " + inFile, af != null);
-    for (SequenceI sq : af.getViewport().getAlignment().getSequences())
-    {
-      SequenceI dsq = sq.getDatasetSequence();
-      while (dsq.getDatasetSequence() != null)
-      {
-        dsq = dsq.getDatasetSequence();
-      }
-      if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
-      {
-        for (int q = 0; q < dsq.getPDBId().size(); q++)
-        {
-          final StructureViewer structureViewer = new StructureViewer(af
-                  .getViewport().getStructureSelectionManager());
-          structureViewer.setViewerType(ViewerType.JMOL);
-          JalviewStructureDisplayI jmolViewer = structureViewer
-                  .viewStructures(dsq.getPDBId().elementAt(q),
-                          new SequenceI[]
-                  { sq }, af.getCurrentView().getAlignPanel());
-          /*
-           * Wait for viewer thread to start
-           */
-          try
-          {
-            Thread.sleep(1000);
-          } catch (InterruptedException e)
-          {
-          }
-
-          jmolViewer.closeViewer(true);
-          // todo: break here means only once through this loop?
-          break;
-        }
-        break;
-      }
-    }
   }
 
   @Test(groups ={ "Functional" })
   public void testSingleSeqViewChimera()
   {
+    Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+            ViewerType.CHIMERA.name());
     String inFile = "examples/1gaq.txt";
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
             inFile, FormatAdapter.FILE);
     assertTrue("Didn't read input file " + inFile, af != null);
     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
     {
+      System.out.println("** sq=" + sq.getName());
       SequenceI dsq = sq.getDatasetSequence();
       while (dsq.getDatasetSequence() != null)
       {
         dsq = dsq.getDatasetSequence();
       }
-      if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
+      if (dsq.getAllPDBEntries() != null && dsq.getAllPDBEntries().size() > 0)
       {
-        for (int q = 0; q < dsq.getPDBId().size(); q++)
+        for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
         {
           final StructureViewer structureViewer = new StructureViewer(af
                   .getViewport().getStructureSelectionManager());
           structureViewer.setViewerType(ViewerType.CHIMERA);
           JalviewStructureDisplayI chimeraViewer = structureViewer
-                  .viewStructures(dsq.getPDBId().elementAt(q),
+                  .viewStructures(dsq.getAllPDBEntries().elementAt(q),
                           new SequenceI[]
                           { sq }, af.getCurrentView().getAlignPanel());
           /*
-           * Wait for viewer thread to start
+           * Wait for viewer load thread to complete
            */
-          try
-          {
-            Thread.sleep(1000);
-          } catch (InterruptedException e)
+          while (!chimeraViewer.getBinding().isFinishedInit())
           {
+            try
+            {
+              Thread.sleep(500);
+            } catch (InterruptedException e)
+            {
+            }
           }
+          assertEquals(1, chimeraViewer.getBinding().getPdbCount());
           chimeraViewer.closeViewer(true);
           // todo: break here means only once through this loop?
           break;