file format enum wip changes

[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 858806b..2a6dc73 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -1,82 +1,113 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.rbvi.chimera;
 
-import static org.junit.Assert.assertTrue;
-import jalview.datamodel.PDBEntry;
+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;
+import jalview.io.DataSourceType;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
+@Test(singleThreaded = true)
 public class JalviewChimeraView
 {
 
   /**
    * @throws java.lang.Exception
    */
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[]
-    { "-noquestionnaire -nonews -props", "test/src/jalview/ext/rbvi/chimera/testProps.jvprops" });
+    jalview.bin.Jalview.main(new String[] {
+        "-noquestionnaire -nonews -props",
+        "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
   }
 
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-
   }
 
-
-  @Test
-  public void testSingleSeqView()
+  @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);
+            inFile, DataSourceType.FILE);
     assertTrue("Didn't read input file " + inFile, af != null);
-    for (SequenceI sq:af.getViewport().getAlignment().getSequences())
+    for (SequenceI sq : af.getViewport().getAlignment().getSequences())
     {
-      SequenceI dsq=sq.getDatasetSequence();
-      while (dsq.getDatasetSequence()!=null)
+      System.out.println("** sq=" + sq.getName());
+      SequenceI dsq = sq.getDatasetSequence();
+      while (dsq.getDatasetSequence() != null)
       {
-        dsq=dsq.getDatasetSequence();
+        dsq = dsq.getDatasetSequence();
       }
-      if (dsq.getPDBId()!=null && dsq.getPDBId().size()>0) {
-        for (int q=0;q<dsq.getPDBId().size();q++) 
+      if (dsq.getAllPDBEntries() != null
+              && dsq.getAllPDBEntries().size() > 0)
+      {
+        for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
         {
-          new StructureViewer(af.getViewport()
-                  .getStructureSelectionManager()).viewStructures(
-                  ViewerType.JMOL,
-                  af.getCurrentView().getAlignPanel(),
-                  new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
-                  new SequenceI[][] { new SequenceI[] { sq } });
-
-          new StructureViewer(af.getViewport()
-                  .getStructureSelectionManager()).viewStructures(
-                  ViewerType.CHIMERA,
-                  af.getCurrentView().getAlignPanel(),
-                  new PDBEntry[] { (PDBEntry)dsq.getPDBId().elementAt(q) },
-                  new SequenceI[][] { new SequenceI[] { sq } });
+          final StructureViewer structureViewer = new StructureViewer(af
+                  .getViewport().getStructureSelectionManager());
+          structureViewer.setViewerType(ViewerType.CHIMERA);
+          JalviewStructureDisplayI chimeraViewer = structureViewer
+                  .viewStructures(dsq.getAllPDBEntries().elementAt(q),
+                          new SequenceI[] { sq }, af.getCurrentView()
+                                  .getAlignPanel());
+          /*
+           * Wait for viewer load thread to complete
+           */
+          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;
         }
         break;
       }
-   }
-    // try {
-      // why?
-//      Thread.sleep(200000);
-//    } catch (InterruptedException q)
-//    {
-    // }
+    }
   }
 }