Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / test / jalview / ext / jmol / JmolViewerTest.java

diff --git a/test/jalview/ext/jmol/JmolViewerTest.java b/test/jalview/ext/jmol/JmolViewerTest.java
index 1100000..a74e51d 100644 (file)
--- a/test/jalview/ext/jmol/JmolViewerTest.java
+++ b/test/jalview/ext/jmol/JmolViewerTest.java
@@ -20,34 +20,53 @@
  */
 package jalview.ext.jmol;
 
+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;
+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;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
+import jalview.io.FileFormat;
+import jalview.io.FileLoader;
 
 @Test(singleThreaded = true)
 public class JmolViewerTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * @throws java.lang.Exception
    */
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[] {
-        "-noquestionnaire -nonews -props",
-        "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
+    Jalview.main(
+            new String[]
+            { "--noquestionnaire", "--nonews", "--props",
+                "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
   }
 
   /**
@@ -56,16 +75,18 @@ 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" })
   public void testSingleSeqViewJMol()
   {
-    Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
+    Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+            ViewerType.JMOL.name());
     String inFile = "examples/1gaq.txt";
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, DataSourceType.FILE);
+    AlignFrame af = new jalview.io.FileLoader()
+            .LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
     assertTrue("Didn't read input file " + inFile, af != null);
     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
     {
@@ -79,13 +100,13 @@ public class JmolViewerTest
       {
         for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
         {
-          final StructureViewer structureViewer = new StructureViewer(af
-                  .getViewport().getStructureSelectionManager());
+          final StructureViewer structureViewer = new StructureViewer(
+                  af.getViewport().getStructureSelectionManager());
           structureViewer.setViewerType(ViewerType.JMOL);
           JalviewStructureDisplayI jmolViewer = structureViewer
                   .viewStructures(dsq.getAllPDBEntries().elementAt(q),
-                          new SequenceI[] { sq }, af.getCurrentView()
-                                  .getAlignPanel());
+                          new SequenceI[]
+                          { sq }, af.getCurrentView().getAlignPanel());
           /*
            * Wait for viewer load thread to complete
            */
@@ -107,4 +128,87 @@ public class JmolViewerTest
       }
     }
   }
+
+  @Test(groups = { "Functional" })
+  public void testAddStrToSingleSeqViewJMol()
+          throws InvocationTargetException, InterruptedException
+  {
+    Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+            ViewerType.JMOL.name());
+    String inFile = "examples/1gaq.txt";
+    AlignFrame af = new jalview.io.FileLoader(true)
+            .LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
+    assertTrue("Didn't read input file " + inFile, af != null);
+    // show a structure for 4th Sequence
+    SequenceI sq1 = af.getViewport().getAlignment().getSequences().get(0);
+    final StructureViewer structureViewer = new StructureViewer(
+            af.getViewport().getStructureSelectionManager());
+    structureViewer.setViewerType(ViewerType.JMOL);
+    JalviewStructureDisplayI jmolViewer = structureViewer.viewStructures(
+            sq1.getDatasetSequence().getAllPDBEntries().elementAt(0),
+            new SequenceI[]
+            { sq1 }, af.getCurrentView().getAlignPanel());
+    /*
+     * Wait for viewer load thread to complete
+     */
+    try
+    {
+      while (!jmolViewer.getBinding().isFinishedInit())
+      {
+        Thread.sleep(500);
+      }
+    } catch (InterruptedException e)
+    {
+    }
+
+    assertTrue(jmolViewer.isVisible());
+
+    // add another pdb file and add it to view
+    final String _inFile = "examples/3W5V.pdb";
+    inFile = _inFile;
+    FileLoader fl = new FileLoader();
+    fl.LoadFile(af.getCurrentView(), _inFile, DataSourceType.FILE,
+            FileFormat.PDB);
+    try
+    {
+      int time = 0;
+      do
+      {
+        Thread.sleep(50); // hope we can avoid race condition
+
+      } while (++time < 30
+              && af.getViewport().getAlignment().getHeight() == 3);
+    } catch (Exception q)
+    {
+    }
+    ;
+    assertTrue("Didn't paste additional structure" + inFile,
+            af.getViewport().getAlignment().getHeight() > 3);
+    SequenceI sq2 = af.getViewport().getAlignment().getSequenceAt(3);
+    PDBEntry pdbe = sq2.getDatasetSequence().getAllPDBEntries().get(0);
+    assertTrue(pdbe.getFile().contains(inFile));
+    structureViewer.viewStructures(pdbe, new SequenceI[] { sq2 },
+            af.alignPanel);
+    /*
+     * Wait for viewer load thread to complete
+     */
+    try
+    {
+      while (structureViewer.isBusy())
+      {
+        Thread.sleep(500);
+      }
+    } catch (InterruptedException e)
+    {
+    }
+    assertEquals(jmolViewer.getBinding().getPdbCount(), 2);
+    String mouseOverTest = "[GLY]293:A.CA/2.1 #2164";
+    ((JalviewJmolBinding) jmolViewer.getBinding()).mouseOverStructure(2164,
+            mouseOverTest);
+    SearchResultsI highlight = af.alignPanel.getSeqPanel()
+            .getLastSearchResults();
+    assertNotNull("Didn't find highlight from second structure mouseover",
+            highlight.getResults(sq2, sq2.getStart(), sq2.getEnd()));
+  }
+
 }