X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolViewerTest.java;h=e451ed211ae38b75b0bbc3cfbfe87ccae915bae2;hb=c65c736a21956464c8e0a01e7c3188f8340c4c5f;hp=4a59044fff66153253e2d8c5a533d3a8698aa91f;hpb=f253e64f1512047a6929e4520ff1a613e1adbd2b;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolViewerTest.java b/test/jalview/ext/jmol/JmolViewerTest.java
index 4a59044..e451ed2 100644
--- a/test/jalview/ext/jmol/JmolViewerTest.java
+++ b/test/jalview/ext/jmol/JmolViewerTest.java
@@ -20,11 +20,15 @@
  */
 package jalview.ext.jmol;
 
+import static org.junit.Assert.assertNotNull;
+import static org.testng.Assert.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
 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.JvOptionPane;
@@ -32,8 +36,11 @@ import jalview.gui.Preferences;
 import jalview.gui.StructureViewer;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileLoader;
+
+import java.lang.reflect.InvocationTargetException;
 
-import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -55,8 +62,10 @@ public class JmolViewerTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    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" });
   }
 
   /**
@@ -71,10 +80,11 @@ public class JmolViewerTest
   @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())
     {
@@ -88,13 +98,13 @@ 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
            */
@@ -117,56 +127,86 @@ public class JmolViewerTest
     }
   }
 
-  @Test(groups = { "Functional", "Network" })
-  public void testStructureLoadingViaURL()
+  @Test(groups = { "Functional" })
+  public void testAddStrToSingleSeqViewJMol()
+          throws InvocationTargetException, InterruptedException
   {
-    Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
-    String inFile = "http://www.jalview.org/builds/develop/examples/3W5V.pdb";
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, DataSourceType.URL);
+    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);
-    for (SequenceI sq : af.getViewport().getAlignment().getSequences())
+    // 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
     {
-      SequenceI dsq = sq.getDatasetSequence();
-      while (dsq.getDatasetSequence() != null)
+      while (!jmolViewer.getBinding().isFinishedInit())
       {
-        dsq = dsq.getDatasetSequence();
+        Thread.sleep(500);
       }
-      if (dsq.getAllPDBEntries() != null
-              && dsq.getAllPDBEntries().size() > 0)
+    } 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
       {
-        for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
-        {
-          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());
-          /*
-          * Wait for viewer load thread to complete
-          */
-          try
-          {
-            while (!jmolViewer.getBinding().isFinishedInit())
-            {
-              Thread.sleep(500);
-            }
-          } catch (InterruptedException e)
-          {
-          }
-          // System.out.println(">>>>>>>>>>>>>>>>> "
-          // + jmolViewer.getBinding().getPdbFile());
-          String[] expectedModelFiles = new String[] { "http://www.jalview.org/builds/develop/examples/3W5V.pdb" };
-          String[] actualModelFiles = jmolViewer.getBinding().getStructureFiles();
-          Assert.assertEqualsNoOrder(actualModelFiles, expectedModelFiles);
-          jmolViewer.closeViewer(true);
-          // todo: break here means only once through this loop?
-          break;
-        }
-        break;
+        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()));
   }
+
 }