From aab90764770d53615070fab825326c5cbc0e263c Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 5 Apr 2018 21:49:38 +0100
Subject: [PATCH] JAL-2945 failing test for structure mapping

---
 test/jalview/ext/jmol/JmolViewerTest.java |   89 +++++++++++++++++++++++++++++
 1 file changed, 89 insertions(+)

diff --git a/test/jalview/ext/jmol/JmolViewerTest.java b/test/jalview/ext/jmol/JmolViewerTest.java
index a1f2344..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;
@@ -32,6 +36,10 @@ 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.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
@@ -119,5 +127,86 @@ 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()));
+  }
 
 }
-- 
1.7.10.2