/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
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;
import jalview.gui.Preferences;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.FormatAdapter;
+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;
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" });
}
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ jalview.gui.Desktop.getInstance().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, FormatAdapter.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())
{
{
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
*/
}
}
}
+
+ @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()));
+ }
+
}