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package jalview.ext.jmol; |
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import static org.junit.Assert.assertNotNull; |
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import static org.testng.Assert.assertEquals; |
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import static org.testng.AssertJUnit.assertTrue; |
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import java.lang.reflect.InvocationTargetException; |
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import org.testng.annotations.AfterClass; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.Test; |
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import jalview.api.structures.JalviewStructureDisplayI; |
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import jalview.bin.Cache; |
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import jalview.bin.Jalview; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SearchResultsI; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AlignFrame; |
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import jalview.gui.Desktop; |
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import jalview.gui.JvOptionPane; |
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import jalview.gui.Preferences; |
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import jalview.gui.StructureViewer; |
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import jalview.gui.StructureViewer.ViewerType; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileFormat; |
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import jalview.io.FileLoader; |
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@Test(singleThreaded = true) |
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| 93.7% |
Uncovered Elements: 5 (79) |
Complexity: 19 |
Complexity Density: 0.33 |
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public class JmolViewerTest |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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} |
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@throws |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@BeforeClass(alwaysRun = true)... |
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public static void setUpBeforeClass() throws Exception |
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{ |
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Jalview.main( |
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new String[] |
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{ "--noquestionnaire", "--nonews", "--props", |
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"test/jalview/ext/rbvi/chimera/testProps.jvprops" }); |
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} |
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@throws |
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| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 1 |
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@AfterClass(alwaysRun = true)... |
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public static void tearDownAfterClass() throws Exception |
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{ |
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if (Desktop.instance != null) |
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Desktop.instance.closeAll_actionPerformed(null); |
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} |
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| 85.2% |
Uncovered Elements: 4 (27) |
Complexity: 7 |
Complexity Density: 0.37 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testSingleSeqViewJMol() |
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{ |
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Cache.setProperty(Preferences.STRUCTURE_DISPLAY, |
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ViewerType.JMOL.name()); |
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String inFile = "examples/1gaq.txt"; |
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AlignFrame af = new jalview.io.FileLoader() |
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.LoadFileWaitTillLoaded(inFile, DataSourceType.FILE); |
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assertTrue("Didn't read input file " + inFile, af != null); |
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for (SequenceI sq : af.getViewport().getAlignment().getSequences()) |
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{ |
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SequenceI dsq = sq.getDatasetSequence(); |
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while (dsq.getDatasetSequence() != null) |
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{ |
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dsq = dsq.getDatasetSequence(); |
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} |
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if (dsq.getAllPDBEntries() != null |
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&& dsq.getAllPDBEntries().size() > 0) |
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{ |
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for (int q = 0; q < dsq.getAllPDBEntries().size(); q++) |
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{ |
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final StructureViewer structureViewer = new StructureViewer( |
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af.getViewport().getStructureSelectionManager()); |
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structureViewer.setViewerType(ViewerType.JMOL); |
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JalviewStructureDisplayI jmolViewer = structureViewer |
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.viewStructures(dsq.getAllPDBEntries().elementAt(q), |
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new SequenceI[] |
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{ sq }, af.getCurrentView().getAlignPanel()); |
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try |
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{ |
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while (!jmolViewer.getBinding().isFinishedInit()) |
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{ |
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Thread.sleep(500); |
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} |
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} catch (InterruptedException e) |
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{ |
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} |
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jmolViewer.closeViewer(true); |
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break; |
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} |
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break; |
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} |
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} |
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} |
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| 100% |
Uncovered Elements: 0 (40) |
Complexity: 8 |
Complexity Density: 0.24 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testAddStrToSingleSeqViewJMol() |
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throws InvocationTargetException, InterruptedException |
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{ |
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Cache.setProperty(Preferences.STRUCTURE_DISPLAY, |
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ViewerType.JMOL.name()); |
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String inFile = "examples/1gaq.txt"; |
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AlignFrame af = new jalview.io.FileLoader(true) |
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.LoadFileWaitTillLoaded(inFile, DataSourceType.FILE); |
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assertTrue("Didn't read input file " + inFile, af != null); |
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SequenceI sq1 = af.getViewport().getAlignment().getSequences().get(0); |
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final StructureViewer structureViewer = new StructureViewer( |
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af.getViewport().getStructureSelectionManager()); |
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structureViewer.setViewerType(ViewerType.JMOL); |
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JalviewStructureDisplayI jmolViewer = structureViewer.viewStructures( |
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sq1.getDatasetSequence().getAllPDBEntries().elementAt(0), |
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new SequenceI[] |
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{ sq1 }, af.getCurrentView().getAlignPanel()); |
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try |
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{ |
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while (!jmolViewer.getBinding().isFinishedInit()) |
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{ |
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Thread.sleep(500); |
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} |
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} catch (InterruptedException e) |
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{ |
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} |
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assertTrue(jmolViewer.isVisible()); |
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final String _inFile = "examples/3W5V.pdb"; |
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inFile = _inFile; |
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FileLoader fl = new FileLoader(); |
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fl.LoadFile(af.getCurrentView(), _inFile, DataSourceType.FILE, |
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FileFormat.PDB); |
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try |
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{ |
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int time = 0; |
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do |
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{ |
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Thread.sleep(50); |
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} while (++time < 30 |
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&& af.getViewport().getAlignment().getHeight() == 3); |
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} catch (Exception q) |
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{ |
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} |
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; |
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assertTrue("Didn't paste additional structure" + inFile, |
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af.getViewport().getAlignment().getHeight() > 3); |
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SequenceI sq2 = af.getViewport().getAlignment().getSequenceAt(3); |
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PDBEntry pdbe = sq2.getDatasetSequence().getAllPDBEntries().get(0); |
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assertTrue(pdbe.getFile().contains(inFile)); |
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structureViewer.viewStructures(pdbe, new SequenceI[] { sq2 }, |
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af.alignPanel); |
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try |
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{ |
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while (structureViewer.isBusy()) |
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{ |
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Thread.sleep(500); |
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} |
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} catch (InterruptedException e) |
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{ |
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} |
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assertEquals(jmolViewer.getBinding().getPdbCount(), 2); |
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String mouseOverTest = "[GLY]293:A.CA/2.1 #2164"; |
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((JalviewJmolBinding) jmolViewer.getBinding()).mouseOverStructure(2164, |
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mouseOverTest); |
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SearchResultsI highlight = af.alignPanel.getSeqPanel() |
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.getLastSearchResults(); |
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assertNotNull("Didn't find highlight from second structure mouseover", |
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highlight.getResults(sq2, sq2.getStart(), sq2.getEnd())); |
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} |
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} |