import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
+import jalview.structure.StructureImportSettings;
import jalview.viewmodel.AlignmentViewport;
import java.io.File;
import java.util.ArrayList;
+import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Jalview.main(new String[] { "-props",
- "test/jalview/io/testProps.jvprops" });
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+
+ /*
+ * set news feed last read to a future time to ensure no
+ * 'unread' news item is displayed
+ */
+ Date oneHourFromNow = new Date(System.currentTimeMillis() + 3600 * 1000);
+ Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
+
+ Jalview.main(new String[] {});
}
/**
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.instance.closeAll_actionPerformed(null);
}
int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
@Test(groups = { "Functional" })
public void viewRefPdbAnnotation() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
- Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("ADD_SS_ANN",
- Boolean.TRUE.toString());
+ // TODO: Make this pass without setting StructureParser.JALVIEW_PARSER
+ // StructureImportSettings
+ // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
+ StructureImportSettings.setProcessSecondaryStructure(true);
+ StructureImportSettings.setVisibleChainAnnotation(true);
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
}
/**
- * test store and recovery of expanded views - currently this is disabled
- * since the Desktop.explodeViews method doesn't seem to result in the views
- * being expanded to distinct align frames when executed programmatically.
+ * test store and recovery of expanded views
*
* @throws Exception
*/
@Test(groups = { "Functional" }, enabled = true)
public void testStoreAndRecoverExpandedviews() throws Exception
{
+ Desktop.instance.closeAll_actionPerformed(null);
+
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
+ Assert.assertEquals(Desktop.getAlignFrames().length, 1);
String afid = af.getViewport().getSequenceSetId();
- {
- final AlignFrame xaf = af;
- af = null;
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- Desktop.instance.explodeViews(xaf);
- }
- }).start();
- Thread.sleep(1000);
- }
- // int times = 0;
- // while (++times < 5 && Desktop.getAlignFrames().length < )
- // {
- // Thread.sleep(300);
- // }
+
+ // check FileLoader returned a reference to the one alignFrame that is
+ // actually on the Desktop
+ assertTrue(
+ "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window",
+ af == Desktop.getAlignFrameFor(af.getViewport()));
+
+ Desktop.explodeViews(af);
+
int oldviews = Desktop.getAlignFrames().length;
Assert.assertEquals(Desktop.getAlignFrames().length,
Desktop.getAlignmentPanels(afid).length);
hidden.size(), hs.getSize());
}
}
+
+ /**
+ * Test save and reload of PDBEntry in Jalview project
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverPDBEntry() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ String exampleFile = "examples/3W5V.pdb";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
+ DataSourceType.FILE);
+ assertTrue("Didn't read in the example file correctly.", af != null);
+ String afid = af.getViewport().getSequenceSetId();
+
+ AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid);
+ System.out.println();
+ AlignmentViewPanel ap = alignPanels[0];
+ String tfileBase = new File(".").getAbsolutePath().replace(".", "");
+ String testFile = tfileBase + exampleFile;
+ AlignmentI alignment = ap.getAlignment();
+ System.out.println("blah");
+ SequenceI[] seqs = alignment.getSequencesArray();
+ Assert.assertNotNull(seqs[0]);
+ Assert.assertNotNull(seqs[1]);
+ Assert.assertNotNull(seqs[2]);
+ Assert.assertNotNull(seqs[3]);
+ Assert.assertNotNull(seqs[0].getDatasetSequence());
+ Assert.assertNotNull(seqs[1].getDatasetSequence());
+ Assert.assertNotNull(seqs[2].getDatasetSequence());
+ Assert.assertNotNull(seqs[3].getDatasetSequence());
+ PDBEntry[] pdbEntries = new PDBEntry[4];
+ pdbEntries[0] = new PDBEntry("3W5V", "A", null, testFile);
+ pdbEntries[1] = new PDBEntry("3W5V", "B", null, testFile);
+ pdbEntries[2] = new PDBEntry("3W5V", "C", null, testFile);
+ pdbEntries[3] = new PDBEntry("3W5V", "D", null, testFile);
+ Assert.assertTrue(seqs[0].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[0]));
+ Assert.assertTrue(seqs[1].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[1]));
+ Assert.assertTrue(seqs[2].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[2]));
+ Assert.assertTrue(seqs[3].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[3]));
+
+ File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ Assert.fail("Didn't save the state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+
+ AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
+ tfile.getAbsolutePath(), DataSourceType.FILE);
+ String rfid = restoredFrame.getViewport().getSequenceSetId();
+ AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
+ AlignmentViewPanel rap = rAlignPanels[0];
+ AlignmentI rAlignment = rap.getAlignment();
+ System.out.println("blah");
+ SequenceI[] rseqs = rAlignment.getSequencesArray();
+ Assert.assertNotNull(rseqs[0]);
+ Assert.assertNotNull(rseqs[1]);
+ Assert.assertNotNull(rseqs[2]);
+ Assert.assertNotNull(rseqs[3]);
+ Assert.assertNotNull(rseqs[0].getDatasetSequence());
+ Assert.assertNotNull(rseqs[1].getDatasetSequence());
+ Assert.assertNotNull(rseqs[2].getDatasetSequence());
+ Assert.assertNotNull(rseqs[3].getDatasetSequence());
+
+ // The Asserts below are expected to fail until the PDB chainCode is
+ // recoverable from a Jalview projects
+ Assert.assertTrue(rseqs[0].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[0]));
+ Assert.assertTrue(rseqs[1].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[1]));
+ Assert.assertTrue(rseqs[2].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[2]));
+ Assert.assertTrue(rseqs[3].getDatasetSequence().getAllPDBEntries()
+ .get(0).equals(pdbEntries[3]));
+ }
}
git://source.jalview.org / jalview.git / blobdiff