import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNotSame;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.api.AlignCalcWorkerI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.util.MapList;
import jalview.viewmodel.ViewportRanges;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
+import jalview.workers.AlignCalcManager;
public class AlignViewportTest
{
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- Jalview.main(new String[] { "-nonews", "-props",
+ Jalview.main(new String[] {
+ //"-jabaws", "none",
+ "-nonews", "-props",
"test/jalview/testProps.jvprops" });
+
+ /*
+ * remove any sequence mappings left lying around by other tests
+ */
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.getInstance());
+ ssm.resetAll();
}
@BeforeMethod(alwaysRun = true)
testee = new AlignViewport(al);
}
- @Test(groups = { "Functional" })
- public void testCollateForPdb()
- {
- // JBP: What behaviour is this supposed to test ?
- /*
- * Set up sequence pdb ids
- */
- PDBEntry pdb1 = new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb");
- PDBEntry pdb2 = new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb");
- PDBEntry pdb3 = new PDBEntry("3ABC", "D", Type.PDB, "3ABC.pdb");
-
- /*
- * seq1 and seq3 refer to 1abcB, seq2 to 2abcC, none to 3abcD
- */
- al.getSequenceAt(0).getDatasetSequence()
- .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
- al.getSequenceAt(2).getDatasetSequence()
- .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
- al.getSequenceAt(1).getDatasetSequence()
- .addPDBId(new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
- /*
- * Add a second chain PDB xref to Seq2 - should not result in a duplicate in
- * the results
- */
- al.getSequenceAt(1).getDatasetSequence()
- .addPDBId(new PDBEntry("2ABC", "D", Type.PDB, "2ABC.pdb"));
- /*
- * Seq3 refers to 3abc - this does not match 3ABC (as the code stands)
- */
- al.getSequenceAt(2).getDatasetSequence()
- .addPDBId(new PDBEntry("3abc", "D", Type.PDB, "3ABC.pdb"));
-
- /*
- * run method under test
- */
- SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2,
- pdb3 });
-
- // seq1 and seq3 refer to PDBEntry[0]
- assertEquals(2, seqs[0].length);
- assertSame(al.getSequenceAt(0), seqs[0][0]);
- assertSame(al.getSequenceAt(2), seqs[0][1]);
-
- // seq2 refers to PDBEntry[1]
- assertEquals(1, seqs[1].length);
- assertSame(al.getSequenceAt(1), seqs[1][0]);
-
- // no sequence refers to PDBEntry[2]
- assertEquals(0, seqs[2].length);
- }
-
/**
* Test that a mapping is not deregistered when a second view is closed but
* the first still holds a reference to the mapping
* mappings
*/
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- assertEquals(2, ssm.getSequenceMappings().size());
- assertTrue(ssm.getSequenceMappings().contains(acf1));
- assertTrue(ssm.getSequenceMappings().contains(acf2));
+ .getStructureSelectionManager(Desktop.getInstance());
+ List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
+ assertEquals(2, sequenceMappings.size());
+ assertTrue(sequenceMappings.contains(acf1));
+ assertTrue(sequenceMappings.contains(acf2));
/*
* Close the second view. Verify that mappings are not removed as the first
* view still holds a reference to them.
*/
af1.closeMenuItem_actionPerformed(false);
- assertEquals(2, ssm.getSequenceMappings().size());
- assertTrue(ssm.getSequenceMappings().contains(acf1));
- assertTrue(ssm.getSequenceMappings().contains(acf2));
+ assertEquals(2, sequenceMappings.size());
+ assertTrue(sequenceMappings.contains(acf1));
+ assertTrue(sequenceMappings.contains(acf2));
}
/**
@Test(groups = { "Functional" })
public void testDeregisterMapping_withNoReference()
{
- Desktop d = Desktop.instance;
+ Desktop d = Desktop.getInstance();
assertNotNull(d);
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.resetAll();
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
@Test(groups = { "Functional" })
public void testDeregisterMapping_withReference()
{
- Desktop d = Desktop.instance;
+ Desktop d = Desktop.getInstance();
assertNotNull(d);
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.resetAll();
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
* Test for JAL-1306 - conservation thread should run even when only Quality
* (and not Conservation) is enabled in Preferences
*/
- @Test(groups = { "Functional" })
+ @Test(groups = { "Functional" }, timeOut=2000)
public void testUpdateConservation_qualityOnly()
{
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Cache.setPropertyNoSave("SHOW_QUALITY",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave("SHOW_CONSERVATION",
Boolean.FALSE.toString());
- Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
+ Cache.setPropertyNoSave("SHOW_OCCUPANCY",
Boolean.FALSE.toString());
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Cache.setPropertyNoSave("SHOW_IDENTITY",
Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignmentAnnotation[] anns = af.viewport.getAlignment()
+
+ /*
+ * wait for Conservation thread to complete
+ */
+ AlignViewport viewport = af.getViewport();
+ waitForCalculations(viewport);
+ AlignmentAnnotation[] anns = viewport.getAlignment()
.getAlignmentAnnotation();
assertNotNull("No annotations found", anns);
assertEquals("More than one annotation found", 1, anns.length);
assertTrue("No quality value in column 1", annotations[0].value > 10f);
}
+ /**
+ * Wait for consensus etc calculation threads to complete
+ *
+ * @param viewport
+ */
+ protected void waitForCalculations(AlignViewport viewport)
+ {
+ synchronized (this)
+ {
+ System.out.print("waiting...");
+ int n = 3;
+ while (--n >= 0 || viewport.getCalcManager().isWorking())
+ {
+ try
+ {
+ System.out.print(((AlignCalcManager) viewport.getCalcManager()).getQueueLength());
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ System.out.println("...done");
+ }
+ }
+
@Test(groups = { "Functional" })
public void testSetGlobalColourScheme()
{
/*
* test for JAL-2283: don't inadvertently turn on colour by conservation
*/
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Cache.setPropertyNoSave("DEFAULT_COLOUR_PROT", "None");
+ Cache.setPropertyNoSave("SHOW_CONSERVATION",
Boolean.TRUE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
ColourSchemeI cs = new PIDColourScheme();
- af.getViewport().setGlobalColourScheme(cs);
- assertFalse(af.getViewport().getResidueShading()
+ AlignViewport viewport = af.getViewport();
+ viewport.setGlobalColourScheme(cs);
+ assertFalse(viewport.getResidueShading()
.conservationApplied());
+
+ /*
+ * JAL-3201 groups have their own ColourSchemeI instances
+ */
+ AlignmentI aln = viewport.getAlignment();
+ SequenceGroup sg1 = new SequenceGroup();
+ sg1.addSequence(aln.getSequenceAt(0), false);
+ sg1.addSequence(aln.getSequenceAt(2), false);
+ SequenceGroup sg2 = new SequenceGroup();
+ sg2.addSequence(aln.getSequenceAt(1), false);
+ sg2.addSequence(aln.getSequenceAt(3), false);
+ aln.addGroup(sg1);
+ aln.addGroup(sg2);
+ viewport.setColourAppliesToAllGroups(true);
+ viewport.setGlobalColourScheme(new ClustalxColourScheme());
+ ColourSchemeI cs0 = viewport.getGlobalColourScheme();
+ ColourSchemeI cs1 = sg1.getColourScheme();
+ ColourSchemeI cs2 = sg2.getColourScheme();
+ assertTrue(cs0 instanceof ClustalxColourScheme);
+ assertTrue(cs1 instanceof ClustalxColourScheme);
+ assertTrue(cs2 instanceof ClustalxColourScheme);
+ assertNotSame(cs0, cs1);
+ assertNotSame(cs0, cs2);
+ assertNotSame(cs1, cs2);
}
@Test(groups = { "Functional" })
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
DataSourceType.PASTE);
AlignViewport testme = af.getViewport();
+ waitForCalculations(testme);
SequenceI cons = testme.getConsensusSeq();
- assertEquals("A-C", cons.getSequenceAsString());
+ String s = cons.getSequenceAsString();
+ System.out.println("s is " + s);
+
+ assertEquals("A-C", s);
}
@Test(groups = { "Functional" })
git://source.jalview.org / jalview.git / blobdiff