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 jalview.api.AlignViewportI;
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.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import java.util.ArrayList;
import java.util.List;
AlignmentI al;
- AlignViewport testee;
+ AlignmentViewport testee;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
Jalview.main(new String[] { "-nonews", "-props",
"test/jalview/testProps.jvprops" });
+
+ /*
+ * remove any sequence mappings left lying around by other tests
+ */
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ 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
*/
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
- assertEquals(2, ssm.getSequenceMappings().size());
- assertTrue(ssm.getSequenceMappings().contains(acf1));
- assertTrue(ssm.getSequenceMappings().contains(acf2));
+ 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 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",
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();
+ synchronized (this)
+ {
+ while (viewport.getAlignmentConservationAnnotation() != null)
+ {
+ try
+ {
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ }
+ AlignmentAnnotation[] anns = viewport.getAlignment()
.getAlignmentAnnotation();
assertNotNull("No annotations found", anns);
assertEquals("More than one annotation found", 1, anns.length);
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(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
SequenceGroup sg1 = new SequenceGroup();
SequenceGroup sg2 = new SequenceGroup();
SequenceGroup sg3 = new SequenceGroup();
jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport av = af.getViewport();
- Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row.");
+ AlignViewportI av = af.getViewport();
+ Assert.assertNull(av.getOccupancyAnnotation(), "Preference did not disable occupancy row.");
int c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
null, "Occupancy"))
af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
av = af.getViewport();
- Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
+ Assert.assertNotNull(av.getOccupancyAnnotation(), "Preference did not enable occupancy row.");
c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
- null, av.getAlignmentGapAnnotation().label))
+ null, av.getOccupancyAnnotation().label))
{
c++;
}
;
Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetConsensusSeq()
+ {
+ /*
+ * A-C
+ * A-C
+ * A-D
+ * --D
+ * consensus expected to be A-C
+ */
+ String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
+ DataSourceType.PASTE);
+ AlignmentViewport testme = af.getViewport();
+ SequenceI cons = testme.getConsensusSeq();
+ assertEquals("A-C", cons.getSequenceAsString());
+ }
+ @Test(groups = { "Functional" })
+ public void testHideRevealSequences()
+ {
+ ViewportRanges ranges = testee.getRanges();
+ assertEquals(3, al.getHeight());
+ assertEquals(0, ranges.getStartSeq());
+ assertEquals(2, ranges.getEndSeq());
+
+ /*
+ * hide first sequence
+ */
+ testee.hideSequence(new SequenceI[] { al.getSequenceAt(0) });
+ assertEquals(2, al.getHeight());
+ assertEquals(0, ranges.getStartSeq());
+ assertEquals(1, ranges.getEndSeq());
+
+ /*
+ * reveal hidden sequences above the first
+ */
+ testee.showSequence(0);
+ assertEquals(3, al.getHeight());
+ assertEquals(0, ranges.getStartSeq());
+ assertEquals(2, ranges.getEndSeq());
+
+ /*
+ * hide first and third sequences
+ */
+ testee.hideSequence(new SequenceI[] { al.getSequenceAt(0),
+ al.getSequenceAt(2) });
+ assertEquals(1, al.getHeight());
+ assertEquals(0, ranges.getStartSeq());
+ assertEquals(0, ranges.getEndSeq());
+
+ /*
+ * reveal all hidden sequences
+ */
+ testee.showAllHiddenSeqs();
+ assertEquals(3, al.getHeight());
+ assertEquals(0, ranges.getStartSeq());
+ assertEquals(2, ranges.getEndSeq());
}
}
git://source.jalview.org / jalview.git / blobdiff