X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=20b4988f01fb0d477f8379e4ad6f332a077cd0e1;hb=53b2ec17b88081e402f60deab2723750bc4867d1;hp=812fd8ff5e6e63436f7994fce03ee6751e357237;hpb=5779b71c22d85070cbb59aa51a612d03f9744cc3;p=jalview.git diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index 812fd8f..20b4988 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -23,18 +23,18 @@ package jalview.gui; 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.bin.Cache; +import jalview.bin.Instance; import jalview.bin.Jalview; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; 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; @@ -42,6 +42,7 @@ import jalview.datamodel.SequenceGroup; 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; @@ -80,7 +81,7 @@ public class AlignViewportTest * remove any sequence mappings left lying around by other tests */ StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Instance.getDesktop()); ssm.resetAll(); } @@ -96,57 +97,6 @@ public class AlignViewportTest 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 @@ -179,7 +129,7 @@ public class AlignViewportTest * mappings */ StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Instance.getDesktop()); List sequenceMappings = ssm.getSequenceMappings(); assertEquals(2, sequenceMappings.size()); assertTrue(sequenceMappings.contains(acf1)); @@ -201,10 +151,10 @@ public class AlignViewportTest @Test(groups = { "Functional" }) public void testDeregisterMapping_withNoReference() { - Desktop d = Desktop.instance; + Desktop d = Instance.getDesktop(); assertNotNull(d); StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Instance.getDesktop()); ssm.resetAll(); AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded( @@ -264,10 +214,10 @@ public class AlignViewportTest @Test(groups = { "Functional" }) public void testDeregisterMapping_withReference() { - Desktop d = Desktop.instance; + Desktop d = Instance.getDesktop(); assertNotNull(d); StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Instance.getDesktop()); ssm.resetAll(); AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded( @@ -328,22 +278,39 @@ public class AlignViewportTest * 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(); + 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); @@ -361,15 +328,40 @@ public class AlignViewportTest /* * 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" })