X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=b3c6b2ae1fb9fbe92c5ce1e03c8aa3ecc3c4d9db;hb=efba321f20b819819c0b1cd9c9133d9d1a2ab314;hp=8c540b0bcdb2cf6b21a0a7ea742d5cfe4b8771e8;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index 8c540b0..b3c6b2a 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -23,31 +23,49 @@ 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 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.bin.Cache; +import jalview.bin.Jalview; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.PDBEntry.Type; +import jalview.datamodel.Annotation; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; +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; import jalview.util.MapList; - -import java.util.ArrayList; -import java.util.List; - -import org.testng.annotations.BeforeClass; -import org.testng.annotations.BeforeMethod; -import org.testng.annotations.Test; +import jalview.viewmodel.ViewportRanges; public class AlignViewportTest { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + AlignmentI al; AlignViewport testee; @@ -55,8 +73,16 @@ public class AlignViewportTest @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - jalview.bin.Jalview.main(new String[] { "-props", - "test/jalview/testProps.jvprops" }); + 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) @@ -71,56 +97,6 @@ public class AlignViewportTest testee = new AlignViewport(al); } - @Test(groups = { "Functional" }) - public void testCollateForPdb() - { - /* - * 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 @@ -131,18 +107,20 @@ public class AlignViewportTest /* * alignment with reference to mappings */ - AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded( - ">Seq1\nCAGT\n", DataSourceType.PASTE); + AlignFrame af1 = new FileLoader() + .LoadFileWaitTillLoaded(">Seq1\nCAGT\n", DataSourceType.PASTE); SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0); AlignedCodonFrame acf1 = new AlignedCodonFrame(); - acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 }, - 1, 1)); + acf1.addMap(s1, s1, + new MapList(new int[] + { 1, 4 }, new int[] { 1, 4 }, 1, 1)); AlignedCodonFrame acf2 = new AlignedCodonFrame(); - acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 }, - 1, 1)); + acf2.addMap(s1, s1, + new MapList(new int[] + { 1, 4 }, new int[] { 4, 1 }, 1, 1)); - List mappings = new ArrayList(); + List mappings = new ArrayList<>(); mappings.add(acf1); mappings.add(acf2); af1.getViewport().getAlignment().setCodonFrames(mappings); @@ -154,18 +132,19 @@ public class AlignViewportTest */ StructureSelectionManager ssm = StructureSelectionManager .getStructureSelectionManager(Desktop.instance); - assertEquals(2, ssm.getSequenceMappings().size()); - assertTrue(ssm.getSequenceMappings().contains(acf1)); - assertTrue(ssm.getSequenceMappings().contains(acf2)); + List 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)); } /** @@ -180,30 +159,33 @@ public class AlignViewportTest .getStructureSelectionManager(Desktop.instance); ssm.resetAll(); - AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded( - ">Seq1\nRSVQ\n", DataSourceType.PASTE); - AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded( - ">Seq2\nDGEL\n", DataSourceType.PASTE); + AlignFrame af1 = new FileLoader() + .LoadFileWaitTillLoaded(">Seq1\nRSVQ\n", DataSourceType.PASTE); + AlignFrame af2 = new FileLoader() + .LoadFileWaitTillLoaded(">Seq2\nDGEL\n", DataSourceType.PASTE); SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA"); SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA"); SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0); SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0); // need to be distinct AlignedCodonFrame acf1 = new AlignedCodonFrame(); - acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 }, - new int[] { 1, 12 }, 1, 3)); + acf1.addMap(cs1, s1, + new MapList(new int[] + { 1, 4 }, new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf2 = new AlignedCodonFrame(); - acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 }, - new int[] { 1, 12 }, 1, 3)); + acf2.addMap(cs2, s2, + new MapList(new int[] + { 1, 4 }, new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf3 = new AlignedCodonFrame(); - acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1, - 12 }, 1, 1)); + acf3.addMap(cs2, cs2, + new MapList(new int[] + { 1, 12 }, new int[] { 1, 12 }, 1, 1)); - List mappings1 = new ArrayList(); + List mappings1 = new ArrayList<>(); mappings1.add(acf1); af1.getViewport().getAlignment().setCodonFrames(mappings1); - List mappings2 = new ArrayList(); + List mappings2 = new ArrayList<>(); mappings2.add(acf2); mappings2.add(acf3); af2.getViewport().getAlignment().setCodonFrames(mappings2); @@ -243,31 +225,34 @@ public class AlignViewportTest .getStructureSelectionManager(Desktop.instance); ssm.resetAll(); - AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded( - ">Seq1\nRSVQ\n", DataSourceType.PASTE); - AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded( - ">Seq2\nDGEL\n", DataSourceType.PASTE); + AlignFrame af1 = new FileLoader() + .LoadFileWaitTillLoaded(">Seq1\nRSVQ\n", DataSourceType.PASTE); + AlignFrame af2 = new FileLoader() + .LoadFileWaitTillLoaded(">Seq2\nDGEL\n", DataSourceType.PASTE); SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA"); SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA"); SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0); SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0); // need to be distinct AlignedCodonFrame acf1 = new AlignedCodonFrame(); - acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 }, - new int[] { 1, 12 }, 1, 3)); + acf1.addMap(cs1, s1, + new MapList(new int[] + { 1, 4 }, new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf2 = new AlignedCodonFrame(); - acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 }, - new int[] { 1, 12 }, 1, 3)); + acf2.addMap(cs2, s2, + new MapList(new int[] + { 1, 4 }, new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf3 = new AlignedCodonFrame(); - acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1, - 12 }, 1, 1)); + acf3.addMap(cs2, cs2, + new MapList(new int[] + { 1, 12 }, new int[] { 1, 12 }, 1, 1)); - List mappings1 = new ArrayList(); + List mappings1 = new ArrayList<>(); mappings1.add(acf1); mappings1.add(acf2); af1.getViewport().getAlignment().setCodonFrames(mappings1); - List mappings2 = new ArrayList(); + List mappings2 = new ArrayList<>(); mappings2.add(acf2); mappings2.add(acf3); af2.getViewport().getAlignment().setCodonFrames(mappings2); @@ -296,4 +281,260 @@ public class AlignViewportTest assertTrue(ssmMappings.contains(acf2)); assertFalse(ssmMappings.contains(acf3)); } + + /** + * Test for JAL-1306 - conservation thread should run even when only Quality + * (and not Conservation) is enabled in Preferences + */ + @Test(groups = { "Functional" }, timeOut = 2000) + public void testUpdateConservation_qualityOnly() + { + Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("SHOW_QUALITY", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("SHOW_CONSERVATION", + Boolean.FALSE.toString()); + Cache.applicationProperties.setProperty("SHOW_OCCUPANCY", + Boolean.FALSE.toString()); + Cache.applicationProperties.setProperty("SHOW_IDENTITY", + Boolean.FALSE.toString()); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + + /* + * 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("Annotation is not Quality", + anns[0].description.startsWith("Alignment Quality")); + Annotation[] annotations = anns[0].annotations; + assertNotNull("Quality annotations are null", annotations); + assertNotNull("Quality in column 1 is null", annotations[0]); + 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) + { + do + { + try + { + wait(50); + } catch (InterruptedException e) + { + } + } while (viewport.getCalcManager().isWorking()); + } + } + + @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", + Boolean.TRUE.toString()); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + ColourSchemeI cs = new PIDColourScheme(); + 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" }) + public void testSetGetHasSearchResults() + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + SearchResultsI sr = new SearchResults(); + SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0); + + // create arbitrary range on first sequence + sr.addResult(s1, s1.getStart() + 10, s1.getStart() + 15); + + // test set + af.getViewport().setSearchResults(sr); + // has -> true + assertTrue(af.getViewport().hasSearchResults()); + // get == original + assertEquals(sr, af.getViewport().getSearchResults()); + + // set(null) results in has -> false + + af.getViewport().setSearchResults(null); + assertFalse(af.getViewport().hasSearchResults()); + } + + /** + * Verify that setting the selection group has the side-effect of setting the + * context on the group, unless it already has one, but does not change + * whether the group is defined or not. + */ + @Test(groups = { "Functional" }) + public void testSetSelectionGroup() + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + AlignViewport av = af.getViewport(); + SequenceGroup sg1 = new SequenceGroup(); + SequenceGroup sg2 = new SequenceGroup(); + SequenceGroup sg3 = new SequenceGroup(); + + av.setSelectionGroup(sg1); + assertSame(sg1.getContext(), av.getAlignment()); // context set + assertFalse(sg1.isDefined()); // group not defined + + sg2.setContext(sg1, false); + av.setSelectionGroup(sg2); + assertFalse(sg2.isDefined()); // unchanged + assertSame(sg2.getContext(), sg1); // unchanged + + // create a defined group + sg3.setContext(av.getAlignment(), true); + av.setSelectionGroup(sg3); + assertTrue(sg3.isDefined()); // unchanged + } + + /** + * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits + * occupancy row from viewport + */ + @Test(groups = { "Functional" }) + public void testShowOrDontShowOccupancy() + { + // disable occupancy + 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."); + int c = 0; + for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null, + null, "Occupancy")) + { + c++; + } + Assert.assertEquals(c, 0, "Expected zero occupancy rows."); + + // enable occupancy + jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", + Boolean.TRUE.toString()); + af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa", + DataSourceType.FILE); + av = af.getViewport(); + Assert.assertNotNull(av.getAlignmentGapAnnotation(), + "Preference did not enable occupancy row."); + c = 0; + for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null, + null, av.getAlignmentGapAnnotation().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); + AlignViewport testme = af.getViewport(); + waitForCalculations(testme); + 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()); + } }