X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=db41f3e94adb152897d65c1afd8650e14ebdbcdb;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=b3c6b2ae1fb9fbe92c5ce1e03c8aa3ecc3c4d9db;hpb=04c8f7bff663aa469127e9eed4164e02933782f1;p=jalview.git diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index b3c6b2a..db41f3e 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -27,6 +27,7 @@ import static org.testng.AssertJUnit.assertNotSame; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; +import jalview.api.AlignViewportI; import java.util.ArrayList; import java.util.List; @@ -54,6 +55,7 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.PIDColourScheme; import jalview.structure.StructureSelectionManager; import jalview.util.MapList; +import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; public class AlignViewportTest @@ -68,7 +70,7 @@ public class AlignViewportTest AlignmentI al; - AlignViewport testee; + AlignmentViewport testee; @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception @@ -81,7 +83,7 @@ public class AlignViewportTest * remove any sequence mappings left lying around by other tests */ StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); ssm.resetAll(); } @@ -107,18 +109,16 @@ 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<>(); mappings.add(acf1); @@ -131,7 +131,7 @@ public class AlignViewportTest * mappings */ StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + .getStructureSelectionManager(Desktop.getInstance()); List sequenceMappings = ssm.getSequenceMappings(); assertEquals(2, sequenceMappings.size()); assertTrue(sequenceMappings.contains(acf1)); @@ -153,33 +153,30 @@ public class AlignViewportTest @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(">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<>(); mappings1.add(acf1); @@ -219,33 +216,30 @@ public class AlignViewportTest @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(">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<>(); mappings1.add(acf1); @@ -286,18 +280,18 @@ 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" }, timeOut = 2000) + @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); @@ -328,7 +322,9 @@ public class AlignViewportTest { synchronized (this) { - do + System.out.print("waiting..."); + int n = 3; + while (--n >= 0 || viewport.getCalcManager().isWorking()) { try { @@ -336,7 +332,8 @@ public class AlignViewportTest } catch (InterruptedException e) { } - } while (viewport.getCalcManager().isWorking()); + } + System.out.println("...done"); } } @@ -346,15 +343,16 @@ 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(); AlignViewport viewport = af.getViewport(); viewport.setGlobalColourScheme(cs); - assertFalse(viewport.getResidueShading().conservationApplied()); + assertFalse(viewport.getResidueShading() + .conservationApplied()); /* * JAL-3201 groups have their own ColourSchemeI instances @@ -415,7 +413,7 @@ public class AlignViewportTest { 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(); @@ -434,20 +432,17 @@ public class AlignViewportTest av.setSelectionGroup(sg3); assertTrue(sg3.isDefined()); // unchanged } - /** - * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits - * occupancy row from viewport + * 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()); + jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString()); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/uniref50.fa", DataSourceType.FILE); - AlignViewport av = af.getViewport(); + AlignViewportI av = af.getViewport(); Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row."); int c = 0; @@ -457,12 +452,11 @@ public class AlignViewportTest 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); + 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.");