import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.api.AlignViewportI;
import java.util.ArrayList;
import java.util.List;
import jalview.schemes.PIDColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.util.MapList;
+import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
public class AlignViewportTest
AlignmentI al;
- AlignViewport testee;
+ AlignmentViewport testee;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
* remove any sequence mappings left lying around by other tests
*/
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
ssm.resetAll();
}
/*
* 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<AlignedCodonFrame> mappings = new ArrayList<>();
mappings.add(acf1);
* mappings
*/
StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ .getStructureSelectionManager(Desktop.getInstance());
List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
assertEquals(2, sequenceMappings.size());
assertTrue(sequenceMappings.contains(acf1));
@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<AlignedCodonFrame> mappings1 = new ArrayList<>();
mappings1.add(acf1);
@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<AlignedCodonFrame> mappings1 = new ArrayList<>();
mappings1.add(acf1);
* 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);
{
synchronized (this)
{
- do
+ System.out.print("waiting...");
+ int n = 3;
+ while (--n >= 0 || viewport.getCalcManager().isWorking())
{
try
{
} catch (InterruptedException e)
{
}
- } while (viewport.getCalcManager().isWorking());
+ }
+ System.out.println("...done");
}
}
/*
* 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
{
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();
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;
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.");
git://source.jalview.org / jalview.git / blobdiff