import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNotSame;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.structure.StructureImportSettings;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.AlignmentViewport.AutoAnnotation;
import java.awt.Color;
import java.io.File;
}
@Test(groups = { "Functional" })
- public void testRNAStructureRecovery() throws Exception
+ public void testRestoreRNAStructure() throws Exception
{
String inFile = "examples/RF00031_folded.stk";
String tfile = File.createTempFile("JalviewTest", ".jvp")
}
@Test(groups = { "Functional" })
- public void testTCoffeeScores() throws Exception
+ public void testRestoreTCoffeeColouring() throws Exception
{
String inFile = "examples/uniref50.fa",
inAnnot = "examples/uniref50.score_ascii";
DataSourceType.FILE);
assertNotNull(af, "Didn't read input file " + inFile);
af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
- assertSame(af.getViewport().getGlobalColourScheme().getClass(),
+ AlignViewport viewport = af.getViewport();
+ assertSame(viewport.getGlobalColourScheme().getClass(),
TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
assertNotNull(
- ColourSchemeProperty.getColourScheme(
- af.getViewport().getAlignment(),
- af.getViewport().getGlobalColourScheme()
+ ColourSchemeProperty.getColourScheme(viewport,
+ viewport.getAlignment(),
+ viewport.getGlobalColourScheme()
.getSchemeName()),
"Recognise T-Coffee score from string");
}
@Test(groups = { "Functional" })
- public void testColourByAnnotScores() throws Exception
+ public void testRestoreColourByAnnotion() throws Exception
{
String inFile = "examples/uniref50.fa",
inAnnot = "examples/testdata/uniref50_iupred.jva";
* @throws Exception
*/
@Test(groups = { "Functional" }, enabled = true)
- public void testStoreAndRecoverExpandedviews() throws Exception
+ public void testRestoreExpandedviews() throws Exception
{
Desktop.instance.closeAll_actionPerformed(null);
int oldviews = Desktop.getAlignFrames().length;
Assert.assertEquals(Desktop.getAlignFrames().length,
Desktop.getAlignmentPanels(afid).length);
- File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
+ File tfile = File.createTempFile("testRestoreExpandedviews", ".jvp");
try
{
new Jalview2XML(false).saveState(tfile);
* @throws Exception
*/
@Test(groups = { "Functional" })
- public void testStoreAndRecoverReferenceSeqSettings() throws Exception
+ public void testRestoreReferenceSeqSettings() throws Exception
{
Desktop.instance.closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
n++;
}
- File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
+ File tfile = File.createTempFile("testRestoreReferenceSeqSettings",
".jvp");
try
{
* @throws Exception
*/
@Test(groups = { "Functional" })
- public void testStoreAndRecoverGroupRepSeqs() throws Exception
+ public void testRestoreGroupRepSeqs() throws Exception
{
Desktop.instance.closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
n++;
}
- File tfile = File.createTempFile("testStoreAndRecoverGroupReps",
- ".jvp");
+ File tfile = File.createTempFile("testRestoreGroupRepSeqs", ".jvp");
try
{
new Jalview2XML(false).saveState(tfile);
* @throws Exception
*/
@Test(groups = { "Functional" })
- public void testStoreAndRecoverPDBEntry() throws Exception
+ public void testRestorePDBEntry() throws Exception
{
Desktop.instance.closeAll_actionPerformed(null);
String exampleFile = "examples/3W5V.pdb";
seqs[3].getDatasetSequence().getAllPDBEntries().get(0),
pdbEntries[3]);
- File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp");
+ File tfile = File.createTempFile("testRestorePDBEntry", ".jvp");
try
{
new Jalview2XML(false).saveState(tfile);
* @throws IOException
*/
@Test(groups = { "Functional" })
- public void testStoreAndRecoverColourThresholds() throws IOException
+ public void testRestoreColourThresholds() throws IOException
{
Desktop.instance.closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
/*
* save project, close windows, reload project, verify
*/
- File tfile = File.createTempFile("testStoreAndRecoverColourThresholds",
+ File tfile = File.createTempFile("testRestoreColourThresholds",
".jvp");
tfile.deleteOnExit();
new Jalview2XML(false).saveState(tfile);
* @throws IOException
*/
@Test(groups = { "Functional" })
- public void testSaveLoadFeatureColoursAndFilters() throws IOException
+ public void testRestoreFeatureColoursAndFilters() throws IOException
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
}
@Test(groups = "Functional")
- public void testPcaViewAssociation() throws IOException
+ public void testRestorePCAViewAssociation() throws IOException
{
Desktop.instance.closeAll_actionPerformed(null);
final String PCAVIEWNAME = "With PCA";
// create a new tempfile
- File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
+ File tempfile = File.createTempFile("testRestorePCAViewAssociation",
+ "jvp");
{
String exampleFile = "examples/uniref50.fa";
.getAlignViewport(),
"Didn't restore correct view association for the PCA view");
}
+
+ /**
+ * Tests that annotation ordering is faithfully restored, on project reload or
+ * New View, even if preference settings have changed
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testRestoreAnnotationOrdering() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ Cache.setProperty("SHOW_ANNOTATION", "true");
+ Cache.setProperty("SHOW_CONSERVATION", "true");
+ Cache.setProperty("SHOW_QUALITY", "false");
+ Cache.setProperty("SHOW_IDENTITY", "false");
+ Cache.setProperty("SHOW_OCCUPANCY", "true");
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ assertEquals(afs.length, 1);
+ AlignmentI alignment = afs[0].getViewport().getAlignment();
+ AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+ assertEquals(anns.length, 2);
+
+ /*
+ * this order is hard wired in AlignmentViewport.initAutoAnnotation()
+ */
+ assertEquals(anns[0].label, "Conservation");
+ assertEquals(anns[1].label, "Occupancy");
+
+ /*
+ * add two user annotations, adjust order, height and visibility
+ */
+ AlignmentAnnotation tmp = anns[0];
+ anns[0] = anns[1];
+ anns[1] = tmp;
+ Annotation[] an1 = new Annotation[] { new Annotation(2f) };
+ Annotation[] an2 = new Annotation[] { new Annotation(3f) };
+ alignment.addAnnotation(new AlignmentAnnotation("hello", "desc1", an1),
+ 1);
+ alignment.addAnnotation(new AlignmentAnnotation("world", "desc2", an2),
+ 3);
+ anns = alignment.getAlignmentAnnotation();
+ assertEquals(anns[0].label, "Occupancy");
+ assertEquals(anns[1].label, "hello");
+ assertEquals(anns[2].label, "Conservation");
+ assertEquals(anns[3].label, "world");
+ anns[0].graphHeight = 60;
+ anns[0].visible = false;
+ anns[1].graphHeight = 70;
+ anns[2].graphHeight = 80;
+ anns[3].graphHeight = 90;
+ anns[3].visible = false;
+
+ /*
+ * save project to temporary file and reload on to an empty desktop,
+ * verify annotation order, height and visibility is restored
+ */
+ File projectFile = File.createTempFile("jvTest", ".jvp");
+ new Jalview2XML(false).saveState(projectFile);
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ projectFile.getAbsolutePath(),
+ DataSourceType.FILE);
+ anns = af.getViewport().getAlignment().getAlignmentAnnotation();
+ assertEquals(anns.length, 4);
+ assertEquals(anns[0].label, "Occupancy");
+ assertEquals(anns[1].label, "hello");
+ assertEquals(anns[2].label, "Conservation");
+ assertEquals(anns[3].label, "world");
+ assertEquals(anns[0].graphHeight, 60);
+ assertEquals(anns[1].graphHeight, 70);
+ assertEquals(anns[2].graphHeight, 80);
+ assertEquals(anns[3].graphHeight, 90);
+ assertFalse(anns[0].visible);
+ assertTrue(anns[1].visible);
+ assertTrue(anns[2].visible);
+ assertFalse(anns[3].visible);
+
+ /*
+ * make a new view of the alignment (uses project save/load code)
+ * and verify annotations are ordered the same
+ */
+ AlignmentPanel newPanel = af.newView("new", true);
+ AlignmentAnnotation[] newAnns = newPanel.getAlignment()
+ .getAlignmentAnnotation();
+ assertEquals(newAnns.length, 4);
+ assertEquals(newAnns[0].label, "Occupancy");
+ assertEquals(newAnns[1].label, "hello");
+ assertEquals(newAnns[2].label, "Conservation");
+ assertEquals(newAnns[3].label, "world");
+ assertEquals(newAnns[0].graphHeight, 60);
+ assertEquals(newAnns[1].graphHeight, 70);
+ assertEquals(newAnns[2].graphHeight, 80);
+ assertEquals(newAnns[3].graphHeight, 90);
+ assertFalse(newAnns[0].visible);
+ assertTrue(newAnns[1].visible);
+ assertTrue(newAnns[2].visible);
+ assertFalse(newAnns[3].visible);
+ newPanel.closePanel();
+
+ /*
+ * reload the project with Preferences set to not create Occupancy, but to
+ * create Quality; annotations should still appear as saved in the project;
+ * preferences should be left unchanged (after temporary override)
+ */
+ Desktop.instance.closeAll_actionPerformed(null);
+ Cache.setProperty("SHOW_OCCUPANCY", "false");
+ Cache.removeProperty("SHOW_QUALITY"); // will default to true
+ Map<String, String> originalPreferences = Cache.getProperties(
+ AutoAnnotation.OCCUPANCY.preferenceKey,
+ AutoAnnotation.CONSERVATION.preferenceKey,
+ AutoAnnotation.QUALITY.preferenceKey,
+ AutoAnnotation.CONSENSUS.preferenceKey);
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ projectFile.getAbsolutePath(), DataSourceType.FILE);
+ alignment = af.getViewport().getAlignment();
+ anns = alignment.getAlignmentAnnotation();
+ assertEquals(anns.length, 4);
+ assertEquals(anns[0].label, "Occupancy");
+ assertEquals(anns[1].label, "hello");
+ assertEquals(anns[2].label, "Conservation");
+ assertEquals(anns[3].label, "world");
+ Map<String, String> newPreferences = Cache.getProperties(
+ AutoAnnotation.OCCUPANCY.preferenceKey,
+ AutoAnnotation.CONSERVATION.preferenceKey,
+ AutoAnnotation.QUALITY.preferenceKey,
+ AutoAnnotation.CONSENSUS.preferenceKey);
+ assertEquals(originalPreferences, newPreferences);
+ assertNull(Cache.getProperty(AutoAnnotation.QUALITY.preferenceKey));
+
+ /*
+ * make a new view, reorder its annotations, and delete and hide
+ * a different annotation in each of the two views
+ */
+ newPanel = af.newView("new", true);
+ af.getViewport().setViewName("Original");
+
+ /*
+ * just for interest - new view has the same manual annotation objects,
+ * but new auto-calculated annotations
+ */
+ AlignmentI newAlignment = newPanel.getAlignment();
+ newAnns = newAlignment.getAlignmentAnnotation();
+ assertNotSame(anns[0], newAnns[0]);
+ assertSame(anns[1], newAnns[1]);
+ assertNotSame(anns[2], newAnns[2]);
+ assertSame(anns[3], newAnns[3]);
+
+ alignment.deleteAnnotation(anns[2]); // delete Conservation view 1
+ anns[1].visible = false; // hide 'hello' view 1
+
+ tmp = newAnns[0];
+ newAnns[0] = newAnns[3]; // 'world' moved to top of new view
+ newAnns[3] = tmp; // then hello, Conservation, Occupancy
+ newAnns[0].visible = false; // hide 'world' in new view
+ newAnns[3].graphHeight = 99; // set height of Occupancy
+ newAlignment.deleteAnnotation(newAnns[1]); // delete 'hello' in new view
+
+ /*
+ * save, reload and verify annotations in both views
+ */
+ ((AlignViewport) newPanel.getAlignViewport()).setViewName("New View");
+ projectFile = File.createTempFile("jvTest", ".jvp");
+ new Jalview2XML(false).saveState(projectFile);
+ Desktop.instance.closeAll_actionPerformed(null);
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ projectFile.getAbsolutePath(), DataSourceType.FILE);
+ assertEquals(af.getAlignPanels().size(), 2);
+
+ /*
+ * check first view
+ */
+ AlignViewportI firstViewport = af.getAlignPanels().get(0)
+ .getAlignViewport();
+ assertEquals(((AlignViewport) firstViewport).getViewName(), "Original");
+ alignment = firstViewport.getAlignment();
+ anns = alignment.getAlignmentAnnotation();
+ assertEquals(anns.length, 3);
+ assertEquals(anns[0].label, "Occupancy");
+ assertEquals(anns[1].label, "hello");
+ assertEquals(anns[2].label, "world");
+ assertFalse(anns[0].visible);
+ assertFalse(anns[1].visible);
+ assertFalse(anns[2].visible);
+
+ /*
+ * check second view
+ */
+ AlignViewportI secondViewport = af.getAlignPanels().get(1)
+ .getAlignViewport();
+ assertEquals(((AlignViewport) secondViewport).getViewName(),
+ "New View");
+ alignment = secondViewport.getAlignment();
+ anns = alignment.getAlignmentAnnotation();
+ assertEquals(anns.length, 3);
+ assertEquals(anns[0].label, "world");
+ assertEquals(anns[1].label, "Conservation");
+ assertEquals(anns[2].label, "Occupancy");
+ assertFalse(anns[0].visible);
+ assertTrue(anns[1].visible);
+ assertFalse(anns[2].visible);
+ assertEquals(anns[2].graphHeight, 99);
+ }
}
git://source.jalview.org / jalview.git / blobdiff