X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=af52edad5c3f42dd974ce358195f19d29c62317d;hb=b3fb6325a8bc315c5c938faf10ffd2e73d965f16;hp=8886394d86cc3962828f322b0912e1d71e838b0f;hpb=a473afe5d67b0368c7627c001c65fe9a6117dd16;p=jalview.git diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 8886394..af52eda 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -23,11 +23,13 @@ package jalview.project; 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 java.awt.Color; +import java.awt.Rectangle; import java.io.File; import java.io.IOException; import java.util.ArrayList; @@ -48,9 +50,13 @@ import jalview.api.AlignViewportI; 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.ContactListI; +import jalview.datamodel.ContactMatrix; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.GeneLocus; import jalview.datamodel.HiddenSequences; @@ -70,8 +76,10 @@ import jalview.gui.AlignViewport; import jalview.gui.AlignmentPanel; import jalview.gui.Desktop; import jalview.gui.JvOptionPane; +import jalview.gui.OverviewPanel; import jalview.gui.PCAPanel; import jalview.gui.PopupMenu; +import jalview.gui.Preferences; import jalview.gui.SliderPanel; import jalview.io.DataSourceType; import jalview.io.FileFormat; @@ -92,6 +100,7 @@ import jalview.util.MapList; import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererModel; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; @Test(singleThreaded = true) public class Jalview2xmlTests extends Jalview2xmlBase @@ -101,6 +110,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() { + if (Desktop.instance != null) + Desktop.instance.closeAll_actionPerformed(null); JvOptionPane.setInteractiveMode(false); JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } @@ -588,6 +599,16 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3")); assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1")); assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1")); + /* + * test for patch release versions + */ + assertFalse(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.2")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.4")); + assertFalse( + Jalview2XML.isVersionStringLaterThan("2.12.2.0b1", "2.12.2.0")); + assertFalse( + Jalview2XML.isVersionStringLaterThan("2.12.2.3", "2.12.2.2")); + } /** @@ -854,8 +875,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase acg.setPredefinedColours(true); af.changeColour(acg); Color seqcol[] = new Color[3]; - for (int iStart=fsq.findIndex(fsq.getStart()),i=0;i<3;i++) { - seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null); + for (int iStart = fsq.findIndex(fsq.getStart()), i = 0; i < 3; i++) + { + seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas + .getSequenceRenderer() + .getResidueColour(fsq, iStart + i, null); } /* * save project, close windows, reload project, verify @@ -864,7 +888,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase "testStoreAndRecoverAnnotRowElemColors", ".jvp"); tfile.deleteOnExit(); new Jalview2XML(false).saveState(tfile); - //Desktop.instance.closeAll_actionPerformed(null); + // Desktop.instance.closeAll_actionPerformed(null); af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), DataSourceType.FILE); Assert.assertNotNull(af, "Failed to reload project"); @@ -872,9 +896,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase * verify alignment annotation has colors */ av = af.getViewport(); - + ColourSchemeI loadedCscheme = av.getGlobalColourScheme(); - Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient,"Didn't apply Annotation colour gradient"); + Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient, + "Didn't apply Annotation colour gradient"); acg = (AnnotationColourGradient) loadedCscheme; assertTrue(acg.isSeqAssociated()); assertTrue(acg.isPredefinedColours()); @@ -887,13 +912,16 @@ public class Jalview2xmlTests extends Jalview2xmlBase for (int iStart = al.getSequenceAt(0) .findIndex(al.getSequenceAt(0).getStart()), i = 0; i < 3; i++) { - Assert.assertTrue(ala.annotations[i].colour!=null); + Assert.assertTrue(ala.annotations[i].colour != null); Assert.assertTrue(ala.annotations[i].colour.equals(annots[i].colour)); - Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null); - Assert.assertTrue(seqcol[i].equals(newseqcol),"Sequence shading is different"); + Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas + .getSequenceRenderer() + .getResidueColour(fsq, iStart + i, null); + Assert.assertTrue(seqcol[i].equals(newseqcol), + "Sequence shading is different"); } - + } /** @@ -1359,4 +1387,227 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertTrue(dbRef instanceof GeneLocus); assertEquals(dbRef, dbref3); } + + /** + * test store and recovery of Overview windows + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = true) + public void testStoreAndRecoverOverview() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + + Cache.setProperty("SHOW_OVERVIEW", "false"); + Cache.setProperty(Preferences.USE_LEGACY_GAP, "false"); + Cache.setColourProperty(Preferences.GAP_COLOUR, Color.green); + Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.yellow); + Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "true"); + + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + + /* + * open and resize / reposition overview + */ + af.overviewMenuItem_actionPerformed(null); + OverviewPanel ov1 = af.alignPanel.getOverviewPanel(); + assertNotNull(ov1); + ov1.setFrameBounds(20, 30, 200, 400); + assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa"); + assertTrue(ov1.isShowHiddenRegions()); + + /* + * open a New View and its Overview and reposition it + */ + af.newView_actionPerformed(null); + af.overviewMenuItem_actionPerformed(null); + OverviewPanel ov2 = af.alignPanel.getOverviewPanel(); + assertNotNull(ov2); + assertNotSame(ov1, ov2); + ov2.setFrameBounds(25, 35, 205, 405); + assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original"); + assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1"); + + File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp"); + new Jalview2XML(false).saveState(tfile); + Desktop.instance.closeAll_actionPerformed(null); + + /* + * change preferences (should _not_ affect reloaded Overviews) + */ + Cache.setProperty("SHOW_OVERVIEW", "true"); + Cache.setProperty(Preferences.USE_LEGACY_GAP, "true"); + Cache.setColourProperty(Preferences.GAP_COLOUR, Color.blue); + Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.orange); + Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "false"); + + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + + /* + * workaround: explicitly select View 1 (not in focus after restore) + */ + af.tabSelectionChanged(1); + + /* + * verify restored overview for View 1 + */ + ov2 = af.alignPanel.getOverviewPanel(); + assertEquals(ov2.getCanvas().getGapColour(), Color.green); + // 'non-legacy' colouring uses white for non-gapped residues + assertEquals(ov2.getCanvas().getResidueColour(), Color.white); + assertEquals(ov2.getCanvas().getHiddenColour(), Color.yellow); + assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1"); + assertEquals(ov2.getFrameBounds(), new Rectangle(25, 35, 205, 405)); + assertTrue(ov2.isShowHiddenRegions()); + + /* + * verify restored overview for Original view + */ + af.tabSelectionChanged(0); + ov1 = af.alignPanel.getOverviewPanel(); + assertEquals(ov1.getCanvas().getGapColour(), Color.green); + // 'non-legacy' colouring uses white for non-gapped residues + assertEquals(ov1.getCanvas().getResidueColour(), Color.white); + assertEquals(ov1.getCanvas().getHiddenColour(), Color.yellow); + assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original"); + assertEquals(ov1.getFrameBounds(), new Rectangle(20, 30, 200, 400)); + assertTrue(ov1.isShowHiddenRegions()); + } + + /** + * Test that a view with no Overview is restored with no Overview, even if + * 'Open Overview' is selected in Preferences + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = true) + public void testStoreAndRecoverNoOverview() throws Exception + { + Cache.setProperty("SHOW_OVERVIEW", "false"); + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE); + + File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp"); + new Jalview2XML(false).saveState(tfile); + Desktop.instance.closeAll_actionPerformed(null); + + Cache.setProperty("SHOW_OVERVIEW", "true"); + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + + assertNull(af.alignPanel.getOverviewPanel()); + } + + /** + * Test that a view from an older version of Jalview is restored with Overview + * automatically shown when the preference is set + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = true) + public void testAutoShowOverviewForLegacyProjects() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + Cache.setProperty("SHOW_OVERVIEW", "true"); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile.jvp", DataSourceType.FILE); + + Cache.setProperty("SHOW_OVERVIEW", "false"); + assertNotNull(af.alignPanel.getOverviewPanel()); + } + + /** + * Test that loading example.jvp, doing some stuff, then hitting reload + * doesn't leave the modified window still open + * + * See JAL-4127 - interactively performing the same actions and reloading + * works fine, but programmatically they do not + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = false) + public void testReloadActuallyReloads() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile.jvp", DataSourceType.FILE); + af.getViewport().getColumnSelection().addElement(3); + af.hideSelColumns_actionPerformed(null); + af.newView("new", true); + af.reload_actionPerformed(null); + Thread.sleep(30); + // af exists still but isn't shown + assertTrue(af.isClosed()); + } + + @Test(groups = { "Functional" }) + public void testPAEsaveRestore() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE); + AlignmentI al = af.getViewport().getAlignment(); + // PAE matrices are added as reference annotation to the dataset sequence + // at least for now. + SequenceI sq = al.getSequenceAt(0).getDatasetSequence(); + int i = sq.getLength(); + float[][] paevals = new float[i][i]; + for (i = i - 1; i >= 0; i--) + { + for (int j = 0; j <= i; j++) + { + paevals[i][j] = ((i - j < 2) + || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f; + paevals[j][i] = paevals[i][j]; + } + } + PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals); + String content = ContactMatrix.contactToFloatString(dummyMat); + Assert.assertTrue(content.contains("\t1.")); // at least one element must be + // 1 + float[][] vals = ContactMatrix.fromFloatStringToContacts(content, + sq.getLength(), sq.getLength()); + assertEquals(vals[3][4], paevals[3][4]); + dummyMat.makeGroups(0.5f, false); + Assert.assertNotSame(dummyMat.getNewick(), ""); + AlignmentAnnotation paeCm = sq.addContactList(dummyMat); + al.addAnnotation(paeCm); + File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix", + ".jvp"); + new Jalview2XML(false).saveState(tfile); + Desktop.instance.closeAll_actionPerformed(null); + + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + AlignmentI newAl = af.getViewport().getAlignment(); + SequenceI newSeq = newAl.getSequenceAt(0).getDatasetSequence(); + // check annotation of the expected type exists + Assert.assertEquals(newSeq.getAnnotation().length, 1); + Assert.assertEquals(newSeq.getAnnotation()[0].graph, paeCm.graph); + + // check a contact matrix was recovered + Assert.assertEquals(newSeq.getContactMaps().size(), 1); + // and can be found for the annotation on the sequence + ContactMatrixI restoredMat = newSeq + .getContactMatrixFor(newSeq.getAnnotation()[0]); + Assert.assertNotNull(restoredMat); + for (i = sq.getLength() - 1; i >= 0; i--) + { + ContactListI oldCM = dummyMat.getContactList(i), + newCM = restoredMat.getContactList(i); + for (int j = oldCM.getContactHeight(); j >= 0; j--) + { + Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j)); + } + } + Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups()); + Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups()); + Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree()); + Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick()); + + } + }