X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=cd8a4b077dc7b6b1d943f6a00c6a8b5b1ae115ec;hb=284b555bcff969e2b92d32241ede65e4c7e538bb;hp=8188a8db8a4f73c89359a8fa2f47375d11538d95;hpb=0b573ed90b14079f7326281f50c0c9cffdace586;p=jalview.git diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 8188a8d..cd8a4b0 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -23,23 +23,44 @@ 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; +import java.util.HashMap; +import java.util.List; +import java.util.Locale; +import java.util.Map; + +import javax.swing.JInternalFrame; + +import org.testng.Assert; +import org.testng.AssertJUnit; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + import jalview.analysis.scoremodels.SimilarityParams; 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.DBRefEntry; import jalview.datamodel.GeneLocus; import jalview.datamodel.HiddenSequences; import jalview.datamodel.Mapping; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; +import jalview.datamodel.Sequence.DBModList; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@ -52,8 +73,10 @@ 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; @@ -75,21 +98,6 @@ import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererModel; -import java.awt.Color; -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import javax.swing.JInternalFrame; - -import org.testng.Assert; -import org.testng.AssertJUnit; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - @Test(singleThreaded = true) public class Jalview2xmlTests extends Jalview2xmlBase { @@ -158,8 +166,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertNotNull( ColourSchemeProperty.getColourScheme(viewport, viewport.getAlignment(), - viewport.getGlobalColourScheme() - .getSchemeName()), + viewport.getGlobalColourScheme().getSchemeName()), "Recognise T-Coffee score from string"); af.saveAlignment(tfile, FileFormat.Jalview); @@ -232,8 +239,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase boolean diffseqcols = false, diffgseqcols = false; SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); - for (int p = 0, pSize = af.getViewport().getAlignment() - .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) + for (int p = 0, + pSize = af.getViewport().getAlignment().getWidth(); p < pSize + && (!diffseqcols || !diffgseqcols); p++) { if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f)) @@ -252,8 +260,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertTrue(__rcs.isSeqAssociated(), "Group Annotation colourscheme wasn't sequence associated"); - for (int p = 0, pSize = af.getViewport().getAlignment() - .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) + for (int p = 0, + pSize = af.getViewport().getAlignment().getWidth(); p < pSize + && (!diffseqcols || !diffgseqcols); p++) { if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null, @@ -448,9 +457,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.assertEquals(Desktop.getAlignFrames().length, Desktop.getAlignmentPanels( af.getViewport().getSequenceSetId()).length); - Assert.assertEquals( - Desktop.getAlignmentPanels( - af.getViewport().getSequenceSetId()).length, + Assert.assertEquals(Desktop + .getAlignmentPanels(af.getViewport().getSequenceSetId()).length, oldviews); } @@ -803,6 +811,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase "Mismatch PDBEntry 'Type'"); Assert.assertNotNull(recov.getFile(), "Recovered PDBEntry should have a non-null file entry"); + Assert.assertEquals( + recov.getFile().toLowerCase(Locale.ENGLISH) + .lastIndexOf("pdb"), + recov.getFile().length() - 3, + "Recovered PDBEntry file should have PDB suffix"); } } @@ -814,6 +827,88 @@ public class Jalview2xmlTests extends Jalview2xmlBase * @throws IOException */ @Test(groups = { "Functional" }) + public void testStoreAndRecoverAnnotationRowElementColours() + throws IOException + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded("SEQ\tMNQ", + DataSourceType.PASTE); + + AlignViewport av = af.getViewport(); + AlignmentI al = av.getAlignment(); + SequenceI fsq; + fsq = al.getSequenceAt(0); + Annotation annots[] = new Annotation[fsq.getLength()]; + AlignmentAnnotation ala = new AlignmentAnnotation("Colour", "Annots", + annots); + annots[0] = new Annotation(1.0f); + annots[1] = new Annotation(2.0f); + annots[2] = new Annotation(3.0f); + annots[0].colour = Color.RED; + annots[1].colour = Color.GREEN; + annots[2].colour = Color.BLUE; + ala.validateRangeAndDisplay(); + al.getSequenceAt(0).addAlignmentAnnotation(ala); + al.addAnnotation(ala); + /* + * and colour by annotation + */ + AnnotationColourGradient acg = new AnnotationColourGradient(ala, + af.alignPanel.av.getGlobalColourScheme(), 0); + acg.setSeqAssociated(true); + 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); + } + /* + * save project, close windows, reload project, verify + */ + File tfile = File.createTempFile( + "testStoreAndRecoverAnnotRowElemColors", ".jvp"); + tfile.deleteOnExit(); + new Jalview2XML(false).saveState(tfile); + //Desktop.instance.closeAll_actionPerformed(null); + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + Assert.assertNotNull(af, "Failed to reload project"); + /* + * verify alignment annotation has colors + */ + av = af.getViewport(); + + ColourSchemeI loadedCscheme = av.getGlobalColourScheme(); + Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient,"Didn't apply Annotation colour gradient"); + acg = (AnnotationColourGradient) loadedCscheme; + assertTrue(acg.isSeqAssociated()); + assertTrue(acg.isPredefinedColours()); + + al = av.getAlignment(); + fsq = al.getSequenceAt(0); + ala = fsq.getAnnotation()[0]; + Assert.assertNotNull(ala, "No annotation row recovered"); + Assert.assertNotNull(ala.annotations); + 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.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"); + + } + + } + + /** + * Configure an alignment and a sub-group each with distinct colour schemes, + * Conservation and PID thresholds, and confirm these are restored from the + * saved project. + * + * @throws IOException + */ + @Test(groups = { "Functional" }) public void testStoreAndRecoverColourThresholds() throws IOException { Desktop.instance.closeAll_actionPerformed(null); @@ -1034,7 +1129,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertEquals(fr.getFeatureFilter("type2").toStableString(), "(Score LE 2.4) AND (Score GT 1.1)"); assertEquals(fr.getFeatureFilter("type3").toStableString(), - "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)"); + "(AF Contains X) OR (CSQ:PolyPhen NE 0)"); } private void addFeature(SequenceI seq, String featureType, int score) @@ -1204,7 +1299,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, DataSourceType.PASTE); assertNotNull(af, "Didn't read in the example file correctly."); - + AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0]; SequenceI pep = ap.getAlignment().getSequenceAt(0); SequenceI cds = ap.getAlignment().getSequenceAt(1); @@ -1236,15 +1331,15 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.fail("Didn't save the state", e); } Desktop.instance.closeAll_actionPerformed(null); - + new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), DataSourceType.FILE); AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0]; SequenceI rpep = rap.getAlignment().getSequenceAt(0); + DBModList dbrefs = rpep.getDBRefs(); assertEquals(rpep.getName(), "P30419"); - DBRefEntry[] dbrefs = rpep.getDBRefs(); - assertEquals(dbrefs.length, 3); - DBRefEntry dbRef = dbrefs[0]; + assertEquals(dbrefs.size(), 3); + DBRefEntry dbRef = dbrefs.get(0); assertFalse(dbRef instanceof GeneLocus); assertNull(dbRef.getMap()); assertEquals(dbRef, dbref1); @@ -1253,7 +1348,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase * restored dbrefs with mapping have a different 'map to' * sequence but otherwise match the original dbrefs */ - dbRef = dbrefs[1]; + dbRef = dbrefs.get(1); assertFalse(dbRef instanceof GeneLocus); assertTrue(dbRef.equalRef(dbref2)); assertNotNull(dbRef.getMap()); @@ -1265,8 +1360,145 @@ public class Jalview2xmlTests extends Jalview2xmlBase /* * GeneLocus map.to is null so can compare Mapping objects */ - dbRef = dbrefs[2]; + dbRef = dbrefs.get(2); 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 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()); + } }