X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=9c1b32ffe4727fe2f03b09aea9a6d1a047c76632;hb=b122ba188c2ffcbb302809bafc02058e355643ee;hp=8188a8db8a4f73c89359a8fa2f47375d11538d95;hpb=0b573ed90b14079f7326281f50c0c9cffdace586;p=jalview.git diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 8188a8d..9c1b32f 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -23,23 +23,52 @@ 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.math.BigInteger; +import java.util.ArrayList; +import java.util.BitSet; +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.AlignmentUtils; 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.ContactListI; +import jalview.datamodel.ContactMatrix; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.GeneLocus; +import jalview.datamodel.GroupSet; import jalview.datamodel.HiddenSequences; import jalview.datamodel.Mapping; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; +import jalview.datamodel.Sequence; +import jalview.datamodel.Sequence.DBModList; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@ -52,8 +81,10 @@ 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; @@ -74,21 +105,8 @@ import jalview.util.MapList; 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; +import jalview.ws.datamodel.MappableContactMatrixI; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; @Test(singleThreaded = true) public class Jalview2xmlTests extends Jalview2xmlBase @@ -98,6 +116,8 @@ 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); } @@ -158,8 +178,7 @@ 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); @@ -270,12 +289,12 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void gatherViewsHere() throws Exception { - int origCount = Desktop.getAlignFrames() == null ? 0 - : Desktop.getAlignFrames().length; + int origCount = Desktop.getDesktopAlignFrames() == null ? 0 + : Desktop.getDesktopAlignFrames().length; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", DataSourceType.FILE); assertNotNull(af, "Didn't read in the example file correctly."); - assertTrue(Desktop.getAlignFrames().length == 1 + origCount, + assertTrue(Desktop.getDesktopAlignFrames().length == 1 + origCount, "Didn't gather the views in the example file."); } @@ -413,7 +432,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", DataSourceType.FILE); - Assert.assertEquals(Desktop.getAlignFrames().length, 1); + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 1); String afid = af.getViewport().getSequenceSetId(); // check FileLoader returned a reference to the one alignFrame that is @@ -423,8 +442,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase Desktop.explodeViews(af); - int oldviews = Desktop.getAlignFrames().length; - Assert.assertEquals(Desktop.getAlignFrames().length, + int oldviews = Desktop.getDesktopAlignFrames().length; + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, Desktop.getAlignmentPanels(afid).length); File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp"); try @@ -438,19 +457,18 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.fail("Didn't save the expanded view state", e); } Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) + if (Desktop.getDesktopAlignFrames() != null) { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); } af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), DataSourceType.FILE); Assert.assertNotNull(af); - Assert.assertEquals(Desktop.getAlignFrames().length, + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, Desktop.getAlignmentPanels( af.getViewport().getSequenceSetId()).length); - Assert.assertEquals( - Desktop.getAlignmentPanels( - af.getViewport().getSequenceSetId()).length, + Assert.assertEquals(Desktop + .getAlignmentPanels(af.getViewport().getSequenceSetId()).length, oldviews); } @@ -503,9 +521,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.fail("Didn't save the expanded view state", e); } Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) + if (Desktop.getDesktopAlignFrames() != null) { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); } af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), @@ -585,6 +603,16 @@ 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")); + } /** @@ -672,9 +700,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.fail("Didn't save the expanded view state", e); } Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) + if (Desktop.getDesktopAlignFrames() != null) { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); } af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), @@ -766,9 +794,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.fail("Didn't save the state", e); } Desktop.instance.closeAll_actionPerformed(null); - if (Desktop.getAlignFrames() != null) + if (Desktop.getDesktopAlignFrames() != null) { - Assert.assertEquals(Desktop.getAlignFrames().length, 0); + Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0); } AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded( @@ -803,6 +831,11 @@ 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 +847,95 @@ 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 +1156,7 @@ 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) @@ -1097,7 +1219,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertNotNull(af); AlignmentI ds = null; - for (AlignFrame alignFrame : Desktop.getAlignFrames()) + for (AlignFrame alignFrame : Desktop.getDesktopAlignFrames()) { if (ds == null) { @@ -1204,7 +1326,7 @@ 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 +1358,15 @@ 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 +1375,7 @@ 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 +1387,355 @@ 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 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 testMatrixToFloatsAndBack() + { + int imax=2000; + int i=imax; + SequenceI sq = new Sequence("dummy","SEQ"); + while (sq.getLength()= 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]); + assertEquals(vals[4][3], paevals[4][3]); + + // test recovery + for (i=0;iseq1\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]); + assertEquals(vals[4][3], paevals[4][3]); + dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false,0.5f, false)); + Assert.assertNotSame(dummyMat.getNewick(), ""); + AlignmentAnnotation paeCm = sq.addContactList(dummyMat); + al.addAnnotation(paeCm); + // verify store/restore of group bitsets + for (BitSet gp : dummyMat.getGroups()) + { + StringBuilder sb = new StringBuilder(); + for (long val : gp.toLongArray()) + { + if (sb.length() > 0) + { + sb.append(","); + } + sb.append(val); + } + String[] longvals = sb.toString().split(","); + long[] newlongvals = new long[longvals.length]; + for (int lv = 0; lv < longvals.length; lv++) + { + try + { + newlongvals[lv] = Long.valueOf(longvals[lv]); + } catch (Exception x) + { + Assert.fail("failed to deserialise bitset element "); + } + } + BitSet newGp = BitSet.valueOf(newlongvals); + assertTrue(gp.equals(newGp)); + } + 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); + MapList oldMap = ((MappableContactMatrixI) dummyMat).getMapFor(sq); + MapList newMap = ((MappableContactMatrixI) restoredMat) + .getMapFor(newSeq); + Assert.assertEquals(oldMap.getFromRanges(), newMap.getFromRanges()); + Assert.assertEquals(oldMap.getToRanges(), newMap.getToRanges()); + Assert.assertEquals(oldMap.getFromRatio(), newMap.getFromRatio()); + Assert.assertEquals(oldMap.getToRatio(), newMap.getToRatio()); + 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--) + { + double old_j = oldCM.getContactAt(j); + double new_j = newCM.getContactAt(j); + Assert.assertEquals(old_j, new_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()); + + // verify no duplicate PAE matrix data when new view created and saved + + // add reference annotations to view first, then copy + AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0), newSeq.getAnnotation()[0],null); + + AlignmentViewPanel newview = af.newView("copy of PAE", true); + + // redundant asserts here check all is good with the new view firest... + AlignmentI newviewAl = newview.getAlignment(); + SequenceI newviewSeq = newviewAl.getSequenceAt(0); + // check annotation of the expected type exists + Assert.assertEquals(newviewSeq.getAnnotation().length, 1); + Assert.assertEquals(newviewSeq.getAnnotation()[0].graph, paeCm.graph); + // check we have just one contact matrix mapping + Assert.assertEquals(newviewSeq.getContactMaps().size(), 1); + + // and can be found for the annotation on the sequence + ContactMatrixI newviewMat = newviewSeq + .getContactMatrixFor(newviewSeq.getAnnotation()[0]); + Assert.assertNotNull(newviewMat); + + Assert.assertTrue(newviewMat == restoredMat); + + // save the two views and restore. Now look at visible annotation to check all views have shared refs. + + tfile = File.createTempFile("testStoreAndRecoverPAEmatrixTwoViews", + ".jvp"); + new Jalview2XML(false).saveState(tfile); + Desktop.instance.closeAll_actionPerformed(null); + + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + newAl = af.getAlignPanels().get(0).getAlignment(); + AlignmentAnnotation view1aa = newAl.getSequenceAt(0).getAnnotation()[0]; + + newviewAl = af.getAlignPanels().get(1).getAlignment(); + AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0).getAnnotation()[0]; + + // annotations are shared across alignment views - so should still have an identical pair of annotations. + Assert.assertTrue(view1aa==view2aa); + // identical annotations means identical contact matrix mappings + Assert.assertEquals(newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1); + + // TODO Verify when distinct mappable PAEs are created, only one PAE dataset is actually held. + // Assert.assertTrue(view1aa!=view2aa); + // restoredMat = newAl.getContactMatrixFor(view1aa); + // newviewMat = newviewAl.getContactMatrixFor(view2aa); + // Assert.assertTrue(restoredMat!=newviewMat); + + } + }