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.ContactListI;
+import jalview.datamodel.ContactMatrixI;
+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;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
-import jalview.gui.FeatureRenderer;
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;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.structure.StructureImportSettings;
+import jalview.util.MapList;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
-
-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.viewmodel.seqfeatures.FeatureRendererModel;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
@Test(singleThreaded = true)
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);
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))
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,
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);
}
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"));
+
}
/**
"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");
}
}
* @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);
/*
* create a group with Strand colouring, 30% Conservation
* and 40% PID threshold
+ * (notice menu action applies to selection group even if mouse click
+ * is at a sequence not in the group)
*/
SequenceGroup sg = new SequenceGroup();
sg.addSequence(al.getSequenceAt(0), false);
sg.setStartRes(15);
sg.setEndRes(25);
av.setSelectionGroup(sg);
- PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
+ PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2),
+ null);
popupMenu.changeColour_actionPerformed(
JalviewColourScheme.Strand.toString());
assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
/*
* set colour schemes for features
*/
- FeatureRenderer fr = af.getFeatureRenderer();
+ FeatureRendererModel fr = af.getFeatureRenderer();
fr.findAllFeatures(true);
// type1: red
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)
.getAlignViewport(),
"Didn't restore correct view association for the PCA view");
}
+
+ /**
+ * Test save and reload of DBRefEntry including GeneLocus in project
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverGeneLocus() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA";
+ 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);
+
+ /*
+ * give 'protein' a dbref to self, a dbref with map to CDS,
+ * and a dbref with map to gene 'locus'
+ */
+ DBRefEntry dbref1 = new DBRefEntry("Uniprot", "1", "P30419", null);
+ pep.addDBRef(dbref1);
+ Mapping cdsmap = new Mapping(cds,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 1, 12 }, 1, 3));
+ DBRefEntry dbref2 = new DBRefEntry("EMBLCDS", "2", "X1235", cdsmap);
+ pep.addDBRef(dbref2);
+ Mapping locusmap = new Mapping(null,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 2674123, 2674135 }, 1, 3));
+ DBRefEntry dbref3 = new GeneLocus("human", "GRCh38", "5", locusmap);
+ pep.addDBRef(dbref3);
+
+ File tfile = File.createTempFile("testStoreAndRecoverGeneLocus",
+ ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable e)
+ {
+ 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<DBRefEntry> dbrefs = rpep.getDBRefs();
+ assertEquals(rpep.getName(), "P30419");
+ assertEquals(dbrefs.size(), 3);
+ DBRefEntry dbRef = dbrefs.get(0);
+ assertFalse(dbRef instanceof GeneLocus);
+ assertNull(dbRef.getMap());
+ assertEquals(dbRef, dbref1);
+
+ /*
+ * restored dbrefs with mapping have a different 'map to'
+ * sequence but otherwise match the original dbrefs
+ */
+ dbRef = dbrefs.get(1);
+ assertFalse(dbRef instanceof GeneLocus);
+ assertTrue(dbRef.equalRef(dbref2));
+ assertNotNull(dbRef.getMap());
+ SequenceI rcds = rap.getAlignment().getSequenceAt(1);
+ assertSame(dbRef.getMap().getTo(), rcds);
+ // compare MapList but not map.to
+ assertEquals(dbRef.getMap().getMap(), dbref2.getMap().getMap());
+
+ /*
+ * GeneLocus map.to is null so can compare Mapping objects
+ */
+ 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 testPAEsaveRestore() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE);
+ AlignmentI al = af.getViewport().getAlignment();
+ SequenceI sq = al.getSequenceAt(0);
+ 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);
+ 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);
+ // 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
+ ContactMatrixI restoredMat = al
+ .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));
+ }
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff