import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+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.Locale;
+import java.util.Map;
+
+import javax.swing.JInternalFrame;
+
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+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.ViewStyleI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLocus;
+import jalview.datamodel.HiddenMarkovModel;
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.PCAPanel;
import jalview.gui.PopupMenu;
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 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 junit.extensions.PA;
@Test(singleThreaded = true)
public class Jalview2xmlTests extends Jalview2xmlBase
{
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ Desktop.getInstance().closeAll_actionPerformed(null);
+ }
@Override
@BeforeClass(alwaysRun = true)
af.getViewport()
.getGlobalColourScheme() instanceof RNAHelicesColour,
"Couldn't apply RNA helices colourscheme");
- assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
DataSourceType.FILE);
assertNotNull(af, "Didn't read input file " + inFile);
af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
- assertSame(af.getViewport().getGlobalColourScheme().getClass(),
+ AlignViewportI 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");
- assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
af.alignPanel.alignmentChanged();
- assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
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,
+ assertEquals(Desktop.getAlignFrames().length,
+ 1 + origCount,
"Didn't gather the views in the example file.");
}
@Test(groups = { "Functional" }, enabled = true)
public void testStoreAndRecoverExpandedviews() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
{
Assert.fail("Didn't save the expanded view state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@Test(groups = { "Functional" })
public void testStoreAndRecoverReferenceSeqSettings() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
{
Assert.fail("Didn't save the expanded view state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@Test(groups = { "Functional" })
public void testStoreAndRecoverGroupRepSeqs() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
{
Assert.fail("Didn't save the expanded view state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
@Test(groups = { "Functional" })
public void testStoreAndRecoverPDBEntry() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
String exampleFile = "examples/3W5V.pdb";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
DataSourceType.FILE);
{
Assert.fail("Didn't save the state", e);
}
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
if (Desktop.getAlignFrames() != null)
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
"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");
}
}
@Test(groups = { "Functional" })
public void testStoreAndRecoverColourThresholds() throws IOException
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
AlignmentI al = av.getAlignment();
/*
* Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
*/
+ av.setColourAppliesToAllGroups(false);
af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
af.abovePIDThreshold_actionPerformed(true);
/*
* 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);
".jvp");
tfile.deleteOnExit();
new Jalview2XML(false).saveState(tfile);
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
DataSourceType.FILE);
Assert.assertNotNull(af, "Failed to reload project");
/*
* set colour schemes for features
*/
- FeatureRenderer fr = af.getFeatureRenderer();
+ FeatureRendererModel fr = af.getFeatureRenderer();
fr.findAllFeatures(true);
// type1: red
File tfile = File.createTempFile("JalviewTest", ".jvp");
tfile.deleteOnExit();
String filePath = tfile.getAbsolutePath();
- assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
+ af.saveAlignment(filePath, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
/*
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)
}
/**
+ * Load an HMM profile to an alignment, and confirm it is correctly restored
+ * when reloaded from project
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverHmmProfile() throws IOException
+ {
+ Desktop.getInstance().closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+
+ AlignViewportI av = af.getViewport();
+ AlignmentI al = av.getAlignment();
+
+ /*
+ * mimic drag and drop of hmm file on to alignment
+ */
+ AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.hmm", DataSourceType.FILE);
+ al.insertSequenceAt(0,
+ af2.getViewport().getAlignment().getSequenceAt(0));
+
+ /*
+ * check it loaded in
+ */
+ SequenceI hmmSeq = al.getSequenceAt(0);
+ assertTrue(hmmSeq.hasHMMProfile());
+ HiddenMarkovModel hmm = hmmSeq.getHMM();
+ assertSame(hmm.getConsensusSequence(), hmmSeq);
+
+ /*
+ * save project, close windows, reload project, verify
+ */
+ File tfile = File.createTempFile("testStoreAndRecoverHmmProfile",
+ ".jvp");
+ tfile.deleteOnExit();
+ new Jalview2XML(false).saveState(tfile);
+ Desktop.getInstance().closeAll_actionPerformed(null);
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ Assert.assertNotNull(af, "Failed to reload project");
+
+ hmmSeq = al.getSequenceAt(0);
+ assertTrue(hmmSeq.hasHMMProfile());
+ assertSame(hmm.getConsensusSequence(), hmmSeq);
+ Mapping mapToHmmConsensus = (Mapping) PA.getValue(hmm,
+ "mapToHmmConsensus");
+ assertNotNull(mapToHmmConsensus);
+ assertSame(mapToHmmConsensus.getTo(), hmmSeq.getDatasetSequence());
+ }
+
+ /**
* pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
* view (JAL-3171) this test ensures we can import and merge those views
*/
@Test(groups = { "Functional" })
public void testMergeDatasetsforManyViews() throws IOException
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
// complex project - one dataset, several views on several alignments
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
@Test(groups = "Functional")
public void testPcaViewAssociation() throws IOException
{
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
final String PCAVIEWNAME = "With PCA";
// create a new tempfile
File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
}
// load again.
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
tempfile.getCanonicalPath(), DataSourceType.FILE);
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ JInternalFrame[] frames = Desktop.getInstance().getAllFrames();
// PCA and the tabbed alignment view should be the only two windows on the
// desktop
assertEquals(frames.length, 2,
.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.getInstance().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.getInstance().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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff