import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+import jalview.analysis.PCA;
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.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Point;
import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
+import jalview.gui.CalculationChooser;
import jalview.gui.Desktop;
+import jalview.gui.FeatureRenderer;
import jalview.gui.Jalview2XML;
import jalview.gui.JvOptionPane;
+import jalview.gui.PCAPanel;
import jalview.gui.PopupMenu;
+import jalview.gui.RotatableCanvas;
import jalview.gui.SliderPanel;
+import jalview.math.MatrixTest;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.FeatureColour;
import jalview.schemes.JalviewColourScheme;
import jalview.schemes.RNAHelicesColour;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.structure.StructureImportSettings;
+import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
+import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
+import javax.swing.JInternalFrame;
+import javax.swing.JRadioButton;
+
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
@Test(singleThreaded = true)
public class Jalview2xmlTests extends Jalview2xmlBase
{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ }
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUpMethod()
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
@Override
@BeforeClass(alwaysRun = true)
}
+ /**
+ * Test for JAL-2223 - multiple mappings in View Mapping report
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void noDuplicatePdbMappingsMade() throws Exception
+ {
+ StructureImportSettings.setProcessSecondaryStructure(true);
+ StructureImportSettings.setVisibleChainAnnotation(true);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+
+ // locate Jmol viewer
+ // count number of PDB mappings the structure selection manager holds -
+ String pdbFile = af.getCurrentView().getStructureSelectionManager()
+ .findFileForPDBId("1A70");
+ assertEquals(
+ af.getCurrentView().getStructureSelectionManager()
+ .getMapping(pdbFile).length,
+ 2, "Expected only two mappings for 1A70");
+
+ }
+
@Test(groups = { "Functional" })
public void viewRefPdbAnnotation() throws Exception
{
String afid = af.getViewport().getSequenceSetId();
// remember reference sequence for each panel
- Map<String, SequenceI> refseqs = new HashMap<String, SequenceI>();
+ Map<String, SequenceI> refseqs = new HashMap<>();
/*
* mark sequence 2, 3, 4.. in panels 1, 2, 3...
* remember representative and hidden sequences marked
* on each panel
*/
- Map<String, SequenceI> repSeqs = new HashMap<String, SequenceI>();
- Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
+ Map<String, SequenceI> repSeqs = new HashMap<>();
+ Map<String, List<String>> hiddenSeqNames = new HashMap<>();
/*
* mark sequence 2, 3, 4.. in panels 1, 2, 3...
repIndex = Math.max(repIndex, 1);
SequenceI repSeq = alignment.getSequenceAt(repIndex);
repSeqs.put(ap.getViewName(), repSeq);
- List<String> hiddenNames = new ArrayList<String>();
+ List<String> hiddenNames = new ArrayList<>();
hiddenSeqNames.put(ap.getViewName(), hiddenNames);
/*
assertTrue(rs.conservationApplied());
assertEquals(rs.getConservationInc(), 30);
}
+
+ /**
+ * Test save and reload of feature colour schemes and filter settings
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testSaveLoadFeatureColoursAndFilters() throws IOException
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
+ SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
+
+ /*
+ * add some features to the sequence
+ */
+ int score = 1;
+ addFeatures(seq1, "type1", score++);
+ addFeatures(seq1, "type2", score++);
+ addFeatures(seq1, "type3", score++);
+ addFeatures(seq1, "type4", score++);
+ addFeatures(seq1, "type5", score++);
+
+ /*
+ * set colour schemes for features
+ */
+ FeatureRenderer fr = af.getFeatureRenderer();
+ fr.findAllFeatures(true);
+
+ // type1: red
+ fr.setColour("type1", new FeatureColour(Color.red));
+
+ // type2: by label
+ FeatureColourI byLabel = new FeatureColour();
+ byLabel.setColourByLabel(true);
+ fr.setColour("type2", byLabel);
+
+ // type3: by score above threshold
+ FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
+ 10);
+ byScore.setAboveThreshold(true);
+ byScore.setThreshold(2f);
+ fr.setColour("type3", byScore);
+
+ // type4: by attribute AF
+ FeatureColourI byAF = new FeatureColour();
+ byAF.setColourByLabel(true);
+ byAF.setAttributeName("AF");
+ fr.setColour("type4", byAF);
+
+ // type5: by attribute CSQ:PolyPhen below threshold
+ FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
+ 1, 10);
+ byPolyPhen.setBelowThreshold(true);
+ byPolyPhen.setThreshold(3f);
+ byPolyPhen.setAttributeName("CSQ", "PolyPhen");
+ fr.setColour("type5", byPolyPhen);
+
+ /*
+ * set filters for feature types
+ */
+
+ // filter type1 features by (label contains "x")
+ FeatureMatcherSetI filterByX = new FeatureMatcherSet();
+ filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
+ fr.setFeatureFilter("type1", filterByX);
+
+ // filter type2 features by (score <= 2.4 and score > 1.1)
+ FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
+ filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
+ filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
+ fr.setFeatureFilter("type2", filterByScore);
+
+ // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
+ FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
+ filterByXY
+ .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
+ filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
+ "PolyPhen"));
+ fr.setFeatureFilter("type3", filterByXY);
+
+ /*
+ * save as Jalview project
+ */
+ File tfile = File.createTempFile("JalviewTest", ".jvp");
+ tfile.deleteOnExit();
+ String filePath = tfile.getAbsolutePath();
+ assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
+ "Failed to store as a project.");
+
+ /*
+ * close current alignment and load the saved project
+ */
+ af.closeMenuItem_actionPerformed(true);
+ af = null;
+ af = new FileLoader()
+ .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
+ assertNotNull(af, "Failed to import new project");
+
+ /*
+ * verify restored feature colour schemes and filters
+ */
+ fr = af.getFeatureRenderer();
+ FeatureColourI fc = fr.getFeatureStyle("type1");
+ assertTrue(fc.isSimpleColour());
+ assertEquals(fc.getColour(), Color.red);
+ fc = fr.getFeatureStyle("type2");
+ assertTrue(fc.isColourByLabel());
+ fc = fr.getFeatureStyle("type3");
+ assertTrue(fc.isGraduatedColour());
+ assertNull(fc.getAttributeName());
+ assertTrue(fc.isAboveThreshold());
+ assertEquals(fc.getThreshold(), 2f);
+ fc = fr.getFeatureStyle("type4");
+ assertTrue(fc.isColourByLabel());
+ assertTrue(fc.isColourByAttribute());
+ assertEquals(fc.getAttributeName(), new String[] { "AF" });
+ fc = fr.getFeatureStyle("type5");
+ assertTrue(fc.isGraduatedColour());
+ assertTrue(fc.isColourByAttribute());
+ assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
+ assertTrue(fc.isBelowThreshold());
+ assertEquals(fc.getThreshold(), 3f);
+
+ assertEquals(fr.getFeatureFilter("type1").toStableString(),
+ "Label Contains x");
+ 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)");
+ }
+
+ private void addFeature(SequenceI seq, String featureType, int score)
+ {
+ SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
+ score, "grp");
+ sf.setValue("AF", score);
+ sf.setValue("CSQ", new HashMap<String, String>()
+ {
+ {
+ put("PolyPhen", Integer.toString(score));
+ }
+ });
+ seq.addSequenceFeature(sf);
+ }
+
+ /**
+ * Adds two features of the given type to the given sequence, also setting the
+ * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
+ *
+ * @param seq
+ * @param featureType
+ * @param score
+ */
+ private void addFeatures(SequenceI seq, String featureType, int score)
+ {
+ addFeature(seq, featureType, score++);
+ addFeature(seq, featureType, score);
+ }
+
+ /**
+ * Test save and reload of a PCA viewer
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testSaveLoadPCA() throws IOException
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ assertEquals(af.getViewport().getAlignment().getHeight(), 15);
+
+ /*
+ * calculate and open PCA (calculates in a separate thread)
+ */
+ CalculationChooser chooser = new CalculationChooser(af);
+ ((JRadioButton) PA.getValue(chooser, "pca")).setSelected(true);
+ PA.invokeMethod(chooser, "calculate_actionPerformed()");
+ PCAPanel pcaPanel = (PCAPanel) PA.getValue(chooser, "pcaPanel");
+ assertNotNull(pcaPanel);
+ waitFor(50); // let it get started!!
+ while (pcaPanel.isWorking())
+ {
+ waitFor(50);
+ }
+ PA.invokeMethod(chooser, "close_actionPerformed()");
+
+ /*
+ * rotate, zoom in, change background colour
+ */
+ RotatableCanvas rc = (RotatableCanvas) PA.getValue(pcaPanel, "rc");
+ PA.setValue(rc, "bgColour", Color.PINK);
+ rc.zoom(1.9f);
+ rc.rotate(20, 40f);
+
+ /*
+ * save as Jalview project
+ */
+ File tfile = File.createTempFile("JalviewTest", ".jvp");
+ tfile.deleteOnExit();
+ String filePath = tfile.getAbsolutePath();
+ assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
+ "Failed to store as a project.");
+
+ /*
+ * load the saved project and locate the restored PCA panel
+ */
+ new FileLoader().LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ PCAPanel pcaPanel2 = null;
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof PCAPanel && frame != pcaPanel)
+ {
+ pcaPanel2 = (PCAPanel) frame;
+ }
+ }
+ assertNotNull(pcaPanel2);
+
+ /*
+ * compare restored and original PCA
+ */
+ PCAModel pcaModel = (PCAModel) PA.getValue(pcaPanel, "pcaModel");
+ PCAModel pcaModel2 = (PCAModel) PA.getValue(pcaPanel2, "pcaModel");
+ RotatableCanvas rc2 = (RotatableCanvas) PA.getValue(pcaPanel2, "rc");
+ assertNotNull(pcaModel);
+ assertNotNull(pcaModel2);
+ assertNotNull(rc2);
+ assertEquals(rc2.getBackgroundColour(), Color.PINK);
+ assertEquals(PA.getValue(rc2, "scaleFactor"), 1.9f);
+
+ // original has input data
+ assertNotNull(pcaModel.getInputData());
+ // restored has no input data (JAL-2647 to do)
+ assertNull(pcaModel2.getInputData());
+
+ // verify sequence points are at the same positions
+ List<SequencePoint> seqPts = pcaModel.getSequencePoints();
+ List<SequencePoint> seqPts2 = pcaModel2.getSequencePoints();
+ assertEquals(seqPts.size(), seqPts2.size());
+ for (int i = 0; i < seqPts.size(); i++)
+ {
+ SequencePoint sp = seqPts.get(i);
+ SequencePoint sp2 = seqPts2.get(i);
+ assertEquals(sp.getSequence().getName(), sp2.getSequence().getName());
+ assertEquals(sp.coord, sp2.coord);
+ }
+
+ // verify axis end points are at the same positions
+ Point[] axes = (Point[]) PA.getValue(rc, "axisEndPoints");
+ Point[] axes2 = (Point[]) PA.getValue(rc2, "axisEndPoints");
+ assertEquals(axes.length, 3);
+ assertEquals(axes2.length, 3);
+ for (int i = 0; i < 3; i++)
+ {
+ assertEquals(axes[i], axes2[i]);
+ }
+
+ // compare PCA data
+ PCA pca = (PCA) PA.getValue(pcaModel, "pca");
+ PCA pca2 = (PCA) PA.getValue(pcaModel2, "pca");
+ assertNotNull(pca);
+ assertNotNull(pca2);
+ // same (BLOSUM62) score model (a singleton object)
+ assertSame(PA.getValue(pca, "scoreModel"),
+ PA.getValue(pca2, "scoreModel"));
+ assertEquals(PA.getValue(pca, "similarityParams"),
+ PA.getValue(pca2, "similarityParams"));
+ MatrixTest.assertMatricesMatch(pca.getPairwiseScores(),
+ pca2.getPairwiseScores());
+ MatrixTest.assertMatricesMatch(pca.getTridiagonal(),
+ pca2.getTridiagonal());
+ MatrixTest.assertMatricesMatch(pca.getEigenmatrix(),
+ pca2.getEigenmatrix());
+ }
+
+ protected void waitFor(long t)
+ {
+ synchronized (this)
+ {
+ try
+ {
+ wait(t);
+ } catch (InterruptedException e)
+ {
+ fail(e.getMessage());
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff