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 jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+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.Desktop;
+import jalview.gui.FeatureRenderer;
import jalview.gui.Jalview2XML;
import jalview.gui.JvOptionPane;
import jalview.gui.PopupMenu;
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 java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
@Test(singleThreaded = true)
public class Jalview2xmlTests extends Jalview2xmlBase
{
}
+ /**
+ * 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);
/*
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
- AlignViewport av = af.getViewport();
+ AlignViewportI av = af.getViewport();
AlignmentI al = av.getAlignment();
/*
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 testStoreAndRecoverFeatureColoursAndFilters()
+ 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);
+ }
+
+ /**
+ * 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.instance.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.instance.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());
+ }
}
git://source.jalview.org / jalview.git / blobdiff