Package org.bioinfo.ngs.qc.qualimap.gui.utils

Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper$Section

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  public void createBeanCreateCloneThenCloneShouldHaveSameStructureAndValuesButEveryElementOfDifferentReference() {
   
    // create some data
    // use a.b.m2.Book which has 1:N relations (collection) to other beans
    Book book = new Book("History of Britain", "John O'Farrel", ImmutableList.copyOf(new Section[] {
      new Section("Section1", "no description", ImmutableSet.copyOf(new Paragraph[] {
          new Paragraph(1, "Bla bla bla"),
          new Paragraph(1, "Bla bla bla"),
      })),
      new Section("Section2", "no description", ImmutableSet.copyOf(new Paragraph[] {
          new Paragraph(1066, "Bla bla bla"),
      })),
      new Section("Section3", "no description", ImmutableSet.copyOf(new Paragraph[] {
          new Paragraph(1, "Bla bla bla"),
          new Paragraph(2, "Bla bla bla"),
          new Paragraph(3, "Bla bla bla"),
      })),
    }));
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public class SimpleApp {
  public static void main(String[] args) {
    // create some data
    // use a.b.m2.Book which has 1:N relations (collection) to other beans
    Book book = new Book("History of Britain", "John O'Farrel", ImmutableList.copyOf(new Section[] {
      new Section("Section1", "no description", ImmutableSet.copyOf(new Paragraph[] {
          new Paragraph(1, "Bla bla bla"),
          new Paragraph(1, "Bla bla bla"),
      })),
      new Section("Section2", "no description", ImmutableSet.copyOf(new Paragraph[] {
          new Paragraph(1066, "Bla bla bla"),
      })),
      new Section("Section3", "no description", ImmutableSet.copyOf(new Paragraph[] {
          new Paragraph(1, "Bla bla bla"),
          new Paragraph(2, "Bla bla bla"),
          new Paragraph(3, "Bla bla bla"),
      })),
    }));
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    Body body = new Body();
    Mdiv mdiv = new Mdiv();
    Score score = new Score();
    ScoreDef scoreDef = createScoreDef(stavesCount);
    score.getGapsAndSbsAndCorrs().add(scoreDef);
    Section section = new Section();
    Measure measureFirst = new Measure();
    Staff staffFirst = new Staff();
    Layer layerFirst = new Layer();
    staffFirst.getSbsAndSymbolsAndOrigs().add(layerFirst);
    measureFirst.getAnnotsAndSlursAndTupletSpen().add(staffFirst);
    for (int stavesIter = 1; stavesIter < stavesCount; stavesIter++) {
      Staff staff = new Staff();
      Layer layer = new Layer();
      staff.getSbsAndSymbolsAndOrigs().add(layer);
      measureFirst.getAnnotsAndSlursAndTupletSpen().add(staff);
    }
    section.getUnclearsAndSbsAndApps().add(measureFirst);

    for (int measureIter = 1; measureIter < measureCount; measureIter++) {
      Measure measure = new Measure();
      for (int stavesIter = 0; stavesIter < stavesCount; stavesIter++) {
        Staff staff = new Staff();
        Layer layer = new Layer();
        staff.getSbsAndSymbolsAndOrigs().add(layer);
        measure.getAnnotsAndSlursAndTupletSpen().add(staff);
      }
      section.getUnclearsAndSbsAndApps().add(measure);
    }
    score.getGapsAndSbsAndCorrs().add(section);
    mdiv.setScore(score);
    body.getMdivs().add(mdiv);
    music.setBody(body);
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    tpd.setDescription(MusicMessages.MEI_documentation_generic_n);
    descriptors.add(tpd);
  }
 
  private void createDefaultSection() {
    setMeiNode(new Section());
  }
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  private static MeiNode handleScoreChild(BasicElement childForm,
      boolean saveAllVariants) {
    if (childForm instanceof SectionForm) {
      SectionForm sectionForm = (SectionForm) childForm;
      Section section = (Section) sectionForm.getMeiNode();
      section.getUnclearsAndSbsAndApps().clear();
      for (BasicElement sectionChildForm : sectionForm.getChildren()) {
        section.getUnclearsAndSbsAndApps().add(
            handleScoreChild(sectionChildForm, saveAllVariants));
      }
      return section;
    } else if (childForm instanceof EndingForm) {
      EndingForm endingForm = (EndingForm) childForm;
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     * <!-- begin-user-doc -->
     * <!-- end-user-doc -->
     * @generated
     */
    public Section createSectionFromString(EDataType eDataType, String initialValue) {
        Section result = Section.get(initialValue);
        if (result == null) throw new IllegalArgumentException("The value '" + initialValue + "' is not a valid enumerator of '" + eDataType.getName() + "'");
        return result;
    }
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        SectionsType owsSections = (SectionsType) kvp.get("sections");
        if(owsSections != null) {
            Sections sections = Wcs20Factory.eINSTANCE.createSections();
            for(Object o : owsSections.getSection()) {
                String sectionName = (String) o;
                Section section = Section.get(sectionName);
                if(section == null) {
                    throw new WCS20Exception("Invalid sections value " + sectionName + ", supported values are " + Arrays.asList(Section.values()),
                            OWSExceptionCode.InvalidParameterValue, "sections");
                }
                sections.getSection().add(section);
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    public StatsReporter() {
        name = "Results";
        namePostfix = "";
        fileName = "qualimapReport";
        inputDataKeeper = new StatsKeeper();
        summaryStatsKeeper = new StatsKeeper();
        tableDataStatsKeeper = new StatsKeeper();
    }
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    }

    private void prepareChromosomeStatsKeeper(BamStats.ChromosomeInfo[] statsArray) {

        tableDataStatsKeeper = new StatsKeeper();
        tableDataStatsKeeper.setName("Chromosome stats" + namePostfix );

        StatsKeeper.Section headerSection = new StatsKeeper.Section(Constants.TABLE_STATS_HEADER);
        String[] header = {
                "Name", "Length", "Mapped bases", "Mean coverage", "Standard deviation"
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    private void createSummaryTable(StatsReporter reporter) throws IOException {

        logLine("Creating summary...\n");

        StatsKeeper summaryKeeper = reporter.getSummaryStatsKeeper();

        StatsKeeper.Section section = new StatsKeeper.Section("Globals");
        section.addRow("Number of samples", Integer.toString( bamQCResults.size() ));
        summaryKeeper.addSection(section);

        StatsKeeper tableDataKeeper = reporter.getTableDataStatsKeeper();

        StatsKeeper.Section headerSection = new StatsKeeper.Section("header");
        String[] header = {"Sample name", "Coverage mean", "Coverage std",
                "GC percentage", "Mapping quality mean", "Insert size median" };
        headerSection.addRow( header );
        tableDataKeeper.addSection(headerSection);

        StatsKeeper.Section dataSection = new StatsKeeper.Section("data");

        for (SampleInfo bamQcResult : bamQCResults) {
            String path = bamQcResult.path + File.separator + "genome_results.txt";
            BamStats stats = loadSummaryStats(path);

            String[] row = new String[header.length];
            row[0] = bamQcResult.name;
            row[1] = Double.toString( stats.getMeanCoverage() );
            row[2] = Double.toString( stats.getStdCoverage() );
            row[3] = Double.toString( stats.getMeanGcRelativeContent() );
            row[4] = Double.toString( stats.getMeanMappingQualityPerWindow() );
            row[5] = Double.toString( stats.getMedianInsertSize() );
            dataSection.addRow(row);

            double[] sample = new double[NUM_FEATURES];
            sample[0] = stats.getMeanCoverage();
            sample[1] = stats.getStdCoverage();
            sample[2] = stats.getMeanGcRelativeContent();
            sample[3] = stats.getMeanMappingQualityPerWindow();
            sample[4] = stats.getMedianInsertSize();
            sampleData.add(sample);


        }
        tableDataKeeper.addSection(dataSection);



    }
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Related Classes of org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper$Section

  • a.b.application.CreateBeanAndCloneTest
  • a.b.z.application.SimpleApp
  • ca.uhn.fhir.model.dstu.composite.CodeableConceptDt
  • ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt
  • ca.uhn.fhir.model.primitive.StringDt
  • com.google.gerrit.common.data.ChangeInfo
  • com.google.gwt.user.client.Element
  • info.textgrid.lab.noteeditor.factories.MusicContainerFactory
  • info.textgrid.lab.noteeditor.MeiFromFormsConverter
  • info.textgrid.lab.noteeditor.model.SectionForm
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