Examples of PeakList

net.sf.mzmine.data.PeakList
org.bmdrc.mass.PeakList
@author SungBo Hwang, CSB @author GiBum Shin, CSB

Examples of net.sf.mzmine.data.PeakList

      });
      dataFiles.addAll(Arrays.asList(files));
    }


    // Produce new PeakList
    PeakList peakList = new SimplePeakList("Mass Candidates",
        dataFiles.toArray(new RawDataFile[dataFiles.size()]));


    // Start the comparison task to filter and sort the candidate masses
    SpectraMatcherComparisonTask comparisonTask = new SpectraMatcherComparisonTask(
        processingTasks, parameters, massCandidatesByFile, peakList);

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Examples of net.sf.mzmine.data.PeakList

        return a.getName().compareTo(b.getName());
      }
    });


    // Produce new PeakList
    PeakList peakList = new SimplePeakList(
        "Retention Index Correction Results",
        dataFiles.toArray(new RawDataFile[dataFiles.size()]));


    // Create PeakListRows
    int id = 0;


    for (String name : FameData.FAME_NAMES) {
      PeakListRow row = new SimplePeakListRow(++id);
      row.setComment(name);


      for (FameAlignmentProcessingTask task : processingTasks) {
        if (task.getResults().containsKey(name))
          row.addPeak(task.getResults().get(name).getDataFile(), task
              .getResults().get(name));
      }


      peakList.addRow(row);
    }


    // Add table to the GUI
    ResultsListTableWindow window = new ResultsListTableWindow(peakList);
    MZmineCore.getDesktop().addInternalFrame(window);

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Examples of net.sf.mzmine.data.PeakList


        currentLoadedObjectName = fileMatcher.group(2);


        InputStream peakListStream = zipFile.getInputStream(entry);


        PeakList newPeakList = peakListOpenHandler
            .readPeakList(peakListStream);


        newProject.addPeakList(newPeakList);
      }

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Examples of net.sf.mzmine.data.PeakList

  @Override
  protected void addDialogComponents() {


    super.addDialogComponents();


    PeakList peakLists[] = MZmineCore.getCurrentProject().getPeakLists();
    if (peakLists.length < 2)
      return;


    PeakList selectedPeakLists[] = MZmineCore.getDesktop()
        .getSelectedPeakLists();


    // Preview check box
    previewCheckBox = new JCheckBox("Show preview of RANSAC alignment");
    previewCheckBox.addActionListener(this);

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Examples of net.sf.mzmine.data.PeakList

    return alignMol;
  }


  private void updatePreview() {


    PeakList peakListX = (PeakList) peakListsComboX.getSelectedItem();
    PeakList peakListY = (PeakList) peakListsComboY.getSelectedItem();


    if ((peakListX == null) || (peakListY == null))
      return;


    // Select the rawDataFile which has more peaks in each peakList
    int numPeaks = 0;
    RawDataFile file = null;
    RawDataFile file2 = null;


    for (RawDataFile rfile : peakListX.getRawDataFiles()) {
      if (peakListX.getPeaks(rfile).length > numPeaks) {
        numPeaks = peakListX.getPeaks(rfile).length;
        file = rfile;
      }
    }
    numPeaks = 0;
    for (RawDataFile rfile : peakListY.getRawDataFiles()) {
      if (peakListY.getPeaks(rfile).length > numPeaks) {
        numPeaks = peakListY.getPeaks(rfile).length;
        file2 = rfile;
      }
    }


    // Update the parameter set from dialog components
    updateParameterSetFromComponents();


    // Check the parameter values
    ArrayList<String> errorMessages = new ArrayList<String>();
    boolean parametersOK = super.parameterSet
        .checkAllParameterValues(errorMessages);
    if (!parametersOK) {
      StringBuilder message = new StringBuilder(
          "Please check the parameter settings:\n\n");
      for (String m : errorMessages) {
        message.append(m);
        message.append("\n");
      }
      MZmineCore.getDesktop().displayMessage(message.toString());
      return;
    }


    // Ransac Alignment
    Vector<AlignStructMol> list = this.getVectorAlignment(peakListX,
        peakListY, file, file2);
    RANSAC ransac = new RANSAC(super.parameterSet);
    ransac.alignment(list);


    // Plot the result
    this.chart.removeSeries();
    this.chart.addSeries(list,
        peakListX.getName() + " vs " + peakListY.getName(),
        super.parameterSet.getParameter(RansacAlignerParameters.Linear)
            .getValue());
    this.chart.printAlignmentChart(peakListX.getName() + " RT",
        peakListY.getName() + " RT");


  }

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Examples of net.sf.mzmine.data.PeakList

  }


  @Override
  public ExitCode showSetupDialog() {


    PeakList selectedPeakList[] = getParameter(peakList).getValue();
    PeakListRow rowChoices[];
    if (selectedPeakList.length == 1) {
      rowChoices = selectedPeakList[0].getRows();
    } else {
      rowChoices = new PeakListRow[0];

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Examples of net.sf.mzmine.data.PeakList

  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {


    PeakList peakLists[] = parameters.getParameter(
        StandardCompoundNormalizerParameters.peakList).getValue();
    for (PeakList peakList : peakLists) {
      Task newTask = new StandardCompoundNormalizerTask(peakList,
          parameters);
      tasks.add(newTask);

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Examples of net.sf.mzmine.data.PeakList

    ExitCode exitCode = BatchModeModule.runBatch(batchFile);
    assert (exitCode == ExitCode.OK);


    assert (MZmineCore.getCurrentProject().getPeakLists().length > 0);


    PeakList peakList = MZmineCore.getCurrentProject().getPeakLists()[0];
    assert (peakList.getNumberOfRows() > 0);


    logger.info("Set #1 Mass Candidates: " + peakList.getNumberOfRows());


    for (PeakListRow row : peakList.getRows()) {
      assert (row.getNumberOfPeaks() > 0);
      assert (row.getRawDataFiles().length > 0);
      assert (row.getNumberOfPeaks() > 0);


      for (ChromatographicPeak p : row.getPeaks()) {

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Examples of net.sf.mzmine.data.PeakList

        alignment.addRow(row);


      }
    }


    PeakList curAlignment = alignment;
    return curAlignment;
  }

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Examples of net.sf.mzmine.data.PeakList

    ExitCode exitCode = BatchModeModule.runBatch(batchFile);
    assert (exitCode == ExitCode.OK);


    assert (MZmineCore.getCurrentProject().getPeakLists().length > 0);


    PeakList peakList = MZmineCore.getCurrentProject().getPeakLists()[0];
    assert (peakList.getNumberOfRows() > 0);


    logger.info("Set #2 Mass Candidates: " + peakList.getNumberOfRows());


    for (PeakListRow row : peakList.getRows()) {
      assert (row.getNumberOfPeaks() > 0);
      assert (row.getRawDataFiles().length > 0);
      assert (row.getNumberOfPeaks() > 0);


      for (ChromatographicPeak p : row.getPeaks()) {

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