Package net.sf.mzmine.util

Examples of net.sf.mzmine.util.Range

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    setBackground(Color.white);

    this.dataFile = dataFile;

    // Retrieve parameter's values
    Range rtRange = parameters.getParameter(
        NeutralLossParameters.retentionTimeRange).getValue();
    Range mzRange = parameters.getParameter(NeutralLossParameters.mzRange)
        .getValue();
    int numOfFragments = parameters.getParameter(
        NeutralLossParameters.numOfFragments).getValue();

    Object xAxisType = parameters.getParameter(
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        }

        double mzMin = ((Number) fieldMinMZ.getValue()).doubleValue();
        double mzMax = ((Number) fieldMaxMZ.getValue()).doubleValue();

        Range range = new Range(mzMin, mzMax);
        if (rangeType.equals("HIGHLIGHT_PRECURSOR"))
          plot.setHighlightedPrecursorRange(range);
        else if (rangeType.equals("HIGHLIGHT_NEUTRALLOSS"))
          plot.setHighlightedNeutralLossRange(range);
        logger.info("Updating Neutral loss plot window");
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  public Scan filterScan(Scan scan, ParameterSet parameters) {

    double binSize = parameters.getParameter(
        ResampleFilterParameters.binSize).getValue();

    Range mzRange = scan.getMZRange();
    int numberOfBins = (int) Math.round((mzRange.getMax() - mzRange
        .getMin()) / binSize);
    if (numberOfBins == 0) {
      numberOfBins++;
    }

    // ScanUtils.binValues needs arrays
    DataPoint dps[] = scan.getDataPoints();
    double[] x = new double[dps.length];
    double[] y = new double[dps.length];
    for (int i = 0; i < dps.length; i++) {
      x[i] = dps[i].getMZ();
      y[i] = dps[i].getIntensity();
    }
    // the new intensity values
    double[] newY = ScanUtils.binValues(x, y, mzRange, numberOfBins,
        !scan.isCentroided(), ScanUtils.BinningType.AVG);
    SimpleDataPoint[] newPoints = new SimpleDataPoint[newY.length];

    // set the new m/z value in the middle of the bin
    double newX = mzRange.getMin() + binSize / 2.0;
    // creates new DataPoints
    for (int i = 0; i < newY.length; i++) {
      newPoints[i] = new SimpleDataPoint(newX, newY[i]);
      newX += binSize;
    }
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  }

  public void updateOnRangeDataPoints(String rangeType) {

    NeutralLossPlot plot = visualizer.getPlot();
    Range prRange = plot.getHighlightedPrecursorRange();
    Range nlRange = plot.getHighlightedNeutralLossRange();

    // Set type of search
    int level = NEUTRALLOSS_LEVEL;
    if (rangeType.equals("HIGHLIGHT_PRECURSOR"))
      level = PRECURSOR_LEVEL;

    // Clean previous selection
    dataSeries.get(level).clear();

    NeutralLossDataPoint point;
    boolean b = false;
    for (int i = 0; i < dataSeries.get(RAW_LEVEL).size(); i++) {
      point = dataSeries.get(RAW_LEVEL).get(i);
      // Verify if the point is on range
      if (level == PRECURSOR_LEVEL)
        b = prRange.contains(point.getPrecursorMass());
      else
        b = nlRange.contains(point.getNeutralLoss());
      if (b)
        dataSeries.get(level).add(point);
    }

    fireDatasetChanged();
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      if (minValue == null)
        minValue = 0;
      Number maxValue = ((Number) maxSearchField.getValue());
      if (maxValue == null)
        maxValue = 0;
      Range searchRange = new Range(minValue.doubleValue(),
          maxValue.doubleValue());
      try {
        SearchDefinition newSearch = new SearchDefinition(searchType,
            searchRegex, searchRange);
        chart.updateSearchDefinition(newSearch);
      } catch (PatternSyntaxException pe) {
        MZmineCore.getDesktop().displayErrorMessage(
            "The regular expression's syntax is invalid: " + pe);
      }
      return;
    }

    if (command.equals("SEARCH_DATA_TYPE")) {

      SearchDefinitionType searchType = (SearchDefinitionType) comboSearchDataType
          .getSelectedItem();

      switch (searchType) {

        case MASS :
          minSearchField.setVisible(true);
          maxSearchField.setVisible(true);
          labelRange.setVisible(true);
          txtSearchField.setVisible(false);
          NumberFormat mzFormatter = MZmineCore.getConfiguration()
              .getMZFormat();
          Range mzRange = peakList.getRowsMZRange();
          DefaultFormatterFactory mzFormatFac = new DefaultFormatterFactory(
              new NumberFormatter(mzFormatter));
          minSearchField.setFormatterFactory(mzFormatFac);
          minSearchField.setValue(mzRange.getMin());
          maxSearchField.setFormatterFactory(mzFormatFac);
          maxSearchField.setValue(mzRange.getMax());
          break;

        case RT :
          minSearchField.setVisible(true);
          maxSearchField.setVisible(true);
          labelRange.setVisible(true);
          txtSearchField.setVisible(false);
          NumberFormat rtFormatter = MZmineCore.getConfiguration()
              .getRTFormat();
          Range rtRange = peakList.getRowsRTRange();
          DefaultFormatterFactory rtFormatFac = new DefaultFormatterFactory(
              new NumberFormatter(rtFormatter));
          minSearchField.setFormatterFactory(rtFormatFac);
          minSearchField.setValue(rtRange.getMin());
          maxSearchField.setFormatterFactory(rtFormatFac);
          maxSearchField.setValue(rtRange.getMax());
          break;

        case NAME :
          minSearchField.setVisible(false);
          maxSearchField.setVisible(false);
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      @Nonnull Collection<Task> tasks) {
    final RawDataFile[] dataFiles = parameters.getParameter(
        TICVisualizerParameters.DATA_FILES).getValue();
    final int msLevel = parameters.getParameter(
        TICVisualizerParameters.MS_LEVEL).getValue();
    final Range rtRange = parameters.getParameter(
        TICVisualizerParameters.RT_RANGE).getValue();
    final Range mzRange = parameters.getParameter(
        TICVisualizerParameters.MZ_RANGE).getValue();
    final PlotType plotType = parameters.getParameter(
        TICVisualizerParameters.PLOT_TYPE).getValue();
    final ChromatographicPeak[] selectionPeaks = parameters.getParameter(
        TICVisualizerParameters.PEAKS).getValue();
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    // if necessary
    for (int row = 0; row < peaks.size(); row++) {
      PeakListRow newRow = processedPeakList.getRow(row);
      // Create a new gap

      Range mzRange = mzTolerance.getToleranceRange(peaks.get(row)
          .getMZ());
      Range rtRange = rtTolerance.getToleranceRange(peaks.get(row)
          .getRT());
      newRow.addPeakIdentity(new SimplePeakIdentity(peaks.get(row)
          .getName()), true);

      Gap newGap = new Gap(newRow, dataFile, mzRange, rtRange,
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    // setBackground(Color.white);

    this.getInfoRange(peakList);

    if (peakList.getNumberOfRows() == 0) {
      mzRange = new Range(0, 0);
      rtRange = new Range(0, 0);
    }

    // Raw data file list
    JList rawDataFileList = new JList(peakList.getRawDataFiles());
    rawDataFileList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
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  public void actionPerformed(ActionEvent event) {

    Object src = event.getSource();

    if (src == setAutoButton) {
      Range rtRange = null;
      RawDataFile currentFiles[] = MZmineCore.getCurrentProject()
          .getDataFiles();
      for (RawDataFile file : currentFiles) {
        Range fileRange = file.getDataRTRange();
        if (rtRange == null)
          rtRange = fileRange;
        else
          rtRange.extendRange(fileRange);
      }
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      double area = 0, height = 0, mz = 0, rt = 0;
      int scanNumbers[] = new int[bestPeakDataPoints.size()];
      DataPoint finalDataPoint[] = new DataPoint[bestPeakDataPoints
          .size()];
      Range finalRTRange = null, finalMZRange = null, finalIntensityRange = null;
      int representativeScan = 0;

      // Process all datapoints
      for (int i = 0; i < bestPeakDataPoints.size(); i++) {

        GapDataPoint dp = bestPeakDataPoints.get(i);

        if (i == 0) {
          finalRTRange = new Range(dp.getRT());
          finalMZRange = new Range(dp.getMZ());
          finalIntensityRange = new Range(dp.getIntensity());
        } else {
          assert finalRTRange != null && finalMZRange != null
              && finalIntensityRange != null;
          finalRTRange.extendRange(dp.getRT());
          finalMZRange.extendRange(dp.getMZ());
          finalIntensityRange.extendRange(dp.getIntensity());
        }

        scanNumbers[i] = bestPeakDataPoints.get(i).getScanNumber();
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Related Classes of net.sf.mzmine.util.Range

  • net.sf.mzmine.data.impl.SimpleChromatographicPeak
  • net.sf.mzmine.data.impl.SimplePeakList
  • net.sf.mzmine.data.impl.SimpleScan
  • net.sf.mzmine.modules.deconvolutedanalysis.CorrectedSpectrum
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameAlignmentProcessingTask
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameCorrection
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.table.ResultsListTable
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.MassCandidate
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.SpectraMatcherComparisonTask
  • net.sf.mzmine.modules.deconvolutedanalysis.spectrafilter.SpectraFilterTest
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