Examples of net.sf.mzmine.data.DataPoint

net.sf.mzmine.data.DataPoint
This interface represents one data point of a spectra (m/z and intensity). Data point is immutable once created, to make things simple.

    for (index = 0; index < dataPoints.length; index++) {
      if (dataPoints[index].getIntensity() >= intensity)
        points.add(dataPoints[index]);
    }


    DataPoint pointsOverIntensity[] = points.toArray(new DataPoint[0]);


    return pointsOverIntensity;
  }

View Full Code Here


    // Update raw data point ranges, height, rt and representative scan
    height = Double.MIN_VALUE;
    for (int i = 0; i < allScanNumbers.length; i++) {


      DataPoint mzPeak = dataPointsMap.get(allScanNumbers[i]);


      // Replace the MzPeak instance with an instance of SimpleDataPoint,
      // to reduce the memory usage. After we finish this extended peak,
      // we
      // don't need the additional data provided by the MzPeak
      SimpleDataPoint newDataPoint = new SimpleDataPoint(mzPeak);
      dataPointsMap.put(allScanNumbers[i], newDataPoint);


      if (i == 0) {
        rawDataPointsIntensityRange = new Range(mzPeak.getIntensity());
        rawDataPointsMZRange = new Range(mzPeak.getMZ());
      } else {
        rawDataPointsIntensityRange.extendRange(mzPeak.getIntensity());
        rawDataPointsMZRange.extendRange(mzPeak.getMZ());
      }


      if (height < mzPeak.getIntensity()) {
        height = mzPeak.getIntensity();
        rt = dataFile.getScan(allScanNumbers[i]).getRetentionTime();
        representativeScan = allScanNumbers[i];
      }
    }

View Full Code Here

    RawDataFile rawFile = oldPeak.getDataFile();
    ExtendedPeak newPeak = new ExtendedPeak(rawFile);
    int totalScanNumber = rawFile.getNumOfScans();
    Range mzRange = mzTolerance.getToleranceRange(oldPeak.getMZ());
    Scan scan;
    DataPoint dataPoint;


    // Look for dataPoint related to this peak to the left
    int scanNumber = originScanNumber;
    scanNumber--;
    while (scanNumber > 0) {


      scan = rawFile.getScan(scanNumber);


      if (scan == null) {
        scanNumber--;
        continue;
      }


      if (scan.getMSLevel() != 1) {
        scanNumber--;
        continue;
      }


      dataPoint = ScanUtils.findBasePeak(scan, mzRange);


      if (dataPoint == null)
        break;
      if (dataPoint.getIntensity() < minimumHeight)
        break;


      newPeak.addMzPeak(scanNumber, dataPoint);
      if (dataPoint.getIntensity() > maxHeight)
        maxHeight = dataPoint.getIntensity();


      scanNumber--;


    }


    // Add original dataPoint
    newPeak.addMzPeak(originScanNumber,
        oldPeak.getDataPoint(originScanNumber));


    // Look to the right
    scanNumber = originScanNumber;
    scanNumber++;
    while (scanNumber <= totalScanNumber) {


      scan = rawFile.getScan(scanNumber);


      if (scan == null) {
        scanNumber++;
        continue;
      }


      if (scan.getMSLevel() != 1) {
        scanNumber++;
        continue;
      }


      dataPoint = ScanUtils.findBasePeak(scan, mzRange);


      if (dataPoint == null)
        break;
      if (dataPoint.getIntensity() < minimumHeight)
        break;


      newPeak.addMzPeak(scanNumber, dataPoint);
      if (dataPoint.getIntensity() > maxHeight)
        maxHeight = dataPoint.getIntensity();


      scanNumber++;


    }

View Full Code Here


  @Override
  public boolean equals(Object obj) {
    if (!(obj instanceof DataPoint))
      return false;
    DataPoint dp = (DataPoint) obj;
    return (this.mz == dp.getMZ()) && (this.intensity == dp.getIntensity());
  }

View Full Code Here


      // Get next scan
      Scan scan = column.getScan(scanNumber);


      // Find most intense m/z peak
      DataPoint basePeak = ScanUtils.findBasePeak(scan, mzRangeWithTol);


      if (basePeak != null) {
        if (basePeak.getIntensity() > 0)
          dataPointFound = true;
        newPeak.addDatapoint(scan.getScanNumber(), basePeak);
      } else {
        DataPoint fakeDataPoint = new SimpleDataPoint(
            mzRangeWithTol.getAverage(), 0);
        newPeak.addDatapoint(scan.getScanNumber(), fakeDataPoint);
      }


    }

View Full Code Here

    for (int i = 0; i < scanNumbers.length; i++)
      retentionTimes[i] = dataFile.getScan(scanNumbers[i])
          .getRetentionTime();
    double intensities[] = new double[scanNumbers.length];
    for (int i = 0; i < scanNumbers.length; i++) {
      DataPoint dp = previewPeak.getDataPoint(scanNumbers[i]);
      if (dp != null)
        intensities[i] = dp.getIntensity();
      else
        intensities[i] = 0;
    }


    // Create shape model

View Full Code Here


    ChromatographicPeak peaks[] = peakList.getPeaks(dataFile);


    Vector<ChromatographicPeak> candidates = new Vector<ChromatographicPeak>();
    for (ChromatographicPeak peak : peaks) {
      DataPoint peakDataPoint = peak.getDataPoint(scanNumber);
      if (peakDataPoint != null)
        candidates.add(peak);
    }
    displayedPeaks = candidates.toArray(new ChromatographicPeak[0]);


    mzValues = new double[displayedPeaks.length];
    intensityValues = new double[displayedPeaks.length];


    for (int i = 0; i < displayedPeaks.length; i++) {
      DataPoint dp = displayedPeaks[i].getDataPoint(scanNumber);
      if (dp == null)
        continue;
      mzValues[i] = dp.getMZ();
      intensityValues[i] = dp.getIntensity();
    }


    label = "Peaks in " + peakList.getName();


  }

View Full Code Here

            retentionTimes[i] = dataFile.getScan(scanNumbers[i])
                .getRetentionTime();


          intensities = new double[scanNumbers.length];
          for (int i = 0; i < scanNumbers.length; i++) {
            DataPoint dp = peak.getDataPoint(scanNumbers[i]);
            if (dp != null)
              intensities[i] = dp.getIntensity();
            else
              intensities[i] = 0;
          }


          ChromatographicPeak shapePeak = (ChromatographicPeak) shapeModelConstruct

View Full Code Here

      return scan;
    }


    // Pickup datapoints inside the m/z range


    DataPoint croppedDataPoints[] = scan.getDataPointsByMass(mzRange);


    // Create updated scan
    SimpleScan newScan = new SimpleScan(scan);
    newScan.setDataPoints(croppedDataPoints);

View Full Code Here

    // Get all scan numbers
    int allScanNumbers[] = CollectionUtils.toIntArray(mzPeakMap.keySet());


    // Find the data point with top intensity and use its RT and height
    for (int i = 0; i < allScanNumbers.length; i++) {
      DataPoint dataPoint = mzPeakMap.get(allScanNumbers[i]);
      double rt = dataFile.getScan(allScanNumbers[i]).getRetentionTime();
      if (dataPoint.getIntensity() > height) {
        height = dataPoint.getIntensity();
        representativeScan = allScanNumbers[i];
        this.rt = rt;
      }
    }

View Full Code Here

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Related Classes of net.sf.mzmine.data.DataPoint

net.sf.mzmine.data.impl.SimpleDataPoint

net.sf.mzmine.data.impl.SimpleScan

net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameAlignmentProcessingTask

net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.Chromatogram

net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderTask

net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.HighestDataPointConnector

net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilter

net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterSetupDialog

net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterTask

net.sf.mzmine.modules.peaklistmethods.gapfilling.peakfinder.Gap

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