Examples of net.sf.mzmine.data.impl.SimpleDataPoint

net.sf.mzmine.data.impl.SimpleDataPoint
This class represents one data point of a spectrum (m/z and intensity pair). Data point is immutable once created, to make things simple.


      double mz = dataPoints[i].getMZ();
      double intensity = dataPoints[i].getIntensity() / maxIntensity
          * normalizedValue;


      newDataPoints[i] = new SimpleDataPoint(mz, intensity);
    }


    SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
        newDataPoints, pattern.getStatus(), pattern.getDescription());

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            + dataPoints[i + 1].getIntensity();
        double newMZ = (dataPoints[i].getMZ()
            * dataPoints[i].getIntensity() + dataPoints[i + 1]
            .getMZ() * dataPoints[i + 1].getIntensity())
            / newIntensity;
        dataPoints[i + 1] = new SimpleDataPoint(newMZ, newIntensity);
        dataPoints[i] = null;
      }
    }


    ArrayList<DataPoint> newDataPoints = new ArrayList<DataPoint>();

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              massOverCharge = (double) peakStream.readFloat();
              intensity = (double) peakStream.readFloat();
            }


            // Copy m/z and intensity data
            completeDataPoints[i] = new SimpleDataPoint(
                massOverCharge, intensity);


          }
        } catch (IOException eof) {
          setStatus(TaskStatus.ERROR);

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        LittleEndianDataInputStream dis = new LittleEndianDataInputStream(
            dumpStream);
        for (int i = 0; i < numOfDataPoints; i++) {
          double mz = dis.readDouble();
          double intensity = dis.readDouble();
          completeDataPoints[i] = new SimpleDataPoint(mz, intensity);
        }


        boolean centroided = ScanUtils.isCentroided(completeDataPoints);


        DataPoint optimizedDataPoints[] = ScanUtils

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      double mz = massValueArray.getDouble(massIndex0)
          * massValueScaleFactor;
      double intensity = intensityValueArray.getDouble(intensityIndex0)
          * intensityValueScaleFactor;
      completeDataPoints[j] = new SimpleDataPoint(mz, intensity);


    }


    scanNum++;

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        DataPoint completeDataPoints[] = new DataPoint[peaksCount];
        spectrumInstrumentFlag = false;


        // Copy m/z and intensity data
        for (int i = 0; i < completeDataPoints.length; i++) {
          completeDataPoints[i] = new SimpleDataPoint(
              (double) mzDataPoints[i],
              (double) intensityDataPoints[i]);
        }


        // Auto-detect whether this scan is centroided

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        scanner.next();


        int spectrumSize = scanner.nextInt();
        DataPoint[] dataPoints = new DataPoint[spectrumSize];
        for (int j = 0; j < spectrumSize; j++) {
          dataPoints[j] = new SimpleDataPoint(scanner.nextDouble(),
              scanner.nextDouble());
        }
        newMZmineFile.addScan(new SimpleScan(null, parsedScans + 1,
            msLevel, retentionTime, -1, 0.0, charge, null,
            dataPoints, ScanUtils.isCentroided(dataPoints)));

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


        processedScans++;

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    Number intensityValues[] = intensityArray.getBinaryDataAsNumberArray();
    DataPoint dataPoints[] = new DataPoint[mzValues.length];
    for (int i = 0; i < dataPoints.length; i++) {
      double mz = mzValues[i].doubleValue();
      double intensity = intensityValues[i].doubleValue();
      dataPoints[i] = new SimpleDataPoint(mz, intensity);
    }
    return dataPoints;


  }

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    if (pattern != null) {
      isotopes = pattern.getDataPoints();
    } else {
      isotopes = new DataPoint[1];
      ChromatographicPeak bestPeak = row.getBestPeak();
      isotopes[0] = new SimpleDataPoint(bestPeak.getMZ(),
          bestPeak.getHeight());
    }


    try {
      FileWriter fileWriter = new FileWriter(outputFile);

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Related Classes of net.sf.mzmine.data.impl.SimpleDataPoint

net.sf.mzmine.data.DataPoint

net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameData

net.sf.mzmine.modules.deconvolutedanalysis.massdetection.MassCandidate

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

net.sf.mzmine.modules.peaklistmethods.gapfilling.samerange.SameRangeTask

net.sf.mzmine.modules.peaklistmethods.identification.camera.CameraSearchTask

net.sf.mzmine.modules.peaklistmethods.isotopes.deisotoper.IsotopeGrouperTask

net.sf.mzmine.modules.peaklistmethods.isotopes.isotopepatternscore.IsotopePatternScoreCalculator

net.sf.mzmine.modules.peaklistmethods.isotopes.isotopeprediction.IsotopePatternCalculator

net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.ResolvedPeak

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