Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.DataPoint

154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
   */
  public @Nonnull
  DataPoint[] getDataPointsOverIntensity(double intensity) {
    int index;
    Vector<DataPoint> points = new Vector<DataPoint>();
    DataPoint dataPoints[] = getDataPoints();

    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
223
224
225
226
227
228
229
230
231
232
233
  public void setRetentionTime(double retentionTime) {
    this.retentionTime = retentionTime;
  }

  void updateValues() {
    DataPoint dataPoints[] = getDataPoints();

    // find m/z range and base peak
    if (dataPoints.length > 0) {

      basePeak = dataPoints[0];
View Full Code Here
332
333
334
335
336
337
338
339
340
341
342
    StorableMassList storedMassList;
    if (massList instanceof StorableMassList) {
      storedMassList = (StorableMassList) massList;
    } else {
      DataPoint massListDataPoints[] = massList.getDataPoints();
      try {
        int mlStorageID = rawDataFile
            .storeDataPoints(massListDataPoints);
        storedMassList = new StorableMassList(rawDataFile, mlStorageID,
            massList.getName(), this);
View Full Code Here
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
          - (binTime / 2.0f), scan.getRetentionTime()
          + (binTime / 2.0f));
      Range mzWindow = new Range(
          scan.getPrecursorMZ() - (binSize / 2.0f),
          scan.getPrecursorMZ() + (binSize / 2.0f));
      DataPoint point;
      DataPoint maxPoint = null;
      int[] regionScanNumbers = dataFile.getScanNumbers(1, rtWindow);
      for (int regionScanNumber : regionScanNumbers) {
        Scan regionScan = dataFile.getScan(regionScanNumber);
        point = ScanUtils.findBasePeak(regionScan, mzWindow);
        // no datapoint found
        if (point == null) {
          continue;
        }
        if (maxPoint == null) {
          maxPoint = point;
        }
        int result = Double.compare(maxPoint.getIntensity(),
            point.getIntensity());
        if (result <= 0) {
          maxPoint = point;
          bestScan = regionScan;
        }

      }

      // if no representative dataPoint
      if (bestScan == null) {
        continue;
      }

      assert maxPoint != null;

      SimpleChromatographicPeak c = new SimpleChromatographicPeak(
          dataFile, scan.getPrecursorMZ(),
          bestScan.getRetentionTime(), maxPoint.getIntensity(),
          maxPoint.getIntensity(),
          new int[]{bestScan.getScanNumber()},
          new DataPoint[]{maxPoint}, PeakStatus.DETECTED,
          bestScan.getScanNumber(), scan.getScanNumber(), new Range(
              bestScan.getRetentionTime()), new Range(
              scan.getPrecursorMZ()), new Range(
              maxPoint.getIntensity()));

      PeakListRow entry = new SimplePeakListRow(scan.getScanNumber());
      entry.addPeak(dataFile, c);

      newPeakList.addRow(entry);
View Full Code Here
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
      // ignore scans of other ms levels
      if (scan.getMSLevel() != msLevel)
        continue;

      DataPoint scanBasePeak = scan.getBasePeak();
      if (scanBasePeak == null)
        continue;

      if ((maxBasePeak == null)
          || (scanBasePeak.getIntensity() > maxBasePeak))
        maxBasePeak = scanBasePeak.getIntensity();

    }

    // return -1 if no scan at this MS level
    if (maxBasePeak == null)
View Full Code Here
373
374
375
376
377
378
379
380
381
382
383
    dataPointsFile.seek(currentOffset);
    dataPointsFile.read(buffer.array(), 0, numOfBytes);

    FloatBuffer floatBuffer = buffer.asFloatBuffer();

    DataPoint dataPoints[] = new DataPoint[numOfDataPoints];

    for (int i = 0; i < numOfDataPoints; i++) {
      float mz = floatBuffer.get();
      float intensity = floatBuffer.get();
      dataPoints[i] = new SimpleDataPoint(mz, intensity);
View Full Code Here
399
400
401
402
403
404
405
406
407
408
409
    if (newScan instanceof StorableScan) {
      scans.put(newScan.getScanNumber(), (StorableScan) newScan);
      return;
    }

    DataPoint dataPoints[] = newScan.getDataPoints();
    final int storageID = storeDataPoints(dataPoints);

    StorableScan storedScan = new StorableScan(newScan, this,
        dataPoints.length, storageID);
View Full Code Here
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
          + " precursor m/z)";
    }

    subTitle += ", RT " + rtFormat.format(currentScan.getRetentionTime());

    DataPoint basePeak = currentScan.getBasePeak();
    if (basePeak != null) {
      subTitle += ", base peak: " + mzFormat.format(basePeak.getMZ())
          + " m/z ("
          + intensityFormat.format(basePeak.getIntensity()) + ")";
    }

    setTitle(title);
    spectrumPlot.setTitle(title, subTitle);
View Full Code Here
67
68
69
70
71
72
73
74
75
76
77
  @Override
  public @Nonnull
  DataPoint[] getDataPoints() {
    try {
      DataPoint result[] = rawDataFile.readDataPoints(storageID);
      return result;

    } catch (IOException e) {
      logger.severe("Could not read data from temporary file "
          + e.toString());
View Full Code Here
105
106
107
108
109
110
111
112
113
114
115
        return;

      Scan scan = dataFile.getScan(scanNumbers[i]);

      MassDetector detector = massDetector.getModule();
      DataPoint mzPeaks[] = detector.getMassValues(scan,
          massDetector.getParameterSet());

      SimpleMassList newMassList = new SimpleMassList(name, scan, mzPeaks);

      // Add new mass list to the scan
View Full Code Here
TOP

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
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.