Package net.sf.mzmine.util

Examples of net.sf.mzmine.util.Range

30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
public class CropFilter implements ScanFilter {

  public Scan filterScan(Scan scan, ParameterSet parameters) {

    Range mzRange = parameters.getParameter(CropFilterParameters.mzRange)
        .getValue();

    // Check if whole m/z range is within cropping region or
    // scan is a fragmentation scan. In such case we copy the
    // scan unmodified.
    if ((scan.getMSLevel() > 1)
        || (mzRange.containsRange(scan.getMZRange()))) {
      return scan;
    }

    // Pickup datapoints inside the m/z range
View Full Code Here
160
161
162
163
164
165
166
167
168
169
170
171
172
  void addDatapoint(int scanNumber, DataPoint dataPoint) {

    double rt = dataFile.getScan(scanNumber).getRetentionTime();

    if (mzPeakMap.isEmpty()) {
      rtRange = new Range(rt);
      mzRange = new Range(dataPoint.getMZ());
      intensityRange = new Range(dataPoint.getIntensity());
    } else {
      rtRange.extendRange(rt);
      mzRange.extendRange(dataPoint.getMZ());
      intensityRange.extendRange(dataPoint.getIntensity());
    }
View Full Code Here
103
104
105
106
107
108
109
110
111
112
113
114
115
    this.rt = p.getRT();
    this.height = p.getHeight();
    this.area = p.getArea();

    // Create a copy of the mutable properties, not a reference
    this.rtRange = new Range(p.getRawDataPointsRTRange());
    this.mzRange = new Range(p.getRawDataPointsMZRange());
    this.intensityRange = new Range(p.getRawDataPointsIntensityRange());

    this.scanNumbers = p.getScanNumbers();

    this.dataPointsPerScan = new DataPoint[scanNumbers.length];
View Full Code Here
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
    this.scanNumbers = scanNumbers;

    rawDataFile = originalDetectedShape.getDataFile();

    // Create a copy of the mutable properties
    rawDataPointsIntensityRange = new Range(
        originalDetectedShape.getRawDataPointsIntensityRange());
    rawDataPointsMZRange = new Range(
        originalDetectedShape.getRawDataPointsMZRange());

    dataPointsMap = new TreeMap<Integer, DataPoint>();
    status = originalDetectedShape.getPeakStatus();

    // Initialize EMG parameters base on intensities and retention times
    initializEMGParameters(intensities, retentionTimes, rt, height);

    // Calculate intensity of each point in the shape.
    double shapeHeight, currentRT, previousRT, previousHeight;

    int allScanNumbers[] = rawDataFile.getScanNumbers(1);
    double allRetentionTimes[] = new double[allScanNumbers.length];
    for (int i = 0; i < allScanNumbers.length; i++)
      allRetentionTimes[i] = rawDataFile.getScan(allScanNumbers[i])
          .getRetentionTime();

    previousHeight = calculateEMGIntensity(H, M, Dp, Ap, C,
        allRetentionTimes[0]);
    previousRT = allRetentionTimes[0] * 60d;
    rawDataPointsRTRange = new Range(allRetentionTimes[0]);

    for (int i = 0; i < allRetentionTimes.length; i++) {

      shapeHeight = calculateEMGIntensity(H, M, Dp, Ap, C,
          allRetentionTimes[i]);
View Full Code Here
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
    mz = originalDetectedShape.getMZ();
    this.scanNumbers = scanNumbers;
    rawDataFile = originalDetectedShape.getDataFile();

    // Create a copy of the mutable properties
    rawDataPointsIntensityRange = new Range(
        originalDetectedShape.getRawDataPointsIntensityRange());
    rawDataPointsMZRange = new Range(
        originalDetectedShape.getRawDataPointsMZRange());
    rawDataPointsRTRange = new Range(
        originalDetectedShape.getRawDataPointsRTRange());

    dataPointsMap = new TreeMap<Integer, DataPoint>();
    status = originalDetectedShape.getPeakStatus();
View Full Code Here
115
116
117
118
119
120
121
122
123
124
125
126
127
128
      dataPointMZValues[i] = dp.getMZ();
      dataPointIntensityValues[i] = dp.getIntensity();

      if (rawDataPointsIntensityRange == null) {
        rawDataPointsIntensityRange = new Range(dp.getIntensity());
        rawDataPointsRTRange = new Range(dataFile.getScan(
            scanNumbers[i]).getRetentionTime());
        rawDataPointsMZRange = new Range(dp.getMZ());
      } else {
        rawDataPointsRTRange.extendRange(dataFile.getScan(
            scanNumbers[i]).getRetentionTime());
        rawDataPointsIntensityRange.extendRange(dp.getIntensity());
        rawDataPointsMZRange.extendRange(dp.getMZ());
View Full Code Here
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
   *            Intensity values to set
   */
  public void setDataPoints(DataPoint[] dataPoints) {

    this.dataPoints = dataPoints;
    mzRange = new Range(0, 0);
    basePeak = null;
    totalIonCurrent = 0;

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

      basePeak = dataPoints[0];
      mzRange = new Range(dataPoints[0].getMZ(), dataPoints[0].getMZ());

      for (DataPoint dp : dataPoints) {

        if (dp.getIntensity() > basePeak.getIntensity())
          basePeak = dp;
View Full Code Here
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
    rt = originalDetectedShape.getRT();
    mz = originalDetectedShape.getMZ();
    rawDataFile = originalDetectedShape.getDataFile();

    // Create a copy of the mutable properties
    rawDataPointsIntensityRange = new Range(
        originalDetectedShape.getRawDataPointsIntensityRange());
    rawDataPointsMZRange = new Range(
        originalDetectedShape.getRawDataPointsMZRange());

    dataPointsMap = new TreeMap<Integer, DataPoint>();
    status = originalDetectedShape.getPeakStatus();

    // FWFM (Full Width at Half Maximum)
    FWHM = calculateWidth(intensities, retentionTimes, resolution, rt, mz,
        height);
    // FWHM = MathUtils.calcStd(intensities) * 2.355;

    partC = FWHM / CONST;
    part2C2 = 2f * (double) Math.pow(partC, 2);

    // Calculate intensity of each point in the shape.
    double shapeHeight, currentRT, previousRT, previousHeight;

    int allScanNumbers[] = rawDataFile.getScanNumbers(1);
    double allRetentionTimes[] = new double[allScanNumbers.length];
    for (int i = 0; i < allScanNumbers.length; i++)
      allRetentionTimes[i] = rawDataFile.getScan(allScanNumbers[i])
          .getRetentionTime();

    previousHeight = calculateIntensity(allRetentionTimes[0]);
    previousRT = allRetentionTimes[0] * 60d;
    rawDataPointsRTRange = new Range(allRetentionTimes[0]);

    for (int i = 0; i < allRetentionTimes.length; i++) {

      currentRT = allRetentionTimes[i] * 60d;
      shapeHeight = calculateIntensity(currentRT);
View Full Code Here
178
179
180
181
182
183
184
185
186
187
188
189
190
191
    for (int rowIndex = 0; rowIndex < rows.length; rowIndex++) {

      if (isCanceled())
        return;

      Range mzTolRange = mzTolerance.getToleranceRange(rows[rowIndex]
          .getAverageMZ());

      if (mzTolRange.contains(lipidIonMass)) {
        rows[rowIndex].addPeakIdentity(lipid, false);

        // Notify the GUI about the change in the project
        MZmineCore.getCurrentProject().notifyObjectChanged(
            rows[rowIndex], false);
View Full Code Here
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
    // <PEAK>
    if (qName.equals(PeakListElementName_2_5.PEAK.getElementName())) {

      DataPoint[] mzPeaks = new DataPoint[numOfMZpeaks];
      Range peakRTRange = null, peakMZRange = null, peakIntensityRange = null;
      RawDataFile dataFile = dataFilesIDMap.get(peakColumnID);

      if (dataFile == null)
        throw new SAXException("Error in project: data file "
            + peakColumnID + " not found");

      for (int i = 0; i < numOfMZpeaks; i++) {

        Scan sc = dataFile.getScan(scanNumbers[i]);
        double retentionTime = sc.getRetentionTime();

        double mz = masses[i];
        double intensity = intensities[i];

        if ((peakRTRange == null) || (peakIntensityRange == null)) {
          peakRTRange = new Range(retentionTime);
          peakIntensityRange = new Range(intensity);
        } else {
          peakRTRange.extendRange(retentionTime);
          peakIntensityRange.extendRange(intensity);
        }
        if (mz > 0.0) {
          mzPeaks[i] = new SimpleDataPoint(mz, intensity);
          if (peakMZRange == null)
            peakMZRange = new Range(mz);
          else
            peakMZRange.extendRange(mz);
        }
      }
View Full Code Here
TOP

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
    • 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.