def _makeScan(self, scanData): """Make scan object from raw data.""" # parse peaks points = self._parsePoints(scanData) if scanData['spectrumType'] == 'discrete': for x, p in enumerate(points): points[x] = obj_peak.peak(p[0], p[1]) scan = obj_scan.scan(peaklist=obj_peaklist.peaklist(points)) else: scan = obj_scan.scan(profile=points) # set metadata scan.title = scanData['title'] scan.scanNumber = scanData['scanNumber'] scan.parentScanNumber = scanData['parentScanNumber'] scan.msLevel = scanData['msLevel'] scan.polarity = scanData['polarity'] scan.retentionTime = scanData['retentionTime'] scan.totIonCurrent = scanData['totIonCurrent'] scan.basePeakMZ = scanData['basePeakMZ'] scan.basePeakIntensity = scanData['basePeakIntensity'] scan.precursorMZ = scanData['precursorMZ'] scan.precursorIntensity = scanData['precursorIntensity'] scan.precursorCharge = scanData['precursorCharge'] return scan
def _makeScan(self, scanData, dataType): """Make scan object from raw data.""" # parse data as peaklist (discrete points) if dataType == 'peaklist' or (dataType == None and len(scanData['data']) < 3000): buff = [] for point in scanData['data']: buff.append(obj_peak.peak(point[0], point[1])) scan = obj_scan.scan(peaklist=obj_peaklist.peaklist(buff)) # parse data as spectrum (continuous line) else: scan = obj_scan.scan(profile=scanData['data']) # set metadata scan.title = scanData['title'] scan.scanNumber = scanData['scanNumber'] scan.parentScanNumber = scanData['parentScanNumber'] scan.msLevel = scanData['msLevel'] scan.polarity = scanData['polarity'] scan.retentionTime = scanData['retentionTime'] scan.totIonCurrent = scanData['totIonCurrent'] scan.basePeakMZ = scanData['basePeakMZ'] scan.basePeakIntensity = scanData['basePeakIntensity'] scan.precursorMZ = scanData['precursorMZ'] scan.precursorIntensity = scanData['precursorIntensity'] scan.precursorCharge = scanData['precursorCharge'] return scan
def _makeScan(self, scanData, dataType): """Make scan object from raw data.""" # parse data as peaklist (discrete points) if dataType == 'peaklist' or (dataType==None and len(scanData['data'])<3000): buff = [] for point in scanData['data']: buff.append(obj_peak.peak(point[0], point[1])) scan = obj_scan.scan(peaklist=obj_peaklist.peaklist(buff)) # parse data as spectrum (continuous line) else: scan = obj_scan.scan(profile=scanData['data']) # set metadata scan.title = scanData['title'] scan.scanNumber = scanData['scanNumber'] scan.parentScanNumber = scanData['parentScanNumber'] scan.msLevel = scanData['msLevel'] scan.polarity = scanData['polarity'] scan.retentionTime = scanData['retentionTime'] scan.totIonCurrent = scanData['totIonCurrent'] scan.basePeakMZ = scanData['basePeakMZ'] scan.basePeakIntensity = scanData['basePeakIntensity'] scan.precursorMZ = scanData['precursorMZ'] scan.precursorIntensity = scanData['precursorIntensity'] scan.precursorCharge = scanData['precursorCharge'] return scan
def _makeScan(self, scanData, dataType): """Make scan object from raw data.""" # parse data as peaklist (discrete points) if dataType == 'discrete': buff = [] for point in scanData: buff.append(obj_peak.peak(point[0], point[1])) scan = obj_scan.scan(peaklist=obj_peaklist.peaklist(buff)) # parse data as spectrum (continuous line) else: scan = obj_scan.scan(profile=scanData) return scan