public Tuple <double, string[, ]> GetStatusLogForScanNum(int nScanNumber, List <double> writtenRetentionTimes)
{
double pdStatusLogRT = 0;
object pvarLabels = null;
object pvarValues = null;
int pnArraySize = 0;
_rawConnection.GetStatusLogForScanNum(nScanNumber, ref pdStatusLogRT, ref pvarLabels, ref pvarValues, ref pnArraySize);
if (writtenRetentionTimes.Count > 0 && writtenRetentionTimes.Last() == pdStatusLogRT)
{
return(null);
}
else
{
writtenRetentionTimes.Add(pdStatusLogRT);
}
var values = (string[])pvarValues;
var labels = (string[])pvarLabels;
var returnArray = new string[2, pnArraySize];
for (int i = 0; i < pnArraySize; i++)
{
returnArray[0, i] = labels[i];
returnArray[1, i] = values[i];
}
return(new Tuple <double, string[, ]>(pdStatusLogRT, returnArray));
}
/// <summary>
/// Reads raw data. Puts spectra into a thread safe queue. Closes queue when done. Parses the rawfile-log into the statusLog object
/// </summary>
/// <param name="raw">Raw file</param>
/// <param name="rawScanQueue">Thread safe queue</param>
private void ReadRawFile(IXRawfile5 raw, BlockingCollection <RawScan> rawScanQueue)
{
int firstScanNumber = -1;
raw.GetFirstSpectrumNumber(ref firstScanNumber);
int lastScanNumber = -1;
raw.GetLastSpectrumNumber(ref lastScanNumber);
for (int scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
string scanFilter = null;
raw.GetFilterForScanNum(scanNumber, ref scanFilter);
//read scan header into key/value arrays
object keyRef = null;
object valueRef = null;
int indexRef = 0;
raw.GetTrailerExtraForScanNum(scanNumber, ref keyRef, ref valueRef, ref indexRef);
string[] trailerKeys = (string[])keyRef;
string[] trailerValues = (string[])valueRef;
//read tic and base peak mass using dummy variables
double tic = 0.0;
int int1 = 0;
int int2 = 0;
int int3 = 0;
double double1 = 0.0;
double double2 = 0.0;
double double3 = 0.0;
double basePeakMass = 0.0;
double double5 = 0.0;
double double6 = 0.0;
raw.GetScanHeaderInfoForScanNum(scanNumber, ref int1, ref double1, ref double2, ref double3, ref tic, ref basePeakMass, ref double5, ref int2, ref int3, ref double6);
//read data (mz,int,...) using dummy variables
object labels_obj = null;
object flags_obj = null;
raw.GetLabelData(ref labels_obj, ref flags_obj, ref scanNumber);
double[,] data = (double[, ])labels_obj;
//read precursorMz
double precursorMz = 0.0;
raw.GetPrecursorMassForScanNum(scanNumber, 2, ref precursorMz);
RawScan rawScan = new RawScan(scanNumber, scanFilter, tic, trailerKeys, trailerValues, data, precursorMz, basePeakMass);
rawScanQueue.Add(rawScan);
//read status log
double rtLog = 0.0;
object statuslogKeys = null;
object statuslogValues = null;
int statuslogN = 0;
raw.GetStatusLogForScanNum(scanNumber, ref rtLog, ref statuslogKeys, ref statuslogValues, ref statuslogN);
statusLog.Add(rtLog, (string[])statuslogKeys, (string[])statuslogValues);
}
rawScanQueue.CompleteAdding();
Log.Information("Read all spectra in base module");
}
public Dictionary <string, string> GetStatusLog(int scanNum)
{
//void GetStatusLogForScanNum(int nScanNumber, ref double pdStatusLogRT, ref object pvarLabels, ref object pvarValues, ref int pnArraySize);
double pdStatusLogRT = double.NaN;
object pvarLabels = null;
object pvarValues = null;
int pnArraySize = -1;
_rawConnection.GetStatusLogForScanNum(scanNum, ref pdStatusLogRT, ref pvarLabels, ref pvarValues, ref pnArraySize);
string[] labelArray = pvarLabels as string[];
string[] valueArray = pvarValues as string[];
Dictionary <string, string> returnDict = new Dictionary <string, string>();
for (int i = 0; i < labelArray.Length; i++)
{
if (!returnDict.ContainsKey(labelArray[i]))
{
returnDict.Add(labelArray[i], valueArray[i]);
}
}
return(returnDict);
}
private MassSpectrum GetSpectrumByScanNum(int scanNum)
{
//if (scanNum >= 24021 && scanNum <= 24021)
//{
// return null;
//}
string scanFilter = null;
_rawReader.GetFilterForScanNum(scanNum, ref scanFilter);
// get scan type;
int nScanType = 0;
_rawReader.GetScanTypeForScanNum(scanNum, ref nScanType);
// get scan header information of the spectrum;
int numPackets = 0, numChannels = 0, uniformTime = 0;
double startTime = 0, lowMass = 0, highMass = 0, tic = 0, basePeakMass = 0, basePeakIntensity = 0, frequency = 0;
_rawReader.GetScanHeaderInfoForScanNum(scanNum, ref numPackets, ref startTime, ref lowMass, ref highMass,
ref tic, ref basePeakMass, ref basePeakIntensity, ref numChannels, ref uniformTime, ref frequency);
// get the instrument type;
InstrumentType instrumentType = InstrumentType.ELSE;
if (scanFilter.StartsWith("FTMS"))
{
instrumentType = InstrumentType.FTMS;
}
else if (scanFilter.StartsWith("ITMS"))
{
instrumentType = InstrumentType.ITMS;
}
// get MS spectrum list;
string spectrumId = "controllerType=0 controllerNumber=1 scan=" + scanNum.ToString();
// get the retention time;
double retentionTime = double.NaN;
_rawReader.RTFromScanNum(scanNum, ref retentionTime);
// get the ion injection time and the precursor information;
object trailerLabelsObj = null;
object trailerValuesObj = null;
int trailer_array_size = -1;
_rawReader.GetTrailerExtraForScanNum(scanNum, ref trailerLabelsObj, ref trailerValuesObj, ref trailer_array_size);
string[] trailerLabels = (string[])trailerLabelsObj;
string[] trailerValues = (string[])trailerValuesObj;
double ionInjectionTime = 0;
double precMz = 0;
int precZ = 0;
int precScanNum = 0;
double isolationWindowSize = 0;
for (int trailerIdx = trailerLabels.GetLowerBound(0); trailerIdx <= trailerLabels.GetUpperBound(0); trailerIdx++)
{
if (trailerLabels[trailerIdx].StartsWith("Ion Injection Time"))
{
ionInjectionTime = double.Parse(trailerValues[trailerIdx]);
}
if (trailerLabels[trailerIdx].StartsWith("Monoisotopic M/Z"))
{
precMz = double.Parse(trailerValues[trailerIdx]);
}
if (trailerLabels[trailerIdx].StartsWith("Charge State"))
{
precZ = int.Parse(trailerValues[trailerIdx]);
}
if (trailerLabels[trailerIdx].StartsWith("Master Scan Number"))
{
precScanNum = int.Parse(trailerValues[trailerIdx]);
}
if (trailerLabels[trailerIdx].StartsWith("MS2 Isolation Width"))
{
isolationWindowSize = double.Parse(trailerValues[trailerIdx]);
}
}
// get the analyzer temperature from the status log;
object logLabelsObj = null;
object logValuesObj = null;
int pnArraySize = 0;
_rawReader.GetStatusLogForScanNum(scanNum, 1.0, ref logLabelsObj, ref logValuesObj, ref pnArraySize);
double analyzerTemperature = -1.0;
if (logLabelsObj != null && logValuesObj != null)
{
string[] logLabels = (string[])logLabelsObj;
string[] logValues = (string[])logValuesObj;
for (int idx = logLabels.GetLowerBound(0); idx <= logLabels.GetUpperBound(0); idx++)
{
if (logLabels[idx].Contains("FT Analyzer Temp"))
{
analyzerTemperature = double.Parse(logValues[idx]);
}
if (logLabels[idx].Contains("Analyzer Temperature"))
{
analyzerTemperature = double.Parse(logValues[idx]);
}
}
}
// create an instance of MassSpectrum;
List <Ion> peaks = null;
MassSpectrum spectrum = new MassSpectrum(
(int)scanNum,
spectrumId,
retentionTime,
peaks,
ionInjectionTime,
instrumentType,
scanFilter,
analyzerTemperature,
correctPrecMz);
// check the MS level;
if (scanFilter.Contains(" ms "))
{
spectrum.MsLevel = 1;
// do not filter peaks for MS1 as all peaks may be needed for later masss/charge correction;
spectrum.Peaks = GetPeaks(scanNum, scanFilter, false);
}
else if (scanFilter.Contains(" ms2 "))
{
spectrum.MsLevel = 2;
int activationType = 0;
//int pnNumMSOrders = 0;
_rawReader.GetActivationTypeForScanNum(scanNum, spectrum.MsLevel, ref activationType);
//_rawReader.GetNumberOfMSOrdersFromScanNum(scanNum, ref pnNumMSOrders);
//_rawReader.GetIsolationWidthForScanNum(scanNum, pnNumMSOrders, ref isolationWindowSize);
spectrum.IsolationWindowSize = isolationWindowSize;
spectrum.ActivationMethod = (Activation)activationType;
spectrum.Peaks = GetPeaks(scanNum, scanFilter, false);
spectrum.Precursors = new List <Tuple <double, int> >();
spectrum.PrecursorIntensity = 0;
spectrum.PrecursorScanNumber = precScanNum;
// get the precMz from the filter;
int begin = scanFilter.IndexOf(" ms2 ") + 5;
int end = begin + 1, len = 1;
while (end < scanFilter.Count() && (scanFilter[end] >= '0' && scanFilter[end] <= '9') || scanFilter[end] == '.')
{
end++;
len++;
}
spectrum.PrecMzFromFilter = double.Parse(scanFilter.Substring(begin, len));
//Console.Write(bypassThermoAlgorithm);
//Console.Write(precMz);
if (precMz == 0 || bypassThermoAlgorithm)
{
precMz = spectrum.PrecMzFromFilter;
}
if (precZ == 0 && ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE)
{
foreach (int z in MS2_PRECURSOR_CHARGES)
{
spectrum.Precursors.Add(new Tuple <double, int>(precMz, z));
}
}
else
{
spectrum.Precursors.Add(new Tuple <double, int>(precMz, precZ));
}
}
else if (scanFilter.Contains(" ms3 "))
{
spectrum.MsLevel = 3;
if (precMz == 0)
{
int end = scanFilter.Count() - 1;
while (end >= 0 && scanFilter[end] != '@')
{
end--;
}
int begin = end - 1, len = 1;
while (begin >= 0 && (scanFilter[begin] >= '0' && scanFilter[begin] <= '9') || scanFilter[begin] == '.')
{
begin--;
len++;
}
begin++;
len--;
precMz = double.Parse(scanFilter.Substring(begin, len));
}
// TODO: MS3 spectrum mass/charge correction need to be taken care;
spectrum.Precursors = new List <Tuple <double, int> >();
spectrum.Precursors.Add(new Tuple <double, int>(precMz, precZ));
spectrum.Peaks = GetPeaks(scanNum, scanFilter, false);
if (precMz < 0.01)
{
for (int trailerIdx = trailerLabels.GetLowerBound(0); trailerIdx <= trailerLabels.GetUpperBound(0); trailerIdx++)
{
if (trailerLabels[trailerIdx].StartsWith("SPS Mass 1"))
{
precMz = double.Parse(trailerValues[trailerIdx]);
break;
}
}
}
spectrum.Precursors = new List <Tuple <double, int> >();
spectrum.PrecursorIntensity = double.NaN;
spectrum.PrecursorScanNumber = precScanNum;
int activationType = 0;
_rawReader.GetActivationTypeForScanNum(scanNum, spectrum.MsLevel, ref activationType);
spectrum.ActivationMethod = (Activation)activationType;
if (precZ == 0 && ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE)
{
int maxCharge = 0;
foreach (int z in MS2_PRECURSOR_CHARGES)
{
if (maxCharge < z)
{
maxCharge = z;
}
}
for (int z = 0; z <= maxCharge; z++)
{
spectrum.Precursors.Add(new Tuple <double, int>(precMz, z));
}
}
else
{
spectrum.Precursors.Add(new Tuple <double, int>(precMz, precZ));
}
}
// get the isolation window size;
//double isoWinSize = 0;
//int numMSOrders = 0;
//_rawReader.GetNumberOfMSOrdersFromScanNum(scanNum, ref numMSOrders);
//for (int i = 0; i <= 10; i++)
//{
// _rawReader.GetIsolationWidthForScanNum(scanNum, i, ref isoWinSize);
// Console.WriteLine(i + "\t" + isoWinSize);
//}
//spectrum.IsolationWindowSize = isoWinSize;
//_rawReader.GetIsolationWidthForScanNum(scanNum, spectrum.MsLevel, ref isoWinSize);
//Console.WriteLine(spectrum.MsLevel + "\t" + isoWinSize);
// set the scan header information;
spectrum.TotIonCurrent = tic;
spectrum.LowMz = lowMass;
spectrum.HighMz = highMass;
spectrum.BasePeakMz = basePeakMass;
spectrum.BasePeakIntensity = basePeakIntensity;
return(spectrum);
}