public DataReaderCSharpClient()
{
string msg = null;
string stackTrace = null;
try
{
// Transition information for MRM data files
TestIsPrimaryChrom(_tMRM_DataFile);
// UV spectra and signals for non-MS detectors
ExtractNonMSData(_nonMs_DataFile1, 10);
//Create an instance of MassSpecDataReader to open up the data file
IMsdrDataReader dataAccess = new MassSpecDataReader();
println("MHDA API Version: " + dataAccess.Version);
dataAccess.OpenDataFile(_tgtMsMs_DataFile);
GetAxisInformation(dataAccess);
PrintFileInfo(dataAccess);
PrintDeviceInfo(dataAccess);
PrintMSScanInfo(dataAccess);
GetAllScansUsingRowIndex(dataAccess);//Get all scans using row Index
GetPrecursorInfo(dataAccess);
DeisotopeTest(dataAccess);
DoSpectrumExtractionTest(dataAccess);
DoSpectrumExtractionTestWithStorage(dataAccess);
GetAllScanRecords(dataAccess);
GetSampleInfoData(dataAccess);
ExtractEIC(dataAccess);
dataAccess.CloseDataFile();
println("\nDone.");
}
catch (Exception ex)
{
msg = ex.Message;
stackTrace = ex.StackTrace;
println("Exception: " + msg);
}
println("Press Enter to close");
Console.ReadLine();
}
// Examine triggered MRM data file transition chromatograms to see which are
// for primary transitions.
private void TestIsPrimaryChrom(string tMrmFilePath)
{
IMsdrDataReader dataReader = new MassSpecDataReader();
dataReader.OpenDataFile(tMrmFilePath);
IBDAChromFilter filter = new BDAChromFilter();
filter.ChromatogramType = ChromType.MultipleReactionMode;
filter.MSScanTypeFilter = MSScanType.MultipleReaction;
filter.ExtractOneChromatogramPerScanSegment = true;
filter.DoCycleSum = false;
IBDAChromData[] chroms = dataReader.GetChromatogram(filter);
foreach (IBDAChromData chrom in chroms)
{
bool val = chrom.IsPrimaryMrm;
string s = string.Format("{0}->{1}, {2}", chrom.MZOfInterest[0].Start, chrom.MeasuredMassRange[0].Start,
val);
println(s);
}
dataReader.CloseDataFile();
}
public DataReaderCSharpClient()
{
//Create an instance of MassSpecDataReader to open up the data file
//ExtractNonMSData();
IMsdrDataReader dataAccess = new MassSpecDataReader();
println("MHDA API Version: " + dataAccess.Version);
dataAccess.OpenDataFile(_dataFilename1);
GetMSLevels(dataAccess);
//PrintFileInfo(dataAccess);
//PrintDeviceInfo(dataAccess);
//PrintMSScanInfo(dataAccess);
//GetAllScansUsingRowIndex(dataAccess);//Get all scans using row Index
//GetPrecursorInfo(dataAccess);
//DeisotopeTest(dataAccess);
//DoSpectrumExtractionTest(dataAccess);
//DoSpectrumExtractionTestWithStorage(dataAccess);
//dataAccess.CloseDataFile();
//DadSignalExtract();
}
// Extract non-MS data from the specified file path, with UV spectra limited to at
// most the specified number.
private void ExtractNonMSData(string dataFilePath, int maxSpectraToReport)
{
IMsdrDataReader dataReader = new MassSpecDataReader();
dataReader.OpenDataFile(dataFilePath);
INonmsDataReader nonMsReader = dataReader as INonmsDataReader;
IDeviceInfo[] deviceInfo = nonMsReader.GetNonmsDevices();
if ((deviceInfo == null) || (deviceInfo.Length == 0))
{
println("No Non MS device found");
}
else
{
foreach (IDeviceInfo device in deviceInfo)
{
println("Device = " + device.DeviceName + " Ordinal number = " + device.OrdinalNumber.ToString() + " Device type = " + device.DeviceType.ToString());
#region DAD Signal & Spectrum
if (device.DeviceType == DeviceType.DiodeArrayDetector ||
device.DeviceType == DeviceType.HDR ||
device.DeviceType == DeviceType.CompactLC1220DAD)
{
//Extracting Signal Information
ISignalInfo[] sigInfo = nonMsReader.GetSignalInfo(device, StoredDataType.Chromatograms);
if (sigInfo.Length == 0)
{
println("No DAD signal found");
}
else
{
StringBuilder sb = new StringBuilder();
sb.AppendFormat("Found info on {0} signals: ", sigInfo.Length);
foreach (ISignalInfo info in sigInfo)
{
sb.AppendFormat("{0}, ", info.SignalName);
}
println(sb.ToString());
IBDAChromData chromData = nonMsReader.GetSignal(sigInfo[0]);
if ((chromData == null) || (chromData.TotalDataPoints == 0))
{
println("No data found for first DAD signal");
}
else
{
int count = chromData.TotalDataPoints;
double[] xArray = chromData.XArray;
float[] yArray = chromData.YArray;
// This information can be exported to a file on disk
FileStream file = new FileStream(@"C:\temp\reportNew.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter sw = new StreamWriter(file);
sw.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArray.Length; i++)
{
sw.WriteLine(i.ToString() + "," + xArray[i].ToString() + "," + yArray[i].ToString());
}
sw.Close();
file.Close();
}
}
//Extracting TWC
IBDAChromData chromDataTWC = nonMsReader.GetTWC(device);
//compare this data with our own file
if ((chromDataTWC == null) || (chromDataTWC.TotalDataPoints == 0))
{
println("No TWC found");
}
else
{
int dataPoints = chromDataTWC.TotalDataPoints;
double[] xArrayTWC = chromDataTWC.XArray;
float[] yArrayTWC = chromDataTWC.YArray;
// Expoting this information to a file on disk
FileStream fileTWC = new FileStream(@"C:\temp\reportTWC.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter swTWC = new StreamWriter(fileTWC);
swTWC.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArrayTWC.Length; i++)
{
swTWC.WriteLine(i.ToString() + "," + xArrayTWC[i].ToString() + "," + yArrayTWC[i].ToString());
}
swTWC.Close();
fileTWC.Close();
}
//Extracting EWC
IRange rangeSignal = new MinMaxRange(40, 250);
IRange rangeRef = new MinMaxRange(40, 250);
IBDAChromData chromDataEWC = nonMsReader.GetEWC(device, rangeSignal, rangeRef);
if ((chromDataEWC == null) || (chromDataEWC.TotalDataPoints == 0))
{
println("No EWC found");
}
else
{
double[] xArrayEWC = chromDataEWC.XArray;
float[] yArrayEWC = chromDataEWC.YArray;
// Expoting this information to a file on disk
FileStream fileEWC = new FileStream(@"C:\temp\reportEWC.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter swEWC = new StreamWriter(fileEWC);
swEWC.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArrayEWC.Length; i++)
{
swEWC.WriteLine(i.ToString() + "," + xArrayEWC[i].ToString() + "," + yArrayEWC[i].ToString());
}
swEWC.Close();
fileEWC.Close();
}
//UV Spectrum: get each UV spectrum in the file
string uvSpectraFilePath = @"C:\temp\reportUV.csv";
if (File.Exists(uvSpectraFilePath))
{
File.Delete(uvSpectraFilePath);
}
for (int k = 0; k < chromDataTWC.XArray.Length && k < maxSpectraToReport; k++)
{
IRange range = new MinMaxRange(chromDataTWC.XArray[k], chromDataTWC.XArray[k]);
IBDASpecData[] uvSpecData = nonMsReader.GetUVSpectrum(device, range);
if (uvSpecData == null)
{
println("No UV spectrum found");
}
else
{
foreach (IBDASpecData uvSpec in uvSpecData)
{
if (uvSpec.TotalDataPoints != 0)
{
int dataPopints = uvSpec.TotalDataPoints;
double[] xArrayUV = uvSpec.XArray;
float[] yArrayUV = uvSpec.YArray;
// Expoting this information to a file on disk
FileStream fileUV = new FileStream(uvSpectraFilePath, FileMode.Append,
FileAccess.Write);
TextWriter swUV = new StreamWriter(fileUV);
swUV.WriteLine("#Point,X(Nanometers),Y(mAU)");
for (int i = 0; i < xArrayUV.Length; i++)
{
swUV.WriteLine(i.ToString() + "," + xArrayUV[i].ToString() + "," +
yArrayUV[i].ToString());
}
swUV.Close();
fileUV.Close();
}
else
{
println("No UV spectrum found");
}
}
}
}
}
#endregion
#region InstrumentCurves - TCC
if (device.DeviceType == DeviceType.ThermostattedColumnCompartment)
{
ISignalInfo[] sigInfo = nonMsReader.GetSignalInfo(device, StoredDataType.InstrumentCurves);
if (sigInfo.Length == 0)
{
println("No TCC Curves found");
}
else
{
IBDAChromData chromData = nonMsReader.GetSignal(sigInfo[0]);
if ((chromData == null) || (chromData.TotalDataPoints == 0))
{
println("No TCC Curves found");
}
else
{
int count = chromData.TotalDataPoints;
double[] xArray = chromData.XArray;
float[] yArray = chromData.YArray;
// Expoting this information to a file on disk
FileStream file = new FileStream(@"C:\temp\reportInstrumentCurve.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter sw = new StreamWriter(file);
sw.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArray.Length; i++)
{
sw.WriteLine(i.ToString() + "," + xArray[i].ToString() + "," + yArray[i].ToString());
}
sw.Close();
file.Close();
}
}
}
#endregion
}
}
}
/// <summary>
/// To extract non MS data
/// </summary>
private void ExtractNonMSData()
{
IMsdrDataReader dataReader = new MassSpecDataReader();
dataReader.OpenDataFile(_NonMSdataFilename);
INonmsDataReader nonMsReader = dataReader as INonmsDataReader;
IDeviceInfo[] deviceInfo = nonMsReader.GetNonmsDevices();
if ((deviceInfo == null) || (deviceInfo.Length == 0))
{
println("No Non MS device found");
}
else
{
foreach (IDeviceInfo device in deviceInfo)
{
println("Device = " + device.DeviceName + " Ordinal number = " + device.OrdinalNumber.ToString() + " Device type = " + device.DeviceType.ToString());
#region DAD Signal & Spectrum
if (device.DeviceType == DeviceType.DiodeArrayDetector)
{
//Extracting Signal Information
ISignalInfo[] sigInfo = nonMsReader.GetSignalInfo(device, StoredDataType.Chromatograms);
if (sigInfo.Length == 0)
{
println("No DAD signal found");
}
else
{
IBDAChromData chromData = nonMsReader.GetSignal(sigInfo[0]);
if ((chromData == null) || (chromData.TotalDataPoints == 0))
{
println("No DAD signal found");
}
else
{
int count = chromData.TotalDataPoints;
double[] xArray = chromData.XArray;
float[] yArray = chromData.YArray;
// This information can be exported to a file on disk
FileStream file = new FileStream(@"C:\temp\reportNew.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter sw = new StreamWriter(file);
sw.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArray.Length; i++)
{
sw.WriteLine(i.ToString() + "," + xArray[i].ToString() + "," + yArray[i].ToString());
}
sw.Close();
file.Close();
}
}
//Extracting TWC
IBDAChromData chromDataTWC = nonMsReader.GetTWC(device);
//compare this data with our own file
if ((chromDataTWC == null) || (chromDataTWC.TotalDataPoints == 0))
{
println("No TWC found");
}
else
{
int dataPoints = chromDataTWC.TotalDataPoints;
double[] xArrayTWC = chromDataTWC.XArray;
float[] yArrayTWC = chromDataTWC.YArray;
// Expoting this information to a file on disk
FileStream fileTWC = new FileStream(@"C:\temp\reportTWC.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter swTWC = new StreamWriter(fileTWC);
swTWC.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArrayTWC.Length; i++)
{
swTWC.WriteLine(i.ToString() + "," + xArrayTWC[i].ToString() + "," + yArrayTWC[i].ToString());
}
swTWC.Close();
fileTWC.Close();
}
//Extracting EWC
IRange rangeSignal = new MinMaxRange(40, 250);
IRange rangeRef = new MinMaxRange(40, 250);
IBDAChromData chromDataEWC = nonMsReader.GetEWC(device, rangeSignal, rangeRef);
if ((chromDataEWC == null) || (chromDataEWC.TotalDataPoints == 0))
{
println("No EWC signal found");
}
else
{
int dataPointsEWC = chromDataEWC.TotalDataPoints;
double[] xArrayEWC = chromDataEWC.XArray;
float[] yArrayEWC = chromDataEWC.YArray;
// Expoting this information to a file on disk
FileStream fileEWC = new FileStream(@"C:\temp\reportEWC.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter swEWC = new StreamWriter(fileEWC);
swEWC.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArrayEWC.Length; i++)
{
swEWC.WriteLine(i.ToString() + "," + xArrayEWC[i].ToString() + "," + yArrayEWC[i].ToString());
}
swEWC.Close();
fileEWC.Close();
}
//UV Spectrum
IRange range = new MinMaxRange(1.109, 1.409);
IMinMaxRange ran = new MinMaxRange(1, 2);
ran.Max = 1;
IBDASpecData[] uvSpecData = nonMsReader.GetUVSpectrum(device, range);
if (uvSpecData == null)
{
println("No UV signal found");
}
else
{
foreach (IBDASpecData uvSpec in uvSpecData)
{
if (uvSpec.TotalDataPoints != 0)
{
int dataPopints = uvSpec.TotalDataPoints;
double[] xArrayUV = uvSpec.XArray;
float[] yArrayUV = uvSpec.YArray;
// Expoting this information to a file on disk
FileStream fileUV = new FileStream(@"C:\temp\reportUV.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter swUV = new StreamWriter(fileUV);
swUV.WriteLine("#Point,X(Nanometers),Y(mAU)");
for (int i = 0; i < xArrayUV.Length; i++)
{
swUV.WriteLine(i.ToString() + "," + xArrayUV[i].ToString() + "," + yArrayUV[i].ToString());
}
swUV.Close();
fileUV.Close();
}
else
{
println("No UV signal found");
}
}
}
}
#endregion
#region InstrumentCurves - TCC
if (device.DeviceType == DeviceType.ThermostattedColumnCompartment)
{
ISignalInfo[] sigInfo = nonMsReader.GetSignalInfo(device, StoredDataType.InstrumentCurves);
if (sigInfo.Length == 0)
{
println("No TCC Curves found");
}
else
{
IBDAChromData chromData = nonMsReader.GetSignal(sigInfo[0]);
if ((chromData == null) || (chromData.TotalDataPoints == 0))
{
println("No TCC Curves found");
}
else
{
int count = chromData.TotalDataPoints;
double[] xArray = chromData.XArray;
float[] yArray = chromData.YArray;
// Expoting this information to a file on disk
FileStream file = new FileStream(@"C:\temp\reportInstrumentCurve.csv", FileMode.Create, FileAccess.ReadWrite);
TextWriter sw = new StreamWriter(file);
sw.WriteLine("#Point,X(Minutes),Y(Response Units)");
for (int i = 0; i < xArray.Length; i++)
{
sw.WriteLine(i.ToString() + "," + xArray[i].ToString() + "," + yArray[i].ToString());
}
sw.Close();
file.Close();
}
}
}
#endregion
}
}
}
public void Load(string agilentDFolderPath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, int maximumThreads)
{
OnReportTaskWithoutProgress(new EventArgs());
IMsdrDataReader agilent_d = new MassSpecDataReader();
agilent_d.OpenDataFile(agilentDFolderPath);
Dictionary <int, IBDASpecData> ms1s;
if (GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary <int, IBDASpecData>();
}
IMsdrPeakFilter ms1_peak_filter = new MsdrPeakFilter();
IMsdrPeakFilter ms2_peak_filter = new MsdrPeakFilter();
ms2_peak_filter.AbsoluteThreshold = absoluteThreshold;
ms2_peak_filter.RelativeThreshold = relativeThresholdPercent;
ms2_peak_filter.MaxNumPeaks = maximumNumberOfPeaks;
ChargeStateAssignmentWrapper csaw = new ChargeStateAssignmentWrapper();
OnReportTaskWithProgress(new EventArgs());
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Parallel.For(0, (int)agilent_d.MSScanFileInformation.TotalScansPresent, parallel_options, row_number =>
{
IMSScanRecord scan_record;
lock (agilent_d)
{
scan_record = agilent_d.GetScanRecord(row_number);
}
if (scan_record.MSLevel == MSLevel.MSMS)
{
IBDASpecData agilent_spectrum;
lock (agilent_d)
{
agilent_spectrum = agilent_d.GetSpectrum(row_number, ms1_peak_filter, ms2_peak_filter);
}
if (agilent_spectrum.TotalDataPoints > 0)
{
int polarity = 0;
if (agilent_spectrum.IonPolarity == IonPolarity.Positive)
{
polarity = 1;
}
else if (agilent_spectrum.IonPolarity == IonPolarity.Negative)
{
polarity = -1;
}
int spectrum_number = row_number + 1;
string scan_id = "scanId=" + agilent_spectrum.ScanId.ToString();
double precursor_mz = agilent_spectrum.MZOfInterest[0].Start;
double precursor_intensity;
if (GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
GetAccurateMZAndIntensity(ms1s, agilent_d, agilent_spectrum.ParentScanId, ref precursor_mz, out precursor_intensity);
}
else
{
agilent_spectrum.GetPrecursorIntensity(out precursor_intensity);
}
int charge;
agilent_spectrum.GetPrecursorCharge(out charge);
if (polarity < 0)
{
charge = -charge;
}
List <MSPeak> peaks = null;
if (!assignChargeStates)
{
peaks = new List <MSPeak>(agilent_spectrum.TotalDataPoints);
for (int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peaks.Add(new MSPeak(agilent_spectrum.XArray[i], agilent_spectrum.YArray[i], 0, polarity));
}
}
for (int c = (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? minimumAssumedPrecursorChargeState : charge);
c <= (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? maximumAssumedPrecursorChargeState : charge); c++)
{
if (assignChargeStates)
{
int[] peak_ids = new int[agilent_spectrum.TotalDataPoints];
double[] peak_mzs = new double[agilent_spectrum.TotalDataPoints];
double[] peak_intensities = new double[agilent_spectrum.TotalDataPoints];
for (int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peak_ids[i] = i;
peak_mzs[i] = agilent_spectrum.XArray[i];
peak_intensities[i] = agilent_spectrum.YArray[i];
}
int[] peak_charge_states = new int[agilent_spectrum.TotalDataPoints];
int[] peak_clusters = new int[agilent_spectrum.TotalDataPoints];
int num_peaks;
lock (csaw)
{
csaw.SetParameters(IsotopeModel.Peptidic, 1, (short)c, false, ACCURACY_C0, ACCURACY_C1);
num_peaks = csaw.AssignChargeStates(peak_ids, peak_mzs, peak_intensities, peak_charge_states, peak_clusters);
}
peaks = new List <MSPeak>(num_peaks);
HashSet <int> observed_peak_clusters = new HashSet <int>();
for (int i = 0; i < num_peaks; i++)
{
bool isotopic_peak = observed_peak_clusters.Contains(peak_clusters[i]);
if (!deisotope || !isotopic_peak)
{
peaks.Add(new MSPeak(peak_mzs[i], peak_intensities[i], peak_charge_states[i], polarity));
if (peak_clusters[i] > 0 && !isotopic_peak)
{
observed_peak_clusters.Add(peak_clusters[i]);
}
}
}
}
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(agilentDFolderPath, spectrum_number, scan_id, null, scan_record.RetentionTime, FRAGMENTATION_METHOD, precursor_mz, precursor_intensity, c, precursor_mass, peaks);
lock (this)
{
Add(spectrum);
}
}
}
}
lock (progress_lock)
{
spectra_processed++;
int new_progress = (int)((double)spectra_processed / agilent_d.MSScanFileInformation.TotalScansPresent * 100);
if (new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
});
agilent_d.CloseDataFile();
}
public void Load(string agilentDFolderPath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, int maximumThreads)
{
OnReportTaskWithoutProgress(new EventArgs());
IMsdrDataReader agilent_d = new MassSpecDataReader();
agilent_d.OpenDataFile(agilentDFolderPath);
Dictionary<int, IBDASpecData> ms1s;
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary<int, IBDASpecData>();
}
IMsdrPeakFilter ms1_peak_filter = new MsdrPeakFilter();
IMsdrPeakFilter ms2_peak_filter = new MsdrPeakFilter();
ms2_peak_filter.AbsoluteThreshold = absoluteThreshold;
ms2_peak_filter.RelativeThreshold = relativeThresholdPercent;
ms2_peak_filter.MaxNumPeaks = maximumNumberOfPeaks;
ChargeStateAssignmentWrapper csaw = new ChargeStateAssignmentWrapper();
OnReportTaskWithProgress(new EventArgs());
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Parallel.For(0, (int)agilent_d.MSScanFileInformation.TotalScansPresent, parallel_options, row_number =>
{
IMSScanRecord scan_record;
lock(agilent_d)
{
scan_record = agilent_d.GetScanRecord(row_number);
}
if(scan_record.MSLevel == MSLevel.MSMS)
{
IBDASpecData agilent_spectrum;
lock(agilent_d)
{
agilent_spectrum = agilent_d.GetSpectrum(row_number, ms1_peak_filter, ms2_peak_filter);
}
if(agilent_spectrum.TotalDataPoints > 0)
{
int polarity = 0;
if(agilent_spectrum.IonPolarity == IonPolarity.Positive)
{
polarity = 1;
}
else if(agilent_spectrum.IonPolarity == IonPolarity.Negative)
{
polarity = -1;
}
int spectrum_number = row_number + 1;
string scan_id = "scanId=" + agilent_spectrum.ScanId.ToString();
double precursor_mz = agilent_spectrum.MZOfInterest[0].Start;
double precursor_intensity;
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
GetAccurateMZAndIntensity(ms1s, agilent_d, agilent_spectrum.ParentScanId, ref precursor_mz, out precursor_intensity);
}
else
{
agilent_spectrum.GetPrecursorIntensity(out precursor_intensity);
}
int charge;
agilent_spectrum.GetPrecursorCharge(out charge);
if(polarity < 0)
{
charge = -charge;
}
List<MSPeak> peaks = null;
if(!assignChargeStates)
{
peaks = new List<MSPeak>(agilent_spectrum.TotalDataPoints);
for(int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peaks.Add(new MSPeak(agilent_spectrum.XArray[i], agilent_spectrum.YArray[i], 0, polarity));
}
}
for(int c = (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? minimumAssumedPrecursorChargeState : charge);
c <= (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? maximumAssumedPrecursorChargeState : charge); c++)
{
if(assignChargeStates)
{
int[] peak_ids = new int[agilent_spectrum.TotalDataPoints];
double[] peak_mzs = new double[agilent_spectrum.TotalDataPoints];
double[] peak_intensities = new double[agilent_spectrum.TotalDataPoints];
for(int i = 0; i < agilent_spectrum.TotalDataPoints; i++)
{
peak_ids[i] = i;
peak_mzs[i] = agilent_spectrum.XArray[i];
peak_intensities[i] = agilent_spectrum.YArray[i];
}
int[] peak_charge_states = new int[agilent_spectrum.TotalDataPoints];
int[] peak_clusters = new int[agilent_spectrum.TotalDataPoints];
int num_peaks;
lock(csaw)
{
csaw.SetParameters(IsotopeModel.Peptidic, 1, (short)c, false, ACCURACY_C0, ACCURACY_C1);
num_peaks = csaw.AssignChargeStates(peak_ids, peak_mzs, peak_intensities, peak_charge_states, peak_clusters);
}
peaks = new List<MSPeak>(num_peaks);
HashSet<int> observed_peak_clusters = new HashSet<int>();
for(int i = 0; i < num_peaks; i++)
{
bool isotopic_peak = observed_peak_clusters.Contains(peak_clusters[i]);
if(!deisotope || !isotopic_peak)
{
peaks.Add(new MSPeak(peak_mzs[i], peak_intensities[i], peak_charge_states[i], polarity));
if(peak_clusters[i] > 0 && !isotopic_peak)
{
observed_peak_clusters.Add(peak_clusters[i]);
}
}
}
}
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(agilentDFolderPath, spectrum_number, scan_id, null, scan_record.RetentionTime, FRAGMENTATION_METHOD, precursor_mz, precursor_intensity, c, precursor_mass, peaks);
lock(this)
{
Add(spectrum);
}
}
}
}
lock(progress_lock)
{
spectra_processed++;
int new_progress = (int)((double)spectra_processed / agilent_d.MSScanFileInformation.TotalScansPresent * 100);
if(new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
});
agilent_d.CloseDataFile();
}