private ThermoDynamicData(IXRawfile5 _rawConnection, IFilteringParams filterParams, int numSpectra, ManagedThermoHelperLayer.PrecursorInfo[] couldBePrecursor, SourceFile sourceFile, ThermoGlobalParams thermoGlobalParams) : base(_rawConnection, numSpectra, couldBePrecursor, sourceFile, thermoGlobalParams)
{
this._rawConnection = _rawConnection;
this.filterParams = filterParams;
}
private ThermoStaticData(MsDataScan[] scans, ThermoGlobalParams thermoGlobalParams, SourceFile sourceFile) : base(scans, sourceFile)
{
this.ThermoGlobalParams = thermoGlobalParams;
}
public static ThermoStaticData LoadAllStaticData(string filePath, IFilteringParams filterParams = null)
{
if (!File.Exists(filePath))
{
throw new FileNotFoundException();
}
if (CheckForMsFileReader() == false)
{
throw new MzLibException("MsFileReader Not Installed");
}
var ok = new ManagedThermoHelperLayer.HelperClass();
IXRawfile5 theConnection = (IXRawfile5) new MSFileReader_XRawfile();
theConnection.Open(filePath);
int pbSMData = 0;
theConnection.IsThereMSData(ref pbSMData);
if (pbSMData == 0)
{
throw new MzLibException("Could not read data from file " + Path.GetFileName(filePath));
}
theConnection.SetCurrentController(0, 1);
var precursorInfosArray = ok.GetAllPrecursorInfos(filePath);
for (int i = 0; i < precursorInfosArray.Length; i++)
{
if (precursorInfosArray[i].nScanNumber == 0)
{
precursorInfosArray[i].nScanNumber = -1;
}
}
int pnFirstSpectrum = 0;
theConnection.GetFirstSpectrumNumber(ref pnFirstSpectrum);
int pnLastSpectrum = 0;
theConnection.GetLastSpectrumNumber(ref pnLastSpectrum);
ThermoGlobalParams p = GetAllGlobalStuff(theConnection, precursorInfosArray, filePath);
MsDataScan[] scans = new MsDataScan[pnLastSpectrum - pnFirstSpectrum + 1];
for (int nScanNumber = pnFirstSpectrum; nScanNumber <= pnLastSpectrum; nScanNumber++)
{
scans[nScanNumber - pnFirstSpectrum] = GetMsDataOneBasedScanFromThermoFile(theConnection, nScanNumber, p, filterParams);
}
theConnection.Close();
string sendCheckSum;
using (FileStream stream = File.OpenRead(filePath))
{
using (SHA1Managed sha = new SHA1Managed())
{
byte[] checksum = sha.ComputeHash(stream);
sendCheckSum = BitConverter.ToString(checksum)
.Replace("-", string.Empty);
}
}
SourceFile sourceFile = new SourceFile(
@"Thermo nativeID format",
@"Thermo RAW format",
sendCheckSum,
@"SHA-1",
filePath,
Path.GetFileNameWithoutExtension(filePath));
return(new ThermoStaticData(scans, p, sourceFile));
}
public static MsDataScan GetMsDataOneBasedScanFromThermoFile(IXRawfile5 theConnection, int nScanNumber, ThermoGlobalParams globalParams, IFilteringParams filterParams = null)
{
int pnNumPackets = 0;
double pdLowMass = 0;
double pdHighMass = 0;
double pdTIC = 0;
double pdBasePeakMass = 0;
double pdBasePeakIntensity = 0;
int pnNumChannels = 0;
int pbUniformTime = 0;
double pdFrequency = 0;
double pdStartTime = 0;
theConnection.GetScanHeaderInfoForScanNum(nScanNumber, ref pnNumPackets, ref pdStartTime, ref pdLowMass, ref pdHighMass, ref pdTIC, ref pdBasePeakMass, ref pdBasePeakIntensity, ref pnNumChannels, ref pbUniformTime, ref pdFrequency);
double?ms2isolationWidthFromTrailerExtra = null;
double?injectionTimeFromTrailerExtra = null;
double?precursorMonoisotopicMZfromTrailierExtra = null;
int? chargeStatefromTrailierExtra = null;
int? masterScanfromTrailierExtra = null;
object pvarValues = null;
object pvarLables = null;
int pnArraySize = 0;
theConnection.GetTrailerExtraForScanNum(nScanNumber, ref pvarLables, ref pvarValues, ref pnArraySize);
string[] labels = (string[])pvarLables;
string[] values = (string[])pvarValues;
for (int i = labels.GetLowerBound(0); i <= labels.GetUpperBound(0); i++)
{
if (labels[i].StartsWith("MS2 Isolation Width", StringComparison.Ordinal))
{
ms2isolationWidthFromTrailerExtra = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Ion Injection Time (ms)", StringComparison.Ordinal))
{
injectionTimeFromTrailerExtra = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Monoisotopic M/Z", StringComparison.Ordinal))
{
precursorMonoisotopicMZfromTrailierExtra = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Charge State", StringComparison.Ordinal))
{
chargeStatefromTrailierExtra = int.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(int?)null :
int.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Master Scan Number", StringComparison.Ordinal))
{
masterScanfromTrailierExtra = int.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(int?)null :
int.Parse(values[i], CultureInfo.InvariantCulture);
}
}
string pbstrFilter = null;
theConnection.GetFilterForScanNum(nScanNumber, ref pbstrFilter);
int pnMSOrder = 0;
theConnection.GetMSOrderForScanNum(nScanNumber, ref pnMSOrder);
int pnMassAnalyzerType = 0;
theConnection.GetMassAnalyzerTypeForScanNum(nScanNumber, ref pnMassAnalyzerType);
object pvarNoisePacket = null;
try //if there is no noise data
{
theConnection.GetNoiseData(ref pvarNoisePacket, nScanNumber);
}
catch
{
//pvarNoisePAcket is already null
}
double[,] noiseData = pvarNoisePacket as double[, ];
double[,] data;
try
{
object pvarFlags = null;
object pvarLabels = null;
theConnection.GetLabelData(ref pvarLabels, ref pvarFlags, ref nScanNumber);
data = pvarLabels as double[, ];
if (data == null || data.Length == 0)
{
throw new MzLibException("For spectrum number " + nScanNumber + " the data is null!");
}
}
catch (MzLibException)
{
// Warning: the masses reported by GetMassListFromScanNum when centroiding are not properly calibrated and thus could be off by 0.3 m/z or more
double pdCentroidPeakWidth = 0;
object pvarnMassList = null;
object pvarPeakFlags = null;
theConnection.GetMassListFromScanNum(ref nScanNumber, null, 0, 0, 0, 1, ref pdCentroidPeakWidth, ref pvarnMassList, ref pvarPeakFlags, ref pnArraySize);
data = (double[, ])pvarnMassList;
}
MzSpectrum thermoSpectrum;
if (filterParams != null && data.GetLength(1) > 0 && (filterParams.MinimumAllowedIntensityRatioToBasePeakM.HasValue || filterParams.NumberOfPeaksToKeepPerWindow.HasValue) && ((filterParams.ApplyTrimmingToMs1 && pnMSOrder == 1) || (filterParams.ApplyTrimmingToMsMs && pnMSOrder > 1)))
{
var count = data.GetLength(1);
var mzArray = new double[count];
var intensityArray = new double[count];
Buffer.BlockCopy(data, 0, mzArray, 0, sizeof(double) * count);
Buffer.BlockCopy(data, sizeof(double) * count, intensityArray, 0, sizeof(double) * count);
if (filterParams.NumberOfWindows == null)
{
int numPeaks = TopNpeakHelper(ref intensityArray, ref mzArray, filterParams);
//the following arrays are modified after TopN helper
Array.Resize(ref intensityArray, numPeaks);
Array.Resize(ref mzArray, numPeaks);
}
//Array reference passed by value, array calues will be modified after calling
else
{
WindowModeHelper(ref intensityArray, ref mzArray, filterParams);
}
Array.Sort(mzArray, intensityArray);
thermoSpectrum = new MzSpectrum(mzArray, intensityArray, false);
}
else
{
thermoSpectrum = new MzSpectrum(data);
}
MZAnalyzerType mzAnalyzerType;
if ((ThermoMzAnalyzer)pnMassAnalyzerType == ThermoMzAnalyzer.FTMS)
{
mzAnalyzerType = MZAnalyzerType.Orbitrap;
}
else
{
mzAnalyzerType = MZAnalyzerType.Unknown;
}
string nativeId = "controllerType=0 controllerNumber=1 scan=" + nScanNumber;
if (pnMSOrder > 1)
{
int pnActivationType = 0;
theConnection.GetActivationTypeForScanNum(nScanNumber, pnMSOrder, ref pnActivationType);
// INITIALIZE globalParams.couldBePrecursor[nScanNumber - 1] (for dynamic connections that don't have it initialized yet)
if (globalParams.CouldBePrecursor[nScanNumber - 1].Equals(default(ManagedThermoHelperLayer.PrecursorInfo)))
{
var ok = new ManagedThermoHelperLayer.HelperClass();
globalParams.CouldBePrecursor[nScanNumber - 1] = ok.GetSingleScanPrecursorInfo(nScanNumber, globalParams.FilePath);
}
var precursorInfo = globalParams.CouldBePrecursor[nScanNumber - 1];
// THIS METHOD IS BUGGY!!! DO NOT USE
//theConnection.FindPrecursorMassInFullScan(nScanNumber, ref pnMasterScan, ref pdFoundMass, ref pdHeaderMass, ref pnChargeState);
int oneBasedPrecursorScanNumber = -1;
if (precursorInfo.nScanNumber > 0)
{
oneBasedPrecursorScanNumber = precursorInfo.nScanNumber;
}
else if (masterScanfromTrailierExtra.HasValue && masterScanfromTrailierExtra > 0)
{
oneBasedPrecursorScanNumber = masterScanfromTrailierExtra.Value;
}
else
{
// we weren't able to get the precursor scan number, so we'll have to guess;
// loop back to find precursor scan
// (assumed to be the first scan before this scan with an MS order of this scan's MS order - 1)
// e.g., if this is an MS2 scan, find the first MS1 scan before this and assume that's the precursor scan
int scanOrder = globalParams.MsOrderByScan[nScanNumber - 1];
int precursorScanOrder = scanOrder - 1;
for (int i = nScanNumber - 1; i >= 0; i--)
{
int msOrder = globalParams.MsOrderByScan[i];
if (msOrder == precursorScanOrder)
{
oneBasedPrecursorScanNumber = i + 1;
break;
}
}
}
if (oneBasedPrecursorScanNumber == -1)
{
throw new MzLibException("Could not find precursor info for scan #" + nScanNumber);
}
int?selectedIonGuessChargeStateGuess = null;
if (precursorInfo.nChargeState > 0)
{
selectedIonGuessChargeStateGuess = precursorInfo.nChargeState;
}
else if (chargeStatefromTrailierExtra.HasValue)
{
selectedIonGuessChargeStateGuess = chargeStatefromTrailierExtra;
}
double?selectedIonGuessMonoisotopicMz = null;
if (precursorMonoisotopicMZfromTrailierExtra.HasValue && precursorMonoisotopicMZfromTrailierExtra.Value > 0)
{
selectedIonGuessMonoisotopicMz = precursorMonoisotopicMZfromTrailierExtra;
}
if (precursorInfo.dMonoIsoMass > 0 && !selectedIonGuessMonoisotopicMz.HasValue)
{
selectedIonGuessMonoisotopicMz = precursorInfo.dMonoIsoMass;
}
Regex matcher;
if (pbstrFilter.ToLower().Contains("msx"))
{
matcher = mFindParentIonOnlyMsx;
}
else
{
matcher = mFindParentIonOnlyNonMsx;
}
double selectedIonGuessMZ = double.Parse(matcher.Match(pbstrFilter).Groups["ParentMZ"].Value);
// int? selectedIonChargeStateGuess, double? selectedIonIntensity, double? isolationMZ, double? isolationWidth, DissociationType dissociationType, int? oneBasedPrecursorScanNumber, double? selectedIonMonoisotopicGuessMz, double? injectionTime, double[,] noiseData, string nativeId)
// double TotalIonCurrent, double selectedIonMZ, int? selectedIonChargeStateGuess, double? selectedIonIntensity, double? isolationMZ, double? isolationWidth, DissociationType dissociationType, int? oneBasedPrecursorScanNumber, double? selectedIonMonoisotopicGuessMz, double? injectionTime, double[,] noiseData, string nativeId)
return(new MsDataScan(
thermoSpectrum,
nScanNumber,
pnMSOrder,
true,
PolarityRegex.IsMatch(pbstrFilter) ? Polarity.Positive : Polarity.Negative,
pdStartTime,
new MzRange(pdLowMass, pdHighMass),
pbstrFilter,
mzAnalyzerType,
pdTIC,
injectionTimeFromTrailerExtra,
noiseData,
nativeId,
selectedIonGuessMZ,
selectedIonGuessChargeStateGuess,
null,
selectedIonGuessMZ,
ms2isolationWidthFromTrailerExtra,
(DissociationType)pnActivationType,
oneBasedPrecursorScanNumber,
selectedIonGuessMonoisotopicMz
));
}
else
{
return(new MsDataScan(
thermoSpectrum,
nScanNumber,
1,
true,
PolarityRegex.IsMatch(pbstrFilter) ? Polarity.Positive : Polarity.Negative,
pdStartTime,
new MzRange(pdLowMass, pdHighMass),
pbstrFilter,
mzAnalyzerType,
pdTIC,
injectionTimeFromTrailerExtra,
noiseData,
nativeId));
}
}
protected ThermoFile(IXRawfile5 _rawConnection, int numSpectra, ManagedThermoHelperLayer.PrecursorInfo[] couldBePrecursor, SourceFile sourceFile, ThermoGlobalParams thermoGlobalParams) : base(numSpectra, sourceFile)
{
this.ThermoGlobalParams = thermoGlobalParams;
}
protected ThermoFile(IThermoScan[] scans, ThermoGlobalParams thermoGlobalParams, SourceFile sourceFile) : base(scans, sourceFile)
{
this.ThermoGlobalParams = thermoGlobalParams;
}
private ThermoStaticData(IThermoScan[] scans, ThermoGlobalParams p, SourceFile sourceFile) : base(scans, p, sourceFile)
{
}
private ThermoDynamicData(IXRawfile5 _rawConnection, IFilteringParams filterParams, int numSpectra, SourceFile sourceFile, ThermoGlobalParams thermoGlobalParams) : base(numSpectra, sourceFile)
{
this._rawConnection = _rawConnection;
this.filterParams = filterParams;
ThermoGlobalParams = thermoGlobalParams;
}