public static int DumpInstrumentMethod(string RawFileName)
{
List <string> _strExportRAW = new List <string>();
XRAWLib.XRawfile _rawfile = new XRAWLib.XRawfile();
//XRAWFILE2Lib.XRawfile _rawfile = new XRawfile();
_rawfile.Open(RawFileName);
_rawfile.SetCurrentController(0, 1);
//_rawfile.GetInstMethod()
/*
* int testSTLog = 0, testTuneData = 0, testerror = 0;
* _rawfile.GetNumStatusLog(ref testSTLog); MessageBox.Show("testSTLog - " + testSTLog.ToString());
* _rawfile.GetNumTuneData(ref testTuneData); MessageBox.Show("testTuneData - " + testTuneData.ToString());
* _rawfile.GetNumErrorLog(ref testerror); MessageBox.Show("testerror - " + testerror.ToString()); */
string pbstrFileName = null, pbstrInstMethod0 = null, pbstrInstMethod1 = null;
int pnNumPackets = 0;
double dStartTime = 0.0, pdRT = 0.0, pdStatusLogRT = 0.0;
double dLowMass = 0.0;
double dHighMass = 0.0;
double dTIC = 0.0;
double dBasePeakMass = 0.0;
double dBasePeakIntensity = 0.0;
int nChannels = 0;
int bUniformTime = 0;
double dFrequency = 0.0;
int pnFirstSpectrum = 0, pnLastSpectrum = 0, pnArraySizeTE = 0, pnArraySizeSL = 0;
DateTime pCreationDate = DateTime.Now;
_rawfile.GetFileName(ref pbstrFileName);
_rawfile.GetInstMethod(0, ref pbstrInstMethod0); _rawfile.GetInstMethod(1, ref pbstrInstMethod1);
_rawfile.GetCreationDate(ref pCreationDate);
File.WriteAllText(Path.ChangeExtension(RawFileName, "inm"), pbstrInstMethod0 + pbstrInstMethod1);
//MessageBox.Show(pbstrInstMethod0);
string AquDate = null;
_rawfile.GetInstSerialNumber(ref AquDate);
MessageBox.Show(pCreationDate.ToString(), "Creatio");
MessageBox.Show(AquDate, "AquDate");
return(1);
}
public static int GetScanNum(string RawFileName)
{
XRAWLib.XRawfile _rawfile = new XRAWLib.XRawfile();
_rawfile.Open(RawFileName);
_rawfile.SetCurrentController(0, 1);
int /*pnFirstSpectrum = 0,*/ pnLastSpectrum = 0;
_rawfile.GetLastSpectrumNumber(ref pnLastSpectrum);
//MessageBox.Show(pnLastSpectrum.ToString());
_rawfile.Close();
return(pnLastSpectrum);
}
public static double GetTotalIntensityOfIonFromScanNumber(XRAWLib.XRawfile Rawfile, int nScanNumber, List <IonData> IonMassList, double Tolerance)
{
double totalIonIntensity = 0.0;
object pvarMassList = null; object pvarPeakFlags = null; int pnArraySize = 0; double pdCentroidWidth = 0.0;
Rawfile.GetMassListFromScanNum(nScanNumber, null, 0, 0, 0, 1, ref pdCentroidWidth, ref pvarMassList, ref pvarPeakFlags, ref pnArraySize);
double[,] scanMassList = (double[, ])pvarMassList;
for (int i = 0; i < pnArraySize; i++)
{
totalIonIntensity += scanMassList[1, i];
for (int j = 0; j < IonMassList.Count; j++)
{
if (scanMassList[0, i] > (IonMassList[j]._MassOverCharge - Tolerance) && scanMassList[0, i] < (IonMassList[j]._MassOverCharge + Tolerance))
{
IonMassList[j].Intensity += scanMassList[1, i];
}
}
// MessageBox.Show(String.Format("Mass - {0}, Intensity - {1} ", mas[0, i], mas[1, i]) );
}
return(totalIonIntensity);
}
public static PeptidePeaksExtra GetPeptideExtrasForCompound(string RawFileName, string Compound, double PeakLeftRT, double PeakRightRT)
{
PeptidePeaksExtra _peptideExtras = new PeptidePeaksExtra();
_peptideExtras._allInjectTimes = new List <CompoundInjectTime>();
_peptideExtras._Peptide = PeptideFromCompound(Compound);
//List<CompoundInjectTime> _listCompVSInj = new List<CompoundInjectTime>();
XRAWLib.XRawfile _rawfile = new XRAWLib.XRawfile();
_rawfile.Open(RawFileName);
_rawfile.SetCurrentController(0, 1);
int pnFirstSpectrum = 0, pnLastSpectrum = 0, pnArraySizeTE = 0;
_rawfile.ScanNumFromRT(PeakLeftRT, ref pnFirstSpectrum); _rawfile.ScanNumFromRT(PeakRightRT, ref pnLastSpectrum);
int count = 0;
for (int nScanNumber = pnFirstSpectrum; nScanNumber <= pnLastSpectrum; nScanNumber++) // all spectrums
{
string pbstrFilter = null, pbstrScanEvent = null;
object pvarLabelsTE = null, pvarValuesTE = null;
_rawfile.GetFilterForScanNum(nScanNumber, ref pbstrFilter);
// MessageBox.Show(nScanNumber.ToString() +" - "+ pbstrFilter+" peakleft " + PeakLeftRT);
// if (pbstrFilter == null) { MessageBox.Show(RawFileName + "have null filter"); continue; }
string compoundName = CompoundFromFilter(pbstrFilter);
string peptideName = PeptideFromFilter(pbstrFilter);
if (!IfCompound(peptideName, Compound))
{
continue;
}
count++;
(_rawfile as XRAWLib.IXRawfile5).GetScanEventForScanNum(nScanNumber, ref pbstrScanEvent);
_rawfile.GetTrailerExtraForScanNum(nScanNumber, ref pvarLabelsTE, ref pvarValuesTE, ref pnArraySizeTE);
string[] strTrailerLabels = (string[])pvarLabelsTE; string[] strTrailerValues = (string[])pvarValuesTE;
string trailerExtra = ""; //, trailerHeader = ""; string statusLog = "", statusHeader = ""; string quantIons = "", quantIonsHeader = "";
int _injectIndex = 2;
for (int i = 0; i < strTrailerLabels.Length; i++)
{
if (strTrailerLabels[i].StartsWith("Ion Injection Time"))
{
trailerExtra = strTrailerValues[i];
_injectIndex = i;
}
}
CompoundInjectTime _compInj = new CompoundInjectTime();
_compInj._ScanNum = nScanNumber;
_compInj._Compound = compoundName;
try
{
_compInj._InjectTime = float.Parse(strTrailerValues[_injectIndex]);
}
catch (Exception _ex)
{
MessageBox.Show("GetPeptideExtrasForCompound():float.Parse", "Cannot parse " + strTrailerValues[_injectIndex] + " to float;");
}
_peptideExtras._allInjectTimes.Add(_compInj);
}
_rawfile.Close();
var AvgInjTimeQuery = from pair in _peptideExtras._allInjectTimes
group pair by pair._Compound into gr
select new { Compound = gr.Key, AvgInjTime = gr.Average(a => a._InjectTime), NumSpec = gr.Count() };
foreach (var _compound in AvgInjTimeQuery)
{
if (_compound.Compound.Contains("C13"))
{
_peptideExtras._AvgC13_InjT = _compound.AvgInjTime; _peptideExtras._NumSpecC13_InjT = _compound.NumSpec;
}
if (_compound.Compound.Contains("C12"))
{
_peptideExtras._AvgC12_InjT = _compound.AvgInjTime; _peptideExtras._NumSpecC12_InjT = _compound.NumSpec;
}
if (_compound.Compound.Contains("N15"))
{
_peptideExtras._AvgN15_InjT = _compound.AvgInjTime; _peptideExtras._NumSpecN15_InjT = _compound.NumSpec;
}
}
_peptideExtras._TotScans = count;
return(_peptideExtras);
}
public static int DumpScanHeaderDataForCompound(string RawFileName, string RawFileOut, bool IfHeader, string Compound, double PeakLeftRT, double PeakRightRT, double Tolerance)
{
List <string> _strExportRAW = new List <string>();
XRAWLib.XRawfile _rawfile = new XRAWLib.XRawfile();
//XRAWFILE2Lib.XRawfile _rawfile = new XRawfile();
_rawfile.Open(RawFileName);
_rawfile.SetCurrentController(0, 1);
//_rawfile.GetInstMethod()
/*
* int testSTLog = 0, testTuneData = 0, testerror = 0;
* _rawfile.GetNumStatusLog(ref testSTLog); MessageBox.Show("testSTLog - " + testSTLog.ToString());
* _rawfile.GetNumTuneData(ref testTuneData); MessageBox.Show("testTuneData - " + testTuneData.ToString());
* _rawfile.GetNumErrorLog(ref testerror); MessageBox.Show("testerror - " + testerror.ToString()); */
string pbstrFileName = null, pbstrInstMethod = null;
int pnNumPackets = 0;
double dStartTime = 0.0, pdRT = 0.0, pdStatusLogRT = 0.0;
double dLowMass = 0.0;
double dHighMass = 0.0;
double dTIC = 0.0;
double dBasePeakMass = 0.0;
double dBasePeakIntensity = 0.0;
int nChannels = 0;
int bUniformTime = 0;
double dFrequency = 0.0;
int pnFirstSpectrum = 0, pnLastSpectrum = 0, pnArraySizeTE = 0, pnArraySizeSL = 0;
DateTime pCreationDate = DateTime.Now;
_rawfile.GetFileName(ref pbstrFileName); _rawfile.GetInstMethod(1, ref pbstrInstMethod); _rawfile.GetCreationDate(ref pCreationDate);
pbstrFileName = Path.GetFileNameWithoutExtension(pbstrFileName);
_rawfile.GetFirstSpectrumNumber(ref pnFirstSpectrum); _rawfile.GetLastSpectrumNumber(ref pnLastSpectrum);
int count = 0;
for (int nScanNumber = pnFirstSpectrum; nScanNumber <= pnLastSpectrum; nScanNumber++) // all spectrums
{
List <IonData> _ScanMSDataList = InitIonsForQuantList();
double _tii = GetTotalIntensityOfIonFromScanNumber(_rawfile, nScanNumber, _ScanMSDataList, Tolerance);
string pbstrFilter = null, pbstrScanEvent = null;
object pvarLabelsTE = null, pvarValuesTE = null;
object pvarLabelsSL = null, pvarValuesSL = null;
_rawfile.GetScanHeaderInfoForScanNum(nScanNumber, ref pnNumPackets, ref dStartTime, ref dLowMass, ref dHighMass, ref dTIC,
ref dBasePeakMass, ref dBasePeakIntensity, ref nChannels, ref bUniformTime, ref dFrequency);
_rawfile.GetTrailerExtraForScanNum(nScanNumber, ref pvarLabelsTE, ref pvarValuesTE, ref pnArraySizeTE);
_rawfile.GetFilterForScanNum(nScanNumber, ref pbstrFilter);
string compoundName = CompoundFromFilter(pbstrFilter);
if (!IfCompound(compoundName, Compound))
{
continue;
}
count++;
bool _ifPeak = false;
_rawfile.RTFromScanNum(nScanNumber, ref pdRT); if (pdRT > PeakLeftRT && pdRT < PeakRightRT)
{
_ifPeak = true;
}
(_rawfile as XRAWLib.IXRawfile5).GetScanEventForScanNum(nScanNumber, ref pbstrScanEvent);
_rawfile.GetStatusLogForScanNum(nScanNumber, ref pdStatusLogRT, ref pvarLabelsSL, ref pvarValuesSL, ref pnArraySizeSL); //MessageBox.Show(pnArraySizeSL.ToString());
string[] strTrailerLabels = (string[])pvarLabelsTE; string[] strTrailerValues = (string[])pvarValuesTE;
string[] strStatusLabels = (string[])pvarLabelsSL; string[] strStatusValues = (string[])pvarValuesSL;
string trailerExtra = "", trailerHeader = ""; string statusLog = "", statusHeader = ""; string quantIons = "", quantIonsHeader = "";
for (int i = 0; i < pnArraySizeTE; i++) // all TrailerExtra
{
trailerExtra += strTrailerValues[i]; trailerExtra += "; ";
if (count == 1 && IfHeader)
{
trailerHeader += strTrailerLabels[i]; trailerHeader += "; ";
}
}
foreach (IonData _ion in _ScanMSDataList) // all Quant MS ions-intens.
{
quantIons += _ion._Intensity.ToString(); quantIons += "; ";
if (count == 1 && IfHeader)
{
quantIonsHeader += _ion._MassOverCharge.ToString(); quantIonsHeader += "; ";
}
}
for (int i = 0; i < pnArraySizeSL; i++) // all StatusLog
{
statusLog += strStatusValues[i]; statusLog += "; "; //MessageBox.Show(strStatusLabels[i] + " - " + strStatusValues[i]);
if (count == 1 && IfHeader)
{
statusHeader += strStatusLabels[i]; statusHeader += "; ";
}
}
if (count == 1 && IfHeader)
{
_strExportRAW.Add("pbstrFileName; pCreationDate; nScanNumber; pbstrFilter; pdRT; pbstrScanEvent; pnNumPackets; dStartTime; dLowMass; " +
"dHighMass; dTIC; dBasePeakMass; dBasePeakIntensity; nChannels; bUniformTime; dFrequency; ifPeak; compound; TII; PeakLeftRT; PeakRightRT; "
+ quantIonsHeader + trailerHeader);
}
_strExportRAW.Add(
String.Format("{0}; {1}; {2}; {3}; {4}; {5}; {6}; {7}; {8}; {9}; {10}; {11}; {12}; {13}; {14}; {15}; {16}; {17}; {18}; {19}; {20}; {21} {22}",
pbstrFileName, pCreationDate,
nScanNumber, pbstrFilter, pdRT, pbstrScanEvent,
pnNumPackets, dStartTime, dLowMass, dHighMass, dTIC, dBasePeakMass, dBasePeakIntensity, nChannels, bUniformTime, dFrequency,
_ifPeak, compoundName, _tii, PeakLeftRT, PeakRightRT,
quantIons,
trailerExtra)
);
}
if (IfHeader)
{
File.WriteAllLines(RawFileOut, _strExportRAW.ToArray());
}
else
{
File.AppendAllLines(RawFileOut, _strExportRAW.ToArray());
}
_rawfile.Close();
return(count);
}
public static void DumpScanHeaderData(string RawFileName, string RawFileOut, bool IfHeader)
{
List <string> _strExportRAW = new List <string>();
XRAWLib.XRawfile _rawfile = new XRAWLib.XRawfile();
//XRAWFILE2Lib.XRawfile _rawfile = new XRawfile();
_rawfile.Open(RawFileName);
_rawfile.SetCurrentController(0, 1);
int testSTLog = 0, testTuneData = 0, testerror = 0;
_rawfile.GetNumStatusLog(ref testSTLog); MessageBox.Show("testSTLog - " + testSTLog.ToString());
_rawfile.GetNumStatusLog(ref testTuneData); MessageBox.Show("testTuneData - " + testTuneData.ToString());
_rawfile.GetNumStatusLog(ref testerror); MessageBox.Show("testerror - " + testerror.ToString());
string pbstrFileName = null, pbstrInstMethod = null;
int pnNumPackets = 0;
double dStartTime = 0.0, pdRT = 0.0, pdStatusLogRT = 0.0;
double dLowMass = 0.0;
double dHighMass = 0.0;
double dTIC = 0.0;
double dBasePeakMass = 0.0;
double dBasePeakIntensity = 0.0;
int nChannels = 0;
int bUniformTime = 0;
double dFrequency = 0.0;
int pnFirstSpectrum = 0, pnLastSpectrum = 0, pnArraySizeTE = 0, pnArraySizeSL = 0;
DateTime pCreationDate = DateTime.Now;
_rawfile.GetFileName(ref pbstrFileName); _rawfile.GetInstMethod(1, ref pbstrInstMethod); _rawfile.GetCreationDate(ref pCreationDate);
_rawfile.GetFirstSpectrumNumber(ref pnFirstSpectrum); _rawfile.GetLastSpectrumNumber(ref pnLastSpectrum);
int count = 0;
for (int nScanNumber = pnFirstSpectrum; nScanNumber <= pnLastSpectrum; nScanNumber++) // all spectrums
{
string pbstrFilter = null, pbstrScanEvent = null;
object pvarLabelsTE = null, pvarValuesTE = null;
object pvarLabelsSL = null, pvarValuesSL = null;
count++;
_rawfile.GetScanHeaderInfoForScanNum(nScanNumber, ref pnNumPackets, ref dStartTime, ref dLowMass, ref dHighMass, ref dTIC,
ref dBasePeakMass, ref dBasePeakIntensity, ref nChannels, ref bUniformTime, ref dFrequency);
_rawfile.GetTrailerExtraForScanNum(nScanNumber, ref pvarLabelsTE, ref pvarValuesTE, ref pnArraySizeTE);
_rawfile.GetFilterForScanNum(nScanNumber, ref pbstrFilter); //MessageBox.Show(pbstrFilter);
_rawfile.RTFromScanNum(nScanNumber, ref pdRT);
(_rawfile as XRAWLib.IXRawfile5).GetScanEventForScanNum(nScanNumber, ref pbstrScanEvent);
_rawfile.GetStatusLogForScanNum(nScanNumber, ref pdStatusLogRT, ref pvarLabelsSL, ref pvarValuesSL, ref pnArraySizeSL); MessageBox.Show(pnArraySizeSL.ToString());
string[] strTrailerLabels = (string[])pvarLabelsTE; string[] strTrailerValues = (string[])pvarValuesTE;
string[] strStatusLabels = (string[])pvarLabelsSL; string[] strStatusValues = (string[])pvarValuesSL;
string trailerExtra = "", trailerHeader = ""; string statusLog = "", statusHeader = "";
for (int i = 0; i < pnArraySizeTE; i++) // all TrailerExtra
{
trailerExtra += strTrailerValues[i]; trailerExtra += "; ";
if (count == 1)
{
trailerHeader += strTrailerLabels[i]; trailerHeader += "; ";
}
}
for (int i = 0; i < pnArraySizeSL; i++) // all StatusLog
{
statusLog += strStatusValues[i]; statusLog += "; "; MessageBox.Show(strStatusLabels[i] + " - " + strStatusValues[i]);
if (count == 1)
{
statusHeader += strStatusLabels[i]; statusHeader += "; ";
}
}
if (count == 1)
{
_strExportRAW.Add("pbstrFileName; pCreationDate; nScanNumber; pbstrFilter; pdRT; pbstrScanEvent; pnNumPackets; dStartTime; dLowMass; " +
"dHighMass; dTIC; dBasePeakMass; dBasePeakIntensity; nChannels; bUniformTime; dFrequency; " + trailerHeader);
}
_strExportRAW.Add(
String.Format("{0}; {1}; {2}; {3}; {4}; {5}; {6}; {7}; {8}; {9}; {10}; {11}; {12}; {13}; {14}; {15}; {16}",
pbstrFileName, pCreationDate,
nScanNumber, pbstrFilter, pdRT, pbstrScanEvent,
pnNumPackets, dStartTime, dLowMass, dHighMass, dTIC, dBasePeakMass, dBasePeakIntensity, nChannels, bUniformTime, dFrequency,
trailerExtra)
);
}
if (IfHeader)
{
File.WriteAllLines(RawFileOut, _strExportRAW.ToArray());
}
else
{
File.AppendAllLines(RawFileOut, _strExportRAW.ToArray());
}
_rawfile.Close();
}