public void Close()
{
_rawReader.Close();
if (_mgfWriter != null)
{
_mgfWriter.Close();
}
if (_ms1Writer != null)
{
_ms1Writer.Close();
}
if (_ms2Writer != null)
{
_ms2Writer.Close();
}
if (_ms3Writer != null)
{
_ms3Writer.Close();
}
if (_mzXMLWriter != null)
{
_mzXMLWriter.Close();
}
if (_chargeNumWriter != null)
{
_chargeNumWriter.Close();
}
}
private bool IsNotRawfile(string fileName)
{
bool returnvar = false;
try
{
//IXRawfile5 raw = (IXRawfile5) new MSFileReader_XRawfile();
RawFileName rawfile = new RawFileName(fileName);
raw.Open(rawfile.FullName);
raw.SetCurrentController(0, 1);
int lastScanNumber = -1;
raw.GetLastSpectrumNumber(ref lastScanNumber);
if (lastScanNumber < 10)
{
returnvar = true;
}
if (raw != null)
{
raw.Close();
}
}
catch//can add specific exception here
{
return(true);
}
finally
{
//if (raw != null)
// raw.Close();
}
return(returnvar);
}
protected virtual void Dispose(bool disposing)
{
if (disposing)
{
if (_rawConnection != null)
{
_rawConnection.Close();
}
}
}
protected override void Dispose(bool disposing)
{
if (disposing)
{
if (_rawConnection != null)
{
_rawConnection.Close();
_rawConnection = null;
}
}
base.Dispose(disposing);
}
public void Dispose()
{
if (disposed)
{
return;
}
if (rawFile != null)
{
rawFile.Close();
}
disposed = true;
}
// Protected implementation of Dispose pattern.
protected virtual void Dispose(bool disposing)
{
if (disposed)
{
return;
}
if (disposing)
{
// Free any other managed objects here.
_rawConnection.Close();
}
// Free any unmanaged objects here.
disposed = true;
}
public RawFileProcessing(IXRawfile5 raw, string rawFileName, SettingsForAnalysis settingName)
{
//open rawfile (add error check)
raw.Open(rawFileName);
raw.SetCurrentController(0, 1);
raw.GetCreationDate(ref _msStart);
double endtime = 0.0;
raw.GetEndTime(ref endtime);
_msEnd = _msStart.AddMinutes(endtime);
_filecreation = File.GetCreationTime(rawFileName);
raw.GetWarningMessage(ref WarningMessage);
ProcessScans(raw, settingName);
raw.Close();
ReduceToMetaVariables(settingName);
}
private void SaveDataToCdf(MsSpectrum spec, string fpath)
{
DataSetFactory.SearchFolder("Microsoft.Research.Science.Data.NetCDF4.dll");
DataSetFactory.SearchFolder("Microsoft.Research.Science.Data.dll");
DataSetFactory.SearchFolder("Microsoft.Research.Science.Data.Imperative.dll");
int nControllerType = 0; // 0 == mass spec device
int nContorllerNumber = 1; // first MS device
int totalNumScans = 0; // Number of scans
int firstScanNumber = 0, lastScanNumber = -1; // Number of first and last scan
string scanFilter = null; // Scan filter line
int numDataPoints = -1; // points in both the m/z and intensity arrays
double retentionTimeInMinutes = -1;
double minObservedMZ = -1;
double maxObservedMZ = -1;
double totalIonCurrent = -1;
double basePeakMZ = -1;
double basePeakIntensity = -1;
int channel = 0; // unused
int uniformTime = 0; // unused
double frequency = 0; // unused
int arraySize = -1;
object rawData = null; // rawData wil come as Double[,]
object peakFlags = null;
string szFilter = null; // No filter
int intensityCutoffType = 1; // No cutoff
int intensityCutoffValue = 0; // No cutoff
int maxNumberOfPeaks = 0; // 0 : return all data peaks
double centroidPeakWidth = 0; // No centroiding
int centroidThisScan = 0; // No centroiding
DateTime creationDate = DateTime.MinValue;
var scanPath = Path.Combine(fpath, $"{spec.Id}.cdf");
var cdf = DataSet.Open(scanPath);
cdf.IsAutocommitEnabled = false;
AddMetadata(cdf);
IXRawfile5 rawFile = (IXRawfile5) new MSFileReader_XRawfile();
rawFile.Open(spec.RawFilePath);
rawFile.SetCurrentController(nControllerType, nContorllerNumber);
rawFile.GetNumSpectra(ref totalNumScans);
rawFile.GetFirstSpectrumNumber(ref firstScanNumber);
rawFile.GetLastSpectrumNumber(ref lastScanNumber);
rawFile.GetCreationDate(ref creationDate);
var massVar = cdf.Add <double>("mass_values", new[] { "point_number" });
var intensities = cdf.Add <Int32>("intensity_values", new[] { "point_number" });
var acqTimeVar = cdf.Add <double>("scan_acquisition_time", new[] { "scan_number" });
var scIndexVar = cdf.Add <int>("scan_index", new[] { "scan_number" });
var scCountVar = cdf.Add <int>("point_count", new[] { "scan_number" });
var totalIntensityVar = cdf.Add <double>("total_intensity", new[] { "scan_number" });
massVar.Metadata["scale_factor"] = 1.0;
intensities.Metadata["scale_factor"] = 1.0;
try
{
var retTimes = new double[lastScanNumber];
var ticArr = new double[lastScanNumber];
var scanIndex = new Int32[lastScanNumber];
var pointCount = new Int32[lastScanNumber];
for (int curScanNum = firstScanNumber; curScanNum <= lastScanNumber; curScanNum++)
{
rawFile.GetScanHeaderInfoForScanNum(curScanNum,
ref numDataPoints,
ref retentionTimeInMinutes,
ref minObservedMZ,
ref maxObservedMZ,
ref totalIonCurrent,
ref basePeakMZ,
ref basePeakIntensity,
ref channel, // unused
ref uniformTime, // unused
ref frequency // unused
);
scanFilter = null;
rawFile.GetFilterForScanNum(curScanNum, ref scanFilter);
peakFlags = null;
centroidPeakWidth = 0;
arraySize = 0;
intensityCutoffType = 1;
intensityCutoffValue = (int)(0.001 * basePeakIntensity);
rawFile.GetMassListFromScanNum(
ref curScanNum,
szFilter, // filter
intensityCutoffType, // intensityCutoffType
intensityCutoffValue, // intensityCutoffValue
maxNumberOfPeaks, // maxNumberOfPeaks
centroidThisScan, // centroid result?
ref centroidPeakWidth, // centroidingPeakWidth
ref rawData, // daw data
ref peakFlags, // peakFlags
ref arraySize); // array size
;
var datArray = (Array)rawData;
var massArr = new double[arraySize];
var intArr = new int[arraySize];
for (var j = 0; j < arraySize; j++)
{
massArr[j] = (double)datArray.GetValue(0, j);
intArr[j] = Convert.ToInt32(datArray.GetValue(1, j));
}
//Console.Write($"curScan = {curScanNum}\n");
var ind = curScanNum - 1;
pointCount[ind] = arraySize;
if (ind == 0)
{
scanIndex[ind] = 0;
scanIndex[ind + 1] = arraySize;
}
else
{
scanIndex[ind] += scanIndex[ind - 1];
if (ind + 1 < lastScanNumber)
{
scanIndex[ind + 1] = arraySize;
}
}
retTimes[ind] = TimeSpan.FromMinutes(retentionTimeInMinutes).TotalSeconds;
ticArr[ind] = totalIonCurrent;
massVar.Append(massArr);
intensities.Append(intArr);
rawData = null;
}
totalIntensityVar.PutData(ticArr);
scIndexVar.PutData(scanIndex);
acqTimeVar.PutData(retTimes);
scCountVar.PutData(pointCount);
cdf.Commit();
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
finally
{
cdf.Dispose();
rawFile.Close();
}
}
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 void Exit()
{
_rawConnect.Close();
}
