private MsDataFileImpl GetDataFile(bool ignoreZeroIntensityPoints)
{
if (_dataFile == null)
{
if (DataFilePath is MsDataFilePath)
{
string dataFilePath = FindDataFilePath();
var lockMassParameters = DataFilePath.GetLockMassParameters();
if (dataFilePath == null)
{
throw new FileNotFoundException(string.Format(
Resources
.ScanProvider_GetScans_The_data_file__0__could_not_be_found__either_at_its_original_location_or_in_the_document_or_document_parent_folder_,
DataFilePath));
}
int sampleIndex = SampleHelp.GetPathSampleIndexPart(dataFilePath);
if (sampleIndex == -1)
{
sampleIndex = 0;
}
// Full-scan extraction always uses SIM as spectra
_dataFile = new MsDataFileImpl(dataFilePath, sampleIndex, lockMassParameters, true,
combineIonMobilitySpectra: DataFilePath.GetCombineIonMobilitySpectra(),
requireVendorCentroidedMS1: DataFilePath.GetCentroidMs1(),
requireVendorCentroidedMS2: DataFilePath.GetCentroidMs2(),
ignoreZeroIntensityPoints: ignoreZeroIntensityPoints);
}
else
{
_dataFile = DataFilePath.OpenMsDataFile(true, 0, null, ignoreZeroIntensityPoints);
}
}
return(_dataFile);
}
private MsDataFileImpl GetDataFile(bool ignoreZeroIntensityPoints)
{
if (_dataFile == null)
{
const bool simAsSpectra = true; // SIM always as spectra here
const bool preferOnlyMs1 = false; // Open with all available spectra indexed
if (DataFilePath is MsDataFilePath)
{
string dataFilePath = FindDataFilePath();
var lockMassParameters = DataFilePath.GetLockMassParameters();
if (dataFilePath == null)
{
throw new FileNotFoundException(string.Format(
Resources
.ScanProvider_GetScans_The_data_file__0__could_not_be_found__either_at_its_original_location_or_in_the_document_or_document_parent_folder_,
DataFilePath));
}
int sampleIndex = SampleHelp.GetPathSampleIndexPart(dataFilePath);
if (sampleIndex == -1)
{
sampleIndex = 0;
}
// Full-scan extraction always uses SIM as spectra
_dataFile = new MsDataFileImpl(dataFilePath, sampleIndex,
lockMassParameters,
simAsSpectra,
combineIonMobilitySpectra: _cachedFile.HasCombinedIonMobility,
requireVendorCentroidedMS1: _cachedFile.UsedMs1Centroids,
requireVendorCentroidedMS2: _cachedFile.UsedMs2Centroids,
ignoreZeroIntensityPoints: ignoreZeroIntensityPoints);
}
else
{
_dataFile = DataFilePath.OpenMsDataFile(simAsSpectra, preferOnlyMs1,
_cachedFile.UsedMs1Centroids, _cachedFile.UsedMs2Centroids, ignoreZeroIntensityPoints);
}
}
return(_dataFile);
}