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);
}
public const double DISPLAY_FILTER_PERCENT = 0.01; // filter peaks less than this percentage of maximum intensity
public ChromatogramLoadingStatus(MsDataFileUri filePath, IEnumerable <string> replicateNames) :
base(SampleHelp.GetFileName(filePath))
{
Transitions = new TransitionData();
FilePath = filePath;
ReplicateNames = replicateNames;
}
public static MsDataFilePath ParseUri(string url)
{
return(new MsDataFilePath(SampleHelp.GetPathFilePart(url),
SampleHelp.GetPathSampleNamePart(url),
SampleHelp.GetPathSampleIndexPart(url),
SampleHelp.GetLockmassParameters(url),
SampleHelp.GetCentroidMs1(url),
SampleHelp.GetCentroidMs2(url),
SampleHelp.GetCombineIonMobilitySpectra(url)));
}
public static MsDataFileUri Parse(string url)
{
if (url.StartsWith(ChorusUrl.ChorusUrlPrefix))
{
return(new ChorusUrl(url));
}
return(new MsDataFilePath(SampleHelp.GetPathFilePart(url),
SampleHelp.GetPathSampleNamePart(url),
SampleHelp.GetPathSampleIndexPart(url),
SampleHelp.GetLockmassParameters(url),
SampleHelp.GetCentroidMs1(url),
SampleHelp.GetCentroidMs2(url)));
}
public static MsDataFileUri Parse(string url)
{
if (url.StartsWith(UnifiUrl.UrlPrefix))
{
return(new UnifiUrl(url));
}
return(new MsDataFilePath(SampleHelp.GetPathFilePart(url),
SampleHelp.GetPathSampleNamePart(url),
SampleHelp.GetPathSampleIndexPart(url),
SampleHelp.GetLockmassParameters(url),
SampleHelp.GetCentroidMs1(url),
SampleHelp.GetCentroidMs2(url),
SampleHelp.GetCombineIonMobilitySpectra(url)));
}
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);
}
public override string ToString()
{
return(SampleHelp.EncodePath(FilePath, SampleName, SampleIndex, LockMassParameters, CentroidMs1, CentroidMs2));
}
public override string ToString()
{
return(SampleHelp.LegacyEncodePath(FilePath, SampleName, SampleIndex, LockMassParameters,
LegacyCentroidMs1, LegacyCentroidMs2, LegacyCombineIonMobilitySpectra));
}