public static string ConvertToPbf(string specFilePath, IMassSpecDataReader specReader,
double precursorSignalToNoiseRatioThreshold, double productSignalToNoiseRatioThreshold, string pbfFilePath = null,
IProgress <ProgressData> progress = null)
{
return(PbfLcMsRun.ConvertToPbf(specFilePath, MassSpecDataReaderFactory.GetMassSpecDataReader(specFilePath),
precursorSignalToNoiseRatioThreshold, productSignalToNoiseRatioThreshold, pbfFilePath, progress));
}
/// <summary>
///
/// </summary>
/// <param name="specFilePath"></param>
/// <param name="precursorSignalToNoiseRatioThreshold"></param>
/// <param name="productSignalToNoiseRatioThreshold"></param>
/// <param name="progress"></param>
/// <returns></returns>
/// <remarks>It is recommended that "MassSpecDataReaderFactory.NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static LcMsRun GetLcMsRun(
string specFilePath,
double precursorSignalToNoiseRatioThreshold,
double productSignalToNoiseRatioThreshold,
IProgress <ProgressData> progress = null)
{
return(GetLcMsRun(specFilePath, MassSpecDataReaderFactory.GetMassSpecDataReader(specFilePath), precursorSignalToNoiseRatioThreshold,
productSignalToNoiseRatioThreshold, progress));
}
/// <summary>
///
/// </summary>
/// <param name="specFilePath"></param>
/// <param name="progress"></param>
/// <returns></returns>
/// <remarks>It is recommended that "MassSpecDataReaderFactory.NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static LcMsRun GetLcMsRun(string specFilePath, IProgress <ProgressData> progress = null)
{
var reader = MassSpecDataReaderFactory.GetMassSpecDataReader(specFilePath);
return(GetLcMsRun(specFilePath, reader, 0.0, 0.0, progress));
}
/// <summary>
///
/// </summary>
/// <param name="specFilePath"></param>
/// <param name="scanStart"></param>
/// <param name="scanEnd"></param>
/// <param name="progress"></param>
/// <returns></returns>
/// <remarks>It is recommended that "MassSpecDataReaderFactory.NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static LcMsRun GetLcMsRunScanRange(string specFilePath, int scanStart, int scanEnd, IProgress <ProgressData> progress = null)
{
var reader = MassSpecDataReaderFactory.GetMassSpecDataReader(specFilePath);
return(GetLcMsRun(specFilePath, reader, 0.0, 0.0, progress, scanStart, scanEnd));
}
/// <summary>
///
/// </summary>
/// <param name="specFilePath"></param>
/// <param name="singleScanNum"></param>
/// <returns></returns>
/// <remarks>It is recommended that "MassSpecDataReaderFactory.NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public static LcMsRun GetLcMsRunScanRange(string specFilePath, int singleScanNum)
{
var reader = MassSpecDataReaderFactory.GetMassSpecDataReader(specFilePath);
return(GetLcMsRun(specFilePath, reader, 0.0, 0.0, null, singleScanNum, singleScanNum));
}
/// <summary>
/// Function to convert a spectra file name/path to a *.pbf name, even when it has multiple extensions (i.e., .mzML.gz)
/// </summary>
/// <param name="specFileName"></param>
/// <returns></returns>
/// <remarks>It is recommended that "MassSpecDataReaderFactory.NormalizeDatasetPath" be called prior to calling this function, and that the returned string be used instead of the original path</remarks>
public new static string GetPbfFileName(string specFileName)
{
return(MassSpecDataReaderFactory.ChangeExtension(specFileName, FileExtensionConst));
}