/// <summary>
/// Performs the NET-Mass Warping; Sets up the mass calibration settings from the options,
/// performs NET warping, calibrates matches based on the NETWarp results, recalibrates the mass
/// tolerance and then performs Warping again using the mass and Net scores
/// </summary>
/// <param name="progress"></param>
private void PerformNetMassWarp(IProgress <ProgressData> progress = null)
{
var progData = new ProgressData(progress);
var prog = new Progress <ProgressData>(p => progData.Report(p.Percent, p.Status));
OnProgress("LCMSWarp phase one", 0);
progData.StepRange(50, "LCMSWarp phase one");
// First, perform the net calibration using a mass tolerance of the same size as the mass window
// and then perform the net calibration again using the appropriate mass tolerance
var massTolerance = _lcmsWarp.MassTolerance;
_lcmsWarp.MassTolerance = _lcmsWarp.MassCalibrationWindow;
_lcmsWarp.UseMassAndNetScore(false);
PerformNetWarp(0, 50, prog);
OnProgress("Calibrating mass", 50);
progData.StepRange(60, "Calibrating mass");
_lcmsWarp.PerformMassCalibration();
_lcmsWarp.CalculateStandardDeviations();
OnProgress("LCMSWarp phase two", 60);
progData.StepRange(100, "LCMSWarp phase two");
_lcmsWarp.MassTolerance = massTolerance;
_lcmsWarp.UseMassAndNetScore(true);
PerformNetWarp(60, 100, prog);
OnProgress("Complete", 100);
progData.Report(100, "Complete");
}
/// <summary>
/// Performs the NET-Mass Warping; Sets up the mass calibration settings from the options,
/// performs NET warping, calibrates matches based on the NETWarp results, recalibrates the mass
/// tolerance and then performs Warping again using the mass and Net scores
/// </summary>
private void PerformNetMassWarp()
{
OnProgress("LCMSWarp phase one", 0);
// First, perform the net calibration using a mass tolerance of the same size as the mass window
// and then perform the net calibration again using the appropriate mass tolerance
var massTolerance = m_lcmsWarp.MassTolerance;
m_lcmsWarp.MassTolerance = m_lcmsWarp.MassCalibrationWindow;
m_lcmsWarp.UseMassAndNetScore(false);
PerformNetWarp(m_progress, 50);
OnProgress("Calibrating mass", 50);
m_lcmsWarp.PerformMassCalibration();
m_lcmsWarp.CalculateStandardDeviations();
OnProgress("LCMSWarp phase two", 60);
m_lcmsWarp.MassTolerance = massTolerance;
m_lcmsWarp.UseMassAndNetScore(true);
PerformNetWarp(m_progress, 100);
OnProgress("Complete", 100);
}