/// <summary>
/// Performs the NET Warping; Generates matches, gets the probabilities,
/// calculates the alignment matrix and alignment function, gets the transformed NETs
/// and then calculates the alignment matches
/// </summary>
private void PerformNetWarp(double percentCompleteAtStart, double percentCompleteAtEnd)
{
OnProgress("NET Warp, get candidate matches", ComputeIncrementalProgress(percentCompleteAtStart, percentCompleteAtEnd, 0));
m_lcmsWarp.GenerateCandidateMatches();
if (m_lcmsWarp.NumCandidateMatches < 10)
{
throw new ApplicationException("Insufficient number of candidate matches by mass alone");
}
OnProgress("NET Warp, get match probabilities", ComputeIncrementalProgress(percentCompleteAtStart, percentCompleteAtEnd, 10));
m_lcmsWarp.GetMatchProbabilities();
OnProgress("NET Warp, calculate alignment matrix", ComputeIncrementalProgress(percentCompleteAtStart, percentCompleteAtEnd, 30));
m_lcmsWarp.CalculateAlignmentMatrix();
OnProgress("NET Warp, calculate alignment function", ComputeIncrementalProgress(percentCompleteAtStart, percentCompleteAtEnd, 50));
m_lcmsWarp.CalculateAlignmentFunction();
OnProgress("NET Warp, get transformed NETs", ComputeIncrementalProgress(percentCompleteAtStart, percentCompleteAtEnd, 70));
m_lcmsWarp.GetTransformedNets();
OnProgress("NET Warp, calculate alignment matches", ComputeIncrementalProgress(percentCompleteAtStart, percentCompleteAtEnd, 90));
m_lcmsWarp.CalculateAlignmentMatches();
}
/// <summary>
/// Performs the NET Warping; Generates matches, gets the probabilities,
/// calculates the alignment matrix and alignment function, gets the transformed NETs
/// and then calculates the alignment matches
/// </summary>
private void PerformNetWarp(double percentCompleteAtStart, double percentCompleteAtEnd, IProgress <ProgressData> progress = null)
{
var progData = new ProgressData(progress);
var prog = new Progress <ProgressData>(p => progData.Report(p.Percent, p.Status));
var percentCompleteOverall = UpdateCurrentTask(percentCompleteAtStart, percentCompleteAtEnd,
CurrentLcmsWarpTask.GenerateCandidateMatches);
OnProgress("NET Warp, get candidate matches", percentCompleteOverall);
progData.StepRange(10, "NET Warp, get candidate matches");
progData.Report(0.0);
_lcmsWarp.GenerateCandidateMatches(prog);
if (_lcmsWarp.NumCandidateMatches < 10)
{
throw new ApplicationException("Insufficient number of candidate matches by mass alone (NumMatches < 10)");
}
percentCompleteOverall = UpdateCurrentTask(percentCompleteAtStart, percentCompleteAtEnd,
CurrentLcmsWarpTask.GetMatchProbabilities);
OnProgress("NET Warp, get match probabilities", percentCompleteOverall);
progData.StepRange(90, "NET Warp, get match probabilities");
_lcmsWarp.GetMatchProbabilities(prog);
percentCompleteOverall = UpdateCurrentTask(percentCompleteAtStart, percentCompleteAtEnd,
CurrentLcmsWarpTask.CalculateAlignmentMatrix);
OnProgress("NET Warp, calculate alignment matrix", percentCompleteOverall);
progData.StepRange(93, "NET Warp, calculate alignment matrix");
_lcmsWarp.CalculateAlignmentMatrix(prog);
percentCompleteOverall = UpdateCurrentTask(percentCompleteAtStart, percentCompleteAtEnd,
CurrentLcmsWarpTask.CalculateAlignmentFunction);
OnProgress("NET Warp, calculate alignment function", percentCompleteOverall);
progData.StepRange(96, "NET Warp, calculate alignment function");
_lcmsWarp.CalculateAlignmentFunction(prog);
percentCompleteOverall = UpdateCurrentTask(percentCompleteAtStart, percentCompleteAtEnd,
CurrentLcmsWarpTask.GetTransformedNets);
OnProgress("NET Warp, get transformed NETs", percentCompleteOverall);
progData.StepRange(98, "NET Warp, get transformed NETs");
_lcmsWarp.GetTransformedNets(prog);
percentCompleteOverall = UpdateCurrentTask(percentCompleteAtStart, percentCompleteAtEnd,
CurrentLcmsWarpTask.CalculateAlignmentMatches);
OnProgress("NET Warp, calculate alignment matches", percentCompleteOverall);
progData.StepRange(100, "NET Warp, calculate alignment matches");
_lcmsWarp.CalculateAlignmentMatches(prog);
UpdateCurrentTask(percentCompleteAtStart, percentCompleteAtEnd, CurrentLcmsWarpTask.Complete);
progData.Report(100.0, "NET Warp, complete");
}