private List <ScanNETPair> PrepareNetAlignmentDataForLoessSmoothing()
{
var scanNetDictionary = new SortedDictionary <decimal, double>();
foreach (var iqResult in IqResultsForNetAlignment)
{
decimal lcScan;
if (iqResult.ChromPeakSelected == null)
{
lcScan = iqResult.LcScanObs;
}
else
{
lcScan = (decimal)Math.Round(iqResult.ChromPeakSelected.XValue, 2);
}
var yval = iqResult.Target.ElutionTimeTheor;
if (!scanNetDictionary.ContainsKey(lcScan))
{
scanNetDictionary.Add(lcScan, yval);
}
}
var scanNETPairs = new List <ScanNETPair>();
foreach (var pair in scanNetDictionary)
{
var scanNETPair = new ScanNETPair((double)pair.Key, pair.Value);
scanNETPairs.Add(scanNETPair);
}
return(scanNETPairs);
}
public NetAlignmentInfo DoNetAlignment(bool recollectResultsIfAlreadyPresent = false)
{
var needToProcessResults = (recollectResultsIfAlreadyPresent ||
(IqResultsForAlignment == null || IqResultsForAlignment.Count == 0));
if (needToProcessResults)
{
Execute(Targets);
IqResultsForAlignment = FilterAlignmentResults();
}
IqResultsForNetAlignment = UpdateMsgfTargetsWithDatabaseNetValues(IqResultsForAlignment);
IqLogger.Log.Info("Applying Loess smoothing to NET alignment data. LoessBandwidth= " + LoessBandwidthNetAlignment);
var netAlignmentDataForLoess = PrepareNetAlignmentDataForLoessSmoothing();
var iterationsForNetAlignment = 2;
var loessInterpolatorForNetAlignment = new LoessInterpolator(LoessBandwidthNetAlignment, iterationsForNetAlignment);
var loessSmoothedData = new XYData();
loessSmoothedData.Xvalues = netAlignmentDataForLoess.Select(p => p.Scan).ToArray();
loessSmoothedData.Yvalues = loessInterpolatorForNetAlignment.Smooth(netAlignmentDataForLoess.Select(p => p.Scan).ToArray(),
netAlignmentDataForLoess.Select(p => p.NET).ToArray());
var scanToNetVals = new List <ScanNETPair>();
for (var i = 0; i < loessSmoothedData.Xvalues.Length; i++)
{
var xval = loessSmoothedData.Xvalues[i];
var yval = loessSmoothedData.Yvalues[i];
if (!double.IsNaN(yval))
{
var scanNETPair = new ScanNETPair(xval, yval);
scanToNetVals.Add(scanNETPair);
}
}
var netAlignmentInfo = new NetAlignmentInfoBasic(Run.MinLCScan, Run.MaxLCScan);
netAlignmentInfo.SetScanToNETAlignmentData(scanToNetVals);
IqLogger.Log.Info("NET alignment complete using " + scanToNetVals.Count + " data points.");
NetAlignmentInfo = netAlignmentInfo;
return(netAlignmentInfo);
}
