protected override string buildIsosResultOutput(DeconTools.Backend.Core.IsosResult result)
{
Check.Require(result is UIMFIsosResult, "UIMF Isos Exporter is only used with UIMF results");
var uimfResult = (UIMFIsosResult)result;
if (MSFeatureIDsWritten.Contains(result.MSFeatureID)) //this prevents duplicate IDs from being written
{
return(string.Empty);
}
MSFeatureIDsWritten.Add(result.MSFeatureID);
var sb = new StringBuilder();
//We wish to report the FrameNum Not the FrameIndex. FrameNum is unique
sb.Append(uimfResult.MSFeatureID);
sb.Append(delimiter);
sb.Append(uimfResult.ScanSet.PrimaryScanNumber);
sb.Append(delimiter);
sb.Append(uimfResult.IMSScanSet.PrimaryScanNumber);
sb.Append(delimiter);
sb.Append(uimfResult.IsotopicProfile.ChargeState);
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.IntensityAggregate, 4, true)); // Abundance
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.IsotopicProfile.GetMZ(), 5));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.IsotopicProfile.GetScore(), 4));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.IsotopicProfile.AverageMass, 5));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.IsotopicProfile.MonoIsotopicMass, 5));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.IsotopicProfile.MostAbundantIsotopeMass, 5));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.IsotopicProfile.GetFWHM(), 4));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.IsotopicProfile.GetSignalToNoise(), 2));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.IsotopicProfile.GetMonoAbundance(), 4, true));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.IsotopicProfile.GetMonoPlusTwoAbundance(), 4, true));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.IsotopicProfile.OriginalIntensity, 4, true));
sb.Append(delimiter);
sb.Append(uimfResult.IsotopicProfile.IsSaturated ? 1 : 0);
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.DriftTime, 3));
sb.Append(delimiter);
sb.Append(ResultValidators.ResultValidationUtils.GetStringFlagCode(result.Flags));
sb.Append(delimiter);
sb.Append(DblToString(uimfResult.InterferenceScore, 5));
return(sb.ToString());
}
public override void ValidateResult(DeconTools.Backend.Core.ResultCollection resultColl, DeconTools.Backend.Core.IsosResult currentResult)
{
if (currentResult.IsotopicProfile == null)
{
return;
}
Check.Require(currentResult != null, String.Format("{0} failed. CurrentResult has not been defined.", this.Name));
if (resultColl.Run.PeakList == null || resultColl.Run.PeakList.Count == 0)
{
currentResult.InterferenceScore = -1;
return;
}
var monoPeak = currentResult.IsotopicProfile.getMonoPeak();
var lastPeak = currentResult.IsotopicProfile.Peaklist[currentResult.IsotopicProfile.Peaklist.Count - 1];
var leftMZBoundary = monoPeak.XValue - 1.1;
var rightMZBoundary = lastPeak.XValue + lastPeak.Width / 2.35 * 2; // 2 sigma
double interferenceVal = -1;
if (UsePeakBasedInterferenceValue)
{
var scanPeaks = resultColl.Run.PeakList.Select <Peak, MSPeak>(i => (MSPeak)i).ToList();
interferenceVal = m_scorer.GetInterferenceScore(scanPeaks, currentResult.IsotopicProfile.Peaklist, leftMZBoundary, rightMZBoundary);
}
else
{
var startIndexOfXYData = MathUtils.BinarySearchWithTolerance(resultColl.Run.XYData.Xvalues, monoPeak.XValue - 3, 0, (resultColl.Run.XYData.Xvalues.Length - 1), 2);
if (startIndexOfXYData < 0)
{
startIndexOfXYData = 0;
}
interferenceVal = m_scorer.GetInterferenceScore(resultColl.Run.XYData, currentResult.IsotopicProfile.Peaklist, leftMZBoundary, rightMZBoundary, startIndexOfXYData);
}
currentResult.InterferenceScore = interferenceVal;
}
public override void ValidateResult(DeconTools.Backend.Core.ResultCollection resultColl, DeconTools.Backend.Core.IsosResult currentResult)
{
Check.Require(currentResult is N14N15_TResult, "Currently, this is only implemented for N14N15 results");
var n14n15result = (N14N15_TResult)currentResult;
Check.Require(n14n15result.Target.IsotopicProfileLabelled != null, "Cannot validate labelled isotopic profile. Theoretical profile was not defined.");
// stop, but don't throw an error if there is no labelled isotopic profile.
if (n14n15result.IsotopicProfileLabeled == null)
{
return;
}
var isoN15 = n14n15result.IsotopicProfileLabeled;
var scanPeaks = resultColl.Run.PeakList.Select <Peak, MSPeak>(i => (MSPeak)i).ToList();
// get i_score
n14n15result.InterferenceScoreN15 = getIScore(scanPeaks, isoN15);
// get fit score
var fitval = getFitValue(resultColl.Run.XYData, n14n15result.Target.IsotopicProfileLabelled, isoN15);
n14n15result.ScoreN15 = fitval;
}
//This is the primary way to add an IsosResult
public void AddIsosResult(IsosResult addedResult)
{
addedResult.MSFeatureID = MSFeatureCounter;
MSFeatureCounter++; // by placing it here, we make the MSFeatureID a zero-based ID, as Kevin requested in an email (Jan 20/2010)
this.IsosResultBin.Add(addedResult);
}
