public RapidDeconvolutor(double minPeptideToBackgroundRatio, DeconResultComboMode comboMode)
{
this.minPeptideToBackgroundRatio = minPeptideToBackgroundRatio;
this.resultCombiningMode = comboMode;
this.IsNewFitCalculationPerformed = true;
this.fitScoreCalculator = new DeconTools.Backend.ProcessingTasks.FitScoreCalculators.DeconToolsFitScoreCalculator();
this.targetedFeatureFinder = new BasicTFF();
}
protected void AddDeconResult(ResultCollection baseResultList, IsosResult addedResult, DeconResultComboMode comboMode = DeconResultComboMode.simplyAddIt)
{
Check.Require(baseResultList != null, "Deconvolutor problem. Can't combine results. Base resultList is null.");
if (baseResultList == null)
{
return;
}
Check.Require(addedResult != null, "Deconvolutor problem. Can't combine results. Added IsosResult is null.");
switch (comboMode)
{
case DeconResultComboMode.simplyAddIt:
baseResultList.AddIsosResult(addedResult);
break;
case DeconResultComboMode.addItIfUnique:
//retrieve IsosResults for CurrentScanSet
//TODO: next line might be a time bottleneck! needs checking
//List<IsosResult> scanSetIsosResults = ResultCollection.GetIsosResultsForCurrentScanSet(baseResultList);
//search isosResults for a (monoPeak = addedResult's monoPeak) AND chargeState = addedResult's chargeState
if (doesResultExist(baseResultList.IsosResultBin, addedResult))
{
//do nothing... isotopic profile already exists
}
else
{
baseResultList.AddIsosResult(addedResult);
}
break;
case DeconResultComboMode.addAndReplaceIfOneDaltonErrorDetected:
throw new NotImplementedException("add and replace isotopic profile mode not yet supported");
}
}
public RapidDeconvolutor(DeconResultComboMode comboMode)
: this(5, comboMode)
{
}
private void GenerateResults(ResultCollection resultList, ref int[] chargeResults,
ref double[] intensityResults, ref double[] mzResults, ref double[] scoreResults,
ref double[] avgmassResults, ref double[] massResults,
ref double[] mostAbundantMassResults, DeconResultComboMode comboMode)
{
ScanSet currentScanset;
if (resultList.Run is UIMFRun)
{
currentScanset = ((UIMFRun)resultList.Run).CurrentIMSScanSet;
}
else
{
currentScanset = resultList.Run.CurrentScanSet;
}
currentScanset.NumIsotopicProfiles = 0; //reset to 0;
for (int i = 0; i < chargeResults.Length; i++)
{
if (chargeResults[i] == 0)
{
continue;
}
double rapidScore = scoreResults[i];
if ((float)rapidScore == 0.9999999999999f)
{
continue; // this is an oddity about the Rapid results. For very poor or immeasurable scores, it will give a score of 1.000000000;
}
IsosResult result = resultList.CreateIsosResult();
result.IntensityAggregate = intensityResults[i];
IsotopicProfile profile = new IsotopicProfile();
profile.ChargeState = chargeResults[i];
profile.Score = scoreResults[i];
MSPeak monoPeak = new MSPeak();
monoPeak.XValue = ConvertMassToMZ(massResults[i], profile.ChargeState);
//TODO: make it so that the entire isotopic profile peak list is populated. Right now, just the monoisotopic peak is found.
GetIsotopicProfilePeaks(resultList.Run.PeakList, profile.ChargeState, monoPeak.XValue, ref profile);
if (profile.Peaklist.Count == 0) // couldn't find original monoIsotopicPeak in the peaklist
{
//So first check and see if it is the most abundant peak (mzResults returns the mz for the most abundant peak); get the m/z from there (This m/z matches with DeconTools peaklist m/z values)
if (Math.Abs(monoPeak.XValue - mzResults[i]) < (1 / profile.ChargeState - 1 / profile.ChargeState * 0.2))
{
monoPeak.XValue = mzResults[i];
profile.Peaklist = new List <MSPeak>();
profile.Peaklist.Add(monoPeak);
}
else // happens if the mono peak is not the most abundant peak. Will have to use Rapid's calculated value for the mono peak
{
profile.Peaklist = new List <MSPeak>();
profile.Peaklist.Add(monoPeak);
}
}
double mostabundantPeakMZ = mzResults[i];
//Console.WriteLine("mostAbundantPeakMZ = " + mostabundantPeakMZ);
//Console.WriteLine("calculated mostAbundantMZ = " + ConvertMassToMZ(mostAbundantMassResults[i], profile.ChargeState));
profile.MonoIsotopicMass = massResults[i];
profile.MostAbundantIsotopeMass = mostAbundantMassResults[i];
profile.AverageMass = avgmassResults[i];
profile.MonoPeakMZ = profile.GetMZ();
result.IsotopicProfile = profile;
//resultList.ResultList.Add(result);
this.AddDeconResult(resultList, result, comboMode);
currentScanset.NumIsotopicProfiles++;
}
}
