private List <DeconTools.Backend.Core.IsotopicProfile> ConvertRapidResultsToProfileList(DeconToolsV2.Peaks.clsPeak[] peaklist, ref int[] chargeResults, ref double[] intensityResults,
ref double[] mzResults, ref double[] scoreResults, ref double[] avgmassResults, ref double[] massResults, ref double[] mostAbundantMassResults)
{
List <IsotopicProfile> isotopicProfileList = new List <IsotopicProfile>();
for (int i = 0; i < chargeResults.Length; i++)
{
if (chargeResults[i] == 0)
{
continue;
}
IsotopicProfile profile = new IsotopicProfile();
profile.ChargeState = chargeResults[i];
profile.IntensityMostAbundant = (float)intensityResults[i];
profile.IntensityMostAbundantTheor = profile.IntensityMostAbundant;
profile.Score = scoreResults[i];
MSPeak monoPeak = new MSPeak();
monoPeak.XValue = ConvertMassToMZ(massResults[i], profile.ChargeState);
GetIsotopicProfilePeaks(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();
isotopicProfileList.Add(profile);
}
return(isotopicProfileList);
}
private void GenerateResults(
IEnumerable <HornTransformResults> transformResults,
ThrashV1Peak[] mspeakList,
ResultCollection resultList,
bool processingWasAborted,
int maxProcessingTimeMinutes)
{
ScanSet currentScanset;
var currentRun = resultList.Run as UIMFRun;
bool processingUIMF;
if (currentRun != null)
{
currentScanset = currentRun.CurrentIMSScanSet;
processingUIMF = true;
}
else
{
currentScanset = resultList.Run.CurrentScanSet;
processingUIMF = false;
}
currentScanset.NumIsotopicProfiles = 0; //reset to 0;
foreach (var hornResult in transformResults)
{
var result = resultList.CreateIsosResult();
var profile = new IsotopicProfile
{
AverageMass = hornResult.AverageMw,
ChargeState = hornResult.ChargeState,
MonoIsotopicMass = hornResult.MonoMw,
Score = hornResult.Fit,
ScoreCountBasis = hornResult.FitCountBasis,
MostAbundantIsotopeMass = hornResult.MostIntenseMw
};
GetIsotopicProfile(hornResult.IsotopePeakIndices, mspeakList, ref profile);
profile.IntensityMostAbundant = (float)hornResult.Abundance;
profile.IntensityMostAbundantTheor = (float)hornResult.Abundance;
if (NumPeaksUsedInAbundance == 1) // fyi... this is typical
{
result.IntensityAggregate = profile.IntensityMostAbundant;
}
else
{
result.IntensityAggregate = SumPeaks(profile, hornResult.Abundance);
}
profile.MonoPlusTwoAbundance = profile.GetMonoPlusTwoAbundance();
profile.MonoPeakMZ = profile.GetMZ();
result.IsotopicProfile = profile;
AddDeconResult(resultList, result, DeconResultComboMode.simplyAddIt);
//resultList.ResultList.Add(result);
currentScanset.NumIsotopicProfiles++;
}
if (!processingWasAborted)
{
return;
}
string messageBase;
if (processingUIMF)
{
// LC-IMS-MS dataset
if (currentScanset.GetScanCount() <= 1)
{
messageBase = string.Format("Aborted processing of frame {0}, IMS scan {1}",
currentScanset.PrimaryScanNumber,
currentScanset.getLowestScanNumber());
}
else
{
messageBase = string.Format("Aborted processing of frame {0}, IMS scans {1}-{2}",
currentScanset.PrimaryScanNumber,
currentScanset.getLowestScanNumber(),
currentScanset.getHighestScanNumber());
}
}
else
{
// LC-MS dataset
if (currentScanset.GetScanCount() <= 1)
{
messageBase = string.Format("Aborted processing of scan {0}",
currentScanset.getLowestScanNumber());
}
else
{
messageBase = string.Format("Aborted processing of summed scans {0}-{1}",
currentScanset.getLowestScanNumber(),
currentScanset.getHighestScanNumber());
}
}
Console.WriteLine("{0}; runtime exceeded {1} minutes. IsotopicProfileCount={2}",
messageBase,
maxProcessingTimeMinutes,
currentScanset.NumIsotopicProfiles);
}
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++;
}
}