public void deconWithRAPID_Then_ValidateTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
ScanSet scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
MSGenerator msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetectorV2 peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
RapidDeconvolutor decon = new RapidDeconvolutor();
ResultValidatorTask validator = new ResultValidatorTask();
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
validator.Execute(run.ResultCollection);
Assert.AreEqual(190, run.ResultCollection.ResultList.Count);
IsosResult testResult = run.ResultCollection.ResultList[0];
Assert.AreEqual(0.0213668719893332m, (decimal)testResult.InterferenceScore);
//TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void findMSFeaturesInOrbitrapData_Test1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
ScanSet scanSet = new ScanSet(6005);
run.CurrentScanSet = scanSet;
MSGenerator msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetectorV2 peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
peakDetector.IsDataThresholded = true;
RapidDeconvolutor decon = new RapidDeconvolutor();
decon.IsNewFitCalculationPerformed = true;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
Assert.AreEqual(192, run.ResultCollection.ResultList.Count);
//order and get the most intense msfeature
run.ResultCollection.ResultList = run.ResultCollection.ResultList.OrderByDescending(p => p.IntensityAggregate).ToList();
IsosResult testIso = run.ResultCollection.ResultList[0];
Assert.AreEqual(20986588.375, testIso.IntensityAggregate);
Assert.AreEqual(2, testIso.IsotopicProfile.ChargeState);
Assert.AreEqual(0.00548633562231413m, (decimal)testIso.IsotopicProfile.Score);
Assert.AreEqual(3, testIso.IsotopicProfile.Peaklist.Count);
Assert.AreEqual(481.274105402604m, (decimal)testIso.IsotopicProfile.Peaklist[0].XValue);
Assert.AreEqual(481.775412188198m, (decimal)testIso.IsotopicProfile.Peaklist[1].XValue);
Assert.AreEqual(482.276820274024m, (decimal)testIso.IsotopicProfile.Peaklist[2].XValue);
TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList);
}
public void Execute()
{
InitializeWorkflow();
if (Run.MSFileType == Globals.MSFileType.PNNL_UIMF)
{
IMSScanSetCollection = CreateIMSScanSetCollection();
}
LcScanSetCollection = CreateLcScanSetCollection();
PrepareOutputDirectory(WorkflowParameters.OutputDirectory);
var outputPeaksFilePath = getOutputPeaksFilename();
peakExporter = new PeakListTextExporter(Run.MSFileType, outputPeaksFilePath);
var numTotalScans = LcScanSetCollection.ScanSetList.Count;
var lastProgress = DateTime.UtcNow;
using (var sw = new StreamWriter(new FileStream(outputPeaksFilePath, FileMode.Append, FileAccess.Write, FileShare.Read)))
{
if (Run.MSFileType == Globals.MSFileType.PNNL_UIMF && Run is UIMFRun uimfRun)
{
var numTotalFrames = LcScanSetCollection.ScanSetList.Count;
var frameCounter = 0;
foreach (var frameSet in LcScanSetCollection.ScanSetList)
{
frameCounter++;
uimfRun.CurrentScanSet = frameSet;
uimfRun.ResultCollection.MSPeakResultList.Clear();
foreach (var scanSet in IMSScanSetCollection.ScanSetList)
{
uimfRun.CurrentIMSScanSet = (IMSScanSet)scanSet;
MSGenerator.Execute(uimfRun.ResultCollection);
_ms1PeakDetector.Execute(uimfRun.ResultCollection);
}
peakExporter.WriteOutPeaks(sw, uimfRun.ResultCollection.MSPeakResultList);
if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 1 || frameCounter == numTotalFrames)
{
lastProgress = DateTime.UtcNow;
var percentProgress = frameCounter * 100 / (double)numTotalFrames;
reportProgress(percentProgress);
}
}
}
else
{
var scanCounter = 0;
foreach (var scan in LcScanSetCollection.ScanSetList)
{
scanCounter++;
Run.CurrentScanSet = scan;
Run.ResultCollection.MSPeakResultList.Clear();
MSGenerator.Execute(Run.ResultCollection);
if (Run.GetMSLevel(scan.PrimaryScanNumber) == 1)
{
_ms1PeakDetector.Execute(Run.ResultCollection);
}
else
{
var dataIsCentroided = Run.IsDataCentroided(scan.PrimaryScanNumber);
if (dataIsCentroided)
{
_ms2PeakDetectorForCentroidedData.Execute(Run.ResultCollection);
}
else
{
_ms2PeakDetectorForProfileData.Execute(Run.ResultCollection);
}
}
peakExporter.WriteOutPeaks(sw, Run.ResultCollection.MSPeakResultList);
if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 1 || scanCounter == numTotalScans)
{
lastProgress = DateTime.UtcNow;
var percentProgress = scanCounter * 100 / (double)numTotalScans;
reportProgress(percentProgress);
}
}
}
}
Run.ResultCollection.MSPeakResultList.Clear();
}
public override void Execute()
{
InitializeWorkflow();
PrepareOutputFolder(_workflowParameters.OutputFolder);
string outputPeaksFileName = getOutputPeaksFilename();
peakExporter = new PeakListTextExporter(Run.MSFileType, outputPeaksFileName);
int numTotalScans = Run.ScanSetCollection.ScanSetList.Count;
int scanCounter = 0;
if (Run.MSFileType == DeconTools.Backend.Globals.MSFileType.PNNL_UIMF)
{
var uimfrun = Run as UIMFRun;
int numTotalFrames = uimfrun.ScanSetCollection.ScanSetList.Count;
int frameCounter = 0;
foreach (var frameSet in uimfrun.ScanSetCollection.ScanSetList)
{
frameCounter++;
uimfrun.CurrentScanSet = frameSet;
uimfrun.ResultCollection.MSPeakResultList.Clear();
foreach (var scanSet in uimfrun.IMSScanSetCollection.ScanSetList)
{
uimfrun.CurrentIMSScanSet = (IMSScanSet)scanSet;
MSGenerator.Execute(uimfrun.ResultCollection);
this._ms1PeakDetector.Execute(uimfrun.ResultCollection);
}
peakExporter.WriteOutPeaks(uimfrun.ResultCollection.MSPeakResultList);
if (frameCounter % 5 == 0 || scanCounter == numTotalFrames)
{
double percentProgress = frameCounter * 100 / numTotalFrames;
reportProgress(percentProgress);
}
}
}
else
{
foreach (var scan in Run.ScanSetCollection.ScanSetList)
{
scanCounter++;
Run.CurrentScanSet = scan;
Run.ResultCollection.MSPeakResultList.Clear();
MSGenerator.Execute(Run.ResultCollection);
if (Run.GetMSLevel(scan.PrimaryScanNumber) == 1)
{
this._ms1PeakDetector.Execute(Run.ResultCollection);
}
else
{
var dataIsCentroided = Run.IsDataCentroided(scan.PrimaryScanNumber);
if (dataIsCentroided)
{
_ms2PeakDetectorForCentroidedData.Execute(Run.ResultCollection);
}
else
{
_ms2PeakDetectorForProfileData.Execute(Run.ResultCollection);
}
}
peakExporter.WriteOutPeaks(Run.ResultCollection.MSPeakResultList);
if (scanCounter % 50 == 0 || scanCounter == numTotalScans)
{
double percentProgress = scanCounter * 100 / numTotalScans;
reportProgress(percentProgress);
}
}
}
Run.ResultCollection.MSPeakResultList.Clear();
}
protected override void IterateOverScans()
{
DeconMSnResults.Clear();
_scanCounter = 0;
var resultCounter = 0;
foreach (var scanSet in Run.ScanSetCollection.ScanSetList)
{
_scanCounter++;
if (BackgroundWorker != null)
{
if (BackgroundWorker.CancellationPending)
{
return;
}
}
//check ms level
var currentMSLevel = Run.GetMSLevel(scanSet.PrimaryScanNumber);
if (currentMSLevel == 1)
{
Run.ResultCollection.IsosResultBin.Clear();
Run.CurrentScanSet = scanSet;
MSGenerator.Execute(Run.ResultCollection);
_currentMS1XYValues = new XYData
{
Xvalues = Run.XYData.Xvalues,
Yvalues = Run.XYData.Yvalues
};
_currentMS1TICIntensity = Run.GetTICFromInstrumentInfo(scanSet.PrimaryScanNumber);
PeakDetector.Execute(Run.ResultCollection);
_currentMS1Peaks = new List <Peak>(Run.PeakList);
}
else if (currentMSLevel == 2)
{
if (_currentMS1Peaks == null || _currentMS1Peaks.Count == 0)
{
continue;
}
var precursorInfo = Run.GetPrecursorInfo(scanSet.PrimaryScanNumber);
Run.CurrentScanSet = scanSet;
var inaccurateParentMZ = precursorInfo.PrecursorMZ;
resultCounter++;
var deconMSnResult = new DeconMSnResult {
ParentScan = Run.GetParentScan(scanSet.PrimaryScanNumber)
};
deconMSnResult.IonInjectionTime = Run.GetIonInjectionTimeInMilliseconds(deconMSnResult.ParentScan);
deconMSnResult.ScanNum = scanSet.PrimaryScanNumber;
deconMSnResult.OriginalMZTarget = inaccurateParentMZ;
deconMSnResult.ParentScanTICIntensity = _currentMS1TICIntensity;
MSGenerator.Execute(Run.ResultCollection);
var lowerMZ = inaccurateParentMZ - 1.1;
var upperMZ = inaccurateParentMZ + 1.1;
var dataIsCentroided = Run.IsDataCentroided(scanSet.PrimaryScanNumber);
if (dataIsCentroided)
{
_ms2PeakDetectorForCentroidData.Execute(Run.ResultCollection);
}
else
{
_ms2PeakDetectorForProfileData.Execute(Run.ResultCollection);
}
var ms2Peaks = new List <Peak>(Run.PeakList);
var filteredMS1Peaks = _currentMS1Peaks.Where(p => p.XValue > lowerMZ && p.XValue < upperMZ).ToList();
IsotopicProfile selectedMS1Feature = null;
for (var attemptNum = 0; attemptNum < NumMaxAttemptsAtLowIntensitySpecies; attemptNum++)
{
var candidateMS1Features = GetCandidateMS1Features(inaccurateParentMZ, filteredMS1Peaks);
//if none were found, will regenerate MS1 spectrum and find peaks again
if (candidateMS1Features.Count == 0)
{
var numSummed = attemptNum * 2 + 3;
var ms1Scan = precursorInfo.PrecursorScan;
var ms1ScanSet = new ScanSetFactory().CreateScanSet(Run, ms1Scan, numSummed);
//get MS1 mass spectrum again. This time sum spectra
Run.CurrentScanSet = ms1ScanSet;
MSGenerator.Execute(Run.ResultCollection);
//run MS1 peak detector, with greater sensitivity
var isLastAttempt = attemptNum >= NumMaxAttemptsAtLowIntensitySpecies - 2; //need to do -2 because of the way the loop advances the counter.
if (isLastAttempt)
{
_superSensitiveMS1PeakDetector.MinX = lowerMZ;
_superSensitiveMS1PeakDetector.MaxX = upperMZ;
_superSensitiveMS1PeakDetector.Execute(Run.ResultCollection);
filteredMS1Peaks = new List <Peak>(Run.PeakList);
}
else
{
_moreSensitiveMS1PeakDetector.Execute(Run.ResultCollection);
var moreSensitiveMS1Peaks = new List <Peak>(Run.PeakList);
filteredMS1Peaks = moreSensitiveMS1Peaks.Where(p => p.XValue > lowerMZ && p.XValue < upperMZ).ToList();
}
}
else if (candidateMS1Features.Count == 1)
{
selectedMS1Feature = candidateMS1Features.First();
break; //we found something, so no need for any further attempts
}
else
{
var highQualityCandidates = candidateMS1Features.Where(p => p.Score < 0.15).ToList();
if (highQualityCandidates.Count == 0)
{
selectedMS1Feature = candidateMS1Features.OrderByDescending(p => p.IntensityMostAbundantTheor).First();
}
else if (highQualityCandidates.Count == 1)
{
selectedMS1Feature = highQualityCandidates.First();
}
else
{
selectedMS1Feature = highQualityCandidates.OrderByDescending(p => p.IntensityMostAbundantTheor).First();
}
deconMSnResult.ExtraInfo = "Warning - multiple MSFeatures found for target parent MZ";
break; //we found something, so no need for any further attempts
}
}
if (selectedMS1Feature != null)
{
deconMSnResult.ParentMZ = selectedMS1Feature.MonoPeakMZ;
deconMSnResult.ParentChargeState = selectedMS1Feature.ChargeState;
deconMSnResult.ParentIntensity = selectedMS1Feature.IntensityMostAbundantTheor;
deconMSnResult.IntensityAggregate = selectedMS1Feature.IntensityMostAbundantTheor;
deconMSnResult.IsotopicProfile = selectedMS1Feature;
}
else
{
var candidatePeaks = new List <Peak>();
foreach (var peak in filteredMS1Peaks)
{
var currentDiff = Math.Abs(peak.XValue - inaccurateParentMZ);
var toleranceInMZ = ToleranceInPPM * peak.XValue / 1e6;
if (currentDiff < toleranceInMZ)
{
candidatePeaks.Add(peak);
}
}
Peak selectedPeak = null;
if (candidatePeaks.Count == 0)
{
//cannot even find a suitable MS1 peak. So can't do anything
}
else if (candidatePeaks.Count == 1)
{
selectedPeak = candidatePeaks.First();
}
else
{
selectedPeak = candidatePeaks.OrderByDescending(p => p.Height).First();
}
if (selectedPeak != null)
{
deconMSnResult.ParentMZ = selectedPeak.XValue;
deconMSnResult.ParentChargeState = 1; //not sure what charge I should assign... Ask SangTae
deconMSnResult.ParentIntensity = selectedPeak.Height;
deconMSnResult.IsotopicProfile = null;
deconMSnResult.ExtraInfo = "Failure code 1: No MSFeature, but peak found";
}
else
{
deconMSnResult.ParentMZ = precursorInfo.PrecursorMZ; //could not find the accurate parentMZ, so just report what the instrument found.
deconMSnResult.ParentChargeState = 1; //not sure what charge I should assign... Ask SangTae
deconMSnResult.ParentIntensity = 0;
deconMSnResult.IsotopicProfile = null;
deconMSnResult.ExtraInfo = "Failure code 2: No MSFeature or peak found";
}
}
//Build export data.
var outputString = GetMGFOutputString(Run, scanSet.PrimaryScanNumber, deconMSnResult, ms2Peaks);
var includeHeader = resultCounter == 1;
var summaryString = GetSummaryString(deconMSnResult, includeHeader);
var parentProfileString = GetParentProfileString(deconMSnResult, includeHeader);
if (ExportData)
{
WriteOutMainData(outputString);
WriteOutDeconMSnSummary(summaryString);
if (IsParentProfileDataExported)
{
WriteOutParentProfileInfoString(parentProfileString);
}
}
if (deconMSnResult.ParentIntensity > 0)
{
DeconMSnResults.Add(deconMSnResult);
}
}
else
{
throw new ApplicationException(
"DeconMSn only works on MS1 and MS2 data; You are attempting MS3");
}
ReportProgress();
}
}
protected override void IterateOverScans()
{
const int CONSOLE_INTERVAL_SECONDS = 15;
const bool SKIP_DECONVOLUTION = false;
var uimfRun = (UIMFRun)Run;
var startTime = DateTime.UtcNow;
var dtLastProgress = DateTime.UtcNow.Subtract(new TimeSpan(1, 0, 0));
var frameCountProcessed = 0;
var maxRuntimeHours = NewDeconToolsParameters.MiscMSProcessingParameters.MaxHoursPerDataset;
// uimfRun.IMSScanSetCollection.ScanSetList =uimfRun.IMSScanSetCollection.ScanSetList.Where(p => p.PrimaryScanNumber == 153).ToList();
// Iterate over unsummed data and fix saturated isotopic profiles. Unsummed will be used during a second iteration (over summed data)
foreach (var lcScanSet in uimfRun.ScanSetCollection.ScanSetList)
{
uimfRun.ResultCollection.MSPeakResultList.Clear();
_unsummedMSFeatures.Clear();
var unsummedFrameSet = new ScanSet(lcScanSet.PrimaryScanNumber);
// Get saturated MSFeatures for unsummed data
uimfRun.CurrentScanSet = unsummedFrameSet;
var forceProgressMessage = true;
var imsScanCountProcessed = 0;
var maxMinutesPerFrame = NewDeconToolsParameters.MiscMSProcessingParameters.MaxMinutesPerFrame;
if (uimfRun.GetNumFrames() <= 10)
{
// Disable the per-frame timeout if we have 10 or fewer frames
maxMinutesPerFrame = int.MaxValue;
}
var frameStartTime = DateTime.UtcNow;
var timeoutReached = false;
foreach (var scanset in uimfRun.IMSScanSetCollection.ScanSetList)
{
if (DateTime.UtcNow.Subtract(dtLastProgress).TotalSeconds >= CONSOLE_INTERVAL_SECONDS || forceProgressMessage)
{
dtLastProgress = DateTime.UtcNow;
forceProgressMessage = false;
Console.WriteLine("Processing frame " + lcScanSet.PrimaryScanNumber + ", scan " + scanset.PrimaryScanNumber + " (Unsummed)");
}
if (DateTime.UtcNow.Subtract(frameStartTime).TotalMinutes >= maxMinutesPerFrame)
{
Console.WriteLine(
"Aborted processing of frame {0} because {1} minutes have elapsed (processing unsummed features); IMSScanCount processed = {2}",
lcScanSet.PrimaryScanNumber,
(int)DateTime.UtcNow.Subtract(frameStartTime).TotalMinutes,
imsScanCountProcessed);
timeoutReached = true;
break;
}
uimfRun.ResultCollection.IsosResultBin.Clear(); //clear any previous MSFeatures
var unsummedIMSScanset = new IMSScanSet(scanset.PrimaryScanNumber);
uimfRun.CurrentIMSScanSet = unsummedIMSScanset;
_msGenerator.Execute(Run.ResultCollection);
_zeroFiller.Execute(Run.ResultCollection);
// For debugging....
// if (scanset.PrimaryScanNumber == 123)
// {
// Console.WriteLine(scanset + "\t being processed!");
// }
_peakDetector.Execute(Run.ResultCollection);
imsScanCountProcessed++;
if (SKIP_DECONVOLUTION)
{
continue;
}
// Deconvolute Unsummed MSFeatures
// This is a preliminary step for Saturation Detection
//#if Disable_DeconToolsV2
// throw new NotImplementedException("Cannot use class SaturationIMSScanBasedWorkflow since support for C++ based DeconToolsV2 is disabled");
//#else
_deconvolutor.Deconvolute(uimfRun.ResultCollection); //adds to IsosResultBin
//#endif
// Note: the deconvolutor automatically increases the MSFeatureCounter.
// Here, we don't want this, since this data is used only for saturation correction,
// not for generating the official MSFeatures list. So we need to
// correct the MSFeatureCounter value.
Run.ResultCollection.MSFeatureCounter = Run.ResultCollection.MSFeatureCounter -
Run.ResultCollection.IsosResultBin.Count;
_unsummedMSFeatures.AddRange(Run.ResultCollection.IsosResultBin);
// Iterate over unsummed MSFeatures and check for saturation
foreach (var isosResult in uimfRun.ResultCollection.IsosResultBin)
{
var msFeatureXYData = Run.XYData.TrimData(isosResult.IsotopicProfile.MonoPeakMZ - 10,
isosResult.IsotopicProfile.MonoPeakMZ + 10);
var tempMZ = isosResult.IsotopicProfile.MonoPeakMZ;
var currentScan = scanset.PrimaryScanNumber;
var isPossiblySaturated = isosResult.IntensityAggregate >
NewDeconToolsParameters.MiscMSProcessingParameters.SaturationThreshold;
// For debugging...
// UIMFIsosResult tempIsosResult = (UIMFIsosResult) isosResult;
// if (tempIsosResult.IMSScanSet.PrimaryScanNumber == 123)
// {
// Console.WriteLine(tempIsosResult + "\t being processed!");
// }
if (isPossiblySaturated)
{
RebuildSaturatedIsotopicProfile(msFeatureXYData, isosResult, uimfRun.PeakList, out var theorIso);
AdjustSaturatedIsotopicProfile(isosResult.IsotopicProfile, theorIso, AdjustMonoIsotopicMasses, true);
}
}
}
// DisplayMSFeatures(_unsummedMSFeatures);
// Now sum across IMSScans, deconvolute and adjust using saturation detection
forceProgressMessage = true;
imsScanCountProcessed = 0;
// Compute a buffer using .MaxMinutesPerFrame times 20%
double maxFrameMinutesAddon = 0;
var bufferMinutes = maxMinutesPerFrame * 0.2;
if (bufferMinutes < 1)
{
bufferMinutes = 1;
}
if (timeoutReached ||
DateTime.UtcNow.Subtract(frameStartTime).TotalMinutes + bufferMinutes >= maxMinutesPerFrame)
{
// Maximum time per frame has been reached (or has almost been reached)
// Allow the next step to run for an additional bufferMinutes
maxFrameMinutesAddon = bufferMinutes;
}
foreach (var scanSet in uimfRun.IMSScanSetCollection.ScanSetList)
{
var scanset = (IMSScanSet)scanSet;
if (DateTime.UtcNow.Subtract(dtLastProgress).TotalSeconds >= CONSOLE_INTERVAL_SECONDS || forceProgressMessage)
{
dtLastProgress = DateTime.UtcNow;
forceProgressMessage = false;
Console.WriteLine("Processing frame " + lcScanSet.PrimaryScanNumber + ", scan " + scanset.PrimaryScanNumber + " (Summed)");
}
if (DateTime.UtcNow.Subtract(frameStartTime).TotalMinutes >= maxMinutesPerFrame + maxFrameMinutesAddon)
{
Console.WriteLine(
"Aborted processing of frame {0} because {1} minutes have elapsed (processing summed features); IMSScanCount processed = {2}",
lcScanSet.PrimaryScanNumber,
(int)DateTime.UtcNow.Subtract(frameStartTime).TotalMinutes,
imsScanCountProcessed);
break;
}
uimfRun.ResultCollection.IsosResultBin.Clear(); //clear any previous MSFeatures
// Get the summed isotopic profile
uimfRun.CurrentScanSet = lcScanSet;
uimfRun.CurrentIMSScanSet = scanset;
ExecuteTask(MSGenerator);
if (NewDeconToolsParameters.MiscMSProcessingParameters.UseZeroFilling)
{
ExecuteTask(ZeroFiller);
}
if (NewDeconToolsParameters.MiscMSProcessingParameters.UseSmoothing)
{
ExecuteTask(Smoother);
}
ExecuteTask(PeakDetector);
imsScanCountProcessed++;
if (!SKIP_DECONVOLUTION)
{
ExecuteTask(Deconvolutor);
foreach (var isosResult in Run.ResultCollection.IsosResultBin)
{
var isPossiblySaturated = isosResult.IntensityAggregate >
NewDeconToolsParameters.MiscMSProcessingParameters.SaturationThreshold;
if (isPossiblySaturated)
{
var msFeatureXYData = Run.XYData.TrimData(isosResult.IsotopicProfile.MonoPeakMZ - 10,
isosResult.IsotopicProfile.MonoPeakMZ + 10);
RebuildSaturatedIsotopicProfile(msFeatureXYData, isosResult, Run.PeakList, out var theorIso);
AdjustSaturatedIsotopicProfile(isosResult.IsotopicProfile, theorIso, AdjustMonoIsotopicMasses, false);
var currentScan = scanset.PrimaryScanNumber;
var currentMZ = isosResult.IsotopicProfile.MonoPeakMZ;
UpdateReportedSummedPeakIntensities(isosResult, lcScanSet, scanset);
}
else
{
}
if (isosResult.IsotopicProfile.IsSaturated)
{
GetRebuiltFitScore(isosResult);
}
}
}
// Need to remove any duplicate MSFeatures (this occurs when incorrectly deisotoped profiles are built).
// Will do this by making the MSFeatureID the same. Then the Exporter will ensure that only one MSFeature per MSFeatureID
// is exported. This isn't ideal. Better to remove the features but this proves to be quite hard to do without large performance hits.
foreach (var isosResult in Run.ResultCollection.IsosResultBin)
{
double ppmToleranceForDuplicate = 20;
var massTolForDuplicate = ppmToleranceForDuplicate *
isosResult.IsotopicProfile.MonoIsotopicMass / 1e6;
var isosResultLocal = isosResult;
var duplicateIsosResults = (from n in Run.ResultCollection.IsosResultBin
where
Math.Abs(n.IsotopicProfile.MonoIsotopicMass -
isosResultLocal.IsotopicProfile.MonoIsotopicMass) <
massTolForDuplicate && n.IsotopicProfile.ChargeState == isosResultLocal.IsotopicProfile.ChargeState
select n);
var minMSFeatureID = int.MaxValue;
foreach (var dup in duplicateIsosResults)
{
if (dup.MSFeatureID < minMSFeatureID)
{
minMSFeatureID = dup.MSFeatureID;
}
else
{
//here we have found a duplicate
dup.MSFeatureID = minMSFeatureID;
//because there are duplicates, we need to maintain the MSFeatureCounter so it doesn't skip values, as will
//happen when there are duplicates
//Run.ResultCollection.MSFeatureCounter--;
}
}
}
ExecuteTask(ResultValidator);
ExecuteTask(ScanResultUpdater);
if (NewDeconToolsParameters.ScanBasedWorkflowParameters.IsRefittingPerformed)
{
ExecuteTask(FitScoreCalculator);
}
// Allows derived classes to execute additional tasks
ExecuteOtherTasksHook();
if (ExportData)
{
// The following exporting tasks should be last
if (NewDeconToolsParameters.ScanBasedWorkflowParameters.ExportPeakData)
{
ExecuteTask(PeakToMSFeatureAssociator);
ExecuteTask(PeakListExporter);
}
ExecuteTask(IsosResultExporter);
ExecuteTask(ScanResultExporter);
}
ReportProgress();
}
frameCountProcessed++;
if (DateTime.UtcNow.Subtract(startTime).TotalHours >= maxRuntimeHours)
{
Console.WriteLine(
"Aborted processing because {0} hours have elapsed; Frames processed = {1}",
(int)DateTime.UtcNow.Subtract(startTime).TotalHours,
frameCountProcessed);
break;
}
}
}
public void GetUnsummedIntensitiesAndDetectSaturation(Run run, IEnumerable <IsosResult> resultList)
{
Check.Require(run != null, "SaturationDetector failed. Run is null");
if (run == null)
{
return;
}
if (_msGenerator == null)
{
_msGenerator = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
}
if (run is UIMFRun uimfRun)
{
if (uimfRun.CurrentScanSet == null)
{
throw new NullReferenceException("CurrentScanSet is null. You need to set it.");
}
if (uimfRun.CurrentIMSScanSet == null)
{
throw new NullReferenceException("CurrentIMSScanSet is null. You need to set it.");
}
//this creates a FrameSet containing only the primary frame. Therefore no summing will occur
var lcScanSet = new ScanSet(uimfRun.CurrentScanSet.PrimaryScanNumber);
//this creates a ScanSet containing only the primary scan. Therefore no summing will occur
var imsScanSet = new IMSScanSet(uimfRun.CurrentIMSScanSet.PrimaryScanNumber);
//get the mass spectrum +/- 5 da from the range of the isotopicProfile
uimfRun.CurrentScanSet = lcScanSet;
uimfRun.CurrentIMSScanSet = imsScanSet;
_msGenerator.Execute(run.ResultCollection);
}
else
{
if (run.CurrentScanSet == null)
{
throw new NullReferenceException("CurrentScanSet is null. You need to set it.");
}
//this creates a ScanSet containing only the primary scan. Therefore no summing will occur
var scanSet = new ScanSet(run.CurrentScanSet.PrimaryScanNumber);
run.CurrentScanSet = scanSet;
_msGenerator.Execute(run.ResultCollection);
}
foreach (var result in resultList)
{
var indexOfObsMostAbundant = result.IsotopicProfile.GetIndexOfMostIntensePeak();
var mzOfMostAbundant = result.IsotopicProfile.Peaklist[indexOfObsMostAbundant].XValue;
var indexOfUnsummedMostAbundantMZ = run.XYData.GetClosestXVal(mzOfMostAbundant);
if (indexOfUnsummedMostAbundantMZ >= 0)
{
result.IsotopicProfile.OriginalIntensity = run.XYData.Yvalues[indexOfUnsummedMostAbundantMZ];
result.IsotopicProfile.IsSaturated = (result.IsotopicProfile.OriginalIntensity >=
SaturationThreshold);
if (result.IsotopicProfile.IsSaturated)
{
//problem is that with these saturated profiles, they are often truncated because another
//isotopic profile was falsely assigned to the back end of it. So we need to find more peaks that should
//belong to the saturated profile.
var theorTarget = new PeptideTarget
{
ChargeState = (short)result.IsotopicProfile.ChargeState,
MonoIsotopicMass = result.IsotopicProfile.MonoIsotopicMass
};
theorTarget.MZ = (theorTarget.MonoIsotopicMass / theorTarget.ChargeState) + Globals.PROTON_MASS;
var averagineFormula = _tomIsotopicPatternGenerator.GetClosestAvnFormula(result.IsotopicProfile.MonoIsotopicMass, false);
theorTarget.IsotopicProfile = _tomIsotopicPatternGenerator.GetIsotopePattern(averagineFormula, _tomIsotopicPatternGenerator.aafIsos);
theorTarget.EmpiricalFormula = averagineFormula;
theorTarget.CalculateMassesForIsotopicProfile(result.IsotopicProfile.ChargeState);
AssignMissingPeaksToSaturatedProfile(run.PeakList, result.IsotopicProfile, theorTarget.IsotopicProfile);
//goal is to find the index of the isotopic profile peaks of a peak that is not saturated
var indexOfGoodUnsaturatedPeak = -1;
for (var i = indexOfObsMostAbundant + 1; i < result.IsotopicProfile.Peaklist.Count; i++)
{
var indexUnsummedData = run.XYData.GetClosestXVal(result.IsotopicProfile.Peaklist[i].XValue);
var unsummedIntensity = run.XYData.Yvalues[indexUnsummedData];
if (unsummedIntensity < _minRelIntTheorProfile * SaturationThreshold)
{
indexOfGoodUnsaturatedPeak = i;
break;
}
}
AdjustSaturatedIsotopicProfile(result.IsotopicProfile, theorTarget.IsotopicProfile,
indexOfGoodUnsaturatedPeak);
}
}
//double summedIntensity = 0;
//foreach (MSPeak peak in result.IsotopicProfile.Peaklist)
//{
// int indexOfMZ = result.Run.XYData.GetClosestXVal(peak.XValue);
// if (indexOfMZ >= 0)
// {
// summedIntensity += result.Run.XYData.Yvalues[indexOfMZ];
// }
//}
//result.IsotopicProfile.OriginalTotalIsotopicAbundance = summedIntensity;
}
}
public override void Execute(ResultCollection resultList)
{
Check.Require(resultList.Run.CurrentMassTag != null, this.Name + " failed. MassTag was not defined.");
var currentResult = resultList.GetTargetedResult(resultList.Run.CurrentMassTag);
if (msgen == null)
{
msgen = MSGeneratorFactory.CreateMSGenerator(resultList.Run.MSFileType);
msgen.IsTICRequested = false;
}
var mt = resultList.Run.CurrentMassTag;
float normalizedElutionTime;
if (currentResult.Run.CurrentMassTag.ElutionTimeUnit == DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum)
{
normalizedElutionTime = resultList.Run.CurrentMassTag.ScanLCTarget / (float)currentResult.Run.GetNumMSScans();
}
else
{
normalizedElutionTime = resultList.Run.CurrentMassTag.NormalizedElutionTime;
}
//collect Chrom peaks that fall within the NET tolerance
var peaksWithinTol = new List <ChromPeak>(); //
foreach (ChromPeak peak in resultList.Run.PeakList)
{
if (Math.Abs(peak.NETValue - normalizedElutionTime) <= Parameters.NETTolerance) //peak.NETValue was determined by the ChromPeakDetector or a future ChromAligner Task
{
peaksWithinTol.Add(peak);
}
}
var peakQualityList = new List <ChromPeakQualityData>();
//iterate over peaks within tolerance and score each peak according to MSFeature quality
var tempMinScanWithinTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime - Parameters.NETTolerance);
var tempMaxScanWithinTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime + Parameters.NETTolerance);
var tempCenterTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime);
IqLogger.Log.Debug("SmartPeakSelector --> NETTolerance= " + Parameters.NETTolerance + "; chromMinCenterMax= " + tempMinScanWithinTol + "\t" + tempCenterTol + "" +
"\t" + tempMaxScanWithinTol);
IqLogger.Log.Debug("MT= " + currentResult.Target.ID + ";z= " + currentResult.Target.ChargeState + "; mz= " + currentResult.Target.MZ.ToString("0.000") + "; ------------------------- PeaksWithinTol = " + peaksWithinTol.Count);
currentResult.NumChromPeaksWithinTolerance = peaksWithinTol.Count;
currentResult.NumQualityChromPeaks = -1;
ChromPeak bestChromPeak;
if (currentResult.NumChromPeaksWithinTolerance > _parameters.NumChromPeaksAllowed)
{
bestChromPeak = null;
}
else
{
foreach (var chromPeak in peaksWithinTol)
{
var pq = new ChromPeakQualityData(chromPeak);
peakQualityList.Add(pq);
var lcscanSet = ChromPeakUtilities.GetLCScanSetForChromPeak(chromPeak, resultList.Run, _parameters.NumMSSummedInSmartSelector);
resultList.Run.CurrentScanSet = lcscanSet;
//This resets the flags and the scores on a given result
currentResult.ResetResult();
//generate a mass spectrum
msgen.Execute(resultList);
//find isotopic profile
TargetedMSFeatureFinder.Execute(resultList);
try
{
//get fit score
fitScoreCalc.Execute(resultList);
//get i_score
resultValidator.Execute(resultList);
}
catch (Exception)
{
currentResult.FailedResult = true;
}
//collect the results together
AddScoresToPeakQualityData(pq, currentResult);
#if DEBUG
IqLogger.Log.Debug(pq.Display() + Environment.NewLine);
#endif
}
//run a algorithm that decides, based on fit score mostly.
bestChromPeak = determineBestChromPeak(peakQualityList, currentResult);
}
currentResult.ChromPeakQualityList = peakQualityList;
if (Parameters.SummingMode == SummingModeEnum.SUMMINGMODE_STATIC)
{
resultList.Run.CurrentScanSet = ChromPeakUtilities.GetLCScanSetForChromPeak(bestChromPeak, resultList.Run, Parameters.NumScansToSum);
}
else
{
resultList.Run.CurrentScanSet = ChromPeakUtilities.GetLCScanSetForChromPeakBasedOnPeakWidth(bestChromPeak, resultList.Run,
Parameters.AreaOfPeakToSumInDynamicSumming, Parameters.MaxScansSummedInDynamicSumming);
}
UpdateResultWithChromPeakAndLCScanInfo(currentResult, bestChromPeak);
}
