/// <summary>
/// Constructor
/// </summary>
/// <param name="run">LcMsRun (for determining minimum and maximum elution time</param>
/// <param name="features">List of features</param>
/// <param name="title">Plot title</param>
/// <param name="minMass">Minimum mass</param>
/// <param name="maxMass">Maximum mass</param>
public LcMsFeatureMap(LcMsRun run, IEnumerable<LcMsFeature> features, string title, double minMass, double maxMass) :
this(features, title,
minMass, maxMass,
Math.Max(run.GetElutionTime(run.MinLcScan) - 5, 0),
run.GetElutionTime(run.MaxLcScan) + 5)
{
}
public IEnumerable<int> GetMatchingMs2ScanNums(double sequenceMass, Tolerance tolerance, LcMsRun run)
{
var massBinNum = GetBinNumber(sequenceMass);
IEnumerable<int> ms2ScanNums;
if (_sequenceMassBinToScanNumsMap.TryGetValue(massBinNum, out ms2ScanNums)) return ms2ScanNums;
return new int[0];
}
public ScanBasedTagSearchEngine(
LcMsRun run,
ISequenceTagFinder seqTagFinder,
LcMsPeakMatrix featureFinder,
FastaDatabase fastaDb,
Tolerance tolerance,
AminoAcidSet aaSet,
CompositeScorerFactory ms2ScorerFactory = null,
int minMatchedTagLength = DefaultMinMatchedTagLength,
double maxSequenceMass = 50000.0,
int minProductIonCharge = 1,
int maxProductIonCharge = 20)
{
_run = run;
_featureFinder = featureFinder;
_searchableDb = new SearchableDatabase(fastaDb);
_tolerance = tolerance;
_aaSet = aaSet;
_minMatchedTagLength = minMatchedTagLength;
_maxSequenceMass = maxSequenceMass;
_minProductIonCharge = minProductIonCharge;
_maxProductIonCharge = maxProductIonCharge;
MinScan = int.MinValue;
MaxScan = int.MaxValue;
_ms2ScorerFactory = ms2ScorerFactory;
_seqTagFinder = seqTagFinder;
}
public Ms1FtFilter(LcMsRun run, Tolerance massTolerance, string ms1FtFileName, double minLikelihoodRatio = 0)
{
_lcMsChargeMap = new LcMsChargeMap(run, massTolerance);
_minLikelihoodRatio = minLikelihoodRatio;
Read(ms1FtFileName);
}
public FeatureBasedTagSearchEngine(
LcMsRun run,
Ms1FtParser featureParser,
ProductScorerBasedOnDeconvolutedSpectra ms2Scorer,
SequenceTagParser tagParser,
FastaDatabase fastaDb,
Tolerance tolerance,
AminoAcidSet aaSet,
double maxSequenceMass = 50000.0,
int minProductIonCharge = 1,
int maxProductIonCharge = 20)
{
_run = run;
_ms2Scorer = ms2Scorer;
_featureParser = featureParser;
_ms1FtFilter = new Ms1FtFilter(run, tolerance, featureParser.Ms1FtFileName);
_tagParser = tagParser;
_fastaDb = fastaDb;
_searchableDb = new SearchableDatabase(fastaDb);
_tolerance = tolerance;
_aaSet = aaSet;
_maxSequenceMass = maxSequenceMass;
_minProductIonCharge = minProductIonCharge;
_maxProductIonCharge = maxProductIonCharge;
}
public LcMsPeakMatrix(LcMsRun run, LcMsFeatureLikelihood scorer = null, int minScanCharge = 1, int maxScanCharge = 60, int maxThreadCount = 0)
{
Run = run;
_maxThreadCount = maxThreadCount;
_ms1PeakList = new List<Ms1Peak>();
Ms1Spectra = new List<Ms1Spectrum>();
var ms1ScanNums = run.GetMs1ScanVector();
NColumns = ms1ScanNums.Length;
MinSearchCharge = minScanCharge;
MaxSearchCharge = maxScanCharge;
NRows = Math.Min(MaxSearchCharge - MinSearchCharge + 1, 35);
for (var i = 0; i < Math.Min(ms1ScanNums.Length, ushort.MaxValue); i++)
{
var ms1Spec = run.GetMs1Spectrum(ms1ScanNums[i]);
Ms1Spectra.Add(ms1Spec);
foreach (var peak in ms1Spec.Peaks) _ms1PeakList.Add(peak as Ms1Peak);
}
_ms1PeakList.Sort();
_distProfileAcrossCharge = new double[NRows];
_corrProfileAcrossCharge = new double[NRows];
_intensityAcrossCharge = new double[NRows];
_summedEnvelopeColRange = new int[NRows, 2];
_featureMatrix = null;
Comparer = new MzComparerWithBinning(27); // 16ppm
_scorer = scorer;
_seedEnvelopes = new List<KeyValuePair<double, ObservedIsotopeEnvelope>>();
_ms1Filter = null;
}
public MsDeconvFilter(LcMsRun run, Tolerance massTolerance, string msDeconvFileName)
{
_run = run;
_massTolerance = massTolerance;
_lcMsMatchMap = new LcMsMatchMap();
Read(msDeconvFileName);
}
public IsosFilter(LcMsRun run, Tolerance massTolerance, string isosFileName, double fitScoreThreshold = 1.0)
{
_run = run;
_massTolerance = massTolerance;
_fitScoreThreshold = fitScoreThreshold;
_lcMsMatchMap = new LcMsMatchMap();
Read(isosFileName);
}
public InformedTopDownScorer(LcMsRun run, AminoAcidSet aaSet, int minProductCharge, int maxProductCharge, Tolerance tolerance, double ms2CorrThreshold = 0.7)
{
Run = run;
AminoAcidSet = aaSet;
MinProductCharge = minProductCharge;
MaxProductCharge = maxProductCharge;
Tolerance = tolerance;
Ms2CorrThreshold = ms2CorrThreshold;
}
public InformedBottomUpScorer(LcMsRun run, AminoAcidSet aaSet, int minProductCharge, int maxProductCharge, Tolerance tolerance)
{
Run = run;
AminoAcidSet = aaSet;
MinProductCharge = minProductCharge;
MaxProductCharge = maxProductCharge;
Tolerance = tolerance;
_rankScorer = new RankScore(ActivationMethod.HCD, Ms2DetectorType.Orbitrap, Enzyme.Trypsin, Protocol.Standard);
_scoredSpectra = new Dictionary<int, ScoredSpectrum>();
}
public SequenceTagGenerator(LcMsRun run, Tolerance tolerance, int minTagLength = 5, int maxTagLength = 8,
AminoAcid[] aminoAcidsArray = null)
{
_run = run;
_tolerance = tolerance;
_minTagLen = minTagLength;
_maxTagLen = maxTagLength;
_aminoAcids = aminoAcidsArray ?? AminoAcid.StandardAminoAcidArr;
_ms2ScanToTagMap = new Dictionary<int, IList<SequenceTag>>();
}
public Ms1BasedFilter(
LcMsRun run,
int minCharge = 3, int maxCharge = 30,
double ppmTolerance = 15)
{
_run = run;
_minCharge = minCharge;
_maxCharge = maxCharge;
_ppmTolerance = ppmTolerance;
_tolerance = new Tolerance(_ppmTolerance);
_sequenceMassBinToScanNumsMap = new Dictionary<int, IList<int>>();
PrecomputeMostAbundantMzToMatches();
}
public LcMsChargeMap(LcMsRun run, Tolerance tolerance, int maxNumMs2ScansPerMass = MaxNumMs2ScansPerFeature)
{
_run = run;
_scanToIsolationWindow = new Dictionary<int, IsolationWindow>();
_maxNumMs2ScansPerMass = maxNumMs2ScansPerMass;
foreach (var ms2ScanNum in _run.GetScanNumbers(2))
{
var isoWindow = _run.GetIsolationWindow(ms2ScanNum);
if (isoWindow != null) _scanToIsolationWindow.Add(ms2ScanNum, isoWindow);
}
_tolerance = tolerance;
_map = new Dictionary<int, BitArray>();
_comparer = new MzComparerWithBinning(30); // 2 ppm binning
_sequenceMassBinToScanNumsMap = new Dictionary<int, IEnumerable<int>>();
_scanNumToMassBin = new Dictionary<int, List<int>>();
}
public Ms1IsotopeCorrFilter(
LcMsRun run,
int minCharge = 3, int maxCharge = 30,
double ppmTolerance = 15,
double corrThreshold = 0.5,
int maxNumDeisotopedPeaksPerIsolationWindow = 40)
{
_run = run;
_minCharge = minCharge;
_maxCharge = maxCharge;
_corrThreshold = corrThreshold;
MaxNumDeisotopedPeaksPerIsolationWindow = maxNumDeisotopedPeaksPerIsolationWindow;
_ppmTolerance = ppmTolerance;
_tolerance = new Tolerance(_ppmTolerance);
_comparer = new MzComparerWithPpmTolerance(ppmTolerance);
_sequenceMassBinToScanNumsMap = new Dictionary<int, IList<int>>();
// _topKFilter = new Ms1IsotopeTopKFilter(run, minCharge, maxCharge, ppmTolerance);
PrecomputePossibleSequenceMasses();
}
public double GetScore(Sequence sequence, int charge, int scan, LcMsRun lcmsRun)
{
var mass = sequence.Composition.Mass + Composition.H2O.Mass;
var spectrum = lcmsRun.GetSpectrum(scan);
var ionTypes = _rankScore.GetIonTypes(charge, mass);
var filteredSpectrum = SpectrumFilter.FilterIonPeaks(sequence, spectrum, ionTypes, _tolerance);
var match = new SpectrumMatch(sequence, filteredSpectrum, charge);
var score = 0.0;
var rankedPeaks = new RankedPeaks(filteredSpectrum);
foreach (var ionType in ionTypes)
{
var ions = match.GetCleavageIons(ionType);
foreach (var ion in ions)
{
var rank = rankedPeaks.RankIon(ion, _tolerance);
score += _rankScore.GetScore(ionType, rank, charge, mass);
}
}
return score;
}
public TopDownScorer(Composition proteinComposition, LcMsRun run, Tolerance tolernace, SubScoreFactory factory)
{
_run = run;
_proteinCompositionPlusWater = proteinComposition + Composition.H2O;
_tolerance = tolernace;
_factory = factory;
_maxIntensityIsotopeIndex = _proteinCompositionPlusWater.GetMostAbundantIsotopeZeroBasedIndex();
var thorethicalIsotopeEnvelope = _proteinCompositionPlusWater.GetIsotopomerEnvelopeRelativeIntensities();
_minIsotopeIndex = 0;
for (var i = 0; i < thorethicalIsotopeEnvelope.Length; i++)
{
if (!(thorethicalIsotopeEnvelope[i] > MinIsotopeIntensity)) continue;
_minIsotopeIndex = i;
break;
}
_isotopeEnvelope = new double[Math.Min(_maxIntensityIsotopeIndex + NumberAfterMaxIsotopeIndex, thorethicalIsotopeEnvelope.Length) - _minIsotopeIndex];
for (var k = 0; k < _isotopeEnvelope.Length; k++)
{
_isotopeEnvelope[k] = thorethicalIsotopeEnvelope[k + _minIsotopeIndex];
}
/*foreach (var iso in thorethicalIsotopeEnvelope)
{
Console.WriteLine(iso);
}
Console.WriteLine();
foreach (var iso in _isotopeEnvelope)
{
Console.WriteLine(iso);
}
System.Environment.Exit(1);
*/
_xicArray = GetXicArray();
_smoothedXicArray = GetSmoothedXicArray();
}
public LcMsPeakCluster(LcMsRun run, TheoreticalIsotopeEnvelope theoreticalIsotopeEnvelope, double mass, int charge, double repMz, int repScanNum, double abundance)
: base(mass, charge, repMz, repScanNum, abundance)
{
_run = run;
TheoreticalEnvelope = theoreticalIsotopeEnvelope;
Flag = 0;
RepresentativeSummedEnvelop = new double[TheoreticalEnvelope.Size];
AbundanceDistributionAcrossCharge = new double[2];
BestCorrelationScoreAcrossCharge = new double[2];
BestDistanceScoreAcrossCharge = new double[2];
BestIntensityScoreAcrossCharge = new double[2];
EnvelopeDistanceScoreAcrossCharge = new double[2];
EnvelopeCorrelationScoreAcrossCharge = new double[2];
EnvelopeIntensityScoreAcrossCharge = new double[2];
BestCharge = new int[2];
XicCorrelationBetweenBestCharges = new double[2];
_initScore = false;
}
public FeatureBasedTagSearchEngine(
LcMsRun run,
Ms1FtParser featureParser,
SequenceTagParser tagParser,
FastaDatabase fastaDb,
Tolerance tolerance,
AminoAcidSet aaSet,
double maxSequenceMass = 50000.0,
int minProductIonCharge = 1,
int maxProductIonCharge = 20)
: this(
run,
featureParser,
null,
tagParser,
fastaDb,
tolerance,
aaSet,
maxSequenceMass,
minProductIonCharge,
maxProductIonCharge)
{
}
public Ms1IsotopeAndChargeCorrFilter(
LcMsRun run,
Tolerance tolerance,
int minCharge = 3, int maxCharge = 30,
double minMass = 3000.0,
double maxMass = 50000.0,
double isotopeCorrThreshold = 0.7,
double chargeCorrThreshold = 0.7,
double mostAbundantPlusOneIsotopeCorrThreshold = 0.7,
int maxNumPeaksToConsider = 40)
{
_run = run;
_minCharge = minCharge;
_maxCharge = maxCharge;
_isotopeCorrThresholdThreshold = isotopeCorrThreshold;
_chargeCorrThresholdThreshold = chargeCorrThreshold;
_mostAbundantPlusOneIsotopeCorrThreshold = mostAbundantPlusOneIsotopeCorrThreshold;
MaxNumPeaksToConsider = maxNumPeaksToConsider;
_tolerance = tolerance;
_comparer = new MzComparerWithTolerance(tolerance);
_lcMsMatchMap = new LcMsMatchMap();
PrecomputePossibleSequenceMasses();
_lcMsMatchMap.CreateSequenceMassToMs2ScansMap(_run, _tolerance, minMass, maxMass);
}
public ProteinSpectrumMathMap(LcMsRun run, int dataid, List<ProteinSpectrumMatch> prsmList, string dataDesc = "")
{
DataId = dataid;
DataDesc = dataDesc;
Run = run;
_scanNumToMatchMap = new Dictionary<int, ProteinSpectrumMatch>();
if (prsmList == null) return;
ProteinSpectrumMatches = prsmList;
_scanNumToMatchMap.Clear();
foreach (var prsm in prsmList)
{
if (_scanNumToMatchMap.ContainsKey(prsm.ScanNum))
{
if (_scanNumToMatchMap[prsm.ScanNum].Score < prsm.Score) _scanNumToMatchMap[prsm.ScanNum] = prsm;
}
else
{
_scanNumToMatchMap.Add(prsm.ScanNum, prsm);
}
}
}
public LcMsPeakCluster(LcMsRun run, ObservedIsotopeEnvelope observedEnvelope)
: this(run, observedEnvelope.TheoreticalEnvelope, observedEnvelope.MonoMass, observedEnvelope.Charge,
observedEnvelope.RepresentativePeak.Mz, observedEnvelope.ScanNum, observedEnvelope.Abundance)
{
}
public bool RunSearch(double corrThreshold)
{
var sw = new Stopwatch();
ErrorMessage = string.Empty;
Console.Write(@"Reading raw file...");
sw.Start();
_run = InMemoryLcMsRun.GetLcMsRun(SpecFilePath, 1.4826, 1.4826);
_bottomUpScorer = new InformedBottomUpScorer(_run, AminoAcidSet, MinProductIonCharge, MaxProductIonCharge, ProductIonTolerance);
sw.Stop();
var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Determining precursor masses...");
sw.Start();
var ms1Filter = new Ms1IsotopeAndChargeCorrFilter(_run, PrecursorIonTolerance, MinPrecursorIonCharge, MaxPrecursorIonCharge,
400, 5000, corrThreshold, 0, 0);
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Deconvoluting MS2 spectra...");
sw.Start();
_ms2ScorerFactory = new ProductScorerBasedOnDeconvolutedSpectra(
_run,
MinProductIonCharge, MaxProductIonCharge,
new Tolerance(10),
0
);
_ms2ScorerFactory.DeconvoluteAllProductSpectra();
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
// Target database
var targetDb = new FastaDatabase(DatabaseFilePath);
// string dirName = OutputDir ?? Path.GetDirectoryName(SpecFilePath);
var baseName = Path.GetFileNameWithoutExtension(SpecFilePath);
var targetOutputFilePath = Path.Combine(OutputDir, baseName + TargetFileExtension);
var decoyOutputFilePath = Path.Combine(OutputDir, baseName + DecoyFileExtension);
var tdaOutputFilePath = Path.Combine(OutputDir, baseName + TdaFileExtension);
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Target))
{
sw.Reset();
Console.Write(@"Reading the target database...");
sw.Start();
targetDb.Read();
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.WriteLine(@"Searching the target database");
sw.Start();
var targetMatches = RunSearch(GetAnnotationsAndOffsets(targetDb), ms1Filter, false);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Target database search elapsed time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Rescoring and writing target results...");
sw.Start();
WriteResultsToFile(targetMatches, targetOutputFilePath, targetDb);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed time: {0:f4} sec", sec);
}
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Decoy))
{
// Decoy database
sw.Reset();
Console.Write(@"Reading the decoy database...");
sw.Start();
var decoyDb = targetDb.Decoy(Enzyme);
decoyDb.Read();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.WriteLine(@"Searching the decoy database");
sw.Start();
var decoyMatches = RunSearch(GetAnnotationsAndOffsets(decoyDb), ms1Filter, true);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Decoy database search elapsed Time: {0:f4} sec", sec);
sw.Reset();
Console.Write(@"Rescoring and writing decoy results...");
sw.Start();
WriteResultsToFile(decoyMatches, decoyOutputFilePath, decoyDb);
sw.Stop();
sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed time: {0:f4} sec", sec);
}
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Both))
{
var fdrCalculator = new FdrCalculator(targetOutputFilePath, decoyOutputFilePath);
if (fdrCalculator.HasError())
{
ErrorMessage = fdrCalculator.ErrorMessage;
Console.WriteLine(@"Error computing FDR: " + fdrCalculator.ErrorMessage);
return false;
}
fdrCalculator.WriteTo(tdaOutputFilePath);
}
Console.WriteLine(@"Done");
return true;
}
private void TestTagBasedSearch(LcMsRun run,
FastaDatabase fastaDb, Tolerance tolerance, AminoAcidSet aaSet)
{
var engine = new ScanBasedTagSearchEngine(run, new SequenceTagGenerator(run, new Tolerance(8)), new LcMsPeakMatrix(run), fastaDb, tolerance, aaSet);
// engine.MinScan = 3400;
// engine.MaxScan = 3900;
engine.RunSearch();
}
private void CreateFeatureMapImage(LcMsRun run, string featuresFilePath, string imgFilePath)
{
var map = new LcMsFeatureMap(run, featuresFilePath, Math.Max(0, Parameters.MinSearchMass - 500), Parameters.MaxSearchMass);
map.SaveImage(imgFilePath);
Console.WriteLine(@" - Feature map image output: {0}", imgFilePath);
}
public Ms1ContainsIonFilter(LcMsRun run, Tolerance mzTolerance)
{
Run = run;
MzTolerance = mzTolerance;
}
public void CreateSequenceMassToMs2ScansMap(LcMsRun run, Tolerance tolerance, double minMass, double maxMass)
{
// Make a bin to scan numbers map without considering tolerance
var massBinToScanNumsMapNoTolerance = new Dictionary<int, List<int>>();
var minBinNum = GetBinNumber(minMass);
var maxBinNum = GetBinNumber(maxMass);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
IList<IntRange> scanRanges;
if (!_map.TryGetValue(binNum, out scanRanges)) continue;
var sequenceMass = GetMass(binNum);
var ms2ScanNums = new List<int>();
foreach (var scanRange in scanRanges)
{
for (var scanNum = scanRange.Min; scanNum <= scanRange.Max; scanNum++)
{
if (scanNum < run.MinLcScan || scanNum > run.MaxLcScan) continue;
if (run.GetMsLevel(scanNum) == 2)
{
var productSpec = run.GetSpectrum(scanNum) as ProductSpectrum;
if (productSpec == null) continue;
var isolationWindow = productSpec.IsolationWindow;
var isolationWindowTargetMz = isolationWindow.IsolationWindowTargetMz;
var charge = (int)Math.Round(sequenceMass / isolationWindowTargetMz);
var mz = Ion.GetIsotopeMz(sequenceMass, charge,
Averagine.GetIsotopomerEnvelope(sequenceMass).MostAbundantIsotopeIndex);
if (productSpec.IsolationWindow.Contains(mz)) ms2ScanNums.Add(scanNum);
}
}
}
ms2ScanNums.Sort();
massBinToScanNumsMapNoTolerance.Add(binNum, ms2ScanNums);
}
// Account for mass tolerance
_sequenceMassBinToScanNumsMap = new Dictionary<int, IEnumerable<int>>();
var sumScanNums = 0L;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var sequenceMass = GetMass(binNum);
var deltaMass = tolerance.GetToleranceAsDa(sequenceMass, 1);
var curMinBinNum = GetBinNumber(sequenceMass - deltaMass);
var curMaxBinNum = GetBinNumber(sequenceMass + deltaMass);
var ms2ScanNums = new HashSet<int>();
for (var curBinNum = curMinBinNum; curBinNum <= curMaxBinNum; curBinNum++)
{
if (curBinNum < minBinNum || curBinNum > maxBinNum) continue;
List<int> existingMs2ScanNums;
if (!massBinToScanNumsMapNoTolerance.TryGetValue(curBinNum, out existingMs2ScanNums)) continue;
foreach (var ms2ScanNum in existingMs2ScanNums)
{
ms2ScanNums.Add(ms2ScanNum);
}
}
_sequenceMassBinToScanNumsMap[binNum] = ms2ScanNums.ToArray();
sumScanNums += ms2ScanNums.Count;
}
Console.WriteLine("#MS/MS matches per sequence: {0}", sumScanNums / (float)(maxBinNum-minBinNum+1));
_map = null;
}
private Tuple<int, int> GetMinMaxMs1ScanNum(LcMsRun run, double minTime, double maxTime)
{
var ms1ScanNums = run.GetMs1ScanVector();
var minScanNum = -1;
var maxScanNum = -1;
for(var i = 1; i < ms1ScanNums.Length; i++)
{
var time = run.GetElutionTime(ms1ScanNums[i]);
if (minScanNum < 0 && time > minTime)
{
minScanNum = ms1ScanNums[i - 1];
}
if (maxScanNum < 0 && time > maxTime)
{
maxScanNum = ms1ScanNums[i];
break;
}
}
return new Tuple<int, int>(minScanNum, maxScanNum);
}
public bool RunSearch(double corrThreshold = 0.7, CancellationToken? cancellationToken = null, IProgress<ProgressData> progress = null)
{
// Get the Normalized spec file/folder path
SpecFilePath = MassSpecDataReaderFactory.NormalizeDatasetPath(SpecFilePath);
var prog = new Progress<ProgressData>();
var progData = new ProgressData(progress);
if (progress != null)
{
prog = new Progress<ProgressData>(p =>
{
progData.Status = p.Status;
progData.StatusInternal = p.StatusInternal;
progData.Report(p.Percent);
});
}
var sw = new Stopwatch();
var swAll = new Stopwatch();
swAll.Start();
ErrorMessage = string.Empty;
Console.Write(@"Reading raw file...");
progData.Status = "Reading spectra file";
progData.StepRange(10.0);
sw.Start();
_run = PbfLcMsRun.GetLcMsRun(SpecFilePath, 0, 0, prog);
_ms2ScanNums = _run.GetScanNumbers(2).ToArray();
_isolationWindowTargetMz = new double[_run.MaxLcScan + 1];
foreach (var ms2Scan in _ms2ScanNums)
{
var ms2Spec = _run.GetSpectrum(ms2Scan) as ProductSpectrum;
if (ms2Spec == null) continue;
_isolationWindowTargetMz[ms2Scan] = ms2Spec.IsolationWindow.IsolationWindowTargetMz;
}
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
progData.StepRange(20.0);
ISequenceFilter ms1Filter;
if (this.ScanNumbers != null && this.ScanNumbers.Any())
{
ms1Filter = new SelectedMsMsFilter(this.ScanNumbers);
}
else if (string.IsNullOrWhiteSpace(FeatureFilePath))
{
// Checks whether SpecFileName.ms1ft exists
var ms1FtFilePath = MassSpecDataReaderFactory.ChangeExtension(SpecFilePath, LcMsFeatureFinderLauncher.FileExtension);
if (!File.Exists(ms1FtFilePath))
{
Console.WriteLine(@"Running ProMex...");
sw.Start();
var param = new LcMsFeatureFinderInputParameter
{
InputPath = SpecFilePath,
MinSearchMass = MinSequenceMass,
MaxSearchMass = MaxSequenceMass,
MinSearchCharge = MinPrecursorIonCharge,
MaxSearchCharge = MaxPrecursorIonCharge,
CsvOutput = false,
ScoreReport = false,
LikelihoodScoreThreshold = -10
};
var featureFinder = new LcMsFeatureFinderLauncher(param);
featureFinder.Run();
}
sw.Reset();
sw.Start();
Console.Write(@"Reading ProMex results...");
ms1Filter = new Ms1FtFilter(_run, PrecursorIonTolerance, ms1FtFilePath, -10);
}
else
{
sw.Reset();
sw.Start();
var extension = Path.GetExtension(FeatureFilePath);
if (extension.ToLower().Equals(".csv"))
{
Console.Write(@"Reading ICR2LS/Decon2LS results...");
ms1Filter = new IsosFilter(_run, PrecursorIonTolerance, FeatureFilePath);
}
else if (extension.ToLower().Equals(".ms1ft"))
{
Console.Write(@"Reading ProMex results...");
ms1Filter = new Ms1FtFilter(_run, PrecursorIonTolerance, FeatureFilePath, -10);
}
else if (extension.ToLower().Equals(".msalign"))
{
Console.Write(@"Reading MS-Align+ results...");
ms1Filter = new MsDeconvFilter(_run, PrecursorIonTolerance, FeatureFilePath);
}
else ms1Filter = null; //new Ms1FeatureMatrix(_run);
}
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
// pre-generate deconvoluted spectra for scoring
_massBinComparer = new FilteredProteinMassBinning(AminoAcidSet, MaxSequenceMass+1000);
_ms2ScorerFactory2 = new CompositeScorerFactory(_run, _massBinComparer, AminoAcidSet,
MinProductIonCharge, MaxProductIonCharge, ProductIonTolerance);
sw.Reset();
Console.WriteLine(@"Generating deconvoluted spectra for MS/MS spectra...");
sw.Start();
var pfeOptions = new ParallelOptions
{
MaxDegreeOfParallelism = MaxNumThreads,
CancellationToken = cancellationToken ?? CancellationToken.None
};
Parallel.ForEach(_ms2ScanNums, pfeOptions, ms2ScanNum =>
{
_ms2ScorerFactory2.DeconvonluteProductSpectrum(ms2ScanNum);
});
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
progData.StepRange(10.0);
progData.Status = "Reading Fasta File";
// Target database
var targetDb = new FastaDatabase(DatabaseFilePath);
targetDb.Read();
// Generate sequence tags for all MS/MS spectra
if (TagBasedSearch)
{
progData.StepRange(25.0);
progData.Status = "Generating Sequence Tags";
sw.Reset();
Console.WriteLine(@"Generating sequence tags for MS/MS spectra...");
sw.Start();
var seqTagGen = GetSequenceTagGenerator();
_tagMs2ScanNum = seqTagGen.GetMs2ScanNumsContainingTags().ToArray();
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
_tagSearchEngine = new ScanBasedTagSearchEngine(_run, seqTagGen, new LcMsPeakMatrix(_run, ms1Filter), targetDb, ProductIonTolerance, AminoAcidSet,
_ms2ScorerFactory2,
ScanBasedTagSearchEngine.DefaultMinMatchedTagLength,
MaxSequenceMass, MinProductIonCharge, MaxProductIonCharge);
}
var specFileName = MassSpecDataReaderFactory.RemoveExtension(Path.GetFileName(SpecFilePath));
var targetOutputFilePath = Path.Combine(OutputDir, specFileName + TargetFileNameEnding);
var decoyOutputFilePath = Path.Combine(OutputDir, specFileName + DecoyFileNameEnding);
var tdaOutputFilePath = Path.Combine(OutputDir, specFileName + TdaFileNameEnding);
progData.StepRange(60.0);
progData.Status = "Running Target search";
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Target))
{
sw.Reset();
Console.Write(@"Reading the target database...");
sw.Start();
targetDb.Read();
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
var targetMatches = new SortedSet<DatabaseSequenceSpectrumMatch>[_run.MaxLcScan + 1];
progData.MaxPercentage = 42.5;
if (TagBasedSearch)
{
sw.Reset();
Console.WriteLine(@"Tag-based searching the target database");
sw.Start();
RunTagBasedSearch(targetMatches, targetDb, null, prog);
Console.WriteLine(@"Target database tag-based search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.MaxPercentage = 60.0;
sw.Reset();
Console.WriteLine(@"Searching the target database");
sw.Start();
RunSearch(targetMatches, targetDb, ms1Filter, null, prog);
Console.WriteLine(@"Target database search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
// calculate spectral e-value usign generating function
sw.Reset();
Console.WriteLine(@"Calculating spectral E-values for target-spectrum matches");
sw.Start();
var bestTargetMatches = RunGeneratingFunction(targetMatches);
WriteResultsToFile(bestTargetMatches, targetOutputFilePath, targetDb);
sw.Stop();
Console.WriteLine(@"Target-spectrum match E-value calculation elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.StepRange(95.0); // total to 95%
progData.Status = "Running Decoy search";
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Decoy))
{
// Decoy database
sw.Reset();
sw.Start();
var decoyDb = targetDb.Decoy(null, true);
Console.Write(@"Reading the decoy database...");
decoyDb.Read();
Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
progData.MaxPercentage = 77.5;
var decoyMatches = new SortedSet<DatabaseSequenceSpectrumMatch>[_run.MaxLcScan + 1];
if (TagBasedSearch)
{
sw.Reset();
Console.WriteLine(@"Tag-based searching the decoy database");
sw.Start();
RunTagBasedSearch(decoyMatches, decoyDb, null, prog);
Console.WriteLine(@"Decoy database tag-based search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.MaxPercentage = 95.0;
sw.Reset();
Console.WriteLine(@"Searching the decoy database");
sw.Start();
RunSearch(decoyMatches, decoyDb, ms1Filter, null, prog);
Console.WriteLine(@"Decoy database search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
// calculate spectral e-value usign generating function
sw.Reset();
Console.WriteLine(@"Calculating spectral E-values for decoy-spectrum matches");
sw.Start();
var bestDecoyMatches = RunGeneratingFunction(decoyMatches);
WriteResultsToFile(bestDecoyMatches, decoyOutputFilePath, decoyDb);
sw.Stop();
Console.WriteLine(@"Decoy-spectrum match E-value calculation elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds);
}
progData.StepRange(100.0);
progData.Status = "Writing combined results file";
if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Both))
{
// Add "Qvalue" and "PepQValue"
var fdrCalculator = new FdrCalculator(targetOutputFilePath, decoyOutputFilePath);
if (fdrCalculator.HasError())
{
ErrorMessage = fdrCalculator.ErrorMessage;
Console.WriteLine(@"Error computing FDR: " + fdrCalculator.ErrorMessage);
return false;
}
fdrCalculator.WriteTo(tdaOutputFilePath);
}
progData.Report(100.0);
Console.WriteLine(@"Done.");
swAll.Stop();
Console.WriteLine(@"Total elapsed time for search: {0:f1} sec ({1:f2} min)", swAll.Elapsed.TotalSeconds, swAll.Elapsed.TotalMinutes);
return true;
}
private List<ProductSpectrum> GetMatchedSpectrums(LcMsRun run, IList<int> ms2List ,Tuple<int,double, double, double, double,double> feature, int fileIndex)
{
var spectrumList = new List<ProductSpectrum>();
var mass = feature.Item2;
var minElution = feature.Item3;
var maxElution = feature.Item4;
var featureId = feature.Item1 - 1;
var det = new Tuple<int, double, int>(-1, -1.0, -1);
for (var i = 0; i < ms2List.Count; i++)
{
var scanElutionTime = run.GetElutionTime(ms2List[i]);
if (scanElutionTime < minElution || scanElutionTime > maxElution) continue;
var spectrum = run.GetSpectrum(ms2List[i]) as ProductSpectrum;
var window = spectrum.IsolationWindow;
var minMz = window.MinMz - .5;
var maxMz = window.MaxMz + .5;
var mzTable = GetFeatureMassTable(mass);
for (var j = 0; j < mzTable.Length; j++)
{
var mz = mzTable[j];
if (mz < minMz || mz > maxMz) continue;
spectrumList.Add(spectrum);
if(!(det.Item1 > -1)) det = new Tuple<int, double, int>(ms2List[i],mz,j+2);
break;
}
_identifiedFeatures[featureId][fileIndex] = det;
}
return spectrumList;
}
public LcMsPeakMatrix(LcMsRun run, ISequenceFilter ms1Filter, LcMsFeatureLikelihood scorer = null, int minScanCharge = 1, int maxScanCharge = 60,
int maxThreadCount = 0)
: this(run, scorer, minScanCharge, maxScanCharge, maxThreadCount)
{
_ms1Filter = ms1Filter;
}
