public void CreateFilter()
{
var filterLogs = new List <int?>();
var filters = new ISequenceFilter <DummySource, DummyContext>[] {
new SpySequenceFilter(() => filterLogs.Add(0)),
new SpySequenceFilter(() => filterLogs.Add(1)),
new SpySequenceFilter(() => filterLogs.Add(2)),
};
new TestCaseRunner()
.Run(() => Pipeline.CreateFilter(filters))
.Verify((actual, _) => {
var source = new DummySource[] { new DummySource(), new DummySource() };
var context = new DummyContext();
var actualSource = actual(source, context).GetAwaiter().GetResult();
CollectionAssert.AreEqual(new int[] { 0, 1, 2 }, filterLogs, "フィルターの適用順序が一致しません。");
Assert.AreEqual(source, actualSource, "入力シーケンスが出力に素通しされていません。");
}, (Type)null);
}
private SortedSet<DatabaseSequenceSpectrumMatch>[] RunSearch(IEnumerable<AnnotationAndOffset> annotationsAndOffsets, ISequenceFilter ms1Filter, bool isDecoy)
{
var sw = new Stopwatch();
var numPeptides = 0;
sw.Reset();
sw.Start();
var matches = new SortedSet<DatabaseSequenceSpectrumMatch>[_run.MaxLcScan + 1];
// TODO: N-term Met cleavage
foreach (var annotationAndOffset in annotationsAndOffsets)
{
++numPeptides;
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
if (numPeptides % 100000 == 0)
{
Console.Write(@"Processing {0}{1} peptides...", numPeptides,
numPeptides == 1 ? "st" : numPeptides == 2 ? "nd" : numPeptides == 3 ? "rd" : "th");
if (numPeptides != 0)
{
sw.Stop();
var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
sw.Start();
}
}
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, annotation);
if (seqGraph == null)
{
// Console.WriteLine("Ignoring illegal protein: {0}", annotation);
continue;
}
//var protCompositions = seqGraph.GetSequenceCompositions();
var numProteoforms = seqGraph.GetNumProteoformCompositions();
var modCombs = seqGraph.GetModificationCombinations();
for (var modIndex = 0; modIndex < numProteoforms; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
var sequenceMass = protCompositionWithH2O.Mass;
var modCombinations = modCombs[modIndex];
foreach (var ms2ScanNum in ms1Filter.GetMatchingMs2ScanNums(sequenceMass))
{
var spec = _run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null) continue;
var charge =
(int)Math.Round(sequenceMass / (spec.IsolationWindow.IsolationWindowTargetMz - Constants.Proton));
var scorer = _ms2ScorerFactory.GetMs2Scorer(ms2ScanNum);
var score = seqGraph.GetFragmentScore(scorer);
if (score <= 2) continue;
var precursorIon = new Ion(protCompositionWithH2O, charge);
var sequence = annotation.Substring(2, annotation.Length - 4);
var pre = annotation[0];
var post = annotation[annotation.Length - 1];
var prsm = new DatabaseSequenceSpectrumMatch(sequence, pre, post, ms2ScanNum, offset, 0, modCombinations,
precursorIon, score, isDecoy);
if (matches[ms2ScanNum] == null)
{
matches[ms2ScanNum] = new SortedSet<DatabaseSequenceSpectrumMatch> { prsm };
}
else // already exists
{
var existingMatches = matches[ms2ScanNum];
if (existingMatches.Count < NumMatchesPerSpectrum) existingMatches.Add(prsm);
else
{
var minScore = existingMatches.Min.Score;
if (score > minScore)
{
existingMatches.Add(prsm);
existingMatches.Remove(existingMatches.Min);
}
}
}
}
}
}
return matches;
}
public void FilteringEfficiencyQcShew()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
sw.Stop();
Console.WriteLine(@"Reading run: {0:f4} sec", sw.Elapsed.TotalSeconds);
const int minPrecursorCharge = 3;
const int maxPrecursorCharge = 30;
const int tolerancePpm = 10;
var tolerance = new Tolerance(tolerancePpm);
sw.Reset();
sw.Start();
var ms1BasedFilter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10.0), minPrecursorCharge, maxPrecursorCharge, 3000, 50000, 0.7, 0.7, 0.7, 40);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, 15, 0.5, 40);
sw.Stop();
Console.WriteLine(@"Ms1 filter: {0:f4} sec", sw.Elapsed.TotalSeconds);
ISequenceFilter ms1Filter = ms1BasedFilter;
sw.Reset();
sw.Start();
const double minProteinMass = 3000.0;
const double maxProteinMass = 30000.0;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minProteinMass);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxProteinMass);
var numComparisons = 0L;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mass = ProductScorerBasedOnDeconvolutedSpectra.GetMz(binNum);
numComparisons += ms1Filter.GetMatchingMs2ScanNums(mass).Count();
}
sw.Stop();
Console.WriteLine(@"Calculating #matches per bin: {0:f4} sec", sw.Elapsed.TotalSeconds);
//const string prot =
// "ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQQEIPDEATMKKTEVSAVSIVVAAAKKLLA";
//var protMass = (new AminoAcidSet().GetComposition(prot) + Composition.H2O).Mass;
//Console.WriteLine("************ScanNums: " + string.Join("\t", ms1Filter.GetMatchingMs2ScanNums(protMass)));
const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\MSAlign\NoMod.tsv";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var tsvReader = new TsvFileParser(resultFilePath);
var scanNums = tsvReader.GetData("Scan(s)");
var charges = tsvReader.GetData("Charge");
var scores = tsvReader.GetData("E-value");
var sequences = tsvReader.GetData("Peptide");
//const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDownQCShew\raw\QC_ShewIntact_2ug_3k_CID_4Apr14_Bane_PL011402_N30_C30.tsv";
//var tsvReader = new TsvFileParser(resultFilePath);
//var scanNums = tsvReader.GetData("ScanNum");
//var charges = tsvReader.GetData("Charge");
//var scores = tsvReader.GetData("Score");
//var sequences = tsvReader.GetData("Sequence");
var aaSet = new AminoAcidSet();
var seqSet = new HashSet <string>();
var allSeqSet = new HashSet <string>();
var numUnfilteredSpecs = 0;
var totalSpecs = 0;
for (var i = 0; i < scores.Count; i++)
{
var score = Convert.ToDouble(scores[i]);
if (score > 1E-4)
{
continue;
}
//if (score < 10) continue;
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var sequence = SimpleStringProcessing.GetStringBetweenDots(sequences[i]);
if (sequence == null || sequence.Contains("("))
{
continue;
}
//var sequence = sequences[i];
var composition = aaSet.GetComposition(sequence) + Composition.H2O;
var precursorIon = new Ion(composition, charge);
var isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid)
{
continue;
}
++totalSpecs;
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var corr1 = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var corr2 = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
if (corr3 == 1)
{
numUnfilteredSpecs++;
seqSet.Add(sequences[i]);
}
allSeqSet.Add(sequences[i]);
var corrMax = new[] { corr1, corr2, corr3 }.Max();
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}", scanNum, precursorScanNum, corr1, nextScanNum, corr2, corr3, corrMax);
}
Console.WriteLine("TotalNumComparisons: {0}", numComparisons);
Console.WriteLine("AverageNumComparisons: {0:f2}", numComparisons / (double)(maxBinNum - minBinNum + 1));
Console.WriteLine("SuccessRate: {0:f2} {1} / {2}", numUnfilteredSpecs / (double)totalSpecs, numUnfilteredSpecs, totalSpecs);
Console.WriteLine("NumUniqueSequences: {0:f2}, {1} / {2}", seqSet.Count / (double)allSeqSet.Count, seqSet.Count, allSeqSet.Count);
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void FilteringEfficiency()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
const string rawFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(rawFilePath, 1.4826, 1.4826);
sw.Stop();
Console.WriteLine(@"Reading run: {0:f4} sec", sw.Elapsed.TotalSeconds);
const int minPrecursorCharge = 3;
const int maxPrecursorCharge = 30;
const int tolerancePpm = 10;
var tolerance = new Tolerance(tolerancePpm);
sw.Reset();
sw.Start();
//var ms1BasedFilter = new Ms1BasedFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm);
//
//var ms1BasedFilter = new Ms1IsotopeTopKFilter(run, minPrecursorCharge, maxPrecursorCharge, tolerancePpm, 20);
//var ms1BasedFilter = new ProductScorerBasedOnDeconvolutedSpectra(run,
// minPrecursorCharge, maxPrecursorCharge,
// 0, 0,
// 600.0, 1800.0, new Tolerance(tolerancePpm), null);
//ms1BasedFilter.CachePrecursorMatchesBinCentric();
var ms1BasedFilter = new Ms1IsotopeAndChargeCorrFilter(run, new Tolerance(10.0), minPrecursorCharge, maxPrecursorCharge, 3000, 50000, 0.5, 0.5, 0.5, 40);
//var ms1BasedFilter = new Ms1IsotopeCorrFilter(run, minPrecursorCharge, maxPrecursorCharge, 15, 0.5, 40);
sw.Stop();
Console.WriteLine(@"Ms1 filter: {0:f4} sec", sw.Elapsed.TotalSeconds);
ISequenceFilter ms1Filter = ms1BasedFilter;
sw.Reset();
sw.Start();
const double minProteinMass = 3000.0;
const double maxProteinMass = 30000.0;
var minBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(minProteinMass);
var maxBinNum = ProductScorerBasedOnDeconvolutedSpectra.GetBinNumber(maxProteinMass);
var numComparisons = 0L;
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
var mass = ProductScorerBasedOnDeconvolutedSpectra.GetMz(binNum);
numComparisons += ms1Filter.GetMatchingMs2ScanNums(mass).Count();
}
sw.Stop();
Console.WriteLine(@"Calculating #matches per bin: {0:f4} sec", sw.Elapsed.TotalSeconds);
const string resultFilePath = @"C:\cygwin\home\kims336\Data\TopDown\raw\SBEP_STM_001_02272012_Aragon_4PTMs.icresult";
if (!File.Exists(resultFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, resultFilePath);
}
var tsvReader = new TsvFileParser(resultFilePath);
var compositions = tsvReader.GetData("Composition");
var scanNums = tsvReader.GetData("ScanNum");
var charges = tsvReader.GetData("Charge");
var scores = tsvReader.GetData("Score");
var qvalues = tsvReader.GetData("QValue");
var sequences = tsvReader.GetData("Sequence");
var sequenceCount = new Dictionary <string, int>();
for (var i = 0; i < compositions.Count; i++)
{
if (qvalues != null)
{
var qValue = Convert.ToDouble(qvalues[i]);
if (qValue > 0.01)
{
continue;
}
}
else
{
var score = Convert.ToDouble(scores[i]);
if (score < 13)
{
continue;
}
}
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var composition = Composition.Parse(compositions[i]);
var precursorIon = new Ion(composition, charge);
var isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid)
{
continue;
}
var sequence = sequences[i];
if (sequenceCount.TryGetValue(sequence, out var count))
{
sequenceCount[sequence] = count + 1;
}
else
{
sequenceCount[sequence] = 1;
}
}
//var sequences = tsvReader.GetData("Annotation");
var seqSet = new HashSet <string>();
var allSeqSet = new HashSet <string>();
var numUnfilteredSpecs = 0;
var totalSpecs = 0;
for (var i = 0; i < compositions.Count; i++)
{
if (qvalues != null)
{
var qValue = Convert.ToDouble(qvalues[i]);
if (qValue > 0.01)
{
continue;
}
}
else
{
var score = Convert.ToDouble(scores[i]);
if (score < 13)
{
continue;
}
}
var scanNum = Convert.ToInt32(scanNums[i]);
var charge = Convert.ToInt32(charges[i]);
var composition = Composition.Parse(compositions[i]);
var precursorIon = new Ion(composition, charge);
var isValid = run.GetSpectrum(scanNum) is ProductSpectrum spec && spec.IsolationWindow.Contains(precursorIon.GetMostAbundantIsotopeMz());
if (!isValid)
{
continue;
}
++totalSpecs;
var precursorScanNum = run.GetPrecursorScanNum(scanNum);
var precursorSpec = run.GetSpectrum(precursorScanNum);
var corr1 = precursorSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var nextScanNum = run.GetNextScanNum(scanNum, 1);
var nextSpec = run.GetSpectrum(nextScanNum);
var corr2 = nextSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corr3 = ms1Filter.GetMatchingMs2ScanNums(composition.Mass).Contains(scanNum) ? 1 : 0;
if (corr3 == 1)
{
numUnfilteredSpecs++;
seqSet.Add(sequences[i]);
}
allSeqSet.Add(sequences[i]);
//var xic = run.GetFullPrecursorIonExtractedIonChromatogram(precursorIon.GetMostAbundantIsotopeMz(), tolerance);
////xic.Display();
//var apexScanNum = xic.GetNearestApexScanNum(run.GetPrecursorScanNum(scanNum), false);
//var apexSpec = run.GetSpectrum(apexScanNum);
//var corr3 = apexSpec.GetCorrScore(precursorIon, tolerance, 0.1);
var corrMax = new[] { corr1, corr2, corr3 }.Max();
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}", scanNum, precursorScanNum, corr1, nextScanNum, corr2, corr3, corrMax, sequenceCount[sequences[i]]);
}
Console.WriteLine("TotalNumComparisons: {0}", numComparisons);
Console.WriteLine("AverageNumComparisons: {0:f2}", numComparisons / (double)(maxBinNum - minBinNum + 1));
Console.WriteLine("SuccessRate: {0:f2} {1} / {2}", numUnfilteredSpecs / (double)totalSpecs, numUnfilteredSpecs, totalSpecs);
Console.WriteLine("NumUniqueSequences: {0:f2}, {1} / {2}", seqSet.Count / (double)allSeqSet.Count, seqSet.Count, allSeqSet.Count);
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
private void RunSearch(SortedSet<DatabaseSequenceSpectrumMatch>[] matches, FastaDatabase db, ISequenceFilter sequenceFilter, CancellationToken? cancellationToken = null, IProgress<ProgressData> progress = null)
{
var progData = new ProgressData(progress)
{
Status = "Searching for matches"
};
var sw = new Stopwatch();
long estimatedProteins;
var annotationsAndOffsets = GetAnnotationsAndOffsets(db, out estimatedProteins, cancellationToken);
Console.WriteLine(@"Estimated proteins: " + estimatedProteins);
var numProteins = 0;
var lastUpdate = DateTime.MinValue; // Force original update of 0%
sw.Reset();
sw.Start();
var pfeOptions = new ParallelOptions
{
MaxDegreeOfParallelism = MaxNumThreads,
CancellationToken = cancellationToken ?? CancellationToken.None
};
var maxNumNTermCleavages = SearchMode == InternalCleavageType.NoInternalCleavage ? MaxNumNTermCleavages : 0;
//foreach (var annotationAndOffset in annotationsAndOffsets)
Parallel.ForEach(annotationsAndOffsets, pfeOptions, annotationAndOffset =>
{
if (cancellationToken != null && cancellationToken.Value.IsCancellationRequested)
{
//return matches;
return;
}
SearchProgressReport(ref numProteins, ref lastUpdate, estimatedProteins, sw, progData);
SearchForMatches(annotationAndOffset, sequenceFilter, matches, maxNumNTermCleavages, db.IsDecoy, cancellationToken);
});
Console.WriteLine(@"Collected candidate matches: {0}", GetNumberOfMatches(matches));
progData.StatusInternal = string.Empty;
progData.Report(100.0);
}
private void SearchForMatches(AnnotationAndOffset annotationAndOffset,
ISequenceFilter sequenceFilter, SortedSet<DatabaseSequenceSpectrumMatch>[] matches, int maxNumNTermCleavages, bool isDecoy, CancellationToken? cancellationToken = null)
{
var pfeOptions = new ParallelOptions
{
MaxDegreeOfParallelism = MaxNumThreads,
CancellationToken = cancellationToken ?? CancellationToken.None
};
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
//var protein = db.GetProteinName(offset);
var protSequence = annotation.Substring(2, annotation.Length - 4);
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, AminoAcid.ProteinNTerm, protSequence,
AminoAcid.ProteinCTerm);
if (seqGraph == null) return; // No matches will be found without a sequence graph.
for (var numNTermCleavages = 0; numNTermCleavages <= maxNumNTermCleavages; numNTermCleavages++)
{
if (numNTermCleavages > 0) seqGraph.CleaveNTerm();
var numProteoforms = seqGraph.GetNumProteoformCompositions();
var modCombs = seqGraph.GetModificationCombinations();
for (var modIndex = 0; modIndex < numProteoforms; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
var sequenceMass = protCompositionWithH2O.Mass;
if (sequenceMass < MinSequenceMass || sequenceMass > MaxSequenceMass) continue;
var modCombinations = modCombs[modIndex];
var ms2ScanNums = this.ScanNumbers ?? sequenceFilter.GetMatchingMs2ScanNums(sequenceMass);
Parallel.ForEach(ms2ScanNums, pfeOptions, ms2ScanNum =>
{
if (ms2ScanNum > _ms2ScanNums.Last() || ms2ScanNum < _ms2ScanNums.First()) return;
var scorer = _ms2ScorerFactory2.GetMs2Scorer(ms2ScanNum);
var score = seqGraph.GetFragmentScore(scorer);
var isoTargetMz = _isolationWindowTargetMz[ms2ScanNum];
if (!(isoTargetMz > 0)) return;
var charge = (int)Math.Round(sequenceMass / (isoTargetMz - Constants.Proton));
var precursorIon = new Ion(protCompositionWithH2O, charge);
var sequence = protSequence.Substring(numNTermCleavages);
var pre = numNTermCleavages == 0 ? annotation[0] : annotation[numNTermCleavages + 1];
var post = annotation[annotation.Length - 1];
var prsm = new DatabaseSequenceSpectrumMatch(sequence, pre, post, ms2ScanNum, offset, numNTermCleavages,
modCombinations, precursorIon, score, isDecoy);
AddMatch(matches, ms2ScanNum, prsm);
});
}
}
}
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;
}
private SortedSet <DatabaseSequenceSpectrumMatch>[] RunSearch(IEnumerable <AnnotationAndOffset> annotationsAndOffsets, ISequenceFilter ms1Filter, bool isDecoy)
{
var sw = new Stopwatch();
var numPeptides = 0;
sw.Reset();
sw.Start();
var matches = new SortedSet <DatabaseSequenceSpectrumMatch> [_run.MaxLcScan + 1];
// TODO: N-term Met cleavage
foreach (var annotationAndOffset in annotationsAndOffsets)
{
++numPeptides;
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
if (numPeptides % 100000 == 0)
{
Console.Write(@"Processing {0}{1} peptides...", numPeptides,
numPeptides == 1 ? "st" : numPeptides == 2 ? "nd" : numPeptides == 3 ? "rd" : "th");
if (numPeptides != 0)
{
sw.Stop();
var sec = sw.ElapsedTicks / (double)Stopwatch.Frequency;
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sec);
sw.Reset();
sw.Start();
}
}
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, annotation);
if (seqGraph == null)
{
// Console.WriteLine("Ignoring illegal protein: {0}", annotation);
continue;
}
//var protCompositions = seqGraph.GetSequenceCompositions();
var numProteoforms = seqGraph.GetNumProteoformCompositions();
var modCombs = seqGraph.GetModificationCombinations();
for (var modIndex = 0; modIndex < numProteoforms; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
var sequenceMass = protCompositionWithH2O.Mass;
var modCombinations = modCombs[modIndex];
foreach (var ms2ScanNum in ms1Filter.GetMatchingMs2ScanNums(sequenceMass))
{
var spec = _run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null)
{
continue;
}
var charge =
(int)Math.Round(sequenceMass / (spec.IsolationWindow.IsolationWindowTargetMz - Constants.Proton));
var scorer = _ms2ScorerFactory.GetMs2Scorer(ms2ScanNum);
var score = seqGraph.GetFragmentScore(scorer);
if (score <= 2)
{
continue;
}
var precursorIon = new Ion(protCompositionWithH2O, charge);
var sequence = annotation.Substring(2, annotation.Length - 4);
var pre = annotation[0];
var post = annotation[annotation.Length - 1];
var prsm = new DatabaseSequenceSpectrumMatch(sequence, pre, post, ms2ScanNum, offset, 0, modCombinations,
precursorIon, score, isDecoy);
if (matches[ms2ScanNum] == null)
{
matches[ms2ScanNum] = new SortedSet <DatabaseSequenceSpectrumMatch> {
prsm
};
}
else // already exists
{
var existingMatches = matches[ms2ScanNum];
if (existingMatches.Count < NumMatchesPerSpectrum)
{
existingMatches.Add(prsm);
}
else
{
var minScore = existingMatches.Min.Score;
if (score > minScore)
{
existingMatches.Add(prsm);
existingMatches.Remove(existingMatches.Min);
}
}
}
}
}
}
return(matches);
}
/// <summary>
/// <see cref="ISequenceFilter{T, TContext}"/> をフィルターパイプラインに追加します。
/// </summary>
/// <typeparam name="T">フィルター処理の対象となる要素の型。</typeparam>
/// <typeparam name="TContext">フィルター処理のコンテキストを表す型。</typeparam>
/// <param name="pipeline"><see cref="IPipelineBuilder{T, TContext}"/> インスタンス。常に非 <c>null</c>。</param>
/// <param name="filter"><typeparamref name="T"/> のシーケンスをフィルター処理する <see cref="ISequenceFilter{T, TContext}"/> インスタンス。常に非 <c>null</c>。</param>
/// <returns>自身の <see cref="IPipelineBuilder{T, TContext}"/> インスタンス。常に非 <c>null</c>。</returns>
public static IPipelineBuilder <T, TContext> Add <T, TContext>(this IPipelineBuilder <T, TContext> pipeline, ISequenceFilter <T, TContext> filter)
{
Debug.Assert(pipeline != null);
Debug.Assert(filter != null);
return(pipeline.Add(filter.ExecuteAsync));
}
private void SearchForMatches(AnnotationAndOffset annotationAndOffset,
ISequenceFilter sequenceFilter, SortedSet <DatabaseSequenceSpectrumMatch>[] matches, int maxNumNTermCleavages, bool isDecoy, CancellationToken?cancellationToken = null)
{
var pfeOptions = new ParallelOptions
{
MaxDegreeOfParallelism = MaxNumThreads,
CancellationToken = cancellationToken ?? CancellationToken.None
};
var annotation = annotationAndOffset.Annotation;
var offset = annotationAndOffset.Offset;
//var protein = db.GetProteinName(offset);
var protSequence = annotation.Substring(2, annotation.Length - 4);
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, AminoAcid.ProteinNTerm, protSequence,
AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return; // No matches will be found without a sequence graph.
}
for (var numNTermCleavages = 0; numNTermCleavages <= maxNumNTermCleavages; numNTermCleavages++)
{
if (numNTermCleavages > 0)
{
seqGraph.CleaveNTerm();
}
var numProteoforms = seqGraph.GetNumProteoformCompositions();
var modCombs = seqGraph.GetModificationCombinations();
for (var modIndex = 0; modIndex < numProteoforms; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
var sequenceMass = protCompositionWithH2O.Mass;
if (sequenceMass < MinSequenceMass || sequenceMass > MaxSequenceMass)
{
continue;
}
var modCombinations = modCombs[modIndex];
var ms2ScanNums = this.ScanNumbers ?? sequenceFilter.GetMatchingMs2ScanNums(sequenceMass);
Parallel.ForEach(ms2ScanNums, pfeOptions, ms2ScanNum =>
{
if (ms2ScanNum > _ms2ScanNums.Last() || ms2ScanNum < _ms2ScanNums.First())
{
return;
}
var scorer = _ms2ScorerFactory2.GetMs2Scorer(ms2ScanNum);
var score = seqGraph.GetFragmentScore(scorer);
var isoTargetMz = _isolationWindowTargetMz[ms2ScanNum];
if (!(isoTargetMz > 0))
{
return;
}
var charge = (int)Math.Round(sequenceMass / (isoTargetMz - Constants.Proton));
var precursorIon = new Ion(protCompositionWithH2O, charge);
var sequence = protSequence.Substring(numNTermCleavages);
var pre = numNTermCleavages == 0 ? annotation[0] : annotation[numNTermCleavages + 1];
var post = annotation[annotation.Length - 1];
var prsm = new DatabaseSequenceSpectrumMatch(sequence, pre, post, ms2ScanNum, offset, numNTermCleavages,
modCombinations, precursorIon, score, isDecoy);
AddMatch(matches, ms2ScanNum, prsm);
});
}
}
}
private void RunSearch(SortedSet <DatabaseSequenceSpectrumMatch>[] matches, FastaDatabase db, ISequenceFilter sequenceFilter, CancellationToken?cancellationToken = null, IProgress <ProgressData> progress = null)
{
var progData = new ProgressData(progress)
{
Status = "Searching for matches"
};
var sw = new Stopwatch();
long estimatedProteins;
var annotationsAndOffsets = GetAnnotationsAndOffsets(db, out estimatedProteins, cancellationToken);
Console.WriteLine(@"Estimated proteins: " + estimatedProteins);
var numProteins = 0;
var lastUpdate = DateTime.MinValue; // Force original update of 0%
sw.Reset();
sw.Start();
var pfeOptions = new ParallelOptions
{
MaxDegreeOfParallelism = MaxNumThreads,
CancellationToken = cancellationToken ?? CancellationToken.None
};
var maxNumNTermCleavages = SearchMode == InternalCleavageType.NoInternalCleavage ? MaxNumNTermCleavages : 0;
//foreach (var annotationAndOffset in annotationsAndOffsets)
Parallel.ForEach(annotationsAndOffsets, pfeOptions, annotationAndOffset =>
{
if (cancellationToken != null && cancellationToken.Value.IsCancellationRequested)
{
//return matches;
return;
}
SearchProgressReport(ref numProteins, ref lastUpdate, estimatedProteins, sw, progData);
SearchForMatches(annotationAndOffset, sequenceFilter, matches, maxNumNTermCleavages, db.IsDecoy, cancellationToken);
});
Console.WriteLine(@"Collected candidate matches: {0}", GetNumberOfMatches(matches));
progData.StatusInternal = string.Empty;
progData.Report(100.0);
}
