public InformedProteomicsAnalysis( InMemoryLcMsRun run, IEnumerable<string> peptideEnumerator, AminoAcidSet aminoAcidSet): this(run, peptideEnumerator, aminoAcidSet, 1, 3) { }
public void Train(string outFileName, InMemoryLcMsRun run, Tolerance tolerance, string annotationFileName) { // charge, scan number, protein _run = run; _tolerance = tolerance; var target = new Dictionary<int, Dictionary<int, Composition>>(); var decoy = new Dictionary<int, Dictionary<int, Composition>>(); _missingXicCounterTarget = new Dictionary<int, int>(); _missingXicCounterDecoy = new Dictionary<int, int>(); _xicCorrScoreCounterTarget = new Dictionary<int, Dictionary<int, int>>(); _xicCorrScoreCounterDecoy = new Dictionary<int, Dictionary<int, int>>(); }
public InformedProteomicsAnalysis( InMemoryLcMsRun run, IEnumerable<string> peptideEnumerator, AminoAcidSet aminoAcidSet, int minCharge, int maxCharge) { Run = run; PeptideEnumerator = peptideEnumerator; AminoAcidSet = aminoAcidSet; MinCharge = minCharge; MaxCharge = maxCharge; }
public Ms1IsotopeMostAbundantPlusOneFilter( InMemoryLcMsRun run, int minCharge = 3, int maxCharge = 30, double ppmTolerance = 10, double minMass = 3000.0, double maxMass = 50000.0, int maxNumPeaksToConsider = 40) { _run = run; _minCharge = minCharge; _maxCharge = maxCharge; MaxNumPeaksToConsider = maxNumPeaksToConsider; _tolerance = new Tolerance(ppmTolerance); _comparer = new MzComparerWithTolerance(ppmTolerance); _lcMsMatchMap = new LcMsMatchMap(); PrecomputePossibleSequenceMasses(); _lcMsMatchMap.CreateSequenceMassToMs2ScansMap(_run, _tolerance, minMass, maxMass); }
public void WriteAsPbf(InMemoryLcMsRun imlr, BinaryWriter writer, IProgress <ProgressData> progress = null) { PbfLcMsRun.WriteAsPbf(this, writer, progress); }
public void WriteAsPbf(InMemoryLcMsRun imlr, BinaryWriter writer, IProgress<ProgressData> progress = null) { PbfLcMsRun.WriteAsPbf(this, writer, progress); }