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 void TestFloatBinning() { var methodName = MethodBase.GetCurrentMethod().Name; ShowStarting(methodName); const double minMass = 200; const double maxMass = 50000; const int numBits = 29; var comparer = new MzComparerWithBinning(numBits); Console.WriteLine(comparer.GetBinNumber(maxMass)); Console.WriteLine(comparer.GetBinNumber(maxMass) - comparer.GetBinNumber(minMass) + 1); Console.WriteLine(LcMsMatchMap.GetBinNumber(maxMass) - LcMsMatchMap.GetBinNumber(minMass) + 1); }
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 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); }