예제 #1
0
        public MsDeconvFilter(LcMsRun run, Tolerance massTolerance, string msDeconvFileName)
        {
            _run           = run;
            _massTolerance = massTolerance;
            _lcMsMatchMap  = new LcMsMatchMap();

            Read(msDeconvFileName);
        }
예제 #2
0
        public IsosFilter(LcMsRun run, Tolerance massTolerance, string isosFileName, double fitScoreThreshold = 1.0)
        {
            _run               = run;
            _massTolerance     = massTolerance;
            _fitScoreThreshold = fitScoreThreshold;
            _lcMsMatchMap      = new LcMsMatchMap();

            Read(isosFileName);
        }
예제 #3
0
        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);
 }
예제 #5
0
 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);
 }