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);
}
