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);
}
