public TurnoverCalculator(Workspace workspace, String sequence)
{
Sequence = sequence;
_errOnSideOfLowerAbundance = workspace.GetErrOnSideOfLowerAbundance();
_aminoAcidFormulas = workspace.GetAminoAcidFormulasWithTracers();
_tracerDefs = new Dictionary <String, TracerDef>();
_traceeSymbols = new HashSet <String>();
foreach (var tracerDef in workspace.GetTracerDefs())
{
if (!_traceeSymbols.Contains(tracerDef.TraceeSymbol))
{
if (tracerDef.GetMaximumTracerCount(sequence) == 0)
{
continue;
}
_traceeSymbols.Add(tracerDef.TraceeSymbol);
}
_tracerDefs.Add(tracerDef.Name, tracerDef);
}
_maxTracerCount = workspace.GetMaxTracerCount(sequence);
_masses = new ReadOnlyCollection <MzRange>(GetMasses());
var tracerFormulae = new List <TracerFormula>();
_tracerFormulaIndexes = new Dictionary <TracerFormula, int>();
var enumerator = new TracerFormulaEnumerator(Sequence, _tracerDefs.Values);
while (enumerator.MoveNext())
{
_tracerFormulaIndexes.Add(enumerator.Current, tracerFormulae.Count);
tracerFormulae.Add(enumerator.Current);
}
_tracerFormulae = ImmutableList.ValueOf(tracerFormulae);
}
public AminoAcidFormulas AddTracerToAminoAcidFormulas(AminoAcidFormulas aminoAcidFormulas)
{
if (AminoAcidSymbol.HasValue)
{
aminoAcidFormulas = aminoAcidFormulas.SetIsotopeAbundances(
aminoAcidFormulas.IsotopeAbundances.SetAbundances(TraceeSymbol, TraceeMasses));
aminoAcidFormulas = aminoAcidFormulas.SetFormula(AminoAcidSymbol.Value, TraceeSymbol);
}
aminoAcidFormulas = aminoAcidFormulas.SetIsotopeAbundances(
aminoAcidFormulas.IsotopeAbundances.SetAbundances(Name, TracerMasses));
return(aminoAcidFormulas);
}
public AminoAcidFormulas GetAminoAcidFormulas()
{
if (_aminoAcidFormulas != null)
{
return(_aminoAcidFormulas);
}
var massShifts = new Dictionary <char, double>();
foreach (var modification in Modifications)
{
massShifts[modification.Key[0]] = modification.Value;
}
return(_aminoAcidFormulas = AminoAcidFormulas.Default.SetMassShifts(massShifts));
}
public MassDistribution GetMassDistribution(AminoAcidFormulas aminoAcidFormulas)
{
return(aminoAcidFormulas.GetMassDistribution(Sequence, Charge));
}
public double GetMonoisotopicMass(AminoAcidFormulas aminoAcidFormulas)
{
return(AminoAcidFormulas.ProtonMass + aminoAcidFormulas.GetMonoisotopicMass(Sequence) / Charge);
}
