private double ComputeProbability(TracerFormulaEnumerator tracerFormulaEnumerator, TracerPercentFormula tracerPercents)
{
var tracerFormula = tracerFormulaEnumerator.Current;
var tracerSymbolCounts = tracerFormulaEnumerator.GetTracerSymbolCounts();
var traceePercents = tracerSymbolCounts.Keys.ToDictionary(s => s, s => 1.0);
var result = 1.0;
foreach (var tracerDef in _tracerDefs.Values)
{
int tracerTraceeCount = tracerSymbolCounts[tracerDef.TraceeSymbol];
int tracerCount = tracerFormula.GetElementCount(tracerDef.Name);
double probability = Math.Pow(tracerPercents.GetElementCount(tracerDef.Name) / 100, tracerCount)
* Choose(tracerTraceeCount, tracerCount);
result *= probability;
tracerSymbolCounts[tracerDef.TraceeSymbol] = tracerTraceeCount - tracerCount;
traceePercents[tracerDef.TraceeSymbol] = traceePercents[tracerDef.TraceeSymbol] -
tracerPercents.GetElementCount(tracerDef.Name) / 100;
}
foreach (var entry in tracerSymbolCounts)
{
result *= Math.Pow(traceePercents[entry.Key], entry.Value);
}
return(result);
}
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 Dictionary <TracerFormula, double> GetDistribution(TracerPercentFormula tracerPercents)
{
var tracerFormulaEnumerator = new TracerFormulaEnumerator(Sequence, _tracerDefs.Values);
var result = new Dictionary <TracerFormula, double>();
while (tracerFormulaEnumerator.MoveNext())
{
result.Add(tracerFormulaEnumerator.Current, ComputeProbability(tracerFormulaEnumerator, tracerPercents));
}
return(result);
}
private List <MzRange> GetMasses()
{
var massesAndFrequency = new Dictionary <double, double>();
var tracerFormulaEnumerator = new TracerFormulaEnumerator(Sequence, _tracerDefs.Values);
while (tracerFormulaEnumerator.MoveNext())
{
MassDistribution massDistribution = _aminoAcidFormulas.GetMassDistribution(
MoleculeFromTracerFormula(tracerFormulaEnumerator.Current), 0);
massDistribution = massDistribution.OffsetAndDivide(_aminoAcidFormulas.GetMassShift(Sequence), 1);
foreach (var entry in massDistribution)
{
if (entry.Value < MinAbundance)
{
continue;
}
double currentAbundance;
massesAndFrequency.TryGetValue(entry.Key, out currentAbundance);
if (currentAbundance >= entry.Value)
{
continue;
}
massesAndFrequency[entry.Key] = entry.Value;
}
}
var allMasses = new List <double>(massesAndFrequency.Keys);
allMasses.Sort();
var result = new List <MzRange>();
foreach (var mass in allMasses)
{
if (result.Count == 0)
{
result.Add(new MzRange(mass));
continue;
}
var lastMass = result[result.Count - 1];
if (lastMass.Distance(mass) > MassResolution)
{
result.Add(new MzRange(mass));
continue;
}
result[result.Count - 1] = lastMass.Union(mass);
}
return(result);
}
