public OptimalResult(OptimalResult source)
{
this._score = source._score;
this._deltaScore = source._deltaScore;
this._peptideCountFromTargetDB = source._peptideCountFromTargetDB;
this._peptideCountFromDecoyDB = source._peptideCountFromDecoyDB;
this._falseDiscoveryRate = source._falseDiscoveryRate;
}
public string OptimalResultToString(OptimalResult or)
{
if (null == or)
{
return("-\t0\t0\t0");
}
else
{
return(MyConvert.Format("{0:0.####}\t{1}\t{2}\t{3:0.####}", or.Score, or.PeptideCountFromTargetDB, or.PeptideCountFromDecoyDB, or.FalseDiscoveryRate));
}
}
private List <IIdentifiedSpectrum> DoCalculateDuplicated(List <IIdentifiedSpectrum> preFiltered, OptimalResult optimalResult)
{
preFiltered.ForEach(m => m.QValue = -1);
ScoreFunc.SortSpectrum(preFiltered);
//Use top score spectra for Qvalue calculation
var topSpectra = new List <IIdentifiedSpectrum>(preFiltered);
IdentifiedSpectrumUtils.KeepTopPeptideFromSameEngineDifferentParameters(topSpectra, ScoreFunc);
//计算QValue。
QValueFunc(topSpectra, ScoreFunc, FdrCalc);
//将非top的肽段的QValue填充。
for (int i = 1; i < preFiltered.Count; i++)
{
if (preFiltered[i].QValue == -1)
{
preFiltered[i].QValue = preFiltered[i - 1].QValue;
}
}
List <IIdentifiedSpectrum> result = new List <IIdentifiedSpectrum>();
optimalResult.PeptideCountFromDecoyDB = 0;
optimalResult.PeptideCountFromTargetDB = 0;
for (int i = preFiltered.Count - 1; i >= 0; i--)
{
if (preFiltered[i].QValue <= FdrValue)
{
result.AddRange(preFiltered.GetRange(0, i + 1));
optimalResult.Score = ScoreFunc.GetScore(preFiltered[i]);
optimalResult.ExpectValue = preFiltered[i].ExpectValue;
optimalResult.FalseDiscoveryRate = preFiltered[i].QValue;
int decoyCount = 0;
int targetCount = 0;
HashSet <string> filenames = new HashSet <string>();
foreach (IIdentifiedSpectrum spectrum in result)
{
if (filenames.Contains(spectrum.Query.FileScan.LongFileName))
{
continue;
}
filenames.Add(spectrum.Query.FileScan.LongFileName);
if (spectrum.FromDecoy)
{
decoyCount++;
}
else
{
targetCount++;
}
}
optimalResult.PeptideCountFromDecoyDB = decoyCount;
optimalResult.PeptideCountFromTargetDB = targetCount;
Console.WriteLine("{0} -> {1} ==> {2} / {3}", preFiltered.Count, topSpectra.Count, decoyCount, targetCount);
break;
}
}
return(result);
}
public virtual List <IIdentifiedSpectrum> Calculate(List <IIdentifiedSpectrum> preFiltered, OptimalResult optimalResult, bool hasDuplicatedSpectrum)
{
if (hasDuplicatedSpectrum)
{
return(DoCalculateDuplicated(preFiltered, optimalResult));
}
else
{
return(DoCalculateNoDuplicated(preFiltered, optimalResult));
}
}
private List <IIdentifiedSpectrum> DoCalculateNoDuplicated(List <IIdentifiedSpectrum> preFiltered, OptimalResult optimalResult)
{
QValueFunc(preFiltered, ScoreFunc, FdrCalc);
List <IIdentifiedSpectrum> result = new List <IIdentifiedSpectrum>();
optimalResult.PeptideCountFromDecoyDB = 0;
optimalResult.PeptideCountFromTargetDB = 0;
for (int i = preFiltered.Count - 1; i >= 0; i--)
{
if (preFiltered[i].QValue <= FdrValue)
{
result.AddRange(preFiltered.GetRange(0, i + 1));
optimalResult.Score = ScoreFunc.GetScore(preFiltered[i]);
optimalResult.ExpectValue = preFiltered[i].ExpectValue;
optimalResult.FalseDiscoveryRate = preFiltered[i].QValue;
int decoyCount = 0;
int targetCount = 0;
foreach (IIdentifiedSpectrum spectrum in result)
{
if (spectrum.FromDecoy)
{
decoyCount++;
}
else
{
targetCount++;
}
}
optimalResult.PeptideCountFromDecoyDB = decoyCount;
optimalResult.PeptideCountFromTargetDB = targetCount;
Console.WriteLine("{0} / {1} ==> {2} / {3}", preFiltered.Count(m => m.FromDecoy), preFiltered.Count(m => !m.FromDecoy), decoyCount, targetCount);
break;
}
}
return(result);
}
public double Calculate(OptimalResult or)
{
return(Calculate(or.PeptideCountFromDecoyDB, or.PeptideCountFromTargetDB));
}
