public static void DoFilterPeptideFromSameEngineDifferentParameters(List <IIdentifiedSpectrum> peptides, IScoreFunction score, Action <List <IIdentifiedSpectrum> > filter)
{
var dic = peptides.ToGroupDictionary(m => m.Query.FileScan.Experimental);
bool changed = false;
foreach (var v in dic.Values)
{
var vdic = v.ToGroupDictionary(m => m.Query.FileScan.FirstScan);
bool currentChanged = false;
foreach (var peps in vdic.Values)
{
if (peps.Count > 1)
{
score.SortSpectrum(peps);
filter(peps);
currentChanged = true;
}
}
if (currentChanged)
{
changed = true;
v.Clear();
foreach (var peps in vdic.Values)
{
v.AddRange(peps);
}
}
}
if (changed)
{
peptides.Clear();
foreach (var v in dic.Values)
{
peptides.AddRange(v);
}
}
}
public void CalculateToleranceScore(IScoreFunction scoreFunc)
{
scoreFunc.SortSpectrum(this.Spectra);
this.Result.Score = this.Spectra.Count > 0 ? scoreFunc.GetScore(this.Spectra.Last()) : 0.0;
}
public static void CalculateUniqueQValue(List <IIdentifiedSpectrum> peptides, IScoreFunction scoreFuncs, IFalseDiscoveryRateCalculator fdrCalc)
{
if (peptides.Count == 0)
{
return;
}
scoreFuncs.SortSpectrum(peptides);
List <IIdentifiedSpectrum> sameScores = new List <IIdentifiedSpectrum>();
HashSet <string> targetSeq = new HashSet <string>();
HashSet <string> decoySeq = new HashSet <string>();
double lastScore = scoreFuncs.GetScore(peptides[0]);
for (int i = 0; i < peptides.Count; i++)
{
IIdentifiedSpectrum spectrum = peptides[i];
double score = scoreFuncs.GetScore(peptides[i]);
if (score == lastScore)
{
sameScores.Add(spectrum);
if (spectrum.FromDecoy)
{
decoySeq.Add(spectrum.Peptide.PureSequence);
}
else
{
targetSeq.Add(spectrum.Peptide.PureSequence);
}
continue;
}
else
{
double qValue = fdrCalc.Calculate(decoySeq.Count, targetSeq.Count);
foreach (IIdentifiedSpectrum sameScoreSpectrum in sameScores)
{
sameScoreSpectrum.QValue = qValue;
}
sameScores.Clear();
lastScore = score;
sameScores.Add(spectrum);
if (spectrum.FromDecoy)
{
decoySeq.Add(spectrum.Peptide.PureSequence);
}
else
{
targetSeq.Add(spectrum.Peptide.PureSequence);
}
continue;
}
}
double lastQValue = fdrCalc.Calculate(decoySeq.Count, targetSeq.Count);
foreach (IIdentifiedSpectrum sameScoreSpectrum in sameScores)
{
sameScoreSpectrum.QValue = lastQValue;
}
}
/// <summary>
/// 根据给定分数排序函数以及FDR计算器对鉴定谱图列表计算QValue。
/// </summary>
/// <param name="peptides">谱图列表</param>
/// <param name="scoreFuncs">与分数提取、排序相关类</param>
/// <param name="fdrCalc">FDR计算器</param>
public static void CalculateQValue(List <IIdentifiedSpectrum> peptides, IScoreFunction scoreFuncs, IFalseDiscoveryRateCalculator fdrCalc)
{
if (peptides.Count == 0)
{
return;
}
scoreFuncs.SortSpectrum(peptides);
int totalTarget = 0;
int totalDecoy = 0;
HashSet <string> filenames = new HashSet <string>();
foreach (IIdentifiedSpectrum spectrum in peptides)
{
spectrum.QValue = 0.0;
if (filenames.Contains(spectrum.Query.FileScan.LongFileName))
{
continue;
}
filenames.Add(spectrum.Query.FileScan.LongFileName);
if (spectrum.FromDecoy)
{
totalDecoy++;
}
else
{
totalTarget++;
}
}
double lastScore = scoreFuncs.GetScore(peptides[peptides.Count - 1]);
double lastQvalue = fdrCalc.Calculate(totalDecoy, totalTarget);
for (int i = peptides.Count - 1; i >= 0; i--)
{
double score = scoreFuncs.GetScore(peptides[i]);
if (score != lastScore)
{
lastScore = score;
lastQvalue = fdrCalc.Calculate(totalDecoy, totalTarget);
if (lastQvalue == 0.0)
{
break;
}
peptides[i].QValue = lastQvalue;
}
else
{
peptides[i].QValue = lastQvalue;
}
if (peptides[i].FromDecoy)
{
totalDecoy--;
}
else
{
totalTarget--;
}
}
}
