public string GenerateFilterReportString(ParameterOptimizationResult selectedResult)
{
if (selectedResult == null) return string.Empty;
StringBuilder sb = new StringBuilder();
sb.Append("Labeled fit <= " + selectedResult.FitScoreLabelled.ToString("0.####"));
sb.Append(Environment.NewLine);
sb.Append("IScore <= " + selectedResult.Iscore.ToString("0.####"));
sb.Append(Environment.NewLine);
sb.Append("SumOfRatios >= " + selectedResult.SumOfRatios.ToString("0.#"));
sb.Append(Environment.NewLine);
sb.Append("ContigScore >= " + selectedResult.ContigScore.ToString("0"));
sb.Append(Environment.NewLine);
sb.Append("PercentIncorp >= " + selectedResult.PercentIncorp.ToString("0.####"));
sb.Append(Environment.NewLine);
sb.Append("PercentPeptide >= " + selectedResult.PercentPeptidePopulation.ToString("0.##"));
sb.Append(Environment.NewLine);
sb.Append("Num unlabeled results at this filter= " + selectedResult.NumUnlabelledPassingFilter);
sb.Append(Environment.NewLine);
sb.Append("Num labeled results at this filter= " + selectedResult.NumLabeledPassingFilter);
sb.Append(Environment.NewLine);
sb.Append("False positive rate = " + selectedResult.FalsePositiveRate.ToString("0.###"));
return sb.ToString();
}
public List<ParameterOptimizationResult> DoCalculationsOnAllFilterCombinations(string outputFileName = null)
{
bool isHeaderWritten = false;
if (!string.IsNullOrEmpty(outputFileName) && File.Exists(outputFileName)) File.Delete(outputFileName);
var parameterOptimizationResults = new List<ParameterOptimizationResult>();
int numCombinations = GetNumCombinations();
IqLogger.Log.Info("Filter optimizer - num combinations to analyze = "+ numCombinations);
StringBuilder sb = new StringBuilder();
int comboCounter = 0;
for (double fitScoreLabelled = LabelFitLower; fitScoreLabelled < LabelFitUpper; fitScoreLabelled = fitScoreLabelled + LabelFitStep)
{
sb.Clear();
var levelOneC13Filter = (from n in LabeledResults
where n.FitScoreLabeledProfile <= fitScoreLabelled
select n).ToList();
var levelOneC12Filter = (from n in UnlabeledResults
where n.FitScoreLabeledProfile <= fitScoreLabelled
select n).ToList();
IqLogger.Log.Info("Current filter combo: " + comboCounter +" out of " + numCombinations);
for (double area = SumOfRatiosLower; area < SumOfRatiosUpper; area = area + SumOfRatiosStep)
{
var levelTwoC13Filter = (from n in levelOneC13Filter
where n.AreaUnderRatioCurveRevised >= area
select n).ToList();
var levelTwoC12Filter = (from n in levelOneC12Filter
where n.AreaUnderRatioCurveRevised >= area
select n).ToList();
for (double iscore = IscoreLower; iscore < IscoreUpper; iscore = iscore + IscoreStep)
{
var levelThreeC13Filter = (from n in levelTwoC13Filter
where n.IScore <= iscore
select n).ToList();
var levelThreeC12Filter = (from n in levelTwoC12Filter
where n.IScore <= iscore
select n).ToList();
for (int contigScore = ContigScoreLower; contigScore <= ContigScoreUpper; contigScore = contigScore + ContigScoreStep)
{
for (double percentIncorp = PercentIncorpLower; percentIncorp < PercentIncorpUpper; percentIncorp = percentIncorp + PercentIncorpStep)
{
for (double peptidePop = PercentPeptidePopulationLower; peptidePop < PercentPeptidePopulationUpper; peptidePop = peptidePop + PercentPeptidePopulationStep)
{
var c13filteredResults = (from n in levelThreeC13Filter
where n.ContiguousnessScore >= contigScore
&& n.PercentCarbonsLabelled >= percentIncorp
&& n.PercentPeptideLabelled >= peptidePop
select n).ToList();
var c12filteredResults = (from n in levelThreeC12Filter
where n.ContiguousnessScore >= contigScore
&& n.PercentCarbonsLabelled >= percentIncorp
&& n.PercentPeptideLabelled >= peptidePop
select n).ToList();
ParameterOptimizationResult optimizationResult = new ParameterOptimizationResult();
optimizationResult.FitScoreLabelled = fitScoreLabelled;
optimizationResult.SumOfRatios = area;
optimizationResult.Iscore = iscore;
optimizationResult.ContigScore = contigScore;
optimizationResult.PercentIncorp = percentIncorp;
optimizationResult.PercentPeptidePopulation = peptidePop;
optimizationResult.NumLabeledPassingFilter = c13filteredResults.Count;
optimizationResult.NumUnlabelledPassingFilter = c12filteredResults.Count;
sb.Append(optimizationResult.ToStringWithDetails());
sb.Append(Environment.NewLine);
parameterOptimizationResults.Add(optimizationResult);
comboCounter++;
}
}
}
}
}
if (!string.IsNullOrEmpty(outputFileName))
{
using (var sw = new StreamWriter(new FileStream(outputFileName, FileMode.Append, FileAccess.Write, FileShare.Read)))
{
sw.AutoFlush = true;
if (!isHeaderWritten)
{
sw.WriteLine("LabeledFit\tSumOfRatios\tIscore\tContigScore\tPercentIncorp\tPercentPeptideLabeled\tUnlabeledCount\tLabeledCount\tFalsePositiveRate");
}
sw.Write(sb.ToString());
}
}
}
return parameterOptimizationResults;
}
