/// <summary>
/// Calculate scores for targets and decoys. A transition is selected from each transition group using the
/// scoring weights, and then its score is calculated using the calculator weights applied to each feature.
/// </summary>
/// <param name="scoringParams">Parameters to choose the best peak</param>
/// <param name="calculatorParams">Parameters to calculate the score of the best peak.</param>
/// <param name="targetScores">Output list of target scores.</param>
/// <param name="decoyScores">Output list of decoy scores.</param>
/// <param name="secondBestScores">Output list of false target scores.</param>
/// <param name="invert">If true, select minimum rather than maximum scores</param>
public void GetScores(LinearModelParams scoringParams, LinearModelParams calculatorParams, out List <double> targetScores, out List <double> decoyScores,
out List <double> secondBestScores, bool invert = false)
{
targetScores = new List <double>();
decoyScores = new List <double>();
secondBestScores = new List <double>();
int invertSign = invert ? -1 : 1;
foreach (var peakTransitionGroupFeatures in _peakTransitionGroupFeaturesList)
{
PeakGroupFeatures maxFeatures = null;
PeakGroupFeatures nextFeatures = null;
double maxScore = Double.MinValue;
double nextScore = Double.MinValue;
// No peaks in this transition group record
if (peakTransitionGroupFeatures.PeakGroupFeatures.Count == 0)
{
continue;
}
// Find the highest and second highest scores among the transitions in this group.
foreach (var peakGroupFeatures in peakTransitionGroupFeatures.PeakGroupFeatures)
{
double score = invertSign * GetScore(scoringParams, peakGroupFeatures);
if (nextScore < score)
{
if (maxScore < score)
{
nextScore = maxScore;
maxScore = score;
nextFeatures = maxFeatures;
maxFeatures = peakGroupFeatures;
}
else
{
nextScore = score;
nextFeatures = peakGroupFeatures;
}
}
}
double currentScore = maxFeatures == null ? Double.NaN : GetScore(calculatorParams, maxFeatures);
if (peakTransitionGroupFeatures.Id.NodePep.IsDecoy)
{
decoyScores.Add(currentScore);
}
else
{
targetScores.Add(currentScore);
// Skip if only one peak
if (peakTransitionGroupFeatures.PeakGroupFeatures.Count == 1)
{
continue;
}
double secondBestScore = nextFeatures == null ? Double.NaN : GetScore(calculatorParams, nextFeatures);
secondBestScores.Add(secondBestScore);
}
}
}
private static double GetScore(LinearModelParams parameters, PeakGroupFeatures peakGroupFeatures)
{
return(GetScore(parameters.Weights, peakGroupFeatures, parameters.Bias));
}
/// <summary>
/// Calculate the score of a set of features given an array of weighting coefficients.
/// </summary>
private static double GetScore(IList <double> weights, PeakGroupFeatures peakGroupFeatures, double bias)
{
return(LinearModelParams.Score(peakGroupFeatures.Features, weights, bias));
}