/// <summary>
/// Get the scores of the nodes in the GeneratingFunction scoring graph.
/// </summary>
/// <param name="scorer">The FLIP scoring model to use.</param>
/// <param name="proteinMass">The precursor mass.</param>
private double?[][] InitNodeScores(FlipScorer <DeconvolutedSpectrum> scorer, double proteinMass)
{
var numNodes = this.massBins.GetBinNumber(proteinMass) + 1;
var nodeScores = new double?[2][];
var nTerminalFragScores = nodeScores[0] = new double?[numNodes];
var cTerminalFragScores = nodeScores[1] = new double?[numNodes];
var deconvPeaks = (DeconvolutedPeak[])scorer.ProductSpectrum.Peaks;
// transform all peaks into being nterminal ions
foreach (var peak in deconvPeaks)
{
foreach (var ionType in scorer.SelectedIonTypes)
{
var scores = ionType.IsPrefix ? nTerminalFragScores : cTerminalFragScores;
double ionMass = peak.Mass;
double fragmentMass = ionMass - ionType.OffsetComposition.Mass;
var binMass = ionType.IsPrefix ? fragmentMass : proteinMass - fragmentMass;
var binIndex = this.massBins.GetBinNumber(binMass);
if (binIndex >= 0 && binIndex < numNodes)
{
var score = scorer.GetFragmentScore(peak, ionType); // Error score will come from the edge weight
if (scores[binIndex] == null || score >= scores[binIndex])
{
scores[binIndex] = score;
}
}
}
}
return(nodeScores);
}
/// <summary>
/// Create a scoring graph that uses the FLIP scoring model.
/// </summary>
/// <param name="flipScorer">The FLIP scoring model to use.</param>
/// <param name="proteinMass">The maximum mass of the scoring graph.</param>
/// <returns>The scoring graph that uses the FLIP scoring model.</returns>
public FlipScoringGraph GetScoringGraph(FlipScorer <DeconvolutedSpectrum> flipScorer, double proteinMass)
{
var proteinMassBin = this.massBins.GetBinNumber(proteinMass);
// Precalculate scores for all nodes
var nodeScores = this.InitNodeScores(flipScorer, proteinMass);
// Filter the edges for the scoring graph.
var graphEdges = this.edges.Where(edge => edge.SinkNodeIndex <= proteinMassBin)
.Select(edge => new FlipScoringGraphEdge(edge.PrevNodeIndex, edge.SinkNodeIndex, edge.Weight, edge.Label, flipScorer))
.GroupBy(edge => edge.SinkNodeIndex)
.ToDictionary(edgeGroup => edgeGroup.Key, edgeGroup => edgeGroup.ToList());
return(new FlipScoringGraph(this.massBins, nodeScores[0], nodeScores[1], graphEdges));
}
/// <summary>
/// Get the scorer by scan number.
/// </summary>
/// <param name="scanNum">The scan number to get the scorer for.</param>
/// <param name="precursorMass">The precursor mass to get the scorer for.</param>
/// <param name="precursorCharge">The precursor charge to get the scorer for.</param>
/// <param name="activationMethod">The activation method to get the scorer for.</param>
/// <returns>The scorer selected based on the arguments.</returns>
public IScorer GetScorer(int scanNum, double precursorMass = 0, int precursorCharge = 1, ActivationMethod activationMethod = ActivationMethod.Unknown)
{
IScorer scorer;
if (this.scorerHash.ContainsKey(scanNum))
{
scorer = this.scorerHash[scanNum];
}
else
{
var parameters = this.scoringParameterSet.GetScoringParameters(activationMethod, precursorMass);
scorer = new FlipScorer <DeconvolutedSpectrum>(parameters, this.lcmsRun.GetSpectrum(scanNum) as DeconvolutedSpectrum);
this.scorerHash.Add(scanNum, scorer);
}
return(scorer);
}
