public void GetCompositeScores(Sequence sequence, int parentIoncharge, int ms2ScanNum, out double score, out int nMatchedFragments)
{
score = 0d;
nMatchedFragments = 0;
var spec = Run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null)
{
return;
}
var preFixIonCheck = new bool[sequence.Count + 1];
var sufFixIonCheck = new bool[sequence.Count + 1];
var scorer = new CompositeScorer(spec, Tolerance, MinProductCharge, Math.Min(MaxProductCharge, parentIoncharge + 2), activationMethod: ActivationMethod);
var cleavages = sequence.GetInternalCleavages();
var cleavageIndex = 0;
foreach (var c in cleavages)
{
bool prefixHit;
bool suffixHit;
score += scorer.GetFragmentScore(c.PrefixComposition, c.SuffixComposition, out prefixHit, out suffixHit);
nMatchedFragments += (prefixHit) ? 1 : 0;
nMatchedFragments += (suffixHit) ? 1 : 0;
if (prefixHit)
{
preFixIonCheck[cleavageIndex] = true;
}
if (suffixHit)
{
sufFixIonCheck[cleavageIndex] = true;
}
cleavageIndex++;
}
var preContCount = 0;
var sufContCount = 0;
for (var i = 0; i < preFixIonCheck.Length - 1; i++)
{
if (preFixIonCheck[i] && preFixIonCheck[i + 1])
{
preContCount++;
}
if (sufFixIonCheck[i] && sufFixIonCheck[i + 1])
{
sufContCount++;
}
}
score += preContCount * CompositeScorer.ScoreParam.Prefix.ConsecutiveMatch;
score += sufContCount * CompositeScorer.ScoreParam.Suffix.ConsecutiveMatch;
}
public IcScores GetScores(ProductSpectrum spec, string seqStr, Composition composition, int charge, int ms2ScanNum)
{
if (spec == null)
{
return(null);
}
var scorer = new CompositeScorer(spec, Tolerance, MinProductCharge, Math.Min(MaxProductCharge, charge), activationMethod: ActivationMethod);
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, AminoAcid.ProteinNTerm, seqStr, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return(null);
}
var bestScore = double.NegativeInfinity;
Tuple <double, string> bestScoreAndModifications = null;
var protCompositions = seqGraph.GetSequenceCompositions();
for (var modIndex = 0; modIndex < protCompositions.Length; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
if (!protCompositionWithH2O.Equals(composition))
{
continue;
}
var curScoreAndModifications = seqGraph.GetFragmentScoreAndModifications(scorer);
var curScore = curScoreAndModifications.Item1;
if (!(curScore > bestScore))
{
continue;
}
bestScoreAndModifications = curScoreAndModifications;
bestScore = curScore;
}
if (bestScoreAndModifications == null)
{
return(null);
}
var modifications = bestScoreAndModifications.Item2;
var seqObj = Sequence.CreateSequence(seqStr, modifications, AminoAcidSet);
double score;
int nMatchedFragments;
GetCompositeScores(seqObj, charge, ms2ScanNum, out score, out nMatchedFragments);
return(new IcScores(nMatchedFragments, score, modifications));
}
public IScorer GetScorer(ProductSpectrum spectrum, double precursorMass, int precursorCharge, ActivationMethod activationMethod = ActivationMethod.Unknown)
{
IScorer scorer = null;
if (spectrum is DeconvolutedSpectrum)
{
var deconSpec = spectrum as DeconvolutedSpectrum;
scorer = new CompositeScorerBasedOnDeconvolutedSpectrum(deconSpec, spectrum, _productTolerance, _comparer, spectrum.ActivationMethod);
}
else
{
scorer = new CompositeScorer(
spectrum,
this._productTolerance,
activationMethod: activationMethod,
minCharge: _minProductCharge,
maxCharge: _maxProductCharge);
}
return(scorer);
}
public IcScores GetScores(ProductSpectrum spec, string seqStr, Composition composition, int charge, int ms2ScanNum)
{
if (spec == null) return null;
var scorer = new CompositeScorer(spec, Tolerance, MinProductCharge, Math.Min(MaxProductCharge, charge));
var seqGraph = SequenceGraph.CreateGraph(AminoAcidSet, AminoAcid.ProteinNTerm, seqStr, AminoAcid.ProteinCTerm);
if (seqGraph == null) return null;
var bestScore = double.NegativeInfinity;
Tuple<double, string> bestScoreAndModifications = null;
var protCompositions = seqGraph.GetSequenceCompositions();
for (var modIndex = 0; modIndex < protCompositions.Length; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
if (!protCompositionWithH2O.Equals(composition)) continue;
var curScoreAndModifications = seqGraph.GetFragmentScoreAndModifications(scorer);
var curScore = curScoreAndModifications.Item1;
if (!(curScore > bestScore)) continue;
bestScoreAndModifications = curScoreAndModifications;
bestScore = curScore;
}
if (bestScoreAndModifications == null) return null;
var modifications = bestScoreAndModifications.Item2;
var seqObj = Sequence.CreateSequence(seqStr, modifications, AminoAcidSet);
double score;
int nMatchedFragments;
GetCompositeScores(seqObj, charge, ms2ScanNum, out score, out nMatchedFragments);
return new IcScores(nMatchedFragments, score, modifications);
}
public void GetCompositeScores(Sequence sequence, int parentIoncharge, int ms2ScanNum, out double score, out int nMatchedFragments)
{
score = 0d;
nMatchedFragments = 0;
var spec = Run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
if (spec == null) return;
var preFixIonCheck = new bool[sequence.Count + 1];
var sufFixIonCheck = new bool[sequence.Count + 1];
var scorer = new CompositeScorer(spec, Tolerance, MinProductCharge, Math.Min(MaxProductCharge, parentIoncharge+2));
var cleavages = sequence.GetInternalCleavages();
var cleavageIndex = 0;
foreach (var c in cleavages)
{
bool prefixHit;
bool suffixHit;
score += scorer.GetFragmentScore(c.PrefixComposition, c.SuffixComposition, out prefixHit, out suffixHit);
nMatchedFragments += (prefixHit) ? 1 : 0;
nMatchedFragments += (suffixHit) ? 1 : 0;
if (prefixHit) preFixIonCheck[cleavageIndex] = true;
if (suffixHit) sufFixIonCheck[cleavageIndex] = true;
cleavageIndex++;
}
var preContCount = 0;
var sufContCount = 0;
for (var i = 0; i < preFixIonCheck.Length - 1; i++)
{
if (preFixIonCheck[i] && preFixIonCheck[i + 1]) preContCount++;
if (sufFixIonCheck[i] && sufFixIonCheck[i + 1]) sufContCount++;
}
score += preContCount * CompositeScorer.ScoreParam.Prefix.ConsecutiveMatch;
score += sufContCount * CompositeScorer.ScoreParam.Suffix.ConsecutiveMatch;
}
