public Probability<double> GetMassErrorProbability(double massError, IonType ionType)
{
var index = _massError[ionType].GetBinIndex(massError);
if (index < 0) return new Probability<double>(massError, 0, _massError[ionType].Total);
var found = _massError[ionType].Bins[index].Count;
var total = _massError[ionType].Total;
return new Probability<double>(massError, found, total);
}
protected FeatureNode(IsotopomerFeatures isotopomerFeatures, IonType ionType, Feature precursorFeature, GroupParameter groupParameter)
{
_isotopomerFeatures = isotopomerFeatures;
FragmentIonClassBase = ionType;
PrecursorFeature = precursorFeature;
GroupParameter = groupParameter;
GetCorrelations();
}
public IdentifiedSequenceTag(Sequence seq, int c1, int c2, IonType[] iontypes)
{
CleavageIndex1 = c1;
CleavageIndex2 = c2;
DerivedFromPrefix = iontypes[0].IsPrefixIon;
IonTypeArray = iontypes;
_sequence = seq;
}
public void AddMatches(List<SpectrumMatch> matches, IonType[] ionTypes, Tolerance tolerance, double relativeIntensityThreshold, bool reduceCharges=true)
{
foreach (var match in matches)
{
var spectrum = match.Spectrum;
var prefixes = match.Prefixes;
var suffixes = match.Suffixes;
StreamWriter debugFile = File.AppendText(@"C:\Users\wilk011\Documents\DataFiles\TestFolder\bCID.txt");
for (int i = 0; i < prefixes.Count; i++)
{
var ionTypeScores = new Dictionary<string, FitScoreList>();
foreach (var ionType in ionTypes)
{
var cleavagePoints = ionType.BaseIonType.IsPrefix ? prefixes : suffixes;
var ion = ionType.GetIon(cleavagePoints[i]);
var mostIntensePeak = GetHighestPeak(ion, spectrum, tolerance, relativeIntensityThreshold);
double score = GetScore(ion, spectrum, tolerance, relativeIntensityThreshold);
double intensity = -1.0;
if (mostIntensePeak != null)
intensity = mostIntensePeak.Intensity;
var name = ionType.Name;
if (reduceCharges)
name = ReducedChargeName(ionType);
if (!ionTypeScores.ContainsKey(name))
ionTypeScores.Add(name, new FitScoreList());
ionTypeScores[name].Add(new FitScore(intensity, score));
}
var bestScores = SelectBestScores(ionTypeScores);
foreach (var bestscore in bestScores)
{
var score = bestscore.Score;
if (_method == ScoreMethod.FitScore)
score = 1 - score;
WorstScore.Total++;
if (score.Equals(0))
WorstScore.Found++;
debugFile.WriteLine("{0}\t{1}", bestscore.Intensity, score);
}
_intensityHistogram.AddData(bestScores);
}
debugFile.Close();
}
}
public double GetScore(IonType ionType, int rankNum, int charge, double mass)
{
var targetRankTable = _trainingParameters.GetRankTable(charge, mass, false);
var decoyRankTable = _trainingParameters.GetRankTable(charge, mass, true);
var prob = targetRankTable.GetRankProbability(rankNum, ionType).Found;
var decoyProb = decoyRankTable.GetRankProbability(rankNum, ionType).Found;
//if (prob == 0) Console.WriteLine("*** Target: {0} {1}", ionType.Name, rankNum);
//if (decoyProb == 0) Console.WriteLine("*** Decoy: {0} {1}", ionType.Name, rankNum);
if (Math.Abs(prob) < 1e-10 || Math.Abs(decoyProb) < 1e-10) return 0;
return (Math.Log(prob) - Math.Log(decoyProb));
}
/// <summary>
/// Filter out all peaks in a spectrum that are not explained by certain ion types.
/// </summary>
/// <param name="sequence">Sequence to calculate ions from.</param>
/// <param name="spectrum">Spectrum to filter.</param>
/// <param name="ionTypes">Ion types to find peaks for.</param>
/// <param name="tolerance"></param>
/// <returns>Filtered Peptide Spectrum Match</returns>
public static Spectrum FilterIonPeaks(Sequence sequence, Spectrum spectrum, IonType[] ionTypes, Tolerance tolerance)
{
var filteredPeaks = new List<Peak>();
var specMatch = new SpectrumMatch(sequence, spectrum);
foreach (var ionType in ionTypes)
{
var ions = specMatch.GetCleavageIons(ionType);
foreach (var ion in ions)
{
var peak = spectrum.FindPeak(ion.GetMonoIsotopicMz(), tolerance);
if (peak != null) filteredPeaks.Add(peak);
}
}
filteredPeaks.Sort();
return new Spectrum(filteredPeaks, spectrum.ScanNum) {MsLevel = 2};
}
public MassErrorTable(IonType[] ionTypes, Tolerance tolerance, double width=0.2, double binWidth=0.01, double offset=0.0)
{
_ionTypes = ionTypes;
_totalPairs = 0;
_tolerance = tolerance;
_width = width;
_binWidth = binWidth;
_offset = offset;
_massError = new Dictionary<IonType, Histogram<double>>();
_ionPairFrequency = new Dictionary<IonType, Histogram<IonPairFound>>();
var binEdges = GenerateEdges();
foreach (var ionType in _ionTypes)
{
_massError.Add(ionType, new Histogram<double>(binEdges));
_ionPairFrequency.Add(ionType, new Histogram<IonPairFound>((IonPairFound[])Enum.GetValues(typeof(IonPairFound))));
}
}
public Probability<double>[] GetProbabilities(IonType ionType)
{
var bins = _massError[ionType].Bins;
var binEdges = _massError[ionType].GetAlignedBinEdges(BinEdgeAlignment.Center, _binWidth);
return binEdges.Select((t, i) => new Probability<double>(t, bins[i].Count, _totalPairs)).ToArray();
}
public FragmentOffsetFrequency(IonType ionType, float frequency)
{
IonType = ionType;
Frequency = frequency;
}
public double[] GetBinEdges(IonType ionType)
{
return _massError[ionType].BinEdges;
}
public static float GetKLDivergence(IonType fragmentIonClassBase, IonType fragmentIonClassBaseType1, int ratio, float lcCorrelation, float imsCorrelation, FragmentParameter parameter)
{
throw new System.NotImplementedException();
}
//public override bool Equals(object obj)
//{
// var type = obj as IonType;
// if (type != null)
// {
// var other = type;
// return other.IsPrefixIon.Equals(IsPrefixIon) && other.OffsetComposition.Equals(OffsetComposition) &&
// other.Charge == Charge;
// }
// return false;
//}
//public override int GetHashCode()
//{
// //return IsPrefixIon.GetHashCode() + OffsetComposition.GetHashCode() + Charge.GetHashCode();
/// <summary>
/// Check for equality
/// </summary>
/// <param name="other"></param>
/// <returns></returns>
protected bool Equals(IonType other)
{
return(Charge == other.Charge && Equals(OffsetComposition, other.OffsetComposition) && IsPrefixIon == other.IsPrefixIon);
}
public void AddIon(IonType ionType, double found)
{
if (!IonFrequencies.ContainsKey(ionType))
IonFrequencies.Add(ionType, 0.0);
IonFrequencies[ionType] += found;
}
/// <summary>
/// Get the number of peaks found for a given rank and ion type.
/// </summary>
/// <param name="rankNum"></param>
/// <param name="ionType"></param>
/// <returns></returns>
public Probability<IonType> GetRankProbability(int rankNum, IonType ionType)
{
var rankIndex = GetRankIndex(rankNum);
var prob = _rankTable[ionType][rankIndex];
var total = _rankTotals[rankIndex];
return new Probability<IonType>(ionType, prob, total);
}
internal static float GetIMSCorrelationScore(IonType fragmentIonClassBaseType1, IonType fragmentIonClassBaseType2, float imsCorr, FragmentParameter fragmentParameter)
{
throw new System.NotImplementedException();
}
public void WriteToFile(StreamWriter file, IonType[] selectedIonTypes)
{
}
private IonType ReducedChargeIonType(IonType ionType)
{
string name = ionType.Name;
if (ionType.Charge > 1 && ionType.Charge < 10)
name = name.Remove(1, 1);
if (ionType.Charge >= 10)
name = name.Remove(1, 2);
return _ionTypeFactory.GetIonType(name);
}
//public override bool Equals(object obj)
//{
// var type = obj as IonType;
// if (type != null)
// {
// var other = type;
// return other.IsPrefixIon.Equals(IsPrefixIon) && other.OffsetComposition.Equals(OffsetComposition) &&
// other.Charge == Charge;
// }
// return false;
//}
//public override int GetHashCode()
//{
// //return IsPrefixIon.GetHashCode() + OffsetComposition.GetHashCode() + Charge.GetHashCode();
/// <summary>
/// Check for equality
/// </summary>
/// <param name="other"></param>
/// <returns></returns>
protected bool Equals(IonType other)
{
return /*string.Equals(this.Name, other.Name) &&*/ (Charge == other.Charge && Equals(this.OffsetComposition, other.OffsetComposition) && this.IsPrefixIon == other.IsPrefixIon);
}
public FragmentFeatureNode(IsotopomerFeatures isotopomerFeatures, IonType fragmentIonClassBase, Feature precursorFeature,
GroupParameter parameter, SubScoreFactory scoringParams)
: base(isotopomerFeatures, fragmentIonClassBase, precursorFeature, parameter)
{
_scoringParams = scoringParams;
}
internal double GetRatioScore(IonType ionType1, IonType ionType2, int ratio, GroupParameter parameter)
{
return GetScoreFromDictionary(_ratioScoreDictionary, ionType1, ionType2, ratio, parameter, LowScoreForIsotopeScore);
}
internal static float GetRatioScore(IonType fragmentIonClassBaseType1, IonType fragmentIonClassBaseType2, int ratio, FragmentParameter fragmentParameter)
{
throw new System.NotImplementedException();
}
internal double GetRatioScore(IonType ionType, int ratio, GroupParameter parameter) // between precursor and frag ion
{
return GetRatioScore(ionType, ionType, ratio, parameter);
}
internal double GetKLDivergence(IonType ionType, IonType ionType1, int ratio, GroupParameter groupParameter)
{
double prob1 = 1, prob2 = 1;
var si = _ionTypeIndexDictionary[groupParameter];
var ionTypeIndices = new Tuple<int, int> ( si[ionType], si[ionType1]);
if(_ratioTargetProbDictionary.ContainsKey(groupParameter))
{
prob1 = prob1 * _ratioTargetProbDictionary[groupParameter][ionTypeIndices][ratio];
prob2 = prob2 * _ratioDecoyProbDictionary[groupParameter][ionTypeIndices][ratio];
}
return GetKLDivergence(prob1, prob2);
}
private void GenerateAllKnownIonTypes()
{
_ionTypeMap = new Dictionary<string, IonType>();
for (int charge = 1; charge <= _maxCharge; charge++)
{
var chargeStr = charge == 1 ? "" : Convert.ToString(charge);
foreach (var baseIonType in _baseIons)
{
foreach (var neutralLoss in _neutralLosses)
{
var name = baseIonType.Symbol + chargeStr + neutralLoss.Name;
var offsetComposition = baseIonType.OffsetComposition -
neutralLoss.Composition;
_ionTypeMap[name] = new IonType(name, offsetComposition, charge, baseIonType, neutralLoss);
}
}
}
}
internal double GetKLDivergence(IonType ionType, int ratio, GroupParameter groupParameter)
{
return GetKLDivergence(ionType, ionType, ratio, groupParameter);
}
public List<Ion> GetCleavageIons(IonType ionType)
{
var compositions = ionType.BaseIonType.IsPrefix ? Prefixes : Suffixes;
return compositions.Select(ionType.GetIon).ToList();
}
private double GetScoreFromDictionary(Dictionary<GroupParameter, Dictionary<Tuple<int, int>, Dictionary<int, double>>> scoreDictionary, IonType ionType1, IonType ionType2, int rawScore, GroupParameter groupParameter, double lowScore)
{
if (!scoreDictionary.ContainsKey(groupParameter)) return lowScore;
var l1 = scoreDictionary[groupParameter];
var si = _ionTypeIndexDictionary[groupParameter];
var key = new Tuple<int, int> ( si[ionType1], si[ionType2] );
if (!l1.ContainsKey(key)) return lowScore;
var l2 = l1[key];
return !l2.ContainsKey(rawScore) ? lowScore : l2[rawScore];
}
/// <summary>
/// Write RankTable to training parameter file.
/// </summary>
/// <param name="file">Open file to write RankTable to.</param>
/// <param name="selectedIonTypes">The ion types to show in the file.
/// All other ion types are averaged and displayed as "unexplained"</param>
public void WriteToFile(StreamWriter file, IonType[] selectedIonTypes)
{
file.WriteLine("MaxRanks\t" + MaxRanks);
var unselectedIonTypes = IonTypes.Except(selectedIonTypes).ToList();
foreach (var ionType in selectedIonTypes)
{
file.Write(ionType.Name + "\t");
for (int i = 0; i < MaxRanks+1; i++)
{
file.Write(Math.Round(_rankTable[ionType][i], 2) + "\t");
}
file.WriteLine();
}
var total = new double[MaxRanks+1];
var count = new double[MaxRanks+1];
var prob = new double[MaxRanks+1];
for (int i = 0; i < MaxRanks+1; i++)
{
total[i] = 0.0;
count[i] = 0.0;
prob[i] = 0.0;
}
foreach (var ionType in unselectedIonTypes)
{
for (int i = 0; i < MaxRanks+1; i++)
{
total[i] += _rankTable[ionType][i];
count[i]++;
}
}
for (int i = 0; i < MaxRanks+1; i++) prob[i] = Math.Round(total[i] / count[i], 2);
file.WriteLine("Unexplained\t" + string.Join("\t", prob));
file.WriteLine("Total\t" + string.Join("\t", _rankTotals));
}
private static string ReducedChargeName(IonType ionType)
{
string name = ionType.Name;
if (ionType.Charge > 1 && ionType.Charge < 10)
name = name.Remove(1, 1);
if (ionType.Charge >= 10)
name = name.Remove(1, 2);
return name;
}