private int GetCorrelationScore(Tuple <List <MSMSSpectrumPeak>, double[]> isotopomerTuple)
{
var observed = isotopomerTuple.Item1;
var theoretical = isotopomerTuple.Item2;
var maxIndex = 0;
var maxAbundance = double.NegativeInfinity;
for (var i = 0; i < theoretical.Length; i++)
{
if (!(maxAbundance < theoretical[i]))
{
continue;
}
maxAbundance = theoretical[i];
maxIndex = i;
}
var c1 = new double[theoretical.Length + FeatureNode.OffsetFromMonoIsotope];
var c2 = new double[theoretical.Length + FeatureNode.OffsetFromMonoIsotope];
for (var i = 0; i < c1.Length; i++)
{
var i1 = maxIndex + i;
var i2 = -FeatureNode.OffsetFromMonoIsotope + maxIndex + i;
c1[i] = observed[Math.Min(i1, observed.Count - 1)].Intensity;
c2[i] = i2 < 0 ? 0 : theoretical[Math.Min(i2, theoretical.Length - 1)];
}
// Console.WriteLine(c1.Length);
return(SubScoreFactory.CorrToIntForIsotopeScore(SimpleMath.GetCorrelation(c1, c2)));
}
private void Normalize()
{
foreach (var groupParameter in GroupParameter.GetAllFragmentGroupParameters(_maxCharge))
{
if (!IsotopeIntensityCorrProbDictionary.ContainsKey(groupParameter))
{
IsotopeIntensityCorrProbDictionary[groupParameter] = new Dictionary <IonType, Dictionary <int, double> >();
}
var si = IsotopeIntensityCorrProbDictionary[groupParameter];
foreach (var ionType in _ionTypes[groupParameter])
{
if (!si.ContainsKey(ionType))
{
si[ionType] = new Dictionary <int, double>();
}
var ssi = si[ionType];
var sum = 0.0;
foreach (var score in SubScoreFactory.GetAllCorrIntScore())
{
if (!ssi.ContainsKey(score))
{
ssi[score] = 1.0;
}
sum = sum + ssi[score];
}
var keys = new List <int>(ssi.Keys);
foreach (var score in keys)
{
ssi[score] = Math.Max(double.MinValue, ssi[score] / sum);
}
}
}
}
public FeatureEdge(FeatureNode l, FeatureNode r, SubScoreFactory scoringParams)
{
LNode = l;
RNode = r;
var ri = r.Feature == null ? 0.0 : r.Feature.IntensityMax;
var li = l.Feature == null ? 0.0 : l.Feature.IntensityMax;
_scoringParams = scoringParams;
if (LNode is PrecursorFeatureNode) // TODO fix later when no summed intensity is used
_ratio = GetRatioIndex(ri, ri);
else
_ratio = GetRatioIndex(li, ri);
Weight = GetWeight();
}
public FeatureEdge(FeatureNode l, FeatureNode r, SubScoreFactory scoringParams)
{
LNode = l;
RNode = r;
var ri = r.Feature == null ? 0.0 : r.Feature.IntensityMax;
var li = l.Feature == null ? 0.0 : l.Feature.IntensityMax;
_scoringParams = scoringParams;
if (LNode is PrecursorFeatureNode) // TODO fix later when no summed intensity is used
{
_ratio = GetRatioIndex(ri, ri);
}
else
{
_ratio = GetRatioIndex(li, ri);
}
Weight = GetWeight();
}
public PrecursorFeatureNode(IsotopomerFeatures isotopomerFeatures, GroupParameter parameter, SubScoreFactory scoringParams)
: base(isotopomerFeatures, null, isotopomerFeatures.GetMostAbundantFeature(), parameter)
{
_scoringParams = scoringParams;
Score = GetScore();
}
public PrecursorFeatureNode(IsotopomerFeatures isotopomerFeatures, GroupParameter parameter, SubScoreFactory scoringParams)
: base(isotopomerFeatures, null, isotopomerFeatures.GetMostAbundantFeature(), parameter)
{
_scoringParams = scoringParams;
Score = GetScore();
}
