} // max index for _theoreticalIsotopomerEnvelope, not for this
private IsotopomerFeatures(ImsDataCached imsData, Ion ion, Feature precursorFeature, bool isPrecurosr)
{
// BinningMultiplyFactor = 6;
if (ion.Charge >= 3)
{
BinningMultiplyFactor = 1;
}
//else if (ion.Charge == 1) BinningMultiplyFactor = 6;
//else if (ion.Charge == 2) BinningMultiplyFactor = 2;
else
{
BinningMultiplyFactor = 2;
}
var te = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
TheoreticalIsotopomerEnvelope = new double[(te.Length + FeatureNode.OffsetFromMonoIsotope) * BinningMultiplyFactor];
for (var i = FeatureNode.OffsetFromMonoIsotope; i < te.Length + FeatureNode.OffsetFromMonoIsotope; i++)
{
TheoreticalIsotopomerEnvelope[i * BinningMultiplyFactor] = te[i - FeatureNode.OffsetFromMonoIsotope];
}
MaxIntensityIndex = GetMaximumIndex(TheoreticalIsotopomerEnvelope);
//
var start = -FeatureNode.OffsetFromMonoIsotope * BinningMultiplyFactor;
for (var i = start; i < TheoreticalIsotopomerEnvelope.Length + start; i++)
{
var mz = ion.GetIsotopeMz((float)i / BinningMultiplyFactor);
if (isPrecurosr)
{
if (mz > imsData.MaxPrecursorMz || mz < imsData.MinPrecursorMz)
{
Add(null);
}
else
{
Add(imsData.GetPrecursorFeature(mz, precursorFeature));
}
}
else
{
if (mz > imsData.MaxFragmentMz || mz < imsData.MinFragmentMz)
{
Add(null);
}
else
{
Add(imsData.GetFramentFeature(mz, precursorFeature));
}
//var tt = imsData.GetFramentFeature(mz, precursorFeature);
// if(mz == 361.198813765)
// Console.WriteLine(mz + " " + (tt == null ? "NULL" : tt.GetHighestPoint().ToString()));
}
}
}
public FragmentFeatureGraph(ImsDataCached imsData, PrecursorFeatureNode precursorNode, Feature precursorFeature,
Ion precursorIon, Composition cutComposition, GroupParameter parameter, SubScoreFactory scoringParams)
{
_scoringParams = scoringParams;
_precursorFeatureNode = precursorNode;
Add(precursorNode, new List <FeatureEdge>());
var fragmentNodes = GetFragmentNodes(imsData, precursorFeature, cutComposition, precursorIon, parameter);
supportingIonTypes = new List <IonType>();
foreach (var node in fragmentNodes)
{
if (node.Feature != null)
{
supportingIonTypes.Add(node.FragmentIonClassBase);
}
}
//var nn = fragmentNodes.Count(no => no.Feature != null);
//Console.WriteLine(this + "Num features : " + nn);
var usedNodes = new List <FeatureNode> {
precursorNode
};
UpdateEdges(fragmentNodes, usedNodes); // from precursor to any of fragment nodes
if (this[precursorNode].Count == 0)
{
NodeScore = RatioScore = -1; //TODO should be trained..
Score = NodeScore + RatioScore;
return;
}
// usedNodes.Remove(precursorNode);// exclude precursorNode
var primeNode = (FragmentFeatureNode)this[precursorNode][0].RNode;
var targetNodes = GetTargetNodes(primeNode, fragmentNodes, true, false);
UpdateEdges(targetNodes, usedNodes); // to the nodes of different terminal ions
targetNodes = GetTargetNodes(primeNode, fragmentNodes, false, false);
UpdateEdges(targetNodes, usedNodes); // to the nodes of the same terminal ions
targetNodes = GetTargetNodes(primeNode, fragmentNodes, true, true);
UpdateEdges(targetNodes, usedNodes); // to the nodes of differently charged ions
GetScore();
}
private List <FragmentFeatureNode> GetFragmentNodes(ImsDataCached imsData, Feature precursorFeature, Composition cutComposition, Ion precursorIon, GroupParameter parameter)
{
var ionTypes = _scoringParams.GetIonTypes(parameter);
var nodes = new List <FragmentFeatureNode>();
var suffixComposition = precursorIon.Composition - Composition.H2O - cutComposition;
//Console.WriteLine(cutComposition.GetMass() + " " + suffixComposition.GetMass());
foreach (var ionType in ionTypes)
{
var composition = ionType.IsPrefixIon ? cutComposition : suffixComposition;
//Console.WriteLine("FragFeatureGraph\t" + ionType.Name + "\t" + composition.GetMass() + "\t" + ionType.GetIon(composition).GetMonoIsotopicMz());
var node = new FragmentFeatureNode(IsotopomerFeatures.GetFramentIsotopomerFeatures(imsData, composition, ionType, precursorFeature), ionType, precursorFeature, parameter, _scoringParams);
//if(node.Feature != null)
// if (20 * node.Feature.IntensityMax < precursorFeature.IntensityMax || node.Feature.IntensityMax > 20 * precursorFeature.IntensityMax) continue; //
nodes.Add(node);
}
return(nodes);
}
public void RegisterImsData(ImsDataCached imsData, ImsScorerFactory imsScorerFactory)
{
_imsData = imsData;
_imsScorerFactory = imsScorerFactory;
}
internal ImsScorer(ImsDataCached imsData, Ion precursorIon, SubScoreFactory scoringParams) // precursorComposition does not have protons; however, protons are incorporated when calculating mz
{
_imsData = imsData;
_precursorIon = precursorIon;
_scoringParams = scoringParams;
}
public ImsScorer GetImsScorer(ImsDataCached imsData, Ion precursorIon)
{
return(new ImsScorer(imsData, precursorIon, _subScoreFactory));
}
static public IsotopomerFeatures GetPrecursorIsotopomerFeatures(ImsDataCached imsData, Ion precursorIon, Feature precursorFeature)
{
return(new IsotopomerFeatures(imsData, precursorIon, precursorFeature, true));
}
static public IsotopomerFeatures GetFramentIsotopomerFeatures(ImsDataCached imsData, Composition cutComposition, IonType fragmentIonClassBase, Feature precursorFeature)
{
return(new IsotopomerFeatures(imsData, fragmentIonClassBase.GetIon(cutComposition), precursorFeature, false));
}