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();
}
public ImsScorerFactory(string paramFilePath)
{
_subScoreFactory = new SubScoreFactory(paramFilePath);
}
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;
}
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 ImsScorerFactory(string paramFilePath)
{
_subScoreFactory = new SubScoreFactory(paramFilePath);
}
public FragmentFeatureNode(IsotopomerFeatures isotopomerFeatures, IonType fragmentIonClassBase, Feature precursorFeature,
GroupParameter parameter, SubScoreFactory scoringParams)
: base(isotopomerFeatures, fragmentIonClassBase, precursorFeature, parameter)
{
_scoringParams = scoringParams;
}
public FragmentFeatureNode(IsotopomerFeatures isotopomerFeatures, IonType fragmentIonClassBase, Feature precursorFeature,
GroupParameter parameter, SubScoreFactory scoringParams)
: base(isotopomerFeatures, fragmentIonClassBase, precursorFeature, parameter)
{
_scoringParams = scoringParams;
}