internal ScoringGraph(AminoAcid[] aminoAcidSequence, Composition sequenceComposition, ScoringGraphNode rootNode,
int minPrecursorCharge, int maxPrecursorCharge)
{
_aminoAcidSequence = aminoAcidSequence;
_sequenceComposition = sequenceComposition;
_rootNode = rootNode;
_minPrecursorCharge = minPrecursorCharge;
_maxPrecursorCharge = maxPrecursorCharge;
_precursorIon = new Dictionary<int, Ion>();
for (var precursorCharge = _minPrecursorCharge; precursorCharge <= _maxPrecursorCharge; precursorCharge++)
{
_precursorIon[precursorCharge] = new Ion(_sequenceComposition, precursorCharge);
}
// store all nodes in an array
var nodes = new HashSet<ScoringGraphNode>();
var curNodes = new HashSet<ScoringGraphNode> { _rootNode };
while (curNodes.Any())
{
var newNodes = new HashSet<ScoringGraphNode>();
foreach (var node in curNodes)
{
if (nodes.Add(node)) // if node is new
{
foreach (var nextNode in node.GetNextNodes())
{
newNodes.Add(nextNode);
}
}
}
curNodes = newNodes;
}
_nodes = nodes.ToArray();
}
public void AddNextNode(ScoringGraphNode nextNode)
{
_nextNodes.Add(nextNode);
}
internal ScoringGraph(AminoAcid[] aminoAcidSequence, Composition sequenceComposition, ScoringGraphNode rootNode)
: this(aminoAcidSequence, sequenceComposition, rootNode, DefaultMinPrecursorCharge, DefaultMaxPrecursorCharge)
{
}
private double GetProductIonScore(ScoringGraphNode node, ImsScorer imsScorer, Feature precursorFeature)
{
//Console.Write("Offset: " + node.Offset);
double cutScore = 0;
if (node.Index > 1 && node.Index <= _aminoAcidSequence.Length-3)
{
var nTermAA = _aminoAcidSequence[node.Index].Residue;
var cTermAA = _aminoAcidSequence[node.Index + 1].Residue;
cutScore = imsScorer.GetCutScore(nTermAA, cTermAA, node.Composition, precursorFeature);
//Console.WriteLine(" " + _aminoAcidSequence[node.Offset].Residue + " " + node.Composition + " " + _aminoAcidSequence[node.Offset + 1].Residue + " " + cutScore);
}
//Console.WriteLine();
if (node.Index > _aminoAcidSequence.Length - 3)
return 0;
var nextNodeScore = node.GetNextNodes().DefaultIfEmpty().Max(nextNode => GetProductIonScore(nextNode, imsScorer, precursorFeature));
return cutScore + nextNodeScore;
}
