/// <summary>
/// Precompute edges for the scoring graph.
/// </summary>
/// <param name="aminoAcidSet">Amino acid set to build the graph edges from.</param>
/// <param name="aminoAcidProbabilities">The amino acid probabilities.</param>
/// <returns>A list of all scoring graph edges.</returns>
private List <FlipScoringGraphEdge> InitEdges(AminoAcidSet aminoAcidSet, Dictionary <char, double> aminoAcidProbabilities)
{
var adjList = new LinkedList <FlipScoringGraphEdge> [this.massBins.NumberOfBins];
for (var i = 0; i < this.massBins.NumberOfBins; i++)
{
adjList[i] = new LinkedList <FlipScoringGraphEdge>();
}
var terminalModifications = FilteredProteinMassBinning.GetTerminalModifications(aminoAcidSet);
var aminoAcidArray = FilteredProteinMassBinning.GetExtendedAminoAcidArray(aminoAcidSet);
for (var i = 0; i < this.massBins.NumberOfBins; i++)
{
var mi = this.massBins.GetMass(i);
var fineNodeMass = mi;
foreach (var aa in aminoAcidArray)
{
var j = this.massBins.GetBinNumber(fineNodeMass + aa.Mass);
if (j < 0 || j >= this.massBins.NumberOfBins)
{
continue;
}
var aaWeight = aminoAcidProbabilities.ContainsKey(aa.Residue) ? Math.Log10(aminoAcidProbabilities[aa.Residue]) : 0;
adjList[j].AddLast(new FlipScoringGraphEdge(i, j, aaWeight, aa, null));
if (i == 0 && !(aa is ModifiedAminoAcid))
{
foreach (var terminalMod in terminalModifications)
{
var modifiedAa = new ModifiedAminoAcid(aa, terminalMod);
j = this.massBins.GetBinNumber(fineNodeMass + modifiedAa.Mass);
if (j < 0 || j >= this.massBins.NumberOfBins)
{
continue;
}
adjList[j].AddLast(new FlipScoringGraphEdge(i, j, aaWeight, modifiedAa, null));
}
}
}
}
return(adjList.SelectMany(edge => edge).ToList());
}
public ProteinScoringGraphFactory(IMassBinning comparer, AminoAcidSet aminoAcidSet)
{
_comparer = comparer;
_adjList = new LinkedList <ScoringGraphEdge> [_comparer.NumberOfBins];
for (var i = 0; i < _comparer.NumberOfBins; i++)
{
_adjList[i] = new LinkedList <ScoringGraphEdge>();
}
var terminalModifications = FilteredProteinMassBinning.GetTerminalModifications(aminoAcidSet);
var aminoAcidArray = FilteredProteinMassBinning.GetExtendedAminoAcidArray(aminoAcidSet);
for (var i = 0; i < _comparer.NumberOfBins; i++)
{
var mi = _comparer.GetMass(i);
var fineNodeMass = mi;
for (var a = 0; a < aminoAcidArray.Length; a++)
{
var aa = aminoAcidArray[a];
var j = _comparer.GetBinNumber(fineNodeMass + aa.Mass);
if (j < 0 || j >= _comparer.NumberOfBins)
{
continue;
}
_adjList[j].AddLast(new ScoringGraphEdge(i));
if (i == 0 && !(aa is ModifiedAminoAcid))
{
foreach (var terminalMod in terminalModifications)
{
var modifiedAa = new ModifiedAminoAcid(aa, terminalMod);
j = _comparer.GetBinNumber(fineNodeMass + modifiedAa.Mass);
if (j < 0 || j >= _comparer.NumberOfBins)
{
continue;
}
_adjList[j].AddLast(new ScoringGraphEdge(i));
}
}
}
}
}