public void Add(DataVertex vertex, DataEdge inEdge)
{
Add(vertex);
Sequence.Add(inEdge.AminoAcid);
}
/// <summary>
/// Build the data graph from a sequence graph.
/// </summary>
private void BuildGraph()
{
var sequenceRev = this._sequence.Reverse();
var sequence = sequenceRev.Aggregate(string.Empty, (current, aa) => current + aa);
sequence = "\0" + sequence;
this.vertices = new DataVertex[this._maxSeqIndex][];
var mods = this.AminoAcidSet.GetModificationParams();
int id = 0;
int ntermIndex = 0;
int start = this._maxSeqIndex - 2;
int end = 0;
int offset = 1;
if (this.nterminal != null)
{
start++;
sequence += this.nterminal.Residue;
}
if (this.cterminal != null)
{
end--;
offset = 0;
sequence = sequence.Insert(1, this.cterminal.Residue.ToString(CultureInfo.InvariantCulture));
}
// create vertices
for (var si = start; si > end; si--)
{
var graphSi = si - offset;
this.vertices[graphSi] = new DataVertex[this._graph[si].Length];
for (var mi = 0; mi < this._graph[si].Length; mi++)
{
var node = this._graph[si][mi];
var mod = mods.GetModificationCombination(node.ModificationCombinationIndex);
this.SetSink(mi);
this.vertices[graphSi][mi] = new DataVertex
{
ID = id++,
NTermIndex = ntermIndex,
ModIndex = mi,
PrefixComposition = this.GetComplementaryComposition(si, mi),
SuffixComposition = this.GetComposition(si, mi),
ModificationCombination = mod,
Text = string.Empty
};
var vertex = this.vertices[graphSi][mi];
this.DataGraph.AddVertex(vertex);
}
ntermIndex++;
}
// connect vertices
for (var si = start; si > (end + 1); si--)
{
var graphSi = si - offset;
for (int mi = 0; mi < this._graph[si].Length; mi++)
{
var node = this._graph[si][mi];
var currVertex = this.vertices[graphSi][mi];
foreach (var nextModIndex in node.GetPrevNodeIndices())
{
var nextVertex = this.vertices[graphSi - 1][nextModIndex];
var currVertexMods = currVertex.ModificationCombination.Modifications;
var nextVertexMods = nextVertex.ModificationCombination.Modifications;
var result = new List <Modification>(currVertexMods);
foreach (var mod in nextVertexMods)
{
if (result.Contains(mod))
{
result.Remove(mod);
}
}
AminoAcid aminoAcid;
if (si == start && this.nterminal != null)
{
aminoAcid = this.nterminal;
}
else if (si == end + 2 && this.cterminal != null)
{
aminoAcid = this.cterminal;
}
else
{
aminoAcid = this.AminoAcidSet.GetAminoAcid(sequence[graphSi]);
}
var modAa = aminoAcid as ModifiedAminoAcid;
Modification aminoAcidMod = null;
if (modAa != null)
{
aminoAcidMod = modAa.Modification;
}
if (aminoAcidMod != null)
{
result.Add(aminoAcidMod);
}
var edgeModifications = new ModificationCombination(result);
var edge = new DataEdge(currVertex, nextVertex)
{
AminoAcid = aminoAcid,
SequenceIndex = graphSi,
Modifications = edgeModifications
};
this.DataGraph.AddEdge(edge);
}
}
}
}
