public List<Cluster> Work3(int cut = 3, int seed = 1, bool setCoreWeights = false)
{
InitEdges();
Console.WriteLine("Запущена кластеризация второго типа для " + _nodes.Length + " узлов");
var sw = Stopwatch.StartNew();
var weights = new int[_nodes.Length][];
for (int i = 0; i < weights.Length; i++)
{
weights[i] = new int[_nodes.Length];
for (int j = 0; j < _nodes.Length; j++)
weights[i][j] = i != j ? GetEdge(i, j).Weight - cut : (setCoreWeights ? _nodes[i].Count : 0);//_nodes[i].Chain.Length;
}
var m = new Modularity(_nodes, weights, seed);
Console.WriteLine("Start with:" + m.CalcTotalModularity());
var iter = 1;
while (m.Iterate())
Console.WriteLine("Iter[" + iter++ + "]:" + m.CalcTotalModularity());
Console.WriteLine("Result:" + m.CalcTotalModularity());
sw.Stop();
Console.WriteLine("Кластеризация завершена за " + sw.Elapsed);
var clusterIds = m.ClasterIds;
var ret = new List<Cluster>();
for (int i = 0; i < m.NodesCount; i++)
{
// переобозначим элементы каждого кластера
int id = 0;
var dic = new Dictionary<int, int>();
for (int j = 0; j < clusterIds.Length; j++)
{
if(clusterIds[j] != i)
continue;
dic.Add(id++,j);
}
var nodes = new ElementGroup[dic.Count];
var edges = new AlignmentResult[dic.Count][];
for (int j = 0; j < dic.Count; j++)
{
nodes[j] = _nodes[dic[j]];
edges[j] = new AlignmentResult[j];
for (int k = 0; k < j; k++)
{
edges[j][k] = _edges[dic[j]][dic[k]];
if (k == 0)
{
var tt = Alignment.Align(nodes[j].NucleoChain, nodes[k].NucleoChain, 0, 0);
Debug.Assert(tt.Mask == edges[j][k].Mask);
}
}
}
ret.Add(new Cluster(ret.Count, nodes, edges));
}
return ret;
}
public Cluster(int clusterId, ElementGroup[] nodes, AlignmentResult[][] edges)
{
ClusterId = clusterId;
Nodes = nodes;
Edges = edges;
}
public void InitEdges()
{
if (_edges != null)
return;
Console.WriteLine("Запущен рассчёт рёбер для " + _nodes.Length + " узлов");
var sw = Stopwatch.StartNew();
var edges = new AlignmentResult[_nodes.Length][];
Parallel.For(0, edges.Length, new ParallelOptions {MaxDegreeOfParallelism = 4},
i =>
{
edges[i] = new AlignmentResult[i];
for (var j = 0; j < i; j++)
edges[i][j] = Alignment.Align(_nodes[i].NucleoChain, _nodes[j].NucleoChain, i, j);
});
//for (var i = 0; i < edges.Length; i++)
//{
// edges[i] = new AlignmentResult[i];
// for (var j = 0; j < i; j++)
// edges[i][j] = Alignment.Align(_nodes[i].NucleoChain, _nodes[j].NucleoChain, i, j);
//}
_edges = edges;
sw.Stop();
Console.WriteLine("Рёбра рассчитаны за " + sw.Elapsed);
}