/// <summary>
/// Combine cluster nextA and nextB into a new cluster
/// </summary>
private void CreateCluster()
{
BinaryGuideTreeNode _node = new BinaryGuideTreeNode(++_currentClusterID);
// link the two nodes nextA and nextB with the new node
_node.LeftChildren = Nodes[_nextA];
_node.RightChildren = Nodes[_nextB];
Nodes[_nextA].Parent = _node;
Nodes[_nextB].Parent = _node;
// use the leftmost leave's sequenceID
_node.SequenceID = Nodes[_nextA].SequenceID;
Nodes.Add(_node);
BinaryGuideTreeEdge _edge1 = new BinaryGuideTreeEdge(Nodes[_nextA].ID);
BinaryGuideTreeEdge _edge2 = new BinaryGuideTreeEdge(Nodes[_nextB].ID);
_edge1.ParentNode = _node;
_edge2.ParentNode = _node;
_edge1.ChildNode = Nodes[_nextA];
_edge2.ChildNode = Nodes[_nextB];
// the length of the edge is the percent identity of two node sequences
// or the average of identities between two sets of sequences
//_edge1.Length = KimuraDistanceScoreCalculator.calculateDistanceScore(
// seqs[nodes[next1].sequenceID], seqs[nodes[next2].sequenceID]);
// modified: define kimura distance as sequence distance
_edge1.Length = _smallestDistance;
_edge2.Length = _smallestDistance;
_edges.Add(_edge1);
_edges.Add(_edge2);
}
/// <summary>
/// Combine cluster nextA and nextB into a new cluster
/// </summary>
/// <param name="distanceMatrix">distance matrix</param>
private void CreateCluster(IDistanceMatrix distanceMatrix)
{
BinaryGuideTreeNode node = new BinaryGuideTreeNode(++_currentClusterID);
// link the two nodes nextA and nextB with the new node
node.LeftChildren = Nodes[_nextA];
node.RightChildren = Nodes[_nextB];
Nodes[_nextA].Parent = node;
Nodes[_nextB].Parent = node;
// use the leftmost leave's sequenceID
int next = Math.Min(_nextA, _nextB);
node.SequenceID = Nodes[next].SequenceID;
_indexToCluster[node.SequenceID] = _currentClusterID;
Nodes.Add(node);
// Add edges
BinaryGuideTreeEdge edgeA = new BinaryGuideTreeEdge(Nodes[_nextA].ID);
BinaryGuideTreeEdge edgeB = new BinaryGuideTreeEdge(Nodes[_nextB].ID);
edgeA.ParentNode = node;
edgeB.ParentNode = node;
edgeA.ChildNode = Nodes[_nextA];
edgeB.ChildNode = Nodes[_nextB];
Nodes[_nextA].ParentEdge = edgeA;
Nodes[_nextB].ParentEdge = edgeB;
// the length of the edge is the percent identity of two node sequences
// or the average of identities between two sets of sequences
//_edge1.Length = KimuraDistanceScoreCalculator.calculateDistanceScore(
// seqs[nodes[nextA].sequenceID], seqs[nodes[nextB].sequenceID]);
// modified: define kimura distance as sequence distance
edgeA.Length = _smallestDistance;
edgeB.Length = _smallestDistance;
_edges.Add(edgeA);
_edges.Add(edgeB);
}