public double IntraClusterDistance(Cluster C, string[] arr_input_file, double[,] Dmatrix, string distance_type)
{
//type of distance measure: single link: singleLink, complete link:completLink, Average Link: AverageLink, median link:MedianLink or MedoidLink
distance_type = distance_type.Trim();
//use UPPERCASE
distance_type = distance_type.ToUpper();
if (distance_type != "SINGLELINK" && distance_type != "COMPLETELINK" && distance_type != "AVERAGELINK" && distance_type != "MEDOIDLINK" && distance_type != "MEDIANLINK")
distance_type = "AVERAGELINK";
// List<Sequence> temp_medoid = new List<Sequence>();
Sequence OP = new Sequence();
Hashtable h_interClusterDistance = new Hashtable();//Host the contribution of each sequence to the InterCluster distance; the key is the sequenceID
/* for each object in cluster C1 compute distance to all object in C2 */
double inter_d = 0.0;
switch (distance_type)
{
case "AVERAGELINK":
{
double interClusterDistance = 0.0;
int totalPairwiseDistances = 0;
// System.Console.WriteLine("C1.clusterID:" + C1.clusterID+ "C2.clusterID :"+ C2.clusterID);
foreach (Sequence seq1 in C.ListOfSeq)
{
foreach (Sequence seq2 in C.ListOfSeq)
{
if (seq1.sequenceValue != seq2.sequenceValue)
{
double d = OP.fetchDistance(seq1, seq2, arr_input_file, Dmatrix);
// System.Console.WriteLine("dD:" + d);
//Console.Read();
inter_d = inter_d + d;
totalPairwiseDistances = totalPairwiseDistances + 1;
}
}
}
interClusterDistance = Math.Round(inter_d / totalPairwiseDistances, 3);
// System.Console.WriteLine("inside distance interClusterDistance:" + interClusterDistance);
return interClusterDistance;
}
case "SINGLELINK":
{
double interClusterDistance = 0.0;
foreach (Sequence seq1 in C.ListOfSeq)
{
foreach (Sequence seq2 in C.ListOfSeq)
{
if (seq1.sequenceValue != seq2.sequenceValue)
{
double d = OP.fetchDistance(seq1, seq2, arr_input_file, Dmatrix);
if (d < inter_d)
inter_d = d;
}
}
}
interClusterDistance = inter_d;
return interClusterDistance;
}
case "COMPLETELINK":
{
double interClusterDistance = 0.0;
foreach (Sequence seq1 in C.ListOfSeq)
{
foreach (Sequence seq2 in C.ListOfSeq)
{
if (seq1.sequenceValue != seq2.sequenceValue)
{
double d = OP.fetchDistance(seq1, seq2, arr_input_file, Dmatrix);
if (d > inter_d)
inter_d = d;
}
}
}
interClusterDistance = inter_d;
return interClusterDistance;
}
case "MEDOIDLINK":
{
double interClusterDistance = 0.0;
//there could be many medoids for a cluster. We select the two with the largest distance
foreach (Sequence seq1 in C.listOfMedoid)
{
foreach (Sequence seq2 in C.listOfMedoid)
{
if (seq1.sequenceValue != seq2.sequenceValue)
{
double d = OP.fetchDistance(seq1, seq2, arr_input_file, Dmatrix);
if (d > inter_d)
inter_d = d;
}
}
}
interClusterDistance = inter_d;
return interClusterDistance;
}
default:
return inter_d;
}//switch
//return interClusterDistance;
}
public List<Sequence> ComputeMedoid(Cluster C, string[] arr_input_file, double[,] Dmatrix)
{
List<Sequence> temp_medoid = new List<Sequence>();
Sequence OP = new Sequence();
Hashtable h_intraClusterDistance = new Hashtable();//Host the contribution of each sequence to the intraCluster distance; the key is the sequenceID
// Hashtable h_sequence = new Hashtable();//Host the contribution of each sequence to the intraCluster distance; the key is the sequenceID
/* for each object in this cluster select the object in middle by computing the distance of each object to all objects*/
double intraCluster = 0.0;
// int numOfSeq=C.ListOfSeq.Count;
// double[] arr_intraClusterD = new double[numOfSeq];
foreach (Sequence seq1 in C.ListOfSeq)
{
intraCluster = 0;
foreach (Sequence seq2 in C.ListOfSeq)
{
if (seq1.sequenceValue != seq2.sequenceValue)
{
double d = OP.fetchDistance(seq1, seq2, arr_input_file, Dmatrix);
intraCluster = intraCluster + d;
}
}
//The contribution of each sequ is in the hash.
seq1.contributionToIntraClusterDistance = intraCluster;
h_intraClusterDistance.Add(seq1.sequenceValue, seq1);
}
// The squence with the minimum distance is the medoid
double minDistance = -1.0;
bool first_time = true;
foreach (DictionaryEntry entry in h_intraClusterDistance)
{
Sequence temp = (Sequence)(entry.Value);
if (first_time)
minDistance = temp.contributionToIntraClusterDistance;
if (temp.contributionToIntraClusterDistance < minDistance)
minDistance = temp.contributionToIntraClusterDistance;
}
// At this point the minimumn value of intra cluster distance is known. What is needed to find out all the sequences with same value
foreach (DictionaryEntry entry in h_intraClusterDistance)
{
Sequence temp = (Sequence)(entry.Value);
if (temp.contributionToIntraClusterDistance == minDistance)
temp_medoid.Add(temp);
}
return temp_medoid;
}
