public static string VectorProteinInterfaceWholeTreeHeader(VectorProteinInterfaceWhole a)
{
if (a == null)
{
throw new ArgumentNullException(nameof(a));
}
return(Newick.TreeHeaderSafeName(a.FullProteinInterfaceId.ToString() + "_" + (a.ReversedSequence ? "R_" : "F_") + (a.ReversedInteractions ? "RI_" : "") + string.Join("", a.InteractionBools().Select(Convert.ToInt32)) + "_" + (a.VectorProteinInterfacePartList.Count(b => b.InteractionToNonProteinInterface) > 0 ? 1 : 0)));
}
public void TestUpgma()
{
//decimal[,] distanceMatrix1 =
//{
// { 0, 0, 0, 0, 0 },
// { 0, 0, 1, 1, 1 },
// { 0, 1, 0, 2, 2 },
// { 0, 1, 2, 0, 3 },
// { 0, 1, 2, 3, 0 },
//};
//var result = UpgmaClustering.Upgma(distanceMatrix1);
decimal[,] distanceMatrix2 =
{
{ 0, 19, 27, 8, 33, 18, 13 },
{ 19, 0, 31, 18, 36, 1, 13 },
{ 27, 31, 0, 26, 41, 32, 29 },
{ 8, 18, 26, 0, 31, 17, 14 },
{ 33, 36, 41, 31, 0, 35, 28 },
{ 18, 1, 32, 17, 35, 0, 12 },
{ 13, 13, 29, 14, 28, 12, 0 }
};
var names = new List <string>();
for (var i = 0; i < distanceMatrix2.GetLength(0); i++)
{
names.Add("" + i);
}
List <string> vectorNames = new List <string>();
var maxVectorLength = distanceMatrix2.GetLength(0) > distanceMatrix2.GetLength(1) ? distanceMatrix2.GetLength(0) : distanceMatrix2.GetLength(1);
for (var i = 0; i < maxVectorLength; i++)
{
vectorNames.Add(SpreadsheetFileHandler.AlphabetLetterRollOver(i) + i);
}
List <List <UpgmaNode> > nodeList;
List <List <string> > treeList;
var minimumOutputTreeLeafs = 1;
List <string> finalTreeLeafOrderList;
UpgmaClustering.Upgma(distanceMatrix2, vectorNames, minimumOutputTreeLeafs, out nodeList, out treeList, out finalTreeLeafOrderList);
CheckUpgmaDistanceConsistency(nodeList[nodeList.Count - 1]);
List <string> treeLeafOrderList;
var tree = Newick.NewickTreeFormat(nodeList[nodeList.Count - 1].ToList <GenericNode>(), names, out treeLeafOrderList, minimumOutputTreeLeafs);
Console.WriteLine(tree);
}
