/// <summary>
/// Reads a .cluster file into a partition
/// </summary>
/// <param name="filename"></param>
public Partition(String filename)
{
Clusters = new List <Cluster>();
using (StreamReader sr = new StreamReader(filename))
{
String dataString = sr.ReadLine();
String dataType = dataString.Substring(0, dataString.IndexOf(' '));
String dataFileName = dataString.Substring(dataString.IndexOf(' ') + 1);
String folder = filename.Substring(0, filename.LastIndexOf('\\'));
//Get the DataPoints
switch (dataType)
{
case "Points":
Data = new PointSet(dataFileName);
break;
case "DistanceMatrix":
Data = new DistanceMatrix(dataFileName);
break;
case "Graph":
String extension = dataFileName.Substring(dataFileName.LastIndexOf('.') + 1);
if (extension == "gml")
{
Data = LightWeightGraph.GetGraphFromGML(dataFileName);
}
else if (extension == "graph")
{
Data = LightWeightGraph.GetGraphFromFile(dataFileName);
}
break;
default:
throw new InvalidDataException("dataType");
}
//Parse the Clusters
String line = sr.ReadLine();
int numClusters = int.Parse(line.Split(' ')[1]);
for (int i = 0; i < numClusters; i++)
{
Cluster C = new Cluster(i);
int numItems = int.Parse(sr.ReadLine());
line = sr.ReadLine();
String[] split = line.Split(' ');
for (int k = 0; k < numItems; k++)
{
int pointIndex = int.Parse(split[k]);
C.AddPoint(new ClusteredItem(pointIndex));
}
Clusters.Add(C);
}
}
}
static void Main(string[] args)
{
if (args.Length != 4)
{
Console.WriteLine(
"Usage: Program.cs <Healthyfile> <Infectedfile> <Outputfile> <Group> ");
Environment.Exit(0);
}
// AUTOMATING IBD
// We need both a healthy network and an IBD network
// COMMAND LINE: clusteringanalysis.exe healthyNet infectedNet VATorINTorTEN
//convert from gml to graph
String healthyfile = BackSlashRemover(args[0]);
String infectedfile = BackSlashRemover(args[1]);
String healthyFileName = "";
String infectedFileName = "";
String workingDir = Directory.GetCurrentDirectory();
String datapath = workingDir + "/Data";
datapath = BackSlashRemover(datapath);
if (!Directory.Exists(datapath))
{
Directory.CreateDirectory(datapath);
}
String outPath = BackSlashRemover(args[2]);
if (outPath.Split('/').Length == 1)
{
outPath = $"{workingDir}/{outPath}";
}
if (healthyfile.Contains("/"))
{
healthyFileName = healthyfile.Split('/').Last().Split('.').First();
}
if (infectedfile.Contains("/"))
{
infectedFileName = infectedfile.Split('/').Last().Split('.').First();
}
LightWeightGraph healthy = LightWeightGraph.GetGraphFromGML(healthyfile);
LightWeightGraph infected = LightWeightGraph.GetGraphFromGML(infectedfile);
healthy.SaveGraph($"{datapath}/{healthyFileName}.graph");
infected.SaveGraph($"{datapath}/{infectedFileName}.graph");
// Makes a list of what the nodes reference
using (StreamWriter sw = new StreamWriter($"{datapath}/{healthyFileName}.txt", true))
{
for (int i = 0; i < healthy.Nodes.Length; i++)
{
sw.WriteLine(healthy.Nodes[i].sharedName);
}
}
using (StreamWriter sw = new StreamWriter($"{datapath}/{infectedFileName}.txt", true))
{
for (int i = 0; i < infected.Nodes.Length; i++)
{
sw.WriteLine(infected.Nodes[i].sharedName);
}
}
//we don't actually know the number of clusters in each graph - we want to cluster for 1 more than we start with
//so cluster for 1 just to get the file.
//HVATClust clust1 = new HVATClust(lwg2, K, useweights, 1, 0, reassign, hillclimb);
HVATClust healthyClust1 = new HVATClust(healthy, 1, false, 1, 0, false, false);
Partition t1 = healthyClust1.GetPartition();
int healthyClusters = t1.Clusters.Count;
HVATClust infectedClust1 = new HVATClust(infected, 1, false, 1, 0, false, false);
Partition t2 = infectedClust1.GetPartition();
int infectedClusters = t2.Clusters.Count;
// Now we know the intital number of clusters, do the actual clustering
//HVATClust clust1 = new HVATClust(lwg2, K, useweights, 1, 0, reassign, hillclimb);
// This sees if the input cluster type can be parsed as the Enum, and if so
// Uses a switch statement to decide which clustering to run.
if (args.Length == 4)
{
List <DataOutStruct> outData = ConstructList(args[3], healthy, infected, healthyFileName, infectedFileName,
healthyClusters, infectedClusters);
outData = CombineOuts(infected, healthy, outData);
using (StreamWriter sw = new StreamWriter(outPath))
{
for (int i = 0; i < outData.Count(); i++)
{
sw.WriteLine($"{outData[i].Bacteria} {outData[i].GroupNum}");
}
}
Console.WriteLine("Done.");
Console.WriteLine($"Output in: {outPath}");
}
else
{
Console.WriteLine(
"Please enter 3 parameters, in this order:\n " +
"Healthy data path(.gml)\n " +
"Unhealthy data path(.gml)\n " +
"Desired Output Group(listed in Readme)\n");
}
}
