//This Generates Graphs when clicked
private void button2_Click(object sender, EventArgs e)
{
int numGraphs = ((int)trackBar2.Value - (int)trackBar1.Value) / (int)numericUpDown1.Value;
//sanity check on gui
if (numGraphs > 20 && MessageBox.Show("Are you sure you want to generate " + numGraphs + " different graphs?", "Generate Graphs", MessageBoxButtons.YesNo) == System.Windows.Forms.DialogResult.No)
{
return;
}
for (int i = trackBar1.Value; i <= trackBar2.Value; i += (int)numericUpDown1.Value)
{
LightWeightGraph lwg = null;
if (embeddingComboBox.SelectedIndex == 0)
{
lwg = LightWeightGraph.GetGeometricGraph(distMatrix, distances[i]);
}
else if (embeddingComboBox.SelectedIndex == 1)
{
lwg = LightWeightGraph.GetKNNGraph(distMatrix, i);
}
else
{
lwg = LightWeightGraph.GetStackedMST(distMatrix, (int)trackBar1.Value);
}
//Save GML
String folder = pointSetFile.Substring(0, pointSetFile.LastIndexOf('\\'));
lwg.SaveGML(folder + "\\" + graphPrefix + i + ".gml");
openFileDialog2.InitialDirectory = folder;
//Save Graph format
lwg.SaveGraph(folder + "\\" + graphPrefix + i + ".graph");
}
MessageBox.Show("Graphs have been Generated!");
}
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");
}
}