private void btnSelectSequence_Click(object sender, EventArgs e)
{
// Check for empty or duplicate Name
if (string.IsNullOrWhiteSpace(this.txtTaxonName.Text))
{
MessageBox.Show(this.FindForm(), "Please select a name for the taxon.");
return;
}
foreach (object objAktuell in this.listBoxTaxa.Items)
{
if (objAktuell is TaxonObject taxObjAktuell)
{
if (this.txtTaxonName.Text == taxObjAktuell.Name)
{
MessageBox.Show(this.FindForm(), "Please choose a different name for the taxon.");
return;
}
}
}
// Now everything is fine. Build a new TaxoObject and add it to the list
TaxonObject objNew = new TaxonObject(this.txtTaxonName.Text, this.controlSequences.SequencesSelected);
this.listBoxTaxa.Items.Add(objNew);
this.controlSequences.ResetSelectedSequences();
// this.ShowUnselectedSequences();
}
private void btnNeighborJoining_Click(object sender, EventArgs e)
{
// We need to build a Matrix with the differences of the Taxas
var lstItems = this.listBoxTaxa.Items.Cast <TaxonObject>();
decimal[,] decsDifferences = new decimal[lstItems.Count(), lstItems.Count()];
Dictionary <int, string> dicLabels2Position = new Dictionary <int, string>();
// Fill the Labels Dictionary
for (int intIndex = 0; intIndex < lstItems.Count(); intIndex++)
{
// Add the item to the Labels2Position Dictionary
dicLabels2Position.Add(intIndex, lstItems.ElementAt(intIndex).Name);
}
Parallel.For(0, lstItems.Count(), intOuter =>
{
TaxonObject objOuter = lstItems.ElementAt(intOuter);
// Add the compare with itself 0 in the identity
decsDifferences[intOuter, intOuter] = 0m;
Parallel.For(intOuter + 1, lstItems.Count(), intInner =>
{
TaxonObject objInner = lstItems.ElementAt(intInner);
NeedlemanWunsch nw = new NeedlemanWunsch(objOuter.Items, objInner.Items, this.controlOptions.Options, true);
decsDifferences[intOuter, intInner] = this.rdbDistance.Checked ? nw.Distance : nw.NumberOfChanges;
decsDifferences[intInner, intOuter] = this.rdbDistance.Checked ? nw.Distance : nw.NumberOfChanges;
});
});
/*
* for (int intOuter = 0; intOuter < lstItems.Count(); intOuter++)
* {
* TaxonObject objOuter = lstItems.ElementAt(intOuter);
* // Add the item to the Labels2Position Dictionary
* dicLabels2Position.Add(intOuter, objOuter.Name);
* // Add the compare with itself 0 in the identity
* decsDifferences[intOuter, intOuter] = 0m;
*
* // Now align it with the remaining Taxas
* for (int intInner = intOuter + 1; intInner < lstItems.Count(); intInner++)
* {
* TaxonObject objInner = lstItems.ElementAt(intInner);
*
* NeedlemanWunsch nw = new NeedlemanWunsch(objOuter.Items, objInner.Items, this.controlOptions.Options, true);
*
* decsDifferences[intOuter, intInner] = this.rdbDistance.Checked ? nw.Distance : nw.NumberOfChanges;
* decsDifferences[intInner, intOuter] = this.rdbDistance.Checked ? nw.Distance : nw.NumberOfChanges;
* }
* }
*/
// Do the thing!
NeighborJoining joining = new NeighborJoining(decsDifferences, dicLabels2Position);
//Write result tree to selected txt
string logFileString = Path.ChangeExtension(this.txtSavePath.Text, ".log");
File.WriteAllText(this.txtSavePath.Text, joining.NewickTree);
// Write fancy log file
// Reset all Text with nothing so that we can append from now on
File.WriteAllText(logFileString, string.Empty);
for (int intIndex = 0; intIndex < dicLabels2Position.Count; intIndex++)
{
File.AppendAllText(logFileString, dicLabels2Position[intIndex] + Environment.NewLine);
}
File.AppendAllText(logFileString, Environment.NewLine + "Start Matrix" + Environment.NewLine + "------" + Environment.NewLine);
// Matrix to string[]
string[] matrixLines = new string[decsDifferences.GetLength(0)], matrixLinesTree = new string[decsDifferences.GetLength(0)];
for (int line = 0; line <= decsDifferences.GetLength(0) - 1; line++)
{
for (int column = 0; column <= decsDifferences.GetLength(0) - 1; column++)
{
matrixLines[line] = matrixLines[line] + decsDifferences[line, column].ToString("0.#####", CultureInfo.CreateSpecificCulture("en-GB")) + "\t";
matrixLinesTree[line] += joining.TreeMatrix[line, column].ToString("0.#####", CultureInfo.CreateSpecificCulture("en-GB")) + "\t";
}
}
File.AppendAllLines(logFileString, matrixLines);
File.AppendAllText(logFileString, Environment.NewLine + "Tree Matrix" + Environment.NewLine + "------" + Environment.NewLine);
File.AppendAllLines(logFileString, matrixLinesTree);
File.AppendAllText(logFileString, Environment.NewLine + "Mimimal Branch Length + Error" + Environment.NewLine + "------" + Environment.NewLine);
File.AppendAllText(logFileString, $"{joining.MinEdge.ToString("0.#####", CultureInfo.CreateSpecificCulture("en-GB"))} \t\t{(joining.MinEdge / 2m).ToString("0.#####", CultureInfo.CreateSpecificCulture("en-GB"))}");
File.AppendAllText(logFileString, Environment.NewLine + Environment.NewLine);
// Append joining.NodesAndEdges
string[] nodesAndEdges = new string[joining.NodesAndEdges.Count + 2];
nodesAndEdges[0] = "Between" + "\t\t" + "And" + "\t\t" + "Length";
nodesAndEdges[1] = "-------" + "\t\t" + "---" + "\t\t" + "------";
for (int count = 2; count <= joining.NodesAndEdges.Count + 1; count++)
{
Tuple <string, decimal, string> current = joining.NodesAndEdges[count - 2];
nodesAndEdges[count] = current.Item1 + "\t\t" + current.Item3 + "\t\t" + current.Item2.ToString("0.#####", CultureInfo.CreateSpecificCulture("en-GB"));
}
File.AppendAllLines(logFileString, nodesAndEdges);
// CSV Export
string strSavepathCSV = Path.Combine(Path.GetDirectoryName(logFileString), Path.GetFileNameWithoutExtension(logFileString) + ".csv");
using (TextWriter csvWriter = new StreamWriter(strSavepathCSV, false))
{
// Writer the Header
for (int intIndexHeader = 0; intIndexHeader < dicLabels2Position.Count; intIndexHeader++)
{
csvWriter.Write($";{dicLabels2Position[intIndexHeader]}");
}
csvWriter.WriteLine();
// Write the Original Matrix
for (int line = 0; line <= decsDifferences.GetLength(0) - 1; line++)
{
csvWriter.Write(dicLabels2Position[line]);
for (int column = 0; column <= decsDifferences.GetLength(0) - 1; column++)
{
csvWriter.Write($";{decsDifferences[line, column].ToString("0.#####")}");
}
csvWriter.WriteLine();
}
// Write as much ';' as needed in the NewLine
csvWriter.WriteLine(new string(';', dicLabels2Position.Count));
// Write the Tree Matrix
for (int line = 0; line <= joining.TreeMatrix.GetLength(0) - 1; line++)
{
csvWriter.Write(dicLabels2Position[line]);
for (int column = 0; column <= joining.TreeMatrix.GetLength(0) - 1; column++)
{
csvWriter.Write($";{joining.TreeMatrix[line, column].ToString("0.#####")}");
}
csvWriter.WriteLine();
}
csvWriter.Flush();
}
MessageBox.Show(this.FindForm(), "Done!");
}
