private void PicFileSave_Click(object sender, EventArgs e)
{
SaveFileDialog popart = new SaveFileDialog
{
Filter = "Nexus files (*.nex)|*.nex|All files (*.*)|*.*",
FileName = "popart.nex",
FilterIndex = 1
};
if (popart.ShowDialog() == DialogResult.OK)
{
txtPopArt.Text = popart.FileName;
if (txtPopArt.Text.Contains(" "))
{
string cfile = txtPopArt.Text;
if (File.Exists(PhyloMain.IfRequired(cfile)))
{
File.Delete(cfile);
}
//MessageBox.Show("Spaces in directory or filename are not allowed.\nIt will throw an error.", "No spaces allowed", MessageBoxButtons.OK, MessageBoxIcon.Warning);
//return;
}
btnWritePopArt.Enabled = txtPopArt.Text != "" ? true : false;
}
}
private void RunFigTree(string file)
{
OpenFileDialog tree = new OpenFileDialog
{
CheckFileExists = true,
CheckPathExists = true,
FileName = file,
FilterIndex = 1,
Title = "Open IQ-tree file",
Filter = "Tree file (*.treefile)|*.treefile|Consensus tree (*.contree)|*.contree",
ReadOnlyChecked = true
};
if (tree.ShowDialog() == DialogResult.OK)
{
file = PhyloMain.IfRequired(tree.FileName);
}
figtree = PhyloMain.IfRequired(figtree);
ProcessStartInfo treeshow = new ProcessStartInfo();
treeshow.FileName = figtree;
treeshow.Arguments = file;
treeshow.UseShellExecute = false;
Process.Start(treeshow);
}
private void RunProg(string prog, string options, bool param)
{
if (!param)
{
MessageBox.Show(options, "Parameters used for calculation", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
prog = PhyloMain.IfRequired(prog);
ProcessStartInfo execute = new ProcessStartInfo();
execute.FileName = prog;
execute.Arguments = options;
execute.WindowStyle = ProcessWindowStyle.Minimized;
execute.UseShellExecute = true;
execute.RedirectStandardOutput = false;
using (Process exeProcess = Process.Start(execute))
{
panel1.Visible = true;
Thread.Sleep(100);
SetParent(exeProcess.MainWindowHandle, panel1.Handle);
SetWindowLong(exeProcess.MainWindowHandle, GWL_STYLE, WS_VISIBLE);
MoveWindow(exeProcess.MainWindowHandle, 0, 0, panel1.Width, panel1.Height, true);
exeProcess.WaitForExit();
}
panel1.Visible = false;
}
private void BtnGblocks_Click(object sender, EventArgs e)
{
string align = txtAlignment.Text;
if (PhyloMain.IDlines(align))
{
MessageBox.Show("GBlocks can't be executed, because there are '>' lines present larger than 50 characters.", "Fasta ID line too long", MessageBoxButtons.OK, MessageBoxIcon.Warning);
return;
}
string gap = cboGaps.Text;
string b5 = "";
switch (gap)
{
case "None":
b5 = "n";
break;
case "With Half":
b5 = "h";
break;
case "All":
b5 = "a";
break;
}
options = " -t=d -b3=" + txtB3.Text + " -b4=" + txtB4.Text + " -b5=" + b5 + " -e=.gb";
if (File.Exists(align))
{
RunGblocks(align, options);
}
}
private void BtnMerge_Click(object sender, EventArgs e)
{
options = " --auto --leavegappyregion --adjustdirection --add " + "\"" + txtFastaFile2.Text + "\" --reorder \"" + txtFastaFile1.Text + "\" > \"" + txtSaveAs.Text + "\"";
btnMerge.Enabled = false;
if (!param)
{
MessageBox.Show(options, "Parameters used for calculation", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
mafft = PhyloMain.IfRequired(mafft);
ProcessStartInfo execute = new ProcessStartInfo();
execute.FileName = mafft;
execute.Arguments = options;
execute.WindowStyle = ProcessWindowStyle.Minimized;
execute.UseShellExecute = false;
execute.RedirectStandardOutput = false;
using (Process exeProcess = Process.Start(execute))
{
panel1.Visible = true;
Thread.Sleep(100);
SetParent(exeProcess.MainWindowHandle, panel1.Handle);
SetWindowLong(exeProcess.MainWindowHandle, GWL_STYLE, WS_VISIBLE);
MoveWindow(exeProcess.MainWindowHandle, 0, 0, panel1.Width, panel1.Height, true);
exeProcess.WaitForExit();
}
panel1.Visible = false;
if (chkOpenAlignment.Checked)
{
RunBioEdit(txtSaveAs.Text);
}
}
private void SequenceMatrix_Load(object sender, EventArgs e)
{
sequencematrix = PhyloMain.IfRequired(sequencematrix);
ProcessStartInfo execute = new ProcessStartInfo();
execute.FileName = sequencematrix;
execute.UseShellExecute = false;
Process.Start(execute);
}
private void BtnWritePopArt_Click(object sender, EventArgs e)
{
string pfile = PhyloMain.IfRequired(txtPopArt.Text);
StreamWriter pop = new StreamWriter(pfile, true);
pop.WriteLine("#NEXUS");
pop.WriteLine("BEGIN TAXA;");
pop.WriteLine("DIMENSIONS NTAX=" + ntax + ";");
pop.WriteLine("TAXLABELS");
for (int x = 1; x <= Convert.ToInt16(ntax); x++)
{
pop.WriteLine("Hap_" + x.ToString());
}
pop.WriteLine(";");
pop.WriteLine("END;");
pop.WriteLine(" ");
pop.WriteLine("BEGIN CHARACTERS;");
pop.WriteLine("DIMENSIONS NCHAR=" + nchar + ";");
pop.WriteLine("FORMAT DATATYPE=DNA MISSING=? GAP=- MATCHCHAR=. ;");
pop.WriteLine("MATRIX");
for (int x = 0; x < Convert.ToInt16(ntax); x++)
{
pop.WriteLine(hapchars[x]);
}
pop.WriteLine(";");
pop.WriteLine("END;");
pop.WriteLine(" ");
pop.WriteLine("BEGIN TRAITS;");
pop.WriteLine("Dimensions NTRAITS=" + numTraits.Value.ToString() + ";");
pop.WriteLine("Format labels=yes missing=? separator=Comma;");
string traitlabels = "";
for (int c = 1; c < dgvTraits.ColumnCount; c++)
{
traitlabels += dgvTraits.Columns[c].HeaderText + " ";
}
pop.WriteLine("TraitLabels " + traitlabels + ";");
pop.WriteLine("Matrix");
string values = "";
for (int r = 0; r < dgvTraits.RowCount; r++)
{
for (int c = 1; c < dgvTraits.ColumnCount; c++)
{
values += dgvTraits.Rows[r].Cells[c].Value + ",";
}
values = values.Substring(0, values.Length - 1);
pop.WriteLine("Hap_" + (r + 1).ToString() + " " + values);
values = "";
}
pop.WriteLine(";");
pop.WriteLine("END;");
pop.Close();
btnWritePopArt.Enabled = false;
}
private void RunBioEdit(string file)
{
string cbioedit = PhyloMain.IfRequired(bioedit);
string cfile = PhyloMain.IfRequired(file);
ProcessStartInfo alignshow = new ProcessStartInfo();
alignshow.FileName = cbioedit;
alignshow.Arguments = cfile;
alignshow.UseShellExecute = false;
Process.Start(alignshow);
}
private void MatGAT_Load(object sender, EventArgs e)
{
similarity = PhyloMain.IfRequired(similarity);
string folder = Path.GetDirectoryName(similarity);
Directory.SetCurrentDirectory(folder);
ProcessStartInfo simid = new ProcessStartInfo();
simid.FileName = similarity;
simid.UseShellExecute = true;
Process.Start(simid);
}
private void RunGblocks(string file, string opt)
{
string cgblocks = PhyloMain.IfRequired(gblocks);
file = PhyloMain.IfRequired(file);
ProcessStartInfo gb = new ProcessStartInfo();
gb.FileName = cgblocks;
gb.Arguments = file + opt;
gb.UseShellExecute = false;
gb.RedirectStandardOutput = false;
Process.Start(gb);
}
private void RunProg(string prog, string options, bool param)
{
if (!param)
{
MessageBox.Show(options, "Parameters used for calculation", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
txtWarning.Visible = true;
prog = PhyloMain.IfRequired(prog);
ProcessStartInfo convert = new ProcessStartInfo();
convert.FileName = prog;
convert.Arguments = options;
convert.UseShellExecute = false;
Process.Start(convert);
txtWarning.Visible = false;
}
private void BtnSave_Click(object sender, EventArgs e)
{
btnSave.Enabled = false;
string line;
SaveFileDialog partition = new SaveFileDialog()
{
Filter = "Nexus files (*.nex)|*.nex|All files (*.*)|*.*",
FilterIndex = 1,
FileName = "partition.nex"
};
if (partition.ShowDialog() == DialogResult.OK)
{
partfile = partition.FileName;
}
else
{
return;
}
string cpartfile = PhyloMain.IfRequired(partfile);
StreamWriter sb = new StreamWriter(cpartfile);
//sb.WriteLine("#NEXUS");
sb.WriteLine("BEGIN SETS;");
for (int r = 0; r < dgvPartitions.RowCount; r++)
{
line = "CHARSET " + dgvPartitions.Rows[r].Cells[0].Value + " = " + dgvPartitions.Rows[r].Cells[1].Value + "-" + dgvPartitions.Rows[r].Cells[2].Value + ";";
sb.WriteLine(line);
charset += line.Substring(8) + ", ";
}
if (chkChar.Checked)
{
string newChar = charset.Replace(" = ", ":");
string newChar2 = newChar.Replace(";", "");
charset = newChar2.Substring(0, newChar2.Length - 2);
sb.WriteLine("CHARPARTITION " + txtMyChar.Text + "=" + charset + ";");
}
sb.WriteLine("END;");
sb.Close();
btnSave.Enabled = true;
txtTo.Clear();
txtFrom.Clear();
btnClear.Focus();
partsaved = true;
btnHomPart.Enabled = true;
Msg("part");
}
private void BtnLikelihood_Click(object sender, EventArgs e)
{
iqtree = PhyloMain.IfRequired(iqtree);
file = PhyloMain.IfRequired(file);
btnLikelihood.Enabled = false;
options = " -s " + "\"" + file + "\"" + " -redo -nt AUTO -lmap 2000 -n 0 -m TESTONLY";
ProcessStartInfo execute = new ProcessStartInfo
{
FileName = iqtree,
Arguments = options,
WindowStyle = ProcessWindowStyle.Minimized,
UseShellExecute = false,
RedirectStandardOutput = false
};
using (Process exeProcess = Process.Start(execute))
{
panel1.Visible = true;
Thread.Sleep(100);
SetParent(exeProcess.MainWindowHandle, panel1.Handle);
SetWindowLong(exeProcess.MainWindowHandle, GWL_STYLE, WS_VISIBLE);
MoveWindow(exeProcess.MainWindowHandle, 0, 0, panel1.Width, panel1.Height, true);
exeProcess.WaitForExit();
}
panel1.Visible = false;
btnLikelihood.Enabled = true;
MessageBox.Show("Three files are created: " + file + ".iqtree, " + file + ".lmap.svg, " + file + ".lmap.eps", "Calculation finished succesfully", MessageBoxButtons.OK, MessageBoxIcon.Information);
if (chkLogfile.Checked)
{
string cfile = "\"" + file + ".iqtree\"";
Process n = new Process();
n.StartInfo.FileName = "notepad.exe";
n.StartInfo.Arguments = cfile; // file + ".iqtree";
n.Start();
n.Close();
}
if (chkDiagram.Checked)
{
string cfile = "\"" + file + ".lmap.svg\"";
Process m = new Process();
m.StartInfo.FileName = magick;
m.StartInfo.Arguments = cfile; // file + ".iqtree";
m.Start();
m.Close();
}
}
private void PicSaveTree_Click(object sender, EventArgs e)
{
string afile = txtFastaFile.Text;
string bfile = Path.GetFileNameWithoutExtension(afile) + ".tre";
SaveFileDialog align = new SaveFileDialog
{
Filter = "Newick tree (*.tre)|*.tre",
FilterIndex = 2,
FileName = bfile
};
if (align.ShowDialog() == DialogResult.OK)
{
txtRaxMLtree.Text = align.FileName;
}
if (txtFastaFile.Text != "")
{
folder = Path.GetDirectoryName(txtFastaFile.Text);
string raxmlfile = Path.GetFileName(txtRaxMLtree.Text);
if (File.Exists(PhyloMain.IfRequired(folder + "\\RAxML_info." + raxmlfile)))
{
DialogResult answer = MessageBox.Show("A calculation with the same name already exists.\nDo you want to delete this session?", "RAxML calculation exists", MessageBoxButtons.YesNo, MessageBoxIcon.Warning);
switch (answer)
{
case DialogResult.Yes:
{
foreach (string f in Directory.EnumerateFiles(PhyloMain.IfRequired(folder), "RAxML*.*"))
{
File.Delete(PhyloMain.IfRequired(f));
}
break;
}
case DialogResult.No:
{
txtRaxMLtree.Clear();
return;
}
}
}
}
}
private void BtnSave_Click(object sender, EventArgs e)
{
OleDbCommand SQLQuery = new OleDbCommand();
OleDbConnection con = new OleDbConnection(PhyloMain.connectionString);
SQLQuery.Connection = con;
saved = true;
btnSave.Enabled = false;
foreach (ListViewItem item in listView1.Items)
{
int id = Convert.ToInt16(item.SubItems[0].Text);
string progname = item.SubItems[1].Text;
string content = item.SubItems[2].Text;
string query = "UPDATE Progs SET ProgName='" + progname + "', Location='" + content + "' WHERE ID=" + id;
SQLQuery.CommandText = query;
con.Open();
SQLQuery.ExecuteNonQuery();
con.Close();
}
PhyloMain.param = listView1.Items[19].SubItems[2].Text == "yes" ? false : true;
Progs_Load(sender, e);
PhyloMain.ReadSettings(sender, e);
}
private void BtnHomPart_Click(object sender, EventArgs e)
{
if (!partsaved)
{
MessageBox.Show("First create and save a partition file with charpartition", "No partition file", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
string cpartfile = PhyloMain.IfRequired(partfile); // + ".log"
string cnexus = PhyloMain.IfRequired(txtNexusFile.Text);
string logfile = Path.GetFileNameWithoutExtension(txtNexusFile.Text);
string curdir = Path.GetDirectoryName(txtNexusFile.Text);
logfile = PhyloMain.IfRequired(curdir + "\\" + logfile + ".log");
StreamReader addpart = new StreamReader(cpartfile);
string all = addpart.ReadToEnd();
string repall = all.Replace("#NEXUS", "");
addpart.Close();
File.AppendAllText(cnexus, repall);
StreamWriter hompart = new StreamWriter(cnexus, true);
hompart.WriteLine(" ");
hompart.WriteLine("BEGIN PAUP;");
hompart.WriteLine("log file=" + logfile + " append;");
//hompart.WriteLine("set increase;");
hompart.WriteLine("exclude uninf;");
hompart.WriteLine("set autoclose=yes;");
hompart.WriteLine("set criterion=parsimony;");
hompart.WriteLine("set increase=auto;");
hompart.WriteLine("hompart partition=" + txtMyChar.Text + " nreps=100 search=heuristic / start=stepwise addseq=random nreps=5 savereps=no randomize=addseq rstatus=no swap=tbr hold=1 multree=yes timelimit=600;");
hompart.WriteLine("include all;");
hompart.WriteLine("log stop;");
hompart.WriteLine("END;");
hompart.Close();
Msg("hompart");
}
private void BtnFastTree_Click(object sender, EventArgs e)
{
SynchronizationContext originalContext = SynchronizationContext.Current;
List <ProcessStartInfo> processes = new List <ProcessStartInfo>();
string align = PhyloMain.IfRequired(txtFastaFile.Text);
string tree = PhyloMain.IfRequired(txtFasttree.Text);
string fastprog = PhyloMain.IfRequired(fasttree);
options = " -gamma -gtr -nt " + align + " > " + tree;
if (!param)
{
MessageBox.Show(options, "Parameters used for calculation", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
ProcessStartInfo process1 = new ProcessStartInfo();
process1.UseShellExecute = false;
process1.RedirectStandardOutput = false;
if (chkCommand.Checked)
{
process1.WindowStyle = ProcessWindowStyle.Normal;
}
else
{
process1.WindowStyle = ProcessWindowStyle.Hidden;
process1.UseShellExecute = true;
process1.RedirectStandardOutput = false;
process1.CreateNoWindow = true;
}
process1.FileName = "cmd.exe ";
process1.Arguments = "/C " + fastprog + " " + options;
processes.Add(process1);
if (chkViewTree.Checked)
{
ProcessStartInfo process2 = new ProcessStartInfo();
string view = PhyloMain.IfRequired(figtree);
process2.FileName = view;
process2.Arguments = tree;
process2.UseShellExecute = false;
process2.RedirectStandardOutput = false;
processes.Add(process2);
}
if (chkCommand.Checked)
{
btnFastTree.Enabled = false;
try
{
using (Process exeProcess = Process.Start(process1))
{
panel1.Visible = true;
Thread.Sleep(100);
SetParent(exeProcess.MainWindowHandle, panel1.Handle);
SetWindowLong(exeProcess.MainWindowHandle, GWL_STYLE, WS_VISIBLE);
MoveWindow(exeProcess.MainWindowHandle, 0, 0, panel1.Width, panel1.Height, true);
exeProcess.WaitForExit();
}
panel1.Visible = false;
btnFastTree.Enabled = true;
}
catch (Exception)
{
MessageBox.Show("The program " + fastprog + " encountered on error.", "Execution halted", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
Thread th = new Thread(() =>
{
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { lblRunning.Visible = true; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnFastTree.Enabled = false; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnNew.Enabled = false; }, null); });
for (int i = 0; i < processes.Count; i++)
{
try
{
using (Process exeProcess = Process.Start(processes[i]))
{
exeProcess.WaitForExit();
}
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message, "End of execution", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { lblRunning.Visible = false; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnFastTree.Enabled = true; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnNew.Enabled = true; }, null); });
}
});
th.Start();
}
if (chkCommand.Checked)
{
if (chkViewTree.Checked)
{
Process.Start(figtree, tree);
}
}
}
private void BtnStartRaxML_Click(object sender, EventArgs e)
{
if (txtFastaFile.Text == "" || txtRaxMLtree.Text == "")
{
return;
}
string fasta = Path.GetFileName(txtFastaFile.Text);
string mltree = Path.GetFileName(txtRaxMLtree.Text);
string program = raxml;
folder = Path.GetDirectoryName(txtRaxMLtree.Text);
options = " -s \"" + fasta + "\" -n \"" + mltree + "\" -m GTRCAT -f a -x 5434 -p 3493";
if (chkAmountTaxa.Checked)
{
options = " -D" + options;
}
else
{
options = " -d" + options;
}
if (chkDefault.Checked)
{
options += " -N autoMRE";
}
else
{
options += " -N " + txtBootstraps.Text;
}
if (chkThreads.Checked)
{
program = threads;
options += " -T " + txtThreads.Text;
}
string bfile = Path.GetFileNameWithoutExtension(txtFastaFile.Text);
string raxmlfile = Path.GetFileName(txtRaxMLtree.Text);
if (File.Exists(PhyloMain.IfRequired(folder + "\\RAxML_info." + raxmlfile)))
{
DialogResult answer = MessageBox.Show("A calculation with the same name already exists.\nDo you want to delete this session?", "RAxML calculation exists", MessageBoxButtons.YesNo, MessageBoxIcon.Warning);
switch (answer)
{
case DialogResult.Yes:
{
foreach (string f in Directory.EnumerateFiles(PhyloMain.IfRequired(folder), "RAxML*.*"))
{
File.Delete(PhyloMain.IfRequired(f));
}
break;
}
case DialogResult.No:
{
txtRaxMLtree.Clear();
return;
}
}
}
if (!param)
{
MessageBox.Show(options, "Parameters used for calculation", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
Directory.SetCurrentDirectory(PhyloMain.IfRequired(folder));
raxml = PhyloMain.IfRequired(raxml);
ProcessStartInfo process1 = new ProcessStartInfo();
process1.UseShellExecute = false;
process1.RedirectStandardOutput = false;
if (chkCommand.Checked)
{
process1.WindowStyle = ProcessWindowStyle.Normal;
}
else
{
process1.WindowStyle = ProcessWindowStyle.Hidden;
process1.UseShellExecute = true;
process1.RedirectStandardOutput = false;
process1.CreateNoWindow = true;
}
process1.FileName = raxml;
process1.Arguments = options;
processes.Add(process1);
if (chkViewTree.Checked)
{
string tree = PhyloMain.IfRequired(folder + "\\RAxML_bipartitions." + bfile + ".tre");
ProcessStartInfo process2 = new ProcessStartInfo();
string view = PhyloMain.IfRequired(figtree);
process2.FileName = view;
process2.Arguments = tree;
process2.UseShellExecute = false;
process2.RedirectStandardOutput = false;
processes.Add(process2);
}
if (chkCommand.Checked)
{
btnStartRaxML.Enabled = false;
btnNew.Enabled = false;
try
{
using (Process exeProcess = Process.Start(process1))
{
panel1.Visible = true;
Thread.Sleep(100);
SetParent(exeProcess.MainWindowHandle, panel1.Handle);
SetWindowLong(exeProcess.MainWindowHandle, GWL_STYLE, WS_VISIBLE);
MoveWindow(exeProcess.MainWindowHandle, 0, 0, panel1.Width, panel1.Height, true);
exeProcess.WaitForExit();
}
panel1.Visible = false;
btnStartRaxML.Enabled = true;
btnNew.Enabled = true;
}
catch (Exception)
{
MessageBox.Show("The program " + raxml + " encountered on error.", "Execution halted", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
Thread th = new Thread(() =>
{
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { lblRunning.Visible = true; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnStartRaxML.Enabled = false; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnNew.Enabled = false; }, null); });
for (int i = 0; i < processes.Count; i++)
{
try
{
using (Process exeProcess = Process.Start(processes[i]))
{
exeProcess.WaitForExit();
}
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message, "End of execution", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { lblRunning.Visible = false; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnStartRaxML.Enabled = true; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnNew.Enabled = true; }, null); });
}
});
th.Start();
}
if (chkCommand.Checked)
{
if (chkViewTree.Checked)
{
string tree = PhyloMain.IfRequired(folder + "\\RAxML_bipartitions." + bfile + ".tre");
Process.Start(figtree, tree);
}
}
//btnStartRaxML.Enabled = false;
//btnNew.Enabled = false;
//RunProg(program, options, param);
//btnStartRaxML.Enabled = true;
//btnNew.Enabled = true;
//if (chkViewTree.Checked)
//{
// string tree = PhyloMain.IfRequired(folder + "\\RAxML_bipartitions." + bfile + ".tre");
// RunFigTree(tree);
//}
}
private void RunProg(string prog, string options, bool param)
{
btnStartBioEdit.Enabled = false;
SynchronizationContext originalContext = SynchronizationContext.Current;
if (!param)
{
MessageBox.Show(options, "Parameters used for calculation", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
prog = PhyloMain.IfRequired(prog);
ProcessStartInfo execute = new ProcessStartInfo();
if (chkCommand.Checked)
{
execute.WindowStyle = ProcessWindowStyle.Normal;
}
else
{
execute.WindowStyle = ProcessWindowStyle.Hidden;
execute.RedirectStandardOutput = true;
execute.CreateNoWindow = true;
}
execute.UseShellExecute = false;
execute.FileName = prog;
execute.Arguments = options;
if (chkCommand.Checked)
{
btnAlign.Enabled = false;
try
{
using (Process exeProcess = Process.Start(execute))
{
panel1.Visible = true;
Thread.Sleep(100);
SetParent(exeProcess.MainWindowHandle, panel1.Handle);
SetWindowLong(exeProcess.MainWindowHandle, GWL_STYLE, WS_VISIBLE);
MoveWindow(exeProcess.MainWindowHandle, 0, 0, panel1.Width, panel1.Height, true);
exeProcess.WaitForExit();
}
}
catch (Exception)
{
MessageBox.Show("The program " + prog + " encountered a problem.", "Execution halted", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
panel1.Visible = false;
//btnAlign.Enabled = true;
}
else
{
Thread th = new Thread(() =>
{
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { label11.Visible = true; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnAlign.Enabled = false; }, null); });
try
{
using (Process exeProcess = Process.Start(execute))
{
exeProcess.WaitForExit();
}
}
catch (Exception ex)
{
MessageBox.Show("The program " + prog + " encountered a problem.\n\n" + ex.Message, "Execution halted", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { label11.Visible = false; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnAlign.Enabled = true; }, null); });
});
th.Start();
}
btnStartBioEdit.Enabled = true;
btnAlign.Enabled = true;
}
private void BtnRun_Click(object sender, EventArgs e)
{
List <ProcessStartInfo> processes = new List <ProcessStartInfo>();
string tree = "";
picFtree.Visible = false;
picView.Visible = false;
picAlign.Visible = true;
string fasta = txtDirectoryPath.Text + "\\" + textBox1.Text;
string[] temp = textBox1.Text.Split('.');
string align = txtDirectoryPath.Text + "\\" + temp[0] + ".afa";
string options = "";
if (PhyloMain.node == "Node31" || PhyloMain.node == "Node32")
{
options = " --localpair --adjustdirection --maxiterate 1000 --reorder \"" + fasta + "\" > \"" + align + "\"";
}
if (PhyloMain.node == "Node33" || PhyloMain.node == "Node34")
{
options = " -in \"" + fasta + "\" -out \"" + align + "\" -maxiters 16";
}
ProcessStartInfo process = new ProcessStartInfo();
process.FileName = aprog;
process.Arguments = options;
process.UseShellExecute = true;
process.RedirectStandardOutput = false;
if (!chkCommand.Checked)
{
process.WindowStyle = ProcessWindowStyle.Hidden;
}
else
{
process.WindowStyle = ProcessWindowStyle.Normal;
}
processes.Add(process);
picFtree.Visible = true;
string fastprog = PhyloMain.IfRequired(tprog);
if (PhyloMain.node == "Node31" || PhyloMain.node == "Node33")
{
tree = txtDirectoryPath.Text + "\\" + temp[0] + ".tre";
options = " -gamma -gtr -nt \"" + align + "\" > \"" + tree + "\"";
ProcessStartInfo process1 = new ProcessStartInfo();
process1.FileName = "cmd.exe ";
process1.Arguments = "/C " + fastprog + " " + options;
process1.UseShellExecute = true;
process1.RedirectStandardOutput = false;
if (!chkCommand.Checked)
{
process1.WindowStyle = ProcessWindowStyle.Hidden;
}
else
{
process1.WindowStyle = ProcessWindowStyle.Normal;
}
processes.Add(process1);
}
else
{
if (PhyloMain.node == "Node32" || PhyloMain.node == "Node34")
{
tree = txtDirectoryPath.Text + "\\" + temp[0] + "_IQ";
options = " -s " + "\"" + align + "\"" + " -redo -nt AUTO -nm 1000 -m MFP+MERGE -abayes -alrt 1000 -bb 1000 -pre " + "\"" + tree + "\"";
ProcessStartInfo process1 = new ProcessStartInfo();
process1.FileName = fastprog;
process1.Arguments = options;
process1.UseShellExecute = false;
process1.RedirectStandardOutput = true;
if (!chkCommand.Checked)
{
process1.WindowStyle = ProcessWindowStyle.Hidden;
}
else
{
process1.WindowStyle = ProcessWindowStyle.Normal;
}
processes.Add(process1);
}
}
picView.Visible = true;
string file = "";
if (PhyloMain.node == "Node31" || PhyloMain.node == "Node33")
{
file = PhyloMain.IfRequired(tree);
}
if (PhyloMain.node == "Node32" || PhyloMain.node == "Node34")
{
file = PhyloMain.IfRequired(tree + ".treefile");
}
string view = PhyloMain.IfRequired(vprog);
ProcessStartInfo process2 = new ProcessStartInfo();
process2.FileName = view;
process2.Arguments = file;
process2.UseShellExecute = false;
process2.RedirectStandardOutput = false;
if (!chkCommand.Checked)
{
process2.WindowStyle = ProcessWindowStyle.Hidden;
}
else
{
process2.WindowStyle = ProcessWindowStyle.Normal;
}
processes.Add(process2);
Thread th = new Thread(() =>
{
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { lblRunning.Visible = true; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnRun.Enabled = false; }, null); });
for (int i = 0; i < processes.Count; i++)
{
try
{
using (Process exeProcess = Process.Start(processes[i]))
{
exeProcess.WaitForExit();
}
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message, "End of execution", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { lblRunning.Visible = false; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnRun.Enabled = false; }, null); });
}
});
th.Start();
picAlign.Visible = false;
picFtree.Visible = false;
picView.Visible = false;
textBox1.Clear();
}
private void BtnAlign_Click(object sender, EventArgs e)
{
btnAlign.Enabled = false;
options = "";
if (rdbClustalW.Checked)
{
string options = " -ALIGN -CONVERT -OUTPUT=fasta -INFILE=\"" + txtFastaFile.Text + "\" -OUTFILE=\"" + txtAlignment.Text + "\" -BOOTSTRAP=" + txtBootstrap.Text;
if (chkNJtree.Checked)
{
options += " -TREE";
}
if (rdbAligned.Checked)
{
options += " -OUTORDER=aligned";
}
else
{
options += " -OUTORDER=input";
}
RunProg(clustalw, options, param);
}
if (rdbMuscle.Checked)
{
string options = " -in \"" + txtFastaFile.Text + "\" -out \"" + txtAlignment.Text + "\" -maxiters " + txtMuscleIterations.Text;
if (chkDiag.Checked)
{
options += " -diags1";
}
RunProg(muscle, options, param);
}
if (rdbMAFFT.Checked)
{
if (rdbFFT1.Checked)
{
options = " --retree " + cboRetree.Text;
}
if (rdbEINS.Checked)
{
options = " --genafpair";
}
if (rdbLINS.Checked)
{
options = " --localpair";
}
if (rdbGINS.Checked)
{
options = " --globalpair";
}
if (chkAdjust.Checked)
{
options += " --adjustdirection";
}
options += " --maxiterate 1000 --reorder \"" + txtFastaFile.Text + "\" > \"" + txtAlignment.Text + "\"";
RunProg(mafft, options, param);
}
if (chkGblocks.Checked)
{
if (PhyloMain.IDlines(txtAlignment.Text))
{
MessageBox.Show("GBlocks can't be executed, because there are '>' lines present larger than 50 characters.", "Fasta ID line too long", MessageBoxButtons.OK, MessageBoxIcon.Warning);
return;
}
string gap = cboGaps.Text;
string b5 = "";
switch (gap)
{
case "None":
b5 = "n";
break;
case "With Half":
b5 = "h";
break;
case "All":
b5 = "a";
break;
}
options = " -t=d -b3=" + txtB3.Text + " -b4=" + txtB4.Text + " -b5=" + b5 + " -e=.gb";
RunGblocks(txtAlignment.Text, options);
}
btnAlign.Enabled = true;
//btnStartBioEdit.Enabled = true;
}
private void BtnSearch_Click_1(object sender, EventArgs e)
{
string length = "";
string output = PhyloMain.IfRequired(txtOutput.Text);
string perlfile = progsdir + "\\ncbi_search.pl";
string query;
string maxitems = txtMaxItems.Text;
if (rdbNucleotide.Checked)
{
if (txtMinLength.Text == "" && txtMaxLength.Text == "")
{
length = "0";
}
if (txtMinLength.Text != "" & txtMaxLength.Text == "")
{
length = txtMinLength.Text + ":" + "99999999";
}
if (txtMaxLength.Text != "" && txtMinLength.Text == "")
{
length = "0" + ":" + txtMaxLength.Text;
}
if (txtMinLength.Text != "" && txtMaxLength.Text != "")
{
length = txtMinLength.Text + ":" + txtMaxLength.Text;
}
if (length == "0")
{
query = "\"" + txtOrganism.Text + "[ORGN] AND " + cboProduct.Text + "\"";
}
else
{
query = "\"" + txtOrganism.Text + "[ORGN] AND " + length + "[SLEN] AND " + cboProduct.Text + "\"";
}
query += " -d nucleotide -r fasta -o " + output;
}
else
{
query = "\"" + txtOrganism.Text + "\" -d pubmed -r abstract -o " + output;
}
if (maxitems != "")
{
query += " -m " + Convert.ToInt16(maxitems);
}
query = perlfile + " -q " + query;
if (!param)
{
MessageBox.Show(query, "Parameters used for calculation", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
if (File.Exists(output))
{
File.Delete(output);
}
ProcessStartInfo process1 = new ProcessStartInfo();
process1.UseShellExecute = false;
process1.RedirectStandardOutput = false;
process1.WindowStyle = ProcessWindowStyle.Hidden;
process1.UseShellExecute = true;
process1.RedirectStandardOutput = false;
process1.CreateNoWindow = true;
process1.FileName = "cmd.exe ";
process1.Arguments = "/C " + perl + " " + query;
processes.Add(process1);
if (chkOpenOutput.Checked)
{
if (rdbNucleotide.Checked)
{
ProcessStartInfo showresult = new ProcessStartInfo();
showresult.FileName = bioedit;
showresult.Arguments = output;
showresult.UseShellExecute = false;
showresult.RedirectStandardOutput = false;
processes.Add(showresult);
}
else
{
ProcessStartInfo showresult = new ProcessStartInfo();
showresult.FileName = "notepad.exe";
showresult.Arguments = output;
showresult.UseShellExecute = false;
showresult.RedirectStandardOutput = false;
processes.Add(showresult);
}
}
Thread th = new Thread(() =>
{
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { txtWarning.Visible = true; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnSearch.Enabled = false; }, null); });
for (int i = 0; i < processes.Count; i++)
{
try
{
using (Process exeProcess = Process.Start(processes[i]))
{
exeProcess.WaitForExit();
}
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message, "End of execution", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { txtWarning.Visible = false; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnSearch.Enabled = true; }, null); });
}
});
th.Start();
}
private void BtnConvert_Click(object sender, EventArgs e)
{
txtWarning.Visible = true;
btnReset.Focus();
btnConvert.Enabled = false;
ConvertedFile = txtConvertedFile.Text;
//in case Fasta is opened
if (txtFastaFile.Text != "")
{
fasta = true;
}
if (txtOpenTree.Text != "")
{
fasta = false;
}
string[] Ci_item = Ci.Split('-');
totRows = Sheet1.Cells.SpecialCells(Excel.XlCellType.xlCellTypeLastCell).Row;
string sFileName = fasta ? txtFastaFile.Text : txtOpenTree.Text;
string[] props_item = props.Split('-');
var content = string.Empty;
StreamReader sBuf = new StreamReader(sFileName);
content = sBuf.ReadToEnd();
sBuf.Close();
StreamWriter sb = new StreamWriter(ConvertedFile);
for (int v = 2; v <= totRows; v++)
{
string FullName = "";
string Details = "";
string DetailList = "";
string StrainID = Sheet1.Cells[v, 1].Value;
string species = Sheet1.Cells[v, 2].Value;
FullName = StrainID + " " + species;
if (props != "")
{
for (int y = 0; y < props_item.Length; y++)
{
int k = Convert.ToInt16(Ci_item[y]);
Details = Sheet1.Cells[v, k + 3].Value;
if (Details != null)
{
DetailList += Details + txtPiping.Text;
Details = null;
}
}
}
if (DetailList != "")
{
DetailList = " [" + DetailList.Substring(0, DetailList.Length - 1) + "]";
content = fasta ? content.Replace(StrainID, FullName + DetailList) : content.Replace(StrainID, "'" + FullName + DetailList + "'");
}
else
{
content = fasta ? content.Replace(StrainID, FullName) : content.Replace(StrainID, "'" + FullName + "'");
}
}
sb.Write(content);
sb.Close();
LabelBook.Close();
MyApp.Quit();
//release objects
releaseObject(LabelBook);
releaseObject(MyApp);
txtFinished.Text = "Conversion finished. File saved as:" + Environment.NewLine + txtConvertedFile.Text;
txtFinished.Visible = true;
txtWarning.Visible = false;
if (chkConvFasta.Checked)
{
bioedit = PhyloMain.IfRequired(bioedit);
Process show = new Process();
show.StartInfo.FileName = bioedit;
show.StartInfo.Arguments = PhyloMain.IfRequired(ConvertedFile);
show.Start();
}
if (chkConvTree.Checked)
{
figtree = PhyloMain.IfRequired(figtree);
Process show = new Process();
show.StartInfo.FileName = figtree;
show.StartInfo.Arguments = PhyloMain.IfRequired(ConvertedFile);
show.Start();
}
}
private void BtnStart_Click(object sender, EventArgs e)
{
//folder = Path.GetDirectoryName(txtFastaFile.Text);
string tempalign = folder + "\\tempalign.fas";
tempalign = PhyloMain.IfRequired(tempalign);
string align = cboAlign.Text;
switch (align)
{
case "Muscle":
options = " -maxiters 12 -in \"" + txtFastaFile.Text + "\" -out " + tempalign;
break;
case "MAFFT":
options = " --maxiterate 1000 --reorder --adjustdirection \"" + txtFastaFile.Text + "\" > " + tempalign;
break;
case "Clustal":
options = " -ALIGN -CONVERT -OUTORDER=aligned -OUTPUT=fasta -INFILE=\"" + txtFastaFile.Text + "\" -OUTFILE=" + tempalign;
break;
}
//start alignment program
RunProg(aprog, options, param);
temptree = Path.GetFileNameWithoutExtension(txtFastaFile.Text);
string tree = cboTree.Text;
switch (tree)
{
case "FastTree":
temptree = PhyloMain.IfRequired(folder + "\\" + temptree + ".tre");
options = "/c " + fasttree + " -gamma -gtr -nt " + tempalign + " > " + temptree;
break;
case "IQ-tree":
temptree = PhyloMain.IfRequired(folder + "\\" + temptree + "_IQ");
options = " -s " + tempalign + " -redo -nt AUTO -nm 1000 -pre " + temptree;
break;
case "RaxML":
tempalign = Path.GetFileName(tempalign);
options = " -s \"" + tempalign + "\" -n \"" + temptree + "\" -m GTRCAT -f a -N autoMRE -x 9363 -p 4301";
temptree = PhyloMain.IfRequired(folder + "\\" + "RAxML_bipartitions." + temptree);
break;
}
//start treebuilding
RunProg(tprog, options, param);
if (chkViewTree.Checked)
{
figtree = PhyloMain.IfRequired(figtree);
ProcessStartInfo treeshow = new ProcessStartInfo();
//Directory.SetCurrentDirectory(folder);
treeshow.FileName = figtree;
treeshow.Arguments = temptree;
treeshow.UseShellExecute = false;
Process.Start(treeshow);
}
if (File.Exists(PhyloMain.IfRequired(tempalign)))
{
File.Delete(PhyloMain.IfRequired(tempalign));
}
}
private void BtnStartBayes_Click(object sender, EventArgs e)
{
SynchronizationContext originalContext = SynchronizationContext.Current;
List <ProcessStartInfo> processes = new List <ProcessStartInfo>();
string tree = "";
if (txtMrBayes.Text != "")
{
if (chkInteractive.Checked)
{
options = " -i ";
}
options += txtMrBayes.Text;
tree = txtMrBayes.Text + ".con.tre";
}
if (txtFasta.Text != "" && txtNewBayes.Text != "")
{
if (txtNrStrains.Text == "" || txtSeqLength.Text == "")
{
MessageBox.Show("When fasta-files are used, MrBayes needs to know the number of taxa and the sequence length.", "Missing data", MessageBoxButtons.OK, MessageBoxIcon.Exclamation);
return;
}
//prepare a nexus file with fasta data to NewBayes file
string fasta = txtFasta.Text;
string export = txtNewBayes.Text;
tree = export + ".con.tre";
string temp = "";
var sb = new StringBuilder();
StreamReader file = new StreamReader(fasta);
StreamWriter sW = new StreamWriter(export, true);
sW.WriteLine("#NEXUS");
sW.WriteLine("BEGIN DATA;");
sW.WriteLine("DIMENSIONS NTAX=" + txtNrStrains.Text + " NCHAR=" + txtSeqLength.Text + ";");
sW.WriteLine("FORMAT DATATYPE=DNA GAP=-;");
sW.WriteLine("MATRIX");
temp = file.ReadLine();
while (!file.EndOfStream)
{
if (temp != "" && temp.Substring(0, 1) == ">")
{
temp = temp.Substring(1, temp.Length - 1) + "\t";
sb.AppendLine(temp);
temp = file.ReadLine();
while (temp.Substring(0, 1) != ">" && !file.EndOfStream)
{
sb.AppendLine(temp);
temp = file.ReadLine();
}
}
else
{
temp = file.ReadLine();
}
}
// write last line
sb.AppendLine(temp);
sW.WriteLine(sb.ToString());
file.Dispose();
file.Close();
sW.WriteLine(";");
sW.WriteLine("END;");
sW.WriteLine(" ");
var bb = new StringBuilder();
// add MrBayes block
string gen = (Convert.ToInt16(txtGenerations.Text) * 1000000).ToString();
bb.AppendLine("BEGIN MRBAYES;");
bb.AppendLine("set autoclose=yes nowarn=yes;");
bb.AppendLine("Lset applyto=(1) nst=6 rates=equal;");
bb.AppendLine("Prset applyto=(1) statefreqpr=Fixed(equal);");
bb.AppendLine("mcmc nruns=2 nchains=" + txtChains.Text + " ngen=" + gen + " samplefreq=1000 savebrlens=yes;");
bb.AppendLine("sump burninfrac=" + txtBurnin.Text + ";");
bb.AppendLine("sumt burninfrac=" + txtBurnin.Text + ";");
bb.AppendLine("quit;");
bb.AppendLine("END;");
sW.WriteLine(bb.ToString());
sW.Close();
sW.Dispose();
options = "\"" + txtNewBayes.Text + "\"";
tree = txtNewBayes.Text + ".con.tre";
}
//if a nexus file is chosen, add Bayes block at the end of the file
if (txtNexus.Text != "" && txtNewBayes.Text != "")
{
string nexus = txtNexus.Text;
string export = txtNewBayes.Text;
var sb = new StringBuilder();
StreamReader file = new StreamReader(nexus);
string line = file.ReadToEnd();
StreamWriter sW = new StreamWriter(export, true);
sW.Write(line);
sW.Flush();
file.Close();
string gen = (Convert.ToInt16(txtGenerations.Text) * 1000000).ToString();
sb.AppendLine("BEGIN MRBAYES;");
sb.AppendLine("set autoclose=yes nowarn=yes;");
sb.AppendLine("Lset applyto=(1) nst=6 rates=equal;");
sb.AppendLine("Prset applyto=(1) statefreqpr=Fixed(equal);");
sb.AppendLine("mcmc nruns=2 nchains=" + txtChains.Text + " ngen=" + gen + " samplefreq=1000 savebrlens=yes;");
sb.AppendLine("sump burninfrac=" + txtBurnin.Text + ";");
sb.AppendLine("sumt burninfrac=" + txtBurnin.Text + ";");
sb.AppendLine("quit;");
sb.AppendLine("END;");
sW.WriteLine(sb.ToString());
sW.Close();
options = "\"" + txtNewBayes.Text + "\"";
tree = txtNewBayes.Text + ".con.tre";
}
ProcessStartInfo process1 = new ProcessStartInfo();
process1.UseShellExecute = false;
process1.RedirectStandardOutput = false;
if (chkCommand.Checked)
{
process1.WindowStyle = ProcessWindowStyle.Normal;
}
else
{
process1.WindowStyle = ProcessWindowStyle.Hidden;
process1.UseShellExecute = true;
process1.RedirectStandardOutput = false;
process1.CreateNoWindow = true;
}
process1.FileName = "cmd.exe ";
process1.Arguments = "/C " + bayes + " " + options;
processes.Add(process1);
if (chkViewTree.Checked)
{
ProcessStartInfo process2 = new ProcessStartInfo();
string view = PhyloMain.IfRequired(figtree);
process2.FileName = view;
process2.Arguments = tree;
process2.UseShellExecute = false;
process2.RedirectStandardOutput = false;
processes.Add(process2);
}
if (chkCommand.Checked)
{
btnStartBayes.Enabled = false;
try
{
using (Process exeProcess = Process.Start(process1))
{
panel1.Visible = true;
Thread.Sleep(100);
SetParent(exeProcess.MainWindowHandle, panel1.Handle);
SetWindowLong(exeProcess.MainWindowHandle, GWL_STYLE, WS_VISIBLE);
MoveWindow(exeProcess.MainWindowHandle, 0, 0, panel1.Width, panel1.Height, true);
exeProcess.WaitForExit();
}
panel1.Visible = false;
btnStartBayes.Enabled = true;
}
catch (Exception)
{
MessageBox.Show("MrBayes wasn't able to execute the created file.", "Corrupted file", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
Thread th = new Thread(() =>
{
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { lblRunning.Visible = true; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnStartBayes.Enabled = false; }, null); });
for (int i = 0; i < processes.Count; i++)
{
try
{
using (Process exeProcess = Process.Start(processes[i]))
{
exeProcess.WaitForExit();
}
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message, "End of execution", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { lblRunning.Visible = false; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnStartBayes.Enabled = true; }, null); });
}
});
th.Start();
}
if (chkCommand.Checked)
{
if (chkViewTree.Checked)
{
Process.Start(figtree, tree);
}
}
}
private void BtnStartIQ_Click(object sender, EventArgs e)
{
btnStartIQ.Enabled = false;
btnNew.Enabled = false;
string fasta = Path.GetFileName(txtFastaFile.Text);
folder = Path.GetDirectoryName(txtFastaFile.Text);
Environment.CurrentDirectory = folder;
options = " -s " + fasta + " -redo -nt AUTO -nm " + txtMaxIterations.Text;
if (chkSubstitution.Checked)
{
options += " -m " + cboModels.Text;
}
else
{
options += " -m MFP+MERGE";
}
if (chkPartition.Checked)
{
options += " -spp" + txtPartition.Text;
}
if (rdbAIC.Checked)
{
options += " -merit AIC";
}
if (rdbAICc.Checked)
{
options += " -merit AICc";
}
if (chkBayes.Checked)
{
options += " -abayes";
}
if (chkLRT.Checked)
{
options += " -alrt " + txtLRTiterations.Text;
}
if (chkBootstraps.Checked)
{
options += " -bb " + txtBootstraps.Text;
}
if (chkNonBS.Checked)
{
options += " -b " + txtNonBS.Text;
}
if (chkShort.Checked)
{
options += " -pers 0.2 -nstop 500";
}
if (chkNNI.Checked)
{
options += " -allnni";
}
if (chkBranch.Checked && chkBootstraps.Checked)
{
options += " -bnni";
}
if (chkTest.Checked)
{
options += " -zb 1000 -zw -au";
}
string bfile = Path.GetFileNameWithoutExtension(txtIQtree.Text);
options += " -pre " + bfile;
if (!param)
{
MessageBox.Show(options, "Parameters used for calculation", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
iqtree = PhyloMain.IfRequired(iqtree);
ProcessStartInfo process1 = new ProcessStartInfo();
process1.UseShellExecute = false;
process1.RedirectStandardOutput = false;
if (chkCommand.Checked)
{
process1.WindowStyle = ProcessWindowStyle.Normal;
}
else
{
process1.WindowStyle = ProcessWindowStyle.Hidden;
process1.UseShellExecute = true;
process1.RedirectStandardOutput = false;
process1.CreateNoWindow = true;
}
process1.FileName = iqtree;
process1.Arguments = options;
processes.Add(process1);
if (chkViewTree.Checked)
{
string tree = bfile + ".treefile";
ProcessStartInfo process2 = new ProcessStartInfo();
string view = PhyloMain.IfRequired(figtree);
process2.FileName = view;
process2.Arguments = tree;
process2.UseShellExecute = false;
process2.RedirectStandardOutput = false;
processes.Add(process2);
}
if (chkCommand.Checked)
{
btnStartIQ.Enabled = false;
btnNew.Enabled = false;
try
{
using (Process exeProcess = Process.Start(process1))
{
panel1.Visible = true;
Thread.Sleep(100);
SetParent(exeProcess.MainWindowHandle, panel1.Handle);
SetWindowLong(exeProcess.MainWindowHandle, GWL_STYLE, WS_VISIBLE);
MoveWindow(exeProcess.MainWindowHandle, 0, 0, panel1.Width, panel1.Height, true);
exeProcess.WaitForExit();
}
panel1.Visible = false;
btnStartIQ.Enabled = true;
btnNew.Enabled = true;
}
catch (Exception)
{
MessageBox.Show("The program " + iqtree + " encountered on error.", "Execution halted", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
Thread th = new Thread(() =>
{
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { lblRunning.Visible = true; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnStartIQ.Enabled = false; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnNew.Enabled = false; }, null); });
for (int i = 0; i < processes.Count; i++)
{
try
{
using (Process exeProcess = Process.Start(processes[i]))
{
exeProcess.WaitForExit();
}
}
catch (Exception ex)
{
MessageBox.Show("Error: " + ex.Message, "End of execution", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { lblRunning.Visible = false; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnStartIQ.Enabled = true; }, null); });
ThreadPool.QueueUserWorkItem(delegate { originalContext.Post(delegate { btnNew.Enabled = true; }, null); });
}
});
th.Start();
}
if (chkCommand.Checked)
{
if (chkViewTree.Checked)
{
string tree = bfile + ".treefile";
Process.Start(figtree, tree);
}
}
}
private void SearchHaplotypes(string temp)
{
temp = PhyloMain.IfRequired(temp);
string sBuf = "";
StreamReader haplotypes = new StreamReader(temp);
sBuf = haplotypes.ReadToEnd();
haplotypes.Close();
if (!sBuf.Contains("DnaSP"))
{
MessageBox.Show("This file doesn't seem to be a DnaSP file.", "Check format", MessageBoxButtons.OK, MessageBoxIcon.Error);
txtDnaSP.Clear();
return;
}
string line = "";
int count = 0;
//find number of taxa (haplotype groups)
StreamReader all = new StreamReader(temp);
line = all.ReadLine();
while (line != null)
{
if (line.Contains("NTAX="))
{
int start = line.IndexOf("NTAX=") + "NTAX=".Length;
int end = line.IndexOf(";") - start;
ntax = line.Substring(start, end);
nrhaplos = new string[Convert.ToInt16(ntax)];
}
if (line.Contains("[Hap#"))
{
line = all.ReadLine();
do
{
int start2 = line.IndexOf(":") + ":".Length;
nrhaplos[count] = line.Substring(start2 + 1, 3);
count++;
line = all.ReadLine();
} while (line.Contains("[Hap_"));
break;
}
line = all.ReadLine();
}
all.Close();
int totalhaps = nrhaplos.Length;
for (int i = 0; i < totalhaps; i++)
{
//dgvTraits.Rows.Add();
string item = "Hap_" + (i + 1).ToString() + ": " + nrhaplos[i].ToString();
dgvTraits.Rows.Insert(i, item);
}
StreamReader chars = new StreamReader(temp);
line = chars.ReadLine();
while (chars != null)
{
if (line.Contains("NCHAR="))
{
int start = line.IndexOf("NCHAR=") + "NCHAR=".Length;
int end = line.IndexOf(";") - start;
nchar = line.Substring(start, end);
hapchars = new string[Convert.ToInt16(nchar)];
}
if (line.Contains("MATRIX"))
{
line = chars.ReadLine();
line = chars.ReadLine();
line = chars.ReadLine();
count = 0;
do
{
hapchars[count] = line;
count++;
line = chars.ReadLine();
} while (line.Contains("Hap_"));
break;
}
line = chars.ReadLine();
}
}
