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 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;
}
