private void buttonGo_Click(object sender, EventArgs e)
{
PatternTools.DNA2Protein translator = new PatternTools.DNA2Protein();
int counter = 0;
foreach (string s in translator.Translate6(textBoxInput.Text))
{
counter++;
richTextBoxOutput.AppendText("Frame " + counter + "\n");
richTextBoxOutput.AppendText(s + "\n\n");
}
}
private void buttonWork_Click(object sender, EventArgs e)
{
buttonWork.Text = "Busy!";
//First, lets get the input DB in RAM
PatternTools.FastaParser.FastaFileParser fp = new PatternTools.FastaParser.FastaFileParser();
fp.ParseFile(new StreamReader(textBoxInputFile.Text), false, PatternTools.FastaParser.DBTypes.IDSpaceDescription);
if (checkBoxQualityFilters.Checked)
{
int itemsRemovedMinNo = fp.MyItems.RemoveAll(a => a.Sequence.Length <= (int)numericUpDownMinNoNT.Value);
labelNoNt.Text = itemsRemovedMinNo.ToString();
}
else
{
labelNoNt.Text = "0";
}
this.Update();
int itemsRemovedStopCoddons = 0;
StreamWriter sw = new StreamWriter(textBoxOutput.Text);
PatternTools.DNA2Protein translator = new PatternTools.DNA2Protein();
foreach (FastaItem fi in fp.MyItems)
{
List <string> translatedFrames = new List <string>();
if (radioButton3Frame.Checked)
{
translatedFrames = translator.Translate3(fi.Sequence);
}
else
{
translatedFrames = translator.Translate6(fi.Sequence);
}
for (int i = 0; i < translatedFrames.Count; i++)
{
if (checkBoxQualityFilters.Checked)
{
int noStopCodons = Regex.Matches(translatedFrames[i], Regex.Escape("*")).Count;
Console.WriteLine(fi.SequenceIdentifier + " Frame{0} StopCodons: {1}", i, noStopCodons);
if (noStopCodons >= (int)numericUpDownMaxNoStopCodons.Value)
{
itemsRemovedStopCoddons++;
labelNoStopCodons.Text = itemsRemovedStopCoddons.ToString();
this.Update();
}
}
else
{
sw.WriteLine(fi.SequenceIdentifier + "_" + i);
sw.WriteLine(translatedFrames[i]);
}
}
}
sw.Close();
Console.WriteLine("Done");
buttonWork.Text = "Go!";
}
