static void Main(string[] args)
{
if (args.Length == 0)
{
MainForm mf = new MainForm();
//mf.ShowDialog();
return;
}
FileInfo file;
file = new FileInfo(args[0]);
RawReaderParams readerParams = new RawReaderParams();
readerParams.LoadDefaults();
Reader reader = new Reader(readerParams);
List <MSLight> allSpectra = reader.GetSpectra(file.FullName, new List <int>(), false);
if (readerParams.ExtractMS1)
{
List <MSLight> msPrint = allSpectra.FindAll(a => a.ActivationType.Equals(""));
SpectraPrinter.PrintFile(file, msPrint, ".ms1", readerParams);
}
if (readerParams.ExtractMS2)
{
List <MSLight> msPrint = allSpectra.FindAll(a => !a.ActivationType.Equals(""));
SpectraPrinter.PrintFile(file, msPrint, ".ms2", readerParams);
}
}
private void buttonExtract_Click(object sender, EventArgs e)
{
richTextBoxMS.Clear();
RawReaderParams myParams = new RawReaderParams();
myParams.LoadDefaults();
Reader r = new Reader(myParams);
List <MSLight> theMS = r.GetSpectra(studyFile.FullName, new List <int>()
{
(int)numericUpDownSpectrumNumber.Value
}, false);
List <Ion> theIons = new List <Ion>();
for (int i = 0; i < theMS[0].MZ.Count; i++)
{
theIons.Add(new Ion(theMS[0].MZ[i], theMS[0].Intensity[i], 0, 0));
}
foreach (Ion i in theIons)
{
richTextBoxMS.AppendText(i.MZ + " " + i.Intensity + "\n");
}
}
private RawReaderParams CaptureParamsFromScreen()
{
RawReaderParams theParams = new RawReaderParams();
theParams.ExtractMS1 = checkBoxMS1.Checked;
theParams.ExtractMS2 = checkBoxMS2.Checked;
theParams.ExtractMS2 = checkBoxMS3.Checked;
theParams.UseThermoMonoIsotopicPrediction = checkBoxUseThermosMonoIsotopicInference.Checked;
theParams.ActivateSpectraCleaner = checkBoxSpectraCleaner.Checked;
theParams.SpectraCleanerWindowSize = (int)numericUpDownWindowSize.Value;
theParams.SpectraCleanerMaxPeaksPerWindow = (int)numericUpDownMaxPeaksPerWindow.Value;
theParams.SpectraCleanerMaxSpectraPerFile = (int)numericUpDownSpectraPerFile.Value;
return(theParams);
}
private void buttonGO_Click(object sender, EventArgs e)
{
if (!Directory.Exists(textBoxInputDirectory.Text))
{
MessageBox.Show("Please enter a valid directory");
return;
}
if (!checkBoxMS1.Checked && !checkBoxMS2.Checked && !checkBoxMGF.Checked)
{
MessageBox.Show("Please enter at least one valid output format.");
return;
}
buttonGO.Text = "Working";
this.Update();
DirectoryInfo di = new DirectoryInfo(textBoxInputDirectory.Text);
List <FileInfo> rawFiles = di.GetFiles("*.raw").ToList();
progressBar1.Value = 0;
this.Update();
RawReaderParams rawReaderParams = CaptureParamsFromScreen();
double fileCounter = 0;
foreach (FileInfo rawFile in rawFiles)
{
try
{
Console.WriteLine("Processing file " + rawFile.Name);
Reader r = new Reader(rawReaderParams);
List <MSLight> theSpectra = r.GetSpectra(rawFile.FullName, new List <int>(), false);
if (theSpectra.Count == 0)
{
WriteMessageToLog(di, "No mass spectra found in file : " + rawFile.Name);
}
else
{
if (rawReaderParams.ExtractMS1)
{
List <MSLight> ms2Print = theSpectra.FindAll(a => a.ZLines.Count == 0);
SpectraPrinter.PrintFile(rawFile, ms2Print, ".ms1", rawReaderParams);
}
//MS2 and MS3 need to be revised to work with MS3.
if (rawReaderParams.ExtractMS2)
{
List <MSLight> ms2Print = theSpectra.FindAll(a => a.ZLines.Count > 0);
SpectraPrinter.PrintFile(rawFile, ms2Print, ".ms2", rawReaderParams);
}
if (rawReaderParams.ExtractMS3)
{
List <MSLight> ms3Print = theSpectra.FindAll(a => a.ZLines.Count > 0);
SpectraPrinter.PrintFile(rawFile, ms3Print, ".ms3", rawReaderParams);
}
if (checkBoxMGF.Checked)
{
List <MSLight> ms2Print = theSpectra.FindAll(a => a.ZLines.Count > 0);
List <MSUltraLight> ms22 = ms2Print.Select(a => new MSUltraLight(a, -1)).ToList();
WriteAsMGF(ms22, rawFile.FullName + ".mgf");
}
}
fileCounter++;
progressBar1.Value = (int)((fileCounter / (double)rawFiles.Count()) * 100);
this.Update();
}
catch (Exception e2)
{
Console.WriteLine("Problem on file : " + rawFile.Name + "\n" + e2.Message);
WriteMessageToLog(di, "Problem on file : " + rawFile.Name + "\n" + e2.Message);
}
}
buttonGO.Text = "GO !";
this.Update();
}
public static void PrintFile(FileInfo rawFile, List <MSLight> ms2Print, string ext, RawReaderParams readerParams)
{
string fileNameWithoutExtension = Path.GetFileNameWithoutExtension(rawFile.FullName);
string outputFileName = rawFile.Directory.FullName + "/" + fileNameWithoutExtension + ext;
if (readerParams.ActivateSpectraCleaner)
{
int fileCounter = 0;
List <MSLight> tmpSpectraList = new List <MSLight>();
foreach (MSLight mslight in ms2Print)
{
tmpSpectraList.Add(mslight);
if (tmpSpectraList.Count == readerParams.SpectraCleanerMaxSpectraPerFile)
{
fileCounter++;
Print(tmpSpectraList, outputFileName + "_" + fileCounter + ext);
tmpSpectraList.Clear();
}
}
if (tmpSpectraList.Count > 0)
{
fileCounter++;
Print(ms2Print, outputFileName + "_" + fileCounter + ext);
tmpSpectraList.Clear();
}
}
else
{
Print(ms2Print, outputFileName);
}
}
