private void MGFRead(string FileName)
{
MGFInFileName.Text = FileName;
MGFin = new MGFParser.MGFFile();
MGFin.MGFRead(FileName);
MGFoutFileName.Text = Path.GetDirectoryName(FileName) + Path.DirectorySeparatorChar +
Path.GetFileNameWithoutExtension(FileName) + "-filtered.mgf";
}
private void backgroundWorker1_DoWork(object sender, DoWorkEventArgs e)
{
//BackgroundWorker worker = sender as BackgroundWorker;
int PercentCompleted = 0;
if (mp == null)
{
if (File.Exists(DatFileName.Text))
{
mp = new Mascot.MascotParser();
mp.ParseFile(DatFileName.Text);
}
else
{
throw new ArgumentException(
"Mascot .DAT file must be specified", "n");
}
}
if (MGFin == null)
{
if (File.Exists(DatFileName.Text))
{
MGFRead(MGFInFileName.Text);
}
else
{
throw new ArgumentException(
"MGF file must be specified", "n");
}
}
if (!Settings.Default.MScore)
{
//сортируем по score
MascotSpectrabyScore mss = new MascotSpectrabyScore();
mp.Spectra.Sort(mss);
int DirectCount = 0, ReversedCount = 0, i;
for (i = 0; i < mp.Spectra.Count; i++)
{
if (mp.Spectra[i].Peptides.Count == 0)
{
break;
}
bool Reversed = true;
for (int j = 0; j < mp.Spectra[i].Peptides[0].ProteinNames.Length; j++)
{
Reversed &= mp.Spectra[i].Peptides[0].ProteinNames[j].ToUpper().Contains("REVERSED");
}
if (Reversed)
{
ReversedCount++;
}
else
{
DirectCount++;
}
double FDRRatio = ((double)ReversedCount / (double)DirectCount) * 100.0;
if (FDRRatio > Convert.ToDouble(Settings.Default.FDRThreshold))
{
break;
}
}
Settings.Default.Mascot_Threshold = Convert.ToString(mp.Spectra[i].Peptides[0].Score);
}
Mascot.MascotSpectra ms;
MGFParser.MGFSpectrum mgfs;
MGFout = new MGFParser.MGFFile();
MGFout.MGFComments.AddRange(MGFin.MGFComments);
MGFout.MGFComments.Add(String.Format("Filtered by {0};", Text));
MGFout.MGFComments.Add(String.Format("Mascot Threshold - {0}", Settings.Default.Mascot_Threshold));
if (!Settings.Default.MScore)
{
MGFout.MGFComments.Add(String.Format("Based on FDR Threshold - {0}%", Settings.Default.FDRThreshold));
}
MGFout.MGFComments.Add(String.Format("Mascot Result File - {0}", DatFileName.Text));
for (int i = 0; i < MGFin.Spectra.Count; i++)
{
mgfs = MGFin.Spectra[i];
//Link to Mascot search results - не работает - мы только что пересортировалми спектры
//ms = mp.AccessByFSN(mgfs.ScanNumber);
ms = null;
for (int j = 0; j < mp.Spectra.Count; j++)
{
if (mp.Spectra[j].ScanNumber == mgfs.ScanNumber)
{
ms = mp.Spectra[j];
break;
}
}
if (ms == null)
{
throw new ArgumentException(
"Probably .dat file does not correspond to .mgf file", "n");
}
if (ms.Peptides.Count == 0 ||
ms.Peptides[0].Score < Convert.ToDouble(Settings.Default.Mascot_Threshold))
{
continue;
}
bool Reversed = true;
for (int j = 0; j < ms.Peptides[0].ProteinNames.Length; j++)
{
Reversed &= ms.Peptides[0].ProteinNames[j].ToUpper().Contains("REVERSED");
}
if (Reversed)
{
continue;
}
if (mgfs.Data.Count == 0)
{
continue;
}
MGFout.Spectra.Add(mgfs);
if (Convert.ToInt32(((i * 100) / MGFin.Spectra.Count)) > PercentCompleted)
{
PercentCompleted = Convert.ToInt32(((i * 100) / MGFin.Spectra.Count));
backgroundWorker1.ReportProgress(PercentCompleted);
}
}
backgroundWorker1.ReportProgress(100);
MGFout.MGFWrite(Settings.Default.MGF_Out);
backgroundWorker1.ReportProgress(0);
}