public void Convert(string omssaCSV, MSDataFile dataFile)
{
string filePath = Path.ChangeExtension(omssaCSV, ".pepxml");
using (PepXmlWriter writer = new PepXmlWriter(filePath))
{
writer.WriteSampleProtease(Protease);
writer.StartSearchSummary("OMSSA", true, true);
writer.WriteProteinDatabase(FastaDatabaseFile);
writer.WriteSearchProtease(Protease, MissedClevages);
foreach (int modNumber in FixedMods)
{
OmssaModification mod;
if (OmssaModification.TryGetModification(modNumber, out mod))
{
writer.WriteModification(mod, mod.Sites, true);
}
}
foreach (int modNumber in VariableMods)
{
OmssaModification mod;
if (OmssaModification.TryGetModification(modNumber, out mod))
{
writer.WriteModification(mod, mod.Sites, false);
}
}
writer.SetCurrentStage(PepXmlWriter.Stage.Spectra, true);
using (OmssaCsvPsmReader reader = new OmssaCsvPsmReader(omssaCSV, UserModFile))
{
reader.AddMSDataFile(dataFile);
reader.LoadProteins(FastaDatabaseFile);
foreach (PeptideSpectralMatch psm in reader.ReadNextPsm())
{
writer.StartSpectrum(psm.SpectrumNumber, psm.Spectrum.RetentionTime, psm.Spectrum.PrecursorMz, psm.Spectrum.PrecursorCharge);
writer.WritePSM(psm);
writer.EndSpectrum();
}
}
}
}
public void Run()
{
logTB.Clear();
logTB.BackColor = Color.White;
string rawFileDirectory = textBox3.Text;
string inputcsvfile = textBox1.Text;
if (!File.Exists(inputcsvfile))
{
UpdateLog("Cannot open input csvfile: " + inputcsvfile + ", aborting!");
return;
}
string outputDirectory = textBox2.Text;
if (string.IsNullOrWhiteSpace(outputDirectory))
{
UpdateLog("Must provide a valid output folder!");
return;
}
if (!Directory.Exists(outputDirectory))
{
UpdateLog("Output directory " + outputDirectory + " doesn't exist, creating it...");
Directory.CreateDirectory(outputDirectory);
}
List <Modification> fixedModifications = listBox2.Items.OfType <Modification>().ToList();
List <Modification> quantifiedModifications = new List <Modification>();
List <string> modNames = checkedListBox1.CheckedItems.OfType <string>().ToList();
if (modNames.Count > 0)
{
foreach (string modName in modNames)
{
if (modName == Phosphorylation.Name)
{
quantifiedModifications.Add(Phosphorylation);
}
else
{
OmssaModification mod;
if (!OmssaModification.TryGetModification(modName, out mod))
{
UpdateLog("Unable to load mod " + modName + ". Did you load the correct modification file?");
return;
}
quantifiedModifications.Add(mod);
}
}
}
else
{
UpdateLog("No modifications were selected to be quantified, please select mods from the list or one of the default options");
return;
}
//double ascoreThreshold = (double)numericUpDown2.Value;
double prodThreshold = (double)numericUpDown3.Value / 100.0;
bool separateGroups = checkBox3.Enabled && checkBox3.Checked;
bool ignoreCTerminal = checkBox2.Checked;
bool reduceSites = checkBox1.Checked;
int scoreCutoff = (int)numericUpDown2.Value;
bool phosphoNeutralLoss = phosphoNeutralLossCB.Checked && quantifiedModifications.Contains(Phosphorylation);
Tolerance prodTolerance = GetProductTolerance();
_lotor = new Lotor(rawFileDirectory, inputcsvfile, outputDirectory, fixedModifications,
quantifiedModifications, prodTolerance, scoreCutoff, separateGroups, prodThreshold, ignoreCTerminal, reduceSites,
FragmentTypes.b | FragmentTypes.y, phosphoNeutralLoss);
_lotor.UpdateLog += lotor_UpdateLog;
_lotor.UpdateProgress += lotor_UpdateProgress;
_lotor.Completed += _lotor_Completed;
localizeB.Enabled = false;
_mainThread = new Thread(_lotor.Localize);
_mainThread.IsBackground = true;
_mainThread.Start();
}