private void writeSingleSpectrum(string sourceFile, string nativeID, string outFileName)
{
MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig();
writeConfig.format = MSDataFile.Format.Format_MGF;
writeConfig.precision = MSDataFile.Precision.Precision_32;
//var predicate = new SpectrumList_FilterPredicate_IndexSet();
//predicate.indexSet.Add(nativeID);
var predicate = new SpectrumList_FilterPredicate_NativeIDSet();
predicate.nativeIDSet.Add(nativeID);
try
{
//Workspace.SetText("\r\nWriting selected spectrum to " + outFileName);
MainForm.SetText(this, "Start writing selected spectrum to " + outFileName + "\r\n");
using (MSDataFile msFile = new MSDataFile(sourceFile))
{
msFile.run.spectrumList = new SpectrumList_Filter(msFile.run.spectrumList, new SpectrumList_FilterAcceptSpectrum(predicate.accept));
msFile.write(outFileName, writeConfig);
}
MainForm.SetText(this, "Finished writing selected spectrum to " + outFileName + "\r\n");
}
catch (Exception exc)
{
//throw new Exception("Error in writiing new spectra file", exc);
//Workspace.SetText("\r\nError in writing new spectra file\r\n");
tbPepNovoResult.AppendText("\r\nError in writing new spectra file\r\n");
throw new Exception(exc.Message);
}
}
/// <summary>
/// run a process and send standard output and standard error to status form
/// </summary>
/// <param name="pathAndExeFile"></param>
/// <param name="args"></param>
public void RunProcess(string pathAndExeFile, string args, string workingDir)
{
Process RunProc = new Process();
RunProc.EnableRaisingEvents = true;
RunProc.StartInfo.CreateNoWindow = true;
RunProc.StartInfo.WorkingDirectory = workingDir;
RunProc.StartInfo.UseShellExecute = false;
RunProc.StartInfo.RedirectStandardError = true;
RunProc.StartInfo.RedirectStandardOutput = true;
RunProc.ErrorDataReceived += new DataReceivedEventHandler(StdErrorHandler);
//RunProc.OutputDataReceived += new DataReceivedEventHandler( StdOutputHandler );
//RunProc.ErrorDataReceived += new DataReceivedEventHandler(StdErrorHandler);
RunProc.StartInfo.FileName = pathAndExeFile;
RunProc.StartInfo.Arguments = args;
RunProc.Start();
//RunProc.BeginOutputReadLine();
RunProc.BeginErrorReadLine();
//string stdOutput = RunProc.StandardOutput.ReadToEnd();
//statusForm.tbStatus.AppendText(stdOutput);
//RunProc.WaitForExit();
StreamReader srOut = RunProc.StandardOutput;
//StreamReader srErr = RunProc.StandardError;
//while (!RunProc.HasExited)
string outLine = string.Empty;
//string errLine = string.Empty;
//while (((outLine = srOut.ReadLine()) != null) || ((errLine = srErr.ReadLine()) != null))
//while (((outLine = srOut.ReadLine()) != null) && (!RunProc.HasExited))
while ((outLine = srOut.ReadLine()) != null)
{
//SetText(outLine+"\r\n");
MainForm.SetText(mainForm, outLine + "\r\n");
//lock(statusForm.tbStatus)
//statusForm.tbStatus.AppendText(outLine + "\n");
// RunProc.WaitForExit(500);
}
//SetText("\r\nError/warning message from " + pathAndExeFile + " :\r\n");
//string srErr = RunProc.StandardError.ReadToEnd();
//SetText(srErr.ReadToEnd().ToString()+"\r\n");
//SetText(srErr + "\r\n");
RunProc.WaitForExit();
RunProc.Close();
}
/// <summary>
/// run pepnovo
/// </summary
public void RunPepNovo()
{
//string fileBaseName = Path.GetFileNameWithoutExtension(file.FullName);
//string outMetricsFileName = fileBaseName + outMetricsSuffix + ".txt";
//string outHighQualSpecFileName = fileBaseName + outputFilenameSuffixForRemoval + "." + outputFormat;
// string outLabelFileName = fileBaseName + outputFilenameSuffixForRecovery + ".txt";
if (!File.Exists(inFile))
{
MessageBox.Show("Error: Cannot find the spectrum file for de novo sequencing!");
return;
}
string EXE = @"PepNovo.exe";
string BIN_DIR = Path.GetDirectoryName(Application.ExecutablePath) + "\\" + "PepNovo";
string pathAndExeFile = BIN_DIR + "\\" + EXE;
string args = " -model CID_IT_TRYP " + " -model_dir " + "\"" + BIN_DIR + "\"" + "\\" + "Models"
+ " -pm_tolerance " + precursorTolerance + " -fragment_tolerance " + fragmentTolerance
+ " -no_quality_filter " + " -num_solutions 10 " + " -PTMs " + ptms
+ useSpectrumCharge + useSpectrumMz + " -file " + " \"" + inFile + "\"";
MainForm.SetText(mainForm, "\r\nStart running PepNovo ...\r\n\r\n");
//MainForm.SetText(mainForm, "PepNovo command: " + pathAndExeFile + args + "\r\n\r\n");
try
{
Workspace workspace = new Workspace(mainForm);
workspace.RunProcess(pathAndExeFile, args, workingDir);
}
catch (Exception exc)
{
//Workspace.SetText("\r\nError in running PepNovo\r\n");
MainForm.SetText(mainForm, "\r\nError in running PepNovo\r\n");
throw new Exception(exc.Message);
}
//if (!File.Exists(outMetricsFile))
//{
// MessageBox.Show("Error in running DirecTag, no metrics file generated");
//}
MainForm.SetText(mainForm, "\r\nFinished PepNovo! \r\n");
if (File.Exists(inFile))
{
File.Delete(inFile);
MainForm.SetText(mainForm, "Deleted " + inFile + "\r\n");
}
}
private void StdErrorHandler(object sendingProcess,
DataReceivedEventArgs errLine)
{
//SetText(errLine.Data + "\r\n");
MainForm.SetText(mainForm, errLine.Data + "\r\n");
// Write the error text to the file if there is something
// to write and an error file has been specified.
//if (!String.IsNullOrEmpty(errLine.Data))
//{
// if (!errorsWritten)
// {
// if (streamError == null)
// {
// // Open the file.
// try
// {
// streamError = new StreamWriter(netErrorFile, true);
// }
// catch (Exception e)
// {
// Console.WriteLine("Could not open error file!");
// Console.WriteLine(e.Message.ToString());
// }
// }
// if (streamError != null)
// {
// // Write a header to the file if this is the first
// // call to the error output handler.
// streamError.WriteLine();
// streamError.WriteLine(DateTime.Now.ToString());
// streamError.WriteLine("Net View error output:");
// }
// errorsWritten = true;
// }
// if (streamError != null)
// {
// // Write redirected errors to the file.
// streamError.WriteLine(errLine.Data);
// streamError.Flush();
// }
//}
}
