private void btnRun_Click(object sender, EventArgs e)
{
ArrayList fileList = new ArrayList();
fileList = GetFileList(tvSelDirs, tbSrcDir.Text.Replace("\\", "/"));
if (fileList.Count == 0)
{
MessageBox.Show("please select input files");
return;
}
List<string> allowedFormat = new List<string>(new string[] { "mzXML", "mzxml", "mzML", "mzml", "mgf", "MGF", "MS2", "ms2" });
// run directag, allow write high quality spectra by directag, allow add identification label and write unidentified spectra
if (cbAssessement.Checked)
{
# region Error checking
if (tbSrcDir.Text.Equals(string.Empty))
{
MessageBox.Show("Error: Please select input file directory!");
return;
}
if (tbOutputDir.Text.Equals(string.Empty) || !Directory.Exists(tbOutputDir.Text))
{
MessageBox.Show("Error: Please select correct output directory!");
return;
}
//List<string> allowedFormat = new List<string>(new string[] { "mzXML", "mzxml", "mzML", "mzml", "mgf", "MGF", "MS2", "ms2" });
if (cbRemoval.Checked)
{
if (!allowedFormat.Exists(element => element.Equals(cmbOutputFileFormat.Text)))
{
MessageBox.Show("Please select proper output format");
return;
}
if (Convert.ToInt32(tbRemovalCutoff.Text) <= 0 || Convert.ToInt32(tbRemovalCutoff.Text) > 100)
{
MessageBox.Show("Please specify proper cutoff between 0 and 100!");
return;
}
if (tbOutFileNameSuffixForRemoval.Text.Equals(string.Empty))
{
MessageBox.Show("Please specify output file suffix!");
return;
}
}
if (cbRecovery.Checked)
{
if (tbPepXMLDir.Text.Equals(string.Empty))
{
MessageBox.Show("Error: Please specify pepXML file directory!");
return;
}
if (tbDBFile.Text.Equals(string.Empty))
{
MessageBox.Show("Error: Please specify database file!");
return;
}
if (tbMaxFDR.Text.Equals(string.Empty))
{
MessageBox.Show("Error: Please specify FDR!");
return;
}
double fdr = Convert.ToDouble(tbMaxFDR.Text);
if (fdr <= 0 || fdr >= 100)
{
MessageBox.Show("Please input proper FDR between 0 and 100");
return;
}
if (cmbScoreInfo.Text.Equals(string.Empty))
{
MessageBox.Show("Error: Please specify database search score weights!");
return;
}
if (tbOutFileNameSuffixForRecovery.Text.Equals(string.Empty))
{
MessageBox.Show("Error: Please specify output file suffix!");
return;
}
if (cbWriteOutUnidentifiedSpectra.Checked)
{
if (Convert.ToInt32(tbRecoveryCutoff.Text) <= 0 || Convert.ToInt32(tbRecoveryCutoff.Text) > 100)
{
MessageBox.Show("Please specify proper recovery cutoff between 0 and 100!");
return;
}
if (!allowedFormat.Exists(element => element.Equals(cmbRecoveryOutFormat.Text)))
{
MessageBox.Show("Please select proper output format");
return;
}
}
}
# endregion
RunDirecTagAction directagAction = new RunDirecTagAction();
directagAction.InFileList = fileList;
directagAction.OutMetricsSuffix = tbOutputMetricsSuffix.Text;
directagAction.OutputDir = tbOutputDir.Text;
if (cbRemoval.Checked)
{
directagAction.OutputFilenameSuffixForRemoval = tbOutFileNameSuffixForRemoval.Text;
directagAction.OutputFormat = cmbOutputFileFormat.Text;
}
if (cbRecovery.Checked)
{
directagAction.AddLabel = true;
//directagAction.IdpickerCfg = idpickerCfg;
directagAction.IdpickerCfg = getIdpickerCfg();
directagAction.OutputFilenameSuffixForRecovery = tbOutFileNameSuffixForRecovery.Text;
if (cbWriteOutUnidentifiedSpectra.Checked)
{
directagAction.WriteOutUnidentifedSpectra = true;
directagAction.RecoveryCutoff = Convert.ToSingle(tbRecoveryCutoff.Text) / 100.0f;
directagAction.RecoveryOutFormat = cmbRecoveryOutFormat.Text;
}
}
if ( cbAdjustScoreByGroup.Checked)
{
directagAction.AdjustScanRankerScoreByGroup = true;
}
string outputDir = tbOutputDir.Text;
Directory.SetCurrentDirectory(outputDir);
if (Workspace.statusForm == null || Workspace.statusForm.IsDisposed)
{
Workspace.statusForm = new TextBoxForm(this);
Workspace.statusForm.Show();
Application.DoEvents();
}
// run directag
bgDirectagRun.WorkerSupportsCancellation = true;
bgDirectagRun.RunWorkerCompleted += bgDirectagRun_RunWorkerCompleted;
DirecTagInfo directagInfo = new DirecTagInfo();
bulidAndWriteDirectagInfo(directagInfo);
//Thread t = new Thread(delegate() { directagAction.RunDirectag(); });
//t.Start();
//t.Join();
//bgDirectagRun.ProgressChanged += bgDirectagRun_ProgressChanged;
bgDirectagRun.RunWorkerAsync(directagAction);
}
/// <summary>
/// write cfg file for DirecTag
/// </summary>
private void bulidAndWriteDirectagInfo(DirecTagInfo directagInfo)
{
directagInfo.NumChargeStates = Convert.ToInt32(tbNumChargeStates.Text);
directagInfo.FragmentMzTolerance = Convert.ToSingle(tbFragmentTolerance.Text);
directagInfo.IsotopeMzTolerance = Convert.ToSingle(tbFragmentTolerance.Text) / 2;
directagInfo.TagLength = Convert.ToInt32(tbTagLength.Text);
directagInfo.PrecursorMzTolerance = Convert.ToSingle(tbPrecursorTolerance.Text);
directagInfo.UseAvgMassOfSequences = (rbAverage.Checked) ? 1 : 0;
directagInfo.UseChargeStateFromMS = (cbUseChargeStateFromMS.Checked) ? 1 : 0;
directagInfo.UseMultipleProcessors = (cbUseMultipleProcessors.Checked) ? 1 : 0;
directagInfo.StaticMods = tbStaticMods.Text;
directagInfo.WriteOutTags = (cbWriteOutTags.Checked) ? 1 : 0;
directagInfo.WriteScanRankerMetrics = (cbAssessement.Checked) ? 1 : 0;
//directagInfo.ScanRankerMetricsFileName; // given in cmd line
directagInfo.WriteHighQualSpectra = (cbRemoval.Checked) ? 1 : 0;
//directagInfo.HighQualSpecFileName = fileBaseName + tbOutFileNameSuffixForRemoval.Text + ".txt"; //given in cmd line
directagInfo.OutputFormat = cmbOutputFileFormat.Text;
directagInfo.HighQualSpecCutoff = Convert.ToSingle(tbRemovalCutoff.Text) / 100.0f;
directagInfo.WriteDirectagCfg();
}