private void btnOK_Click(object sender, EventArgs e)
{
//Error check
if (tbPepXMLFile.Text.Equals(string.Empty) || tbDBfile.Text.Equals(string.Empty) ||
tbDecoyPrefix.Text.Equals(string.Empty) || tbMaxFDR.Text.Equals(string.Empty) ||
cmbScoreWeights.Text.Equals(string.Empty))
{
MessageBox.Show("Please specify all required parameters");
return;
}
double fdr = Convert.ToDouble(tbMaxFDR.Text);
if (fdr <= 0 || fdr >= 1)
{
MessageBox.Show("Please input proper FDR between 0 and 1");
return;
}
idpCfg = new IDPickerInfo();
idpCfg.PepXMLFile = tbPepXMLFile.Text;
idpCfg.DBFile = tbDBfile.Text;
idpCfg.DecoyPrefix = tbDecoyPrefix.Text;
idpCfg.MaxFDR = fdr;
idpCfg.ScoreWeights = cmbScoreWeights.Text;
idpCfg.NormalizeSearchScores = (cbNormSearchScores.Checked) ? 1 : 0;
idpCfg.OptimizeScoreWeights = (cbOptimizeScoreWeights.Checked) ? 1 : 0;
DialogResult = DialogResult.OK;
Close();
}
/// <summary>
/// run idpQonvert to create idpXML file to determine identified spectra
/// </summary>
/// <param name="idpCfg"></param>
/// <param name="outDir"></param>
private void runIdpQonvert(IDPickerInfo idpCfg, string outDir)
{
// run idpQonvert and create idpXML file
string EXE = @"idpQonvert.exe";
string BIN_DIR = Path.GetDirectoryName(Application.ExecutablePath);
string pathAndExeFile = BIN_DIR + "\\" + EXE;
// string outputFilename = Path.GetFileNameWithoutExtension(idpCfg.PepXMLFile) + ".idpXML";
//// IDPicker 2 args
//string args =
// " -MaxFDR " + idpCfg.MaxFDR
// + " -NormalizeSearchScores " + idpCfg.NormalizeSearchScores
// + " -OptimizeScoreWeights " + idpCfg.OptimizeScoreWeights
// + " -SearchScoreWeights " + "\"" + idpCfg.ScoreInfo + "\""
// + " -DecoyPrefix " + "\"" + idpCfg.DecoyPrefix + "\""
// + " -WriteQonversionDetails 0 "
// + " -ProteinDatabase " + "\"" + idpCfg.DBFile + "\"" + " "
// + idpCfg.PepXMLFiles; // each file enclosed by "..." and separated by a space
//// IDPicker 3 args
// MaxImportFDR equal to MaxFDR to reduce idpDB size
string args =
" -MaxImportFDR " + idpCfg.MaxFDR
+ " -MaxFDR " + idpCfg.MaxFDR
+ " -QonverterMethod " + "\"" + idpCfg.QonverterMethod + "\""
+ " -ScoreInfo " + "\"" + idpCfg.ScoreInfo + "\""
+ " -DecoyPrefix " + "\"" + idpCfg.DecoyPrefix + "\""
+ " -WriteQonversionDetails 0 "
+ " -ProteinDatabase " + "\"" + idpCfg.DBFile + "\"" + " "
+ idpCfg.PepXMLFiles; // each file enclosed by "..." and separated by a space
// Workspace.SetText("\r\nidpQonvert cmd\r\n" + pathAndExeFile + " " + args + "\r\n\r\n");
try
{
//if (File.Exists(outputFilename))
//{
// File.Delete(outputFilename);
//}
Workspace.SetText("\r\nidpQonvert command:\r\n" + pathAndExeFile + args + "\r\n");
Workspace.RunProcess(pathAndExeFile, args, outDir);
}
catch (Exception exc)
{
//throw new Exception("Error running idpQonvert\r\n", exc);
Workspace.SetText("\r\nError in running idpQonvert\r\n");
Workspace.ChangeButtonTo("Close");
throw new Exception(exc.Message);
}
//if (!File.Exists(outputFilename))
//{
// throw new Exception("Error in running idpQonvert, no idpXML file generated");
//}
}
public RunDirecTagAction()
{
addLabel = false;
idpickerCfg = null;
outputFilenameSuffixForRecovery = string.Empty;
}
/// <summary>
/// get IDPicker cfg from MainForm
/// </summary>
/// <returns></returns>
private IDPickerInfo getIdpickerCfg()
{
IDPickerInfo idpickerCfg = new IDPickerInfo();
idpickerCfg.PepXMLFileDir = tbPepXMLDir.Text;
idpickerCfg.DBFile = tbDBFile.Text;
idpickerCfg.MaxFDR = Convert.ToDouble(tbMaxFDR.Text) / 100;
idpickerCfg.DecoyPrefix = tbDecoyPrefix.Text;
idpickerCfg.ScoreInfo = cmbScoreInfo.Text;
idpickerCfg.QonverterMethod = cmbQonverterMethod.Text;
//idpickerCfg.NormalizeSearchScores = (cbNormSearchScores.Checked) ? 1 : 0;
//idpickerCfg.OptimizeScoreWeights = (cbOptimizeScoreWeights.Checked) ? 1 : 0;
//idpickerCfg.PepXMLFile given when running idpqonvert
return idpickerCfg;
}
public RunDirecTagAction()
{
addLabel = false;
idpickerCfg = null;
outputFilenameSuffixForRecovery = string.Empty;
}
private void btnOK_Click(object sender, EventArgs e)
{
//Error check
if (tbPepXMLFile.Text.Equals(string.Empty) || tbDBfile.Text.Equals(string.Empty)
|| tbDecoyPrefix.Text.Equals(string.Empty) || tbMaxFDR.Text.Equals(string.Empty)
|| cmbScoreWeights.Text.Equals(string.Empty))
{
MessageBox.Show("Please specify all required parameters");
return;
}
double fdr = Convert.ToDouble(tbMaxFDR.Text);
if (fdr <= 0 || fdr >= 1)
{
MessageBox.Show("Please input proper FDR between 0 and 1");
return;
}
idpCfg = new IDPickerInfo();
idpCfg.PepXMLFile = tbPepXMLFile.Text;
idpCfg.DBFile = tbDBfile.Text;
idpCfg.DecoyPrefix = tbDecoyPrefix.Text;
idpCfg.MaxFDR = fdr;
idpCfg.ScoreWeights = cmbScoreWeights.Text;
idpCfg.NormalizeSearchScores = (cbNormSearchScores.Checked) ? 1 : 0;
idpCfg.OptimizeScoreWeights = (cbOptimizeScoreWeights.Checked) ? 1 : 0;
DialogResult = DialogResult.OK;
Close();
}
