private ParametersContainer GetOutParameters()
{
ParametersContainer Pars = new ParametersContainer();
Pars.ChromatogramBP = checkBoxChroBP.Checked;
Pars.ChromatogramMs1 = checkBoxChroMs1.Checked;
Pars.ChromatogramMs2 = checkBoxChroMs2.Checked;
Pars.ChromatogramTIC = checkBoxChroTIC.Checked;
Pars.RawFileDirectory = textBoxRawFileDirectory.Text;
Pars.RawFileList = textBoxRawFiles.Text;
Pars.UseRawFileDirectory = radioButtonSelectDirectory.Checked;
Pars.DataOutputDirectoryString = textBoxDataOutputDir.Text;
Pars.MGFLowMassCutoff = checkBoxMgfLowMass.Checked;
Pars.ParseMode = checkBoxModeParse.Checked;
Pars.QcMode = checkBoxModeQC.Checked;
Pars.RefinePrecursorMassCharge = checkBoxRefinePrecursor.Checked;
Pars.MinCharge = comboBoxMinCharge.Text;
Pars.MaxCharge = comboBoxMaxCharge.Text;
Pars.DataOutputChromatograms = ckbxOutputChromatograms.Checked;
Pars.DataOutputMetrics = ckbxOutputMetrics.Checked;
Pars.DataOutputMGF = ckbxOutputMGF.Checked;
Pars.FaimsOutputMgf = checkBoxFaims.Checked;
Pars.DataOutputParseMatrix = ckbxOutputParse.Checked;
Pars.DataOutputDirectory = checkBoxDataOutputDirectory.Checked;
Pars.SearchEngineNone = radioButtonSearchNone.Checked;
Pars.SearchEngineXTandem = radioButtonSearchXTandem.Checked;
Pars.QcDataDirectory = textBoxQcDataDirectory.Text;
Pars.XTandemDirectory = textBoxXTandemDir.Text;
Pars.FastaFile = textBoxFastaFile.Text;
Pars.NumberSpectraToSearch = textBoxNumSpectra.Text;
Pars.PeptideModifications = peptideModifications;
Pars.QuantifyReporterIons = ckbxOutputQuant.Checked;
Pars.Reagents = comboBoxLabelingReagents.Text;
Pars.MGFLowMassCutoff = checkBoxMgfLowMass.Checked;
Pars.MGFLowMassCutoffValue = textBoxMgfLowMass.Text;
return(Pars);
}
private void LoadParameters(ParametersContainer Pars)
{
checkBoxChroBP.Checked = Pars.ChromatogramBP;
checkBoxChroMs1.Checked = Pars.ChromatogramMs1;
checkBoxChroMs2.Checked = Pars.ChromatogramMs2;
checkBoxChroTIC.Checked = Pars.ChromatogramTIC;
textBoxRawFileDirectory.Text = Pars.RawFileDirectory;
textBoxRawFiles.Text = Pars.RawFileList;
radioButtonSelectDirectory.Checked = Pars.UseRawFileDirectory;
textBoxDataOutputDir.Text = Pars.DataOutputDirectoryString;
checkBoxMgfLowMass.Checked = Pars.MGFLowMassCutoff;
checkBoxModeParse.Checked = Pars.ParseMode;
checkBoxModeQC.Checked = Pars.QcMode;
checkBoxRefinePrecursor.Checked = Pars.RefinePrecursorMassCharge;
comboBoxMinCharge.Text = "0";
comboBoxMaxCharge.Text = "100";
comboBoxMinCharge.Text = Pars.MinCharge;
comboBoxMaxCharge.Text = Pars.MaxCharge;
ckbxOutputChromatograms.Checked = Pars.DataOutputChromatograms;
ckbxOutputMetrics.Checked = Pars.DataOutputMetrics;
ckbxOutputMGF.Checked = Pars.DataOutputMGF;
checkBoxFaims.Checked = Pars.FaimsOutputMgf;
ckbxOutputParse.Checked = Pars.DataOutputParseMatrix;
checkBoxDataOutputDirectory.Checked = Pars.DataOutputDirectory;
radioButtonSearchNone.Checked = Pars.SearchEngineNone;
radioButtonSearchXTandem.Checked = Pars.SearchEngineXTandem;
textBoxQcDataDirectory.Text = Pars.QcDataDirectory;
textBoxXTandemDir.Text = Pars.XTandemDirectory;
textBoxFastaFile.Text = Pars.FastaFile;
textBoxNumSpectra.Text = Pars.NumberSpectraToSearch;
peptideModifications = Pars.PeptideModifications;
ckbxOutputQuant.Checked = Pars.QuantifyReporterIons;
comboBoxLabelingReagents.Text = Pars.Reagents;
checkBoxMgfLowMass.Checked = Pars.MGFLowMassCutoff;
textBoxMgfLowMass.Text = Pars.MGFLowMassCutoffValue;
}
private void toolStripMenuItemOpenParameters_Click(object sender, EventArgs e)
{
OpenFileDialog openParameters = new OpenFileDialog();
openParameters.Filter = "RawTools Parameters|*.rtxml";
openParameters.Title = "Load RawTools Parameters";
openParameters.ShowDialog();
if (openParameters.FileName != "")
{
var serializer = new XmlSerializer(typeof(ParametersContainer));
using (StreamReader reader = new StreamReader(openParameters.FileName))
{
ParametersContainer Pars = (ParametersContainer)serializer.Deserialize(reader);
LoadParameters(Pars);
}
}
}
private void toolStripMenuItemSaveParameters_Click(object sender, EventArgs e)
{
SaveFileDialog saveParameters = new SaveFileDialog();
ParametersContainer Pars = GetOutParameters();
saveParameters.Filter = "RawTools Parameters|*.rtxml";
saveParameters.Title = "Save RawTools Parameters";
saveParameters.ShowDialog();
// If the file name is not an empty string open it for saving.
if (saveParameters.FileName != "")
{
var serializer = new XmlSerializer(typeof(ParametersContainer));
using (StreamWriter writer = new StreamWriter(saveParameters.FileName))
{
serializer.Serialize(writer, Pars);
}
}
}