private void PreparingMultiGlycan(Dictionary <COL.GlycoLib.enumLabelingTag, float> argLabeling)
{
DoLog = chkLog.Checked;
//saveFileDialog1.Filter = "Excel Files (*.xslx)|*.xslx";
//saveFileDialog1.Filter = "CSV Files (*.csv)|*.csv";
DateTime time = DateTime.Now; // Use current time
string TimeFormat = "yyMMdd HHmm"; // Use this format
if (DoLog)
{
Logger.WriteLog(System.Environment.NewLine + System.Environment.NewLine + "-----------------------------------------------------------");
Logger.WriteLog("Start Process");
}
saveFileDialog1.FileName = Path.GetDirectoryName(txtRawFile.Text) + "\\" + Path.GetFileNameWithoutExtension(txtRawFile.Text) + "-" + time.ToString(TimeFormat);
if (txtRawFile.Text == "" || (rdoUserList.Checked && txtGlycanList.Text == "") || txtMaxLCTime.Text == "")
{
MessageBox.Show("Please check input values.");
if (DoLog)
{
Logger.WriteLog("End Process- because input value not complete");
}
return;
}
if (saveFileDialog1.ShowDialog() == DialogResult.OK)
{
string glycanlist = System.Windows.Forms.Application.StartupPath + "\\Default_Combination.csv";
if (!rdoDefaultList.Checked)
{
glycanlist = txtGlycanList.Text;
}
if (DoLog)
{
Logger.WriteLog("Start initial program");
}
List <float> AdductMasses = new List <float>();
Dictionary <float, string> AdductLabel = new Dictionary <float, string>();
if (chkAdductK.Checked)
{
AdductMasses.Add(MassLib.Atoms.Potassium);
AdductLabel.Add(MassLib.Atoms.Potassium, "K");
}
if (chkAdductNH4.Checked)
{
AdductMasses.Add(MassLib.Atoms.NitrogenMass + 4 * MassLib.Atoms.HydrogenMass);
AdductLabel.Add(MassLib.Atoms.NitrogenMass + 4 * MassLib.Atoms.HydrogenMass, "NH4");
}
if (chkAdductNa.Checked)
{
AdductMasses.Add(MassLib.Atoms.SodiumMass);
AdductLabel.Add(MassLib.Atoms.SodiumMass, "Na");
}
if (chkAdductProton.Checked)
{
AdductMasses.Add(MassLib.Atoms.ProtonMass);
AdductLabel.Add(MassLib.Atoms.ProtonMass, "H");
}
float outMass = 0.0f;
if (chkAdductUser.Checked && float.TryParse(txtAdductMass.Text, out outMass))
{
AdductMasses.Add(outMass);
AdductLabel.Add(outMass, "User");
}
// MultiNGlycanESIMultiThreads MultiESIs = new MultiNGlycanESIMultiThreads(glycanlist, txtRawFile.Text, Convert.ToInt32(cboCPU.SelectedItem), _peakParameter, _transformParameters);
MultiGlycanESI ESI = null;
if (argLabeling.Count != 0)
{
ESI = new MultiGlycanESI(txtRawFile.Text, Convert.ToInt32(txtStartScan.Text), Convert.ToInt32(txtEndScan.Text), glycanlist, Convert.ToDouble(txtPPM.Text), Convert.ToDouble(txtGlycanPPM.Text), chkPermethylated.Checked, chkReducedReducingEnd.Checked, cboSia.SelectedIndex, argLabeling, AdductLabel, AdductMasses, DoLog, rdoPositive.Checked);
}
else
{
ESI = new MultiGlycanESI(txtRawFile.Text, Convert.ToInt32(txtStartScan.Text), Convert.ToInt32(txtEndScan.Text), glycanlist, Convert.ToDouble(txtPPM.Text), Convert.ToDouble(txtGlycanPPM.Text), chkPermethylated.Checked, chkReducedReducingEnd.Checked, cboSia.SelectedIndex, DoLog, rdoPositive.Checked);
}
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.None;
if (rdoDRAG.Checked)
{
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.DRAG;
}
else if (rdoMultiplePemrthylated.Checked)
{
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.MultiplexPermethylated;
}
ESI.PositiveChargeMode = rdoPositive.Checked;
ESI.MergeDifferentChargeIntoOne = chkMergeDffCharge.Checked;
ESI.ExportFilePath = saveFileDialog1.FileName;
ESI.MaxLCBackMin = Convert.ToSingle(txtMaxLCTime.Text);
ESI.MaxLCFrontMin = Convert.ToSingle(txtMinLCTime.Text);
ESI.IsotopePPM = Convert.ToSingle(txtIsotopeEnvTolerence.Text);
ESI.MininumIsotopePeakCount = Convert.ToInt32(txtIsotopeEnvMinPeakCount.Text);
ESI.PeakSNRatio = Convert.ToSingle(txtSN.Text);
ESI.IsMatchMonoisotopicOnly = chkMonoOnly.Checked;
ESI.ApplyLinearRegLC = chkApplyLinearRegLC.Checked;
ESI.MinPeakHeightPrecentage = Convert.ToSingle(txtMinPeakHeight.Text);
if (chkAbundance.Checked)
{
ESI.MinAbundance = Convert.ToDouble(txtAbundanceMin.Text);
}
else
{
ESI.MinAbundance = 0;
}
if (chkMinLengthOfLC.Checked)
{
ESI.MinLengthOfLC = Convert.ToSingle(txtScanCount.Text);
}
else
{
ESI.MinLengthOfLC = 0;
}
if (chkMZMatch.Checked)
{
ESI.IncludeMZMatch = true;
}
ESI.ForceProtonatedGlycan = chkForceProtonated.Checked;
// ESI.AdductMass = AdductMasses;
//ESI.AdductMassToLabel = AdductLabel;
ESI.IndividualImgs = chkIndividualImg.Checked;
ESI.QuantificationImgs = chkQuantImgs.Checked;
ESI.TotalLCTime = Convert.ToSingle(txtLCTime.Text);
ESI.LCTimeTolerance = Convert.ToSingle(txtLCTolerance.Text) / 100.0f;
if (lstGU != null && lstGU.Count > 0)
{
ESI.GlycanUnits = lstGU;
double[] x = lstGU.Select(ti => Convert.ToDouble(ti.EluctionTime)).ToArray();
double[] y = lstGU.Select(gu => Convert.ToDouble(gu.GU)).ToArray();
ESI.GUFitFunction = new ViliPetek.LinearAlgebra.PolyFit(x, y, 5);
}
if (DoLog)
{
Logger.WriteLog("Initial program complete");
}
frmProcessing frmProcess = new frmProcessing(ESI, DoLog);
frmProcess.ShowDialog();
if (DoLog)
{
Logger.WriteLog("Finish process");
}
}
}
private void PreparingMultiGlycan(Dictionary<COL.GlycoLib.enumLabelingTag,float> argLabeling)
{
DoLog = chkLog.Checked;
//saveFileDialog1.Filter = "Excel Files (*.xslx)|*.xslx";
//saveFileDialog1.Filter = "CSV Files (*.csv)|*.csv";
DateTime time = DateTime.Now; // Use current time
string TimeFormat = "yyMMdd HHmm"; // Use this format
if (DoLog)
{
Logger.WriteLog(System.Environment.NewLine + System.Environment.NewLine + "-----------------------------------------------------------");
Logger.WriteLog("Start Process");
}
saveFileDialog1.FileName = Path.GetDirectoryName(txtRawFile.Text) + "\\" + Path.GetFileNameWithoutExtension(txtRawFile.Text) + "-" + time.ToString(TimeFormat);
if (txtRawFile.Text == "" || (rdoUserList.Checked && txtGlycanList.Text == "") || txtMaxLCTime.Text == "")
{
MessageBox.Show("Please check input values.");
if (DoLog)
{
Logger.WriteLog("End Process- because input value not complete");
}
return;
}
if (saveFileDialog1.ShowDialog() == DialogResult.OK)
{
string glycanlist = System.Windows.Forms.Application.StartupPath + "\\Default_Combination.csv";
if (!rdoDefaultList.Checked)
{
glycanlist = txtGlycanList.Text;
}
if (DoLog)
{
Logger.WriteLog("Start initial program");
}
List<float> AdductMasses = new List<float>();
Dictionary<float, string> AdductLabel = new Dictionary<float, string>();
if (chkAdductK.Checked)
{
AdductMasses.Add(MassLib.Atoms.Potassium);
AdductLabel.Add(MassLib.Atoms.Potassium, "K");
}
if (chkAdductNH4.Checked)
{
AdductMasses.Add(MassLib.Atoms.NitrogenMass + 4 * MassLib.Atoms.HydrogenMass);
AdductLabel.Add(MassLib.Atoms.NitrogenMass + 4 * MassLib.Atoms.HydrogenMass, "NH4");
}
if (chkAdductNa.Checked)
{
AdductMasses.Add(MassLib.Atoms.SodiumMass);
AdductLabel.Add(MassLib.Atoms.SodiumMass, "Na");
}
if (chkAdductProton.Checked)
{
AdductMasses.Add(MassLib.Atoms.ProtonMass);
AdductLabel.Add(MassLib.Atoms.ProtonMass, "H");
}
float outMass = 0.0f;
if (chkAdductUser.Checked && float.TryParse(txtAdductMass.Text, out outMass))
{
AdductMasses.Add(outMass);
AdductLabel.Add(outMass, "User");
}
// MultiNGlycanESIMultiThreads MultiESIs = new MultiNGlycanESIMultiThreads(glycanlist, txtRawFile.Text, Convert.ToInt32(cboCPU.SelectedItem), _peakParameter, _transformParameters);
MultiGlycanESI ESI = null;
if (argLabeling.Count != 0)
{
ESI = new MultiGlycanESI(txtRawFile.Text, Convert.ToInt32(txtStartScan.Text), Convert.ToInt32(txtEndScan.Text), glycanlist, Convert.ToDouble(txtPPM.Text), Convert.ToDouble(txtGlycanPPM.Text), chkPermethylated.Checked, chkReducedReducingEnd.Checked,cboSia.SelectedIndex, argLabeling, AdductLabel,AdductMasses, DoLog, rdoPositive.Checked);
}
else
{
ESI = new MultiGlycanESI(txtRawFile.Text, Convert.ToInt32(txtStartScan.Text), Convert.ToInt32(txtEndScan.Text), glycanlist, Convert.ToDouble(txtPPM.Text), Convert.ToDouble(txtGlycanPPM.Text), chkPermethylated.Checked, chkReducedReducingEnd.Checked, cboSia.SelectedIndex, DoLog, rdoPositive.Checked);
}
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.None;
if (rdoDRAG.Checked)
{
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.DRAG;
}
else if (rdoMultiplePemrthylated.Checked)
{
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.MultiplexPermethylated;
}
ESI.PositiveChargeMode = rdoPositive.Checked;
ESI.MergeDifferentChargeIntoOne = chkMergeDffCharge.Checked;
ESI.ExportFilePath = saveFileDialog1.FileName;
ESI.MaxLCBackMin = Convert.ToSingle(txtMaxLCTime.Text);
ESI.MaxLCFrontMin = Convert.ToSingle(txtMinLCTime.Text);
ESI.IsotopePPM = Convert.ToSingle(txtIsotopeEnvTolerence.Text);
ESI.MininumIsotopePeakCount = Convert.ToInt32(txtIsotopeEnvMinPeakCount.Text);
ESI.PeakSNRatio = Convert.ToSingle(txtSN.Text);
ESI.IsMatchMonoisotopicOnly = chkMonoOnly.Checked;
ESI.ApplyLinearRegLC = chkApplyLinearRegLC.Checked;
ESI.MinPeakHeightPrecentage = Convert.ToSingle(txtMinPeakHeight.Text);
if (chkAbundance.Checked)
{
ESI.MinAbundance = Convert.ToDouble(txtAbundanceMin.Text);
}
else
{
ESI.MinAbundance = 0;
}
if (chkMinLengthOfLC.Checked)
{
ESI.MinLengthOfLC = Convert.ToSingle(txtScanCount.Text);
}
else
{
ESI.MinLengthOfLC = 0;
}
if (chkMZMatch.Checked)
{
ESI.IncludeMZMatch = true;
}
ESI.ForceProtonatedGlycan = chkForceProtonated.Checked;
// ESI.AdductMass = AdductMasses;
//ESI.AdductMassToLabel = AdductLabel;
ESI.IndividualImgs = chkIndividualImg.Checked;
ESI.QuantificationImgs = chkQuantImgs.Checked;
ESI.TotalLCTime = Convert.ToSingle(txtLCTime.Text);
ESI.LCTimeTolerance = Convert.ToSingle(txtLCTolerance.Text)/100.0f;
if (DoLog)
{
Logger.WriteLog("Initial program complete");
}
frmProcessing frmProcess = new frmProcessing(ESI, DoLog);
frmProcess.ShowDialog();
if (DoLog)
{
Logger.WriteLog("Finish process");
}
}
}