Ejemplo n.º 1
0
        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");
                }
            }
        }
Ejemplo n.º 2
0
        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");
                }
            }
        }