public frmProcessing(MultiGlycanESI argMultiNGlycan, bool argLog)
{
InitializeComponent();
DoLog = argLog;
_MultiNGlycan = argMultiNGlycan;
_MultiNGlycan.MaxGlycanCharge = 5;
int StartScan = argMultiNGlycan.StartScan;
int EndScan = argMultiNGlycan.EndScan;
LstScanNumber = new List <int>();
for (int i = StartScan; i <= EndScan; i++)
{
if (_MultiNGlycan.RawReader.GetMsLevel(i) == 1)
{
LstScanNumber.Add(i);
}
}
Start = DateTime.Now;
if (DoLog)
{
Logger.WriteLog("Start process each scan");
}
try
{
bgWorker_Process.RunWorkerAsync();
}
catch (Exception ex)
{
MessageBox.Show(ex.Message);
}
}
public frmProcessing(MultiGlycanESI argMultiNGlycan, bool argLog )
{
InitializeComponent();
DoLog = argLog;
_MultiNGlycan = argMultiNGlycan;
_MultiNGlycan.MaxGlycanCharge = 5;
int StartScan = argMultiNGlycan.StartScan;
int EndScan = argMultiNGlycan.EndScan;
LstScanNumber = new List<int>();
for (int i = StartScan; i <= EndScan; i++)
{
if (_MultiNGlycan.RawReader.GetMsLevel(i) == 1)
{
LstScanNumber.Add(i);
}
}
Start = DateTime.Now;
if (DoLog)
{
Logger.WriteLog("Start process each scan");
}
try
{
bgWorker_Process.RunWorkerAsync();
}
catch (Exception ex)
{
MessageBox.Show(ex.Message);
}
}
public frmBatchProcessing(MultiGlycanESI argMultiNGlycan, List <string> argRawFiles, int argConCurrent, bool argLog)
{
NumberOfParallel = argConCurrent;
InitializeComponent();
DoLog = argLog;
_MultiNGlycan = argMultiNGlycan;
_MultiNGlycan.MaxGlycanCharge = 5;
_RawFilesList = argRawFiles;
//ProcessMultiGlycan();
ProgressUpdate = new Dictionary <string, int>();
TotalScanNum = new Dictionary <string, int>();
_MultiNGlycan.ReadGlycanList();
_MultiNGlycan.CandidateMzList = _MultiNGlycan.GenerateCandidateGlycanMZList(_MultiNGlycan.GlycanList);
ProcessingFile = new string[] { "0", "0", "0" };
ProcessingStatus = new string[] { "ProcessingStatus", "ProcessingStatus", "ProcessingStatus" };
progressBar1.Maximum = 100;
progressBar2.Maximum = 100;
progressBar3.Maximum = 100;
lblCurrentFile.Text = "0 / " + _RawFilesList.Count.ToString();
bgWorker_Process.RunWorkerAsync();
}
public frmBatchProcessing(MultiGlycanESI argMultiNGlycan, List<string> argRawFiles, int argConCurrent, bool argLog)
{
NumberOfParallel = argConCurrent;
InitializeComponent();
DoLog = argLog;
_MultiNGlycan = argMultiNGlycan;
_MultiNGlycan.MaxGlycanCharge = 5;
_RawFilesList = argRawFiles;
//ProcessMultiGlycan();
ProgressUpdate = new Dictionary<string, int>();
TotalScanNum = new Dictionary<string, int>();
_MultiNGlycan.ReadGlycanList();
_MultiNGlycan.CandidateMzList = _MultiNGlycan.GenerateCandidateGlycanMZList(_MultiNGlycan.GlycanList);
ProcessingFile = new string[] { "0", "0", "0" };
ProcessingStatus = new string[] { "ProcessingStatus", "ProcessingStatus", "ProcessingStatus" };
progressBar1.Maximum = 100;
progressBar2.Maximum = 100;
progressBar3.Maximum = 100;
lblCurrentFile.Text = "0 / " + _RawFilesList.Count.ToString();
bgWorker_Process.RunWorkerAsync();
}
private void PreparingMultiGlycan(Dictionary<COL.GlycoLib.enumLabelingTag,float> argLabeling, List<string> argRawFiles )
{
//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;
}
//folderBrowserDialog1.SelectedPath = txtRawFile.Text;
string defaultOutputFolder = txtRawFile.Text + "\\" +DateTime.Now.ToString("yyMMdd-HHmm");
if (!Directory.Exists(defaultOutputFolder))
{
Directory.CreateDirectory(defaultOutputFolder);
}
folderBrowserDialog1.SelectedPath = defaultOutputFolder;
if (folderBrowserDialog1.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, 0,99999, glycanlist, Convert.ToDouble(txtPPM.Text), Convert.ToDouble(txtGlycanPPM.Text), chkPermethylated.Checked, chkReducedReducingEnd.Checked,cboSia.SelectedIndex, argLabeling, AdductLabel,AdductMasses, DoLog);
}
else
{
ESI = new MultiGlycanESI(txtRawFile.Text,0, 99999, glycanlist, Convert.ToDouble(txtPPM.Text), Convert.ToDouble(txtGlycanPPM.Text), chkPermethylated.Checked, chkReducedReducingEnd.Checked, cboSia.SelectedIndex, DoLog);
}
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.None;
if (rdoDRAG.Checked)
{
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.DRAG;
}
else if (rdoMultiplePemrthylated.Checked)
{
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.MultiplexPermethylated;
}
ESI.MergeDifferentChargeIntoOne = chkMergeDffCharge.Checked;
ESI.ExportFilePath = folderBrowserDialog1.SelectedPath;
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.ForceProtonatedGlycan = chkForceProtonated.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;
}
// 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");
}
this.Visible = false;
int concurrent = Convert.ToInt32(cboConcurrent.Text);
frmBatchProcessing frmProcess = new frmBatchProcessing(ESI, argRawFiles, concurrent,DoLog);
frmProcess.ProtonatedResult = chkProtonatedResult.Checked;
if (concurrent == 1)
{
frmProcess.Size = new Size(370, 120);
}
else if (concurrent ==2)
{
frmProcess.Size = new Size(370, 180);
}
else
{
frmProcess.Size = new Size(370, 240);
}
frmProcess.ShowDialog();
this.Visible = true;
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 (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");
}
}
}
public static void Processing(ref MultiGlycanESI argMultiGlycan)
{
GlycanCompound processed;
try
{
List<string> identifiedGlycan =argMultiGlycan.IdentifiedGlycanCompounds.Select(x => x.GlycanKey).Distinct().ToList();
Dictionary<string,List<int>> dictGlycanKeySearchRange = new Dictionary<string, List<int>>();
int LastScan = argMultiGlycan.RawReader.NumberOfScans;
foreach (string glycanKey in identifiedGlycan)
{
List<int> identifedScans =
argMultiGlycan.MatchedPeakInScan.Where(x => x.GlycanComposition.GlycanKey == glycanKey)
.Select(y => y.ScanNum)
.ToList();
identifedScans.Sort();
int frontEdge = identifedScans[0];
double FirstIdentifiedTime = argMultiGlycan.RawReader.ReadScan(frontEdge).Time;
while (frontEdge>1)
{
frontEdge -= 1;
if (argMultiGlycan.RawReader.GetMsLevel(frontEdge) != 1)
{
continue;
}
MSScan s = argMultiGlycan.RawReader.ReadScan(frontEdge);
if (FirstIdentifiedTime - s.Time > 5)
{
break;
}
}
int backEdge = identifedScans[identifedScans.Count - 1];
double LastIdentifedTime = argMultiGlycan.RawReader.ReadScan(backEdge).Time;
while (backEdge < LastScan)
{
backEdge += 1;
if (argMultiGlycan.RawReader.GetMsLevel(backEdge) != 1)
{
continue;
}
MSScan s = argMultiGlycan.RawReader.ReadScan(backEdge);
if (s.Time - LastIdentifedTime > 5)
{
break;
}
}
dictGlycanKeySearchRange.Add(glycanKey, new List<int>(){frontEdge,backEdge});
}
List<MSScan> msScans = new List<MSScan>();
string previousGlycanKey = "";
foreach (GlycanCompound g in argMultiGlycan.GlycanList.OrderBy(x=> x.GlycanKey))
{
if (!identifiedGlycan.Contains(g.GlycanKey))
{
continue;
}
if (previousGlycanKey != g.GlycanKey)
{
msScans.Clear();
//Read Scans
int startScan = dictGlycanKeySearchRange[g.GlycanKey][0] >= 1 ? dictGlycanKeySearchRange[g.GlycanKey][0] : 1;
int endScan = dictGlycanKeySearchRange[g.GlycanKey][1] <= LastScan ? dictGlycanKeySearchRange[g.GlycanKey][1] : LastScan;
msScans.AddRange(argMultiGlycan.RawReader.ReadScanWMSLevel(startScan, endScan,1));
previousGlycanKey = g.GlycanKey;
}
//FindPeaks
int charge = g.Charge;
List<List<MSScan>> scanSectionsContainPeaks = new List<List<MSScan>>();
for (int i = 0; i < msScans.Count; i++)
{
MSScan scan = msScans[i];
int closedIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float) g.MZ);
if (MassUtility.GetMassPPM(scan.MZs[closedIdx], g.MZ) <=argMultiGlycan.MassPPM)
{
List<int> peaks = FindPeakIdx(scan.MZs, closedIdx, charge, argMultiGlycan.IsotopePPM);
if (peaks.Count - peaks.IndexOf(closedIdx) < argMultiGlycan.MininumIsotopePeakCount)
{
continue;
}
//Found peaks
if (scanSectionsContainPeaks.Count > 0)
{
MSScan lastSectionLastScan = scanSectionsContainPeaks.Last().Last();
if (scan.Time - lastSectionLastScan.Time > 2.5)
{
scanSectionsContainPeaks.Add(new List<MSScan>(){scan});
}
else
{
scanSectionsContainPeaks.Last().Add(scan);
}
}
else
{
scanSectionsContainPeaks.Add(new List<MSScan>(){scan});
}
}
}
//If scans can form an elution profile add to identifed result;
foreach (List<MSScan> sectionScans in scanSectionsContainPeaks)
{
if (sectionScans.Count < 3)
{
continue;
}
else
{
//Add matched peak
foreach (MSScan s in sectionScans)
{
int PeakIdx = MassUtility.GetClosestMassIdx(s.MZs, (float)g.MZ);
MatchedGlycanPeak mPeak = new MatchedGlycanPeak(s.ScanNo, s.Time, s.MSPeaks[PeakIdx], g);
List<int> peaks = FindPeakIdx(s.MZs, PeakIdx, charge, argMultiGlycan.IsotopePPM);
int startIdx = peaks.IndexOf(PeakIdx);
List<MSPoint> lstIsotopes= new List<MSPoint>();
for (int i = startIdx; i < peaks.Count; i++)
{
lstIsotopes.Add(new MSPoint(s.MZs[peaks[i]],s.Intensities[peaks[i]]));
}
mPeak.MSPoints = lstIsotopes;
if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
{
argMultiGlycan.MatchedPeakInScan.Add(mPeak);
}
}
}
}
}
//foreach (GlycanCompound g in argMultiGlycan.IdentifiedGlycanCompounds)
//{
// processed = g;
// //Search Peak in front of the peak
// ThermoRawReader raw = (ThermoRawReader)argMultiGlycan.RawReader;
// List<int> identifedScans = argMultiGlycan.MatchedPeakInScan.Where(x => x.GlycanComposition == g).Select(y => y.ScanNum).ToList();
// for (int i = 0; i < identifedScans.Count; i++)
// {
// int identifiedScanNum = identifedScans[i];
// while (true)
// {
// identifiedScanNum -= 1;
// if (identifiedScanNum < 1 || raw.GetRetentionTime(identifedScans[i]) - raw.GetRetentionTime(identifiedScanNum) > argMultiGlycan.MaxLCFrontMin)
// {
// break;
// }
// if (raw.GetMsLevel((identifiedScanNum)) != 1)
// {
// continue;
// }
// MSScan scan = raw.ReadScan(identifiedScanNum);
// int PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], g.MZ) > argMultiGlycan.MassPPM)
// {
// continue;
// }
// //Find isotope cluster
// List<MSPoint> lstIsotopes = new List<MSPoint>();
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx],scan.Intensities[PeakIdx]));
// float targetMZ = (float)g.MZ;
// do
// {
// targetMZ += 1.0f/g.Charge;
// PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, targetMZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], targetMZ) <= argMultiGlycan.MassPPM)
// {
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx],scan.Intensities[PeakIdx]));
// }
// else
// {
// break;
// }
// } while (true);
// if (lstIsotopes.Count < argMultiGlycan.MininumIsotopePeakCount)
// {
// continue;
// }
// MatchedGlycanPeak mPeak = new MatchedGlycanPeak(scan.ScanNo, scan.Time, scan.MSPeaks[PeakIdx], g);
// mPeak.MSPoints = lstIsotopes;
// if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
// {
// argMultiGlycan.MatchedPeakInScan.Add(mPeak);
// }
// }
// identifiedScanNum = identifedScans[i];
// while (true)
// {
// identifiedScanNum += 1;
// if (identifiedScanNum > raw.NumberOfScans || raw.GetRetentionTime(identifiedScanNum) - raw.GetRetentionTime(identifedScans[i]) > argMultiGlycan.MaxLCBackMin)
// {
// break;
// }
// if (raw.GetMsLevel((identifiedScanNum)) != 1)
// {
// continue;
// }
// MSScan scan = raw.ReadScan(identifiedScanNum);
// int PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], g.MZ) > argMultiGlycan.MassPPM)
// {
// continue;
// }
// //Find isotope cluster
// List<MSPoint> lstIsotopes = new List<MSPoint>();
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx], scan.Intensities[PeakIdx]));
// float targetMZ = (float)g.MZ;
// do
// {
// targetMZ += 1.0f / g.Charge;
// PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, targetMZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], targetMZ) <= argMultiGlycan.MassPPM)
// {
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx], scan.Intensities[PeakIdx]));
// }
// else
// {
// break;
// }
// } while (true);
// if (lstIsotopes.Count < argMultiGlycan.MininumIsotopePeakCount)
// {
// continue;
// }
// MatchedGlycanPeak mPeak = new MatchedGlycanPeak(scan.ScanNo, scan.Time, scan.MSPeaks[PeakIdx], g);
// mPeak.MSPoints = lstIsotopes;
// if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
// {
// argMultiGlycan.MatchedPeakInScan.Add(mPeak);
// }
// }
// }
//}
}
catch (Exception ex)
{
throw ex;
}
}
private void PreparingMultiGlycan(Dictionary <COL.GlycoLib.enumLabelingTag, float> argLabeling, List <string> argRawFiles)
{
//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;
}
//folderBrowserDialog1.SelectedPath = txtRawFile.Text;
string defaultOutputFolder = txtRawFile.Text + "\\" + DateTime.Now.ToString("yyMMdd-HHmm");
if (!Directory.Exists(defaultOutputFolder))
{
Directory.CreateDirectory(defaultOutputFolder);
}
folderBrowserDialog1.SelectedPath = defaultOutputFolder;
if (folderBrowserDialog1.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, 0, 99999, glycanlist, Convert.ToDouble(txtPPM.Text), Convert.ToDouble(txtGlycanPPM.Text), chkPermethylated.Checked, chkReducedReducingEnd.Checked, cboSia.SelectedIndex, argLabeling, AdductLabel, AdductMasses, DoLog);
}
else
{
ESI = new MultiGlycanESI(txtRawFile.Text, 0, 99999, glycanlist, Convert.ToDouble(txtPPM.Text), Convert.ToDouble(txtGlycanPPM.Text), chkPermethylated.Checked, chkReducedReducingEnd.Checked, cboSia.SelectedIndex, DoLog);
}
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.None;
if (rdoDRAG.Checked)
{
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.DRAG;
}
else if (rdoMultiplePemrthylated.Checked)
{
ESI.LabelingMethod = GlycoLib.enumGlycanLabelingMethod.MultiplexPermethylated;
}
ESI.MergeDifferentChargeIntoOne = chkMergeDffCharge.Checked;
ESI.ExportFilePath = folderBrowserDialog1.SelectedPath;
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.ForceProtonatedGlycan = chkForceProtonated.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;
}
// 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");
}
this.Visible = false;
int concurrent = Convert.ToInt32(cboConcurrent.Text);
frmBatchProcessing frmProcess = new frmBatchProcessing(ESI, argRawFiles, concurrent, DoLog);
frmProcess.ProtonatedResult = chkProtonatedResult.Checked;
if (concurrent == 1)
{
frmProcess.Size = new Size(370, 120);
}
else if (concurrent == 2)
{
frmProcess.Size = new Size(370, 180);
}
else
{
frmProcess.Size = new Size(370, 240);
}
frmProcess.ShowDialog();
this.Visible = true;
if (DoLog)
{
Logger.WriteLog("Finish process");
}
}
}
private void ProcessMultiGlycanAsync(string argFile)
{
int runningSlot = -1;
for (int i = 0; i < 3; i++)
{
if (ProcessingFile[i] == "0")
{
ProcessingFile[i] = argFile;
runningSlot = i;
break;
}
}
MultiGlycanESI multiGlycan = null;
//ZedGraphControl zedGraphControl = new ZedGraphControl();
try
{
//debugWriter.WriteLine("---------------------Process file:" + argFile + "------------------------");
ProcessingStatus[runningSlot] = "Status: Reading Raw file";
bgWorker_Process.ReportProgress(0);
ProgressUpdate.Add(argFile, 0);
TotalScanNum.Add(argFile, 99999);
if (_MultiNGlycan.LabelingRatio.Count != 0)
{
multiGlycan = new MultiGlycanESI(argFile, 1, 99999, _MultiNGlycan.GlycanFile, _MultiNGlycan.MassPPM, _MultiNGlycan.GlycanPPM, _MultiNGlycan.IsPermethylated, _MultiNGlycan.IsReducedReducingEnd, _MultiNGlycan.SiaType, _MultiNGlycan.LabelingRatio, _MultiNGlycan.AdductMassToLabel, _MultiNGlycan.AdductMass, _MultiNGlycan.DoLOG);
}
else
{
multiGlycan = new MultiGlycanESI(argFile, 1, 99999, _MultiNGlycan.GlycanFile, _MultiNGlycan.MassPPM, _MultiNGlycan.GlycanPPM, _MultiNGlycan.IsPermethylated, _MultiNGlycan.IsReducedReducingEnd, _MultiNGlycan.SiaType, _MultiNGlycan.DoLOG);
}
//debugWriter.WriteLine("init finish");
multiGlycan.LabelingMethod = _MultiNGlycan.LabelingMethod;
multiGlycan.MergeDifferentChargeIntoOne = _MultiNGlycan.MergeDifferentChargeIntoOne;
multiGlycan.ExportFilePath = _MultiNGlycan.ExportFilePath + "\\" + Path.GetFileNameWithoutExtension(argFile);
multiGlycan.MaxLCBackMin = _MultiNGlycan.MaxLCBackMin;
multiGlycan.MaxLCFrontMin = _MultiNGlycan.MaxLCFrontMin;
multiGlycan.IsotopePPM = _MultiNGlycan.IsotopePPM;
multiGlycan.MininumIsotopePeakCount = _MultiNGlycan.MininumIsotopePeakCount;
multiGlycan.PeakSNRatio = _MultiNGlycan.PeakSNRatio;
multiGlycan.IsMatchMonoisotopicOnly = _MultiNGlycan.IsMatchMonoisotopicOnly;
multiGlycan.MinAbundance = _MultiNGlycan.MinAbundance;
multiGlycan.MinLengthOfLC = _MultiNGlycan.MinLengthOfLC;
multiGlycan.IncludeMZMatch = _MultiNGlycan.IncludeMZMatch;
multiGlycan.IndividualImgs = _MultiNGlycan.IndividualImgs;
multiGlycan.QuantificationImgs = _MultiNGlycan.QuantificationImgs;
multiGlycan.GlycanList = _MultiNGlycan.GlycanList;
multiGlycan.CandidateMzList = _MultiNGlycan.CandidateMzList;
multiGlycan.MinPeakHeightPrecentage = _MultiNGlycan.MinPeakHeightPrecentage;
if (_MultiNGlycan.ApplyLinearRegLC)
{
multiGlycan.ApplyLinearRegLC = _MultiNGlycan.ApplyLinearRegLC;
multiGlycan.TotalLCTime = _MultiNGlycan.TotalLCTime;
multiGlycan.LCTimeTolerance = _MultiNGlycan.LCTimeTolerance;
}
TotalScanNum[argFile] = multiGlycan.RawReader.NumberOfScans;
//ProcessingStatus[runningSlot] = "Status: Processing";
//Parallel.ForEach(Enumerable.Range(1, multiGlycan.RawReader.NumberOfScans),
// new ParallelOptions() { MaxDegreeOfParallelism = 4 }, (i) =>
// {
// //Console.WriteLine(argFile + "-" + i.ToString());
// ProgressUpdate[argFile] = ProgressUpdate[argFile] + 1;
// bgWorker_Process.ReportProgress(Convert.ToInt32(ProgressUpdate[argFile] / TotalScanNum[argFile]));
// if (multiGlycan.RawReader.GetMsLevel(i) == 1)
// {
// multiGlycan.ProcessSingleScan(i);
// }
// });
// debugWriter.WriteLine("Start processing");
for (int i = 1; i <= multiGlycan.RawReader.NumberOfScans; i++)
{
ProgressUpdate[argFile] = ProgressUpdate[argFile] + 1;
bgWorker_Process.ReportProgress(Convert.ToInt32(ProgressUpdate[argFile] / TotalScanNum[argFile]));
if (multiGlycan.RawReader.GetMsLevel(i) == 1)
{
multiGlycan.ProcessSingleScan(i);
// debugWriter.WriteLine("Processed scen:" + i.ToString());
}
}
//debugWriter.WriteLine("Merge");
ProcessingStatus[runningSlot] = "Status: Mergeing Result";
multiGlycan.MergeSingleScanResultToPeak();
multiGlycan.SolveDuplicateAssignment();
multiGlycan.MergeSingleScanResultToPeak();
//debugWriter.WriteLine("Merge completed");
if (multiGlycan.GlycanLCorderExist)
{
multiGlycan.ApplyLCordrer();
}
if (!Directory.Exists(multiGlycan.ExportFilePath + "\\Pic") && (multiGlycan.IndividualImgs || multiGlycan.QuantificationImgs))
{
Directory.CreateDirectory(multiGlycan.ExportFilePath + "\\Pic");
}
if (multiGlycan.LabelingMethod == GlycoLib.enumGlycanLabelingMethod.MultiplexPermethylated)
{
multiGlycan.EstimatePurity();
foreach (GlycoLib.enumLabelingTag tag in multiGlycan.LabelingRatio.Keys)
{
if (tag == enumLabelingTag.MP_CH3 || !multiGlycan.HasEstimatePurity((tag)))
continue;
multiGlycan.GetPurityEstimateImage(tag,multiGlycan.ExportFilePath + "\\Pic\\EstimatePurity_" + tag.ToString() + ".png");
}
}
ProcessingStatus[runningSlot] = "Status: Waiting for Export";
bgWorker_Process.ReportProgress(0);
ProcessingStatus[runningSlot] = "Status: Exporting";
bgWorker_Process.ReportProgress(0);
//debugWriter.WriteLine("Export to CSV");
multiGlycan.ExportToCSV();
ProcessingStatus[runningSlot] = "Export completed";
//debugWriter.WriteLine("Export completed");
ProcessingStatus[runningSlot] = "Generate Pics";
if (multiGlycan.IndividualImgs &&
File.Exists(multiGlycan.ExportFilePath+"\\" +Path.GetFileNameWithoutExtension(argFile)+ "_FullList.csv"))
{
//GenerateImages.GenGlycanLcImg(
// _MultiNGlycan.ExportFilePath + "\\" + Path.GetFileName(_MultiNGlycan.ExportFilePath) +"_FullList.csv",
// _MultiNGlycan.ExportFilePath);
GenerateImages.GenGlycanLcImg(multiGlycan);
}
bgWorker_Process.ReportProgress(0);
SucceedFileCount = SucceedFileCount + 1;
//debugWriter.WriteLine("Finish");
//debugWriter.Flush();
}
catch (Exception e)
{
ErrMsg = ErrMsg + (argFile + " error. ErrMSG:" + e.ToString() + "\n");
}
finally
{
ProcessingStatus[runningSlot] = "Status: Ready";
ProcessingFile[runningSlot] = "0";
ProcessedFileCount = ProcessedFileCount + 1;
}
}
private void ProcessMultiGlycanAsync(string argFile)
{
int runningSlot = -1;
for (int i = 0; i < 3; i++)
{
if (ProcessingFile[i] == "0")
{
ProcessingFile[i] = argFile;
runningSlot = i;
break;
}
}
MultiGlycanESI multiGlycan = null;
//ZedGraphControl zedGraphControl = new ZedGraphControl();
try
{
//debugWriter.WriteLine("---------------------Process file:" + argFile + "------------------------");
ProcessingStatus[runningSlot] = "Status: Reading Raw file";
bgWorker_Process.ReportProgress(0);
ProgressUpdate.Add(argFile, 0);
TotalScanNum.Add(argFile, 99999);
if (_MultiNGlycan.LabelingRatio.Count != 0)
{
multiGlycan = new MultiGlycanESI(argFile, 1, 99999, _MultiNGlycan.GlycanFile, _MultiNGlycan.MassPPM, _MultiNGlycan.GlycanPPM, _MultiNGlycan.IsPermethylated, _MultiNGlycan.IsReducedReducingEnd, _MultiNGlycan.SiaType, _MultiNGlycan.LabelingRatio, _MultiNGlycan.AdductMassToLabel, _MultiNGlycan.AdductMass, _MultiNGlycan.DoLOG);
}
else
{
multiGlycan = new MultiGlycanESI(argFile, 1, 99999, _MultiNGlycan.GlycanFile, _MultiNGlycan.MassPPM, _MultiNGlycan.GlycanPPM, _MultiNGlycan.IsPermethylated, _MultiNGlycan.IsReducedReducingEnd, _MultiNGlycan.SiaType, _MultiNGlycan.DoLOG);
}
//debugWriter.WriteLine("init finish");
multiGlycan.LabelingMethod = _MultiNGlycan.LabelingMethod;
multiGlycan.MergeDifferentChargeIntoOne = _MultiNGlycan.MergeDifferentChargeIntoOne;
multiGlycan.ExportFilePath = _MultiNGlycan.ExportFilePath + "\\" + Path.GetFileNameWithoutExtension(argFile);
multiGlycan.MaxLCBackMin = _MultiNGlycan.MaxLCBackMin;
multiGlycan.MaxLCFrontMin = _MultiNGlycan.MaxLCFrontMin;
multiGlycan.IsotopePPM = _MultiNGlycan.IsotopePPM;
multiGlycan.MininumIsotopePeakCount = _MultiNGlycan.MininumIsotopePeakCount;
multiGlycan.PeakSNRatio = _MultiNGlycan.PeakSNRatio;
multiGlycan.IsMatchMonoisotopicOnly = _MultiNGlycan.IsMatchMonoisotopicOnly;
multiGlycan.MinAbundance = _MultiNGlycan.MinAbundance;
multiGlycan.MinLengthOfLC = _MultiNGlycan.MinLengthOfLC;
multiGlycan.IncludeMZMatch = _MultiNGlycan.IncludeMZMatch;
multiGlycan.IndividualImgs = _MultiNGlycan.IndividualImgs;
multiGlycan.QuantificationImgs = _MultiNGlycan.QuantificationImgs;
multiGlycan.GlycanList = _MultiNGlycan.GlycanList;
multiGlycan.CandidateMzList = _MultiNGlycan.CandidateMzList;
multiGlycan.MinPeakHeightPrecentage = _MultiNGlycan.MinPeakHeightPrecentage;
if (_MultiNGlycan.ApplyLinearRegLC)
{
multiGlycan.ApplyLinearRegLC = _MultiNGlycan.ApplyLinearRegLC;
multiGlycan.TotalLCTime = _MultiNGlycan.TotalLCTime;
multiGlycan.LCTimeTolerance = _MultiNGlycan.LCTimeTolerance;
}
TotalScanNum[argFile] = multiGlycan.RawReader.NumberOfScans;
//ProcessingStatus[runningSlot] = "Status: Processing";
//Parallel.ForEach(Enumerable.Range(1, multiGlycan.RawReader.NumberOfScans),
// new ParallelOptions() { MaxDegreeOfParallelism = 4 }, (i) =>
// {
// //Console.WriteLine(argFile + "-" + i.ToString());
// ProgressUpdate[argFile] = ProgressUpdate[argFile] + 1;
// bgWorker_Process.ReportProgress(Convert.ToInt32(ProgressUpdate[argFile] / TotalScanNum[argFile]));
// if (multiGlycan.RawReader.GetMsLevel(i) == 1)
// {
// multiGlycan.ProcessSingleScan(i);
// }
// });
// debugWriter.WriteLine("Start processing");
for (int i = 1; i <= multiGlycan.RawReader.NumberOfScans; i++)
{
ProgressUpdate[argFile] = ProgressUpdate[argFile] + 1;
bgWorker_Process.ReportProgress(Convert.ToInt32(ProgressUpdate[argFile] / TotalScanNum[argFile]));
if (multiGlycan.RawReader.GetMsLevel(i) == 1)
{
multiGlycan.ProcessSingleScan(i);
// debugWriter.WriteLine("Processed scen:" + i.ToString());
}
}
//debugWriter.WriteLine("Merge");
ProcessingStatus[runningSlot] = "Status: Mergeing Result";
multiGlycan.MergeSingleScanResultToPeak();
multiGlycan.SolveDuplicateAssignment();
multiGlycan.MergeSingleScanResultToPeak();
//debugWriter.WriteLine("Merge completed");
if (multiGlycan.GlycanLCorderExist)
{
multiGlycan.ApplyLCordrer();
}
if (!Directory.Exists(multiGlycan.ExportFilePath + "\\Pic") && (multiGlycan.IndividualImgs || multiGlycan.QuantificationImgs))
{
Directory.CreateDirectory(multiGlycan.ExportFilePath + "\\Pic");
}
if (multiGlycan.LabelingMethod == GlycoLib.enumGlycanLabelingMethod.MultiplexPermethylated)
{
multiGlycan.EstimatePurity();
foreach (GlycoLib.enumLabelingTag tag in multiGlycan.LabelingRatio.Keys)
{
if (tag == enumLabelingTag.MP_CH3 || !multiGlycan.HasEstimatePurity((tag)))
{
continue;
}
multiGlycan.GetPurityEstimateImage(tag, multiGlycan.ExportFilePath + "\\Pic\\EstimatePurity_" + tag.ToString() + ".png");
}
}
ProcessingStatus[runningSlot] = "Status: Waiting for Export";
bgWorker_Process.ReportProgress(0);
ProcessingStatus[runningSlot] = "Status: Exporting";
bgWorker_Process.ReportProgress(0);
//debugWriter.WriteLine("Export to CSV");
multiGlycan.ExportToCSV();
ProcessingStatus[runningSlot] = "Export completed";
//debugWriter.WriteLine("Export completed");
ProcessingStatus[runningSlot] = "Generate Pics";
if (multiGlycan.IndividualImgs &&
File.Exists(multiGlycan.ExportFilePath + "\\" + Path.GetFileNameWithoutExtension(argFile) + "_FullList.csv"))
{
//GenerateImages.GenGlycanLcImg(
// _MultiNGlycan.ExportFilePath + "\\" + Path.GetFileName(_MultiNGlycan.ExportFilePath) +"_FullList.csv",
// _MultiNGlycan.ExportFilePath);
GenerateImages.GenGlycanLcImg(multiGlycan);
}
bgWorker_Process.ReportProgress(0);
SucceedFileCount = SucceedFileCount + 1;
//debugWriter.WriteLine("Finish");
//debugWriter.Flush();
}
catch (Exception e)
{
ErrMsg = ErrMsg + (argFile + " error. ErrMSG:" + e.ToString() + "\n");
}
finally
{
ProcessingStatus[runningSlot] = "Status: Ready";
ProcessingFile[runningSlot] = "0";
ProcessedFileCount = ProcessedFileCount + 1;
}
}
public static void GenGlycanLcImg(MultiGlycanESI argMultiGlycanESI)
{
string dir = argMultiGlycanESI.ExportFilePath + "\\Pic";
if (!Directory.Exists(dir))
{
Directory.CreateDirectory(dir);
}
List <Color> LstColor = new List <Color>()
{
Color.DarkCyan, Color.DarkGoldenrod, Color.DarkGray, Color.DarkGreen, Color.DarkKhaki, Color.DarkMagenta, Color.DarkOliveGreen, Color.DarkOrchid, Color.DarkRed, Color.DarkSalmon, Color.DarkSeaGreen, Color.DarkSlateBlue, Color.DarkSlateGray, Color.DarkTurquoise, Color.DarkViolet, Color.DeepPink, Color.DeepSkyBlue
};
Dictionary <string, List <ClusteredPeak> > dictCluster = new Dictionary <string, List <ClusteredPeak> >();
foreach (ClusteredPeak clsPeak in argMultiGlycanESI.MergedResultList)
{
string Key = clsPeak.GlycanKey;
if (argMultiGlycanESI.LabelingMethod != enumGlycanLabelingMethod.None)
{
Key = clsPeak.GlycanKey + "-" + clsPeak.GlycanComposition.LabelingTag;
}
if (!dictCluster.ContainsKey(Key))
{
dictCluster.Add(Key, new List <ClusteredPeak>());
}
dictCluster[Key].Add(clsPeak);
}
//Parallel.ForEach(dictCluster.Keys, new ParallelOptions() {MaxDegreeOfParallelism = MaxDegreeParallelism},Gkey =>
foreach (string Gkey in dictCluster.Keys)
{
string ProcessingGlycanKey = "";
try
{
Dictionary <string, List <LCPointPair> > dictAdductPoints = new Dictionary <string, List <LCPointPair> >();
Dictionary <float, float> MergeIntensity = new Dictionary <float, float>();
List <float> Time = new List <float>();
float maxIntensity = 0;
List <Tuple <double, double> > lstPeakMargin = new List <Tuple <double, double> >();
foreach (ClusteredPeak clsPeak in dictCluster[Gkey])
{
lstPeakMargin.Add(new Tuple <double, double>(clsPeak.StartTime, clsPeak.EndTime));
foreach (MatchedGlycanPeak Peak in clsPeak.MatchedPeaksInScan)
{
if (!dictAdductPoints.ContainsKey(Peak.AdductString))
{
dictAdductPoints.Add(Peak.AdductString, new List <LCPointPair>());
}
float TimeKey = Convert.ToSingle(Peak.ScanTime.ToString("0.00"));
dictAdductPoints[Peak.AdductString].Add(new LCPointPair(Peak.ScanTime, Peak.MSPoints[0].Intensity));
if (!MergeIntensity.ContainsKey(TimeKey))
{
MergeIntensity.Add(TimeKey, 0);
}
MergeIntensity[TimeKey] = MergeIntensity[TimeKey] + Peak.MSPoints[0].Intensity;
if (maxIntensity <= MergeIntensity[TimeKey])
{
maxIntensity = MergeIntensity[TimeKey];
}
if (!Time.Contains(TimeKey))
{
Time.Add(TimeKey);
}
}
}
#region LC Images
using (Chart cht = new Chart())
{
//---------------Generate Graph-----------------
ProcessingGlycanKey = Gkey;
cht.Size = new Size(2400, 1200);
cht.ChartAreas.Add("Default");
cht.ChartAreas["Default"].AxisX.Title = "Scan time (min)";
cht.ChartAreas["Default"].AxisX.TitleFont = new Font("Arial", 24, FontStyle.Bold);
cht.ChartAreas["Default"].AxisX.LabelStyle.Format = "{F2}";
cht.ChartAreas["Default"].AxisX.LabelStyle.Font = new Font("Arial", 24, FontStyle.Bold);
cht.ChartAreas["Default"].AxisX.MajorGrid.LineDashStyle = ChartDashStyle.Dash;
cht.ChartAreas["Default"].AxisX.IsMarginVisible = true;
cht.ChartAreas["Default"].AxisY.Title = "Abundance";
cht.ChartAreas["Default"].AxisY.TitleFont = new Font("Arial", 24, FontStyle.Bold);
cht.ChartAreas["Default"].AxisY.LabelStyle.Format = "{0.#E+00}";
cht.ChartAreas["Default"].AxisY.LabelStyle.Font = new Font("Arial", 24, FontStyle.Bold);
cht.ChartAreas["Default"].AxisY.MajorGrid.LineDashStyle = ChartDashStyle.Dash;
cht.ChartAreas["Default"].AxisY.IsMarginVisible = true;
cht.Titles.Add("Default");
cht.Titles[0].Text = "Glycan: " + Gkey;
cht.Titles[0].Font = new Font("Arial", 24, FontStyle.Bold);
cht.Legends.Add("Default");
cht.Legends["Default"].Docking = Docking.Bottom;
cht.Legends["Default"].Alignment = StringAlignment.Center;
cht.Legends["Default"].LegendStyle = LegendStyle.Row;
cht.Legends["Default"].Font = new Font("Arial", 24, FontStyle.Bold);
int ColorIdx = 0;
// int SymbolIdx = 0;
foreach (string Adduct in dictAdductPoints.Keys)
{
dictAdductPoints[Adduct].OrderBy(x => x.Time); //Sort by time
Series series = cht.Series.Add(Adduct);
series.ChartArea = "Default";
series.ChartType = SeriesChartType.Spline;
series.MarkerStyle = MarkerStyle.Circle;
series.MarkerSize = 15;
series.BorderWidth = 2;
series.Color = LstColor[ColorIdx];
foreach (LCPointPair pp in dictAdductPoints[Adduct])
{
float TimeKey = Convert.ToSingle(pp.Time.ToString("0.00"));
if (series.Points.Where(x => x.XValue == TimeKey).Count() != 0)
{
series.Points.Where(x => x.XValue == TimeKey).ToList()[0].YValues[0] += pp.Intensity;
}
else
{
series.Points.AddXY(TimeKey, pp.Intensity);
}
}
series.Points.OrderBy(x => x.XValue);
ColorIdx = (ColorIdx + 1) % LstColor.Count;
}
//Merge Intensity
Time.Sort();
List <LCPointPair> PPLMerge = new List <LCPointPair>();
foreach (float tim in Time)
{
PPLMerge.Add(new LCPointPair(Convert.ToSingle(tim.ToString("0.00")), MergeIntensity[tim]));
}
Series merge = cht.Series.Add("Merge");
merge.ChartArea = "Default";
merge.ChartType = SeriesChartType.Spline;
merge.BorderWidth = 2;
merge.MarkerStyle = MarkerStyle.Diamond;
merge.MarkerSize = 15;
merge.Color = Color.Black;
merge.BorderDashStyle = ChartDashStyle.Dot;
foreach (LCPointPair pp in PPLMerge)
{
merge.Points.AddXY(pp.Time, pp.Intensity);
}
merge.Points.OrderBy(x => x.XValue);
cht.SaveImage(dir + "\\" + Gkey + ".png", ChartImageFormat.Png);
}
#endregion
}
catch (Exception ex)
{
throw new Exception("GetLC Pic failed " + ProcessingGlycanKey + " Err Msg:" + ex.ToString());
}
}//);
}
public static void GenGlycanLcImg(MultiGlycanESI argMultiGlycanESI)
{
string dir = argMultiGlycanESI.ExportFilePath + "\\Pic";
if (!Directory.Exists(dir))
{
Directory.CreateDirectory(dir);
}
List<Color> LstColor = new List<Color>() { Color.DarkCyan, Color.DarkGoldenrod, Color.DarkGray, Color.DarkGreen, Color.DarkKhaki, Color.DarkMagenta, Color.DarkOliveGreen, Color.DarkOrchid, Color.DarkRed, Color.DarkSalmon, Color.DarkSeaGreen, Color.DarkSlateBlue, Color.DarkSlateGray, Color.DarkTurquoise, Color.DarkViolet, Color.DeepPink, Color.DeepSkyBlue };
Dictionary<string, List<ClusteredPeak>> dictCluster = new Dictionary<string, List<ClusteredPeak>>();
foreach (ClusteredPeak clsPeak in argMultiGlycanESI.MergedResultList)
{
string Key = clsPeak.GlycanKey;
if (argMultiGlycanESI.LabelingMethod != enumGlycanLabelingMethod.None)
{
Key = clsPeak.GlycanKey + "-" + clsPeak.GlycanComposition.LabelingTag;
}
if (!dictCluster.ContainsKey(Key))
{
dictCluster.Add(Key, new List<ClusteredPeak>());
}
dictCluster[Key].Add(clsPeak);
}
//Parallel.ForEach(dictCluster.Keys, new ParallelOptions() {MaxDegreeOfParallelism = MaxDegreeParallelism},Gkey =>
foreach (string Gkey in dictCluster.Keys)
{
string ProcessingGlycanKey = "";
try
{
Dictionary<string, List<LCPointPair>> dictAdductPoints = new Dictionary<string, List<LCPointPair>>();
Dictionary<float, float> MergeIntensity = new Dictionary<float, float>();
List<float> Time = new List<float>();
float maxIntensity = 0;
List<Tuple<double, double>> lstPeakMargin = new List<Tuple<double, double>>();
foreach (ClusteredPeak clsPeak in dictCluster[Gkey])
{
lstPeakMargin.Add(new Tuple<double, double>(clsPeak.StartTime,clsPeak.EndTime));
foreach (MatchedGlycanPeak Peak in clsPeak.MatchedPeaksInScan)
{
if (!dictAdductPoints.ContainsKey(Peak.AdductString))
{
dictAdductPoints.Add(Peak.AdductString, new List<LCPointPair>());
}
float TimeKey = Convert.ToSingle(Peak.ScanTime.ToString("0.00"));
dictAdductPoints[Peak.AdductString].Add(new LCPointPair(Peak.ScanTime, Peak.MSPoints[0].Intensity));
if (!MergeIntensity.ContainsKey(TimeKey))
{
MergeIntensity.Add(TimeKey, 0);
}
MergeIntensity[TimeKey] = MergeIntensity[TimeKey] + Peak.MSPoints[0].Intensity;
if (maxIntensity <= MergeIntensity[TimeKey])
{
maxIntensity = MergeIntensity[TimeKey];
}
if (!Time.Contains(TimeKey))
{
Time.Add(TimeKey);
}
}
}
#region LC Images
using (Chart cht = new Chart())
{
//---------------Generate Graph-----------------
ProcessingGlycanKey = Gkey;
cht.Size = new Size(2400, 1200);
cht.ChartAreas.Add("Default");
cht.ChartAreas["Default"].AxisX.Title = "Scan time (min)";
cht.ChartAreas["Default"].AxisX.TitleFont = new Font("Arial", 24, FontStyle.Bold);
cht.ChartAreas["Default"].AxisX.LabelStyle.Format = "{F2}";
cht.ChartAreas["Default"].AxisX.LabelStyle.Font = new Font("Arial", 24, FontStyle.Bold);
cht.ChartAreas["Default"].AxisX.MajorGrid.LineDashStyle = ChartDashStyle.Dash;
cht.ChartAreas["Default"].AxisX.IsMarginVisible = true;
cht.ChartAreas["Default"].AxisY.Title = "Abundance";
cht.ChartAreas["Default"].AxisY.TitleFont = new Font("Arial", 24, FontStyle.Bold);
cht.ChartAreas["Default"].AxisY.LabelStyle.Format = "{0.#E+00}";
cht.ChartAreas["Default"].AxisY.LabelStyle.Font = new Font("Arial", 24, FontStyle.Bold);
cht.ChartAreas["Default"].AxisY.MajorGrid.LineDashStyle = ChartDashStyle.Dash;
cht.ChartAreas["Default"].AxisY.IsMarginVisible = true;
cht.Titles.Add("Default");
cht.Titles[0].Text = "Glycan: " + Gkey;
cht.Titles[0].Font = new Font("Arial",24,FontStyle.Bold);
cht.Legends.Add("Default");
cht.Legends["Default"].Docking = Docking.Bottom;
cht.Legends["Default"].Alignment = StringAlignment.Center;
cht.Legends["Default"].LegendStyle = LegendStyle.Row;
cht.Legends["Default"].Font = new Font("Arial", 24, FontStyle.Bold);
int ColorIdx = 0;
// int SymbolIdx = 0;
foreach (string Adduct in dictAdductPoints.Keys)
{
dictAdductPoints[Adduct].OrderBy(x=> x.Time); //Sort by time
Series series = cht.Series.Add(Adduct);
series.ChartArea = "Default";
series.ChartType = SeriesChartType.Spline;
series.MarkerStyle = MarkerStyle.Circle;
series.MarkerSize = 15;
series.BorderWidth = 2;
series.Color = LstColor[ColorIdx];
foreach (LCPointPair pp in dictAdductPoints[Adduct])
{
float TimeKey = Convert.ToSingle(pp.Time.ToString("0.00"));
if (series.Points.Where(x => x.XValue == TimeKey).Count()!=0)
{
series.Points.Where(x => x.XValue == TimeKey).ToList()[0].YValues[0]+=pp.Intensity;
}
else
{
series.Points.AddXY(TimeKey, pp.Intensity);
}
}
series.Points.OrderBy(x => x.XValue);
ColorIdx = (ColorIdx + 1) % LstColor.Count;
}
//Merge Intensity
Time.Sort();
List<LCPointPair> PPLMerge = new List<LCPointPair>();
foreach (float tim in Time)
{
PPLMerge.Add(new LCPointPair(Convert.ToSingle(tim.ToString("0.00")), MergeIntensity[tim]));
}
Series merge = cht.Series.Add("Merge");
merge.ChartArea = "Default";
merge.ChartType = SeriesChartType.Spline;
merge.BorderWidth = 2;
merge.MarkerStyle = MarkerStyle.Diamond;
merge.MarkerSize = 15;
merge.Color = Color.Black;
merge.BorderDashStyle = ChartDashStyle.Dot;
foreach (LCPointPair pp in PPLMerge)
{
merge.Points.AddXY(pp.Time, pp.Intensity);
}
merge.Points.OrderBy(x => x.XValue);
cht.SaveImage(dir + "\\" + Gkey + ".png", ChartImageFormat.Png);
}
#endregion
}
catch (Exception ex)
{
throw new Exception("GetLC Pic failed " + ProcessingGlycanKey + " Err Msg:" + ex.ToString());
}
}//);
}
public static void Processing(ref MultiGlycanESI argMultiGlycan)
{
try
{
List <string> identifiedGlycan = argMultiGlycan.IdentifiedGlycanCompounds.Select(x => x.GlycanKey).Distinct().ToList();
Dictionary <string, List <int> > dictGlycanKeySearchRange = new Dictionary <string, List <int> >();
int LastScan = argMultiGlycan.RawReader.NumberOfScans;
foreach (string glycanKey in identifiedGlycan)
{
List <int> identifedScans =
argMultiGlycan.MatchedPeakInScan.Where(x => x.GlycanComposition.GlycanKey == glycanKey)
.Select(y => y.ScanNum)
.ToList();
identifedScans.Sort();
int frontEdge = identifedScans[0];
double FirstIdentifiedTime = argMultiGlycan.RawReader.ReadScan(frontEdge).Time;
while (frontEdge > 1)
{
frontEdge -= 1;
if (argMultiGlycan.RawReader.GetMsLevel(frontEdge) != 1)
{
continue;
}
MSScan s = argMultiGlycan.RawReader.ReadScan(frontEdge);
if (FirstIdentifiedTime - s.Time > 5)
{
break;
}
}
int backEdge = identifedScans[identifedScans.Count - 1];
double LastIdentifedTime = argMultiGlycan.RawReader.ReadScan(backEdge).Time;
while (backEdge < LastScan)
{
backEdge += 1;
if (argMultiGlycan.RawReader.GetMsLevel(backEdge) != 1)
{
continue;
}
MSScan s = argMultiGlycan.RawReader.ReadScan(backEdge);
if (s.Time - LastIdentifedTime > 5)
{
break;
}
}
dictGlycanKeySearchRange.Add(glycanKey, new List <int>()
{
frontEdge, backEdge
});
}
List <MSScan> msScans = new List <MSScan>();
string previousGlycanKey = "";
foreach (GlycanCompound g in argMultiGlycan.GlycanList.OrderBy(x => x.GlycanKey))
{
if (!identifiedGlycan.Contains(g.GlycanKey))
{
continue;
}
if (previousGlycanKey != g.GlycanKey)
{
msScans.Clear();
//Read Scans
int startScan = dictGlycanKeySearchRange[g.GlycanKey][0] >= 1 ? dictGlycanKeySearchRange[g.GlycanKey][0] : 1;
int endScan = dictGlycanKeySearchRange[g.GlycanKey][1] <= LastScan ? dictGlycanKeySearchRange[g.GlycanKey][1] : LastScan;
msScans.AddRange(argMultiGlycan.RawReader.ReadScanWMSLevel(startScan, endScan, 1));
previousGlycanKey = g.GlycanKey;
}
//FindPeaks
int charge = g.Charge;
List <List <MSScan> > scanSectionsContainPeaks = new List <List <MSScan> >();
for (int i = 0; i < msScans.Count; i++)
{
MSScan scan = msScans[i];
int closedIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
if (MassUtility.GetMassPPM(scan.MZs[closedIdx], g.MZ) <= argMultiGlycan.MassPPM)
{
List <int> peaks = FindPeakIdx(scan.MZs, closedIdx, charge, argMultiGlycan.IsotopePPM);
if (peaks.Count - peaks.IndexOf(closedIdx) < argMultiGlycan.MininumIsotopePeakCount)
{
continue;
}
//Found peaks
if (scanSectionsContainPeaks.Count > 0)
{
MSScan lastSectionLastScan = scanSectionsContainPeaks.Last().Last();
if (scan.Time - lastSectionLastScan.Time > 2.5)
{
scanSectionsContainPeaks.Add(new List <MSScan>()
{
scan
});
}
else
{
scanSectionsContainPeaks.Last().Add(scan);
}
}
else
{
scanSectionsContainPeaks.Add(new List <MSScan>()
{
scan
});
}
}
}
//If scans can form an elution profile add to identifed result;
foreach (List <MSScan> sectionScans in scanSectionsContainPeaks)
{
if (sectionScans.Count < 3)
{
continue;
}
else
{
//Add matched peak
foreach (MSScan s in sectionScans)
{
int PeakIdx = MassUtility.GetClosestMassIdx(s.MZs, (float)g.MZ);
MatchedGlycanPeak mPeak = new MatchedGlycanPeak(s.ScanNo, s.Time, s.MSPeaks[PeakIdx], g);
List <int> peaks = FindPeakIdx(s.MZs, PeakIdx, charge, argMultiGlycan.IsotopePPM);
int startIdx = peaks.IndexOf(PeakIdx);
List <MSPoint> lstIsotopes = new List <MSPoint>();
for (int i = startIdx; i < peaks.Count; i++)
{
lstIsotopes.Add(new MSPoint(s.MZs[peaks[i]], s.Intensities[peaks[i]]));
}
mPeak.MSPoints = lstIsotopes;
if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
{
argMultiGlycan.MatchedPeakInScan.Add(mPeak);
}
}
}
}
}
//foreach (GlycanCompound g in argMultiGlycan.IdentifiedGlycanCompounds)
//{
// processed = g;
// //Search Peak in front of the peak
// ThermoRawReader raw = (ThermoRawReader)argMultiGlycan.RawReader;
// List<int> identifedScans = argMultiGlycan.MatchedPeakInScan.Where(x => x.GlycanComposition == g).Select(y => y.ScanNum).ToList();
// for (int i = 0; i < identifedScans.Count; i++)
// {
// int identifiedScanNum = identifedScans[i];
// while (true)
// {
// identifiedScanNum -= 1;
// if (identifiedScanNum < 1 || raw.GetRetentionTime(identifedScans[i]) - raw.GetRetentionTime(identifiedScanNum) > argMultiGlycan.MaxLCFrontMin)
// {
// break;
// }
// if (raw.GetMsLevel((identifiedScanNum)) != 1)
// {
// continue;
// }
// MSScan scan = raw.ReadScan(identifiedScanNum);
// int PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], g.MZ) > argMultiGlycan.MassPPM)
// {
// continue;
// }
// //Find isotope cluster
// List<MSPoint> lstIsotopes = new List<MSPoint>();
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx],scan.Intensities[PeakIdx]));
// float targetMZ = (float)g.MZ;
// do
// {
// targetMZ += 1.0f/g.Charge;
// PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, targetMZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], targetMZ) <= argMultiGlycan.MassPPM)
// {
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx],scan.Intensities[PeakIdx]));
// }
// else
// {
// break;
// }
// } while (true);
// if (lstIsotopes.Count < argMultiGlycan.MininumIsotopePeakCount)
// {
// continue;
// }
// MatchedGlycanPeak mPeak = new MatchedGlycanPeak(scan.ScanNo, scan.Time, scan.MSPeaks[PeakIdx], g);
// mPeak.MSPoints = lstIsotopes;
// if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
// {
// argMultiGlycan.MatchedPeakInScan.Add(mPeak);
// }
// }
// identifiedScanNum = identifedScans[i];
// while (true)
// {
// identifiedScanNum += 1;
// if (identifiedScanNum > raw.NumberOfScans || raw.GetRetentionTime(identifiedScanNum) - raw.GetRetentionTime(identifedScans[i]) > argMultiGlycan.MaxLCBackMin)
// {
// break;
// }
// if (raw.GetMsLevel((identifiedScanNum)) != 1)
// {
// continue;
// }
// MSScan scan = raw.ReadScan(identifiedScanNum);
// int PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, (float)g.MZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], g.MZ) > argMultiGlycan.MassPPM)
// {
// continue;
// }
// //Find isotope cluster
// List<MSPoint> lstIsotopes = new List<MSPoint>();
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx], scan.Intensities[PeakIdx]));
// float targetMZ = (float)g.MZ;
// do
// {
// targetMZ += 1.0f / g.Charge;
// PeakIdx = MassUtility.GetClosestMassIdx(scan.MZs, targetMZ);
// if (MassUtility.GetMassPPM(scan.MZs[PeakIdx], targetMZ) <= argMultiGlycan.MassPPM)
// {
// lstIsotopes.Add(new MSPoint(scan.MZs[PeakIdx], scan.Intensities[PeakIdx]));
// }
// else
// {
// break;
// }
// } while (true);
// if (lstIsotopes.Count < argMultiGlycan.MininumIsotopePeakCount)
// {
// continue;
// }
// MatchedGlycanPeak mPeak = new MatchedGlycanPeak(scan.ScanNo, scan.Time, scan.MSPeaks[PeakIdx], g);
// mPeak.MSPoints = lstIsotopes;
// if (!argMultiGlycan.MatchedPeakInScan.Contains(mPeak))
// {
// argMultiGlycan.MatchedPeakInScan.Add(mPeak);
// }
// }
// }
//}
}
catch (Exception ex)
{
throw ex;
}
}
