private void btnMergeTest_Click(object sender, EventArgs e)
{
GenerateImages.GenQuantImg(@"E:\!MultiGlycanbatch\1\1_Quant.csv", enumGlycanLabelingMethod.MultiplexPermethylated, @"E:\!MultiGlycanbatch\1");
//StreamReader sr = new StreamReader(@"D:\Dropbox\for_Yunli_Hu\b1_19_1_07142012-121002 1349_FullList.csv");
//string tmp = sr.ReadLine();
//List<ClusteredPeak> clu = new List<ClusteredPeak>();
//do
//{
// tmp = sr.ReadLine();
// string[] tmpArray = tmp.Split(',');
// ClusteredPeak tnpCluPeak = new ClusteredPeak(Convert.ToInt32(tmpArray[1]));
// tnpCluPeak.StartTime = Convert.ToDouble(tmpArray[0]);
// tnpCluPeak.EndTime = Convert.ToDouble(tmpArray[0]);
// tnpCluPeak.EndScan = Convert.ToInt32(tmpArray[1]);
// tnpCluPeak.Intensity = Convert.ToSingle(tmpArray[2]);
// tnpCluPeak.GlycanComposition = new COL.GlycoLib.GlycanCompound(
// Convert.ToInt32(tmpArray[8]),
// Convert.ToInt32(tmpArray[9]),
// Convert.ToInt32(tmpArray[10]),
// Convert.ToInt32(tmpArray[11]));
// tnpCluPeak.Charge = Convert.ToInt32(Math.Ceiling( Convert.ToSingle(tmpArray[12]) / Convert.ToSingle(tmpArray[3])));
// clu.Add(tnpCluPeak);
//} while (!sr.EndOfStream);
//sr.Close();
////MultiNGlycanESI.MergeCluster(clu, 8.0);
}
private void bgWorkerGenerateImages_DoWork(object sender, DoWorkEventArgs e)
{
foreach (string resultFile in ResultFiles)
{
currentFile = resultFile;
if (resultFile.Contains("_FullList.csv"))
{
currentFile = resultFile.Remove(resultFile.IndexOf("_FullList.csv")) + ".csv";
}
bgWorkerGenerateImages.ReportProgress(0);
string FullListFile = currentFile.Replace(".csv", "_FullList.csv");
string QuantFile = currentFile.Replace(".csv", "_Quant.csv");
//Get individual image
if (isIndividualImg && File.Exists(FullListFile))
{
GenerateImages.GenGlycanLcImg(
FullListFile,
ExportFilePath + "\\" + Path.GetFileNameWithoutExtension(currentFile),
out lstImgErrors);
}
//Get Quant Image
if (isQuantImg && File.Exists(QuantFile))
{
GenerateImages.GenQuantImg(
QuantFile,
LabelingMethod,
ExportFilePath + "\\" + Path.GetFileNameWithoutExtension(currentFile));
}
CompletedCount = CompletedCount + 1;
bgWorkerGenerateImages.ReportProgress(0);
}
}
private void bgWorker_Process_RunWorkerCompleted(object sender, RunWorkerCompletedEventArgs e)
{
try
{
// _MultiNGlycan.ExportParametersToExcel();
if (DoLog)
{
Logger.WriteLog("Start merge peaks");
}
lblStatus.Text = "Mergeing Peaks";
if (_MultiNGlycan.LabelingMethod == enumGlycanLabelingMethod.MultiplexPermethylated)
{
SecondPassedForMultiplexPermethylated.Processing(ref _MultiNGlycan);
}
//if (_MultiNGlycan.TwoPassedID)
//{
// // _MultiNGlycan.Merge2PassedCluster();
// _MultiNGlycan.MergeSingleScanResultToPeak();
//}
//else
//{
// _MultiNGlycan.MergeCluster();
_MultiNGlycan.MergeSingleScanResultToPeak();
_MultiNGlycan.SolveDuplicateAssignment();
_MultiNGlycan.MergeSingleScanResultToPeak();
//}
if (DoLog)
{
Logger.WriteLog("End merge peaks");
}
if (_MultiNGlycan.GlycanLCorderExist)
{
_MultiNGlycan.ApplyLCordrer();
}
if (!Directory.Exists(_MultiNGlycan.ExportFilePath + "\\Pic") && (_MultiNGlycan.IndividualImgs || _MultiNGlycan.QuantificationImgs))
{
Directory.CreateDirectory(_MultiNGlycan.ExportFilePath + "\\Pic");
}
if (_MultiNGlycan.LabelingMethod == GlycoLib.enumGlycanLabelingMethod.MultiplexPermethylated)
{
_MultiNGlycan.EstimatePurity();
foreach (GlycoLib.enumLabelingTag tag in _MultiNGlycan.LabelingRatio.Keys)
{
if (tag == enumLabelingTag.MP_CH3 || !_MultiNGlycan.HasEstimatePurity((tag)))
{
continue;
}
_MultiNGlycan.GetPurityEstimateImage(tag, _MultiNGlycan.ExportFilePath + "\\Pic\\EstimatePurity_" + tag.ToString() + ".png");
}
//Correct Intensity;
//_MultiNGlycan.CorrectIntensityByIsotope();
}
if (DoLog)
{
;
Logger.WriteLog("Start export");
}
lblStatus.Text = "Exporting";
_MultiNGlycan.ExportToCSV();
//Get individual image
if (_MultiNGlycan.IndividualImgs &&
File.Exists(_MultiNGlycan.ExportFilePath + "\\" + Path.GetFileName(_MultiNGlycan.ExportFilePath) +
"_FullList.csv"))
{
//GenerateImages.GenGlycanLcImg(
// _MultiNGlycan.ExportFilePath + "\\" + Path.GetFileName(_MultiNGlycan.ExportFilePath) +"_FullList.csv",
// _MultiNGlycan.ExportFilePath);
GenerateImages.GenGlycanLcImg(_MultiNGlycan);
}
//Get Quant Image
if (_MultiNGlycan.LabelingMethod != enumGlycanLabelingMethod.None && _MultiNGlycan.QuantificationImgs &&
File.Exists(_MultiNGlycan.ExportFilePath + "\\" + Path.GetFileName(_MultiNGlycan.ExportFilePath) +
"_Quant.csv"))
{
GenerateImages.GenQuantImg(
_MultiNGlycan.ExportFilePath + "\\" + Path.GetFileName(_MultiNGlycan.ExportFilePath) + "_Quant.csv",
_MultiNGlycan.LabelingMethod,
_MultiNGlycan.ExportFilePath);
}
//_MultiNGlycan.ExportToExcel();
if (DoLog)
{
Logger.WriteLog("End export");
}
TimeSpan TDiff = DateTime.Now.Subtract(Start);
lblStatus.Text = "Finish in " + TDiff.TotalMinutes.ToString("0.00") + " mins";
lblNumberOfMerge.Text = _MultiNGlycan.MergedResultList.Count.ToString();
progressBar1.Value = 100;
lblPercentage.Text = "100%";
FlashWindow.Flash(this);
this.Text = "Done";
if (DoLog)
{
Logger.WriteLog("End process each scan");
}
}
catch (Exception ex)
{
throw ex;
}
}
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;
}
}