public RawFileViz(string rawFile)
{
this.InitializeComponent();
#region initialize fields and containers
nextScanButton.Text = Char.ConvertFromUtf32(0x2192);
previousScanButton.Text = Char.ConvertFromUtf32(0x2190);
rawFileThreadManager = RawFileReaderFactory.CreateThreadManager(rawFile);
RawData = rawFileThreadManager.CreateThreadAccessor();
RawData.SelectMsData();
TotalNumScans = RawData.RunHeaderEx.SpectraCount;
FirstScan = RawData.RunHeader.FirstSpectrum;
LastScan = RawData.RunHeader.LastSpectrum;
currentScan = FirstScan;
TotalTime = RawData.RunHeader.EndTime;
this.Text = "ParseDataViz - " + RawData.FileName;
totalScansLabel.Text = String.Format("/ {0}", TotalNumScans);
splitContainer1.SplitterDistance = this.Size.Width - 300;
UpdateChromatogramData();
InitializeChromatogramPlot();
ChroMsLevelComboBox.SelectedIndex = 0;
initializeMassSpecData();
initializeMassSpectrum();
scanNumber.Text = FirstScan.ToString();
y = 0;
x = 1;
#endregion
//#region initial chromatogram
this.plotViewChromatogram.Model = chromatogram;
UpdateChromatogramPlot();
}
public List <ScanMetadata> ReadScanMetadata()
{
var data = new List <ScanMetadata>();
using (var rawReader = rawReaderThreader.CreateThreadAccessor())
{
if (!rawReader.SelectMsData())
{
// Dataset has no MS data. Return.
return(data);
}
var header = rawReader.RunHeaderEx;
var minScan = header.FirstSpectrum;
var maxScan = header.LastSpectrum;
var numScans = header.SpectraCount;
data.Capacity = numScans + 5;
for (var i = minScan; i <= maxScan; i++)
{
var scan = new ScanMetadata {
ScanNumber = i
};
//scan.RetentionTime = rawReader.RetentionTimeFromScanNumber(i);
var scanStats = rawReader.GetScanStatsForScanNumber(i);
scan.RetentionTime = scanStats.StartTime;
scan.TIC = scanStats.TIC;
scan.BPI = scanStats.BasePeakIntensity;
//scan.MSLevel = scanStats.ScanEventNumber;
var scanEvents = rawReader.GetScanEventForScanNumber(i);
scan.MSLevel = (int)scanEvents.MSOrder;
var extra = rawReader.GetTrailerExtraInformation(i);
var converted = Enumerable.Range(0, extra.Length).Select(x => new KeyValuePair <string, string>(extra.Labels[x], extra.Values[x]))
.ToList();
scan.IonInjectionTime = double.Parse(converted.FirstOrDefault(x => x.Key.StartsWith("Ion Injection Time", StringComparison.OrdinalIgnoreCase)).Value ?? "0");
data.Add(scan);
}
}
return(data);
}
public static void ParseDIA(IRawFileThreadManager rawFile, WorkflowParameters parameters)
{
var staticRawFile = rawFile.CreateThreadAccessor();
staticRawFile.SelectInstrument(Device.MS, 1);
staticRawFile.CheckIfBoxcar();
ScanIndex Index = Extract.ScanIndices(rawFile.CreateThreadAccessor());
TrailerExtraCollection trailerExtras = Extract.TrailerExtras(rawFile.CreateThreadAccessor(), Index);
MethodDataContainer methodData = Extract.MethodData(rawFile.CreateThreadAccessor(), Index);
PrecursorScanCollection precursorScans = Extract.PrecursorScansByMasterScanMs2Only(rawFile.CreateThreadAccessor(), trailerExtras, Index);
(CentroidStreamCollection centroidStreams, SegmentScanCollection segmentScans) =
Extract.MsData(rawFile: rawFile.CreateThreadAccessor(), index: Index);
RetentionTimeCollection retentionTimes = Extract.RetentionTimes(rawFile.CreateThreadAccessor(), Index);
ScanMetaDataCollectionDIA metaData = MetaDataProcessingDIA.AggregateMetaDataDIA(centroidStreams, segmentScans, methodData,
trailerExtras, retentionTimes, Index);
RawMetricsDataDIA metrics = null;
if (parameters.ParseParams.Metrics)
{
metrics = MetaDataProcessingDIA.GetMetricsDataDIA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index);
MetricsWriter.WriteMatrix(metrics, staticRawFile.FileName, parameters.ParseParams.OutputDirectory);
}
if (parameters.ParseParams.Parse)
{
string matrixFileName = ReadWrite.GetPathToFile(parameters.ParseParams.OutputDirectory, staticRawFile.FileName, "._parse.txt");
//MatrixWriter.ParseQuantDIA()
//ParseWriter writerDIA = new ParseWriter(matrixFileName, centroidStreams, segmentScans, metaData,
// retentionTimes, trailerExtras, precursorScans, Index);
//writerDIA.WriteMatrixDIA();
}
// I'm not sure what goes into a DIA mgf file, so we aren't making one yet
//if (parameters.ParseParams.WriteMgf)
//{
// ParseWriter writerMGF = new ParseWriter(centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
// writerMGF.WriteMGF(staticRawFile.FileName);
//}
}
DependentsAndPrecursorScansByScanDependentsParallel(IRawFileThreadManager rawFileManager, ScanIndex index)
{
//rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Extracting scan dependents/precursor scans");
ConcurrentDictionary <int, PrecursorScanData> precursorScans = new ConcurrentDictionary <int, PrecursorScanData>();
ConcurrentDictionary <int, IScanDependents> dependents = new ConcurrentDictionary <int, IScanDependents>();
//Dictionary<int, PrecursorScanData> precursorScans = new Dictionary<int, PrecursorScanData>();
//Dictionary<int, IScanDependents> dependents = new Dictionary<int, IScanDependents>();
//ConcurrentBag<(int scan, PrecursorScanData data)> precursorBag = new ConcurrentBag<(int scan, PrecursorScanData data)>();
//ConcurrentBag<(int scan, IScanDependents data)> dependentsBag = new ConcurrentBag<(int scan, IScanDependents data)>();
var updateProgressLock = new object();
var addLockTarget = new object();
IEnumerable <int> scans = index.ScanEnumerators[MSOrderType.Ms];
ProgressIndicator progress = new ProgressIndicator(scans.Count(), "Indexing linked scan events");
var batches = scans.Chunk(Constants.MultiThreading.ChunkSize(scans.Count()));
Parallel.ForEach(batches, Constants.MultiThreading.Options(), batch =>
{
int ms2Scan = -1;
int ms3Scan = -1;
IScanDependents scanDependents;
var rawFile = rawFileManager.CreateThreadAccessor();
rawFile.SelectInstrument(Device.MS, 1);
foreach (int scan in batch)
{
scanDependents = rawFile.GetScanDependents(scan, 2);
dependents.AddOrUpdate(scan, scanDependents, (a, b) => b);
// check if the ms1 scan has dependent scans
if (scanDependents == null)
{
return;
}
for (int i = 0; i < scanDependents.ScanDependentDetailArray.Length; i++)
{
if (index.AnalysisOrder == MSOrderType.Ms2) // it is ms2
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
//precursorScans.AddOrUpdate(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan), (a, b) => b);
precursorScans.TryAdd(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
}
else // it is ms3
{
ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
var ms2Dependents = rawFile.GetScanDependents(ms2Scan, 2).ScanDependentDetailArray;
if (ms2Dependents.Length != 0) // make sure there is ms3 data
{
ms3Scan = ms2Dependents[0].ScanIndex;
precursorScans.AddOrUpdate(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan), (a, b) => b);
precursorScans.AddOrUpdate(ms3Scan, new PrecursorScanData(ms3scan: ms3Scan, ms2Scan: ms2Scan, masterScan: scan), (a, b) => b);
}
else
{
// there is no ms3 scan, so we only add the ms2 scan
precursorScans.AddOrUpdate(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan), (a, b) => b);
}
}
}
lock (updateProgressLock)
{
progress.Update();
}
}
});
progress.Done();
var outScans = new PrecursorScanCollection();
var outDependents = new ScanDependentsCollections();
foreach (var item in precursorScans)
{
outScans.Add(item.Key, item.Value);
}
foreach (var item in dependents)
{
outDependents.Add(item.Key, item.Value);
}
// check for missing precursor information
/*
* foreach (int scan in index.ScanEnumerators[MSOrderType.Ms2])
* {
* if (outScans.Keys.Contains(scan))
* {
* outScans.HasPrecursorData.Add(scan, true);
* }
* else
* {
* outScans.HasPrecursorData.Add(scan, false);
* }
* }*/
return(outScans, outDependents);
}
public static (ScanIndex, PrecursorScanCollection, ScanDependentsCollections) ScanIndicesPrecursorsDependents(IRawFileThreadManager rawFileAccessor)
{
Log.Information("Extracting scan indices");
ConcurrentDictionary <int, ScanData> allScans;
allScans = new ConcurrentDictionary <int, ScanData>();
Dictionary <int, ScanData> orphanScans = new Dictionary <int, ScanData>();
MSOrderType AnalysisOrder;
ConcurrentBag <int> ms1 = new ConcurrentBag <int>();
ConcurrentBag <int> ms2 = new ConcurrentBag <int>();
ConcurrentBag <int> ms3 = new ConcurrentBag <int>();
ConcurrentBag <int> msAny = new ConcurrentBag <int>();
ConcurrentDictionary <int, PrecursorScanData> precursorScans = new ConcurrentDictionary <int, PrecursorScanData>();
ConcurrentDictionary <int, IScanDependents> dependents = new ConcurrentDictionary <int, IScanDependents>();
var staticRawFile = rawFileAccessor.CreateThreadAccessor();
staticRawFile.SelectMsData();
// populate the scan indices
IEnumerable <int> scans = staticRawFile.GetFilteredScanEnumerator(staticRawFile.GetFilterFromString("")); // get all scans
// get ms order of experiment
Console.Write("Determing MS analysis order... ");
AnalysisOrder = (from x in scans select staticRawFile.GetScanEventForScanNumber(x).MSOrder).Max();
Console.WriteLine("Done!");
object lockTarget = new object();
ProgressIndicator P = new ProgressIndicator(scans.Count(), "Extracting scan indices");
int chunkSize = Constants.MultiThreading.ChunkSize(scans.Count());
var batches = scans.Chunk(chunkSize);
Parallel.ForEach(batches, batch =>
{
ScanData ms1ScanData;
ScanData ms2ScanData;
ScanData ms3ScanData;
foreach (int scan in batch)
{
//var rawFile = rawFileAccessor.CreateThreadAccessor();
using (var rawFile = rawFileAccessor.CreateThreadAccessor())
{
rawFile.SelectMsData();
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(scan);
ms1ScanData = new ScanData();
ms2ScanData = new ScanData();
ms3ScanData = new ScanData();
ms1ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms1ScanData.MSOrder = scanEvent.MSOrder;
if (ms1ScanData.MSOrder == MSOrderType.Ms)
{
ms1.Add(scan);
msAny.Add(scan);
var scanDependents = rawFile.GetScanDependents(scan, 4);
dependents.TryAdd(scan, scanDependents);
// check if the ms1 scan has dependent scans
if (scanDependents == null)
{
// there are no scan dependents
ms1ScanData.HasDependents = false;
allScans.TryAdd(scan, ms1ScanData);
return;
}
else
{
ms1ScanData.HasDependents = true;
allScans.TryAdd(scan, ms1ScanData);
}
for (int i = 0; i < scanDependents.ScanDependentDetailArray.Length; i++)
{
int ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
ms2.Add(ms2Scan);
msAny.Add(ms2Scan);
if (AnalysisOrder == MSOrderType.Ms2) // it is ms2
{
ms2ScanData = new ScanData();
scanEvent = rawFile.GetScanEventForScanNumber(ms2Scan);
ms2ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms2ScanData.MSOrder = scanEvent.MSOrder;
ms2ScanData.HasDependents = false;
ms2ScanData.HasPrecursors = true;
allScans.TryAdd(ms2Scan, ms2ScanData);
precursorScans.TryAdd(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
}
else // it is ms3
{
var ms2Dependents = rawFile.GetScanDependents(ms2Scan, 4).ScanDependentDetailArray;
ms2ScanData = new ScanData();
scanEvent = rawFile.GetScanEventForScanNumber(ms2Scan);
ms2ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms2ScanData.MSOrder = scanEvent.MSOrder;
ms2ScanData.HasPrecursors = true;
if (ms2Dependents.Length != 0) // make sure there is ms3 data
{
int ms3Scan = ms2Dependents[0].ScanIndex;
ms3.Add(ms3Scan);
msAny.Add(ms3Scan);
scanEvent = rawFile.GetScanEventForScanNumber(ms3Scan);
precursorScans.TryAdd(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
precursorScans.TryAdd(ms3Scan, new PrecursorScanData(ms3scan: ms3Scan, ms2Scan: ms2Scan, masterScan: scan));
ms2ScanData.HasDependents = true;
ms3ScanData = new ScanData();
ms3ScanData.HasPrecursors = true;
ms3ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms3ScanData.MSOrder = scanEvent.MSOrder;
allScans.TryAdd(ms3Scan, ms3ScanData);
}
else
{
// there is no ms3 scan, so we only add the ms2 scan
precursorScans.TryAdd(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
ms2ScanData.HasDependents = false;
}
allScans.TryAdd(ms2Scan, ms2ScanData);
}
}
}
lock (lockTarget)
{
P.Update();
}
}
}
});
P.Done();
HashSet <int> allKeys = new HashSet <int>(allScans.Keys);
P = new ProgressIndicator(scans.Count(), "Checking for orphaned scans");
foreach (int scan in scans)
{
if (allKeys.Contains(scan))
{
continue;
}
else
{
ScanData scanData = new ScanData();
var scanEvent = staticRawFile.GetScanEventForScanNumber(scan);
scanData.MassAnalyzer = scanEvent.MassAnalyzer;
scanData.MSOrder = scanEvent.MSOrder;
orphanScans.Add(scan, scanData);
}
P.Update();
}
P.Done();
Console.WriteLine();
Console.WriteLine("================ Scan indexing report ================");
Console.WriteLine($"Total scans in file: {staticRawFile.RunHeaderEx.SpectraCount}");
Console.WriteLine($"Scans linked: {allScans.Count()}");
Console.WriteLine();
Console.WriteLine("Orphan scans:");
if (orphanScans.Count() > 0)
{
foreach (var scan in orphanScans)
{
Console.WriteLine($"\tScan: {scan.Key}, MSOrder: {scan.Value.MSOrder}");
}
Console.WriteLine("\nThe above scans will not be present in the output data. You should");
Console.WriteLine("manually check them to ensure they are not critical to you analysis.");
}
else
{
Console.WriteLine("None!");
}
Console.WriteLine();
if (staticRawFile.RunHeaderEx.SpectraCount == allScans.Count() + orphanScans.Count())
{
Console.WriteLine("All scans accounted for!");
}
else
{
Console.WriteLine($"Number of scans unaccounted for: {staticRawFile.RunHeaderEx.SpectraCount - (allScans.Count() + orphanScans.Count())}");
Console.WriteLine("If this number is alarming, please contact the RawTools authors\n" +
"by posting an issue at:\n" +
"https://github.com/kevinkovalchik/RawTools/issues");
}
Console.WriteLine("======================================================");
Console.WriteLine();
// we need to order the scan enumerators before sending them out
var orderedMs1 = ms1.ToList();
var orderedMs2 = ms2.ToList();
var orderedMs3 = ms3.ToList();
var orderedMsAny = msAny.ToList();
orderedMs1.Sort();
orderedMs2.Sort();
orderedMs3.Sort();
orderedMsAny.Sort();
ScanIndex scanIndex = new ScanIndex();
scanIndex.allScans = allScans.ConvertToDictionary();
scanIndex.AnalysisOrder = AnalysisOrder;
scanIndex.ScanEnumerators.Add(MSOrderType.Any, orderedMsAny.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms, orderedMs1.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms2, orderedMs2.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms3, orderedMs3.ToArray());
scanIndex.TotalScans = staticRawFile.RunHeaderEx.SpectraCount;
return(scanIndex, new PrecursorScanCollection(precursorScans), new ScanDependentsCollections(dependents));
}
public static void UniversalDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters, QcDataCollection qcDataCollection)
{
MethodDataContainer methodData;
CentroidStreamCollection centroidStreams;
SegmentScanCollection segmentScans;
TrailerExtraCollection trailerExtras;
PrecursorMassCollection precursorMasses;
RetentionTimeCollection retentionTimes;
ScanEventReactionCollection reactions;
ScanMetaDataCollectionDDA metaData = null;
PrecursorPeakCollection peakData = null;
int nScans;
var staticRawFile = rawFileThreadManager.CreateThreadAccessor();
staticRawFile.SelectInstrument(Device.MS, 1);
var err = staticRawFile.FileError;
if (err.HasError)
{
Console.WriteLine("ERROR: {0} reports error code: {1}. The associated message is: {2}",
Path.GetFileName(staticRawFile.FileName), err.ErrorCode, err.ErrorMessage);
Console.WriteLine("Skipping this file");
Log.Error("{FILE} reports error code: {ERRORCODE}. The associated message is: {ERRORMESSAGE}",
Path.GetFileName(staticRawFile.FileName), err.ErrorCode, err.ErrorMessage);
return;
}
//staticRawFile.CheckIfBoxcar();
(ScanIndex Index, PrecursorScanCollection precursorScans, ScanDependentsCollections scanDependents) =
Extract.ScanIndicesPrecursorsDependents(rawFileThreadManager, MaxProcesses: parameters.MaxProcesses);
nScans = Index.ScanEnumerators[MSOrderType.Ms2].Length;
using (var rawFile = rawFileThreadManager.CreateThreadAccessor())
{
reactions = Extract.ScanEvents(rawFile, Index);
methodData = Extract.MethodData(rawFile, Index);
(centroidStreams, segmentScans) = Extract.MsData(rawFile: rawFile, index: Index);
trailerExtras = Extract.TrailerExtras(rawFile, Index);
precursorMasses = Extract.PrecursorMasses(rawFile, precursorScans, trailerExtras, Index);
retentionTimes = Extract.RetentionTimes(rawFile, Index);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant | parameters.ParseParams.Metrics | parameters.RefineMassCharge | parameters.QcParams.QcDirectory != null)
{
peakData = AnalyzePeaks.AnalyzeAllPeaks(centroidStreams, retentionTimes, precursorMasses, precursorScans, Index, parameters.MaxProcesses);
if (parameters.RefineMassCharge)
{
MonoIsoPredictor.RefineMonoIsoMassChargeValues(parameters, centroidStreams, precursorMasses, trailerExtras, peakData, precursorScans);
}
metaData = MetaDataProcessingDDA.AggregateMetaDataDDA(centroidStreams, segmentScans, methodData, precursorScans,
trailerExtras, precursorMasses, retentionTimes, scanDependents, reactions, Index, parameters.MaxProcesses);
}
QuantDataCollection quantData = null;
if (parameters.ParseParams.Quant)
{
quantData = Quantification.Quantify(centroidStreams, segmentScans, parameters, methodData, Index);
}
RawMetricsDataDDA rawMetrics = null;
if (parameters.ParseParams.Metrics | parameters.QcParams.QcDirectory != null)
{
rawMetrics = MetaDataProcessingDDA.GetMetricsDataDDA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index, peakData, precursorScans, quantData);
}
if (parameters.ParseParams.Metrics)
{
MetricsWriter.WriteMatrix(rawMetrics, null, staticRawFile.FileName, parameters.ParseParams.OutputDirectory);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant)
{
string matrixFileName = ReadWrite.GetPathToFile(parameters.ParseParams.OutputDirectory, staticRawFile.FileName, "_Matrix.txt");
/*
* ParseWriter writerDDA = new ParseWriter(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
* precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
* writerDDA.WriteMatrixDDA(methodData.AnalysisOrder);
*/
MatrixWriter.ParseQuantDDA(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
}
if (parameters.ParseParams.WriteMgf)
{
//ParseWriter writerMGF = new ParseWriter(centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
//writerMGF.WriteMGF(staticRawFile.FileName);
MgfWriter.WriteMGF(staticRawFile.FileName, centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
}
if (parameters.ParseParams.Chromatogram != null)
{
ChromatogramWriter.WriteChromatogram(centroidStreams, segmentScans, retentionTimes, methodData, Index, parameters, staticRawFile.FileName);
}
if (parameters.QcParams.QcDirectory != null)
{
qcDataCollection = QC.QcWorkflow.LoadOrCreateQcCollection(parameters);
SearchMetricsContainer searchMetrics = new SearchMetricsContainer(staticRawFile.FileName, staticRawFile.CreationDate, methodData);
// check if the raw file already exists in the QC data with a different name
if (QcWorkflow.CheckIfFilePresentInQcCollection(staticRawFile.FileName, qcDataCollection))
{
Log.Information("A file with the same creation date and time as {File} already exists in the QC data", staticRawFile.FileName);
Console.WriteLine("A file with the same creation date and time as {File} already exists in the QC data. Skipping to next file.",
staticRawFile.FileName);
}
else
{
if (parameters.QcParams.PerformSearch)
{
Search.WriteSearchMGF(parameters, centroidStreams, segmentScans, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData,
Index, staticRawFile.FileName, parameters.QcParams.FixedScans);
Search.RunSearch(parameters, methodData, staticRawFile.FileName);
searchMetrics = SearchQC.ParseSearchResults(searchMetrics, parameters, staticRawFile.FileName, nScans);
}
QcDataContainer qcData = new QcDataContainer();
qcData.DDA = rawMetrics;
qcData.SearchMetrics = searchMetrics;
QC.QcWorkflow.UpdateQcCollection(qcDataCollection, qcData, methodData, staticRawFile.FileName);
}
}
}
public static void ParseDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters)
{
MethodDataContainer methodData;
CentroidStreamCollection centroidStreams;
SegmentScanCollection segmentScans;
TrailerExtraCollection trailerExtras;
PrecursorMassCollection precursorMasses;
RetentionTimeCollection retentionTimes;
ScanEventReactionCollection reactions;
ScanMetaDataCollectionDDA metaData = null;
PrecursorPeakCollection peakData = null;
RawMetricsDataDDA rawMetrics = null;
QuantDataCollection quantData = null;
var staticRawFile = rawFileThreadManager.CreateThreadAccessor();
staticRawFile.SelectInstrument(Device.MS, 1);
//staticRawFile.CheckIfBoxcar();
(ScanIndex Index, PrecursorScanCollection precursorScans, ScanDependentsCollections scanDependents) =
Extract.ScanIndicesPrecursorsDependents(rawFileThreadManager);
using (var rawFile = rawFileThreadManager.CreateThreadAccessor())
{
reactions = Extract.ScanEvents(rawFile, Index);
methodData = Extract.MethodData(rawFile, Index);
(centroidStreams, segmentScans) = Extract.MsData(rawFile: rawFile, index: Index);
trailerExtras = Extract.TrailerExtras(rawFile, Index);
precursorMasses = Extract.PrecursorMasses(rawFile, precursorScans, trailerExtras, Index);
retentionTimes = Extract.RetentionTimes(rawFile, Index);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant | parameters.ParseParams.Metrics | parameters.RefineMassCharge)
{
peakData = AnalyzePeaks.AnalyzeAllPeaks(centroidStreams, retentionTimes, precursorMasses, precursorScans, Index);
if (parameters.RefineMassCharge)
{
MonoIsoPredictor.RefineMonoIsoMassChargeValues(centroidStreams, precursorMasses, trailerExtras, peakData, precursorScans);
}
metaData = MetaDataProcessingDDA.AggregateMetaDataDDA(centroidStreams, segmentScans, methodData, precursorScans,
trailerExtras, precursorMasses, retentionTimes, scanDependents, reactions, Index);
}
if (parameters.ParseParams.Quant)
{
quantData = Quantification.Quantify(centroidStreams, segmentScans, parameters, methodData, Index);
}
if (parameters.ParseParams.Metrics)
{
rawMetrics = MetaDataProcessingDDA.GetMetricsDataDDA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index, peakData, precursorScans, quantData);
MetricsWriter.WriteMatrix(rawMetrics, null, staticRawFile.FileName, parameters.ParseParams.OutputDirectory);
}
if (parameters.ParseParams.Parse | parameters.ParseParams.Quant)
{
string matrixFileName = ReadWrite.GetPathToFile(parameters.ParseParams.OutputDirectory, staticRawFile.FileName, "_Matrix.txt");
/*
* ParseWriter writerDDA = new ParseWriter(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
* precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
* writerDDA.WriteMatrixDDA(methodData.AnalysisOrder);
*/
MatrixWriter.ParseQuantDDA(matrixFileName, centroidStreams, segmentScans, metaData, retentionTimes,
precursorMasses, precursorScans, peakData, trailerExtras, Index, quantData);
}
if (parameters.ParseParams.WriteMgf)
{
//ParseWriter writerMGF = new ParseWriter(centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
//writerMGF.WriteMGF(staticRawFile.FileName);
MgfWriter.WriteMGF(staticRawFile.FileName, centroidStreams, segmentScans, parameters, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData, Index);
}
if (parameters.ParseParams.Chromatogram != null)
{
ChromatogramWriter.WriteChromatogram(centroidStreams, segmentScans, retentionTimes, methodData, Index, parameters, staticRawFile.FileName);
}
}
public static void QcDDA(IRawFileThreadManager rawFileThreadManager, WorkflowParameters parameters)
{
MethodDataContainer methodData;
CentroidStreamCollection centroidStreams;
SegmentScanCollection segmentScans;
TrailerExtraCollection trailerExtras;
PrecursorMassCollection precursorMasses;
RetentionTimeCollection retentionTimes;
ScanEventReactionCollection reactions;
var staticRawFile = rawFileThreadManager.CreateThreadAccessor();
staticRawFile.SelectInstrument(Device.MS, 1);
staticRawFile.CheckIfBoxcar();
(ScanIndex Index, PrecursorScanCollection precursorScans, ScanDependentsCollections scanDependents) =
Extract.ScanIndicesPrecursorsDependents(rawFileThreadManager);
using (var rawFile = rawFileThreadManager.CreateThreadAccessor())
{
methodData = Extract.MethodData(rawFile, Index);
reactions = Extract.ScanEvents(rawFile, Index);
(centroidStreams, segmentScans) = Extract.MsData(rawFile: rawFile, index: Index);
trailerExtras = Extract.TrailerExtras(rawFile, Index);
precursorMasses = Extract.PrecursorMasses(rawFile, precursorScans, trailerExtras, Index);
retentionTimes = Extract.RetentionTimes(rawFile, Index);
}
PrecursorPeakCollection peakData = AnalyzePeaks.AnalyzeAllPeaks(centroidStreams, retentionTimes, precursorMasses, precursorScans, Index);
if (parameters.RefineMassCharge)
{
MonoIsoPredictor.RefineMonoIsoMassChargeValues(centroidStreams, precursorMasses, trailerExtras, peakData, precursorScans);
}
ScanMetaDataCollectionDDA metaData = MetaDataProcessingDDA.AggregateMetaDataDDA(centroidStreams, segmentScans, methodData, precursorScans,
trailerExtras, precursorMasses, retentionTimes, scanDependents, reactions, Index);
RawMetricsDataDDA rawMetrics = MetaDataProcessingDDA.GetMetricsDataDDA(metaData, methodData, staticRawFile.FileName, retentionTimes, Index, peakData, precursorScans);
QcDataCollection qcDataCollection = QC.QcWorkflow.LoadOrCreateQcCollection(parameters);
SearchMetricsContainer searchMetrics = new SearchMetricsContainer(staticRawFile.FileName, staticRawFile.CreationDate, methodData);
if (parameters.QcParams.PerformSearch)
{
Search.WriteSearchMGF(parameters, centroidStreams, segmentScans, retentionTimes, precursorMasses, precursorScans, trailerExtras, methodData,
Index, staticRawFile.FileName, parameters.QcParams.FixedScans);
Search.RunSearch(parameters, methodData, staticRawFile.FileName);
searchMetrics = SearchQC.ParseSearchResults(searchMetrics, parameters, staticRawFile.FileName);
}
QcDataContainer qcData = new QcDataContainer();
qcData.DDA = rawMetrics;
qcData.SearchMetrics = searchMetrics;
QC.QcWorkflow.UpdateQcCollection(qcDataCollection, qcData, methodData, staticRawFile.FileName);
staticRawFile.Dispose();
}