public static void QcDIA(IRawDataPlus rawFile, WorkflowParameters parameters)
{
rawFile.SelectInstrument(Device.MS, 1);
rawFile.CheckIfBoxcar();
ScanIndex Index = Extract.ScanIndices(rawFile);
MethodDataContainer methodData = Extract.MethodData(rawFile, Index);
CentroidStreamCollection centroidStreams = new CentroidStreamCollection();
SegmentScanCollection segmentScans = new SegmentScanCollection();
(centroidStreams, segmentScans) = Extract.MsData(rawFile: rawFile, index: Index);
TrailerExtraCollection trailerExtras = Extract.TrailerExtras(rawFile, Index);
RetentionTimeCollection retentionTimes = Extract.RetentionTimes(rawFile, Index);
ScanMetaDataCollectionDIA metaData = MetaDataProcessingDIA.AggregateMetaDataDIA(centroidStreams, segmentScans, methodData,
trailerExtras, retentionTimes, Index);
RawMetricsDataDIA metrics = MetaDataProcessingDIA.GetMetricsDataDIA(metaData, methodData, rawFile.FileName, retentionTimes, Index);
QcDataContainer qcData = new QcDataContainer();
qcData.DIA = metrics;
QcDataCollection qcDataCollection = QC.QcWorkflow.LoadOrCreateQcCollection(parameters);
QC.QcWorkflow.UpdateQcCollection(qcDataCollection, qcData, methodData, rawFile.FileName);
}
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);
//}
}