public ChromDataCollectorSet(ChromSource chromSource, TimeSharing timeSharing,
ChromatogramLoadingStatus.TransitionData allChromData, BlockWriter blockWriter)
{
ChromSource = chromSource;
TypeOfScans = timeSharing;
PrecursorCollectorMap = new List<Tuple<PrecursorTextId, ChromDataCollector>>();
if (timeSharing == TimeSharing.shared)
{
SharedTimesCollector = new SortedBlockedList<float>();
ScanIdsCollector = new BlockedList<int>();
}
_allChromData = allChromData;
_blockWriter = blockWriter;
}
public SpectraChromDataProvider(MsDataFileImpl dataFile,
ChromFileInfo fileInfo,
SrmDocument document,
IRetentionTimePredictor retentionTimePredictor,
string cachePath, // We'll write tempfiles in this directory
ProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_document = document;
_filePath = dataFile.FilePath;
_cachePath = cachePath;
// If no SRM spectra, then full-scan filtering must be enabled
_isSrm = dataFile.HasSrmSpectra;
if (!_isSrm)
{
if (!document.Settings.TransitionSettings.FullScan.IsEnabled)
throw new NoFullScanFilteringException(dataFile.FilePath);
// Only use the retention time predictor on non-SRM data, and only when
// there are enough transitions to cause performance issues with extracting
// full-gradient in a single pass, and then trimming.
if (_document.Settings.TransitionSettings.FullScan.RetentionTimeFilterType == RetentionTimeFilterType.scheduling_windows &&
_document.MoleculeTransitionCount > MAX_FULL_GRADIENT_TRANSITIONS)
{
_retentionTimePredictor = retentionTimePredictor;
}
}
// Only mzXML from mzWiff requires the introduction of zero values
// during interpolation.
_isProcessedScans = dataFile.IsMzWiffXml;
UpdatePercentComplete();
// Create the filter responsible for chromatogram extraction
bool firstPass = (_retentionTimePredictor != null);
_filter = new SpectrumFilter(_document, FileInfo.FilePath, new DataFileInstrumentInfo(dataFile),
_retentionTimePredictor, firstPass);
if (!_isSrm && (_filter.EnabledMs || _filter.EnabledMsMs))
{
// Full-scan filtering should always match a single precursor
// m/z value to a single precursor node in the document tree,
// because that is the way the filters are constructed in the
// first place.
_isSingleMzMatch = true;
}
// Get data object used to graph all of the chromatograms.
if (_loader.HasUI)
_allChromData = LoadingStatus.Transitions;
try
{
InitSpectrumReader(dataFile);
InitChromatogramExtraction();
}
catch(Exception)
{
// If exception thrown before construction is complete than Dispose will not be called.
if (_spectra == null)
dataFile.Dispose();
else
_spectra.Dispose();
throw;
}
}
public Spectra(SrmDocument document, SpectrumFilter filter, ChromatogramLoadingStatus.TransitionData allChromData, MsDataFileImpl dataFile)
{
_document = document;
_filter = filter;
_dataFile = dataFile;
_allChromData = allChromData;
_lookaheadContext = new LookaheadContext(_filter, _dataFile);
_countSpectra = dataFile.SpectrumCount;
HasSrmSpectra = dataFile.HasSrmSpectra;
// If possible, find the maximum retention time in order to scale the chromatogram graph.
if (_allChromData != null && (_filter.EnabledMsMs || _filter.EnabledMs))
{
var retentionTime = _dataFile.GetStartTime(_countSpectra - 1);
if (retentionTime.HasValue)
{
_allChromData.MaxRetentionTime = (float)retentionTime.Value;
_allChromData.MaxRetentionTimeKnown = true;
_allChromData.Progressive = true;
}
}
}
