protected ChromInfoData(MeasuredResults measuredResults, int replicateIndex, ChromFileInfo chromFileInfo, ChromInfo chromInfo)
{
MeasuredResults = measuredResults;
ReplicateIndex = replicateIndex;
ChromFileInfo = chromFileInfo;
ChromInfo = chromInfo;
}
public RemoteChromDataProvider(SrmDocument document, IRetentionTimePredictor retentionTimePredictor, ChromFileInfo chromFileInfo, ProgressStatus progressStatus, int startPercent,
int endPercent, ILoadMonitor loader)
: base(chromFileInfo, progressStatus, startPercent, endPercent, loader)
{
_document = document;
ChorusUrl chorusUrl = (ChorusUrl)chromFileInfo.FilePath;
_chorusAccount = chorusUrl.FindChorusAccount(Settings.Default.ChorusAccountList);
var chromatogramRequestProviders = new List<ChromatogramRequestProvider>();
foreach (bool firstPass in new[] {true, false})
{
if (null == retentionTimePredictor && !firstPass)
{
continue;
}
var chromatogramRequestProvider = new ChromatogramRequestProvider(document, chorusUrl,
retentionTimePredictor, firstPass);
if (0 == chromatogramRequestProvider.ChromKeys.Count)
{
continue;
}
chromatogramRequestProviders.Add(chromatogramRequestProvider);
}
_chromatogramRequestProviders = chromatogramRequestProviders.ToArray();
_chromTaskLists = new ChromTaskList[_chromatogramRequestProviders.Length];
}
public PeptideChromDataSets(PeptideDocNode nodePep,
SrmDocument document,
ChromFileInfo fileInfo,
IList <DetailedPeakFeatureCalculator> detailedPeakFeatureCalculators,
bool isProcessedScans)
{
NodePep = nodePep;
FileInfo = fileInfo;
DetailedPeakFeatureCalculators = detailedPeakFeatureCalculators;
_document = document;
_retentionTimes = new double[0];
_isProcessedScans = isProcessedScans;
}
protected ChromDataProvider(ChromFileInfo fileInfo,
IProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
{
FileInfo = fileInfo;
Status = status;
_startPercent = startPercent;
_endPercent = endPercent;
_loader = loader;
}
public ChromatogramDataProvider(MsDataFileImpl dataFile,
ChromFileInfo fileInfo,
ProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_dataFile = dataFile;
if (_dataFile.IsThermoFile)
{
_readMaxMinutes = 4;
}
int len = dataFile.ChromatogramCount;
_chromIndices = new int[len];
bool fixCEOptForShimadzu = dataFile.IsShimadzuFile;
int indexPrecursor = -1;
double lastPrecursor = 0;
for (int i = 0; i < len; i++)
{
int index;
string id = dataFile.GetChromatogramId(i, out index);
if (!ChromKey.IsKeyId(id))
continue;
var chromKey = ChromKey.FromId(id, fixCEOptForShimadzu);
if (chromKey.Precursor != lastPrecursor)
{
lastPrecursor = chromKey.Precursor;
indexPrecursor++;
}
var ki = new KeyValuePair<ChromKey, int>(chromKey, index);
_chromIndices[index] = indexPrecursor;
_chromIds.Add(ki);
}
// Shimadzu can't do the necessary product m/z stepping for itself.
// So, they provide the CE values in their IDs and we need to adjust
// product m/z values for them to support CE optimization.
if (fixCEOptForShimadzu)
FixCEOptForShimadzu();
if (_chromIds.Count == 0)
throw new NoSrmDataException(dataFile.FilePath);
SetPercentComplete(50);
}
public override void ReadXml(XmlReader reader)
{
// Read tag attributes
base.ReadXml(reader);
UseForRetentionTimeFilter = reader.GetBoolAttribute(ATTR.use_for_retention_time_prediction, false);
AnalyteConcentration = reader.GetNullableDoubleAttribute(ATTR.analyte_concentration);
SampleType = SampleType.FromName(reader.GetAttribute(ATTR.sample_type));
// Consume tag
reader.Read();
// Check if there is an optimization function element, and read
// if if there is.
IXmlElementHelper <OptimizableRegression> helper =
reader.FindHelper(OPTIMIZATION_HELPERS);
if (helper != null)
{
OptimizationFunction = helper.Deserialize(reader);
}
var chromFileInfos = new List <ChromFileInfo>();
var fileLoadIds = new List <string>();
while (reader.IsStartElement(EL.sample_file) ||
reader.IsStartElement(EL.replicate_file) ||
reader.IsStartElement(EL.chromatogram_file))
{
// Note that the file path is actually be a URI that encodes things like lockmass correction as well as filename
ChromFileInfo chromFileInfo = new ChromFileInfo(MsDataFileUri.Parse(reader.GetAttribute(ATTR.file_path)));
chromFileInfo = chromFileInfo.ChangeHasMidasSpectra(reader.GetBoolAttribute(ATTR.has_midas_spectra, false));
chromFileInfos.Add(chromFileInfo);
string id = reader.GetAttribute(ATTR.id) ?? GetOrdinalSaveId(fileLoadIds.Count);
fileLoadIds.Add(id);
reader.Read();
if (reader.IsStartElement(EL.instrument_info_list))
{
reader.Skip();
reader.Read();
}
}
Annotations = SrmDocument.ReadAnnotations(reader);
MSDataFileInfos = chromFileInfos;
_fileLoadIds = fileLoadIds.ToArray();
// Consume end tag
reader.ReadEndElement();
}
public bool Equals(ChromFileInfo other)
{
if (ReferenceEquals(null, other))
{
return(false);
}
if (ReferenceEquals(this, other))
{
return(true);
}
if (!Equals(other.Id, Id))
{
return(false);
}
if (!Equals(other.FilePath, FilePath))
{
return(false);
}
if (!other.FileWriteTime.Equals(FileWriteTime))
{
return(false);
}
if (!other.RunStartTime.Equals(RunStartTime))
{
return(false);
}
if (!other.MaxIntensity.Equals(MaxIntensity))
{
return(false);
}
if (!other.MaxRetentionTime.Equals(MaxRetentionTime))
{
return(false);
}
if (HasMidasSpectra != other.HasMidasSpectra)
{
return(false);
}
if (!ArrayUtil.EqualsDeep(other.InstrumentInfoList, InstrumentInfoList))
{
return(false);
}
if (!ArrayUtil.EqualsDeep(other.RetentionTimeAlignments, RetentionTimeAlignments))
{
return(false);
}
return(true);
}
public ChorusResponseChromDataProvider(SrmDocument document, ChromFileInfo chromFileInfo, ProgressStatus progressStatus, int startPercent,
int endPercent, ILoadMonitor loader)
: base(chromFileInfo, progressStatus, startPercent, endPercent, loader)
{
ChromatogramCache.RawData rawData;
MsDataFilePath msDataFilePath = (MsDataFilePath) chromFileInfo.FilePath;
IPooledStream stream = loader.StreamManager.CreatePooledStream(msDataFilePath.FilePath, false);
ChromatogramCache.LoadStructs(stream.Stream, out rawData);
var chromCacheFile = rawData.ChromCacheFiles[0];
rawData.ChromCacheFiles = new[]
{
new ChromCachedFile(chromFileInfo.FilePath, chromCacheFile.Flags, chromCacheFile.FileWriteTime,
chromCacheFile.RunStartTime, chromCacheFile.MaxRetentionTime, chromCacheFile.MaxIntensity,
chromCacheFile.InstrumentInfoList),
};
var cache = new ChromatogramCache("cachePath", rawData, stream); // Not L10N
_cachedChromatogramDataProvider = new CachedChromatogramDataProvider(cache, document,
chromFileInfo.FilePath, chromFileInfo, null, progressStatus, startPercent, endPercent, loader);
}
public ChorusResponseChromDataProvider(SrmDocument document, ChromFileInfo chromFileInfo, IProgressStatus progressStatus, int startPercent,
int endPercent, ILoadMonitor loader) : base(chromFileInfo, progressStatus, startPercent, endPercent, loader)
{
ChromatogramCache.RawData rawData;
MsDataFilePath msDataFilePath = (MsDataFilePath)chromFileInfo.FilePath;
IPooledStream stream = loader.StreamManager.CreatePooledStream(msDataFilePath.FilePath, false);
ChromatogramCache.LoadStructs(stream.Stream, out rawData);
var chromCacheFile = rawData.ChromCacheFiles[0];
rawData.ChromCacheFiles = new[]
{
new ChromCachedFile(chromFileInfo.FilePath, chromCacheFile.Flags, chromCacheFile.FileWriteTime,
chromCacheFile.RunStartTime, chromCacheFile.MaxRetentionTime, chromCacheFile.MaxIntensity,
chromCacheFile.InstrumentInfoList),
};
var cache = new ChromatogramCache("cachePath", rawData, stream); // Not L10N
_cachedChromatogramDataProvider = new CachedChromatogramDataProvider(cache, document,
chromFileInfo.FilePath, chromFileInfo, null, progressStatus, startPercent, endPercent, loader);
}
public CachedChromatogramDataProvider(ChromatogramCache cache,
SrmDocument document,
MsDataFileUri dataFilePath,
ChromFileInfo fileInfo,
bool? singleMatchMz,
ProgressStatus status,
int startPercent,
int endPercent,
ILoadMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_cache = cache;
_fileIndex = cache.CachedFiles.IndexOf(f => Equals(f.FilePath, dataFilePath));
_chromKeyIndices = cache.GetChromKeys(dataFilePath).OrderBy(v => v.LocationPoints).ToArray();
_cache.GetStatusDimensions(dataFilePath, out _maxRetentionTime, out _maxIntensity);
_singleMatchMz = singleMatchMz.HasValue
? singleMatchMz.Value
// Unfortunately, before the single matching status was
// written into the cache file, we can only guess about its
// status based on the overall document settings
: document.Settings.TransitionSettings.FullScan.IsEnabled;
}
public CachedChromatogramDataProvider(ChromatogramCache cache,
SrmDocument document,
MsDataFileUri dataFilePath,
ChromFileInfo fileInfo,
bool?singleMatchMz,
ProgressStatus status,
int startPercent,
int endPercent,
ILoadMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_cache = cache;
_fileIndex = cache.CachedFiles.IndexOf(f => Equals(f.FilePath, dataFilePath));
_chromKeyIndices = cache.GetChromKeys(dataFilePath).OrderBy(v => v.LocationPoints).ToArray();
_cache.GetStatusDimensions(dataFilePath, out _maxRetentionTime, out _maxIntensity);
_singleMatchMz = singleMatchMz.HasValue
? singleMatchMz.Value
// Unfortunately, before the single matching status was
// written into the cache file, we can only guess about its
// status based on the overall document settings
: document.Settings.TransitionSettings.FullScan.IsEnabled;
}
public CachedChromatogramDataProvider(ChromatogramCache cache,
SrmDocument document,
MsDataFileUri dataFilePath,
ChromFileInfo fileInfo,
bool?singleMatchMz,
IProgressStatus status,
int startPercent,
int endPercent,
ILoadMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
// Deal with older cache formats where we did not record chromatogram polarity
var assumeNegativeChargesInPreV11Caches = document.MoleculeTransitionGroups.All(p => p.PrecursorMz.IsNegative);
// Need a newly loaded copy to allow for concurrent loading for multiple cached files
_cache = ChromatogramCache.Load(cache.CachePath, new ProgressStatus(), loader, assumeNegativeChargesInPreV11Caches);
_fileIndex = cache.CachedFiles.IndexOf(f => Equals(f.FilePath, dataFilePath));
_chromKeyIndices = cache.GetChromKeys(dataFilePath).OrderBy(v => v.LocationPoints).ToArray();
foreach (var c in _chromKeyIndices.Where(i => i.Key.Precursor != 0))
{
if (c.Key.Precursor.IsNegative)
{
_sourceHasNegativePolarityData = true;
}
else
{
_sourceHasPositivePolarityData = true;
}
}
_cache.GetStatusDimensions(dataFilePath, out _maxRetentionTime, out _maxIntensity);
_singleMatchMz = singleMatchMz.HasValue
? singleMatchMz.Value
// Unfortunately, before the single matching status was
// written into the cache file, we can only guess about its
// status based on the overall document settings
: document.Settings.TransitionSettings.FullScan.IsEnabled;
}
private TransitionChromInfoData(MeasuredResults measuredResults, int replicateIndex, ChromFileInfo chromFileInfo, TransitionChromInfo transitionChromInfo)
: base(measuredResults, replicateIndex, chromFileInfo, transitionChromInfo)
{
}
private static double?GetApexRT(TransitionGroupDocNode nodeGroup, int resultIndex, ChromFileInfo chromFileInfo, bool ms1Trans)
{
double?apexRT = null;
float ms1Max = 0;
var trans = ms1Trans
? nodeGroup.GetMsTransitions(true)
: nodeGroup.GetMsMsTransitions(true);
foreach (var nodeTran in trans)
{
foreach (var peakInfo in nodeTran.GetChromInfos(resultIndex).Where(c =>
ReferenceEquals(c.FileId, chromFileInfo.FileId)))
{
if (peakInfo.Area > ms1Max)
{
apexRT = peakInfo.RetentionTime;
ms1Max = peakInfo.Area;
}
}
}
return(apexRT);
}
private bool IsCachedFile(SrmDocument doc, ChromFileInfo info)
{
return doc.Settings.MeasuredResults.IsCachedFile(info.FilePath);
}
public ChromatogramDataProvider(MsDataFileImpl dataFile,
ChromFileInfo fileInfo,
IProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_dataFile = dataFile;
if (_dataFile.IsThermoFile)
{
_readMaxMinutes = 4;
}
int len = dataFile.ChromatogramCount;
_chromIndices = new int[len];
bool fixCEOptForShimadzu = dataFile.IsShimadzuFile;
int indexPrecursor = -1;
var lastPrecursor = SignedMz.ZERO;
for (int i = 0; i < len; i++)
{
int index;
string id = dataFile.GetChromatogramId(i, out index);
if (!ChromKey.IsKeyId(id))
{
continue;
}
var chromKey = ChromKey.FromId(id, fixCEOptForShimadzu);
if (chromKey.Precursor != lastPrecursor)
{
lastPrecursor = chromKey.Precursor;
indexPrecursor++;
}
var ki = new ChromKeyProviderIdPair(chromKey, index);
_chromIndices[index] = indexPrecursor;
_chromIds.Add(ki);
}
// Shimadzu can't do the necessary product m/z stepping for itself.
// So, they provide the CE values in their IDs and we need to adjust
// product m/z values for them to support CE optimization.
if (fixCEOptForShimadzu)
{
FixCEOptForShimadzu();
}
if (_chromIds.Count == 0)
{
throw new NoSrmDataException(FileInfo.FilePath);
}
// CONSIDER(kaipot): Some way to support mzML files converted from MIDAS wiff files
_hasMidasSpectra = (dataFile.IsABFile) && SpectraChromDataProvider.HasSpectrumData(dataFile);
SetPercentComplete(50);
}
public void RemoveResults(DateTime? removeBefore)
{
if (removeBefore.HasValue)
_out.WriteLine(Resources.CommandLine_RemoveResults_Removing_results_before_ + removeBefore.Value.ToShortDateString() + "..."); // Not L10N
else
_out.WriteLine(Resources.CommandLine_RemoveResults_Removing_all_results);
var filteredChroms = new List<ChromatogramSet>();
if (_doc.Settings.MeasuredResults == null)
{
// No imported results in the document.
return;
}
foreach (var chromSet in _doc.Settings.MeasuredResults.Chromatograms)
{
var listFileInfosRemaining = new ChromFileInfo[0];
if (removeBefore.HasValue)
{
listFileInfosRemaining = chromSet.MSDataFileInfos.Where(fileInfo =>
fileInfo.RunStartTime == null || fileInfo.RunStartTime >= removeBefore).ToArray();
}
if (ArrayUtil.ReferencesEqual(listFileInfosRemaining, chromSet.MSDataFileInfos))
filteredChroms.Add(chromSet);
else
{
foreach (var fileInfo in chromSet.MSDataFileInfos.Except(listFileInfosRemaining))
_out.WriteLine(Resources.CommandLine_RemoveResults_Removed__0__, fileInfo.FilePath);
if (listFileInfosRemaining.Any())
filteredChroms.Add(chromSet.ChangeMSDataFileInfos(listFileInfosRemaining));
}
}
if (!ArrayUtil.ReferencesEqual(filteredChroms, _doc.Settings.MeasuredResults.Chromatograms))
{
MeasuredResults newMeasuredResults = filteredChroms.Any() ?
_doc.Settings.MeasuredResults.ChangeChromatograms(filteredChroms) : null;
_doc = _doc.ChangeMeasuredResults(newMeasuredResults);
}
}
private TransitionChromInfoData(MeasuredResults measuredResults, int replicateIndex, ChromFileInfo chromFileInfo, TransitionChromInfo transitionChromInfo)
: base(measuredResults, replicateIndex, chromFileInfo, transitionChromInfo)
{
}
public bool Equals(ChromFileInfo other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
if (!Equals(other.Id, Id))
return false;
if (!Equals(other.FilePath, FilePath))
return false;
if (!other.FileWriteTime.Equals(FileWriteTime))
return false;
if (!other.RunStartTime.Equals(RunStartTime))
return false;
if (!other.MaxIntensity.Equals(MaxIntensity))
return false;
if (!other.MaxRetentionTime.Equals(MaxRetentionTime))
return false;
if (!ArrayUtil.EqualsDeep(other.InstrumentInfoList, InstrumentInfoList))
return false;
if (!ArrayUtil.EqualsDeep(other.RetentionTimeAlignments, RetentionTimeAlignments))
return false;
return true;
}
public ChromatogramDataProvider(MsDataFileImpl dataFile,
ChromFileInfo fileInfo,
IProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_dataFile = dataFile;
_globalChromatogramExtractor = new GlobalChromatogramExtractor(dataFile);
if (_dataFile.IsThermoFile)
{
_readMaxMinutes = 4;
}
int len = dataFile.ChromatogramCount;
_chromIndices = new int[len];
bool fixCEOptForShimadzu = dataFile.IsShimadzuFile;
int indexPrecursor = -1;
var lastPrecursor = SignedMz.ZERO;
for (int i = 0; i < len; i++)
{
int index;
string id = dataFile.GetChromatogramId(i, out index);
if (!ChromKey.IsKeyId(id))
{
continue;
}
var chromKey = ChromKey.FromId(id, fixCEOptForShimadzu);
if (chromKey.Precursor != lastPrecursor)
{
lastPrecursor = chromKey.Precursor;
indexPrecursor++;
}
if (chromKey.Precursor.IsNegative)
{
_sourceHasNegativePolarityData = true;
}
else
{
_sourceHasPositivePolarityData = true;
}
var ki = new ChromKeyProviderIdPair(chromKey, index);
_chromIndices[index] = indexPrecursor;
_chromIds.Add(ki);
}
// Shimadzu can't do the necessary product m/z stepping for itself.
// So, they provide the CE values in their IDs and we need to adjust
// product m/z values for them to support CE optimization.
if (fixCEOptForShimadzu)
{
FixCEOptForShimadzu();
}
if (_chromIds.Count == 0)
{
throw new NoSrmDataException(FileInfo.FilePath);
}
// CONSIDER: TIC and BPC are not well defined for SRM and produced chromatograms with over 100,000 points in
// Agilent CE optimization data. So, keep them off for now.
// foreach (int globalIndex in _globalChromatogramExtractor.GlobalChromatogramIndexes)
// {
// _chromIndices[globalIndex] = globalIndex;
// _chromIds.Add(new ChromKeyProviderIdPair(ChromKey.FromId(_globalChromatogramExtractor.GetChromatogramId(globalIndex, out int indexId), false), globalIndex));
// }
foreach (var qcTracePair in _globalChromatogramExtractor.QcTraceByIndex)
{
_chromIndices[qcTracePair.Key] = qcTracePair.Key;
_chromIds.Add(new ChromKeyProviderIdPair(ChromKey.FromQcTrace(qcTracePair.Value), qcTracePair.Key));
}
// CONSIDER(kaipot): Some way to support mzML files converted from MIDAS wiff files
_hasMidasSpectra = (dataFile.IsABFile) && SpectraChromDataProvider.HasSpectrumData(dataFile);
_ionMobilityUnits = dataFile.IonMobilityUnits;
_hasIonMobilityCombined = dataFile.HasCombinedIonMobilitySpectra; // When true, data source provides IMS data in 3-array format, which affects spectrum ID format
SetPercentComplete(50);
}
public ChromatogramSet ChangeMSDataFilePaths(IList<MsDataFileUri> prop)
{
var set = ImClone(this);
// Be sure to preserve existing file info objects
var dictPathToFileInfo = MSDataFileInfos.ToDictionary(info => info.FilePath);
var listFileInfos = new List<ChromFileInfo>();
foreach (var filePath in prop)
{
ChromFileInfo chromFileInfo;
if (!dictPathToFileInfo.TryGetValue(filePath, out chromFileInfo))
{
chromFileInfo = new ChromFileInfo(filePath);
}
listFileInfos.Add(chromFileInfo);
}
set.MSDataFileInfos = listFileInfos;
if (ReferenceEquals(MSDataFileInfos, set.MSDataFileInfos))
return this;
return set;
}
/// <summary>
/// Calculates the fileCacheFlags from a collection of cached paths.
/// This function modifies 'this', and should only be called on a clone
/// before it is returned from a change operation.
/// <para>
/// If a path is not found in the cached set, its name is checked in
/// the names set, and if found, then disk is checked to see if the
/// file location has been moved.</para>
/// </summary>
/// <param name="cachedPaths">Set of known cached paths</param>
/// <param name="cachedFileNames">Set of known cached file names</param>
/// <param name="cachePath">Final cache path</param>
private void CalcCachedFlags(IDictionary<MsDataFileUri, ChromCachedFile> cachedPaths,
ICollection<string> cachedFileNames, string cachePath)
{
ChromFileInfo[] fileInfos = new ChromFileInfo[FileCount];
for (int i = 0; i < fileInfos.Length; i++)
{
fileInfos[i] = MSDataFileInfos[i];
var path = fileInfos[i].FilePath;
ChromCachedFile fileInfo;
if (cachedPaths.TryGetValue(path, out fileInfo))
fileInfos[i] = fileInfos[i].ChangeInfo(fileInfo);
else if (cachedFileNames == null || cachedFileNames.Contains(path.GetFileName()))
{
// If the name but not the file was found, check for an
// existing file in the cache file's directory.
var dataFilePath = GetExistingDataFilePath(cachePath, path);
if (dataFilePath != null && cachedPaths.TryGetValue(dataFilePath, out fileInfo))
fileInfos[i] = fileInfos[i].ChangeInfo(fileInfo);
}
}
if (!ArrayUtil.EqualsDeep(MSDataFileInfos, fileInfos))
MSDataFileInfos = fileInfos;
}
private PeptideChromInfoData(MeasuredResults measuredResults, int replicateIndex, ChromFileInfo chromFileInfo, PeptideChromInfo peptideChromInfo, PeptideDocNode peptideDocNode)
: base(measuredResults, replicateIndex, chromFileInfo, peptideChromInfo, peptideDocNode, null)
{
}
private TransitionChromInfoData(MeasuredResults measuredResults, int replicateIndex, ChromFileInfo chromFileInfo, TransitionChromInfo transitionChromInfo, PeptideDocNode peptideDocNode, TransitionGroupDocNode transitionGroupDocNode, TransitionDocNode transitionDocNode)
: base(measuredResults, replicateIndex, chromFileInfo, transitionChromInfo, peptideDocNode, transitionGroupDocNode)
{
TransitionDocNode = transitionDocNode;
}
private ChromFileInfo StripFilePathInfo(ChromFileInfo chromFileInfo)
{
// Remove the everything but the filename from the FilePath, and zero out the FileModifiedTime.
var chromCachedFile = new ChromCachedFile(new MsDataFilePath(chromFileInfo.FilePath.GetFileName()), 0,
new DateTime(0), chromFileInfo.RunStartTime, (float) chromFileInfo.MaxRetentionTime,
(float) chromFileInfo.MaxIntensity, chromFileInfo.InstrumentInfoList);
return chromFileInfo.ChangeInfo(chromCachedFile);
}
public RemoteChromDataProvider(SrmDocument document, IRetentionTimePredictor retentionTimePredictor, ChromFileInfo chromFileInfo, IProgressStatus progressStatus, int startPercent,
int endPercent, ILoadMonitor loader)
: base(chromFileInfo, progressStatus, startPercent, endPercent, loader)
{
_document = document;
ChorusUrl chorusUrl = (ChorusUrl)chromFileInfo.FilePath;
_chorusAccount = chorusUrl.FindChorusAccount(Settings.Default.RemoteAccountList);
var chromatogramRequestProviders = new List <ChromatogramRequestProvider>();
foreach (bool firstPass in new[] { true, false })
{
if (null == retentionTimePredictor && !firstPass)
{
continue;
}
var chromatogramRequestProvider = new ChromatogramRequestProvider(document, chorusUrl,
retentionTimePredictor, firstPass);
if (0 == chromatogramRequestProvider.ChromKeys.Count)
{
continue;
}
chromatogramRequestProviders.Add(chromatogramRequestProvider);
}
_chromatogramRequestProviders = chromatogramRequestProviders.ToArray();
_chromTaskLists = new ChromTaskList[_chromatogramRequestProviders.Length];
}
private static double? GetApexRT(TransitionGroupDocNode nodeGroup, int resultIndex, ChromFileInfo chromFileInfo, bool ms1Trans)
{
double? apexRT = null;
float ms1Max = 0;
var trans = ms1Trans
? nodeGroup.GetMsTransitions(true)
: nodeGroup.GetMsMsTransitions(true);
foreach (var nodeTran in trans)
{
foreach (var peakInfo in nodeTran.GetChromInfos(resultIndex).Where(c =>
ReferenceEquals(c.FileId, chromFileInfo.FileId)))
{
if (peakInfo.Area > ms1Max)
{
apexRT = peakInfo.RetentionTime;
ms1Max = peakInfo.Area;
}
}
}
return apexRT;
}
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;
}
}
protected ChromDataProvider(ChromFileInfo fileInfo,
ProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
{
FileInfo = fileInfo;
Status = status;
_startPercent = startPercent;
_endPercent = endPercent;
_loader = loader;
}
