public override void WriteToStream(Stream stream)
{
PrimitiveArrays.Write(stream, TransitionTimeIntensities.First().Times.ToArray());
foreach (var timeIntensities in TransitionTimeIntensities)
{
PrimitiveArrays.Write(stream, timeIntensities.Intensities.ToArray());
}
foreach (var timeIntensities in TransitionTimeIntensities)
{
if (timeIntensities.MassErrors == null)
{
continue;
}
WriteMassErrors(stream, timeIntensities.MassErrors);
}
var scanIdsByChromSource = ScanIdsByChromSource();
foreach (var chromSource in PERSISTED_CHROM_SOURCES)
{
ImmutableList <int> scanIds;
if (!scanIdsByChromSource.TryGetValue(chromSource, out scanIds))
{
continue;
}
PrimitiveArrays.Write(stream, scanIds.ToArray());
}
}
// ReSharper restore LocalizableElement
private void WriteCache(ILoadMonitor loader)
{
using (FileSaver fs = new FileSaver(CachePath, loader.StreamManager))
{
using (var stream = loader.StreamManager.CreateStream(fs.SafeName, FileMode.Create, true))
{
PrimitiveArrays.WriteOneValue(stream, FORMAT_VERSION_CACHE);
PrimitiveArrays.WriteOneValue(stream, _sourceFiles.Count);
foreach (var file in _sourceFiles)
{
byte[] fileNameBytes = Encoding.UTF8.GetBytes(file);
PrimitiveArrays.WriteOneValue(stream, fileNameBytes.Length);
PrimitiveArrays.Write(stream, fileNameBytes);
}
PrimitiveArrays.WriteOneValue(stream, _libraryEntries.Length);
foreach (var elibSpectrumInfo in _libraryEntries)
{
elibSpectrumInfo.Write(stream);
}
loader.StreamManager.Finish(stream);
fs.Commit();
loader.StreamManager.SetCache(FilePath, CachePath);
}
}
}
private void WriteData(Block block, Stream fileStream)
{
// Create back link to previous spilled block.
var lastFilePosition = _filePosition;
_filePosition = (int)fileStream.Position;
PrimitiveArrays.WriteOneValue(fileStream, lastFilePosition);
PrimitiveArrays.Write(fileStream, block._data);
}
public void Write(Stream stream)
{
Key.Write(stream);
PrimitiveArrays.WriteOneValue(stream, Id);
PrimitiveArrays.WriteOneValue(stream, PeakArea);
RetentionTimesByFileId.Write(stream);
PrimitiveArrays.WriteOneValue(stream, TransitionAreas.Count);
PrimitiveArrays.Write(stream, TransitionAreas.Select(mi => mi.Mz).ToArray());
PrimitiveArrays.Write(stream, TransitionAreas.Select(mi => mi.Intensity).ToArray());
}
public void Write(Stream stream)
{
PrimitiveArrays.WriteOneValue(stream, PeptideModSeq.Length);
PrimitiveArrays.Write(stream, Encoding.UTF8.GetBytes(PeptideModSeq));
PrimitiveArrays.WriteOneValue(stream, Key.Charge);
PrimitiveArrays.WriteOneValue(stream, BestFileId);
PrimitiveArrays.WriteOneValue(stream, FileDatas.Count);
foreach (var peakBoundEntry in FileDatas)
{
PrimitiveArrays.WriteOneValue(stream, peakBoundEntry.Key);
PrimitiveArrays.WriteOneValue(stream, peakBoundEntry.Value.PeakBounds.StartTime);
PrimitiveArrays.WriteOneValue(stream, peakBoundEntry.Value.PeakBounds.EndTime);
if (peakBoundEntry.Value.ApexTime.HasValue)
{
PrimitiveArrays.WriteOneValue <byte>(stream, 1);
PrimitiveArrays.WriteOneValue(stream, peakBoundEntry.Value.ApexTime.Value);
}
else
{
PrimitiveArrays.WriteOneValue <byte>(stream, 0);
}
}
}
private static void WriteMassErrors(Stream stream, IList <float> values)
{
PrimitiveArrays.Write(stream, values.Select(value => ChromPeak.To10x(value)).ToArray());
}
private bool JoinNextPart()
{
// Check for cancellation on every part.
if (_loader.IsCanceled)
{
_loader.UpdateProgress(_status = _status.Cancel());
Complete(null);
return(false);
}
if (_currentPartIndex >= CacheFilePaths.Count)
{
Complete(null);
return(false);
}
// If not cancelled, update progress.
string cacheFilePath = CacheFilePaths[_currentPartIndex];
string message = string.Format(Resources.ChromCacheJoiner_JoinNextPart_Joining_file__0__, cacheFilePath);
int percent = _currentPartIndex * 100 / CacheFilePaths.Count;
_status = _status.ChangeMessage(message).ChangePercentComplete(percent);
_loader.UpdateProgress(_status);
try
{
using (var inStream = _loader.StreamManager.CreateStream(cacheFilePath, FileMode.Open, false))
{
if (_fs.Stream == null)
{
_fs.Stream = _loader.StreamManager.CreateStream(_fs.SafeName, FileMode.Create, true);
}
ChromatogramCache.RawData rawData;
long bytesData = ChromatogramCache.LoadStructs(inStream, out rawData);
// If joining, then format version should have already been checked.
Assume.IsTrue(ChromatogramCache.IsVersionCurrent(rawData.FormatVersion) ||
// WatersCacheTest uses older format partial caches
rawData.FormatVersion == ChromatogramCache.FORMAT_VERSION_CACHE_2);
int offsetFiles = _listCachedFiles.Count;
int offsetTransitions = _listTransitions.Count;
int offsetPeaks = _peakCount;
int offsetScores = _scoreCount;
long offsetPoints = _fs.Stream.Position;
// Scan ids
long offsetScanIds = _fsScans.Stream.Position;
_listCachedFiles.AddRange(rawData.ChromCacheFiles.Select(f => f.RelocateScanIds(f.LocationScanIds + offsetScanIds)));
if (rawData.CountBytesScanIds > 0)
{
inStream.Seek(rawData.LocationScanIds, SeekOrigin.Begin);
inStream.TransferBytes(_fsScans.Stream, rawData.CountBytesScanIds);
}
_peakCount += rawData.ChromatogramPeaks.Length;
rawData.ChromatogramPeaks.WriteArray(block => ChromPeak.WriteArray(_fsPeaks.FileStream.SafeFileHandle, block));
_listTransitions.AddRange(rawData.ChromTransitions);
// Initialize the score types the first time through
if (_scoreTypesCount == -1)
{
_listScoreTypes.AddRange(rawData.ScoreTypes);
_scoreTypesCount = _listScoreTypes.Count;
}
else if (!ArrayUtil.EqualsDeep(_listScoreTypes, rawData.ScoreTypes))
{
// If the existing score types in the caches are not the same, the caches cannot be joined
if (_listScoreTypes.Intersect(rawData.ScoreTypes).Count() != _listScoreTypes.Count)
{
throw new InvalidDataException("Data cache files with different score types cannot be joined."); // Not L10N
}
}
_scoreCount += rawData.Scores.Length;
rawData.Scores.WriteArray(block => PrimitiveArrays.Write(_fsScores.Stream, block));
for (int i = 0; i < rawData.ChromatogramEntries.Length; i++)
{
rawData.RecalcEntry(i,
offsetFiles,
offsetTransitions,
offsetPeaks,
offsetScores,
offsetPoints,
_dictTextIdToByteIndex,
_listTextIdBytes);
}
_listGroups.AddRange(rawData.ChromatogramEntries);
inStream.Seek(0, SeekOrigin.Begin);
long copyBytes = bytesData;
while (copyBytes > 0)
{
int read = inStream.Read(_buffer, 0, (int)Math.Min(_buffer.Length, copyBytes));
_fs.Stream.Write(_buffer, 0, read);
copyBytes -= read;
}
_currentPartIndex++;
return(true);
}
}
catch (InvalidDataException x)
{
Complete(x);
}
catch (IOException x)
{
Complete(x);
}
catch (Exception x)
{
Complete(new Exception(String.Format(Resources.ChromCacheJoiner_JoinNextPart_Failed_to_create_cache__0__, CachePath), x));
}
return(false);
}
public void WriteChromGroup(ChromatogramGroupInfo originalChromGroup, MinimizedChromGroup minimizedChromGroup)
{
if (minimizedChromGroup.RetainedTransitionIndexes.Count == 0)
{
return;
}
var originalHeader = originalChromGroup.Header;
int fileIndex = originalHeader.FileIndex;
int startTransitionIndex = _transitions.Count;
int startPeakIndex = _peakCount;
int startScoreIndex = _scoreCount;
for (int iPeak = 0; iPeak < originalHeader.NumPeaks; iPeak++)
{
int iScores = originalHeader.StartScoreIndex + iPeak * _scoreTypes.Count;
var scores = _originalCache.GetCachedScores(iScores).ToArray();
PrimitiveArrays.Write(_outputStreamScores, scores);
_scoreCount += scores.Length;
}
int numPoints = minimizedChromGroup.OptimizedLastScan - minimizedChromGroup.OptimizedFirstScan + 1;
var retainedPeakIndexes = new HashSet <int>();
if (minimizedChromGroup.OptimizedStartTime.HasValue && minimizedChromGroup.OptimizedEndTime.HasValue)
{
for (int iPeak = 0; iPeak < originalHeader.NumPeaks; iPeak++)
{
bool outsideRange = false;
for (var transitionIndex = 0; transitionIndex < originalHeader.NumTransitions; transitionIndex++)
{
if (!minimizedChromGroup.RetainedTransitionIndexes.Contains(transitionIndex))
{
continue;
}
var peak = _originalCache.GetPeak(originalHeader.StartPeakIndex +
transitionIndex * originalHeader.NumPeaks + iPeak);
if (peak.StartTime < minimizedChromGroup.OptimizedStartTime.Value ||
peak.EndTime > minimizedChromGroup.OptimizedEndTime.Value)
{
outsideRange = true;
break;
}
}
if (!outsideRange)
{
retainedPeakIndexes.Add(iPeak);
}
}
}
else
{
retainedPeakIndexes.UnionWith(Enumerable.Range(0, originalHeader.NumPeaks));
}
int numPeaks = retainedPeakIndexes.Count;
int maxPeakIndex;
if (retainedPeakIndexes.Contains(originalHeader.MaxPeakIndex))
{
maxPeakIndex = retainedPeakIndexes.Count(index => index < originalHeader.MaxPeakIndex);
}
else
{
maxPeakIndex = -1;
}
long location = _outputStream.Position;
float[] times = originalChromGroup.Times.Skip(minimizedChromGroup.OptimizedFirstScan).Take(numPoints).ToArray();
List <float[]> intensities = new List <float[]>();
List <short[]> massError10Xs = originalChromGroup.MassError10XArray != null
? new List <short[]>()
: null;
int[][] scanIndexes = null;
if (originalChromGroup.ScanIndexes != null)
{
scanIndexes = new int[originalChromGroup.ScanIndexes.Length][];
for (int i = 0; i < scanIndexes.Length; i++)
{
if (originalChromGroup.ScanIndexes[i] != null)
{
scanIndexes[i] =
originalChromGroup.ScanIndexes[i].Skip(minimizedChromGroup.OptimizedFirstScan)
.Take(numPoints)
.ToArray();
}
}
}
foreach (var originalIndex in minimizedChromGroup.RetainedTransitionIndexes)
{
_transitions.Add(_originalCache.GetTransition(originalIndex + originalHeader.StartTransitionIndex));
for (int originalPeakIndex = 0; originalPeakIndex < originalHeader.NumPeaks; originalPeakIndex++)
{
if (!retainedPeakIndexes.Contains(originalPeakIndex))
{
continue;
}
var originalPeak = _originalCache.GetPeak(originalHeader.StartPeakIndex +
originalIndex * originalHeader.NumPeaks +
originalPeakIndex);
_peakCount++;
ChromPeak.WriteArray(_outputStreamPeaks.SafeFileHandle, new[] { originalPeak });
}
intensities.Add(originalChromGroup.IntensityArray[originalIndex]
.Skip(minimizedChromGroup.OptimizedFirstScan)
.Take(numPoints).ToArray());
if (massError10Xs != null)
{
massError10Xs.Add(originalChromGroup.MassError10XArray[originalIndex]
.Skip(minimizedChromGroup.OptimizedFirstScan)
.Take(numPoints).ToArray());
}
}
var massError10XArray = massError10Xs != null?massError10Xs.ToArray() : null;
byte[] points = ChromatogramCache.TimeIntensitiesToBytes(times, intensities.ToArray(), massError10XArray, scanIndexes);
// Compress the data (can be huge for AB data with lots of zeros)
byte[] pointsCompressed = points.Compress(3);
int lenCompressed = pointsCompressed.Length;
_outputStream.Write(pointsCompressed, 0, lenCompressed);
var header = new ChromGroupHeaderInfo5(originalHeader.Precursor,
originalHeader.TextIdIndex,
originalHeader.TextIdLen,
fileIndex,
_transitions.Count - startTransitionIndex,
startTransitionIndex,
numPeaks,
startPeakIndex,
startScoreIndex,
maxPeakIndex,
numPoints,
pointsCompressed.Length,
location,
originalHeader.Flags,
originalHeader.StatusId,
originalHeader.StatusRank);
_chromGroupHeaderInfos.Add(header);
}
public void WriteChromGroup(ChromatogramGroupInfo originalChromGroup, MinimizedChromGroup minimizedChromGroup)
{
if (minimizedChromGroup.RetainedTransitionIndexes.Count == 0)
{
return;
}
var originalHeader = originalChromGroup.Header;
int fileIndex = originalHeader.FileIndex;
int startTransitionIndex = _transitions.Count;
int startPeakIndex = _peakCount;
int startScoreIndex = _scoreCount;
_scoreCount += minimizedChromGroup.PeakScores.Length;
PrimitiveArrays.Write(_outputStreamScores, minimizedChromGroup.PeakScores);
_peakCount += minimizedChromGroup.TotalPeakCount;
_transitions.AddRange(minimizedChromGroup.Transitions);
var flags = originalHeader.Flags;
MemoryStream pointsStream = new MemoryStream();
var transitionChromSources = minimizedChromGroup.Transitions.Select(tran => tran.Source).ToArray();
var timeIntensitiesGroup = minimizedChromGroup.MinimizedTimeIntensitiesGroup;
if (timeIntensitiesGroup is RawTimeIntensities && _cacheFormat.FormatVersion < CacheFormatVersion.Twelve)
{
timeIntensitiesGroup = ((RawTimeIntensities)minimizedChromGroup.MinimizedTimeIntensitiesGroup)
.Interpolate(transitionChromSources);
}
timeIntensitiesGroup.WriteToStream(pointsStream);
if (timeIntensitiesGroup is RawTimeIntensities)
{
flags |= ChromGroupHeaderInfo.FlagValues.raw_chromatograms;
}
else
{
flags &= ~ChromGroupHeaderInfo.FlagValues.raw_chromatograms;
var interpolatedTimeIntensities = timeIntensitiesGroup as InterpolatedTimeIntensities;
if (interpolatedTimeIntensities != null)
{
flags &=
~(ChromGroupHeaderInfo.FlagValues.has_frag_scan_ids |
ChromGroupHeaderInfo.FlagValues.has_sim_scan_ids |
ChromGroupHeaderInfo.FlagValues.has_ms1_scan_ids);
var scanIdsByChromSource = interpolatedTimeIntensities.ScanIdsByChromSource();
if (scanIdsByChromSource.ContainsKey(ChromSource.fragment))
{
flags |= ChromGroupHeaderInfo.FlagValues.has_frag_scan_ids;
}
if (scanIdsByChromSource.ContainsKey(ChromSource.ms1))
{
flags |= ChromGroupHeaderInfo.FlagValues.has_ms1_scan_ids;
}
if (scanIdsByChromSource.ContainsKey(ChromSource.sim))
{
flags |= ChromGroupHeaderInfo.FlagValues.has_sim_scan_ids;
}
}
}
int numPeaks = minimizedChromGroup.NumPeaks;
int maxPeakIndex = minimizedChromGroup.MaxPeakIndex;
_cacheFormat.ChromPeakSerializer().WriteItems(_outputStreamPeaks, minimizedChromGroup.MinimizedPeaks);
long location = _outputStream.Position;
int lenUncompressed = (int)pointsStream.Length;
byte[] pointsCompressed = pointsStream.ToArray().Compress(3);
int lenCompressed = pointsCompressed.Length;
_outputStream.Write(pointsCompressed, 0, lenCompressed);
int textIdIndex;
int textIdLen;
var newTextId = GetNewTextId(originalHeader);
if (newTextId == null)
{
textIdIndex = -1;
textIdLen = 0;
}
else
{
textIdIndex = CalcTextIdOffset(newTextId);
textIdLen = newTextId.Count;
}
var header = new ChromGroupHeaderInfo(originalHeader.Precursor,
textIdIndex,
textIdLen,
fileIndex,
_transitions.Count - startTransitionIndex,
startTransitionIndex,
numPeaks,
startPeakIndex,
startScoreIndex,
maxPeakIndex,
timeIntensitiesGroup.NumInterpolatedPoints,
lenCompressed,
lenUncompressed,
location,
flags,
originalHeader.StatusId,
originalHeader.StatusRank,
originalHeader.StartTime, originalHeader.EndTime,
originalHeader.CollisionalCrossSection,
originalHeader.IonMobilityUnits);
_chromGroupHeaderInfos.Add(header);
}
