public static InterpolatedTimeIntensities ReadFromStream(Stream stream, ChromGroupHeaderInfo chromGroupHeaderInfo, ChromTransition[] chromTransitions)
{
Dictionary <ChromSource, int[]> scanIds = new Dictionary <ChromSource, int[]>();
int numTrans = chromTransitions.Length;
Assume.IsTrue(numTrans == chromGroupHeaderInfo.NumTransitions);
int numPoints = chromGroupHeaderInfo.NumPoints;
var sharedTimes = PrimitiveArrays.Read <float>(stream, numPoints);
var transitionIntensities = new IList <float> [numTrans];
for (int i = 0; i < numTrans; i++)
{
transitionIntensities[i] = PrimitiveArrays.Read <float>(stream, numPoints);
}
IList <float>[] transitionMassErrors = new IList <float> [numTrans];
if (chromGroupHeaderInfo.HasMassErrors)
{
for (int i = 0; i < numTrans; i++)
{
transitionMassErrors[i] = ReadMassErrors(stream, numPoints);
}
}
if (chromGroupHeaderInfo.HasFragmentScanIds)
{
scanIds.Add(ChromSource.fragment, PrimitiveArrays.Read <int>(stream, numPoints));
}
if (chromGroupHeaderInfo.HasSimScanIds)
{
scanIds.Add(ChromSource.sim, PrimitiveArrays.Read <int>(stream, numPoints));
}
if (chromGroupHeaderInfo.HasMs1ScanIds)
{
scanIds.Add(ChromSource.ms1, PrimitiveArrays.Read <int>(stream, numPoints));
}
List <TimeIntensities> listOfTimeIntensities = new List <TimeIntensities>();
for (int i = 0; i < numTrans; i++)
{
var chromSource = chromTransitions[i].Source;
int[] transitionScanIds;
scanIds.TryGetValue(chromSource, out transitionScanIds);
var timeIntensities = new TimeIntensities(sharedTimes, transitionIntensities[i], transitionMassErrors[i], transitionScanIds);
listOfTimeIntensities.Add(timeIntensities);
}
return(new InterpolatedTimeIntensities(listOfTimeIntensities, chromTransitions.Select(chromTransition => chromTransition.Source)));
}
public static ChromLibSpectrumInfo Read(Stream stream)
{
LibKey key = LibKey.Read(stream);
int id = PrimitiveArrays.ReadOneValue <int>(stream);
double peakArea = PrimitiveArrays.ReadOneValue <double>(stream);
var retentionTimesByFileId = IndexedRetentionTimes.Read(stream);
int mzCount = PrimitiveArrays.ReadOneValue <int>(stream);
var mzs = PrimitiveArrays.Read <double>(stream, mzCount);
var areas = PrimitiveArrays.Read <float>(stream, mzCount);
var mzAreas = ImmutableList.ValueOf(Enumerable.Range(0, mzCount)
.Select(index => new SpectrumPeaksInfo.MI
{
Mz = mzs[index],
Intensity = areas[index]
}));
return(new ChromLibSpectrumInfo(key, id, peakArea, retentionTimesByFileId, mzAreas));
}
private static float[] ReadMassErrors(Stream stream, int count)
{
return(PrimitiveArrays.Read <short>(stream, count).Select(value => value / 10f).ToArray());
}
protected void Complete(Exception x)
{
lock (this)
{
ChromatogramCache result = null;
try
{
if (x == null && !_status.IsFinal)
{
long locationScanIds = 0, countBytesScanIds = 0;
if (_fs.Stream != null)
{
try
{
locationScanIds = _fs.Stream.Position;
countBytesScanIds = _fsScans.Stream.Position;
ChromatogramCache.WriteStructs(_fs.Stream,
_fsScans.Stream,
_fsPeaks.Stream,
_fsScores.Stream,
_listCachedFiles,
_listGroups,
_listTransitions,
_listTextIdBytes,
_listScoreTypes,
_scoreCount,
_peakCount);
_loader.StreamManager.Finish(_fs.Stream);
_fs.Stream = null;
// Allow cancelation right up to the final commit
if (!_loader.IsCanceled)
{
_fs.Commit(_destinationStream);
}
else
{
_loader.UpdateProgress(_status = _status.Cancel());
}
}
catch (Exception xWrite)
{
throw new IOException(TextUtil.LineSeparate(string.Format(Resources.ChromCacheWriter_Complete_Failure_attempting_to_write_the_file__0_, _fs.RealName), xWrite.Message));
}
}
if (!_status.IsCanceled)
{
// Create stream identifier, but do not open. The stream will be opened
// the first time the document uses it.
var readStream = _loader.StreamManager.CreatePooledStream(CachePath, false);
// DebugLog.Info("{0}. {1} - created", readStream.GlobalIndex, CachePath);
_fsPeaks.Stream.Seek(0, SeekOrigin.Begin);
_fsScores.Stream.Seek(0, SeekOrigin.Begin);
var rawData = new ChromatogramCache.RawData
{
FormatVersion = ChromatogramCache.FORMAT_VERSION_CACHE,
ChromCacheFiles = _listCachedFiles.ToArray(),
ChromatogramEntries = _listGroups.ToArray(),
ChromTransitions = _listTransitions.ToArray(),
ChromatogramPeaks = new BlockedArray <ChromPeak>(
count => ChromPeak.ReadArray(_fsPeaks.FileStream, count), _peakCount,
ChromPeak.SizeOf, ChromPeak.DEFAULT_BLOCK_SIZE),
ScoreTypes = _listScoreTypes.ToArray(),
Scores = new BlockedArray <float>(
count => PrimitiveArrays.Read <float>(_fsScores.FileStream, count), _scoreCount,
sizeof(float), ChromatogramCache.DEFAULT_SCORES_BLOCK_SIZE),
TextIdBytes = _listTextIdBytes.ToArray(),
LocationScanIds = locationScanIds,
CountBytesScanIds = countBytesScanIds,
};
result = new ChromatogramCache(CachePath, rawData, readStream);
_status = _status.Complete();
_loader.UpdateProgress(_status);
}
}
}
catch (Exception x2)
{
x = x2;
}
finally
{
Dispose();
}
try
{
_completed(result, x == null ? _status : _status.ChangeErrorException(x));
}
catch (Exception x2)
{
_completed(null, _status.ChangeErrorException(x2));
}
}
}
protected void Complete(Exception x)
{
lock (this)
{
ChromatogramCache result = null;
try
{
if (x == null && !_status.IsFinal)
{
long locationScanIds = 0, countBytesScanIds = 0;
if (_fs.Stream != null)
{
locationScanIds = _fs.Stream.Position;
countBytesScanIds = _fsScans.Stream.Position;
ChromatogramCache.WriteStructs(_fs.Stream,
_fsScans.Stream,
_fsPeaks.Stream,
_fsScores.Stream,
_listCachedFiles,
_listGroups,
_listTransitions,
_listTextIdBytes,
_listScoreTypes,
_scoreCount,
_peakCount);
_loader.StreamManager.Finish(_fs.Stream);
_fs.Stream = null;
_fs.Commit(_destinationStream);
}
// Create stream identifier, but do not open. The stream will be opened
// the first time the document uses it.
var readStream = _loader.StreamManager.CreatePooledStream(CachePath, false);
_fsPeaks.Stream.Seek(0, SeekOrigin.Begin);
_fsScores.Stream.Seek(0, SeekOrigin.Begin);
var rawData = new ChromatogramCache.RawData
{
FormatVersion = ChromatogramCache.FORMAT_VERSION_CACHE,
ChromCacheFiles = _listCachedFiles.ToArray(),
ChromatogramEntries = _listGroups.ToArray(),
ChromTransitions = _listTransitions.ToArray(),
ChromatogramPeaks = new BlockedArray <ChromPeak>(
count => ChromPeak.ReadArray(_fsPeaks.FileStream.SafeFileHandle, count), _peakCount,
ChromPeak.SizeOf, ChromPeak.DEFAULT_BLOCK_SIZE),
ScoreTypes = _listScoreTypes.ToArray(),
Scores = new BlockedArray <float>(
count => PrimitiveArrays.Read <float>(_fsScores.FileStream, count), _scoreCount,
sizeof(float), ChromatogramCache.DEFAULT_SCORES_BLOCK_SIZE),
TextIdBytes = _listTextIdBytes.ToArray(),
LocationScanIds = locationScanIds,
CountBytesScanIds = countBytesScanIds,
};
result = new ChromatogramCache(CachePath, rawData, readStream);
_loader.UpdateProgress(_status.Complete());
}
}
catch (Exception x2)
{
x = x2;
}
finally
{
Dispose();
}
try
{
_completed(result, x);
}
catch (Exception x2)
{
_completed(null, x2);
}
}
}
