public ChromGroups(
IList <IList <int> > chromatogramRequestOrder,
IList <ChromKey> chromKeys,
float maxRetentionTime,
int cycleCount,
string cachePath)
{
RequestOrder = chromatogramRequestOrder;
_chromKeys = chromKeys;
_maxRetentionTime = maxRetentionTime;
_cycleCount = cycleCount;
_cachePath = cachePath;
if (RequestOrder == null)
{
return;
}
// Sanity check.
foreach (var group in RequestOrder)
{
foreach (var chromIndex in group)
{
Assume.IsTrue(chromIndex >= 0 && chromIndex < _chromKeys.Count);
}
}
// Create array to map a provider id back to the peptide group that contains it.
_idToGroupId = new int[_chromKeys.Count];
for (int groupId = 0; groupId < chromatogramRequestOrder.Count; groupId++)
{
foreach (var id in chromatogramRequestOrder[groupId])
{
_idToGroupId[id] = groupId;
}
}
// Decide how groups will be allocated to spill files.
long maxSpillFileSize = 0;
long estimateSpillFileSize = 0;
SpillFile spillFile = new SpillFile();
_spillFiles = new SpillFile[chromatogramRequestOrder.Count];
for (int groupId = 0; groupId < _spillFiles.Length; groupId++)
{
long maxGroupSize = GetMaxSize(groupId);
long estimateGroupSize = EstimateGroupSize(groupId);
maxSpillFileSize += maxGroupSize;
estimateSpillFileSize += estimateGroupSize;
if (maxSpillFileSize > MAX_SPILL_FILE_SIZE || estimateSpillFileSize > TARGET_SPILL_FILE_SIZE)
{
spillFile = new SpillFile();
maxSpillFileSize = maxGroupSize;
estimateSpillFileSize = estimateGroupSize;
}
_spillFiles[groupId] = spillFile;
spillFile.MaxTime = Math.Max(spillFile.MaxTime, GetMaxTime(groupId));
}
}
/// <summary>
/// Release a chromatogram if its collector is complete (indicated by retention time).
/// </summary>
/// <returns>-1 if chromatogram is not finished yet.</returns>
public int ReleaseChromatogram(
int chromatogramIndex, float retentionTime, ChromCollector collector,
out TimeIntensities timeIntensities)
{
int groupIndex = GetGroupIndex(chromatogramIndex);
var spillFile = _spillFiles[groupIndex];
// Not done reading yet.
if (retentionTime < spillFile.MaxTime || (collector != null && !collector.IsSetTimes))
{
timeIntensities = null;
return(-1);
}
// No chromatogram information collected.
if (collector == null)
{
timeIntensities = TimeIntensities.EMPTY;
return(0);
}
if (ReferenceEquals(_cachedSpillFile, spillFile))
{
if (spillFile.Stream != null)
{
if (_bytesFromSpillFile == null || spillFile.Stream.Length != _bytesFromSpillFile.Length)
{
// Need to reread spill file if more bytes were written since the time it was cached.
_cachedSpillFile = null;
}
}
}
if (!ReferenceEquals(_cachedSpillFile, spillFile))
{
_cachedSpillFile = spillFile;
_bytesFromSpillFile = null;
var fileStream = spillFile.Stream;
if (fileStream != null)
{
fileStream.Seek(0, SeekOrigin.Begin);
_bytesFromSpillFile = new byte[fileStream.Length];
int bytesRead = fileStream.Read(_bytesFromSpillFile, 0, _bytesFromSpillFile.Length);
Assume.IsTrue(bytesRead == _bytesFromSpillFile.Length);
// TODO: Would be nice to have something that releases spill files progressively, as they are
// no longer needed.
// spillFile.CloseStream();
}
}
collector.ReleaseChromatogram(_bytesFromSpillFile, out timeIntensities);
return(collector.StatusId);
}
/// <summary>
/// Release a chromatogram if its collector is complete (indicated by retention time).
/// </summary>
/// <returns>-1 if chromatogram is not finished yet.</returns>
public int ReleaseChromatogram(
int chromatogramIndex, float retentionTime, ChromCollector collector,
out float[] times, out float[] intensities, out float[] massErrors, out int[] scanIds)
{
int groupIndex = GetGroupIndex(chromatogramIndex);
var spillFile = _spillFiles[groupIndex];
// Not done reading yet.
if (retentionTime < spillFile.MaxTime)
{
times = null;
intensities = null;
massErrors = null;
scanIds = null;
return(-1);
}
// No chromatogram information collected.
if (collector == null)
{
times = EMPTY_FLOAT_ARRAY;
intensities = EMPTY_FLOAT_ARRAY;
massErrors = null;
scanIds = null;
return(0);
}
if (!ReferenceEquals(_cachedSpillFile, spillFile))
{
_cachedSpillFile = spillFile;
_bytesFromSpillFile = null;
var fileStream = spillFile.Stream;
if (fileStream != null)
{
fileStream.Seek(0, SeekOrigin.Begin);
_bytesFromSpillFile = new byte[fileStream.Length];
int bytesRead = fileStream.Read(_bytesFromSpillFile, 0, _bytesFromSpillFile.Length);
Assume.IsTrue(bytesRead == _bytesFromSpillFile.Length);
// TODO: Would be nice to have something that releases spill files progressively, as they are
// no longer needed.
// spillFile.CloseStream();
}
}
collector.ReleaseChromatogram(_bytesFromSpillFile, out times, out intensities, out massErrors, out scanIds);
return(collector.StatusId);
}
SpillFile AcquireFile(Int64 sizeNeeded)
{
SpillFile f;
if (sizeNeeded < 0)
{
f = new SpillFile(MintFileName());
}
else
{
lock (availableFiles)
{
var fitFiles = availableFiles.Where(x => x.BufferedSpace >= sizeNeeded);
// XXX
f = fitFiles.First();
}
}
return(f);
}
public RecvFiberSpillBank(Vertex <T> vertex, int bufferSize)
{
this.vertex = vertex;
this.spillFile = new SpillFile <Pair <S, T> >(System.IO.Path.GetRandomFileName(), bufferSize, new AutoSerializedMessageEncoder <S, T>(1, 1, DummyBufferPool <byte> .Pool, vertex.Stage.InternalGraphManager.Controller.Configuration.SendPageSize, vertex.CodeGenerator), new AutoSerializedMessageDecoder <S, T>(vertex.CodeGenerator), vertex.Stage.InternalGraphManager.Controller.Configuration.SendPageSize, vertex.CodeGenerator.GetSerializer <MessageHeader>());
}
public RecvFiberSpillBank(Vertex <T> shard, int bufferSize)
{
this.Shard = shard;
this.spillFile = new SpillFile <Pair <S, T> >(System.IO.Path.GetRandomFileName(), bufferSize, new AutoSerializedMessageEncoder <S, T>(1, 1, DummyBufferPool <byte> .Pool, shard.Stage.InternalGraphManager.Controller.Configuration.SendPageSize, AutoSerializationMode.OneTimePerMessage), new AutoSerializedMessageDecoder <S, T>(), shard.Stage.InternalGraphManager.Controller.Configuration.SendPageSize);
}
SpillFile AcquireFile(Int64 sizeNeeded)
{
SpillFile f;
if (sizeNeeded < 0)
{
f = new SpillFile(MintFileName());
}
else
{
lock (availableFiles)
{
var fitFiles = availableFiles.Where(x => x.BufferedSpace >= sizeNeeded);
// XXX
f = fitFiles.First();
}
}
return f;
}
