public override bool GetChromatogram(
int id,
Target modifiedSequence,
Color peptideColor,
out ChromExtra extra,
out TimeIntensities timeIntensities)
{
bool loaded = false;
extra = null;
timeIntensities = null;
int idRemain = id;
for (int iTaskList = 0; iTaskList < _chromatogramRequestProviders.Length; iTaskList++)
{
ChromatogramRequestProvider requestProvider = _chromatogramRequestProviders[iTaskList];
if (requestProvider.ChromKeys.Count <= idRemain)
{
idRemain -= requestProvider.ChromKeys.Count;
continue;
}
ChromTaskList chromTaskList = _chromTaskLists[iTaskList];
if (null == chromTaskList)
{
chromTaskList = _chromTaskLists[iTaskList] = new ChromTaskList(CheckCancelled, _document, _chorusAccount, requestProvider.ChorusUrl, ChromTaskList.ChunkChromatogramRequest(requestProvider.GetChromatogramRequest(), 1000));
chromTaskList.SetMinimumSimultaneousTasks(3);
}
ChromKey chromKey = requestProvider.ChromKeys[idRemain];
loaded = chromTaskList.GetChromatogram(chromKey, out timeIntensities);
if (loaded)
{
extra = new ChromExtra(id, chromKey.Precursor == 0 ? 0 : -1);
if (chromKey.Precursor.IsNegative)
{
_sourceHasNegativePolarityData = true;
}
else
{
_sourceHasPositivePolarityData = true;
}
if (timeIntensities.NumPoints > 0 && Status is ChromatogramLoadingStatus)
{
((ChromatogramLoadingStatus)Status).Transitions.AddTransition(
modifiedSequence,
peptideColor,
extra.StatusId,
extra.StatusRank,
timeIntensities.Times,
timeIntensities.Intensities);
}
}
break;
}
int percentComplete = _chromTaskLists.Sum(taskList => taskList == null ? 0 : taskList.PercentComplete) /
_chromTaskLists.Length;
percentComplete = Math.Min(percentComplete, 99);
SetPercentComplete(percentComplete);
return(loaded);
}
public static IPeakFinder CreatePeakFinder(TimeIntensities interpolatedTimeIntensities)
{
var peakFinder = PeakFinders.NewDefaultPeakFinder();
peakFinder.SetChromatogram(interpolatedTimeIntensities.Times, interpolatedTimeIntensities.Intensities);
return(peakFinder);
}
/// <summary>
/// Get a chromatogram with properly sorted time values.
/// </summary>
public void ReleaseChromatogram(byte[] bytesFromDisk, out TimeIntensities timeIntensities)
{
var times = Times.ToArray(bytesFromDisk);
var intensities = Intensities.ToArray(bytesFromDisk);
var massErrors = MassErrors != null
? MassErrors.ToArray(bytesFromDisk)
: null;
var scanIds = Scans != null
? Scans.ToArray(bytesFromDisk)
: null;
// Make sure times and intensities match in length.
if (times.Length != intensities.Length)
{
throw new InvalidDataException(
string.Format(Resources.ChromCollected_ChromCollected_Times__0__and_intensities__1__disagree_in_point_count,
times.Length, intensities.Length));
}
if (massErrors != null && massErrors.Length != intensities.Length)
{
throw new InvalidDataException(
string.Format(Resources.ChromCollector_ReleaseChromatogram_Intensities___0___and_mass_errors___1___disagree_in_point_count_,
intensities.Length, massErrors.Length));
}
timeIntensities = new TimeIntensities(times, intensities, massErrors, scanIds);
// Release memory.
Times = null;
Intensities = null;
MassErrors = null;
Scans = null;
}
public override bool GetChromatogram(int id, Target modifiedSequence, Color color, out ChromExtra extra, out TimeIntensities timeIntensities)
{
// No mass errors in SRM
if (_readChromatograms == 0)
{
_readStartTime = DateTime.UtcNow; // Said to be 117x faster than Now and this is for a delta
}
float[] times, intensities;
if (!_globalChromatogramExtractor.GetChromatogram(id, out times, out intensities))
{
_dataFile.GetChromatogram(id, out string chromId, out times, out intensities);
}
timeIntensities = new TimeIntensities(times, intensities, null, null);
// Assume that each chromatogram will be read once, though this may
// not always be completely true.
_readChromatograms++;
if (!System.Diagnostics.Debugger.IsAttached)
{
double predictedMinutes = ExpectedReadDurationMinutes;
if (_readMaxMinutes > 0 && predictedMinutes > _readMaxMinutes)
{
// TODO: This warning isn't checked in the command line version of Skyline. Maybe we should do that.
if (Status is ChromatogramLoadingStatus)
{
Status =
((ChromatogramLoadingStatus)Status).ChangeWarningMessage(Resources.ChromatogramDataProvider_GetChromatogram_This_import_appears_to_be_taking_longer_than_expected__If_importing_from_a_network_drive__consider_canceling_this_import__copying_to_local_disk_and_retrying_);
}
}
}
if (_readChromatograms < _chromIds.Count)
{
SetPercentComplete(50 + _readChromatograms * 50 / _chromIds.Count);
}
int index = _chromIndices[id];
extra = new ChromExtra(index, -1); // TODO: is zero the right value?
// Display in AllChromatogramsGraph
var loadingStatus = Status as ChromatogramLoadingStatus;
if (loadingStatus != null)
{
loadingStatus.Transitions.AddTransition(
modifiedSequence,
color,
index, -1,
times,
intensities);
}
return(true);
}
/// <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>
/// Adds the intensities from the other TimeIntensities to the intensities in this.
/// The returned TimeIntensities whill have a set of times which is the union of the
/// times in this and <paramref name="other"/>.
/// </summary>
public TimeIntensities MergeTimesAndAddIntensities(TimeIntensities other)
{
if (Times.Equals(other.Times))
{
return(AddIntensities(other));
}
var mergedTimes = ImmutableList.ValueOf(Times.Concat(other.Times).Distinct().OrderBy(time => time));
if (mergedTimes.Equals(Times))
{
return(AddIntensities(other));
}
return(Interpolate(mergedTimes, false).AddIntensities(other));
}
public static RawTimeIntensities FromChromatogramGroupData(ChromatogramGroupData chromatogramGroupData)
{
var timeIntensitiesList = new List <TimeIntensities>();
var timeLists = chromatogramGroupData.TimeLists.Select(timeList => ImmutableList.ValueOf(timeList.Times)).ToArray();
var scanIdLists = chromatogramGroupData.ScanIdLists
.Select(scanIdList => ImmutableList.ValueOf(scanIdList.ScanIds)).ToArray();
foreach (var chromatogram in chromatogramGroupData.Chromatograms)
{
IEnumerable <float> massErrors = null;
if (chromatogram.MassErrors100X.Count > 0)
{
massErrors = chromatogram.MassErrors100X.Select(error => error / 100.0f);
}
else if (chromatogram.MassErrorsDeprecated.Count > 0)
{
massErrors = chromatogram.MassErrorsDeprecated;
}
var timeIntensities = new TimeIntensities(timeLists[chromatogram.TimeListIndex - 1],
chromatogram.Intensities,
massErrors,
chromatogram.ScanIdListIndex == 0 ? null : scanIdLists[chromatogram.ScanIdListIndex - 1]);
timeIntensitiesList.Add(timeIntensities);
}
InterpolationParams interpolationParams;
if (chromatogramGroupData.InterpolatedNumPoints == 0)
{
interpolationParams = null;
}
else
{
interpolationParams = new InterpolationParams(chromatogramGroupData.InterpolatedStartTime, chromatogramGroupData.InterpolatedEndTime, chromatogramGroupData.InterpolatedNumPoints, chromatogramGroupData.InterpolatedDelta)
.ChangeInferZeroes(chromatogramGroupData.InferZeroes);
}
var rawTimeIntensities = new RawTimeIntensities(timeIntensitiesList, interpolationParams);
if (chromatogramGroupData.TimeIntervals != null)
{
var startTimes = chromatogramGroupData.TimeIntervals.StartTimes;
var endTimes = chromatogramGroupData.TimeIntervals.EndTimes;
var timeIntervals = TimeIntervals.FromIntervals(Enumerable.Range(0, startTimes.Count)
.Select(i => new KeyValuePair <float, float>(startTimes[i], endTimes[i])));
rawTimeIntensities = rawTimeIntensities.ChangeTimeIntervals(timeIntervals);
}
return(rawTimeIntensities);
}
/// <summary>
/// Adds the intensities from the other TimeIntensities to the intensities in this.
/// The returned TimeIntensities will have the same set of times as this.
/// </summary>
public TimeIntensities AddIntensities(TimeIntensities other)
{
if (!Times.Equals(other.Times))
{
other = other.Interpolate(Times, false);
}
float[] newIntensities = new float[Times.Count];
for (int i = 0; i < Times.Count; i++)
{
// Avoid arithmetic overflow
double intensitySum = Intensities[i] + other.Intensities[i];
newIntensities[i] = intensitySum < float.MaxValue ? (float)intensitySum : float.MaxValue;
}
return(new TimeIntensities(Times, newIntensities, null, null));
}
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 override bool GetChromatogram(int id, Target modifiedSequence, Color color, out ChromExtra extra, out TimeIntensities timeIntensities)
{
float[] times, intensities;
if (!_globalChromatogramExtractor.GetChromatogram(id, out times, out intensities))
{
_dataFile.GetChromatogram(id, out _, out times, out intensities);
}
timeIntensities = new TimeIntensities(times, intensities, null, null);
// Assume that each chromatogram will be read once, though this may
// not always be completely true.
_readChromatograms++;
if (_readChromatograms < _chromIds.Count)
{
SetPercentComplete(50 + _readChromatograms * 50 / _chromIds.Count);
}
int index = _chromIndices[id];
extra = new ChromExtra(index, -1); // TODO: is zero the right value?
// Display in AllChromatogramsGraph
var loadingStatus = Status as ChromatogramLoadingStatus;
if (loadingStatus != null)
{
loadingStatus.Transitions.AddTransition(
modifiedSequence,
color,
index, -1,
times,
intensities);
}
return(true);
}
public override bool GetChromatogram(int id, Target modifiedSequence, Color peptideColor, out ChromExtra extra, out TimeIntensities timeIntensities)
{
return(_cachedChromatogramDataProvider.GetChromatogram(
id, modifiedSequence, peptideColor,
out extra, out timeIntensities));
}
public override bool GetChromatogram(int id, Target modifiedSequence, Color peptideColor, out ChromExtra extra, out TimeIntensities timeIntensities)
{
var chromKeyIndices = _chromKeyIndices[id];
if (_lastChromGroupInfo == null || _lastIndices.GroupIndex != chromKeyIndices.GroupIndex)
{
_lastChromGroupInfo = _cache.LoadChromatogramInfo(chromKeyIndices.GroupIndex);
_lastChromGroupInfo.ReadChromatogram(_cache);
}
_lastIndices = chromKeyIndices;
var tranInfo = _lastChromGroupInfo.GetTransitionInfo(chromKeyIndices.TranIndex);
timeIntensities = tranInfo.TimeIntensities;
// Assume that each chromatogram will be read once, though this may
// not always be completely true.
_readChromatograms++;
// But avoid reaching 100% before reading is actually complete
SetPercentComplete(Math.Min(99, 100 * _readChromatograms / _chromKeyIndices.Length));
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0 && Status is ChromatogramLoadingStatus)
{
((ChromatogramLoadingStatus)Status).Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
timeIntensities.Times,
timeIntensities.Intensities);
}
return(true);
}
public abstract bool GetChromatogram(int id, Target modifiedSequence, Color color, out ChromExtra extra, out TimeIntensities timeIntensities);
public SingletonImpl(TimeIntensities timeIntensities) : base(ImmutableList.Singleton(timeIntensities))
{
}
public static TimeIntensitiesGroup Singleton(TimeIntensities timeIntensities)
{
return(new SingletonImpl(timeIntensities));
}
public PeakIntegrator(TimeIntensities interpolatedTimeIntensities)
: this(interpolatedTimeIntensities, null)
{
}
public void Interpolate(float[] timesNew, bool inferZeros)
{
var chromatogramTimeIntensities = new TimeIntensities(RawTimes, RawIntensities, RawMassErrors, RawScanIds);
TimeIntensities = chromatogramTimeIntensities.Interpolate(timesNew, inferZeros);
}
public void FixChromatogram(float[] timesNew, float[] intensitiesNew, int[] scanIndexesNew)
{
TimeIntensities = RawTimeIntensities = new TimeIntensities(timesNew, intensitiesNew, null, scanIndexesNew);
}
public PeakIntegrator(TimeIntensities interpolatedTimeIntensities, IPeakFinder peakFinder)
{
InterpolatedTimeIntensities = interpolatedTimeIntensities;
PeakFinder = peakFinder;
}
