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 override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
return(_cachedChromatogramDataProvider.GetChromatogram(
id, modifiedSequence, peptideColor,
out extra, out times, out scanIndexes, out intensities, out massErrors));
}
public override bool GetChromatogram(
int id,
string modifiedSequence,
Color peptideColor,
out ChromExtra extra,
out float[] times,
out int[] scanIndexes,
out float[] intensities,
out float[] massErrors)
{
bool loaded = false;
extra = null;
times = null;
scanIndexes = null;
intensities = null;
massErrors = 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 times, out scanIndexes, out intensities, out massErrors);
if (loaded)
{
extra = new ChromExtra(id, chromKey.Precursor == 0 ? 0 : -1);
if (times.Length > 0)
{
LoadingStatus.Transitions.AddTransition(
modifiedSequence,
peptideColor,
extra.StatusId,
extra.StatusRank,
times,
intensities);
}
}
break;
}
int percentComplete = _chromTaskLists.Sum(taskList => taskList == null ? 0 : taskList.PercentComplete) /
_chromTaskLists.Length;
percentComplete = Math.Min(percentComplete, 99);
SetPercentComplete(percentComplete);
return(loaded);
}
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);
}
public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
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);
times = tranInfo.Times;
intensities = tranInfo.Intensities;
massErrors = null;
if (tranInfo.MassError10Xs != null)
{
massErrors = tranInfo.MassError10Xs.Select(m => m / 10.0f).ToArray();
}
scanIndexes = null;
if (tranInfo.ScanIndexes != null)
{
scanIndexes = tranInfo.ScanIndexes[(int)chromKeyIndices.Key.Source];
}
// 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,
times,
intensities);
}
return(true);
}
public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
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);
times = tranInfo.Times;
intensities = tranInfo.Intensities;
massErrors = null;
if (tranInfo.MassError10Xs != null)
{
massErrors = tranInfo.MassError10Xs.Select(m => m / 10.0f).ToArray();
}
scanIndexes = null;
if (tranInfo.ScanIndexes != null)
{
scanIndexes = tranInfo.ScanIndexes[(int)chromKeyIndices.Key.Source];
}
SetPercentComplete(100 * id / _chromKeyIndices.Length);
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0)
{
LoadingStatus.Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
times,
intensities);
}
return(true);
}
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)
{
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, string modifiedSequence, Color color, out ChromExtra extra,
out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors);
public abstract bool GetChromatogram(int id, Target modifiedSequence, Color color, out ChromExtra extra, out TimeIntensities timeIntensities);
public abstract bool GetChromatogram(int id, string modifiedSequence, Color color, out ChromExtra extra,
out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors);
public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
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);
times = tranInfo.Times;
intensities = tranInfo.Intensities;
massErrors = null;
if (tranInfo.MassError10Xs != null)
massErrors = tranInfo.MassError10Xs.Select(m => m/10.0f).ToArray();
scanIndexes = null;
if (tranInfo.ScanIndexes != null)
scanIndexes = tranInfo.ScanIndexes[(int) chromKeyIndices.Key.Source];
SetPercentComplete(100 * id / _chromKeyIndices.Length);
extra = new ChromExtra(chromKeyIndices.StatusId, chromKeyIndices.StatusRank);
// Display in AllChromatogramsGraph
if (chromKeyIndices.Key.Precursor != 0)
{
LoadingStatus.Transitions.AddTransition(
modifiedSequence,
peptideColor,
chromKeyIndices.StatusId,
chromKeyIndices.StatusRank,
times,
intensities);
}
return true;
}
public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
var statusId = _collectors.ReleaseChromatogram(id, _chromGroups,
out times, out intensities, out massErrors, out scanIndexes);
extra = new ChromExtra(statusId, LoadingStatus.Transitions.GetRank(id)); // TODO: Get rank
// Each chromatogram will be read only once!
_readChromatograms++;
UpdatePercentComplete();
return times.Length > 0;
}
public override bool GetChromatogram(
int id,
string modifiedSequence,
Color peptideColor,
out ChromExtra extra,
out float[] times,
out int[] scanIndexes,
out float[] intensities,
out float[] massErrors)
{
bool loaded = false;
extra = null;
times = null;
scanIndexes = null;
intensities = null;
massErrors = 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 times, out scanIndexes, out intensities, out massErrors);
if (loaded)
{
extra = new ChromExtra(id, chromKey.Precursor == 0 ? 0 : -1);
if (times.Length > 0)
{
LoadingStatus.Transitions.AddTransition(
modifiedSequence,
peptideColor,
extra.StatusId,
extra.StatusRank,
times,
intensities);
}
}
break;
}
int percentComplete = _chromTaskLists.Sum(taskList => taskList == null ? 0 : taskList.PercentComplete)/
_chromTaskLists.Length;
percentComplete = Math.Min(percentComplete, 99);
SetPercentComplete(percentComplete);
return loaded;
}
public override bool GetChromatogram(
int id, string modifiedSequence, Color peptideColor,
out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
return _cachedChromatogramDataProvider.GetChromatogram(
id, modifiedSequence, peptideColor,
out extra, out times, out scanIndexes, out intensities, out massErrors);
}
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, string modifiedSequence, Color color, out ChromExtra extra, out float[] times, out int[] scanIndexes, out float[] intensities, out float[] massErrors)
{
// No mass errors in SRM
massErrors = null;
if (_readChromatograms == 0)
{
_readStartTime = DateTime.Now;
}
string chromId;
_dataFile.GetChromatogram(id, out chromId, out times, out intensities);
scanIndexes = 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.
Status =
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
LoadingStatus.Transitions.AddTransition(
modifiedSequence,
color,
index, -1,
times,
intensities);
return true;
}
