private void AddChromKeys(ChromSource source, SpectrumProductFilter[] productFilters, bool highEnergy,
List <ChromKey> listChromKeys)
{
if (null != productFilters)
{
var ionMobility = GetIonMobilityWindow(highEnergy);
foreach (var spectrumProductFilter in productFilters)
{
spectrumProductFilter.FilterId = listChromKeys.Count;
var key = new ChromKey(ModifiedSequence,
Q1,
ionMobility,
spectrumProductFilter.TargetMz,
0, // CE value (Shimadzu SRM only)
spectrumProductFilter.FilterWidth,
source,
Extractor,
true,
true,
MinTime,
MaxTime);
listChromKeys.Add(key);
}
}
}
private void AddChromKeys(ChromSource source, SpectrumProductFilter[] productFilters, bool highEnergy,
List <ChromKey> listChromKeys)
{
if (null != productFilters)
{
double?imCenterOpt = null;
double imCenter, imWidth;
if (GetDriftTimeWindow(out imCenter, out imWidth, highEnergy))
{
imCenterOpt = imCenter;
}
foreach (var spectrumProductFilter in productFilters)
{
spectrumProductFilter.FilterId = listChromKeys.Count;
var key = new ChromKey(ModifiedSequence,
Q1,
imCenterOpt,
imWidth,
spectrumProductFilter.TargetMz,
0, // CE value (Shimadzu SRM only)
spectrumProductFilter.FilterWidth,
source,
Extractor,
true,
true,
MinTime,
MaxTime);
listChromKeys.Add(key);
}
}
}
public bool GetDriftRange(out double minDrift, out double maxDrift, ChromSource sourceType)
{
minDrift = double.MaxValue;
maxDrift = double.MinValue;
var hasDriftInfo = false;
foreach (var transition in ScanProvider.Transitions)
{
if (!transition.IonMobilityValue.HasValue || !transition.IonMobilityExtractionWidth.HasValue)
{
// Accept all values
minDrift = double.MinValue;
maxDrift = double.MaxValue;
}
else if (sourceType == ChromSource.unknown || transition.Source == sourceType)
{
// Products and precursors may have different expected drift time values in Waters MsE
double startDrift = transition.IonMobilityValue.Value -
transition.IonMobilityExtractionWidth.Value / 2;
double endDrift = startDrift + transition.IonMobilityExtractionWidth.Value;
minDrift = Math.Min(minDrift, startDrift);
maxDrift = Math.Max(maxDrift, endDrift);
hasDriftInfo = true;
}
}
return(hasDriftInfo);
}
private void AddChromKeys(ChromSource source, SpectrumProductFilter[] productFilters, bool highEnergy,
List <ChromKey> listChromKeys)
{
if (null != productFilters)
{
var ionMobilityFilter = GetIonMobilityWindow();
foreach (var spectrumProductFilter in productFilters)
{
spectrumProductFilter.FilterId = listChromKeys.Count;
var key = new ChromKey(ModifiedSequence,
Q1,
ionMobilityFilter.ApplyOffset(highEnergy ? spectrumProductFilter.HighEnergyIonMobilityValueOffset : 0),
spectrumProductFilter.TargetMz,
0, // CE value (Shimadzu SRM only)
spectrumProductFilter.FilterWidth,
source,
Extractor,
true,
true);
if (_filterByTime)
{
key = key.ChangeOptionalTimes(_minTime, _maxTime);
}
listChromKeys.Add(key);
}
}
}
private ChromatogramRequestDocumentChromatogramGroup MakeChromatogramRequestDocumentChromatogramGroup(
ChromSource chromSource, bool calculateMassErrors, IEnumerable <ChromatogramRequestDocumentChromatogramGroupChromatogram> chromatograms)
{
ChromatogramRequestDocumentChromatogramGroup docFilterPair = new ChromatogramRequestDocumentChromatogramGroup
{
ModifiedSequence = ModifiedSequence != null?ModifiedSequence.ToString() : null,
PrecursorMz = Q1.RawValue, // A negative ion mode precursor will be serialized as a negative mz value
MassErrors = calculateMassErrors,
};
switch (Extractor)
{
case ChromExtractor.base_peak:
docFilterPair.Extractor = RemoteApi.GeneratedCode.ChromExtractor.BasePeak;
break;
case ChromExtractor.summed:
docFilterPair.Extractor = RemoteApi.GeneratedCode.ChromExtractor.Summed;
break;
}
if (MinTime.HasValue)
{
docFilterPair.MinTime = MinTime.Value;
docFilterPair.MinTimeSpecified = true;
}
if (MaxTime.HasValue)
{
docFilterPair.MaxTime = MaxTime.Value;
docFilterPair.MaxTimeSpecified = true;
}
if (MinIonMobilityValue.HasValue && MaxIonMobilityValue.HasValue)
{
docFilterPair.DriftTime = (MinIonMobilityValue.Value + MaxIonMobilityValue.Value) / 2;
if (ChromSource.fragment == chromSource) // Use high energy offset for fragments
{
docFilterPair.DriftTime += HighEnergyIonMobilityValueOffset;
}
docFilterPair.DriftTimeSpecified = true;
docFilterPair.DriftTimeWindow = MaxIonMobilityValue.Value - MinIonMobilityValue.Value;
docFilterPair.DriftTimeWindowSpecified = true;
}
switch (chromSource)
{
case ChromSource.ms1:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Ms1;
break;
case ChromSource.fragment:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Ms2;
break;
case ChromSource.sim:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Sim;
break;
}
docFilterPair.Chromatogram = chromatograms.ToArray();
return(docFilterPair);
}
private ChromatogramRequestDocumentChromatogramGroup MakeChromatogramRequestDocumentChromatogramGroup(
ChromSource chromSource, bool calculateMassErrors, IEnumerable <ChromatogramRequestDocumentChromatogramGroupChromatogram> chromatograms)
{
ChromatogramRequestDocumentChromatogramGroup docFilterPair = new ChromatogramRequestDocumentChromatogramGroup
{
ModifiedSequence = ModifiedSequence,
PrecursorMz = Q1,
MassErrors = calculateMassErrors,
};
switch (Extractor)
{
case ChromExtractor.base_peak:
docFilterPair.Extractor = RemoteApi.GeneratedCode.ChromExtractor.BasePeak;
break;
case ChromExtractor.summed:
docFilterPair.Extractor = RemoteApi.GeneratedCode.ChromExtractor.Summed;
break;
}
if (MinTime.HasValue)
{
docFilterPair.MinTime = MinTime.Value;
docFilterPair.MinTimeSpecified = true;
}
if (MaxTime.HasValue)
{
docFilterPair.MaxTime = MaxTime.Value;
docFilterPair.MaxTimeSpecified = true;
}
if (MinDriftTimeMsec.HasValue && MaxDriftTimeMsec.HasValue)
{
docFilterPair.DriftTime = (MinDriftTimeMsec.Value + MaxDriftTimeMsec.Value) / 2;
if (ChromSource.fragment == chromSource && HighEnergyDriftTimeOffsetMsec.HasValue)
{
docFilterPair.DriftTime += HighEnergyDriftTimeOffsetMsec.Value;
}
docFilterPair.DriftTimeSpecified = true;
docFilterPair.DriftTimeWindow = MaxDriftTimeMsec.Value - MinDriftTimeMsec.Value;
docFilterPair.DriftTimeWindowSpecified = true;
}
switch (chromSource)
{
case ChromSource.ms1:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Ms1;
break;
case ChromSource.fragment:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Ms2;
break;
case ChromSource.sim:
docFilterPair.Source = RemoteApi.GeneratedCode.ChromSource.Sim;
break;
}
docFilterPair.Chromatogram = chromatograms.ToArray();
return(docFilterPair);
}
private MsDataFileScanIds _msDataFileScanIds; // Indexed container of MsDataFileImpl ids
#endregion Fields
#region Constructors
public ScanProvider(string docFilePath, MsDataFileUri dataFilePath, ChromSource source,
float[] times, TransitionFullScanInfo[] transitions, Func<MsDataFileScanIds> getMsDataFileScanIds)
{
DocFilePath = docFilePath;
DataFilePath = dataFilePath;
Source = source;
Times = times;
Transitions = transitions;
_getMsDataFileScanIds = getMsDataFileScanIds;
}
public ScanProvider(string docFilePath, MsDataFileUri dataFilePath, ChromSource source,
IList <float> times, TransitionFullScanInfo[] transitions, MeasuredResults measuredResults, Func <MsDataFileScanIds> getMsDataFileScanIds)
{
DocFilePath = docFilePath;
DataFilePath = dataFilePath;
Source = source;
Times = times;
Transitions = transitions;
_measuredResultsReference = new WeakReference <MeasuredResults>(measuredResults);
_getMsDataFileScanIds = getMsDataFileScanIds;
}
public ChorusScanProvider(string docFilePath, ChorusUrl chorusUrl, ChromSource source, float[] times,
TransitionFullScanInfo[] transitions)
{
ChorusUrl = chorusUrl;
DocFilePath = docFilePath;
DataFilePath = chorusUrl;
Source = source;
Times = times;
Transitions = transitions;
_chorusSession = new ChorusSession();
}
public ChorusScanProvider(string docFilePath, ChorusUrl chorusUrl, ChromSource source, float[] times,
TransitionFullScanInfo[] transitions)
{
ChorusUrl = chorusUrl;
DocFilePath = docFilePath;
DataFilePath = chorusUrl;
Source = source;
Times = times;
Transitions = transitions;
_chorusSession = new ChorusSession();
}
public ScanProvider(string docFilePath, MsDataFileUri dataFilePath, ChromSource source,
float[] times, TransitionFullScanInfo[] transitions, Func <MsDataFileScanIds> getMsDataFileScanIds)
{
DocFilePath = docFilePath;
DataFilePath = dataFilePath;
Source = source;
Times = times;
Transitions = transitions;
_getMsDataFileScanIds = getMsDataFileScanIds;
}
public MsDataSpectrum[] GetSpectra(ChorusUrl chorusUrl, ChromSource source,
SignedMz precursor, int scanId)
{
string strSource;
int msLevel = 1;
// ReSharper disable NonLocalizedString
switch (source)
{
case ChromSource.ms1:
strSource = "ms1";
break;
case ChromSource.sim:
strSource = "sim";
break;
case ChromSource.fragment:
strSource = "ms2";
msLevel = 2;
break;
default:
throw new ArgumentException("Unknown source " + source);
}
string strUri = string.Format(CultureInfo.InvariantCulture,
"{0}/skyline/api/chroextract-drift/file/{1}/source/{2}/precursor/{3}/{4}",
chorusUrl.ServerUrl,
chorusUrl.FileId,
strSource,
precursor.RawValue, // This will be a negative value for negative ion mode data
scanId);
// ReSharper restore NonLocalizedString
var webRequest = (HttpWebRequest)WebRequest.Create(new Uri(strUri));
AddAuthHeader(ChorusAccount, webRequest);
return(SendRequest(webRequest, response =>
{
string strResponse = string.Empty;
var responseStream = response.GetResponseStream();
if (null != responseStream)
{
var streamReader = new StreamReader(responseStream);
strResponse = streamReader.ReadToEnd();
}
JObject jObject = JsonConvert.DeserializeObject <JObject>(strResponse);
JArray array = (JArray)jObject["results"]; // Not L10N
return array.OfType <JObject>().Select(obj => GetSpectrumFromJObject(obj, msLevel)).ToArray();
}));
}
public ChorusScanProvider(string docFilePath, ChorusUrl chorusUrl, ChromSource source, IList <float> times,
TransitionFullScanInfo[] transitions)
{
ChorusUrl = chorusUrl;
DocFilePath = docFilePath;
DataFilePath = chorusUrl;
Source = source;
Times = times;
Transitions = transitions;
ChorusAccount chorusAccount = ChorusUrl.FindChorusAccount(Settings.Default.RemoteAccountList);
_chorusSession = new ChorusSession(chorusAccount);
}
public IList <int> GetScanIndexes(ChromSource source)
{
if (ScanProvider != null)
{
foreach (var transition in ScanProvider.Transitions)
{
if (transition.Source == source)
{
return(transition.ScanIndexes);
}
}
}
return(null);
}
public TimeIntensities GetTimeIntensities(ChromSource source)
{
if (ScanProvider != null)
{
foreach (var transition in ScanProvider.Transitions)
{
if (transition.Source == source)
{
return(transition.TimeIntensities);
}
}
}
return(null);
}
public void UpdateScanProvider(IScanProvider scanProvider, int transitionIndex, int scanIndex)
{
ScanProvider.SetScanProvider(scanProvider);
if (scanProvider != null)
{
Source = scanProvider.Transitions[transitionIndex].Source;
Assume.IsTrue(Source == ScanProvider.Source);
TransitionIndex = transitionIndex;
ScanIndex = scanIndex;
FileName = scanProvider.DataFilePath.GetFileName();
}
else
{
MsDataSpectra = null;
FileName = null;
}
}
public void SelectScanType(ChromSource source)
{
comboBoxScanType.SelectedItem = _msDataFileScanHelper.NameFromSource(source);
}
private bool IsMs1(ChromSource source)
{
return(source != ChromSource.fragment); // TODO: source == ChromSource.ms1 || source == ChromSource.sim;
}
private static void SetScanType(ChromSource source, double x, double y)
{
RunUI(() => SkylineWindow.GraphFullScan.SelectScanType(source));
CheckFullScanSelection(x, y);
}
public IList <int> GetScanIndexes(ChromSource source)
{
return(GetTimeIntensities(source)?.ScanIds);
}
public string NameFromSource(ChromSource source)
{
return(SourceNames[(int)source]);
}
private static void SetScanType(ChromSource source, double x, double y)
{
RunUI(() => SkylineWindow.GraphFullScan.SelectScanType(source));
CheckFullScanSelection(x, y);
}
public bool GetIonMobilityRange(out double minIonMobility, out double maxIonMobility, ChromSource sourceType)
{
minIonMobility = double.MaxValue;
maxIonMobility = double.MinValue;
var hasIonMobilityInfo = false;
foreach (var transition in ScanProvider.Transitions)
{
if (!transition._ionMobilityInfo.HasIonMobilityValue || !transition._ionMobilityInfo.IonMobilityExtractionWindowWidth.HasValue)
{
// Accept all values
minIonMobility = double.MinValue;
maxIonMobility = double.MaxValue;
}
else if (sourceType == ChromSource.unknown || transition.Source == sourceType)
{
// Products and precursors may have different expected ion mobility values in Waters MsE
double startIM = transition._ionMobilityInfo.IonMobility.Mobility.Value -
transition._ionMobilityInfo.IonMobilityExtractionWindowWidth.Value / 2;
double endIM = startIM + transition._ionMobilityInfo.IonMobilityExtractionWindowWidth.Value;
minIonMobility = Math.Min(minIonMobility, startIM);
maxIonMobility = Math.Max(maxIonMobility, endIM);
hasIonMobilityInfo = true;
}
}
return(hasIonMobilityInfo);
}
private ChromTransition MakeChromTransition(ChromSource chromSource)
{
return(new ChromTransition(0, 0, 0, 0, chromSource));
}
public void SelectScanType(ChromSource source)
{
comboBoxScanType.SelectedItem = _msDataFileScanHelper.NameFromSource(source);
}
public ChromDataCollectorSet(ChromSource chromSource, TimeSharing timeSharing,
ChromatogramLoadingStatus.TransitionData allChromData, BlockWriter blockWriter)
{
ChromSource = chromSource;
TypeOfScans = timeSharing;
PrecursorCollectorMap = new List<Tuple<PrecursorTextId, ChromDataCollector>>();
if (timeSharing == TimeSharing.shared)
{
SharedTimesCollector = new SortedBlockedList<float>();
ScanIdsCollector = new BlockedList<int>();
}
_allChromData = allChromData;
_blockWriter = blockWriter;
}
