private ChromatogramRequestDocument GetChromatogramRequestDocument(SpectrumFilter spectrumFilter)
{
ChromatogramRequestDocument chromatogramRequestDocument = spectrumFilter.ToChromatogramRequestDocument();
if (null == _retentionTimePredictor)
{
return(chromatogramRequestDocument);
}
var peptidesBySequence = new Dictionary <string, PeptideDocNode>();
foreach (var peptide in _srmDocument.Molecules)
{
peptidesBySequence[peptide.RawTextId] = peptide;
}
var chromatogramGroups = new List <ChromatogramRequestDocumentChromatogramGroup>();
foreach (var chromatogramGroup in chromatogramRequestDocument.ChromatogramGroup)
{
PeptideDocNode peptideDocNode = null;
if (!string.IsNullOrEmpty(chromatogramGroup.ModifiedSequence))
{
peptidesBySequence.TryGetValue(chromatogramGroup.ModifiedSequence, out peptideDocNode);
}
bool isFirstPassPeptide = peptideDocNode != null &&
_retentionTimePredictor.IsFirstPassPeptide(peptideDocNode);
if (_firstPass == isFirstPassPeptide)
{
chromatogramGroups.Add(chromatogramGroup);
}
}
chromatogramRequestDocument.ChromatogramGroup = chromatogramGroups.ToArray();
return(chromatogramRequestDocument);
}
public ChromatogramGeneratorTask(ChromTaskList chromTaskList, ChorusAccount chorusAccount, ChorusUrl chorusUrl,
ChromatogramRequestDocument chromatogramRequestDocument)
{
ChromTaskList = chromTaskList;
ChorusAccount = chorusAccount;
ChorusUrl = chorusUrl;
ChromatogramRequestDocument = chromatogramRequestDocument;
}
public ChromatogramCache GenerateChromatograms(ChorusAccount chorusAccount,
ChorusUrl chorusUrl,
ChromatogramRequestDocument chromatogramRequestDocument)
{
var webRequest = (HttpWebRequest)WebRequest.Create(chorusUrl.GetChromExtractionUri());
AddAuthHeader(chorusAccount, webRequest);
webRequest.Method = "POST"; // Not L10N
var xmlSerializer = new XmlSerializer(typeof(ChromatogramRequestDocument));
xmlSerializer.Serialize(webRequest.GetRequestStream(), chromatogramRequestDocument);
webRequest.GetRequestStream().Close();
return(SendRequest(webRequest, response =>
{
MemoryStream memoryStream = new MemoryStream();
var responseStream = response.GetResponseStream();
if (responseStream != null)
{
byte[] buffer = new byte[65536];
int count;
while ((count = responseStream.Read(buffer, 0, buffer.Length)) != 0)
{
memoryStream.Write(buffer, 0, count);
}
}
if (0 == memoryStream.Length)
{
if (response.StatusCode != HttpStatusCode.OK)
{
throw new IOException(string.Format("Empty response: status = {0}", response.StatusCode)); // Not L10N
}
Debug.WriteLine("Zero byte response"); // Not L10N
return null;
}
ChromatogramCache.RawData rawData;
ChromatogramCache.LoadStructs(memoryStream, out rawData);
var chromCacheFile = rawData.ChromCacheFiles[0];
rawData.ChromCacheFiles = new[]
{
new ChromCachedFile(chorusUrl, chromCacheFile.Flags, chromCacheFile.FileWriteTime,
chromCacheFile.RunStartTime, chromCacheFile.MaxRetentionTime, chromCacheFile.MaxIntensity,
chromCacheFile.InstrumentInfoList),
};
return new ChromatogramCache(string.Empty, rawData,
new ChromatogramGeneratorTask.MemoryPooledStream(memoryStream));
}));
}
internal static IEnumerable <ChromKey> ListChromKeys(ChromatogramRequestDocument chromatogramRequestDocument)
{
foreach (var chromatogramGroup in chromatogramRequestDocument.ChromatogramGroup)
{
ChromSource chromSource;
switch (chromatogramGroup.Source)
{
case GeneratedCode.ChromSource.Ms1:
chromSource = ChromSource.ms1;
break;
case GeneratedCode.ChromSource.Ms2:
chromSource = ChromSource.fragment;
break;
case GeneratedCode.ChromSource.Sim:
chromSource = ChromSource.sim;
break;
default:
chromSource = ChromSource.unknown;
break;
}
ChromExtractor chromExtractor;
switch (chromatogramGroup.Extractor)
{
case GeneratedCode.ChromExtractor.BasePeak:
chromExtractor = ChromExtractor.base_peak;
break;
default:
chromExtractor = ChromExtractor.summed;
break;
}
foreach (var chromatogram in chromatogramGroup.Chromatogram)
{
yield return(new ChromKey(chromatogramGroup.ModifiedSequence, new SignedMz(chromatogramGroup.PrecursorMz),
null, 0,
new SignedMz(chromatogram.ProductMz), 0, chromatogram.MzWindow, chromSource, chromExtractor, false, false,
null, null)); // Optional retention and drift times not used in this provider
}
}
}
public static List <ChromatogramRequestDocument> ChunkChromatogramRequest(ChromatogramRequestDocument chromatogramRequestDocument, int targetChromatogramCount)
{
var chunks = new List <ChromatogramRequestDocument>();
List <ChromatogramRequestDocumentChromatogramGroup> currentGroups = new List <ChromatogramRequestDocumentChromatogramGroup>();
int currentChromatogramCount = 0;
foreach (var chromatogramGroup in chromatogramRequestDocument.ChromatogramGroup)
{
currentGroups.Add(chromatogramGroup);
currentChromatogramCount += chromatogramGroup.Chromatogram.Length;
if (currentChromatogramCount >= targetChromatogramCount)
{
chunks.Add(chromatogramRequestDocument.CloneWithChromatogramGroups(currentGroups));
currentGroups.Clear();
currentChromatogramCount = 0;
}
}
if (currentGroups.Any())
{
chunks.Add(chromatogramRequestDocument.CloneWithChromatogramGroups(currentGroups));
}
return(chunks);
}
public ChromatogramRequestDocument ToChromatogramRequestDocument()
{
var document = new ChromatogramRequestDocument
{
MaxMz = _instrument.MaxMz,
MinMz = _instrument.MinMz,
MzMatchTolerance = _instrument.MzMatchTolerance,
};
if (_minTime.HasValue)
{
document.MinTime = _minTime.Value;
document.MinTimeSpecified = true;
}
if (_maxTime.HasValue)
{
document.MaxTime = _maxTime.Value;
document.MaxTimeSpecified = true;
}
switch (_acquisitionMethod)
{
case FullScanAcquisitionMethod.DIA:
document.Ms2FullScanAcquisitionMethod = Ms2FullScanAcquisitionMethod.DIA;
break;
case FullScanAcquisitionMethod.None:
document.Ms2FullScanAcquisitionMethod = Ms2FullScanAcquisitionMethod.None;
break;
case FullScanAcquisitionMethod.Targeted:
document.Ms2FullScanAcquisitionMethod = Ms2FullScanAcquisitionMethod.Targeted;
break;
}
if (null != _filterMzValues)
{
var chromatogramGroups = new List <ChromatogramRequestDocumentChromatogramGroup>();
var sources = new HashSet <RemoteApi.GeneratedCode.ChromSource>();
if (EnabledMs)
{
sources.Add(RemoteApi.GeneratedCode.ChromSource.Ms1);
}
if (EnabledMsMs)
{
sources.Add(RemoteApi.GeneratedCode.ChromSource.Ms2);
}
foreach (var filterPair in _filterMzValues)
{
foreach (var chromatogramGroup in filterPair.ToChromatogramRequestDocumentChromatogramGroups())
{
if (chromatogramGroup.PrecursorMz == 0 || sources.Contains(chromatogramGroup.Source))
{
chromatogramGroups.Add(chromatogramGroup);
}
}
}
document.ChromatogramGroup = chromatogramGroups.ToArray();
}
var isolationScheme = _fullScan.IsolationScheme;
if (null != _fullScan.IsolationScheme)
{
document.IsolationScheme = new ChromatogramRequestDocumentIsolationScheme();
if (_fullScan.IsolationScheme.PrecursorFilter.HasValue)
{
document.IsolationScheme.PrecursorFilter = _fullScan.IsolationScheme.PrecursorFilter.Value;
document.IsolationScheme.PrecursorFilterSpecified = true;
}
if (isolationScheme.PrecursorRightFilter.HasValue)
{
document.IsolationScheme.PrecursorRightFilter = isolationScheme.PrecursorRightFilter.Value;
document.IsolationScheme.PrecursorRightFilterSpecified = true;
}
if (null != isolationScheme.SpecialHandling)
{
document.IsolationScheme.SpecialHandling = isolationScheme.SpecialHandling;
}
if (isolationScheme.WindowsPerScan.HasValue)
{
document.IsolationScheme.WindowsPerScan = isolationScheme.WindowsPerScan.Value;
document.IsolationScheme.WindowsPerScanSpecified = true;
}
document.IsolationScheme.IsolationWindow =
isolationScheme.PrespecifiedIsolationWindows.Select(
isolationWindow =>
{
var result = new ChromatogramRequestDocumentIsolationSchemeIsolationWindow
{
Start = isolationWindow.Start,
End = isolationWindow.End,
};
if (isolationWindow.Target.HasValue)
{
result.Target = isolationWindow.Target.Value;
}
if (isolationWindow.StartMargin.HasValue)
{
result.StartMargin = isolationWindow.StartMargin.Value;
}
if (isolationWindow.EndMargin.HasValue)
{
result.EndMargin = isolationWindow.EndMargin.Value;
}
return(result);
}).ToArray();
}
return(document);
}
internal static IEnumerable <ChromKey> ListChromKeys(ChromatogramRequestDocument chromatogramRequestDocument)
{
return(ChromatogramRequestProvider.ListChromKeys(chromatogramRequestDocument));
}
