public ChromLibSpectrumInfo(LibKey key, int id, double peakArea, IndexedRetentionTimes retentionTimesByFileId, IEnumerable<SpectrumPeaksInfo.MI> transitionAreas)
{
Key = key;
Id = id;
PeakArea = peakArea;
RetentionTimesByFileId = retentionTimesByFileId;
TransitionAreas = ImmutableList.ValueOf(transitionAreas) ?? ImmutableList.Empty<SpectrumPeaksInfo.MI>();
}
public ChromLibSpectrumInfo(LibKey key, int id, double peakArea, IndexedRetentionTimes retentionTimesByFileId, IEnumerable <SpectrumPeaksInfo.MI> transitionAreas)
{
Key = key;
Id = id;
PeakArea = peakArea;
RetentionTimesByFileId = retentionTimesByFileId;
TransitionAreas = ImmutableList.ValueOf(transitionAreas) ?? ImmutableList.Empty <SpectrumPeaksInfo.MI>();
}
public static ChromLibSpectrumInfo Read(Stream stream)
{
LibKey key = LibKey.Read(stream);
int id = PrimitiveArrays.ReadOneValue <int>(stream);
double peakArea = PrimitiveArrays.ReadOneValue <double>(stream);
var retentionTimesByFileId = IndexedRetentionTimes.Read(stream);
int mzCount = PrimitiveArrays.ReadOneValue <int>(stream);
var mzs = PrimitiveArrays.Read <double>(stream, mzCount);
var areas = PrimitiveArrays.Read <float>(stream, mzCount);
var mzAreas = ImmutableList.ValueOf(Enumerable.Range(0, mzCount)
.Select(index => new SpectrumPeaksInfo.MI
{
Mz = mzs[index],
Intensity = areas[index]
}));
return(new ChromLibSpectrumInfo(key, id, peakArea, retentionTimesByFileId, mzAreas));
}
private bool LoadLibraryFromDatabase(ILoadMonitor loader)
{
try
{
var status = new ProgressStatus(string.Format(Resources.ChromatogramLibrary_LoadLibraryFromDatabase_Reading_precursors_from__0_, Name));
loader.UpdateProgress(status);
// _pooledSessionFactory = new PooledSessionFactory(loader.StreamManager.ConnectionPool,
// typeof (ChromLibEntity), FilePath);
using (var session = _pooledSessionFactory.Connection.OpenSession())
{
var libInfo =
session.CreateSQLQuery("SELECT PanoramaServer, LibraryRevision, SchemaVersion FROM LibInfo") // Not L10N
.UniqueResult <object[]>();
PanoramaServer = Convert.ToString(libInfo[0]);
LibraryRevision = Convert.ToInt32(libInfo[1]);
SchemaVersion = Convert.ToString(libInfo[2]);
try
{
var irtQuery = session.CreateQuery("SELECT PeptideModSeq, Irt, TimeSource FROM IrtLibrary"); // Not L10N
_libraryIrts = irtQuery.List <object[]>().Select(
irt => new ChromatogramLibraryIrt(new Target((string)irt[0]), (TimeSource)irt[2], Convert.ToDouble(irt[1]))
).ToArray();
}
catch (GenericADOException)
{
// IrtLibrary table probably doesn't exist
}
var rtQuery = session.CreateQuery("SELECT Precursor.Id, SampleFile.Id, RetentionTime FROM PrecursorRetentionTime"); // Not L10N
var rtDictionary = new Dictionary <int, List <KeyValuePair <int, double> > >(); // PrecursorId -> [SampleFileId -> RetentionTime]
foreach (object[] row in rtQuery.List <object[]>())
{
var precursorId = (int)row[0];
var sampleFileId = (int)row[1];
var rt = Convert.ToDouble(row[2]);
if (!rtDictionary.ContainsKey(precursorId))
{
rtDictionary.Add(precursorId, new List <KeyValuePair <int, double> >());
}
rtDictionary[precursorId].Add(new KeyValuePair <int, double>(sampleFileId, rt));
}
var precursorQuery =
session.CreateQuery("SELECT P.Id, P.ModifiedSequence, P.Charge, P.TotalArea FROM " + typeof(Precursor) + // Not L10N
" P"); // Not L10N
var allTransitionAreas = ReadAllTransitionAreas(session);
var spectrumInfos = new List <ChromLibSpectrumInfo>();
foreach (object[] row in precursorQuery.List <object[]>())
{
var id = (int)row[0];
if (row[1] == null || row[2] == null)
{
continue; // Throw an error?
}
var modifiedSequence = new Target((string)row[1]);
var charge = (int)row[2]; // TODO(bspratt) generalize chromatogram libs to small mol
double totalArea = Convert.ToDouble(row[3]);
List <KeyValuePair <int, double> > retentionTimes;
var indexedRetentionTimes = new IndexedRetentionTimes();
if (rtDictionary.TryGetValue(id, out retentionTimes))
{
indexedRetentionTimes = new IndexedRetentionTimes(retentionTimes);
}
Target modSeqNormal;
try
{
modSeqNormal = SequenceMassCalc.NormalizeModifiedSequence(modifiedSequence);
}
catch (ArgumentException)
{
continue;
}
var libKey = new LibKey(modSeqNormal.Sequence, charge);
IList <SpectrumPeaksInfo.MI> transitionAreas;
allTransitionAreas.TryGetValue(id, out transitionAreas);
spectrumInfos.Add(new ChromLibSpectrumInfo(libKey, id, totalArea, indexedRetentionTimes, transitionAreas));
}
SetLibraryEntries(spectrumInfos);
var sampleFileQuery =
session.CreateQuery("SELECT Id, FilePath, SampleName, AcquiredTime, ModifiedTime, InstrumentIonizationType, " + // Not L10N
"InstrumentAnalyzer, InstrumentDetector FROM SampleFile"); // Not L10N
var sampleFiles = new List <ChromatogramLibrarySourceInfo>();
foreach (object[] row in sampleFileQuery.List <object[]>())
{
var id = (int)row[0];
if (row[1] == null || row[2] == null)
{
continue; // Throw an error?
}
var filePath = row[1].ToString();
var sampleName = row[2].ToString();
var acquiredTime = row[3] != null ? row[3].ToString() : string.Empty;
var modifiedTime = row[4] != null ? row[4].ToString() : string.Empty;
var instrumentIonizationType = row[5] != null ? row[5].ToString() : string.Empty;
var instrumentAnalyzer = row[6] != null ? row[6].ToString() : string.Empty;
var instrumentDetector = row[7] != null ? row[7].ToString() : string.Empty;
sampleFiles.Add(new ChromatogramLibrarySourceInfo(id, filePath, sampleName, acquiredTime, modifiedTime, instrumentIonizationType,
instrumentAnalyzer, instrumentDetector));
}
_librarySourceFiles = sampleFiles.ToArray();
loader.UpdateProgress(status.Complete());
return(true);
}
}
catch (Exception e)
{
Trace.TraceWarning(Resources.ChromatogramLibrary_LoadLibraryFromDatabase_Error_loading_chromatogram_library__0_, e);
return(false);
}
}
