private SpectrumPeaksInfo.MI[] ReadSpectrum(ElibSpectrumInfo info, int sourceFileId)
{
if (sourceFileId < 0)
{
return(null);
}
return(_pooledSqliteConnection.ExecuteWithConnection(connection =>
{
HashSet <double> mzs = new HashSet <double>();
List <SpectrumPeaksInfo.MI> spectrum = new List <SpectrumPeaksInfo.MI>();
// First read all of the quantifiable transitions from the PeptideQuants table.
var peptideQuantSpectrum = ReadSpectrumFromPeptideQuants(connection, info);
if (peptideQuantSpectrum != null)
{
foreach (var mi in peptideQuantSpectrum)
{
if (mzs.Add(mi.Mz))
{
spectrum.Add(mi);
}
}
}
// Then read the spectrum for the specific file
var entriesSpectrum = ReadSpectrumFromEntriesTable(connection, info, sourceFileId);
foreach (var mi in entriesSpectrum)
{
if (mzs.Add(mi.Mz))
{
var miToAdd = mi;
if (peptideQuantSpectrum != null)
{
// If we successfully read from the PeptideQuants table, then the
// rest of the mzs we find in the entries table are non-quantitative.
miToAdd.Quantitative = false;
}
else
{
// If we were unable to read from the PeptideQuants table, then
// the non-quantitative transitions are the ones with really low intensity.
miToAdd.Quantitative = miToAdd.Intensity >= MIN_QUANTITATIVE_INTENSITY;
}
spectrum.Add(miToAdd);
}
}
return spectrum.ToArray();
}));
}
private bool LoadFromCache(ILoadMonitor loader)
{
if (!loader.StreamManager.IsCached(FilePath, CachePath))
{
return(false);
}
try
{
ValueCache valueCache = new ValueCache();
using (var stream = loader.StreamManager.CreateStream(CachePath, FileMode.Open, true))
{
int version = PrimitiveArrays.ReadOneValue <int>(stream);
if (version != FORMAT_VERSION_CACHE)
{
return(false);
}
int fileCount = PrimitiveArrays.ReadOneValue <int>(stream);
List <String> sourceFiles = new List <string>(fileCount);
while (sourceFiles.Count < fileCount)
{
int byteCount = PrimitiveArrays.ReadOneValue <int>(stream);
byte[] bytes = new byte[byteCount];
stream.Read(bytes, 0, bytes.Length);
sourceFiles.Add(Encoding.UTF8.GetString(bytes));
}
int spectrumInfoCount = PrimitiveArrays.ReadOneValue <int>(stream);
_sourceFiles = ImmutableList.ValueOf(sourceFiles);
List <ElibSpectrumInfo> spectrumInfos = new List <ElibSpectrumInfo>();
while (spectrumInfos.Count < spectrumInfoCount)
{
spectrumInfos.Add(ElibSpectrumInfo.Read(valueCache, stream));
}
SetLibraryEntries(spectrumInfos);
return(true);
}
}
catch (Exception exception)
{
Trace.TraceWarning(@"Exception loading cache: {0}", exception);
return(false);
}
}
protected override SpectrumHeaderInfo CreateSpectrumHeaderInfo(ElibSpectrumInfo info)
{
return(new ChromLibSpectrumHeaderInfo(Name, 0));
}
private IEnumerable <SpectrumPeaksInfo.MI> ReadSpectrumFromEntriesTable(SQLiteConnection connection, ElibSpectrumInfo info,
int sourceFileId)
{
using (var cmd = new SQLiteCommand(connection))
{
cmd.CommandText =
@"SELECT MassEncodedLength, MassArray, IntensityEncodedLength, IntensityArray FROM entries WHERE PrecursorCharge = ? AND PeptideModSeq = ? AND SourceFile = ?";
cmd.Parameters.Add(new SQLiteParameter(DbType.Int32)
{
Value = info.Key.Charge
});
cmd.Parameters.Add(new SQLiteParameter(DbType.String)
{
Value = info.PeptideModSeq
});
cmd.Parameters.Add(new SQLiteParameter(DbType.String)
{
Value = _sourceFiles[sourceFileId]
});
using (var reader = cmd.ExecuteReader())
{
if (reader.Read())
{
double[] mzs = PrimitiveArrays.FromBytes <double>(
PrimitiveArrays.ReverseBytesInBlocks(
UncompressEncyclopeDiaData((byte[])reader.GetValue(1), reader.GetInt32(0)),
sizeof(double)));
float[] intensities =
PrimitiveArrays.FromBytes <float>(PrimitiveArrays.ReverseBytesInBlocks(
UncompressEncyclopeDiaData((byte[])reader.GetValue(3), reader.GetInt32(2)),
sizeof(float)));
return(mzs.Select((mz, index) => new SpectrumPeaksInfo.MI
{
Mz = mz,
Intensity = intensities[index],
}) // CONSIDER(bspratt): annotation?
.ToArray());
}
return(null);
}
}
}
private IEnumerable <SpectrumPeaksInfo.MI> ReadSpectrumFromPeptideQuants(SQLiteConnection connection, ElibSpectrumInfo info)
{
using (var cmd = new SQLiteCommand(connection))
{
cmd.CommandText = @"SELECT QuantIonMassLength, QuantIonMassArray, QuantIonIntensityLength, QuantIonIntensityArray FROM peptidequants WHERE PrecursorCharge = ? AND PeptideModSeq = ?";
cmd.Parameters.Add(new SQLiteParameter(DbType.Int32)
{
Value = info.Key.Charge
});
cmd.Parameters.Add(new SQLiteParameter(DbType.String)
{
Value = info.PeptideModSeq
});
SQLiteDataReader reader;
try
{
reader = cmd.ExecuteReader();
}
catch (DbException)
{
// Older .elib files do not have these columns, so just return null
return(null);
}
using (reader)
{
if (!reader.Read())
{
// None of the transitions are considered Quantifiable.
return(new SpectrumPeaksInfo.MI[0]);
}
double[] mzs = PrimitiveArrays.FromBytes <double>(
PrimitiveArrays.ReverseBytesInBlocks(
UncompressEncyclopeDiaData((byte[])reader.GetValue(1), reader.GetInt32(0)),
sizeof(double)));
float[] intensities =
PrimitiveArrays.FromBytes <float>(PrimitiveArrays.ReverseBytesInBlocks(
UncompressEncyclopeDiaData((byte[])reader.GetValue(3), reader.GetInt32(2)), sizeof(float)));
return(mzs.Select(
(mz, index) => new SpectrumPeaksInfo.MI {
Mz = mz, Intensity = intensities[index]
}));
}
}
}
protected override SpectrumPeaksInfo.MI[] ReadSpectrum(ElibSpectrumInfo info)
{
return(ReadSpectrum(info, info.BestFileId));
}
