private MsDataSpectrum GetSpectrumFromJObject(JObject jObject, int msLevel)
{
// ReSharper disable NonLocalizedString
string strMzs = jObject["mzs-base64"].ToString();
string strIntensities = jObject["intensities-base64"].ToString();
byte[] mzBytes = Convert.FromBase64String(strMzs);
byte[] intensityBytes = Convert.FromBase64String(strIntensities);
double[] mzs = PrimitiveArrays.FromBytes <double>(
PrimitiveArrays.ReverseBytesInBlocks(mzBytes, sizeof(double)));
float[] intensityFloats = PrimitiveArrays.FromBytes <float>(
PrimitiveArrays.ReverseBytesInBlocks(intensityBytes, sizeof(float)));
double[] intensities = intensityFloats.Select(f => (double)f).ToArray();
double? driftTime = null;
JToken jDriftTime;
if (jObject.TryGetValue("driftTime", out jDriftTime))
{
driftTime = jDriftTime.ToObject <double>();
}
MsDataSpectrum spectrum = new MsDataSpectrum
{
Index = jObject["index"].ToObject <int>(),
RetentionTime = jObject["rt"].ToObject <double>(),
Mzs = mzs,
Intensities = intensities,
DriftTimeMsec = driftTime,
};
return(spectrum);
// ReSharper restore NonLocalizedString
}
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]
}));
}
}
}
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 MsDataSpectrum GetSpectrumFromJObject(JObject jObject, int msLevel)
{
// ReSharper disable NonLocalizedString
string strMzs = jObject["mzs-base64"].ToString();
string strIntensities = jObject["intensities-base64"].ToString();
byte[] mzBytes = Convert.FromBase64String(strMzs);
byte[] intensityBytes = Convert.FromBase64String(strIntensities);
double[] mzs = PrimitiveArrays.FromBytes <double>(
PrimitiveArrays.ReverseBytesInBlocks(mzBytes, sizeof(double)));
float[] intensityFloats = PrimitiveArrays.FromBytes <float>(
PrimitiveArrays.ReverseBytesInBlocks(intensityBytes, sizeof(float)));
double[] intensities = intensityFloats.Select(f => (double)f).ToArray();
IonMobilityValue ionMobility = IonMobilityValue.EMPTY;
JToken jDriftTime;
if (jObject.TryGetValue("driftTime", out jDriftTime))
{
var driftTime = jDriftTime.ToObject <double>();
if (driftTime != 0)
{
ionMobility = IonMobilityValue.GetIonMobilityValue(driftTime, MsDataFileImpl.eIonMobilityUnits.drift_time_msec);
}
}
MsDataSpectrum spectrum = new MsDataSpectrum
{
Index = jObject["index"].ToObject <int>(),
RetentionTime = jObject["rt"].ToObject <double>(),
Mzs = mzs,
Intensities = intensities,
IonMobility = ionMobility,
};
return(spectrum);
// ReSharper restore NonLocalizedString
}
