コード例 #1
0
ファイル: ChorusSession.cs プロジェクト: tomas-pluskal/pwiz
        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
        }
コード例 #2
0
 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]
             }));
         }
     }
 }
コード例 #3
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);
         }
     }
 }
コード例 #4
0
ファイル: ChorusSession.cs プロジェクト: zrolfs/pwiz
        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
        }