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caeteracaetera
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Total Absorbance Chromatogram
1 parent 1755627 commit 0a1934c

3 files changed

Lines changed: 170 additions & 2 deletions

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‎MainClass.cs‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -409,6 +409,11 @@ private static void RegularParametersParsing(string[] args)
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"Don't use zlib compression for the m/z ratios and intensities. By default zlib compression is enabled.",
410410
v => parseInput.NoZlibCompression = v != null
411411
},
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{
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"a|allDetectors",
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"Extract additonal detector data: UV/PDA etc",
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v => parseInput.AllDetectors = v != null
416+
},
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{
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"l=|logging=", "Optional logging level: 0 for silent, 1 for verbose.",
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v => logFormatString = v

‎ParseInput.cs‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -65,6 +65,8 @@ public string RawFilePath
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public bool NoZlibCompression { get; set; }
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public bool AllDetectors { get; set; }
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6870
public LogFormat LogFormat { get; set; }
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public bool IgnoreInstrumentErrors { get; set; }
@@ -98,6 +100,7 @@ public ParseInput()
98100
NoZlibCompression = false;
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LogFormat = LogFormat.DEFAULT;
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IgnoreInstrumentErrors = false;
103+
AllDetectors = false;
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}
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103106
public ParseInput(string rawFilePath, string rawDirectoryPath, string outputDirectory, OutputFormat outputFormat

‎Writer/MzMlSpectrumWriter.cs‎

Lines changed: 162 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -640,6 +640,7 @@ private List<ChromatogramType> ConstructChromatograms(int firstScanNumber, int l
640640
{
641641
var chromatograms = new List<ChromatogramType>();
642642

643+
//MS chromatograms
643644
// Define the settings for getting the Base Peak chromatogram
644645
var settings = new ChromatogramTraceSettings(TraceType.BasePeak);
645646

@@ -671,8 +672,8 @@ private List<ChromatogramType> ConstructChromatograms(int firstScanNumber, int l
671672
};
672673
chromatogram.cvParam[0] = new CVParamType
673674
{
674-
accession = "MS:1000235",
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name = "total ion current chromatogram",
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accession = "MS:1000628",
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name = "basepeak chromatogram",
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cvRef = "MS",
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value = ""
678679
};
@@ -791,8 +792,167 @@ private List<ChromatogramType> ConstructChromatograms(int firstScanNumber, int l
791792

792793
chromatograms.Add(chromatogram);
793794
}
795+
794796
}
795797

798+
//UV chromatograms
799+
if (ParseInput.AllDetectors)
800+
{
801+
for (int nrI = 0; nrI < _rawFile.GetInstrumentCountOfType(Device.Pda); nrI++)
802+
{
803+
_rawFile.SelectInstrument(Device.Pda, nrI + 1);
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805+
var settingsPDA = new ChromatogramTraceSettings(TraceType.TotalAbsorbance);
806+
807+
var dataPDA = _rawFile.GetChromatogramData(new IChromatogramSettings[] { settingsPDA },
808+
firstScanNumber, lastScanNumber);
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810+
var tracePDA = ChromatogramSignal.FromChromatogramData(dataPDA);
811+
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for (var i = 0; i < tracePDA.Length; i++)
813+
{
814+
if (tracePDA[i].Length > 0)
815+
{
816+
// Binary data array list
817+
var binaryData = new List<BinaryDataArrayType>();
818+
819+
var chromatogram = new ChromatogramType
820+
{
821+
index = i.ToString(),
822+
id = String.Format("PDA_{0}_TotalAbsorbance_{1}", nrI, i),
823+
defaultArrayLength = 0,
824+
binaryDataArrayList = new BinaryDataArrayListType
825+
{
826+
count = "2",
827+
binaryDataArray = new BinaryDataArrayType[2]
828+
},
829+
cvParam = new CVParamType[1]
830+
};
831+
chromatogram.cvParam[0] = new CVParamType
832+
{
833+
accession = "MS:1000812",
834+
name = "absorption chromatogram",
835+
cvRef = "MS",
836+
value = ""
837+
};
838+
839+
// Chromatogram times
840+
if (!trace[i].Times.IsNullOrEmpty())
841+
{
842+
// Set the chromatogram default array length
843+
chromatogram.defaultArrayLength = trace[i].Times.Count;
844+
845+
var timesBinaryData =
846+
new BinaryDataArrayType
847+
{
848+
binary = ParseInput.NoZlibCompression
849+
? Get64BitArray(trace[i].Times)
850+
: GetZLib64BitArray(trace[i].Times)
851+
};
852+
timesBinaryData.encodedLength =
853+
(4 * Math.Ceiling((double)timesBinaryData
854+
.binary.Length / 3)).ToString(CultureInfo.InvariantCulture);
855+
var timesBinaryDataCvParams = new List<CVParamType>
856+
{
857+
new CVParamType
858+
{
859+
accession = "MS:1000595",
860+
name = "time array",
861+
cvRef = "MS",
862+
unitName = "minute",
863+
value = "",
864+
unitCvRef = "UO",
865+
unitAccession = "UO:0000031"
866+
},
867+
new CVParamType
868+
{
869+
accession = "MS:1000523", name = "64-bit float", cvRef = "MS", value = ""
870+
}
871+
};
872+
if (!ParseInput.NoZlibCompression)
873+
{
874+
timesBinaryDataCvParams.Add(
875+
new CVParamType
876+
{
877+
accession = "MS:1000574",
878+
name = "zlib compression",
879+
cvRef = "MS",
880+
value = ""
881+
});
882+
}
883+
884+
timesBinaryData.cvParam = timesBinaryDataCvParams.ToArray();
885+
886+
binaryData.Add(timesBinaryData);
887+
}
888+
889+
// Chromatogram intensities
890+
if (!trace[i].Times.IsNullOrEmpty())
891+
{
892+
// Set the spectrum default array length if necessary
893+
if (chromatogram.defaultArrayLength == 0)
894+
{
895+
chromatogram.defaultArrayLength = trace[i].Intensities.Count;
896+
}
897+
898+
var intensitiesBinaryData =
899+
new BinaryDataArrayType
900+
{
901+
binary = ParseInput.NoZlibCompression
902+
? Get64BitArray(trace[i].Intensities)
903+
: GetZLib64BitArray(trace[i].Intensities)
904+
};
905+
intensitiesBinaryData.encodedLength =
906+
(4 * Math.Ceiling((double)intensitiesBinaryData
907+
.binary.Length / 3)).ToString(CultureInfo.InvariantCulture);
908+
var intensitiesBinaryDataCvParams = new List<CVParamType>
909+
{
910+
new CVParamType
911+
{
912+
accession = "MS:1000515",
913+
name = "intensity array",
914+
cvRef = "MS",
915+
unitName = "absorbance unit",
916+
value = "",
917+
unitCvRef = "UO",
918+
unitAccession = "UO:0000269"
919+
},
920+
new CVParamType
921+
{
922+
accession = "MS:1000523", name = "64-bit float", cvRef = "MS", value = ""
923+
}
924+
};
925+
if (!ParseInput.NoZlibCompression)
926+
{
927+
intensitiesBinaryDataCvParams.Add(
928+
new CVParamType
929+
{
930+
accession = "MS:1000574",
931+
name = "zlib compression",
932+
cvRef = "MS",
933+
value = ""
934+
});
935+
}
936+
937+
intensitiesBinaryData.cvParam = intensitiesBinaryDataCvParams.ToArray();
938+
939+
binaryData.Add(intensitiesBinaryData);
940+
}
941+
942+
if (!binaryData.IsNullOrEmpty())
943+
{
944+
chromatogram.binaryDataArrayList = new BinaryDataArrayListType
945+
{
946+
count = binaryData.Count.ToString(),
947+
binaryDataArray = binaryData.ToArray()
948+
};
949+
}
950+
951+
chromatograms.Add(chromatogram);
952+
}
953+
}
954+
}
955+
}
796956
return chromatograms;
797957
}
798958

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