public XicData(XicData copy)
{
OutputMeta = new XicOutputMeta(copy.OutputMeta);
Content = new List <XicUnit>();
foreach (XicUnit unit in copy.Content)
{
Content.Add(new XicUnit(unit));
}
}
public static void run(XicParameters parameters)
{
var jsonString = File.ReadAllText(parameters.jsonFilePath, Encoding.UTF8);
var validationErrors = JSONParser.ValidateJson(jsonString);
if (!validationErrors.IsNullOrEmpty())
{
var validationMessage = new StringBuilder("JSON validation error(s):\n");
foreach (var validationError in validationErrors)
{
if (validationError.ToString().Contains("ExcludedSchemaValidates"))
{
validationMessage.Append(
"Use M/Z and tolerance, M/Z start and M/Z end or sequence and tolerance, not a combination (with optional RT start and/or end).\n");
}
validationMessage.Append(
$"element start line number: {validationError.LineNumber}\n{validationError.ToString()}");
}
throw new RawFileParserException(validationMessage.ToString());
}
var xicData = JSONParser.ParseJSON(jsonString);
foreach (string rawFile in parameters.rawFileList)
{
var dataInstance = new XicData(xicData);
XicReader.ReadXic(rawFile, parameters.base64, dataInstance);
if (parameters.stdout)
{
StdOutputXicData(dataInstance);
}
else
{
// if outputDirectory has been defined, put output there.
string directory;
if (parameters.outputDirectory != null)
{
directory = parameters.outputDirectory;
}
// otherwise put output files into the same directory as the raw file input
else
{
directory = Path.GetDirectoryName(rawFile);
}
var outputFileName = Path.Combine(directory ?? throw new NoNullAllowedException(),
Path.GetFileNameWithoutExtension(rawFile) + ".json");
OutputXicData(dataInstance, outputFileName);
}
}
}
public static void ReadXic(string rawFilePath, bool base64, XicData xicData)
{
IRawDataPlus rawFile;
using (rawFile = RawFileReaderFactory.ReadFile(rawFilePath))
{
if (!rawFile.IsOpen)
{
throw new RawFileParserException("Unable to access the RAW file using the native Thermo library.");
}
// Check for any errors in the RAW file
if (rawFile.IsError)
{
throw new RawFileParserException(
$"Error opening ({rawFile.FileError}) - {rawFilePath}");
}
// Check if the RAW file is being acquired
if (rawFile.InAcquisition)
{
throw new RawFileParserException("RAW file still being acquired - " + rawFilePath);
}
// Get the number of instruments (controllers) present in the RAW file and set the
// selected instrument to the MS instrument, first instance of it
rawFile.SelectInstrument(Device.MS, 1);
// Get the first and last scan from the RAW file
var firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
var lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
// Get the start and end time from the RAW file
var startTime = rawFile.RunHeaderEx.StartTime;
var endTime = rawFile.RunHeaderEx.EndTime;
// Get the mass range from the RAW file
var minMass = rawFile.RunHeaderEx.LowMass;
var maxMass = rawFile.RunHeaderEx.HighMass;
// Update global metadata
xicData.OutputMeta.base64 = base64;
xicData.OutputMeta.timeunit = "minutes";
foreach (var xicUnit in xicData.Content)
{
IChromatogramSettings settings = null;
if (!xicUnit.Meta.MzStart.HasValue && !xicUnit.Meta.MzEnd.HasValue)
{
settings = new ChromatogramTraceSettings()
{
Filter = xicUnit.Meta.Filter ?? "ms"
};
}
if (!xicUnit.Meta.MzStart.HasValue)
{
xicUnit.Meta.MzStart = minMass;
}
if (!xicUnit.Meta.MzEnd.HasValue)
{
xicUnit.Meta.MzEnd = maxMass;
}
if (settings == null)
{
settings = new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = xicUnit.Meta.Filter ?? "ms",
MassRanges = new[]
{
new Range(xicUnit.Meta.MzStart.Value,
xicUnit.Meta.MzEnd.Value)
}
};
}
List <int> rtFilteredScans = null;
if (!xicUnit.Meta.RtStart.HasValue && !xicUnit.Meta.RtEnd.HasValue)
{
rtFilteredScans = new List <int>();
}
if (!xicUnit.Meta.RtStart.HasValue)
{
xicUnit.Meta.RtStart = startTime;
}
if (!xicUnit.Meta.RtEnd.HasValue)
{
xicUnit.Meta.RtEnd = endTime;
}
IChromatogramData data = null;
if (rtFilteredScans == null)
{
rtFilteredScans = rawFile.GetFilteredScansListByTimeRange(MsFilter,
xicUnit.Meta.RtStart.Value, xicUnit.Meta.RtEnd.Value);
if (rtFilteredScans.Count != 0)
{
data = GetChromatogramData(rawFile, settings, rtFilteredScans[0],
rtFilteredScans[rtFilteredScans.Count - 1]);
if (data != null && data.PositionsArray.Length == 1 && data.PositionsArray[0].Length == 1 &&
(Math.Abs(data.PositionsArray[0][0] - startTime) < 0.001 ||
Math.Abs(data.PositionsArray[0][0] - endTime) < 0.001))
{
Log.Warn(
$"Only the minimum or maximum retention time was returned. This is an indication that the provided retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}] lies outside the max. window [{startTime}-{endTime}]");
}
}
else
{
Log.Warn(
$"No scans found in retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}]. This is an indication that the provided retention time window lies outside the max. window [{startTime}-{endTime}]");
}
}
else
{
data = GetChromatogramData(rawFile, settings, firstScanNumber, lastScanNumber);
}
if (data != null)
{
var chromatogramTrace = ChromatogramSignal.FromChromatogramData(data);
if (chromatogramTrace[0].Scans.Count != 0)
{
if (!base64)
{
xicUnit.RetentionTimes = chromatogramTrace[0].Times;
xicUnit.Intensities = chromatogramTrace[0].Intensities;
}
else
{
xicUnit.RetentionTimes = GetBase64String(chromatogramTrace[0].Times);
xicUnit.Intensities = GetBase64String(chromatogramTrace[0].Intensities);
}
}
}
}
}
}
public static XicData ParseJSON(string jsonString)
{
List <JSONInputUnit> jsonIn;
XicData data = new XicData();
jsonIn = JsonConvert.DeserializeObject <List <JSONInputUnit> >(jsonString);
foreach (JSONInputUnit xic in jsonIn)
{
XicUnit xicUnit = null;
if (xic.HasSequence())
{
Peptide p = new Peptide(xic.Sequence);
xic.Mz = p.GetMz(xic.Charge);
}
if (xic.HasMz())
{
double delta;
switch (xic.ToleranceUnit.ToLower())
{
case "ppm":
delta = xic.Mz.Value * xic.Tolerance.Value * 1e-6;
break;
case "amu":
delta = xic.Tolerance.Value;
break;
case "mmu":
delta = xic.Tolerance.Value * 1e-3;
break;
case "da":
delta = xic.Tolerance.Value;
break;
case "":
delta = xic.Mz.Value * xic.Tolerance.Value * 1e-6;
break;
default:
delta = 10;
break;
}
xicUnit = new XicUnit(xic.Mz.Value - delta, xic.Mz.Value + delta, xic.RtStart,
xic.RtEnd, xic.Filter);
}
else if (xic.HasMzRange())
{
xicUnit = new XicUnit(xic.MzStart.Value, xic.MzEnd.Value, xic.RtStart, xic.RtEnd, xic.Filter);
}
if (xicUnit == null || !xicUnit.HasValidRanges())
{
throw new RawFileParserException(
$"Invalid M/Z and/or retention time range:\n{JsonConvert.SerializeObject(xic, Formatting.Indented)}");
}
data.Content.Add(xicUnit);
}
return(data);
}
private static void OutputXicData(XicData outputData, string outputFileName)
{
var outputString = JsonConvert.SerializeObject(outputData, Formatting.Indented);
File.WriteAllText(outputFileName, outputString);
}
private static void StdOutputXicData(XicData outputData)
{
var outputString = JsonConvert.SerializeObject(outputData, Formatting.Indented);
Console.WriteLine(outputString);
}
