public TrailerExtraIndices(IRawDataPlus rawFile)
{
HeaderItem[] header = rawFile.GetTrailerExtraHeaderInformation();
for (int i = 0; i < header.Length; i++)
{
//Console.WriteLine("{0} {1}", header[i].Label, i);
if (header[i].Label.ToLower().Contains("injection time") & !header[i].Label.ToLower().Contains("reagent"))
{
InjectionTime = i;
}
if (header[i].Label.ToLower().Contains("master scan") | header[i].Label.ToLower().Contains("master index"))
{
MasterScan = i;
}
if (header[i].Label.ToLower().Contains("monoisotopic"))
{
MonoisotopicMZ = i;
}
if (header[i].Label.ToLower().Contains("charge state"))
{
ChargeState = i;
}
if (header[i].Label.ToLower().Contains("hcd energy") & !header[i].Label.ToLower().Contains("ev"))
{
HCDEnergy = i;
}
if (header[i].Label.ToLower().Contains("sps"))
{
SPSMasses.Add(i);
}
}
}
public string GetMonoisotopicMz(int scanNumber)
{
var trailerFields = rawFile.GetTrailerExtraHeaderInformation();
var scanTrailer = rawFile.GetTrailerExtraInformation(scanNumber);
try
{
var idx = trailerFields
.Select((item, index) => new
{
name = item.Label.ToString().CleanRawfileTrailerHeader(),
Position = index
})
.First(x => x.name.Contains("MonoisotopicmZ")).Position;
return(scanTrailer.Values.ToArray()[idx]);
}
catch
{
return(null);
}
}
/// <summary>
/// implements
/// https://github.com/fgcz/rawrr/issues/43
/// </summary>
/// <param name="rawFile"></param>
/// <param name="filename"></param>
/// <param name="L"></param>
public static void WriteCentroidSpectrumAsRcode(this IRawDataPlus rawFile, string filename, List <int> L)
{
int count = 1;
var trailerFields = rawFile.GetTrailerExtraHeaderInformation();
int indexCharge = rawFile.GetIndexOfPattern("Charge State");
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(filename))
{
foreach (int scanNumber in L)
{
var scan = Scan.FromFile(rawFile, scanNumber);
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
var centroidStream = rawFile.GetCentroidStream(scanNumber, false);
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
var scanTrailer = rawFile.GetTrailerExtraInformation(scanNumber);
file.WriteLine("e$Spectrum[[{0}]] <- list(", count++);
file.WriteLine("\tscan = {0},", scanNumber);
file.WriteLine("\trtinseconds = {0},", Math.Round(scanStatistics.StartTime * 60 * 1000) / 1000);
if (indexCharge > 0)
{
file.WriteLine("\tcharge = {0},", int.Parse(scanTrailer.Values.ToArray()[indexCharge]));
}
else
{
file.WriteLine("\tcharge = NA,");
}
try{
var reaction0 = scanEvent.GetReaction(0);
file.WriteLine("\tpepmass = {0},", reaction0.PrecursorMass);
}catch {
file.WriteLine("\tpepmass = NA,");
}
if (scanStatistics.IsCentroidScan && centroidStream.Length > 0)
{
file.WriteLine("\tmZ = c(" + string.Join(", ", centroidStream.Masses) + "),");
file.WriteLine("\tintensity = c(" + string.Join(", ", centroidStream.Intensities) + ")");
}
else
{
file.WriteLine("\tmZ = NULL,\n\tintensity = NULL");
}
file.WriteLine("\t)");
}
}
}
private static int GetIndexOfPattern(this IRawDataPlus rawFile, string pattern = "Charge State")
{
var trailerFields = rawFile.GetTrailerExtraHeaderInformation();
int idx = -1;
try
{
idx = trailerFields
.Select((item, index) => new
{
name = item.Label.ToString(),
Position = index
})
.First(x => x.name.Contains(pattern)).Position;
}
catch
{
}
return(idx);
}
private static int GetChargeIdx(this IRawDataPlus rawFile)
{
var trailerFields = rawFile.GetTrailerExtraHeaderInformation();
int idx_CHARGE = -1;
try
{
idx_CHARGE = trailerFields
.Select((item, index) => new
{
name = item.Label.ToString(),
Position = index
})
.First(x => x.name.Contains("Charge State")).Position;
}
catch
{
}
return(idx_CHARGE);
}
/// <summary>
/// </summary>
/// <param name="rawFile"></param>
/// <param name="filename"></param>
/// <param name="L"></param>
public static void WriteSpectrumAsRcode(this IRawDataPlus rawFile, string filename, List <int> L)
{
int count = 1;
var trailerFields = rawFile.GetTrailerExtraHeaderInformation();
int indexCharge = rawFile.GetIndexOfPattern("Charge State");
int indexMonoisotopicmZ = rawFile.GetIndexOfPattern("MonoisotopicmZ");
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(filename))
{
foreach (int scanNumber in L)
{
var basepeakMass = -1.0;
var basepeakIntensity = -1.0;
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
var centroidStream = rawFile.GetCentroidStream(scanNumber, false);
var scanTrailer = rawFile.GetTrailerExtraInformation(scanNumber);
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
var scan = Scan.FromFile(rawFile, scanNumber);
file.WriteLine("e$Spectrum[[{0}]] <- list(", count++);
file.WriteLine("\tscan = {0},", scanNumber);
try
{
basepeakMass = (scanStatistics.BasePeakMass);
basepeakIntensity = Math.Round(scanStatistics.BasePeakIntensity);
file.WriteLine("\tbasePeak = c({0}, {1}),", basepeakMass, basepeakIntensity);
}
catch
{
file.WriteLine("\tbasePeak = c(NA, NA),");
}
file.WriteLine("\tTIC = {0},", scanStatistics.TIC.ToString());
file.WriteLine("\tmassRange = c({0}, {1}),", scanStatistics.LowMass.ToString(), scanStatistics.HighMass.ToString());
file.WriteLine("\tscanType = \"{0}\",", scanStatistics.ScanType.ToString());
file.WriteLine("\trtinseconds = {0},", Math.Round(scanStatistics.StartTime * 60 * 1000) / 1000);
try
{
var reaction0 = scanEvent.GetReaction(0);
file.WriteLine("\tpepmass = {0},", reaction0.PrecursorMass);
}
catch
{
file.WriteLine("\tpepmass = NA,");
}
if (scanStatistics.IsCentroidScan && centroidStream.Length > 0)
{
// Get the centroid (label) data from the RAW file for this scan
file.WriteLine("\tcentroidStream = TRUE,");
file.WriteLine("\tHasCentroidStream = '{0}, Length={1}',", scan.HasCentroidStream, scan.CentroidScan.Length);
if (scan.HasCentroidStream)
{
file.WriteLine("\tcentroid.mZ = c(" + string.Join(", ", scan.CentroidScan.Masses.ToArray()) + "),");
file.WriteLine("\tcentroid.intensity = c(" + string.Join(", ", scan.CentroidScan.Intensities.ToArray()) + "),");
}
file.WriteLine("\ttitle = \"File: {0}; SpectrumID: {1}; scans: {2}\",",
Path.GetFileName(rawFile.FileName),
null,
scanNumber);
if (indexMonoisotopicmZ > 0)
{
file.WriteLine("\tmonoisotopicMz = {0},", Convert.ToDouble(scanTrailer.Values.ToArray()[indexMonoisotopicmZ]));
}
else
{
file.WriteLine("\tmonoisotopicMz = NA,");
}
if (indexCharge > 0)
{
file.WriteLine("\tcharge = {0},", int.Parse(scanTrailer.Values.ToArray()[indexCharge]));
}
else
{
file.WriteLine("\tcharge = NA,");
}
file.WriteLine("\tmZ = c(" + string.Join(", ", centroidStream.Masses) + "),");
file.WriteLine("\tintensity = c(" + string.Join(", ", centroidStream.Intensities) + "),");
file.WriteLine("\tnoises = c(" + string.Join(", ", centroidStream.Noises) + "),");
file.WriteLine("\tresolutions = c(" + string.Join(", ", centroidStream.Resolutions.ToArray()) + "),");
file.WriteLine("\tcharges = c(" + string.Join(", ", centroidStream.Charges) + "),");
file.WriteLine("\tbaselines = c(" + string.Join(", ", centroidStream.Baselines) + "),");
}
else
{
file.WriteLine("\tcentroidStream = FALSE,");
file.WriteLine("\tHasCentroidStream = '{0}, Length={1}',", scan.HasCentroidStream, scan.CentroidScan.Length);
if (scan.HasCentroidStream)
{
file.WriteLine("\tcentroid.mZ = c(" + string.Join(",", scan.CentroidScan.Masses.ToArray()) + "),");
file.WriteLine("\tcentroid.intensity = c(" + string.Join(",", scan.CentroidScan.Intensities.ToArray()) + "),");
}
file.WriteLine("\ttitle = \"File: {0}; SpectrumID: {1}; scans: {2}\",",
Path.GetFileName(rawFile.FileName),
null,
scanNumber);
if (indexCharge > 0)
{
file.WriteLine("\tcharge = {0},", int.Parse(scanTrailer.Values.ToArray()[indexCharge]));
}
else
{
file.WriteLine("\tcharge = NA,");
}
if (indexMonoisotopicmZ > 0)
{
file.WriteLine("\tmonoisotopicMz = {0},", Convert.ToDouble(scanTrailer.Values.ToArray()[indexMonoisotopicmZ]));
}
else
{
file.WriteLine("\tmonoisotopicMz = NA,");
}
file.WriteLine("\tmZ = c(" + string.Join(",", scan.SegmentedScan.Positions) + "),");
file.WriteLine("\tintensity = c(" + string.Join(",", scan.SegmentedScan.Intensities) + "),");
// file.WriteLine("\tnoises = c(" + string.Join(",", scan.SegmentedScan.Noises) + "),");
}
// ============= Instrument Data =============
// write scan Trailer
var trailerValues = scanTrailer.Values;
var trailerLabels = scanTrailer.Labels;
var zipTrailer = trailerLabels.ToArray().Zip(trailerValues, (a, b) => string.Format("\t\"{0}\" = \"{1}\"", a, b));
file.WriteLine(string.Join(", \n", zipTrailer));
file.WriteLine(")");
}
}
return;
}
