public static void GetIndex(this IRawDataPlus rawFile)
{
int firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
int lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
int idxCharge = rawFile.GetIndexOfPattern();
int idxMasterScan = rawFile.GetIndexOfPattern("Master Scan Number:");
int idxDependencyType = rawFile.GetIndexOfPattern("Dependency Type:");
double charge, precursorMass;
int masterScan, dependencyType;
Console.WriteLine("scan;scanType;rtinseconds;precursorMass;MSOrder;charge;masterScan;dependencyType");
for (int scanNumber = firstScanNumber; scanNumber < lastScanNumber; scanNumber++)
{
var scanTrailer = rawFile.GetTrailerExtraInformation(scanNumber);
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
try{
var reaction0 = scanEvent.GetReaction(0);
precursorMass = reaction0.PrecursorMass;
} catch {
precursorMass = -1;
}
try{
charge = int.Parse(scanTrailer.Values.ToArray()[idxCharge]);
} catch {
charge = -1;
}
try{
masterScan = int.Parse(scanTrailer.Values.ToArray()[idxMasterScan]);
} catch {
masterScan = -1;
}
try{
dependencyType = int.Parse(scanTrailer.Values.ToArray()[idxDependencyType]);
} catch {
dependencyType = -1;
}
Console.WriteLine("{0};{1};{2};{3};{4};{5};{6};{7}", scanNumber,
scanStatistics.ScanType.ToString(),
Math.Round(scanStatistics.StartTime * 60 * 1000) / 1000,
precursorMass,
scanFilter.MSOrder.ToString(),
charge, masterScan, dependencyType);
}
}
/// <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$Spectrum[[{0}]] <- list(", count++);
file.WriteLine("\tscan = {0},", scanNumber);
file.WriteLine("\trtinseconds = {0},", Math.Round(scanStatistics.StartTime * 60 * 1000) / 1000);
if (indexCharge > 0)
{
file.WriteLine("\tcharge = {0},", int.Parse(scanTrailer.Values.ToArray()[indexCharge]));
}
else
{
file.WriteLine("\tcharge = NA,");
}
try{
var reaction0 = scanEvent.GetReaction(0);
file.WriteLine("\tpepmass = {0},", reaction0.PrecursorMass);
}catch {
file.WriteLine("\tpepmass = NA,");
}
if (scanStatistics.IsCentroidScan && centroidStream.Length > 0)
{
file.WriteLine("\tmZ = c(" + string.Join(", ", centroidStream.Masses) + "),");
file.WriteLine("\tintensity = c(" + string.Join(", ", centroidStream.Intensities) + ")");
}
else
{
file.WriteLine("\tmZ = NULL,\n\tintensity = NULL");
}
file.WriteLine("\t)");
}
}
}
public static void WriteSpectrumAsRcode0(this IRawDataPlus rawFile, string filename)
{
int idxCharge = rawFile.GetIndexOfPattern();
int firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
int lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
int charge = -1;
double pc = -1;
using (System.IO.StreamWriter file =
new System.IO.StreamWriter(filename))
{
for (int scanNumber = firstScanNumber; scanNumber < lastScanNumber; scanNumber++)
{
var scanTrailer = rawFile.GetTrailerExtraInformation(scanNumber);
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
var scanEvent = rawFile.GetScanEventForScanNumber(scanNumber);
var scanFilter = rawFile.GetFilterForScanNumber(scanNumber);
try{
var reaction0 = scanEvent.GetReaction(0);
pc = reaction0.PrecursorMass;
}
catch {
pc = -1;
}
try{
charge = int.Parse(scanTrailer.Values.ToArray()[idxCharge]);
}
catch {
charge = -1;
}
file.WriteLine("e$Spectrum[[{0}]] <- list(", scanNumber);
file.WriteLine("\tscan = {0};", scanNumber);
file.WriteLine("\tscanType = \"{0}\";", scanStatistics.ScanType.ToString());
file.WriteLine("\trtinseconds = {0};", Math.Round(scanStatistics.StartTime * 60 * 1000) / 1000);
file.WriteLine("\tprecursorMass = {0};", pc);
file.WriteLine("\tMSOrder = '{0}';", scanFilter.MSOrder.ToString());
file.WriteLine("\tcharge = {0}", charge);
file.WriteLine(")");
}
}
}
/// <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;
}