FLASHDeconvSpectrumFile Class Reference

FLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats. More...

#include <OpenMS/FORMAT/FLASHDeconvSpectrumFile.h>

Collaboration diagram for FLASHDeconvSpectrumFile:

Static Public Member Functions
static void	writeDeconvolvedMassesHeader (std::ostream &os, uint ms_level, bool detail, bool report_decoy)
	write the header in the tsv output file (spectrum level) More...
static void	writeDeconvolvedMasses (const DeconvolvedSpectrum &dspec, std::ostream &os, const String &file_name, const FLASHHelperClasses::PrecalculatedAveragine &avg, const FLASHHelperClasses::PrecalculatedAveragine &decoy_avg, double tol, bool write_detail, bool record_decoy, double noise_decoy_weight)
static void	writeMzML (const MSExperiment &map, std::vector< DeconvolvedSpectrum > &deconvolved_spectra, const String &deconvolved_mzML_file, const String &annotated_mzML_file, int mzml_charge, DoubleList tols)
static void	writeIsobaricQuantification (std::ostream &os, std::vector< DeconvolvedSpectrum > &deconvolved_spectra)
static void	writeTopFDHeader (std::ostream &os, const Param &param)
	write topFD header More...
static void	writeTopFD (const DeconvolvedSpectrum &dspec, std::ostream &os, const String &filename, double qval_threshold=1.0, uint min_ms_level=1, bool randomize_precursor_mass=false, bool randomize_fragment_mass=false)
	write the deconvolved masses TopFD output (*.msalign) More...

Static Private Attributes
static const int	topFD_min_peak_count_ = 3
	number of minimum peak count in topFD msalign file More...
static const int	topFD_max_peak_count_ = 500
	number of maximum peak count in topFD msalign file More...

Detailed Description

FLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats.

Member Function Documentation

writeDeconvolvedMasses()

static void writeDeconvolvedMasses ( const DeconvolvedSpectrum &  dspec, std::ostream &  os, const String &  file_name, const FLASHHelperClasses::PrecalculatedAveragine &  avg, const FLASHHelperClasses::PrecalculatedAveragine &  decoy_avg, double  tol, bool  write_detail, bool  record_decoy, double  noise_decoy_weight  )

static

@brief write the deconvolved masses in the output file (spectrum level)
@param dspec deconvolved spectrum to write
@param fs file stream to the output file
@param file_name the output file name that the deconvolved masses will be written.
@param avg averagine information to calculate monoisotopic and average mass difference within this function. In PeakGroup (peaks of DeconvolvedSpectrum) only monoisotopic mass is recorded. To write both monoisotopic and average masses, their mass difference should be calculated using this averagine information.
@param decoy_avg averagine for noise decoy
@param tol mass tolerance
@param write_detail if this is set, more detailed information on each mass will be written in the output file.
@param record_decoy if set true, decoy and qvalue information will be written.
@param noise_decoy_weight noise decoy weight. Determines how often the noise decoy masses will be written
Default MS1 headers are:
  FileName, ScanNum, TargetDecoyType, RetentionTime, MassCountInSpec, AverageMass, MonoisotopicMass,
  SumIntensity, MinCharge, MaxCharge,
  PeakCount, IsotopeCosine, ChargeScore, MassSNR, ChargeSNR, RepresentativeCharge, RepresentativeMzStart, RepresentativeMzEnd, setQscore, PerChargeIntensity, PerIsotopeIntensity

Default MS2 headers include MS1 headers plus: PrecursorScanNum, PrecursorMz, PrecursorIntensity, PrecursorCharge, PrecursorSNR, PrecursorMonoisotopicMass, PrecursorQscore

Detailed MS1 and MS2 headers include all corresponding headers above plus: PeakMZs, PeakIntensities, PeakCharges, PeakMasses, PeakIsotopeIndices, PeakPPMErrors

Referenced by TOPPFLASHDeconv::main_().

writeDeconvolvedMassesHeader()

static void writeDeconvolvedMassesHeader ( std::ostream &  os, uint  ms_level, bool  detail, bool  report_decoy  )

static

write the header in the tsv output file (spectrum level)

Parameters

os	output stream to the output file
ms_level	ms level of the spectrum
detail	if set true, detailed information of the mass (e.g., peak list for the mass) is written
report_decoy	if set true, decoy and qvalue information will be written.

Referenced by TOPPFLASHDeconv::main_().

writeIsobaricQuantification()

static void writeIsobaricQuantification ( std::ostream &  os, std::vector< DeconvolvedSpectrum > &  deconvolved_spectra  )

static

write isobaric quantification results

Parameters

os	output stream
deconvolved_spectra	deconvolved spectra to write

Referenced by TOPPFLASHDeconv::main_().

writeMzML()

static void writeMzML ( const MSExperiment &  map, std::vector< DeconvolvedSpectrum > &  deconvolved_spectra, const String &  deconvolved_mzML_file, const String &  annotated_mzML_file, int  mzml_charge, DoubleList  tols  )

static

Parameters

map
deconvolved_spectra
deconvolved_mzML_file
annotated_mzML_file
mzml_charge
tols

Referenced by TOPPFLASHDeconv::main_().

writeTopFD()

static void writeTopFD ( const DeconvolvedSpectrum &  dspec, std::ostream &  os, const String &  filename, double  qval_threshold = 1.0, uint  min_ms_level = 1, bool  randomize_precursor_mass = false, bool  randomize_fragment_mass = false  )

static

write the deconvolved masses TopFD output (*.msalign)

Parameters

dspec	deconvolved spectrum to write
os	output stream to the output file
filename	mzml file name
qval_threshold	qvalue threshold to filter out high qvalue precursors.
min_ms_level	min ms level of the dataset
randomize_precursor_mass	if set, a random number between -100 to 100 is added to precursor mass
randomize_fragment_mass	if set, a random number between -100 to 100 is added to fragment mass

Referenced by TOPPFLASHDeconv::main_().

writeTopFDHeader()

static void writeTopFDHeader ( std::ostream &  os, const Param &  param  )

static

write topFD header

Referenced by TOPPFLASHDeconv::main_().

Member Data Documentation

topFD_max_peak_count_

const int topFD_max_peak_count_ = 500

staticprivate

number of maximum peak count in topFD msalign file

topFD_min_peak_count_

const int topFD_min_peak_count_ = 3

staticprivate

number of minimum peak count in topFD msalign file