FLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats.
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#include <OpenMS/FORMAT/FLASHDeconvSpectrumFile.h>
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| static void | writeDeconvolvedMassesHeader (std::fstream &fs, const int ms_level, const bool detail, const bool decoy) |
| | write the header in the tsv output file (spectrum level) More...
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| static void | writeDeconvolvedMasses (DeconvolvedSpectrum &dspec, std::fstream &fs, const String &file_name, const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, const bool write_detail, const bool decoy) |
| | write the deconvolved masses in the output file (spectrum level) More...
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| static void | writeTopFD (const DeconvolvedSpectrum &dspec, std::fstream &fs, const double snr_threshold=1.0, const double decoy_harmonic_factor=1.0, const double decoy_precursor_offset=.0) |
| | write the deconvolved masses TopFD output (*.msalign) More...
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FLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats.
◆ writeDeconvolvedMasses()
write the deconvolved masses in the output file (spectrum level)
- Parameters
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| dspec | deconvolved spectrum to write |
| fs | file stream to the output file |
| file_name | the output file name that the deconvolved masses will be written. |
| 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. |
| write_detail | if this is set, more detailed information on each mass will be written in the output file. |
| decoy | if set true, decoy and qvalue information will be written. Default MS1 headers are: TODO modify FileName, ScanNum, Decoy, RetentionTime, MassCountInSpec, AverageMass, MonoisotopicMass, SumIntensity, MinCharge, MaxCharge, PeakCount, IsotopeCosine, ChargeScore, MassSNR, ChargeSNR, RepresentativeCharge, RepresentativeMzStart, RepresentativeMzEnd, QScore, 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 |
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std::fstream & |
fs, |
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const int |
ms_level, |
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const bool |
detail, |
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const bool |
decoy |
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static |
write the header in the tsv output file (spectrum level)
- Parameters
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| fs | file 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 |
| decoy | if set true, decoy and qvalue information will be written. |
Referenced by TOPPFLASHDeconv::main_().
◆ writeTopFD()
| static void writeTopFD |
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const DeconvolvedSpectrum & |
dspec, |
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std::fstream & |
fs, |
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const double |
snr_threshold = 1.0, |
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const double |
decoy_harmonic_factor = 1.0, |
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const double |
decoy_precursor_offset = .0 |
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) |
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static |
write the deconvolved masses TopFD output (*.msalign)
- Parameters
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| dspec | deconvolved spectrum to write |
| fs | file stream to the output file |
| snr_threshold | SNR threshold to filter out low SNR precursors. Even if a PeakGroup has a high deconvolution quality, it should be still discarded for identification when its precursor SNR (SNR within the isolation window) is too low. |
| decoy_harmonic_factor | this factor will be multiplied to precursor mass and charge. To generate decoy spectra |
| decoy_precursor_offset | this value will be added to precursor mass. To generate decoy spectra |
Referenced by TOPPFLASHDeconv::main_().
◆ topFD_max_peak_count_
| const int topFD_max_peak_count_ = 500 |
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staticprivate |
number of maximum peak count in topFD msalign file
◆ topFD_min_peak_count_
| const int topFD_min_peak_count_ = 3 |
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staticprivate |
number of minimum peak count in topFD msalign file
1.9.1 
