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, uint ms_level, bool detail, bool dummy) |
| | write the header in the tsv output file (spectrum level) More...
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| static void | writeDeconvolvedMasses (DeconvolvedSpectrum &dspec, DeconvolvedSpectrum &target_spec, std::fstream &fs, const String &file_name, const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, double tol, bool write_detail, bool record_dummy) |
| | write the deconvolved masses in the output file (spectrum level) More...
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| static void | writeTopFD (DeconvolvedSpectrum &dspec, std::fstream &fs, double snr_threshold=1.0, const uint min_ms_level=1, bool randomize_precursor_mass=false, bool randomize_fragment_mass=false) |
| | 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 |
| target_spec | target spectrum only used for dummy spectrum output |
| 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. |
| tol | mass tolerance |
| write_detail | if this is set, more detailed information on each mass will be written in the output file. |
| dummy | if set true, dummy and qvalue information will be written. Default MS1 headers are: FileName, ScanNum, TargetDummyType, 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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uint |
ms_level, |
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bool |
detail, |
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bool |
dummy |
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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 |
| dummy | if set true, dummy and qvalue information will be written. |
Referenced by TOPPFLASHDeconv::main_().
◆ writeTopFD()
| static void writeTopFD |
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DeconvolvedSpectrum & |
dspec, |
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std::fstream & |
fs, |
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double |
snr_threshold = 1.0, |
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const uint |
min_ms_level = 1, |
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bool |
randomize_precursor_mass = false, |
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bool |
randomize_fragment_mass = false |
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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. |
| 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_().
◆ 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 
