![]() |
OpenMS
2.7.0
|
Public Member Functions | |
TOPPGNPSExport () | |
Protected Member Functions | |
void | registerOptionsAndFlags_ () override |
ExitCodes | main_ (int, const char **) override |
Private Member Functions | |
void | binPeaks_ (const vector< Peak1D > &peaks, const double bin_width, vector< Peak1D > &binned_peaks) |
Bin peaks by similar m/z position and averaged intensities. More... | |
void | flattenAndBinSpectra_ (MSExperiment &exp, const double bin_width, vector< Peak1D > &merged_peaks) |
Flatten spectra from MSExperiment into a single vector of Peak1D peaks. More... | |
void | writeMSMSBlockHeader_ (ofstream &output_file, const String &output_type, const int &scan_index, const String &feature_id, const int &feature_charge, const String &feature_mz, const String &spec_index, const String &feature_rt) |
Private function that outputs MS/MS Block Header. More... | |
void | writeMSMSBlock_ (ofstream &output_file, const vector< Peak1D > &peaks) |
Private function to write peak mass and intensity to output file. More... | |
void | sortElementMapsByIntensity_ (const ConsensusFeature &feature, vector< pair< int, double >> &element_maps) |
Private method used to sort PeptideIdentification map indices in order of annotation's intensity. More... | |
void | getElementPeptideIdentificationsByElementIntensity_ (const ConsensusFeature &feature, vector< pair< int, double >> &sorted_element_maps, vector< pair< int, int >> &pepts) |
Retrieve list of PeptideIdentification parameters from ConsensusFeature metadata, sorted by map intensity. More... | |
Static Private Attributes | |
static constexpr double | DEF_COSINE_SIMILARITY = 0.9 |
static constexpr double | DEF_MERGE_BIN_SIZE = static_cast<double>(BinnedSpectrum::DEFAULT_BIN_WIDTH_HIRES) |
static constexpr double | DEF_PREC_MASS_TOL = 0.5 |
static constexpr bool | DEF_PREC_MASS_TOL_ISPPM = false |
static constexpr double | DEF_PEPT_CUTOFF = 5 |
static constexpr double | DEF_MSMAP_CACHE = 50 |
|
inline |
|
inlineprivate |
Bin peaks by similar m/z position and averaged intensities.
peaks | Vector of Peak1D peaks sorted by m/z position |
bin_width | Size of bin |
binned_peaks | Result vector with binned peaks passed in by reference |
|
inlineprivate |
Flatten spectra from MSExperiment into a single vector of Peak1D peaks.
exp | MSExperiment containing at least 1 spectrum |
bin_width | Size of binned scan (m/z) |
merged_peaks | Result vector of peaks passed in by reference |
|
inlineprivate |
Retrieve list of PeptideIdentification parameters from ConsensusFeature metadata, sorted by map intensity.
feature | ConsensusFeature feature containing PeptideIdentification annotations |
sorted_element_maps | Sorted list of element_maps |
pepts | Result vector of <map_index,spectrum_index> of PeptideIdentification annotations sorted by map intensity in feature |
|
inlineoverrideprotected |
|
inlineoverrideprotected |
|
inlineprivate |
Private method used to sort PeptideIdentification map indices in order of annotation's intensity.
feature | ConsensusFeature annotated with PeptideIdentifications |
featureMaps_sortedByInt | Result vector of map indices in order of PeptideIdentification intensity |
|
inlineprivate |
Private function to write peak mass and intensity to output file.
output_file | Stream that will write to file |
peaks | Vector of peaks that will be outputted |
|
inlineprivate |
Private function that outputs MS/MS Block Header.
output_file | Stream that will write to file |
scan_index | Current scan index in GNPSExport formatted output |
feature_id | ConsensusFeature Id found in input mzXML file |
feature_charge | ConsensusFeature's highest charge as mentioned in the input mzXML file |
feature_mz | m/z position of PeptideIdentification with highest intensity |
spec_index | Spectrum index of PeptideIdentification with highest intensity |
feature_rt | ConsensusFeature's retention time specified in input mzXML file |
|
staticconstexprprivate |
|
staticconstexprprivate |
|
staticconstexprprivate |
|
staticconstexprprivate |
|
staticconstexprprivate |
|
staticconstexprprivate |