RescoreInput Struct Reference

Input to domain-agnostic Percolator::rescore. More...

#include <OpenMS/ANALYSIS/ID/PercolatorTypes.h>

Public Member Functions
size_t	rowCount () const
	Number of rows: of features, or else of the dense feature_matrix.
size_t	featureCount () const
	Number of features per row: of the first row of features, or else feature_names.size() (0 without rows)
const double *	row (size_t i) const
	The featureCount() values of row i: of features, or else of the dense feature_matrix.

Public Attributes
std::vector< std::vector< double > >	features
std::vector< bool >	is_decoy
	Target (false) or decoy (true) label per row.
std::vector< int >	cv_group_keys
StringList	feature_names
	Names aligned 1:1 with feature columns; used for logging only.
std::vector< int >	scan_numbers
	Optional per-row PIN-compatible fields.
std::vector< int >	spec_file_numbers
std::vector< double >	exp_masses
std::vector< double >	calc_masses
std::vector< double >	feature_matrix
	The feature matrix in one dense block, in place of features.
std::vector< std::string >	peptide_keys

Detailed Description

Input to domain-agnostic Percolator::rescore.

Row ordering is preserved in the output. Each row corresponds to one data point — the row's semantics (PSM, transition, peak group, etc.) are determined by the caller.

Member Function Documentation

featureCount()

size_t featureCount ( ) const

inline

Number of features per row: of the first row of features, or else feature_names.size() (0 without rows)

row()

const double * row ( size_t  i ) const

inline

The featureCount() values of row i: of features, or else of the dense feature_matrix.

rowCount()

size_t rowCount ( ) const

inline

Number of rows: of features, or else of the dense feature_matrix.

Member Data Documentation

calc_masses

std::vector<double> calc_masses

cv_group_keys

std::vector<int> cv_group_keys

Per-row integer key used to group rows into the same cross-validation fold. Rows sharing a key will never be split across folds. Leave empty to use row index (each row in its own group). Supply this when rows have natural duplication (e.g., multiple PSMs from one spectrum, multiple transitions from one precursor).

exp_masses

std::vector<double> exp_masses

feature_matrix

std::vector<double> feature_matrix

The feature matrix in one dense block, in place of features.

Row-major: row i holds the values of the feature_names.size() features at [i * feature_names.size(), (i + 1) * feature_names.size()). Used when features is empty (at most one of the two may hold rows); the number of rows is then is_decoy.size(). rowCount(), featureCount() and row() read the rows of either layout.

Percolator::buildPSMRescoreInput() builds the feature matrix of PSM rescoring this way, straight from the PSMs.

feature_names

StringList feature_names

Names aligned 1:1 with feature columns; used for logging only.

features

std::vector<std::vector<double> > features

[n_rows][n_features] scalar features per row. Rows must all have the same length. Empty if the rows are in the dense feature_matrix.

is_decoy

std::vector<bool> is_decoy

Target (false) or decoy (true) label per row.

peptide_keys

std::vector<std::string> peptide_keys

Optional per-row peptide key for peptide-level q-values (Percolator parameter 'peptide_level'): rows with the same key and label are one peptide, as the percolator executable groups PSMs by the PIN 'Peptide' string between the flanks (incl. modifications). Empty, or one entry per row.

scan_numbers

std::vector<int> scan_numbers

Optional per-row PIN-compatible fields.

When supplied, these override the synthetic defaults (scan = row_index, specFileNr = 0, expMass = calcMass = 0.0) that the wrapper uses internally. Populate them when the in-process output must be bitwise-identical to running the external percolator binary on a .pin file derived from the same PSMs: Percolator's internal PSM sort order (OrderScanHash hashes specFileNr and scan) determines the CV fold assignment, so scan_numbers and spec_file_numbers must match those that PercolatorInfile::store would emit.

Percolator::fillPINCompatibleFields() is a helper that derives all four vectors from a vector of PeptideIdentifications using the same conventions as PercolatorInfile::store.

Each vector is either empty (in which case the default is used) or contains exactly n_rows entries, one per feature row.

spec_file_numbers

std::vector<int> spec_file_numbers