IDFreeMassErrorEstimator.h File Reference

#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <deque>
#include <map>
#include <limits>
#include <optional>
#include <string>
#include <utility>
#include <vector>

Go to the source code of this file.

Classes
class	IDFreeMassErrorEstimator
	Identification-free precursor and fragment mass-precision estimator. More...
struct	IDFreeMassErrorEstimator::Parameters
	Tunable estimator thresholds. Defaults match the validated prideQC implementation. More...
struct	IDFreeMassErrorEstimator::RobustError
	Robust summary of pairwise repeated-measurement differences. More...
struct	IDFreeMassErrorEstimator::ToleranceSuggestion
	Precision-derived search-tolerance suggestion for one unit system. More...
struct	IDFreeMassErrorEstimator::Diagnostics
	Estimator support/accounting counters. More...
struct	IDFreeMassErrorEstimator::Result
	Current precision estimates, optional tolerance suggestions and diagnostics. More...
struct	IDFreeMassErrorEstimator::PrecursorCluster
struct	IDFreeMassErrorEstimator::FragmentFingerprint
struct	IDFreeMassErrorEstimator::GaussianUniformFit

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::IDFreeMassErrorEstimator::Parameters

struct OpenMS::IDFreeMassErrorEstimator::Parameters

Tunable estimator thresholds. Defaults match the validated prideQC implementation.

Class Members
double	fragment_high_intensity_quantile {0.75}
double	fragment_high_res_max_sigma_da {0.01}
double	fragment_high_res_max_sigma_ppm {10.0}
double	fragment_low_res_match_da {0.5}
double	fragment_low_res_min_sigma_da {0.01}
double	fragment_low_res_min_sigma_ppm {20.0}
double	fragment_match_da {0.2}
double	fragment_tolerance_sigma_multiplier {6.0}
double	fragment_very_low_res_match_da {1.0}
Size	max_candidates_per_bin {32}
Size	min_fragment_pairs {200}
Size	min_fragment_tolerance_pairs {1000}
Size	min_fragment_tolerance_spectra {50}
Size	min_matched_peaks {8}
double	min_overlap_fraction {0.25}
Size	min_precursor_cluster_size {3}
Size	min_precursor_clusters {10}
Size	min_spectrum_pairs {25}
Size	min_tolerance_clusters {100}
Size	min_tolerance_pairs {200}
double	precursor_candidate_ppm {20.0}
double	rt_window_seconds {120.0}
double	tolerance_sigma_multiplier {6.0}
Size	top_peaks {50}

OpenMS::IDFreeMassErrorEstimator::RobustError

struct OpenMS::IDFreeMassErrorEstimator::RobustError

Robust summary of pairwise repeated-measurement differences.

Class Members
double	pairwise_median {0.0}
double	pairwise_p95_abs {0.0}
double	pairwise_sigma {0.0}
Size	robust_inlier_count {0}
double	robust_inlier_fraction {0.0}
double	robust_inlier_p95_abs_centered {0.0}
double	robust_inlier_threshold_3sigma {0.0}
Size	robust_outlier_count {0}
double	single_measurement_sigma {0.0}

OpenMS::IDFreeMassErrorEstimator::ToleranceSuggestion

struct OpenMS::IDFreeMassErrorEstimator::ToleranceSuggestion

Precision-derived search-tolerance suggestion for one unit system.

Class Members
string	confidence
double	sigma_multiplier {0.0}
double	single_measurement_sigma {0.0}
Size	support {0}
double	tolerance {0.0}
string	unit

OpenMS::IDFreeMassErrorEstimator::Diagnostics

struct OpenMS::IDFreeMassErrorEstimator::Diagnostics

Estimator support/accounting counters.

Class Members
Size	excluded_fragment_profile_or_unknown {0}
Size	excluded_fragment_unknown {0}
Size	excluded_low_fragment_peaks {0}
Size	excluded_missing_precursor {0}
Size	excluded_profile_peak_pick_failure {0}
Size	fragment_centroid_spectra {0}
Size	fragment_eligible_ms2 {0}
bool	fragment_high_intensity_fallback_used {false}
bool	fragment_high_intensity_mixture_converged {false}
Size	fragment_high_intensity_pairs {0}
double	fragment_high_intensity_signal_fraction {0.0}
Size	fragment_high_intensity_signal_pairs {0}
double	fragment_high_intensity_threshold {0.0}
Size	fragment_low_res_pairs {0}
bool	fragment_mixture_converged {false}
Size	fragment_mixture_iterations {0}
double	fragment_mixture_mean_ppm {0.0}
Size	fragment_mixture_pairs {0}
double	fragment_mixture_reference_mz {0.0}
bool	fragment_mixture_rejected_zero_quantization {false}
double	fragment_mixture_signal_fraction {0.0}
Size	fragment_mixture_signal_pairs {0}
Size	fragment_paired_spectra {0}
Size	fragment_pairs {0}
Size	fragment_profile_centroids {0}
Size	fragment_profile_spectra {0}
Size	fragment_very_low_res_pairs {0}
double	fragment_zero_delta_fraction {0.0}
Size	fragment_zero_delta_pairs {0}
Size	precursor_clusters_used {0}
Size	precursor_eligible_ms2 {0}
Size	precursor_paired_spectra {0}

OpenMS::IDFreeMassErrorEstimator::Result

struct OpenMS::IDFreeMassErrorEstimator::Result

Current precision estimates, optional tolerance suggestions and diagnostics.

Class Members
Diagnostics	diagnostics
optional< RobustError >	fragment_da
double	fragment_match_window_da {0.2}
optional< RobustError >	fragment_ppm
FragmentResolutionRegime	fragment_resolution_regime {FragmentResolutionRegime::UNAVAILABLE}
optional< ToleranceSuggestion >	fragment_tolerance_da
optional< ToleranceSuggestion >	fragment_tolerance_ppm
bool	fragment_window_censored {false}
optional< RobustError >	precursor_da
optional< RobustError >	precursor_ppm
optional< ToleranceSuggestion >	precursor_tolerance_ppm

OpenMS::IDFreeMassErrorEstimator::PrecursorCluster

struct OpenMS::IDFreeMassErrorEstimator::PrecursorCluster

Class Members
bool	committed {false}
Size	count {1}
double	last_mz {0.0}
double	last_rt {0.0}
double	mean_mz {0.0}
vector< double >	pending_da
vector< double >	pending_ppm

OpenMS::IDFreeMassErrorEstimator::FragmentFingerprint

struct OpenMS::IDFreeMassErrorEstimator::FragmentFingerprint

Class Members
vector< double >	mz
double	precursor_mz {0.0}
vector< double >	relative_intensity
double	rt {0.0}

OpenMS::IDFreeMassErrorEstimator::GaussianUniformFit

struct OpenMS::IDFreeMassErrorEstimator::GaussianUniformFit

Class Members
bool	converged {false}
Size	iterations {0}
double	log_likelihood {-std::numeric_limits<double>::infinity()}
double	mean {0.0}
double	pairwise_sigma {0.0}
double	signal_fraction {0.0}