Fragment-index-based peptide database search algorithm (experimental). More...

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

Inheritance diagram for ProSEAlgorithm:

Collaboration diagram for ProSEAlgorithm:

Classes
struct	AnnotatedHit_
	Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space. More...

struct	CalibrationResult_
	Result of a calibration pass. More...

struct	DecoyStrategy_
	Resolved decoy handling for one concrete input database. More...

struct	MultiFileSearchResult
	Multi-file search result bundle. More...

struct	RunStatistics
	Per-run identification statistics for the end-of-search report. More...

struct	SearchContext
	Prepared per-database state shared across multiple spectrum files. More...

struct	SearchResult
	Comprehensive search result including modification analysis. More...

struct	SharedSearchStats
	Configuration, database and fragment-index facts shared across all input files of one ProSE invocation. More...

Public Types
enum class	ExitCodes { EXECUTION_OK , INPUT_FILE_EMPTY , UNEXPECTED_RESULT , UNKNOWN_ERROR , ILLEGAL_PARAMETERS }
	Exit codes. More...

Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Public Member Functions
	ProSEAlgorithm ()

ExitCodes	search (const std::string &in_spectra, const std::string &in_db, std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids) const
	Search spectra in a spectrum file (mzML or Bruker .d) against a protein database using an FI-backed workflow.

SearchResult	searchWithModificationAnalysis (const std::string &in_spectra, const std::string &in_db, const std::string &output_base_name="") const
	Search with comprehensive results including modification analysis tables.

ExitCodes	search (PeakMap &spectra, const std::vector< FASTAFile::FASTAEntry > &fasta_db, std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids) const
	In-memory search: search spectra against a protein database without file I/O.

SearchContext	prepareContext (const std::vector< FASTAFile::FASTAEntry > &fasta_db) const
	Build a SearchContext (decoy-augmented database + FragmentIndex) for reuse.

ExitCodes	search (PeakMap &spectra, SearchContext &ctx, std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids) const
	In-memory search using a pre-built SearchContext.

SearchResult	searchWithModificationAnalysis (PeakMap &spectra, const std::vector< FASTAFile::FASTAEntry > &fasta_db, const std::string &output_base_name="") const
	In-memory search with modification analysis: no file I/O required.

MultiFileSearchResult	searchWithModificationAnalysis (const std::vector< std::string > &in_spectra_files, const std::vector< FASTAFile::FASTAEntry > &fasta_db, const std::vector< std::string > &output_base_names={}, const std::string &aggregate_base_name="") const
	Multi-file search with modification analysis (in-memory FASTA).

MultiFileSearchResult	searchWithModificationAnalysis (const std::vector< std::string > &in_spectra_files, const std::string &in_db, const std::vector< std::string > &output_base_names={}, const std::string &aggregate_base_name="") const
	Multi-file search with modification analysis (FASTA file path).

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.

virtual	~DefaultParamHandler ()
	Destructor.

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.

void	setParameters (const Param &param)
	Sets the parameters.

const Param &	getParameters () const
	Non-mutable access to the parameters.

const Param &	getDefaults () const
	Non-mutable access to the default parameters.

const std::string &	getName () const
	Non-mutable access to the name.

void	setName (const std::string &name)
	Mutable access to the name.

const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.

virtual	~ProgressLogger ()
	Destructor.

	ProgressLogger (const ProgressLogger &other)
	Copy constructor.

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!

LogType	getLogType () const
	Returns the type of progress log being used.

void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.

void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.

void	setProgress (SignedSize value) const
	Sets the current progress.

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end)

Static Public Member Functions
static void	applyCompleteSetProteinFDR (std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids, const std::string &decoy_string, bool decoy_is_prefix, double protein_fdr)
	Finalize protein-level FDR on a COMPLETE protein set (a single input file, or a merged cross-file aggregate).

static void	updateFinalStats (RunStatistics &stats, const PeptideIdentificationList &peptide_ids, const std::string &enzyme, bool fdr_applied)

static void	renderRunSummary (const RunStatistics &stats, const SharedSearchStats &shared, const OpenSearchModificationAnalysis::OpenSearchAnalysisResult &mod_analysis, bool is_open_search, std::ostream &os)

static void	renderModificationSummary (const OpenSearchModificationAnalysis::OpenSearchAnalysisResult &mod_analysis, std::ostream &os)

static std::string	renderRunSummaryYaml (const MultiFileSearchResult &mfres, const std::vector< std::pair< std::string, std::vector< std::string > > > &manifest, Size files_failed, Size files_total)

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.

Protected Types
enum class	DecoyMode_ { AUTO , GENERATE , IGNORE }
	How decoys are obtained/recognised for a search (parameter "decoys"). More...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method.

DecoyStrategy_	resolveDecoyStrategy_ (const std::vector< FASTAFile::FASTAEntry > &db) const
	Decide how to obtain/recognise decoys for `db`.

Param	fragmentIndexParameters_ () const
	ProSE parameters made safe to hand to a FragmentIndex.

std::vector< FASTAFile::FASTAEntry >	buildDecoyAugmentedDB_ (const std::vector< FASTAFile::FASTAEntry > &fasta_db, const DecoyStrategy_ &strategy) const
	Build the searched database according to `strategy`.

std::vector< FASTAFile::FASTAEntry >	buildCalibrationSample_ (const std::vector< FASTAFile::FASTAEntry > &full_db) const
	Build a strided protein sample for chunked calibration.

ExitCodes	searchChunked_ (PeakMap &spectra, std::vector< FASTAFile::FASTAEntry > &full_db, const DecoyStrategy_ &strategy, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids) const
	Chunked database search implementation.

void	scoreSpectraAgainstIndex_ (const PeakMap &spectra, FragmentIndex &fi, const std::vector< FASTAFile::FASTAEntry > &db, const TheoreticalSpectrumGenerator &spectrum_generator, double effective_fragment_tol, bool fragment_mass_tolerance_unit_ppm, bool open_search_mode, std::vector< std::vector< AnnotatedHit_ > > &annotated_hits, const std::string &progress_label) const
	Score all spectra against one FragmentIndex.

void	postProcessHits_ (const PeakMap &exp, std::vector< std::vector< ProSEAlgorithm::AnnotatedHit_ > > &annotated_hits, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids, Size top_hits, const StringList &modifications_fixed, const StringList &modifications_variable, Int peptide_missed_cleavages, double precursor_mass_tolerance, double fragment_mass_tolerance, const std::string &precursor_mass_tolerance_unit_ppm, const std::string &fragment_mass_tolerance_unit_ppm, const Int precursor_min_charge, const Int precursor_max_charge, const std::string &enzyme, const std::string &database_name) const
	Filter and annotate search results.

double	computeModMatchTolerance_ () const

CalibrationResult_	runCalibrationPass_ (PeakMap &spectra, FragmentIndex &fragment_index, const std::vector< FASTAFile::FASTAEntry > &db) const
	Run a fast calibration pass on a subset of spectra to estimate mass accuracy.

void	collectRunStatistics_ (const PeakMap &spectra, const std::vector< ProteinIdentification > &protein_ids, const PeptideIdentificationList &peptide_ids, RunStatistics &stats) const

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

Static Protected Member Functions
static void	preprocessSpectra_ (PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool deisotope_requested, Size peaks_keep_n, Int peaks_window_top)
	filter, deisotope, decharge spectra

static bool	accessionHasDecoyMarker_ (const std::string &accession, const std::string &marker, bool is_prefix)

static void	capturePreFdrStats_ (const PeptideIdentificationList &peptide_ids, RunStatistics &stats)

static double	maxRetainedScore_ (const PeptideIdentificationList &peptide_ids)

Protected Attributes
double	precursor_mass_tolerance_lower_ {10.0}
	positive magnitude (default matches the param)

double	precursor_mass_tolerance_upper_ {10.0}
	positive magnitude (default matches the param)

std::string	precursor_mass_tolerance_unit_ {"ppm"}

Size	precursor_min_charge_

Size	precursor_max_charge_

IntList	precursor_isotopes_

double	fragment_mass_tolerance_

std::string	fragment_mass_tolerance_unit_

bool	deisotope_requested_ {true}

Size	peaks_keep_n_ {0}
	NLargest cap on MS2 peaks before scoring; 0 = resolution-aware auto (peaks:keep_n)

Int	peaks_window_top_ {20}
	WindowMower peaks-per-100Da before scoring (peaks:window_top)

StringList	modifications_fixed_

StringList	modifications_variable_

Size	modifications_max_variable_mods_per_peptide_

std::string	enzyme_

DecoyMode_	decoy_mode_ {DecoyMode_::AUTO}

std::string	decoy_prefix_

double	fdr_psm_ {0.0}

double	fdr_protein_ {0.0}

StringList	annotate_psm_

Size	peptide_min_size_

Size	peptide_max_size_

Size	peptide_missed_cleavages_

EnzymaticDigestion::Specificity	peptide_enzyme_specificity_ {EnzymaticDigestion::SPEC_FULL}

std::string	peptide_motif_

Size	report_top_hits_

bool	add_a_ions_ {false}

bool	add_b_ions_ {true}

bool	add_c_ions_ {false}

bool	add_x_ions_ {false}

bool	add_y_ions_ {true}

bool	add_z_ions_ {false}

Size	database_chunk_size_ {0}
	0 = disabled; >0 = chunk DB into groups of this many proteins

bool	calibration_enabled_ {false}

double	calibration_subset_ratio_ {0.1}

Size	calibration_min_psms_ {50}

CalibrationResult_	last_calibration_result_

RunStatistics	last_run_stats_

double	last_mod_match_tolerance_used_ {-1.0}

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!

std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!

std::string	error_name_
	Name that is displayed in error messages during the parameter checking.

bool	check_defaults_
	If this member is set to false no checking if parameters in done;.

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Private Member Functions
bool	isOpenSearchMode_ () const
	Helper function to determine if open search should be used based on tolerance.

Additional Inherited Members
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Fragment-index-based peptide database search algorithm (experimental).

Provides a self-contained search engine that matches MS/MS spectra against a protein database using an FI (Fragment Index). Typical usage:

Configure parameters via DefaultParamHandler (mass tolerances, enzyme, charges, etc.)
Call search() with an input spectrum file (mzML or Bruker .d) and a FASTA database to populate identification outputs (ProteinIdentification and PeptideIdentificationList)
Intended for educational/prototyping use and to demonstrate FI-backed searching

Notes:

Used by the ProSE TOPP tool
Experimental; interfaces and behavior may change

Class Documentation

◆ OpenMS::ProSEAlgorithm::CalibrationResult_

struct OpenMS::ProSEAlgorithm::CalibrationResult_

Result of a calibration pass.

Holds the estimated precursor and fragment tolerances computed from confident PSMs during the calibration pass. When success is false, the tolerance values are undefined and should not be used.

Collaboration diagram for ProSEAlgorithm::CalibrationResult_:

[legend]

Class Members
double	cal_lower {0}	calibrated lower magnitude (valid iff !extreme_bias && success)
double	cal_upper {0}	calibrated upper magnitude (valid iff !extreme_bias && success)
bool	extreme_bias {false}	\|shift\| >= spread — writeback skipped (test observability)
double	fragment_shift {0}	reserved for future fragment m/z shift correction
double	fragment_tolerance {0}	estimated fragment tolerance (same unit as configured)
double	precursor_shift {0}	signed median of precursor errors (calibration bias)
double	precursor_spread {0}	median(\|e - shift\|) + 3 * MAD(\|e - shift\|)
bool	success {false}	true if enough PSMs were found for reliable estimation

◆ OpenMS::ProSEAlgorithm::DecoyStrategy_

struct OpenMS::ProSEAlgorithm::DecoyStrategy_

Resolved decoy handling for one concrete input database.

Produced by resolveDecoyStrategy_() and consumed by buildDecoyAugmentedDB_() and the downstream PeptideIndexing / FDR steps, so the same decoys that are searched are also the ones scored.

Collaboration diagram for ProSEAlgorithm::DecoyStrategy_:

[legend]

Class Members
string	decoy_string	effective marker for PeptideIndexing + protein FDR
bool	generate {false}	reverse target proteins to synthesise decoys
bool	have_decoys {false}	searched DB will contain decoys (FDR possible)
bool	is_prefix {true}	position of decoy_string
bool	strip_existing {false}	drop pre-existing decoy entries before searching
bool	strip_is_prefix {true}	position of strip_string
string	strip_string	marker of pre-existing decoys to strip

◆ OpenMS::ProSEAlgorithm::MultiFileSearchResult

struct OpenMS::ProSEAlgorithm::MultiFileSearchResult

Multi-file search result bundle.

Returned by the file-list searchWithModificationAnalysis() overloads. Holds one SearchResult per input file (in per_file, in input order) and a single aggregate result whose peptide_ids are the concatenation of all per-file PSMs and whose modification_analysis is computed once on the pooled set of PSMs.

Special cases for aggregate:

When the input list contains exactly one file, aggregate is left almost-empty (only is_open_search and exit_code are set) — the single-file pooled aggregate would just duplicate per_file[0] and re-run modification analysis on the same PSMs. Callers should use per_file[0] for the result in this case.
When every per-file run failed, aggregate.exit_code is set to the first non-OK per-file exit code (so callers can inspect it without walking the per_file vector).

The aggregate's protein_ids template is taken from the first successful per-file result (search parameters are identical across files by construction), with the primary MS run path overwritten to list every input file.

Collaboration diagram for ProSEAlgorithm::MultiFileSearchResult:

[legend]

Class Members
SearchResult	aggregate
bool	decoy_is_prefix = true	Position of `decoy_string` (true = prefix, false = suffix).
string	decoy_string	Effective decoy marker resolved from the shared database, for a caller-side merged-PSM protein-FDR step (e.g. the ProSE TOPP tool's -out_merged path). Empty when the search was target-only (decoys=ignore).
bool	have_decoys = false	True when the searched databases contained decoys (FDR possible).
vector< SearchResult >	per_file
SharedSearchStats	shared	Configuration / database / fragment-index facts shared across all input files (the index is built once and reused), for the end-of-search report.

◆ OpenMS::ProSEAlgorithm::RunStatistics

struct OpenMS::ProSEAlgorithm::RunStatistics

Per-run identification statistics for the end-of-search report.

Populated by collectRunStatistics_() once a single spectrum file has been searched (post-FDR), plus a few fields captured at well-defined points during search() (target/decoy counts pre-FDR, achieved q-value, timing). All counts refer to one input file. Cross-file/shared facts (database, fragment index, configuration) live in SharedSearchStats instead.

Collaboration diagram for ProSEAlgorithm::RunStatistics:

[legend]

Class Members
double	achieved_psm_fdr = -1.0	max retained q-value after FDR (<0 = n/a)
map< Int, Size >	charge_histogram	precursor charge -> PSM count
Size	decoy_psms = 0	decoy PSMs in the final IDs (after FDR, if applied)
bool	fdr_applied = false	true if PSM-level FDR filtering ran
double	frag_err_mad = 0.0
double	frag_err_median = 0.0
double	frag_err_recommended = 0.0
bool	frag_tol_valid = false	true if fragment-error estimate present
double	hyperscore_max = 0.0
double	hyperscore_median = 0.0
double	hyperscore_min = 0.0
string	input_file	spectrum file this run searched (basename or path)
Size	matched_spectra = 0	spectra with >=1 retained PSM in the final IDs (after FDR, if applied)
map< Size, Size >	missed_cleavage_histogram	missed cleavages -> PSM count
Size	ms2_spectra = 0	number of MS2 spectra in the input
double	prec_err_mad = 0.0
double	prec_err_median = 0.0
double	prec_err_recommended = 0.0
bool	prec_tol_valid = false	true if precursor-error estimate present
bool	score_stats_valid = false	true if hyperscore_* below are meaningful
double	seconds_calibration = 0.0	calibration pass wall time (0 if disabled)
double	seconds_fdr = 0.0	FDR filtering wall time (0 if not applied)
double	seconds_search = 0.0	scoring + post-processing wall time
Size	target_psms = 0	target PSMs in the final IDs (after FDR, if applied)
Size	unique_peptides = 0	distinct peptide sequences among top hits
Size	unique_proteins = 0	distinct protein accessions among top hits

◆ OpenMS::ProSEAlgorithm::SearchContext

struct OpenMS::ProSEAlgorithm::SearchContext

Prepared per-database state shared across multiple spectrum files.

Holds the (decoy-augmented) protein database and the built FragmentIndex so that searching N spectrum files against the same FASTA pays the index build cost only once. Construct via prepareContext() and pass to the context-taking search() overload.

Collaboration diagram for ProSEAlgorithm::SearchContext:

[legend]

Class Members
vector< FASTAEntry >	db
bool	decoy_is_prefix = true	Position of `decoy_string` (true = prefix, false = suffix).
string	decoy_string	Effective decoy marker carried by `db` (auto-detected for external decoys, or the configured prefix for internally generated ones). Empty when the search is target-only. Feeds PeptideIndexing and the protein-level FDR so they recognise the same decoys that were searched.
FragmentIndex	fragment_index
bool	have_decoys = false	True when `db` contains decoy entries (generated or external), i.e. target-decoy FDR is possible.
bool	release_fragment_index_after_scoring = false	When true, the context-taking search() overload will release `fragment_index` (via clear()) after scoreSpectraAgainstIndex_ returns, reclaiming its heap footprint before the PeptideIndexing Aho-Corasick pass — which is otherwise the RSS high-water mark on large databases. Set by single-use callers (e.g. the internal search(spectra, fasta_db, ...) wrapper that creates a throw-away ctx). Default false preserves the reuse contract for callers that built ctx via prepareContext() and want to run multiple search() calls against it.

◆ OpenMS::ProSEAlgorithm::SearchResult

struct OpenMS::ProSEAlgorithm::SearchResult

Comprehensive search result including modification analysis.

This structure contains all outputs from an open search including:

Standard protein and peptide identifications
Delta mass statistics table (histogram of mass shifts)
PTM statistics table (mapped modifications with residue analysis)
Per-run identification statistics for the end-of-search report

Collaboration diagram for ProSEAlgorithm::SearchResult:

[legend]

Class Members
ExitCodes	exit_code = ExitCodes::EXECUTION_OK
bool	is_open_search = false
OpenSearchAnalysisResult	modification_analysis
PeptideIdentificationList	peptide_ids
vector< ProteinIdentification >	protein_ids
RunStatistics	stats

◆ OpenMS::ProSEAlgorithm::SharedSearchStats

struct OpenMS::ProSEAlgorithm::SharedSearchStats

Configuration, database and fragment-index facts shared across all input files of one ProSE invocation.

Computed once (the fragment index is built once and reused), so these costs/counts must NOT be summed per file. Populated by the multi-file searchWithModificationAnalysis() overloads.

Collaboration diagram for ProSEAlgorithm::SharedSearchStats:

[legend]

Class Members
bool	calibration_enabled = false
bool	chunked = false
string	database_file	FASTA path (empty for in-memory db)
Size	db_decoy_proteins = 0	decoy entries in the searched (augmented) db
Size	db_target_proteins = 0	target entries in the searched (augmented) db
string	decoy_mode	"generated" \| "external" \| "none (target-only)"
string	enzyme
vector< string >	fixed_mods
double	fragment_tol = 0.0
string	fragment_tol_unit
Size	indexed_fragments = 0	theoretical fragments in the index (summed over chunks)
Size	indexed_peptides = 0	peptides in the fragment index (summed over chunks)
vector< string >	ion_series
Int	max_charge = 0
Int	min_charge = 0
Size	missed_cleavages = 0
bool	open_search = false
double	precursor_tol_lower = 0.0
string	precursor_tol_unit
double	precursor_tol_upper = 0.0
double	protein_fdr_threshold = 0.0
double	psm_fdr_threshold = 0.0
double	seconds_index_build = 0.0	decoy generation + fragment index build wall time
double	seconds_total = 0.0	whole-search wall time (set by the caller)
bool	snes_mode = false
vector< string >	variable_mods

Member Enumeration Documentation

◆ DecoyMode_

enum class DecoyMode_

strongprotected

How decoys are obtained/recognised for a search (parameter "decoys").

Enumerator
AUTO	ensure decoys: use those already present, otherwise generate
GENERATE	always (re)generate decoys from the targets (strip existing first)
IGNORE	search targets only; remove any decoys present in the database

◆ ExitCodes

enum class ExitCodes

strong

Exit codes.

Enumerator
EXECUTION_OK
INPUT_FILE_EMPTY
UNEXPECTED_RESULT
UNKNOWN_ERROR
ILLEGAL_PARAMETERS

Constructor & Destructor Documentation

◆ ProSEAlgorithm()

ProSEAlgorithm ( )

Member Function Documentation

◆ accessionHasDecoyMarker_()

static bool accessionHasDecoyMarker_	(	const std::string &	accession,
		const std::string &	marker,
		bool	is_prefix
	)

staticprotected

Helper: does accession carry the decoy marker at the given position? Empty marker → false. Pure std::string (no String dependency).

◆ applyCompleteSetProteinFDR()

static void applyCompleteSetProteinFDR	(	std::vector< ProteinIdentification > &	protein_ids,
		PeptideIdentificationList &	peptide_ids,
		const std::string &	decoy_string,
		bool	decoy_is_prefix,
		double	protein_fdr
	)

static

Finalize protein-level FDR on a COMPLETE protein set (a single input file, or a merged cross-file aggregate).

Runs protein inference (BasicProteinInferenceAlgorithm), picked-protein FDR (Savitski et al. 2015), threshold filtering at protein_fdr, then removes decoys and repairs indistinguishable-protein / protein-group / peptide-evidence references so the result stores as schema-valid, decoy-free idXML.

Shared by the file-based single-file search() above and the ProSE TOPP tool's single-file finalization, so the exact IDFilter sequence and ordering live in one place (they previously existed as two copies that could drift).

Precondition: protein_ids is non-empty and the set is statistically complete — picked-protein FDR does not compose across runs. The caller gates on "decoys present" and "FDR requested"; this helper additionally skips (with a warning) when no decoy proteins survive inference, to avoid target-only q-values.

Parameters

[in,out]	protein_ids	Protein identifications (operates on protein_ids[0]).
[in,out]	peptide_ids	PSMs feeding inference; decoy PSMs are removed.
[in]	decoy_string	Accession marker identifying decoy proteins.
[in]	decoy_is_prefix	Whether `decoy_string` is a prefix (true) or suffix (false).
[in]	protein_fdr	Picked-protein q-value threshold (expected > 0).

◆ buildCalibrationSample_()

std::vector< FASTAFile::FASTAEntry > buildCalibrationSample_ ( const std::vector< FASTAFile::FASTAEntry > & full_db ) const

protected

Build a strided protein sample for chunked calibration.

Sample size is tied to database_chunk_size_ so the calibration FI never exceeds the user's declared memory budget. Crucial for immunopeptidomics (non-specific digestion) where a fixed-size 5000-protein sample would generate tens of GB of fragment index. Strided rather than first-N so small chunk_size values don't starve the calibration pool (#9182).

Note: very small chunk_size may still produce a calibration pool below calibration_min_psms_; calibration then no-ops silently (follow-up issue: pool PSMs across first-K chunks of the main search loop).

◆ buildDecoyAugmentedDB_()

std::vector< FASTAFile::FASTAEntry > buildDecoyAugmentedDB_	(	const std::vector< FASTAFile::FASTAEntry > &	fasta_db,
		const DecoyStrategy_ &	strategy
	)		const

protected

Build the searched database according to strategy.

Optionally strips pre-existing decoys and/or generates fresh decoys by reversing the target proteins. Produces FASTA entries only — does not construct a FragmentIndex.

◆ capturePreFdrStats_()

static void capturePreFdrStats_	(	const PeptideIdentificationList &	peptide_ids,
		RunStatistics &	stats
	)

staticprotected

Helper: capture statistics that must be read BEFORE FDR filtering, namely target/decoy PSM counts (via the "target_decoy" meta set by PeptideIndexing; "target+decoy" counts as target, matching OpenMS FDR semantics) and the HyperScore distribution (FDR overwrites each hit's score with its q-value). Fills stats.target_psms, stats.decoy_psms, stats.hyperscore_* and stats.score_stats_valid.

◆ collectRunStatistics_()

void collectRunStatistics_	(	const PeakMap &	spectra,
		const std::vector< ProteinIdentification > &	protein_ids,
		const PeptideIdentificationList &	peptide_ids,
		RunStatistics &	stats
	)		const

protected

Helper: fill a RunStatistics with identification counts, distributions and per-run tolerance estimation for one searched file (post-FDR). Silent; rendering is done separately (ProSE TOPP tool or renderRunSummary()). Fields filled at other points (target/decoy counts, achieved FDR, timing) are left untouched.

◆ computeModMatchTolerance_()

double computeModMatchTolerance_ ( ) const

inlineprotected

Scalar tolerance passed to OpenSearchModificationAnalysis under asymmetric bounds. Uses the tighter of the two positive magnitudes — semantically correct for UniMod Δmass matching precision. OpenSearchModificationAnalysis internally clamps this at MAX_MOD_MAPPING_TOL_ = 0.02 Da; see spec §7 for rationale.

Zero on one side is a legal one-sided window (e.g., [0, 500] Da = "search only positive mass shifts"). In that case std::min() would collapse to 0, passing a useless zero tolerance into the mod analyzer — masked in ppm mode by the internal clamp, but genuinely broken in Da mode. Fall back to the non-zero side so the mod-matching precision reflects the configured tolerance.

◆ fragmentIndexParameters_()

Param fragmentIndexParameters_ ( ) const

protected

ProSE parameters made safe to hand to a FragmentIndex.

FragmentIndex declares its own (unused) boolean "decoys" flag with restrictions {true,false}. ProSE's "decoys" parameter is the richer auto/generate/ignore enum and manages decoys at the database level, so forwarding it verbatim would trip FragmentIndex's validation. This returns getParameters() with "decoys" overridden to "false".

◆ isOpenSearchMode_()

bool isOpenSearchMode_ ( ) const

inlineprivate

Helper function to determine if open search should be used based on tolerance.

◆ maxRetainedScore_()

static double maxRetainedScore_ ( const PeptideIdentificationList & peptide_ids )

staticprotected

Helper: maximum top-hit score among retained PSMs. After PSM-FDR the score is the q-value, so this is the achieved FDR of the filtered set (-1.0 if empty).

◆ postProcessHits_()

void postProcessHits_	(	const PeakMap &	exp,
		std::vector< std::vector< ProSEAlgorithm::AnnotatedHit_ > > &	annotated_hits,
		std::vector< ProteinIdentification > &	protein_ids,
		PeptideIdentificationList &	peptide_ids,
		Size	top_hits,
		const StringList &	modifications_fixed,
		const StringList &	modifications_variable,
		Int	peptide_missed_cleavages,
		double	precursor_mass_tolerance,
		double	fragment_mass_tolerance,
		const std::string &	precursor_mass_tolerance_unit_ppm,
		const std::string &	fragment_mass_tolerance_unit_ppm,
		const Int	precursor_min_charge,
		const Int	precursor_max_charge,
		const std::string &	enzyme,
		const std::string &	database_name
	)		const

protected

Filter and annotate search results.

Trims per-spectrum candidate hits to the top N and converts them into PeptideIdentification objects, adding requested PSM annotations and populating protein-level search metadata.

Parameters

[in]	exp	Input MS experiment providing spectra/metadata for annotation.
[in,out]	annotated_hits	Per-spectrum candidate hits (trimmed to `top_hits` in-place).
[out]	protein_ids	Output container for protein-level identification and search metadata.
[out]	peptide_ids	Output container for spectrum-level peptide identifications (PSMs).
[in]	top_hits	Number of top-scoring hits to retain per spectrum (report_top_hits_).
[in]	modifications_fixed	Fixed modifications (by name) used during the search.
[in]	modifications_variable	Variable modifications (by name) used during the search.
[in]	peptide_missed_cleavages	Allowed missed cleavages in digestion.
[in]	precursor_mass_tolerance	Precursor mass tolerance value.
[in]	fragment_mass_tolerance	Fragment mass tolerance value.
[in]	precursor_mass_tolerance_unit_ppm	Precursor tolerance unit ("true"->ppm, "false"->Da).
[in]	fragment_mass_tolerance_unit_ppm	Fragment tolerance unit ("true"->ppm, "false"->Da).
[in]	precursor_min_charge	Minimum precursor charge considered.
[in]	precursor_max_charge	Maximum precursor charge considered.
[in]	enzyme	Digestion enzyme name.
[out]	database_name	Database file name used for the search (stored in protein_ids).

◆ prepareContext()

SearchContext prepareContext ( const std::vector< FASTAFile::FASTAEntry > & fasta_db ) const

Build a SearchContext (decoy-augmented database + FragmentIndex) for reuse.

Performs the database preparation and FragmentIndex construction steps so that subsequent calls to search(spectra, ctx, ...) can reuse the same index across many spectrum files. If decoy generation is enabled (parameter "decoys"), decoys are generated and shuffled into the returned context's db member exactly once here.

Parameters

[in] fasta_db Protein sequence database as FASTA entries.

Returns: Prepared SearchContext containing the (possibly decoy-augmented) database and the built FragmentIndex.

Thread-safety: the returned context's FragmentIndex is read-only during subsequent search() calls; concurrent search() calls reading the same SearchContext are safe (per FragmentIndex query thread-safety contract). Do not call prepareContext() concurrently on the same algorithm instance.

◆ preprocessSpectra_()

static void preprocessSpectra_	(	PeakMap &	exp,
		double	fragment_mass_tolerance,
		bool	fragment_mass_tolerance_unit_ppm,
		bool	deisotope_requested,
		Size	peaks_keep_n,
		Int	peaks_window_top
	)

staticprotected

filter, deisotope, decharge spectra

◆ renderModificationSummary()

static void renderModificationSummary	(	const OpenSearchModificationAnalysis::OpenSearchAnalysisResult &	mod_analysis,
		std::ostream &	os
	)

static

Render the modification-discovery section (top PTMs, unknown delta masses) to os. Shared by the per-file and aggregate report blocks.

◆ renderRunSummary()

static void renderRunSummary	(	const RunStatistics &	stats,
		const SharedSearchStats &	shared,
		const OpenSearchModificationAnalysis::OpenSearchAnalysisResult &	mod_analysis,
		bool	is_open_search,
		std::ostream &	os
	)

static

Render a human-readable single-run summary block (configuration recap, database/index stats, identification results, tolerance estimate, timing and — for open searches — modification discovery) to os. shared carries the configuration/db/index context (built once).

◆ renderRunSummaryYaml()

static std::string renderRunSummaryYaml	(	const MultiFileSearchResult &	mfres,
		const std::vector< std::pair< std::string, std::vector< std::string > > > &	manifest,
		Size	files_failed,
		Size	files_total
	)

static

Serialize the complete end-of-search report to a machine-readable YAML string: shared configuration/database/index facts, per-file identification statistics, the output-file manifest (label -> written paths) and failed/total file counts. Hand-rolled (no YAML library dependency); every string scalar is double-quoted so values containing ':' (e.g. Windows paths) or other YAML metacharacters round-trip safely, and non-finite numbers are emitted as null.

◆ resolveDecoyStrategy_()

DecoyStrategy_ resolveDecoyStrategy_ ( const std::vector< FASTAFile::FASTAEntry > & db ) const

protected

Decide how to obtain/recognise decoys for db.

Detects pre-existing decoys via the common-marker heuristic (OpenMS::DecoyHelper), falling back to the configured decoy_prefix for custom markers, then maps the "decoys" mode (auto/generate/ignore) onto a concrete DecoyStrategy_.

◆ runCalibrationPass_()

CalibrationResult_ runCalibrationPass_	(	PeakMap &	spectra,
		FragmentIndex &	fragment_index,
		const std::vector< FASTAFile::FASTAEntry > &	db
	)		const

protected

Run a fast calibration pass on a subset of spectra to estimate mass accuracy.

Scores a TIC-ranked subset of spectra against the fragment index, collects precursor and fragment mass errors from high-confidence PSMs, and returns calibrated tolerances using median + 3*MAD estimation.

Parameters

[in]	spectra	Preprocessed MS/MS spectra (subset is selected internally by TIC).
[in,out]	fragment_index	Pre-built fragment index for candidate lookup.
[in]	db	Protein database (for sequence reconstruction of candidates).

Returns: CalibrationResult_ with estimated tolerances, or success=false if insufficient PSMs.

◆ scoreSpectraAgainstIndex_()

void scoreSpectraAgainstIndex_	(	const PeakMap &	spectra,
		FragmentIndex &	fi,
		const std::vector< FASTAFile::FASTAEntry > &	db,
		const TheoreticalSpectrumGenerator &	spectrum_generator,
		double	effective_fragment_tol,
		bool	fragment_mass_tolerance_unit_ppm,
		bool	open_search_mode,
		std::vector< std::vector< AnnotatedHit_ > > &	annotated_hits,
		const std::string &	progress_label
	)		const

protected

Score all spectra against one FragmentIndex.

Shared by the non-chunked and chunked search paths. Appends per-scan AnnotatedHit_ entries to annotated_hits; does not prune or sort. Expects a pre-built FragmentIndex whose parameters already reflect any calibrated tolerances the caller wants to apply.

◆ search() [1/3]

ExitCodes search	(	const std::string &	in_spectra,
		const std::string &	in_db,
		std::vector< ProteinIdentification > &	prot_ids,
		PeptideIdentificationList &	pep_ids
	)		const

Search spectra in a spectrum file (mzML or Bruker .d) against a protein database using an FI-backed workflow.

Populates protein and peptide identifications, including search meta data, PSM hits, and search engine annotations. Parameters are taken from this instance (DefaultParamHandler).

Parameters

[in]	in_spectra	Input path to the spectra file (mzML or Bruker .d) containing MS/MS spectra to search.
[in]	in_db	Input path to the protein sequence database in FASTA format.
[out]	prot_ids	Output container receiving search meta data and protein-level information.
[out]	pep_ids	Output container receiving spectrum-level peptide identifications (PSMs).

Returns: ExitCodes indicating success (EXECUTION_OK) or the encountered error condition.

Side effects:

Updates ProgressLogger during processing.
Assigns identifiers and sets search engine name/version in prot_ids/pep_ids.

Errors:

May signal invalid parameters via ILLEGAL_PARAMETERS exit code.
May propagate OpenMS exceptions (e.g., I/O or parse errors) from underlying components.

◆ search() [2/3]

ExitCodes search	(	PeakMap &	spectra,
		const std::vector< FASTAFile::FASTAEntry > &	fasta_db,
		std::vector< ProteinIdentification > &	prot_ids,
		PeptideIdentificationList &	pep_ids
	)		const

In-memory search: search spectra against a protein database without file I/O.

Same as the file-based search() but takes pre-loaded spectra and FASTA entries directly. Spectra are preprocessed in-place (filtered, deisotoped, normalized).

Parameters

[in,out]	spectra	MS/MS spectra to search (preprocessed in-place).
[in]	fasta_db	Protein sequence database as FASTA entries.
[out]	prot_ids	Output protein-level identifications.
[out]	pep_ids	Output spectrum-level peptide identifications (PSMs).

Returns: ExitCodes indicating success or error.

Internally this is a thin wrapper around prepareContext() + the context-taking search() overload, so the FragmentIndex is rebuilt on every call. For repeated searches against the same database, prefer calling prepareContext() once and reusing the resulting SearchContext.

◆ search() [3/3]

ExitCodes search	(	PeakMap &	spectra,
		SearchContext &	ctx,
		std::vector< ProteinIdentification > &	prot_ids,
		PeptideIdentificationList &	pep_ids
	)		const

In-memory search using a pre-built SearchContext.

Searches spectra against the database and FragmentIndex held in ctx. The fragment index build cost (decoy generation, peptide/fragment generation, sorting, bucketing) is paid by prepareContext() and is not repeated here, making this overload the right choice when searching many spectrum files against the same database.

Parameters

[in,out]	spectra	MS/MS spectra to search (preprocessed in-place).
[in,out]	ctx	Pre-built SearchContext from prepareContext(). Taken by non-const reference because the underlying FragmentIndex query API is non-const, even though the index content is not modified during the search; the `db` member is also handed non-const to the downstream PeptideIndexing step (which requires a non-const reference).
[out]	prot_ids	Output protein-level identifications.
[out]	pep_ids	Output spectrum-level peptide identifications (PSMs).

Returns: ExitCodes indicating success or error.

◆ searchChunked_()

ExitCodes searchChunked_	(	PeakMap &	spectra,
		std::vector< FASTAFile::FASTAEntry > &	full_db,
		const DecoyStrategy_ &	strategy,
		std::vector< ProteinIdentification > &	protein_ids,
		PeptideIdentificationList &	peptide_ids
	)		const

protected

Chunked database search implementation.

Splits full_db into chunks of database_chunk_size_ proteins, builds a FragmentIndex per chunk, scores all spectra against each chunk, and accumulates hits before a single post-processing pass. full_db is the already-resolved database (decoys generated/stripped per strategy); strategy carries the effective decoy marker for PeptideIndexing and FDR. Taken by non-const reference because PeptideIndexing::run() mutates it.

Returns: EXECUTION_OK on success; INPUT_FILE_EMPTY / UNEXPECTED_RESULT / UNKNOWN_ERROR on PeptideIndexing failure.

◆ searchWithModificationAnalysis() [1/4]

SearchResult searchWithModificationAnalysis	(	const std::string &	in_spectra,
		const std::string &	in_db,
		const std::string &	output_base_name = `""`
	)		const

Search with comprehensive results including modification analysis tables.

This method performs a peptide database search and additionally returns structured modification analysis results for open search mode. This is the recommended method for modification discovery workflows.

The method automatically:

Detects open search mode based on precursor tolerance
Computes delta mass statistics
Maps delta masses to known modifications
Generates PTM statistics with residue localization
Writes TSV output files if output_base_name is provided

Parameters

in_spectra	Input path to the spectra file (mzML or Bruker .d) containing MS/MS spectra
in_db	Input path to the protein sequence database in FASTA format
output_base_name	Optional base name for output files (TSV tables)

Returns: SearchResult containing identifications and modification analysis

Example usage:

ProSEAlgorithm algo;
Param p = algo.getParameters();
p.setValue("precursor:mass_tolerance_lower", 500.0);  // Open search
p.setValue("precursor:mass_tolerance_upper", 500.0);
p.setValue("precursor:mass_tolerance_unit", "Da");
algo.setParameters(p);
 
auto result = algo.searchWithModificationAnalysis("spectra.mzML", "database.fasta", "output");
if (result.exit_code == ExitCodes::EXECUTION_OK && result.is_open_search)
{
  // Access PTM statistics
  for (const auto& ptm : result.modification_analysis.ptm_stats.entries)
  {
    std::cout << ptm.name << ": " << ptm.count << " PSMs" << std::endl;
  }
 
  // Access delta mass statistics
  for (const auto& dm : result.modification_analysis.delta_mass_stats.entries)
  {
    std::cout << dm.delta_mass << " Da: " << dm.count << " PSMs" << std::endl;
  }
}

◆ searchWithModificationAnalysis() [2/4]

MultiFileSearchResult searchWithModificationAnalysis	(	const std::vector< std::string > &	in_spectra_files,
		const std::string &	in_db,
		const std::vector< std::string > &	output_base_names = `{}`,
		const std::string &	aggregate_base_name = `""`
	)		const

Multi-file search with modification analysis (FASTA file path).

Convenience overload that loads the FASTA database from in_db and delegates to the in-memory multi-file overload. The database file path is recorded in each per-file ProteinIdentification's SearchParameters (and on the aggregate result).

See also: searchWithModificationAnalysis(const std::vector<std::string>&, const std::vector<FASTAFile::FASTAEntry>&, const std::vector<std::string>&, const std::string&) const

◆ searchWithModificationAnalysis() [3/4]

MultiFileSearchResult searchWithModificationAnalysis	(	const std::vector< std::string > &	in_spectra_files,
		const std::vector< FASTAFile::FASTAEntry > &	fasta_db,
		const std::vector< std::string > &	output_base_names = `{}`,
		const std::string &	aggregate_base_name = `""`
	)		const

Multi-file search with modification analysis (in-memory FASTA).

Builds a single SearchContext (decoy generation + FragmentIndex) from fasta_db and reuses it across all input spectrum files. Each input file produces its own SearchResult including a per-file modification analysis (TSV written if a non-empty per-file base name is provided). An additional aggregate SearchResult is computed by pooling all per-file peptide identifications and running modification analysis once on the pooled set.

Parameters

[in]	in_spectra_files	Spectrum file paths (mzML or Bruker .d).
[in]	fasta_db	Protein sequence database as FASTA entries.
[in]	output_base_names	Optional per-file base names for modification-analysis TSV outputs. Must be empty or have the same length as `in_spectra_files`. Empty entries skip TSV writing for that file.
[in]	aggregate_base_name	Optional base name for the aggregate modification-analysis TSV output. Empty disables aggregate TSV writing (the aggregate analysis is still computed).

Returns: MultiFileSearchResult bundling per-file results and aggregate.

Errors:

Throws Exception::InvalidParameter if output_base_names is non-empty and its size differs from in_spectra_files.

◆ searchWithModificationAnalysis() [4/4]

SearchResult searchWithModificationAnalysis	(	PeakMap &	spectra,
		const std::vector< FASTAFile::FASTAEntry > &	fasta_db,
		const std::string &	output_base_name = `""`
	)		const

In-memory search with modification analysis: no file I/O required.

Same as the file-based searchWithModificationAnalysis() but takes pre-loaded data.

Parameters

[in,out]	spectra	MS/MS spectra (preprocessed in-place).
[in]	fasta_db	Protein sequence database as FASTA entries.
[in]	output_base_name	Optional base name for TSV output files.

Returns: SearchResult containing identifications and modification analysis.

◆ updateFinalStats()

static void updateFinalStats	(	RunStatistics &	stats,
		const PeptideIdentificationList &	peptide_ids,
		const std::string &	enzyme,
		bool	fdr_applied
	)

static

Recompute result-level statistics (matched count, unique peptide/protein counts, charge & missed-cleavage histograms, target/decoy counts and achieved PSM FDR) from a FINAL, post-processed PSM list. Use this when the identifications are mutated AFTER search() returns — e.g. the ProSE TOPP tool's Percolator rescoring + deferred FDR — so the report reflects what the user actually receives. Does NOT touch ms2_spectra, the HyperScore distribution (captured pre-FDR during the search) or any timing field. fdr_applied records whether a PSM-level FDR filter was applied; when true achieved_psm_fdr is set to the maximum retained q-value.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ add_a_ions_

bool add_a_ions_ {false}

protected

◆ add_b_ions_

bool add_b_ions_ {true}

protected

◆ add_c_ions_

bool add_c_ions_ {false}

protected

◆ add_x_ions_

bool add_x_ions_ {false}

protected

◆ add_y_ions_

bool add_y_ions_ {true}

protected

◆ add_z_ions_

bool add_z_ions_ {false}

protected

◆ annotate_psm_

StringList annotate_psm_

protected

◆ calibration_enabled_

bool calibration_enabled_ {false}

protected

◆ calibration_min_psms_

Size calibration_min_psms_ {50}

protected

◆ calibration_subset_ratio_

double calibration_subset_ratio_ {0.1}

protected

◆ database_chunk_size_

Size database_chunk_size_ {0}

protected

0 = disabled; >0 = chunk DB into groups of this many proteins

◆ decoy_mode_

DecoyMode_ decoy_mode_ {DecoyMode_::AUTO}

protected

◆ decoy_prefix_

std::string decoy_prefix_

protected

◆ deisotope_requested_

bool deisotope_requested_ {true}

protected

Resolved MS2 deisotoping request (param fragment:deisotope != "false"). preprocessSpectra_ still gates on Deisotoper::isToleranceSupported() so the deisotoper is never called out of range (it would throw -> terminate in the OpenMP region). See OpenMS#9619.

◆ enzyme_

std::string enzyme_

protected

◆ fdr_protein_

double fdr_protein_ {0.0}

protected

◆ fdr_psm_

double fdr_psm_ {0.0}

protected

◆ fragment_mass_tolerance_

double fragment_mass_tolerance_

protected

◆ fragment_mass_tolerance_unit_

std::string fragment_mass_tolerance_unit_

protected

◆ last_calibration_result_

CalibrationResult_ last_calibration_result_

mutableprotected

Most recent calibration result (valid after any search that invoked runCalibrationPass_). Stored for test observability and diagnostics. Marked mutable because it is pure diagnostic/telemetry state that doesn't affect the logical const-ness of search().

◆ last_mod_match_tolerance_used_

double last_mod_match_tolerance_used_ {-1.0}

mutableprotected

Scalar tolerance passed to OpenSearchModificationAnalysis on the most recent search() call. Stored for test observability: because the calibration writeback restores the tolerance members on exit (to avoid per-file state leaks in the multi-file wrapper), tests that want to verify "the mod analyzer received the calibrated value, not the user-configured one" can't just read the members post-search — they need to see what was actually passed to the analyzer. Default -1.0 (sentinel: no search has run yet).

◆ last_run_stats_

RunStatistics last_run_stats_

mutableprotected

Per-run statistics of the most recent search(spectra, ctx, ...) call. Bridges the const search() (which returns ExitCodes, not a SearchResult) to its callers, which copy this into SearchResult::stats. Reset at the start of each search() call. mutable for the same reason as above: pure diagnostic state, orthogonal to logical const-ness.

◆ modifications_fixed_

StringList modifications_fixed_

protected

◆ modifications_max_variable_mods_per_peptide_

Size modifications_max_variable_mods_per_peptide_

protected

◆ modifications_variable_

StringList modifications_variable_

protected

◆ peaks_keep_n_

Size peaks_keep_n_ {0}

protected

NLargest cap on MS2 peaks before scoring; 0 = resolution-aware auto (peaks:keep_n)

◆ peaks_window_top_

Int peaks_window_top_ {20}

protected

WindowMower peaks-per-100Da before scoring (peaks:window_top)

◆ peptide_enzyme_specificity_

EnzymaticDigestion::Specificity peptide_enzyme_specificity_ {EnzymaticDigestion::SPEC_FULL}

protected

◆ peptide_max_size_

Size peptide_max_size_

protected

◆ peptide_min_size_

Size peptide_min_size_

protected

◆ peptide_missed_cleavages_

Size peptide_missed_cleavages_

protected

◆ peptide_motif_

std::string peptide_motif_

protected

◆ precursor_isotopes_

IntList precursor_isotopes_

protected

◆ precursor_mass_tolerance_lower_

double precursor_mass_tolerance_lower_ {10.0}

mutableprotected

positive magnitude (default matches the param)

Calibration overwrites these with the calibrated magnitudes for the duration of search(); pure runtime-state mutation that does not affect the logical const-ness of search(), matching the mutable pattern used by last_calibration_result_.

◆ precursor_mass_tolerance_unit_

std::string precursor_mass_tolerance_unit_ {"ppm"}

protected

◆ precursor_mass_tolerance_upper_

double precursor_mass_tolerance_upper_ {10.0}

mutableprotected

positive magnitude (default matches the param)

◆ precursor_max_charge_

Size precursor_max_charge_

protected

◆ precursor_min_charge_

Size precursor_min_charge_

protected

◆ report_top_hits_

Size report_top_hits_

protected

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::ProSEAlgorithm::CalibrationResult_

◆ OpenMS::ProSEAlgorithm::DecoyStrategy_

◆ OpenMS::ProSEAlgorithm::MultiFileSearchResult

◆ OpenMS::ProSEAlgorithm::RunStatistics

◆ OpenMS::ProSEAlgorithm::SearchContext

◆ OpenMS::ProSEAlgorithm::SearchResult

◆ OpenMS::ProSEAlgorithm::SharedSearchStats

Member Enumeration Documentation

◆ DecoyMode_

◆ ExitCodes

Constructor & Destructor Documentation

◆ ProSEAlgorithm()

Member Function Documentation

◆ accessionHasDecoyMarker_()

◆ applyCompleteSetProteinFDR()

◆ buildCalibrationSample_()

◆ buildDecoyAugmentedDB_()

◆ capturePreFdrStats_()

◆ collectRunStatistics_()

◆ computeModMatchTolerance_()

◆ fragmentIndexParameters_()

◆ isOpenSearchMode_()

◆ maxRetainedScore_()

◆ postProcessHits_()

◆ prepareContext()

◆ preprocessSpectra_()

◆ renderModificationSummary()

◆ renderRunSummary()

◆ renderRunSummaryYaml()

◆ resolveDecoyStrategy_()

◆ runCalibrationPass_()

◆ scoreSpectraAgainstIndex_()

◆ search() [1/3]

◆ search() [2/3]

◆ search() [3/3]

◆ searchChunked_()

◆ searchWithModificationAnalysis() [1/4]

◆ searchWithModificationAnalysis() [2/4]

◆ searchWithModificationAnalysis() [3/4]

◆ searchWithModificationAnalysis() [4/4]

◆ updateFinalStats()

◆ updateMembers_()

Member Data Documentation

◆ add_a_ions_

◆ add_b_ions_

◆ add_c_ions_

◆ add_x_ions_

◆ add_y_ions_

◆ add_z_ions_

◆ annotate_psm_

◆ calibration_enabled_

◆ calibration_min_psms_

◆ calibration_subset_ratio_

◆ database_chunk_size_

◆ decoy_mode_

◆ decoy_prefix_

◆ deisotope_requested_

◆ enzyme_

◆ fdr_protein_

◆ fdr_psm_

◆ fragment_mass_tolerance_

◆ fragment_mass_tolerance_unit_

◆ last_calibration_result_

◆ last_mod_match_tolerance_used_

◆ last_run_stats_

◆ modifications_fixed_

◆ modifications_max_variable_mods_per_peptide_

◆ modifications_variable_