ProSEAlgorithm Class Reference

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	MultiFileSearchResult
	Multi-file search result bundle. More...
struct	SearchContext
	Prepared per-database state shared across multiple spectrum files. More...
struct	SearchResult
	Comprehensive search result including modification analysis. 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 String &in_spectra, const 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 String &in_spectra, const String &in_db, const 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 String &output_base_name="") const
	In-memory search with modification analysis: no file I/O required.
MultiFileSearchResult	searchWithModificationAnalysis (const std::vector< String > &in_spectra_files, const std::vector< FASTAFile::FASTAEntry > &fasta_db, const std::vector< String > &output_base_names={}, const String &aggregate_base_name="") const
	Multi-file search with modification analysis (in-memory FASTA).
MultiFileSearchResult	searchWithModificationAnalysis (const std::vector< String > &in_spectra_files, const String &in_db, const std::vector< String > &output_base_names={}, const String &aggregate_base_name="") const
	Multi-file search with modification analysis (FASTA file path).
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const 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 String &	getName () const
	Non-mutable access to the name.
void	setName (const String &name)
	Mutable access to the name.
const std::vector< 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 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)

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method.
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 String &precursor_mass_tolerance_unit_ppm, const String &fragment_mass_tolerance_unit_ppm, const Int precursor_min_charge, const Int precursor_max_charge, const String &enzyme, const 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	logModificationAnalysisSummary_ (const SearchResult &result, const String &output_base_name) const
	Helper: log the modification analysis summary (shared by in-memory and file-based paths)
void	logSearchDiagnostics_ (const PeakMap &spectra, const std::vector< ProteinIdentification > &protein_ids, const PeptideIdentificationList &peptide_ids) const
	Helper: log search summary statistics and per-run tolerance estimation.
bool	isOpenSearchMode_ () const
	Helper function to determine if open search should be used based on tolerance.
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)
	filter, deisotope, decharge spectra

Protected Attributes
double	precursor_mass_tolerance_lower_ {20.0}
	positive magnitude
double	precursor_mass_tolerance_upper_ {20.0}
	positive magnitude
String	precursor_mass_tolerance_unit_ {"ppm"}
Size	precursor_min_charge_
Size	precursor_max_charge_
IntList	precursor_isotopes_
double	fragment_mass_tolerance_
String	fragment_mass_tolerance_unit_
StringList	modifications_fixed_
StringList	modifications_variable_
Size	modifications_max_variable_mods_per_peptide_
String	enzyme_
bool	decoys_
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}
String	peptide_motif_
Size	report_top_hits_
bool	calibration_enabled_ {false}
double	calibration_subset_ratio_ {0.1}
Size	calibration_min_psms_ {50}
CalibrationResult_	last_calibration_result_
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< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!
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_

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

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::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:

Class Members
SearchResult	aggregate
vector< SearchResult >	per_file

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:

Class Members
vector< FASTAEntry >	db
FragmentIndex	fragment_index

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)

Collaboration diagram for ProSEAlgorithm::SearchResult:

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

Member Enumeration Documentation

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

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.

isOpenSearchMode_()

bool isOpenSearchMode_ ( ) const

inlineprotected

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

logModificationAnalysisSummary_()

void logModificationAnalysisSummary_ ( const SearchResult &  result, const String &  output_base_name  ) const

protected

Helper: log the modification analysis summary (shared by in-memory and file-based paths)

logSearchDiagnostics_()

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

protected

Helper: log search summary statistics and per-run tolerance estimation.

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 String &  precursor_mass_tolerance_unit_ppm, const String &  fragment_mass_tolerance_unit_ppm, const Int  precursor_min_charge, const Int  precursor_max_charge, const String &  enzyme, const 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  )

staticprotected

filter, deisotope, decharge spectra

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.

search() [1/3]

ExitCodes search	(	const String &	in_spectra,
		const 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.

searchWithModificationAnalysis() [1/4]

MultiFileSearchResult searchWithModificationAnalysis	(	const std::vector< String > &	in_spectra_files,
		const std::vector< FASTAFile::FASTAEntry > &	fasta_db,
		const std::vector< String > &	output_base_names = {},
		const 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() [2/4]

MultiFileSearchResult searchWithModificationAnalysis	(	const std::vector< String > &	in_spectra_files,
		const String &	in_db,
		const std::vector< String > &	output_base_names = {},
		const 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<String>&, const std::vector<FASTAFile::FASTAEntry>&, const std::vector<String>&, const String&) const

searchWithModificationAnalysis() [3/4]

SearchResult searchWithModificationAnalysis	(	const String &	in_spectra,
		const String &	in_db,
		const 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() [4/4]

SearchResult searchWithModificationAnalysis	(	PeakMap &	spectra,
		const std::vector< FASTAFile::FASTAEntry > &	fasta_db,
		const 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.

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

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

decoy_prefix_

String decoy_prefix_

protected

decoys_

bool decoys_

protected

enzyme_

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_

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).

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

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_

String peptide_motif_

protected

precursor_isotopes_

IntList precursor_isotopes_

protected

precursor_mass_tolerance_lower_

double precursor_mass_tolerance_lower_ {20.0}

mutableprotected

positive magnitude

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_

String precursor_mass_tolerance_unit_ {"ppm"}

protected

precursor_mass_tolerance_upper_

double precursor_mass_tolerance_upper_ {20.0}

mutableprotected

positive magnitude

precursor_max_charge_

Size precursor_max_charge_

protected

precursor_min_charge_

Size precursor_min_charge_

protected

report_top_hits_

Size report_top_hits_

protected