Minimal in-memory peptide-spectrum search engine. More...

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

Inheritance diagram for SimpleSearchEngineAlgorithm:

Collaboration diagram for SimpleSearchEngineAlgorithm:

Classes
struct	AnnotatedHit_
	Compact internal record for one scored peptide candidate against one spectrum. More...

Public Types
enum class	ExitCodes { EXECUTION_OK , INPUT_FILE_EMPTY , UNEXPECTED_RESULT , UNKNOWN_ERROR , ILLEGAL_PARAMETERS }
	Outcome of search(), distinguishing recoverable input issues from execution errors. More...

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

Public Member Functions
	SimpleSearchEngineAlgorithm ()
	Default constructor; installs the search parameters (see class docs)

ExitCodes	search (const std::string &in_spectra, const std::string &in_db, std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids) const
	Search the MS2 spectra in `in_spectra` against the protein database in `in_db`.

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)

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< SimpleSearchEngineAlgorithm::AnnotatedHit_ > > &annotated_hits, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids, Size top_hits, const ModifiedPeptideGenerator::MapToResidueType &fixed_modifications, const ModifiedPeptideGenerator::MapToResidueType &variable_modifications, Size max_variable_mods_per_peptide, 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
	Materialise top-N scored candidates per spectrum into PeptideHit / ProteinIdentification objects.

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)
	Preprocess MS2 spectra in place: filter, deisotope, decharge.

Protected Attributes
double	precursor_mass_tolerance_
	Precursor mass tolerance (value); unit in `precursor_mass_tolerance_unit_`.

std::string	precursor_mass_tolerance_unit_
	"ppm" or "Da"

Size	precursor_min_charge_
	Minimum precursor charge considered.

Size	precursor_max_charge_
	Maximum precursor charge considered.

IntList	precursor_isotopes_
	Allowed precursor isotope offsets (0 = monoisotopic, 1 = +1 Da, etc.)

double	fragment_mass_tolerance_
	Fragment mass tolerance (value); unit in `fragment_mass_tolerance_unit_`.

std::string	fragment_mass_tolerance_unit_
	"ppm" or "Da"

StringList	modifications_fixed_
	UniMod names of fixed modifications.

StringList	modifications_variable_
	UniMod names of variable modifications.

Size	modifications_max_variable_mods_per_peptide_
	Cap on simultaneous variable modifications per peptide.

std::string	enzyme_
	Enzyme name as recognised by EnzymaticDigestion.

bool	decoys_
	If true, generate target/decoy results.

double	fdr_psm_
	q-value threshold for PSM filtering (0 = disabled); requires `decoys_`

StringList	annotate_psm_
	PSM meta-value annotations to add (see `annotate:PSM` defaults)

Size	peptide_min_size_
	Minimum peptide length after digestion.

Size	peptide_max_size_
	Maximum peptide length after digestion (0 = unlimited)

Size	peptide_missed_cleavages_
	Allowed missed cleavages in digestion.

EnzymaticDigestion::Specificity	peptide_enzyme_specificity_ {EnzymaticDigestion::SPEC_FULL}
	full / semi / none

std::string	peptide_motif_
	Optional regex motif; only peptides matching are considered.

Size	report_top_hits_
	Number of top-scoring PSMs reported per spectrum.

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_

Additional Inherited Members
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.

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Minimal in-memory peptide-spectrum search engine.

Searches MS2 spectra against a protein FASTA database and produces protein- and peptide-level identifications. Designed as a self-contained reference / teaching implementation; it is not intended as a feature-complete replacement for external engines such as MSGF+, Comet, Sage, or MSFragger.

The pipeline run by search():

Load spectra from in_spectra and the protein database from in_db.
Preprocess MS2 spectra (filtering, deisotoping, decharging) via preprocessSpectra_() using the configured fragment tolerance.
In-silico digest each protein with the configured enzyme/specificity/missed cleavages, generate all combinatorial fixed/variable modification variants (capped at modifications:variable_max_per_peptide), and score them against MS2 spectra whose precursor m/z matches the candidate peptide mass within precursor:mass_tolerance (with optional 1/-1 isotope correction per precursor:isotopes).
Collect the top-N scoring candidates per spectrum (report:top_hits), optionally generate target/decoy results (decoys), filter by FDR (FDR:PSM, q-value) and annotate PSMs (annotate:PSM) in postProcessHits_().

Configuration is exposed through the DefaultParamHandler base — see the defaults installed by the constructor for the full list of supported keys (precursor/fragment tolerances and units, charge range, modifications, enzyme, peptide size/motif/missed-cleavage filters, FDR threshold, top-hits, etc.).

Member Enumeration Documentation

◆ ExitCodes

enum class ExitCodes

strong

Outcome of search(), distinguishing recoverable input issues from execution errors.

Enumerator
EXECUTION_OK	Search completed; `prot_ids` and `pep_ids` contain the result.
INPUT_FILE_EMPTY	Spectrum input contained no usable MS2 spectra after loading/filtering.
UNEXPECTED_RESULT	Internal post-condition violated (e.g. no candidates scored at all)
UNKNOWN_ERROR	Caught a generic exception; details written to the log.
ILLEGAL_PARAMETERS	Configuration is internally inconsistent or unsupported.

Constructor & Destructor Documentation

◆ SimpleSearchEngineAlgorithm()

SimpleSearchEngineAlgorithm ( )

Default constructor; installs the search parameters (see class docs)

Member Function Documentation

◆ postProcessHits_()

void postProcessHits_	(	const PeakMap &	exp,
		std::vector< std::vector< SimpleSearchEngineAlgorithm::AnnotatedHit_ > > &	annotated_hits,
		std::vector< ProteinIdentification > &	protein_ids,
		PeptideIdentificationList &	peptide_ids,
		Size	top_hits,
		const ModifiedPeptideGenerator::MapToResidueType &	fixed_modifications,
		const ModifiedPeptideGenerator::MapToResidueType &	variable_modifications,
		Size	max_variable_mods_per_peptide,
		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

Materialise top-N scored candidates per spectrum into PeptideHit / ProteinIdentification objects.

Converts the in-memory AnnotatedHit_ records produced by the scoring loop into first-class identification objects: re-applies the modification variant indicated by peptide_mod_index, annotates PSM meta values (per annotate:PSM), populates protein references, and stamps search-engine settings (tolerances, modifications, enzyme, etc.) onto the resulting ProteinIdentification so the output is self-describing.

Most parameters mirror the algorithm's own configuration and are passed in explicitly so this routine can also be reused outside member context.

Parameters

[in]	exp	Preprocessed spectra used as scoring input.
[in]	annotated_hits	Per-spectrum vectors of scored candidates (already top-N filtered).
[out]	protein_ids	Protein identifications to populate.
[out]	peptide_ids	Peptide-spectrum matches to populate.
[in]	top_hits	Maximum number of PSMs per spectrum to materialise.
[in]	fixed_modifications	Resolved fixed-modification table.
[in]	variable_modifications	Resolved variable-modification table.
[in]	max_variable_mods_per_peptide	Cap on simultaneous variable modifications.
[in]	modifications_fixed	UniMod names of fixed modifications (for the ID metadata stamp).
[in]	modifications_variable	UniMod names of variable modifications (for the ID metadata stamp).
[in]	peptide_missed_cleavages	Allowed missed cleavages (for the ID metadata stamp).
[in]	precursor_mass_tolerance	Precursor mass tolerance value.
[in]	fragment_mass_tolerance	Fragment mass tolerance value.
[in]	precursor_mass_tolerance_unit_ppm	"ppm" or "Da"; recorded in the ID metadata.
[in]	fragment_mass_tolerance_unit_ppm	"ppm" or "Da"; recorded in the ID metadata.
[in]	precursor_min_charge	Minimum precursor charge considered.
[in]	precursor_max_charge	Maximum precursor charge considered.
[in]	enzyme	Enzyme name (for the ID metadata stamp).
[in]	database_name	FASTA database path/name (for the ID metadata stamp).

◆ preprocessSpectra_()

static void preprocessSpectra_	(	PeakMap &	exp,
		double	fragment_mass_tolerance,
		bool	fragment_mass_tolerance_unit_ppm
	)

staticprotected

Preprocess MS2 spectra in place: filter, deisotope, decharge.

Applies the standard search-engine spectrum normalisation used before scoring: filtering out low-quality peaks, charge state deconvolution, and isotope-pattern deisotoping using the supplied fragment tolerance.

Parameters

[in,out]	exp	Spectra to preprocess in place.
[in]	fragment_mass_tolerance	Tolerance for deisotoping and decharging.
[in]	fragment_mass_tolerance_unit_ppm	If true, `fragment_mass_tolerance` is ppm; otherwise Th.

◆ search()

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

Search the MS2 spectra in in_spectra against the protein database in in_db.

Spectra and database are loaded from disk; the result is written into the two output arguments. Existing contents of prot_ids and pep_ids are not cleared by this call. The current parameter set (see the class brief) controls tolerances, modifications, enzyme, FDR, etc.

Parameters

[in]	in_spectra	Path to the spectrum input (mzML or any format readable by FileHandler).
[in]	in_db	Path to the protein FASTA database to search against.
[out]	prot_ids	Protein identifications produced by the search (one run per call).
[out]	pep_ids	Peptide-spectrum matches (PSMs) produced by the search.

Returns: Status code; see ExitCodes.

◆ 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

PSM meta-value annotations to add (see annotate:PSM defaults)

◆ decoys_

bool decoys_

protected

If true, generate target/decoy results.

◆ enzyme_

std::string enzyme_

protected

Enzyme name as recognised by EnzymaticDigestion.

◆ fdr_psm_

double fdr_psm_

protected

q-value threshold for PSM filtering (0 = disabled); requires decoys_

◆ fragment_mass_tolerance_

double fragment_mass_tolerance_

protected

Fragment mass tolerance (value); unit in fragment_mass_tolerance_unit_.

◆ fragment_mass_tolerance_unit_

std::string fragment_mass_tolerance_unit_

protected

"ppm" or "Da"

◆ modifications_fixed_

StringList modifications_fixed_

protected

UniMod names of fixed modifications.

◆ modifications_max_variable_mods_per_peptide_

Size modifications_max_variable_mods_per_peptide_

protected

Cap on simultaneous variable modifications per peptide.

◆ modifications_variable_

StringList modifications_variable_

protected

UniMod names of variable modifications.

◆ peptide_enzyme_specificity_

EnzymaticDigestion::Specificity peptide_enzyme_specificity_ {EnzymaticDigestion::SPEC_FULL}

protected

full / semi / none

◆ peptide_max_size_

Size peptide_max_size_

protected

Maximum peptide length after digestion (0 = unlimited)

◆ peptide_min_size_

Size peptide_min_size_

protected

Minimum peptide length after digestion.

◆ peptide_missed_cleavages_

Size peptide_missed_cleavages_

protected

Allowed missed cleavages in digestion.

◆ peptide_motif_

std::string peptide_motif_

protected

Optional regex motif; only peptides matching are considered.

◆ precursor_isotopes_

IntList precursor_isotopes_

protected

Allowed precursor isotope offsets (0 = monoisotopic, 1 = +1 Da, etc.)

◆ precursor_mass_tolerance_

double precursor_mass_tolerance_

protected

Precursor mass tolerance (value); unit in precursor_mass_tolerance_unit_.

◆ precursor_mass_tolerance_unit_

std::string precursor_mass_tolerance_unit_

protected

"ppm" or "Da"

◆ precursor_max_charge_

Size precursor_max_charge_

protected

Maximum precursor charge considered.

◆ precursor_min_charge_

Size precursor_min_charge_

protected

Minimum precursor charge considered.

◆ report_top_hits_

Size report_top_hits_

protected

Number of top-scoring PSMs reported per spectrum.

Classes

Public Types

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ExitCodes

Constructor & Destructor Documentation

◆ SimpleSearchEngineAlgorithm()

Member Function Documentation

◆ postProcessHits_()

◆ preprocessSpectra_()

◆ search()

◆ updateMembers_()

Member Data Documentation

◆ annotate_psm_

◆ decoys_

◆ enzyme_

◆ fdr_psm_

◆ fragment_mass_tolerance_

◆ fragment_mass_tolerance_unit_

◆ modifications_fixed_

◆ modifications_max_variable_mods_per_peptide_

◆ modifications_variable_

◆ peptide_enzyme_specificity_

◆ peptide_max_size_

◆ peptide_min_size_

◆ peptide_missed_cleavages_

◆ peptide_motif_

◆ precursor_isotopes_

◆ precursor_mass_tolerance_

◆ precursor_mass_tolerance_unit_

◆ precursor_max_charge_

◆ precursor_min_charge_

◆ report_top_hits_