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

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

Inheritance diagram for PeptideSearchEngineFIAlgorithm:

Collaboration diagram for PeptideSearchEngineFIAlgorithm:

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

ExitCodes	search (const String &in_mzML, const String &in_db, std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids) const
	Search spectra in an mzML file against a protein database using an FI-backed workflow. More...

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

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

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

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

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

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

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

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

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

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

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

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

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

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

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

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

void	endProgress (UInt64 bytes_processed=0) const

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

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

void	postProcessHits_ (const PeakMap &exp, std::vector< std::vector< PeptideSearchEngineFIAlgorithm::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. More...

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

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

Static Protected Member Functions
static void	preprocessSpectra_ (PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm)
	filter, deisotope, decharge spectra More...

Protected Attributes
double	precursor_mass_tolerance_

String	precursor_mass_tolerance_unit_

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_

StringList	annotate_psm_

Size	peptide_min_size_

Size	peptide_max_size_

Size	peptide_missed_cleavages_

String	peptide_motif_

Size	report_top_hits_

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

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

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

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

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

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

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. More...

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 mzML file 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 PeptideDataBaseSearchFI TOPP tool
Experimental; interfaces and behavior may change

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 mzML file 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 PeptideDataBaseSearchFI TOPP tool
Experimental; interfaces and behavior may change

Member Enumeration Documentation

◆ ExitCodes

enum ExitCodes

strong

Exit codes.

Enumerator
EXECUTION_OK
INPUT_FILE_EMPTY
UNEXPECTED_RESULT
UNKNOWN_ERROR
ILLEGAL_PARAMETERS

Constructor & Destructor Documentation

◆ PeptideSearchEngineFIAlgorithm()

PeptideSearchEngineFIAlgorithm ( )

Member Function Documentation

◆ isOpenSearchMode_()

bool isOpenSearchMode_ ( ) const

inlineprotected

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

◆ postProcessHits_()

void postProcessHits_	(	const PeakMap &	exp,
		std::vector< std::vector< PeptideSearchEngineFIAlgorithm::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

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

◆ preprocessSpectra_()

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

staticprotected

filter, deisotope, decharge spectra

◆ search()

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

Search spectra in an mzML file 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_mzML	Input path to the mzML file containing MS/MS spectra to search.
in_db	Input path to the protein sequence database in FASTA format.
prot_ids	Output container receiving search meta data and protein-level information.
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.

◆ 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

◆ decoys_

bool decoys_

protected

◆ enzyme_

String enzyme_

protected

◆ fragment_mass_tolerance_

double fragment_mass_tolerance_

protected

◆ fragment_mass_tolerance_unit_

String fragment_mass_tolerance_unit_

protected

◆ 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_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_

double precursor_mass_tolerance_

protected

◆ precursor_mass_tolerance_unit_

String precursor_mass_tolerance_unit_

protected

◆ 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

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ExitCodes

Constructor & Destructor Documentation

◆ PeptideSearchEngineFIAlgorithm()

Member Function Documentation

◆ isOpenSearchMode_()

◆ postProcessHits_()

◆ preprocessSpectra_()

◆ search()

◆ updateMembers_()

Member Data Documentation

◆ annotate_psm_

◆ decoys_

◆ enzyme_

◆ fragment_mass_tolerance_

◆ fragment_mass_tolerance_unit_

◆ modifications_fixed_

◆ modifications_max_variable_mods_per_peptide_

◆ modifications_variable_

◆ 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_