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

Inheritance diagram for SimpleSearchEngineAlgorithm:

Collaboration diagram for SimpleSearchEngineAlgorithm:

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
	SimpleSearchEngineAlgorithm ()

ExitCodes	search (const String &in_mzML, const String &in_db, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids) const
	search spectra against database 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	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< SimpleSearchEngineAlgorithm::AnnotatedHit_ > > &annotated_hits, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &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 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 most of the parameters are used to properly add meta data to the id objects 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...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. 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_

Member Enumeration Documentation

◆ ExitCodes

enum ExitCodes

strong

Exit codes.

Enumerator
EXECUTION_OK
INPUT_FILE_EMPTY
UNEXPECTED_RESULT
UNKNOWN_ERROR
ILLEGAL_PARAMETERS

Constructor & Destructor Documentation

◆ SimpleSearchEngineAlgorithm()

SimpleSearchEngineAlgorithm ( )

Member Function Documentation

◆ postProcessHits_()

void postProcessHits_	(	const PeakMap &	exp,
		std::vector< std::vector< SimpleSearchEngineAlgorithm::AnnotatedHit_ > > &	annotated_hits,
		std::vector< ProteinIdentification > &	protein_ids,
		std::vector< PeptideIdentification > &	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 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 most of the parameters are used to properly add meta data to the id objects

◆ 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,
		std::vector< PeptideIdentification > &	pep_ids
	)		const

search spectra against database

◆ 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

Member Enumeration Documentation

◆ ExitCodes

Constructor & Destructor Documentation

◆ SimpleSearchEngineAlgorithm()

Member Function Documentation

◆ 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_