Search parameters of the DB search. More...

#include <OpenMS/METADATA/ProteinIdentification.h>

Inheritance diagram for ProteinIdentification::SearchParameters:

Collaboration diagram for ProteinIdentification::SearchParameters:

Public Member Functions
	SearchParameters ()

	SearchParameters (const SearchParameters &)=default
	Copy constructor. More...

	SearchParameters (SearchParameters &&)=default
	Move constructor. More...

	~SearchParameters ()=default
	Destructor. More...

SearchParameters &	operator= (const SearchParameters &)=default
	Assignment operator. More...

SearchParameters &	operator= (SearchParameters &&) &=default
	Move assignment operator. More...

bool	operator== (const SearchParameters &rhs) const

bool	operator!= (const SearchParameters &rhs) const

std::pair< int, int >	getChargeRange () const
	returns the charge range from the search engine settings as a pair of ints More...

bool	mergeable (const ProteinIdentification::SearchParameters &sp, const String &experiment_type) const

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

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

	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor. More...

	~MetaInfoInterface ()
	Destructor. More...

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

MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator. More...

void	swap (MetaInfoInterface &rhs)
	Swap contents. More...

bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator. More...

bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator. More...

const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found. More...

DataValue	getMetaValue (const String &name, const DataValue &default_value) const
	Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found. More...

const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found. More...

DataValue	getMetaValue (UInt index, const DataValue &default_value) const
	Returns the value corresponding to the index, or a default value (e.g.: DataValue::EMPTY) if not found. More...

bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists. More...

bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists. More...

void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name. More...

void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index. More...

void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to `name` if it exists. More...

void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to `index` if it exists. More...

void	addMetaValues (const MetaInfoInterface &from)
	function to copy all meta values from one object to this one More...

void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

bool	isMetaEmpty () const
	Returns if the MetaInfo is empty. More...

void	clearMetaInfo ()
	Removes all meta values. More...

Public Attributes
String	db
	The used database. More...

String	db_version
	The database version. More...

String	taxonomy
	The taxonomy restriction. More...

String	charges
	The allowed charges for the search. More...

PeakMassType	mass_type
	Mass type of the peaks. More...

std::vector< String >	fixed_modifications
	Used fixed modifications. More...

std::vector< String >	variable_modifications
	Allowed variable modifications. More...

UInt	missed_cleavages
	The number of allowed missed cleavages. More...

double	fragment_mass_tolerance
	Mass tolerance of fragment ions (Dalton or ppm) More...

bool	fragment_mass_tolerance_ppm
	Mass tolerance unit of fragment ions (true: ppm, false: Dalton) More...

double	precursor_mass_tolerance
	Mass tolerance of precursor ions (Dalton or ppm) More...

bool	precursor_mass_tolerance_ppm
	Mass tolerance unit of precursor ions (true: ppm, false: Dalton) More...

Protease	digestion_enzyme
	The cleavage site information in details (from ProteaseDB) More...

EnzymaticDigestion::Specificity	enzyme_term_specificity
	The number of required cutting-rule matching termini during search (none=0, semi=1, or full=2) More...

Private Member Functions
int	getChargeValue_ (String &charge_str) const

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...

Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...

Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Detailed Description

Search parameters of the DB search.

Constructor & Destructor Documentation

◆ SearchParameters() [1/3]

SearchParameters ( )

◆ SearchParameters() [2/3]

SearchParameters ( const SearchParameters & )

default

Copy constructor.

◆ SearchParameters() [3/3]

SearchParameters ( SearchParameters && )

default

Move constructor.

◆ ~SearchParameters()

~SearchParameters ( )

default

Destructor.

Member Function Documentation

◆ getChargeRange()

std::pair<int,int> getChargeRange ( ) const

returns the charge range from the search engine settings as a pair of ints

◆ getChargeValue_()

int getChargeValue_ ( String & charge_str ) const

private

◆ mergeable()

bool mergeable	(	const ProteinIdentification::SearchParameters &	sp,
		const String &	experiment_type
	)		const

Tests if these search engine settings are mergeable with

Parameters

sp	depending on the given
experiment_type.	Modifications are compared as sets. Databases based on filename. "labeled_MS1" experiments additionally allow different modifications.

◆ operator!=()

bool operator!= ( const SearchParameters & rhs ) const

◆ operator=() [1/2]

SearchParameters& operator= ( const SearchParameters & )

default

Assignment operator.

◆ operator=() [2/2]

SearchParameters& operator= ( SearchParameters && ) &

default

Move assignment operator.

◆ operator==()

bool operator== ( const SearchParameters & rhs ) const

Member Data Documentation

◆ charges

String charges

The allowed charges for the search.

◆ db

String db

The used database.

◆ db_version

String db_version

The database version.

◆ digestion_enzyme

Protease digestion_enzyme

The cleavage site information in details (from ProteaseDB)

◆ enzyme_term_specificity

EnzymaticDigestion::Specificity enzyme_term_specificity

The number of required cutting-rule matching termini during search (none=0, semi=1, or full=2)

◆ fixed_modifications

std::vector<String> fixed_modifications

Used fixed modifications.

◆ fragment_mass_tolerance

double fragment_mass_tolerance

Mass tolerance of fragment ions (Dalton or ppm)

◆ fragment_mass_tolerance_ppm

bool fragment_mass_tolerance_ppm

Mass tolerance unit of fragment ions (true: ppm, false: Dalton)

◆ mass_type

PeakMassType mass_type

Mass type of the peaks.

◆ missed_cleavages

UInt missed_cleavages

The number of allowed missed cleavages.

◆ precursor_mass_tolerance

double precursor_mass_tolerance

Mass tolerance of precursor ions (Dalton or ppm)

◆ precursor_mass_tolerance_ppm

bool precursor_mass_tolerance_ppm

Mass tolerance unit of precursor ions (true: ppm, false: Dalton)

◆ taxonomy

String taxonomy

The taxonomy restriction.

◆ variable_modifications

std::vector<String> variable_modifications

Allowed variable modifications.

Public Member Functions

Public Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SearchParameters() [1/3]

◆ SearchParameters() [2/3]

◆ SearchParameters() [3/3]

◆ ~SearchParameters()

Member Function Documentation

◆ getChargeRange()

◆ getChargeValue_()

◆ mergeable()

◆ operator!=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

Member Data Documentation

◆ charges

◆ db

◆ db_version

◆ digestion_enzyme

◆ enzyme_term_specificity

◆ fixed_modifications

◆ fragment_mass_tolerance

◆ fragment_mass_tolerance_ppm

◆ mass_type

◆ missed_cleavages

◆ precursor_mass_tolerance

◆ precursor_mass_tolerance_ppm

◆ taxonomy

◆ variable_modifications