ProteinIdentification::SearchParameters Struct Reference

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.
	SearchParameters (SearchParameters &&)=default
	Move constructor.
	~SearchParameters ()=default
	Destructor.
SearchParameters &	operator= (const SearchParameters &)=default
	Assignment operator.
SearchParameters &	operator= (SearchParameters &&) &=default
	Move assignment operator.
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
bool	mergeable (const ProteinIdentification::SearchParameters &sp, const String &experiment_type) const
Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()=default
	Constructor.
	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor.
	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor.
	~MetaInfoInterface ()
	Destructor.
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator.
MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator.
void	swap (MetaInfoInterface &rhs)
	Swap contents.
bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator.
bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator.
const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found.
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
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found.
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
bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists.
bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists.
void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name.
void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index.
void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to name if it exists.
void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to index if it exists.
void	addMetaValues (const MetaInfoInterface &from)
void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set.
bool	isMetaEmpty () const
	Returns if the MetaInfo is empty.
void	clearMetaInfo ()
	Removes all meta values.

Public Attributes
String	db
	The used database.
String	db_version
	The database version.
String	taxonomy
	The taxonomy restriction.
String	charges
	The allowed charges for the search.
PeakMassType	mass_type
	Mass type of the peaks.
std::vector< String >	fixed_modifications
	Used fixed modifications.
std::vector< String >	variable_modifications
	Allowed variable modifications.
UInt	missed_cleavages
	The number of allowed missed cleavages.
double	fragment_mass_tolerance
	Mass tolerance of fragment ions (Dalton or ppm)
bool	fragment_mass_tolerance_ppm
	Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
double	precursor_mass_tolerance
	Mass tolerance of precursor ions (Dalton or ppm)
bool	precursor_mass_tolerance_ppm
	Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Protease	digestion_enzyme
	The cleavage site information in details (from ProteaseDB)
EnzymaticDigestion::Specificity	enzyme_term_specificity
	The number of required cutting-rule matching termini during search (none=0, semi=1, or full=2)

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.
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist.
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_ = nullptr
	Pointer to the MetaInfo object.

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 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.