OpenMS
ProteinIdentification::SearchParameters Struct Reference

Search parameters of the DB search. More...

#include <OpenMS/METADATA/ProteinIdentification.h>

Inheritance diagram for ProteinIdentification::SearchParameters:
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Collaboration diagram for ProteinIdentification::SearchParameters:
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Public Member Functions

 SearchParameters ()
 
 SearchParameters (const SearchParameters &)=default
 Copy constructor. More...
 
 SearchParameters (SearchParameters &&)=default
 Move constructor. More...
 
 ~SearchParameters ()=default
 Destructor. More...
 
SearchParametersoperator= (const SearchParameters &)=default
 Assignment operator. More...
 
SearchParametersoperator= (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...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
 
MetaInfoInterfaceoperator= (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 DataValuegetMetaValue (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 DataValuegetMetaValue (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< Stringfixed_modifications
 Used fixed modifications. More...
 
std::vector< Stringvariable_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 MetaInfoRegistrymetaRegistry ()
 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
MetaInfometa_
 Pointer to the MetaInfo object (0 by default) More...
 

Detailed Description

Search parameters of the DB search.

Constructor & Destructor Documentation

◆ SearchParameters() [1/3]

◆ SearchParameters() [2/3]

SearchParameters ( const SearchParameters )
default

Copy constructor.

◆ SearchParameters() [3/3]

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.