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OpenMS
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Search parameters of the DB search. More...
#include <OpenMS/METADATA/ProteinIdentification.h>
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... | |
Search parameters of the DB search.
| SearchParameters | ( | ) |
|
default |
Copy constructor.
|
default |
Move constructor.
|
default |
Destructor.
| std::pair<int,int> getChargeRange | ( | ) | const |
returns the charge range from the search engine settings as a pair of ints
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private |
| 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.
| bool operator!= | ( | const SearchParameters & | rhs | ) | const |
|
default |
Assignment operator.
|
default |
Move assignment operator.
| bool operator== | ( | const SearchParameters & | rhs | ) | const |
| String charges |
The allowed charges for the search.
| String db |
The used database.
| String db_version |
The database version.
| 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)
| std::vector<String> fixed_modifications |
Used fixed modifications.
| 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)
| PeakMassType mass_type |
Mass type of the peaks.
| UInt missed_cleavages |
The number of allowed missed cleavages.
| 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)
| String taxonomy |
The taxonomy restriction.
| std::vector<String> variable_modifications |
Allowed variable modifications.
1.9.1 
