| OpenMS 2.5.0

Public Member Functions | Public Attributes | Private Member Functions | List of all members
ProteinIdentification::SearchParameters Struct Reference

Search parameters of the DB search. More...

`#include <OpenMS/METADATA/ProteinIdentification.h>`

Inheritance 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...
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 DataValue &default_value=DataValue::EMPTY) const
| Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...
const DataValue & | getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
| Returns the value corresponding to an index, or a default value (default: 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 | 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...

## 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)

## ◆ 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.