| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | List of all members
CrossLinksDB Class Reference

`#include <OpenMS/CHEMISTRY/CrossLinksDB.h>`

Inheritance diagram for CrossLinksDB:

## Public Member Functions

void | readFromOBOFile (const String &filename)
| Adds modifications from a given file in OBO format. More...
void | getAllSearchModifications (std::vector< String > &modifications) const
| Collects all modifications that can be used for identification searches. More...
Public Member Functions inherited from ModificationsDB
Size | getNumberOfModifications () const
| Returns the number of modifications read from the unimod.xml file. More...
const ResidueModification * | getModification (Size index) const
| Returns the modification with the given index. note: out-of-bounds check is only performed in debug mode. More...
void | searchModifications (std::set< const ResidueModification *> &mods, const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
| Collects all modifications which have the given name as synonym. More...
const ResidueModification * | getModification (const String &mod_name, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY) const
| Returns the modification with the given name. More...
bool | has (String modification) const
| Returns true if the modification exists. More...
void | addModification (ResidueModification *new_mod)
| Add a new modification to ModificationsDB. Will skip adding if modification already exists (based on its fullID) More...
Size | findModificationIndex (const String &mod_name) const
| Returns the index of the modification in the mods_ vector; a unique name must be given. More...
void | searchModificationsByDiffMonoMass (std::vector< String > &mods, double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)
| Collects all modifications with matching delta mass. More...
const ResidueModification * | getBestModificationByDiffMonoMass (double mass, double max_error, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY)
| Returns the best matching modification for the given delta mass and residue. More...
void | getAllSearchModifications (std::vector< String > &modifications) const
| Collects all modifications that can be used for identification searches. More...

## Static Public Member Functions

static CrossLinksDB * | getInstance ()
| Returns a pointer to the modifications DB (singleton) More...
Static Public Member Functions inherited from ModificationsDB
static ModificationsDB * | getInstance ()
| Returns a pointer to the modifications DB (singleton) More...
static ModificationsDB * | initializeModificationsDB (OpenMS::String unimod_file="CHEMISTRY/unimod.xml", OpenMS::String psimod_file="CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file="CHEMISTRY/XLMOD.obo")
| Initializes the modification DB with non-default modification files (can only be done once) More...
static bool | isInstantiated ()
| Check whether ModificationsDB was instantiated before. More...

## Private Member Functions

Constructors and Destructors
| CrossLinksDB ()
| Default constructor. More...
| CrossLinksDB (const CrossLinksDB &residue_db)
| Copy constructor. More...
| ~CrossLinksDB () override
| Destructor. More...
Assignment
CrossLinksDB & | operator= (const CrossLinksDB &aa)
| Assignment operator. More...

## Additional Inherited Members

Protected Member Functions inherited from ModificationsDB
bool | residuesMatch_ (const String &residue, const ResidueModification *origin) const
| Helper function to check if a residue matches the origin for a modification. More...
Protected Attributes inherited from ModificationsDB
std::vector< ResidueModification * > | mods_
| Stores the modifications. More...
Map< String, std::set< const ResidueModification * > > | modification_names_
| Stores the mappings of (unique) names to the modifications. More...
Static Protected Attributes inherited from ModificationsDB
static bool | is_instantiated_
| Stores whether ModificationsDB was instantiated before. More...

## Constructor & Destructor Documentation

## ◆ CrossLinksDB() [1/2]

CrossLinksDB | ( |  | ) |

private

Default constructor.

## ◆ CrossLinksDB() [2/2]

CrossLinksDB | ( | const CrossLinksDB & | residue_db | ) |

private

Copy constructor.

## ◆ ~CrossLinksDB()

~CrossLinksDB | ( |  | ) |

override private

Destructor.

## Member Function Documentation

## ◆ getAllSearchModifications()

void getAllSearchModifications | ( | std::vector< String > & | modifications | ) | const

Collects all modifications that can be used for identification searches.

## ◆ getInstance()

static CrossLinksDB* getInstance | ( |  | ) |

inline static

Returns a pointer to the modifications DB (singleton)

## ◆ operator=()

CrossLinksDB& operator= | ( | const CrossLinksDB & | aa | ) |

private

Assignment operator.

## ◆ readFromOBOFile()

void readFromOBOFile | ( | const String & | filename | ) |

Adds modifications from a given file in OBO format.

Note
  readFromOBOFile should be called in a single threaded context with no other threads accessing the CrossLinkDB

Exceptions

  Exception::ParseError | if the file cannot be parsed correctly