enzyme database which holds enzymes More...
#include <OpenMS/CHEMISTRY/EnzymesDB.h>
Public Types | |
Typedefs | |
typedef std::set< const Enzyme * >::const_iterator | ConstEnzymeIterator |
typedef std::set< const Enzyme * >::iterator | EnzymeIterator |
Public Member Functions | |
Constructors and Destructors | |
virtual | ~EnzymesDB () |
destructor More... | |
Accessors | |
const Enzyme * | getEnzyme (const String &name) const |
const Enzyme * | getEnzymeByRegEx (const String &cleavage_regex) const |
void | setEnzymes (const String &filename) |
load enzymes from given file More... | |
void | addEnzyme (const Enzyme &enzyme) |
void | clear () |
deletes all enzymes, resulting in an empty database More... | |
void | getAllNames (std::vector< String > &all_names) const |
returns all the enzyme names (does NOT include synonym names) More... | |
void | getAllXTandemNames (std::vector< String > &all_names) const |
returns all the enzyme names available for XTandem More... | |
void | getAllCometNames (std::vector< String > &all_names) const |
returns all the enzyme names available for Comet More... | |
void | getAllOMSSANames (std::vector< String > &all_names) const |
returns all the enzyme names available for OMSSA More... | |
void | getAllMSGFNames (std::vector< String > &all_names) const |
returns all the enzyme names available for MSGFPlus More... | |
Predicates | |
bool | hasEnzyme (const String &name) const |
returns true if the db contains a enzyme with the given name (supports synonym names) More... | |
bool | hasRegEx (const String &cleavage_regex) const |
returns true if the db contains a enzyme with the given regex More... | |
bool | hasEnzyme (const Enzyme *enzyme) const |
returns true if the db contains the enzyme of the given pointer More... | |
Iterators | |
ConstEnzymeIterator | beginEnzyme () const |
ConstEnzymeIterator | endEnzyme () const |
Static Public Member Functions | |
static EnzymesDB * | getInstance () |
this member function serves as a replacement of the constructor More... | |
Protected Member Functions | |
EnzymesDB () | |
EnzymesDB (const EnzymesDB &enzyme_db) | |
copy constructor More... | |
void | readEnzymesFromFile_ (const String &filename) |
reads enzymes from the given file More... | |
const Enzyme * | parseEnzyme_ (Map< String, String > &values) const |
parses a enzyme, given the key/value pairs from i.e. an XML file More... | |
void | addEnzyme_ (const Enzyme *enzyme) |
Assignment | |
EnzymesDB & | operator= (const EnzymesDB &enzymes_db) |
assignment operator More... | |
Protected Attributes | |
boost::unordered_map< String, const Enzyme * > | enzyme_names_ |
Map< String, const Enzyme * > | enzyme_regex_ |
std::set< const Enzyme * > | const_enzymes_ |
enzyme database which holds enzymes
The enzymes stored in this DB are defined in a XML file under share/CHEMISTRY/Enzymes.xml
typedef std::set<const Enzyme*>::const_iterator ConstEnzymeIterator |
typedef std::set<const Enzyme*>::iterator EnzymeIterator |
|
virtual |
destructor
|
protected |
void addEnzyme | ( | const Enzyme & | enzyme | ) |
adds a new enzyme, e.g. a new enzyme, where only the cleavage regex is known
|
protected |
|
inline |
void clear | ( | ) |
deletes all enzymes, resulting in an empty database
|
inline |
void getAllCometNames | ( | std::vector< String > & | all_names | ) | const |
returns all the enzyme names available for Comet
void getAllMSGFNames | ( | std::vector< String > & | all_names | ) | const |
returns all the enzyme names available for MSGFPlus
void getAllNames | ( | std::vector< String > & | all_names | ) | const |
returns all the enzyme names (does NOT include synonym names)
Referenced by SimpleSearchEngine::registerOptionsAndFlags_(), and RNPxlSearch::registerOptionsAndFlags_().
void getAllOMSSANames | ( | std::vector< String > & | all_names | ) | const |
returns all the enzyme names available for OMSSA
void getAllXTandemNames | ( | std::vector< String > & | all_names | ) | const |
returns all the enzyme names available for XTandem
returns a pointer to the enzyme with name (supports synonym names)
Exception::ElementNotFound | if enzyme is unknown |
Referenced by SimpleSearchEngine::postProcessHits_().
returns a pointer to the enzyme with cleavage regex
Exception::IllegalArgument | if enzyme regex is unregistered. |
|
inlinestatic |
this member function serves as a replacement of the constructor
Referenced by SimpleSearchEngine::postProcessHits_(), SimpleSearchEngine::registerOptionsAndFlags_(), and RNPxlSearch::registerOptionsAndFlags_().
bool hasEnzyme | ( | const String & | name | ) | const |
returns true if the db contains a enzyme with the given name (supports synonym names)
bool hasEnzyme | ( | const Enzyme * | enzyme | ) | const |
returns true if the db contains the enzyme of the given pointer
bool hasRegEx | ( | const String & | cleavage_regex | ) | const |
returns true if the db contains a enzyme with the given regex
parses a enzyme, given the key/value pairs from i.e. an XML file
|
protected |
reads enzymes from the given file
void setEnzymes | ( | const String & | filename | ) |
load enzymes from given file
|
protected |
OpenMS / TOPP release 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:08 using doxygen 1.8.13 |