EnzymesDB Class Reference

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_

Detailed Description

enzyme database which holds enzymes

The enzymes stored in this DB are defined in a XML file under share/CHEMISTRY/Enzymes.xml

Member Typedef Documentation

ConstEnzymeIterator

typedef std::set<const Enzyme*>::const_iterator ConstEnzymeIterator

EnzymeIterator

typedef std::set<const Enzyme*>::iterator EnzymeIterator

Constructor & Destructor Documentation

~EnzymesDB()

virtual ~EnzymesDB ( )

virtual

destructor

EnzymesDB() [1/2]

EnzymesDB ( )

protected

EnzymesDB() [2/2]

EnzymesDB ( const EnzymesDB &  enzyme_db )

protected

copy constructor

Member Function Documentation

addEnzyme()

void addEnzyme

(

const Enzyme &

enzyme

)

adds a new enzyme, e.g. a new enzyme, where only the cleavage regex is known

Note

name of enzyme is registered also in a toLowercase() variant

addEnzyme_()

void addEnzyme_ ( const Enzyme *  enzyme )

protected

beginEnzyme()

ConstEnzymeIterator beginEnzyme ( ) const

inline

clear()

void clear

(

)

deletes all enzymes, resulting in an empty database

endEnzyme()

ConstEnzymeIterator endEnzyme ( ) const

inline

getAllCometNames()

void getAllCometNames

(

std::vector< String > &

all_names

)

const

returns all the enzyme names available for Comet

getAllMSGFNames()

void getAllMSGFNames

(

std::vector< String > &

all_names

)

const

returns all the enzyme names available for MSGFPlus

getAllNames()

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_().

getAllOMSSANames()

void getAllOMSSANames

(

std::vector< String > &

all_names

)

const

returns all the enzyme names available for OMSSA

getAllXTandemNames()

void getAllXTandemNames

(

std::vector< String > &

all_names

)

const

returns all the enzyme names available for XTandem

getEnzyme()

const Enzyme* getEnzyme

(

const String &

name

)

const

returns a pointer to the enzyme with name (supports synonym names)

Exceptions

Exception::ElementNotFound

if enzyme is unknown

Note

enzymes are registered in regular and in toLowercase() style, if unsure use toLowercase

Referenced by SimpleSearchEngine::postProcessHits_().

getEnzymeByRegEx()

const Enzyme* getEnzymeByRegEx

(

const String &

cleavage_regex

)

const

returns a pointer to the enzyme with cleavage regex

Exceptions

Exception::IllegalArgument

if enzyme regex is unregistered.

getInstance()

static EnzymesDB* getInstance ( )

inlinestatic

this member function serves as a replacement of the constructor

Referenced by SimpleSearchEngine::postProcessHits_(), SimpleSearchEngine::registerOptionsAndFlags_(), and RNPxlSearch::registerOptionsAndFlags_().

hasEnzyme() [1/2]

bool hasEnzyme

(

const String &

name

)

const

returns true if the db contains a enzyme with the given name (supports synonym names)

hasEnzyme() [2/2]

bool hasEnzyme

(

const Enzyme *

enzyme

)

const

returns true if the db contains the enzyme of the given pointer

hasRegEx()

bool hasRegEx

(

const String &

cleavage_regex

)

const

returns true if the db contains a enzyme with the given regex

operator=()

EnzymesDB& operator= ( const EnzymesDB &  enzymes_db )

protected

assignment operator

parseEnzyme_()

const Enzyme* parseEnzyme_ ( Map< String, String > &  values ) const

protected

parses a enzyme, given the key/value pairs from i.e. an XML file

readEnzymesFromFile_()

void readEnzymesFromFile_ ( const String &  filename )

protected

reads enzymes from the given file

setEnzymes()

void setEnzymes

(

const String &

filename

)

load enzymes from given file

Member Data Documentation

const_enzymes_

std::set<const Enzyme*> const_enzymes_

protected

enzyme_names_

boost::unordered_map<String, const Enzyme*> enzyme_names_

protected

enzyme_regex_

Map<String, const Enzyme*> enzyme_regex_

protected