DigestionEnzymeDB< DigestionEnzymeType, InstanceType > Class Template Reference

Digestion enzyme database (base class) More...

#include <OpenMS/CHEMISTRY/DigestionEnzymeDB.h>

Inheritance diagram for DigestionEnzymeDB< DigestionEnzymeType, InstanceType >:

Collaboration diagram for DigestionEnzymeDB< DigestionEnzymeType, InstanceType >:

Public Member Functions
Constructors and Destructors
virtual	~DigestionEnzymeDB ()
	destructor More...
Accessors
const DigestionEnzymeType *	getEnzyme (const String &name) const
const DigestionEnzymeType *	getEnzymeByRegEx (const String &cleavage_regex) const
void	getAllNames (std::vector< String > &all_names) const
	returns all the enzyme names (does NOT include synonym names) 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 DigestionEnzymeType *enzyme) const
	returns true if the db contains the enzyme of the given pointer More...

Typedefs
typedef std::set< const DigestionEnzymeType * >::const_iterator	ConstEnzymeIterator
typedef std::set< const DigestionEnzymeType * >::iterator	EnzymeIterator
static InstanceType *	getInstance ()
	this member function serves as a replacement of the constructor More...

Assignment
Map< String, const DigestionEnzymeType * >	enzyme_names_
	index by names More...
Map< String, const DigestionEnzymeType * >	enzyme_regex_
	index by regex More...
std::set< const DigestionEnzymeType * >	const_enzymes_
	set of enzymes More...
DigestionEnzymeDB &	operator= (const DigestionEnzymeDB &enzymes_db)=delete
	assignment operator More...
void	readEnzymesFromFile_ (const String &filename)
	reads enzymes from the given file More...
const DigestionEnzymeType *	parseEnzyme_ (Map< String, String > &values) const
	parses an enzyme, given the key/value pairs from an XML file More...
void	addEnzyme_ (const DigestionEnzymeType *enzyme)
	add to internal data; also update indices for search by name and regex More...

Iterators
ConstEnzymeIterator	beginEnzyme () const
ConstEnzymeIterator	endEnzyme () const
	DigestionEnzymeDB (const String &db_file="")
	DigestionEnzymeDB (const DigestionEnzymeDB &enzymes_db)=delete
	copy constructor More...

Detailed Description

template<typename DigestionEnzymeType, typename InstanceType>
class OpenMS::DigestionEnzymeDB< DigestionEnzymeType, InstanceType >

Digestion enzyme database (base class)

Template parameters: DigestionEnzymeType should be a subclass of DigestionEnzyme. InstanceType should be a subclass of DigestionEnzymeDB ("Curiously Recurring Template Pattern", see https://stackoverflow.com/a/34519373).

Member Typedef Documentation

ConstEnzymeIterator

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

EnzymeIterator

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

Constructor & Destructor Documentation

~DigestionEnzymeDB()

virtual ~DigestionEnzymeDB ( )

inlinevirtual

destructor

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::const_enzymes_.

DigestionEnzymeDB() [1/2]

DigestionEnzymeDB ( const String &  db_file = "" )

inlineprotected

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::readEnzymesFromFile_().

DigestionEnzymeDB() [2/2]

DigestionEnzymeDB ( const DigestionEnzymeDB< DigestionEnzymeType, InstanceType > &  enzymes_db )

protecteddelete

copy constructor

Member Function Documentation

addEnzyme_()

void addEnzyme_ ( const DigestionEnzymeType *  enzyme )

inlineprotected

add to internal data; also update indices for search by name and regex

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::const_enzymes_, DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::enzyme_names_, DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::enzyme_regex_, and String::toLower().

Referenced by DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::readEnzymesFromFile_().

beginEnzyme()

ConstEnzymeIterator beginEnzyme ( ) const

inline

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::const_enzymes_.

endEnzyme()

ConstEnzymeIterator endEnzyme ( ) const

inline

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::const_enzymes_.

getAllNames()

void getAllNames ( std::vector< String > &  all_names ) const

inline

returns all the enzyme names (does NOT include synonym names)

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::const_enzymes_.

Referenced by NucleicAcidSearchEngine::registerOptionsAndFlags_().

getEnzyme()

const DigestionEnzymeType* getEnzyme ( const String &  name ) const

inline

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

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::enzyme_names_.

Referenced by NucleicAcidSearchEngine::main_().

getEnzymeByRegEx()

const DigestionEnzymeType* getEnzymeByRegEx ( const String &  cleavage_regex ) const

inline

returns a pointer to the enzyme with cleavage regex

Exceptions

Exception::IllegalArgument

if enzyme regex is unregistered.

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::enzyme_regex_.

getInstance()

static InstanceType* getInstance ( )

inlinestatic

this member function serves as a replacement of the constructor

hasEnzyme() [1/2]

bool hasEnzyme ( const DigestionEnzymeType *  enzyme ) const

inline

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

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::const_enzymes_.

hasEnzyme() [2/2]

bool hasEnzyme ( const String &  name ) const

inline

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

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::enzyme_names_.

hasRegEx()

bool hasRegEx ( const String &  cleavage_regex ) const

inline

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

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::enzyme_regex_.

operator=()

DigestionEnzymeDB& operator= ( const DigestionEnzymeDB< DigestionEnzymeType, InstanceType > &  enzymes_db )

protecteddelete

assignment operator

parseEnzyme_()

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

inlineprotected

parses an enzyme, given the key/value pairs from an XML file

References OPENMS_LOG_ERROR.

Referenced by DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::readEnzymesFromFile_().

readEnzymesFromFile_()

void readEnzymesFromFile_ ( const String &  filename )

inlineprotected

reads enzymes from the given file

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::addEnzyme_(), Param::begin(), Param::empty(), Param::end(), File::find(), Param::ParamIterator::getName(), ParamXMLFile::load(), DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::parseEnzyme_(), and String::split().

Referenced by DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::DigestionEnzymeDB().

Member Data Documentation

const_enzymes_

std::set<const DigestionEnzymeType*> const_enzymes_

protected

set of enzymes

Referenced by DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::addEnzyme_(), DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::beginEnzyme(), DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::endEnzyme(), DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::getAllNames(), DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::hasEnzyme(), and DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::~DigestionEnzymeDB().

enzyme_names_

Map<String, const DigestionEnzymeType*> enzyme_names_

protected

index by names

Referenced by DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::addEnzyme_(), DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::getEnzyme(), and DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::hasEnzyme().

enzyme_regex_

Map<String, const DigestionEnzymeType*> enzyme_regex_

protected

index by regex

Referenced by DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::addEnzyme_(), DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::getEnzymeByRegEx(), and DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::hasRegEx().