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
std::map< String, const DigestionEnzymeType * >	enzyme_names_
	index by names More...

std::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_ (std::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_, and DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::hasRegEx().

◆ 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_.

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

◆ operator=()

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

protecteddelete

assignment operator

◆ parseEnzyme_()

const DigestionEnzymeType* parseEnzyme_ ( std::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_(), String::split(), and OpenMS::StringUtils::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_

std::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_

std::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().

Public Member Functions

Typedefs

Assignment

Iterators

Detailed Description

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

Member Typedef Documentation

◆ ConstEnzymeIterator

◆ EnzymeIterator

Constructor & Destructor Documentation

◆ ~DigestionEnzymeDB()

◆ DigestionEnzymeDB() [1/2]

◆ DigestionEnzymeDB() [2/2]

Member Function Documentation

◆ addEnzyme_()

◆ beginEnzyme()

◆ endEnzyme()

◆ getAllNames()

◆ getEnzyme()

◆ getEnzymeByRegEx()

◆ getInstance()

◆ hasEnzyme() [1/2]

◆ hasEnzyme() [2/2]

◆ hasRegEx()

◆ operator=()

◆ parseEnzyme_()

◆ readEnzymesFromFile_()

Member Data Documentation

◆ const_enzymes_

◆ enzyme_names_

◆ enzyme_regex_

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