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
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)
Predicates
bool	hasEnzyme (const String &name) const
	returns true if the db contains a enzyme with the given name (supports synonym names)
bool	hasRegEx (const String &cleavage_regex) const
	returns true if the db contains a enzyme with the given regex
bool	hasEnzyme (const DigestionEnzymeType *enzyme) const
	returns true if the db contains the enzyme of the given pointer

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

Assignment
std::map< String, const DigestionEnzymeType * >	enzyme_names_
	index by names
std::map< String, const DigestionEnzymeType * >	enzyme_regex_
	index by regex
std::set< const DigestionEnzymeType * >	const_enzymes_
	set of enzymes
DigestionEnzymeDB &	operator= (const DigestionEnzymeDB &enzymes_db)=delete
	assignment operator
bool	readEnzymesFromFileIfPresent_ (const String &filename)
	Reads enzymes from the given file if it exists.
void	readEnzymesFromFile_ (const String &filename)
	reads enzymes from the given file
const DigestionEnzymeType *	parseEnzyme_ (std::map< String, String > &values) const
	parses an enzyme, given the key/value pairs from an XML file
void	addEnzyme_ (const DigestionEnzymeType *enzyme)

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

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

template<typename DigestionEnzymeType , typename InstanceType >

typedef std::set<constDigestionEnzymeType*>::const_iterator ConstEnzymeIterator

EnzymeIterator

template<typename DigestionEnzymeType , typename InstanceType >

typedef std::set<constDigestionEnzymeType*>::iterator EnzymeIterator

Constructor & Destructor Documentation

~DigestionEnzymeDB()

template<typename DigestionEnzymeType , typename InstanceType >

virtual ~DigestionEnzymeDB ( )

inlinevirtual

destructor

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::const_enzymes_.

DigestionEnzymeDB() [1/2]

template<typename DigestionEnzymeType , typename InstanceType >

DigestionEnzymeDB ( const String &  db_file = "" )

inlineprotected

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

DigestionEnzymeDB() [2/2]

template<typename DigestionEnzymeType , typename InstanceType >

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

protecteddelete

copy constructor

Member Function Documentation

addEnzyme_()

template<typename DigestionEnzymeType , typename InstanceType >

void addEnzyme_ ( const DigestionEnzymeType *  enzyme )

inlineprotected

add to internal data; also update indices for search by name and regex. If an enzyme with the same name already exists, it is replaced.

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()

template<typename DigestionEnzymeType , typename InstanceType >

ConstEnzymeIterator beginEnzyme ( ) const

inline

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::const_enzymes_.

endEnzyme()

template<typename DigestionEnzymeType , typename InstanceType >

ConstEnzymeIterator endEnzyme ( ) const

inline

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::const_enzymes_.

getAllNames()

template<typename DigestionEnzymeType , typename InstanceType >

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_.

getEnzyme()

template<typename DigestionEnzymeType , typename InstanceType >

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_.

getEnzymeByRegEx()

template<typename DigestionEnzymeType , typename InstanceType >

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()

template<typename DigestionEnzymeType , typename InstanceType >

static InstanceType * getInstance ( )

inlinestatic

this member function serves as a replacement of the constructor

hasEnzyme() [1/2]

template<typename DigestionEnzymeType , typename InstanceType >

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]

template<typename DigestionEnzymeType , typename InstanceType >

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()

template<typename DigestionEnzymeType , typename InstanceType >

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=()

template<typename DigestionEnzymeType , typename InstanceType >

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

protecteddelete

assignment operator

parseEnzyme_()

template<typename DigestionEnzymeType , typename InstanceType >

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_()

template<typename DigestionEnzymeType , typename InstanceType >

void readEnzymesFromFile_ ( const String &  filename )

inlineprotected

reads enzymes from the given file

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

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

readEnzymesFromFileIfPresent_()

template<typename DigestionEnzymeType , typename InstanceType >

bool readEnzymesFromFileIfPresent_ ( const String &  filename )

inlineprotected

Reads enzymes from the given file if it exists.

Returns

true if file was found and loaded successfully, false if file was not found

Note

Only FileNotFound exceptions are caught. ParseError exceptions are intentionally re-thrown to indicate XML parsing issues with an existing file.

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

Member Data Documentation

const_enzymes_

template<typename DigestionEnzymeType , typename InstanceType >

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_

template<typename DigestionEnzymeType , typename InstanceType >

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_

template<typename DigestionEnzymeType , typename InstanceType >

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().