Database for enzymes that digest RNA (RNases) More...

Inheritance diagram for RNaseDB:

Collaboration diagram for RNaseDB:

Public Member Functions
	RNaseDB (std::vector< std::unique_ptr< DigestionEnzymeDataProvider< DigestionEnzymeRNA > > > providers)
	Construct from custom data providers (for testing / dependency injection)

Public Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
virtual	~DigestionEnzymeDB ()
	destructor

const DigestionEnzymeRNA *	getEnzyme (const String &name) const

const DigestionEnzymeRNA *	getEnzymeByRegEx (const String &cleavage_regex) const

void	getAllNames (std::vector< String > &all_names) const
	returns all the enzyme names (does NOT include synonym names)

bool	hasEnzyme (const String &name) const
	returns true if the db contains a enzyme with the given name (supports synonym names)

bool	hasEnzyme (const DigestionEnzymeRNA *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

ConstEnzymeIterator	beginEnzyme () const

ConstEnzymeIterator	endEnzyme () const

Protected Member Functions
	RNaseDB ()
	default constructor: loads enzymes from XML file

Protected Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
DigestionEnzymeDB &	operator= (const DigestionEnzymeDB &enzymes_db)=delete
	assignment operator

void	addEnzyme_ (const DigestionEnzymeRNA *enzyme)

void	loadFromProviders_ (std::vector< std::unique_ptr< DigestionEnzymeDataProvider< DigestionEnzymeRNA > > > &providers)

	DigestionEnzymeDB ()=default

	DigestionEnzymeDB (const DigestionEnzymeDB &enzymes_db)=delete
	copy constructor

Friends
class	DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >

Additional Inherited Members
Public Types inherited from DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
typedef std::set< constDigestionEnzymeType * >::const_iterator	ConstEnzymeIterator

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

Static Public Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
static RNaseDB *	getInstance ()
	this member function serves as a replacement of the constructor

Protected Attributes inherited from DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
std::map< String, const DigestionEnzymeRNA * >	enzyme_names_
	index by names

std::map< String, const DigestionEnzymeRNA * >	enzyme_regex_
	index by regex

std::set< const DigestionEnzymeRNA * >	const_enzymes_
	set of enzymes

Detailed Description

Database for enzymes that digest RNA (RNases)

The enzymes stored in this DB are defined in an XML file under "share/CHEMISTRY/Enzymes_RNA.xml".

Supports dependency injection via a provider-based constructor for testing and custom enzyme sources.

Constructor & Destructor Documentation

RNaseDB ( )

protected

default constructor: loads enzymes from XML file

RNaseDB ( std::vector< std::unique_ptr< DigestionEnzymeDataProvider< DigestionEnzymeRNA > > > providers )

explicit

Construct from custom data providers (for testing / dependency injection)

Parameters

[in] providers Data providers supplying enzyme definitions

friend