IntaRNA::OutputHandlerInteractionList Class Reference

#include <OutputHandlerInteractionList.h>

Inheritance diagram for IntaRNA::OutputHandlerInteractionList:

Collaboration diagram for IntaRNA::OutputHandlerInteractionList:

Public Types
typedef StorageContainer::const_iterator	const_iterator
	const iterator on stored interactions
typedef StorageContainer::iterator	iterator
	iterator on stored interactions

Public Member Functions
	OutputHandlerInteractionList (const OutputConstraint &outConstraint, const size_t maxToStore)
virtual	~OutputHandlerInteractionList ()
	destruction
virtual void	add (const Interaction &interaction)
bool	empty () const
const_iterator	begin () const
const_iterator	end () const
iterator	begin ()
iterator	end ()
Public Member Functions inherited from IntaRNA::OutputHandler
	OutputHandler (const OutputConstraint &outConstraint)
virtual	~OutputHandler ()
virtual size_t	reported () const
virtual void	incrementZ (const Z_type subZ)
virtual Z_type	getZ () const
const OutputConstraint &	getOutputConstraint () const

Protected Types
typedef std::list< Interaction * >	StorageContainer
	the container used internally for storing interactions

Static Protected Member Functions
static bool	lessThan_StorageContainer (const Interaction *const a, const Interaction *const b)
	'less-than' comparison struct dereferencing storage pointer

Protected Attributes
StorageContainer	storage
	container where interactions are stored
const size_t	maxToStore
	number of elements to store within storage (only maxToStore best)
size_t	reportedInteractions
	counter of reported interactions
Protected Attributes inherited from IntaRNA::OutputHandler
const OutputConstraint	outConstraint
	the output constraints to be applied
size_t	reportedInteractions
	number of reported interactions
Z_type	Z
	overall partition function for the sequences provided in Z_energy

Additional Inherited Members
Static Public Member Functions inherited from IntaRNA::OutputHandler
static std::string	reverse (const std::string &str)

Detailed Description

OutputHandler that stores all reported interactions in a list

NOTE: this handler does NOT support InteractionRange instances

Member Typedef Documentation

const_iterator

typedef StorageContainer::const_iterator IntaRNA::OutputHandlerInteractionList::const_iterator

const iterator on stored interactions

iterator

typedef StorageContainer::iterator IntaRNA::OutputHandlerInteractionList::iterator

iterator on stored interactions

StorageContainer

typedef std::list<Interaction*> IntaRNA::OutputHandlerInteractionList::StorageContainer

protected

the container used internally for storing interactions

Constructor & Destructor Documentation

OutputHandlerInteractionList()

IntaRNA::OutputHandlerInteractionList::OutputHandlerInteractionList	(	const OutputConstraint &	outConstraint,
		const size_t	maxToStore
	)

construction of empty container

Parameters

maxToStore	the maximal number of (best) elements to be stored
outConstraint	the output constraint applied to find the reported interaction

~OutputHandlerInteractionList()

virtual IntaRNA::OutputHandlerInteractionList::~OutputHandlerInteractionList ( )

virtual

destruction

Member Function Documentation

add()

virtual void IntaRNA::OutputHandlerInteractionList::add ( const Interaction &  interaction )

virtual

Adds a given RNA-RNA interaction to the storage/output.

Parameters

interaction

the interaction to add

Implements IntaRNA::OutputHandler.

begin() [1/2]

OutputHandlerInteractionList::iterator IntaRNA::OutputHandlerInteractionList::begin ( )

inline

iterator to first stored interaction or end() if empty

Returns

first stored interaction (pointer) or end() if empty

begin() [2/2]

OutputHandlerInteractionList::const_iterator IntaRNA::OutputHandlerInteractionList::begin ( ) const

inline

constant iterator to first stored interaction or end() if empty

Returns

first stored interaction (pointer) or end() if empty

empty()

bool IntaRNA::OutputHandlerInteractionList::empty ( ) const

inline

whether or not the container is empty

Returns

true if no elements are stored

end() [1/2]

OutputHandlerInteractionList::iterator IntaRNA::OutputHandlerInteractionList::end ( )

inline

iterator pointing AFTER last interaction (non-valid)

Returns

iterator pointing after last element

end() [2/2]

OutputHandlerInteractionList::const_iterator IntaRNA::OutputHandlerInteractionList::end ( ) const

inline

constant iterator pointing AFTER last interaction (non-valid)

Returns

iterator pointing after last element

lessThan_StorageContainer()

static bool IntaRNA::OutputHandlerInteractionList::lessThan_StorageContainer ( const Interaction *const  a, const Interaction *const  b  )

inlinestaticprotected

'less-than' comparison struct dereferencing storage pointer

Member Data Documentation

maxToStore

const size_t IntaRNA::OutputHandlerInteractionList::maxToStore

protected

number of elements to store within storage (only maxToStore best)

reportedInteractions

size_t IntaRNA::OutputHandler::reportedInteractions

protected

counter of reported interactions

storage

StorageContainer IntaRNA::OutputHandlerInteractionList::storage

protected

container where interactions are stored

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The documentation for this class was generated from the following file:

• src/IntaRNA/OutputHandlerInteractionList.h