BALL::Enumerator< Container, SiteIterator, Variant > Class Template Reference

#include <BALL/CONCEPT/enumerator.h>

List of all members.

Classes
class	IteratorTraits_
Public Types
Type definitions
typedef void(*	MutatorFunction )(Variant &, const Variant &)
typedef std::vector< Variant >	VariantVector
typedef std::pair < SiteIterator, VariantVector >	Site
typedef std::list< Site >	SiteList
typedef ForwardIterator < Enumerator< Container, SiteIterator, Variant > , Container, EnumeratorIndex *, IteratorTraits_ >	Iterator
typedef ConstForwardIterator < Enumerator< Container, SiteIterator, Variant > , Container, EnumeratorIndex *, IteratorTraits_ >	ConstIterator
Public Member Functions
Constructors and Destructors
	Enumerator ()
	Enumerator (Container &container)
	Enumerator (Container &container, MutatorFunction mutator)
	~Enumerator ()
Accessors
void	addVariants (const SiteIterator &it, const VariantVector &variants)
void	deleteVariants (const SiteIterator &it, const VariantVector &variants)
Size	countVariants ()
Container &	getCurrent ()
void	createCombination (const Position index) throw (Exception::IndexOverflow)
void	createCombination (const EnumeratorIndex &index) throw (EnumeratorIndex::IncompatibleIndex)
Iterators
Iterator	begin ()
Iterator	end ()
ConstIterator	begin () const
ConstIterator	end () const
Protected Member Functions
void	mutate_ (SiteIterator &it, const Variant &v)
Static Protected Member Functions
static void	defaultAssign_ (Variant &a, const Variant &b)
Protected Attributes
Container &	container_
MutatorFunction	mutator_
SiteList	variant_sites_
EnumeratorIndex	position_
bool	is_valid_position_
Friends
class	IteratorTraits_

---

Detailed Description

template<class Container, class SiteIterator, class Variant>
class BALL::Enumerator< Container, SiteIterator, Variant >

Enumerator class. The EnumeratorIndex class is designed to enumerate all possible combinations of things. Applications are e.g. the enumeration of all possible sequences defined through a multisequence or enumerating all possible rotamers of a peptide or a bindings site.

Enumerator uses EnumeratorIndex as an inhomogeneous counter class. It is also highly templatized in order to be adaptable to most problem instances. In general, the enumeration problem can be seen as counting with a mixed-base number. For an example of the Enumerator's usage, please refer to the tutorial.

The Enumerator's template arguments are

• the Container it operates on (e.g. the String representing the sequence or the protein containing the amino acids)
• the SiteIterator (i.e. an iterator pointing to a defined position within the container)
• the Variant type (i.e. the type of the object to be enumerated). It has to be the same type as the dereferenced SiteIterator.

In the case of a string sequence that has to be mutated, the Container is of class String , the SiteIterator is of type String::Iterator, and Variant is obviously of type char.

---

Member Typedef Documentation

template<class Container, class SiteIterator, class Variant>

typedef ConstForwardIterator<Enumerator<Container, SiteIterator, Variant>, Container, EnumeratorIndex*, IteratorTraits_> BALL::Enumerator< Container, SiteIterator, Variant >::ConstIterator

Constant forward iterator

template<class Container, class SiteIterator, class Variant>

typedef ForwardIterator<Enumerator<Container, SiteIterator, Variant>, Container, EnumeratorIndex*, IteratorTraits_> BALL::Enumerator< Container, SiteIterator, Variant >::Iterator

Mutable forward iterator

template<class Container, class SiteIterator, class Variant>

typedef void(* BALL::Enumerator< Container, SiteIterator, Variant >::MutatorFunction)(Variant &, const Variant &)

Site mutator function. A function used to assing one variant of a site in the container to another. In the trivial case, this is just the assignment operator (as implemented in the default case), but more involved enumeration problems (e.g. side chain rotamer enumeration) might require additional code for the assignment of the true variant.

template<class Container, class SiteIterator, class Variant>

typedef std::pair<SiteIterator, VariantVector> BALL::Enumerator< Container, SiteIterator, Variant >::Site

A combination of a site position and all its possible variants.

template<class Container, class SiteIterator, class Variant>

typedef std::list<Site> BALL::Enumerator< Container, SiteIterator, Variant >::SiteList

A list of sites.

template<class Container, class SiteIterator, class Variant>

typedef std::vector<Variant> BALL::Enumerator< Container, SiteIterator, Variant >::VariantVector

A vector containing all possible variants for a specific site.

---

Constructor & Destructor Documentation

template<typename Container , typename SiteIterator , typename Variant >

BALL::Enumerator< Container, SiteIterator, Variant >::Enumerator

(

)

[inline]

Default Constructor

template<typename Container , typename SiteIterator , typename Variant >

BALL::Enumerator< Container, SiteIterator, Variant >::Enumerator

(

Container &

container

)

[inline]

Detailed Constructor. The mutator function is set to a default mutator, using the assignment operator for Variant.

Parameters:

container

a Container class to be mutated

template<class Container, class SiteIterator, class Variant>

BALL::Enumerator< Container, SiteIterator, Variant >::Enumerator	(	Container &	container,
		MutatorFunction	mutator
	)

Detailed Constructor

Parameters:

	container	a Container class to be mutated
	mutator	the function defining the mutations to be applied

template<class Container, class SiteIterator, class Variant>

BALL::Enumerator< Container, SiteIterator, Variant >::~Enumerator

(

)

[inline]

Default Destructor

---

Member Function Documentation

template<class Container, class SiteIterator, class Variant>

void BALL::Enumerator< Container, SiteIterator, Variant >::addVariants	(	const SiteIterator &	it,
		const VariantVector &	variants
	)			[inline]

Add variants to the list of variants

template<typename Container , typename VariantConstIterator , typename Variant >

BALL_INLINE Enumerator< Container, VariantConstIterator, Variant >::ConstIterator BALL::Enumerator< Container, VariantConstIterator, Variant >::begin

(

)

const [inline]

References BALL::ConstForwardIterator< Container, DataType, Position, Traits >::begin().

template<typename Container , typename SiteIterator , typename Variant >

BALL_INLINE Enumerator< Container, SiteIterator, Variant >::Iterator BALL::Enumerator< Container, SiteIterator, Variant >::begin

(

)

[inline]

References BALL::ForwardIterator< Container, DataType, Position, Traits >::begin().

template<class Container, class SiteIterator, class Variant>

Size BALL::Enumerator< Container, SiteIterator, Variant >::countVariants

(

)

[inline]

Count all variants.

Returns:

the number of all possible variants

template<typename Container , typename SiteIterator , typename Variant >

void BALL::Enumerator< Container, SiteIterator, Variant >::createCombination

(

const EnumeratorIndex &

index

)

throw (EnumeratorIndex::IncompatibleIndex) [inline]

Create a combination denoted by an instance of EnumeratorIndex.

Parameters:

index

the instance of EnumeratorIndex that describes the combination to be created

template<typename Container , typename SiteIterator , typename Variant >

void BALL::Enumerator< Container, SiteIterator, Variant >::createCombination

(

const Position

index

)

throw (Exception::IndexOverflow) [inline]

Create a combination denoted by its number.

Parameters:

index

the number of the combination to be created

template<class Container, class SiteIterator, class Variant>

static void BALL::Enumerator< Container, SiteIterator, Variant >::defaultAssign_	(	Variant &	a,
		const Variant &	b
	)			[inline, static, protected]

template<class Container, class SiteIterator, class Variant>

void BALL::Enumerator< Container, SiteIterator, Variant >::deleteVariants	(	const SiteIterator &	it,
		const VariantVector &	variants
	)			[inline]

Delete variants from the list of variants

template<typename Container , typename VariantConstIterator , typename Variant >

BALL_INLINE Enumerator< Container, VariantConstIterator, Variant >::ConstIterator BALL::Enumerator< Container, VariantConstIterator, Variant >::end

(

)

const [inline]

References BALL::ConstForwardIterator< Container, DataType, Position, Traits >::end().

template<typename Container , typename SiteIterator , typename Variant >

BALL_INLINE Enumerator< Container, SiteIterator, Variant >::Iterator BALL::Enumerator< Container, SiteIterator, Variant >::end

(

)

[inline]

References BALL::ForwardIterator< Container, DataType, Position, Traits >::end().

template<typename Container , typename SiteIterator , typename Variant >

BALL_INLINE Container & BALL::Enumerator< Container, SiteIterator, Variant >::getCurrent

(

)

[inline]

Access the current content

Returns:

a reference to the container class of this enumerator

References BALL::Enumerator< Container, SiteIterator, Variant >::container_.

template<class Container, class SiteIterator, class Variant>

void BALL::Enumerator< Container, SiteIterator, Variant >::mutate_	(	SiteIterator &	it,
		const Variant &	v
	)			[inline, protected]

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Friends And Related Function Documentation

template<class Container, class SiteIterator, class Variant>

friend class IteratorTraits_ [friend]

---

Member Data Documentation

template<class Container, class SiteIterator, class Variant>

Container& BALL::Enumerator< Container, SiteIterator, Variant >::container_ [protected]

Referenced by BALL::Enumerator< Container, SiteIterator, Variant >::getCurrent().

template<class Container, class SiteIterator, class Variant>

bool BALL::Enumerator< Container, SiteIterator, Variant >::is_valid_position_ [protected]

template<class Container, class SiteIterator, class Variant>

MutatorFunction BALL::Enumerator< Container, SiteIterator, Variant >::mutator_ [protected]

template<class Container, class SiteIterator, class Variant>

EnumeratorIndex BALL::Enumerator< Container, SiteIterator, Variant >::position_ [protected]

template<class Container, class SiteIterator, class Variant>

SiteList BALL::Enumerator< Container, SiteIterator, Variant >::variant_sites_ [protected]