Enumerator< Container, SiteIterator, Variant > Class Template Reference

Enumerator class. More...

#include <enumerator.h>

List of all members.

Public Types
Type definitions
typedef void(*	MutatorFunction )(Variant &, const Variant &)
	Site mutator function.
typedef std::vector< Variant >	VariantVector
	A vector containing all possible variants for a specific site.
typedef std::pair< SiteIterator, VariantVector >	Site
	A combination of a site position and all its possible variants.
typedef std::list< Site >	SiteList
	A list of sites.
typedef ForwardIterator< Enumerator< Container, SiteIterator, Variant >, Container, EnumeratorIndex *, IteratorTraits_ >	Iterator
	Mutable forward iterator.
typedef ConstForwardIterator< Enumerator< Container, SiteIterator, Variant >, Container, EnumeratorIndex *, IteratorTraits_ >	ConstIterator
	Constant forward iterator.
Public Member Functions
Constructors and Destructors
	Enumerator () throw ()
	Default Constructor.
	Enumerator (Container &container) throw ()
	Detailed Constructor.
	Enumerator (Container &container, MutatorFunction mutator) throw ()
	Detailed Constructor.
	~Enumerator () throw ()
	Default Destructor.
Accessors
void	addVariants (const SiteIterator &it, const VariantVector &variants) throw ()
	Add variants to the list of variants.
void	deleteVariants (const SiteIterator &it, const VariantVector &variants) throw ()
	Delete variants from the list of variants.
Size	countVariants () throw ()
	Count all variants.
Container &	getCurrent () throw ()
	Access the current content.
void	createCombination (const Position index) throw (Exception::IndexOverflow)
	Create a combination denoted by its number.
void	createCombination (const EnumeratorIndex &index) throw (EnumeratorIndex::IncompatibleIndex)
	Create a combination denoted by an instance of EnumeratorIndex.
Iterators
Iterator	begin () throw ()
Iterator	end () throw ()
ConstIterator	begin () const throw ()
ConstIterator	end () const throw ()
Protected Member Functions
void	mutate_ (SiteIterator &it, const Variant &v) throw ()
Static Protected Member Functions
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_

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Detailed Description

template<class Container, class SiteIterator, class Variant>
class 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.

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Member Typedef Documentation

template<class Container, class SiteIterator, class Variant> typedef void(* 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> 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> Enumerator< Container, SiteIterator, Variant >::SiteList

A list of sites.

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

A vector containing all possible variants for a specific site.

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Constructor & Destructor Documentation

template<typename Container, typename SiteIterator, typename Variant> Enumerator< Container, SiteIterator, Variant >::Enumerator (  Container &  container  )  throw ()

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

Detailed Constructor. Parameters: container  a Container class to be mutated mutator  the function defining the mutations to be applied

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Member Function Documentation

template<class Container, class SiteIterator, class Variant> Size Enumerator< Container, SiteIterator, Variant >::countVariants (   )  throw ()

Count all variants. Returns: the number of all possible variants

template<typename Container, typename SiteIterator, typename Variant> void Enumerator< Container, SiteIterator, Variant >::createCombination (  const EnumeratorIndex &  index  )  throw (EnumeratorIndex::IncompatibleIndex)

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 Enumerator< Container, SiteIterator, Variant >::createCombination (  const Position  index  )  throw (Exception::IndexOverflow)

Create a combination denoted by its number. Parameters: index  the number of the combination to be created

template<typename Container, typename SiteIterator, typename Variant> Container & Enumerator< Container, SiteIterator, Variant >::getCurrent (   )  throw ()

Access the current content. Returns: a reference to the container class of this enumerator