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ell::State Class Reference

#include <State.hh>

Inheritance diagram for ell::State:

[legend]

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Detailed Description

An object of the class State represents a state in the energy landscape. It handles its fitness and neighborhood concerning the landscape.

A State is always valid in the subclass.

Author:

Martin Mann, Sebastian Will, Andreas Richter

Definition at line 37 of file State.hh.

Public Types
typedef biu::VirtualList< State >	NeighborList
typedef std::auto_ptr< NeighborList >	NeighborListPtr
Public Member Functions
virtual State *	clone (State *toFill=NULL) const=0
virtual CSequence &	compress (CSequence &toFill) const=0
virtual CSequence	compress (void) const =0
virtual State *	fromString (const std::string &stringRep) const =0
virtual double	getEnergy () const=0
virtual const std::string &	getID (void) const =0
virtual unsigned int	getMinimalDistance (const State &state2) const =0
virtual NeighborListPtr	getNeighborList () const=0
virtual State *	getRandomNeighbor (State *inPlaceNeigh=NULL) const=0
virtual NeighborListPtr	getRandomNeighborList () const=0
virtual bool	operator!= (const State &state2) const =0
virtual bool	operator< (const State &state2) const
virtual bool	operator== (const State &state2) const =0
	State ()
virtual std::string &	toString (std::string &toFill) const =0
virtual std::string	toString () const=0
virtual State *	uncompress (const CSequence &cseq)=0
virtual State *	uncompress (const CSequence &cseq, State *toFill) const =0
virtual	~State ()
Static Public Member Functions
static bool	less (const State *s1, const State *s2)

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Member Typedef Documentation

typedef biu::VirtualList<State> ell::State::NeighborList

Virtual list of neighbor states which can be accessed by a STL-like iterator.

Definition at line 44 of file State.hh.

typedef std::auto_ptr<NeighborList> ell::State::NeighborListPtr

An autopointer to a NeighborList.

Definition at line 47 of file State.hh.

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Constructor & Destructor Documentation

ell::State::State

(

)

[inline]

Definition at line 49 of file State.hh.

virtual ell::State::~State

(

)

[inline, virtual]

Definition at line 52 of file State.hh.

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Member Function Documentation

virtual State* ell::State::clone

(

State *

toFill = NULL

)

const [pure virtual]

Returns a pointer to a clone of the current state.

Parameters:

toFill

a State to make a copy of this, or NULL if a new State should be created

Returns:

a pointer to a copy of this state, if toFill is != NULL the return value corresponds to the updated state pointed to by toFill, otherwise a new object is created !!!

Implemented in ell::S_LP, ell::S_LP_PullM, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, ell::S_SG_Ising, and ell::S_SG_NPP.

virtual CSequence& ell::State::compress

(

CSequence &

toFill

)

const [pure virtual]

Access to a compressed sequence representation of the state.

Parameters:

toFill

a data structure to write the compressed representation too

Returns:

the compressed sequence representation

Implemented in ell::S_LP, ell::S_LP_PullM, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, and ell::S_SG_Ising.

virtual CSequence ell::State::compress

(

void

)

const [pure virtual]

Access to a compressed sequence representation of the state.

Returns:

the compressed sequence representation

Implemented in ell::S_LP, ell::S_LP_PullM, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, and ell::S_SG_Ising.

virtual State* ell::State::fromString

(

const std::string &

stringRep

)

const [pure virtual]

Returns a new State based on the current state. The new state differs only by the information given by stringRep.

Implemented in ell::S_LP, ell::S_LP_PullM, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, ell::S_SG_Ising, and ell::S_SG_NPP.

virtual double ell::State::getEnergy

(

)

const [pure virtual]

Returns the state specific energy.

Implemented in ell::S_LP, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, ell::S_SG_Ising, and ell::S_SG_NPP.

virtual const std::string& ell::State::getID

(

void

)

const [pure virtual]

Access to a State subclass specific ID string to identify instances of this class.

Returns:

the subclass specific ID string

Implemented in ell::S_LP_PullM, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, ell::S_SG_Ising, and ell::S_SG_NPP.

virtual unsigned int ell::State::getMinimalDistance

(

const State &

state2

)

const [pure virtual]

Returns the minimal number of steps via valid neighbored states from this to another valid State.

Parameters:

state2

the State to reach

Implemented in ell::S_LP_PullM, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, and ell::S_SG_Ising.

virtual NeighborListPtr ell::State::getNeighborList

(

)

const [pure virtual]

Returns a virtual list of all VALID neighbored states in the energy landscape in a specific order.

Implemented in ell::S_LP, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, and ell::S_SG_Ising.

virtual State* ell::State::getRandomNeighbor

(

State *

inPlaceNeigh = NULL

)

const [pure virtual]

Returns a VALID random neighbored state. If a state is given, this is changed to a neighbor.

Implemented in ell::S_LP, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, ell::S_SG_Ising, and ell::S_SG_NPP.

virtual NeighborListPtr ell::State::getRandomNeighborList

(

)

const [pure virtual]

Returns a virtual list of all VALID neighbored states in the energy landscape in a random order. If a state is given, this is changed to a neighbor.

Implemented in ell::S_LP, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, and ell::S_SG_Ising.

bool ell::State::less	(	const State *	s1,
		const State *	s2
	)			[inline, static]

Comparison function that compares two State pointer based on the less than operator '<' of the first State. The function can be used in STL algorithms, e.g. if only State pointer are stored but the ordering should be based on the object order.

Parameters:

	s1	the State pointer of the object that is asked to be smaller (!=NULL)
	s2	the State pointer of the object that is asked to be bigger (!=NULL)

Returns:

s1->operator <(*s1);

Reimplemented in ell::S_Explicit.

Definition at line 206 of file State.hh.

virtual bool ell::State::operator!=

(

const State &

state2

)

const [pure virtual]

Implemented in ell::S_LP, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, ell::S_SG_Ising, and ell::S_SG_NPP.

bool ell::State::operator<

(

const State &

state2

)

const [inline, virtual]

Implements a unique order on states based on their energy and string representation. A state is smaller than another one iff it has smaller energy or it has equal energy and a lexicographically smaller string representation (tie breaker).

This function will be overwritten to achive a better performance than calling getEnergy() and getString().

If the energy function is non-degenerate the string comparison is obsolete.

Parameters:

state2

the State object to compare to

Returns:

true if this state is smaller than state2 according to the unique order of the states

Reimplemented in ell::S_LP, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, and ell::S_Explicit.

Definition at line 190 of file State.hh.

virtual bool ell::State::operator==

(

const State &

state2

)

const [pure virtual]

Implemented in ell::S_LP, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, ell::S_SG_Ising, and ell::S_SG_NPP.

virtual std::string& ell::State::toString

(

std::string &

toFill

)

const [pure virtual]

Fill the given string with a specific std::string representation of this State.

Parameters:

toFill

the string to overwrite

Returns:

the changed toFill in parameter

Implemented in ell::S_LP, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, and ell::S_SG_Ising.

virtual std::string ell::State::toString

(

)

const [pure virtual]

Returns a specific std::string representation of this State.

Implemented in ell::S_LP, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, and ell::S_SG_Ising.

virtual State* ell::State::uncompress

(

const CSequence &

cseq

)

[pure virtual]

Uncompresses a compressed sequencce representation into a this State object.

Parameters:

cseq

the compressed sequence representation of a state

Returns:

this or NULL in error case

Implemented in ell::S_LP, ell::S_LP_PullM, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, and ell::S_SG_Ising.

virtual State* ell::State::uncompress	(	const CSequence &	cseq,
		State *	toFill
	)			const [pure virtual]

Uncompresses a compressed sequencce representation into a new State object.

Parameters:

	cseq	the compressed sequence representation of a state
	toFill	a state object to uncompress too or NULL if a new object has to be created

Returns:

new State object that is encoded in cseq or NULL in error case.

Implemented in ell::S_LP, ell::S_LP_PullM, ell::S_RNAfe_SingleM, ell::S_RNAfe_SingleM_TB, ell::S_Explicit, ell::S_SG_Ising, and ell::S_SG_NPP.

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

• src/ell/State.hh