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ell::S_LP_PullM Class Reference

#include <S_LP_PullM.hh>

Inheritance diagram for ell::S_LP_PullM:

[legend]

---

Detailed Description

Definition at line 13 of file S_LP_PullM.hh.

Public Types
typedef size_t	Move
typedef biu::VirtualList< State >	NeighborList
typedef std::auto_ptr< NeighborList >	NeighborListPtr
Public Member Functions
virtual State *	applyNeighborChange (const size_t index, State *const neigh) const
virtual S_LP_PullM *	clone (State *toFill=NULL) const
virtual CSequence &	compress (CSequence &toFill) const
virtual CSequence	compress (void) const
virtual State *	fromString (const std::string &stringRep) const
virtual double	getEnergy () const
virtual const std::string &	getID (void) const
virtual unsigned int	getMinimalDistance (const State &state2) const
virtual State *	getNeighbor (const size_t index, State *neigh) const
virtual NeighborListPtr	getNeighborList () const
virtual size_t	getNeighborNumber (void) const
virtual State *	getRandomNeighbor (State *inPlaceNeigh=NULL) const
virtual NeighborListPtr	getRandomNeighborList () const
virtual bool	operator!= (const State &state2) const
virtual bool	operator< (const State &lp2) const
virtual bool	operator== (const State &state2) const
	S_LP_PullM (const S_LP_PullM &)
	S_LP_PullM (biu::LatticeProtein_I *latProt, biu::LatticeMoveSet *moveSet)
virtual std::string &	toString (std::string &toFill) const
virtual std::string	toString () const
virtual State *	uncompress (const CSequence &cseq)
virtual State *	uncompress (const CSequence &cseq, State *toFill) const
virtual State *	undoNeighborChange (const size_t index, State *const neigh) const
virtual	~S_LP_PullM ()
Static Public Member Functions
static bool	less (const State *s1, const State *s2)
Static Public Attributes
static const std::string	ID
Protected Attributes
biu::LatticeProtein_I *	latProt
biu::LatticeMoveSet *	moveSet

---

Member Typedef Documentation

typedef size_t ell::S_LP::Move [inherited]

Each move is defined by a value of type Move.

Definition at line 22 of file S_LP.hh.

typedef biu::VirtualList<State> ell::State::NeighborList [inherited]

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 [inherited]

An autopointer to a NeighborList.

Definition at line 47 of file State.hh.

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Constructor & Destructor Documentation

ell::S_LP_PullM::S_LP_PullM	(	biu::LatticeProtein_I *	latProt,
		biu::LatticeMoveSet *	moveSet
	)

Constructs a State using a LatticeProtein and a PullMoveSet.

Parameters:

	latProt	the lattice protein used by this State
	moveSet	the move set used by this State

Definition at line 15 of file S_LP_PullM.cc.

ell::S_LP_PullM::S_LP_PullM

(

const S_LP_PullM &

)

Definition at line 20 of file S_LP_PullM.cc.

ell::S_LP_PullM::~S_LP_PullM

(

)

[virtual]

Definition at line 24 of file S_LP_PullM.cc.

---

Member Function Documentation

State * ell::S_LP::applyNeighborChange	(	const size_t	index,
		State *const	neigh
	)			const [virtual, inherited]

Applies the necessary changes to a given state to get the neighbor. Note: neigh is expected to be a copy (i.e. *this == *neigh) and therefore direct changes are possible or to be NULL. If (neigh==NULL) a copy of this has to be generated, modified, and returned.

Parameters:

	index	the neighbor to generate
	neigh	a copy of this the changes should be applied to

Returns:

the neighbor state of the given index or NULL if the index is out of range

Implements ell::IterableNeighbors.

Definition at line 164 of file S_LP.cc.

S_LP_PullM * ell::S_LP_PullM::clone

(

State *

toFill = NULL

)

const [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 !!!

Implements ell::S_LP.

Definition at line 34 of file S_LP_PullM.cc.

CSequence & ell::S_LP_PullM::compress

(

CSequence &

toFill

)

const [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

Implements ell::S_LP.

Definition at line 79 of file S_LP_PullM.cc.

CSequence ell::S_LP_PullM::compress

(

void

)

const [virtual]

Access to a compressed sequence representation of the state.

Returns:

the compressed sequence representation

Implements ell::S_LP.

Definition at line 68 of file S_LP_PullM.cc.

State * ell::S_LP_PullM::fromString

(

const std::string &

stringRep

)

const [virtual]

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

Implements ell::S_LP.

Definition at line 55 of file S_LP_PullM.cc.

double ell::S_LP::getEnergy

(

)

const [virtual, inherited]

Returns the state specific energy.

Implements ell::State.

Definition at line 25 of file S_LP.cc.

const std::string & ell::S_LP_PullM::getID

(

void

)

const [virtual]

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

Returns:

the subclass specific ID string

Implements ell::State.

Definition at line 28 of file S_LP_PullM.cc.

virtual unsigned int ell::S_LP_PullM::getMinimalDistance

(

const State &

state2

)

const [inline, virtual]

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

Parameters:

state2

the State to reach

Implements ell::State.

Definition at line 83 of file S_LP_PullM.hh.

State * ell::S_LP::getNeighbor	(	const size_t	index,
		State *	neigh
	)			const [virtual, inherited]

Access to a specific neighbor.

Parameters:

	index	the index of the neighbor in [0, getNeighborNumber())
	neigh	if != NULL this state should be converted into the neighbor otherwise a new one is created and returned

Returns:

the new neighbor state or NULL if the index is >= getNeighborNumber()

Implements ell::IterableNeighbors.

Definition at line 127 of file S_LP.cc.

State::NeighborListPtr ell::S_LP::getNeighborList

(

)

const [virtual, inherited]

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

Implements ell::State.

Definition at line 87 of file S_LP.cc.

size_t ell::S_LP::getNeighborNumber

(

void

)

const [virtual, inherited]

How many neighbor indices are accessible.

Returns:

the number of neighbors

Implements ell::IterableNeighbors.

Definition at line 121 of file S_LP.cc.

State * ell::S_LP::getRandomNeighbor

(

State *

inPlaceNeigh = NULL

)

const [virtual, inherited]

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

Implements ell::State.

Definition at line 96 of file S_LP.cc.

State::NeighborListPtr ell::S_LP::getRandomNeighborList

(

)

const [virtual, inherited]

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.

Implements ell::State.

Definition at line 92 of file S_LP.cc.

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

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.

bool ell::S_LP::operator!=

(

const State &

state2

)

const [virtual, inherited]

Implements ell::State.

Definition at line 61 of file S_LP.cc.

bool ell::S_LP::operator<

(

const State &

lp2

)

const [virtual, inherited]

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

Parameters:

lp2

the S_LP object to compare to

Returns:

true if this state is smaller than lp2 according to the unique order of the states

Reimplemented from ell::State.

Definition at line 66 of file S_LP.cc.

bool ell::S_LP::operator==

(

const State &

state2

)

const [virtual, inherited]

Implements ell::State.

Definition at line 51 of file S_LP.cc.

std::string & ell::S_LP::toString

(

std::string &

toFill

)

const [virtual, inherited]

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

Parameters:

toFill

the string to overwrite

Returns:

the changed toFill in parameter

Implements ell::State.

Definition at line 42 of file S_LP.cc.

std::string ell::S_LP::toString

(

)

const [virtual, inherited]

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

Implements ell::State.

Definition at line 31 of file S_LP.cc.

State * ell::S_LP_PullM::uncompress

(

const CSequence &

cseq

)

[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

Implements ell::S_LP.

Definition at line 124 of file S_LP_PullM.cc.

State * ell::S_LP_PullM::uncompress	(	const CSequence &	cseq,
		State *	toFill
	)			const [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.

Implements ell::S_LP.

Definition at line 94 of file S_LP_PullM.cc.

State * ell::S_LP::undoNeighborChange	(	const size_t	index,
		State *const	neigh
	)			const [virtual, inherited]

Undo the changes done to this state to generate the given neighbor. The goal is to do less operations than doing a full copy like (*neigh = *this).

Parameters:

	index	the neighbor index that was applied last [ 0, getNeighborNumber() )
	neigh	the state resulting from the last changes ( != NULL)

Returns:

the copy of this object via undoing the last changes in neigh

Implements ell::IterableNeighbors.

Definition at line 150 of file S_LP.cc.

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Field Documentation

const std::string ell::S_LP_PullM::ID [static]

the specific ID string of this class

Definition at line 19 of file S_LP_PullM.hh.

biu::LatticeProtein_I* ell::S_LP::latProt [protected, inherited]

Definition at line 16 of file S_LP.hh.

biu::LatticeMoveSet* ell::S_LP::moveSet [protected, inherited]

Definition at line 17 of file S_LP.hh.

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

• src/ell/protein/S_LP_PullM.hh
• src/ell/protein/S_LP_PullM.cc