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ell::S_LP_PullM Class Reference

#include <S_LP_PullM.hh>

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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< NeighborListNeighborListPtr

Public Member Functions

virtual StateapplyNeighborChange (const size_t index, State *const neigh) const
virtual S_LP_PullMclone (State *toFill=NULL) const
virtual CSequencecompress (CSequence &toFill) const
virtual CSequence compress (void) const
virtual StatefromString (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 StategetNeighbor (const size_t index, State *neigh) const
virtual NeighborListPtr getNeighborList () const
virtual size_t getNeighborNumber (void) const
virtual StategetRandomNeighbor (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 Stateuncompress (const CSequence &cseq)
virtual Stateuncompress (const CSequence &cseq, State *toFill) const
virtual StateundoNeighborChange (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.


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.


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.


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