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ell::S_RNAfe_SingleM Class Reference

#include <S_RNAfe_SingleM.hh>

Inheritance diagram for ell::S_RNAfe_SingleM:

[legend]

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Detailed Description

This class represents an RNA structure in the energy landscape. Neighbors are generated by adding or removing one bond to the RNA structure known as single moves.

The free energy calculated using Vienna RNA package functionality.

Author:

Martin Mann, Sebastian Will, Andreas Richter

Definition at line 19 of file S_RNAfe_SingleM.hh.

Public Types
typedef biu::VirtualList< State >	NeighborList
typedef std::auto_ptr< NeighborList >	NeighborListPtr
Public Member Functions
virtual S_RNAfe_SingleM *	clone () 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 int	getFitness () const
virtual unsigned int	getMinimalDistance (const State &state2) const
virtual NeighborListPtr	getNeighborList () const
virtual State *	getRandomNeighbor (State *inPlaceNeigh=NULL) const
virtual NeighborListPtr	getRandomNeighborList () const
virtual bool	operator!= (const State &state2) const
virtual bool	operator== (const State &state2) const
	S_RNAfe_SingleM (const S_RNAfe_SingleM &rnaFESMS)
	S_RNAfe_SingleM (const RNAFreeEnergy &rna)
	S_RNAfe_SingleM (const std::string &rnaSeqStr, const std::string &rnaStructBracketNotStr)
virtual std::string	toString () const
virtual State *	uncompress (const CSequence &cseq)
virtual State *	uncompress (const CSequence &cseq, State *toFill) const
virtual	~S_RNAfe_SingleM ()
Protected Types
typedef RNAFreeEnergy::SingleMove	SingleMove
Protected Member Functions
SingleMove	firstValidSingleMove () const
SingleMove	nextValidSingleMove (const SingleMove lastSingleMove) const
SingleMove	searchForNextValidSingleMove (size_t pos1, size_t pos2) const
Protected Attributes
biu::Alphabet::AlphElem	close
biu::Alphabet::AlphElem	none
biu::Alphabet::AlphElem	open
RNAFreeEnergy	rnaFreeEnergy
Data Structures
class	NeighborList
class	RandomNeighborList

---

Member Typedef Documentation

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 43 of file State.hh.

typedef std::auto_ptr<NeighborList> ell::State::NeighborListPtr [inherited]

An autopointer to a NeighborList.

Definition at line 46 of file State.hh.

typedef RNAFreeEnergy::SingleMove ell::S_RNAfe_SingleM::SingleMove [protected]

Definition at line 22 of file S_RNAfe_SingleM.hh.

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Constructor & Destructor Documentation

ell::S_RNAfe_SingleM::S_RNAfe_SingleM	(	const std::string &	rnaSeqStr,
		const std::string &	rnaStructBracketNotStr
	)

Definition at line 17 of file S_RNAfe_SingleM.cc.

ell::S_RNAfe_SingleM::S_RNAfe_SingleM

(

const RNAFreeEnergy &

rna

)

Definition at line 27 of file S_RNAfe_SingleM.cc.

ell::S_RNAfe_SingleM::S_RNAfe_SingleM

(

const S_RNAfe_SingleM &

rnaFESMS

)

Definition at line 35 of file S_RNAfe_SingleM.cc.

ell::S_RNAfe_SingleM::~S_RNAfe_SingleM

(

)

[virtual]

Definition at line 41 of file S_RNAfe_SingleM.cc.

---

Member Function Documentation

S_RNAfe_SingleM * ell::S_RNAfe_SingleM::clone

(

)

const [virtual]

Returns a pointer to a clone of the current state.

Implements ell::State.

Definition at line 176 of file S_RNAfe_SingleM.cc.

CSequence & ell::S_RNAfe_SingleM::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::State.

Definition at line 418 of file S_RNAfe_SingleM.cc.

CSequence ell::S_RNAfe_SingleM::compress

(

void

)

const [virtual]

Access to a compressed sequence representation of the state.

Returns:

the compressed sequence representation

Implements ell::State.

Definition at line 408 of file S_RNAfe_SingleM.cc.

S_RNAfe_SingleM::SingleMove ell::S_RNAfe_SingleM::firstValidSingleMove

(

)

const [protected]

Returns the first VALID single move. Returns SingleMove(0,RNAStructure::INVALID_INDEX) if no first valid single move exits.

Definition at line 45 of file S_RNAfe_SingleM.cc.

State * ell::S_RNAfe_SingleM::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::State.

Definition at line 181 of file S_RNAfe_SingleM.cc.

double ell::S_RNAfe_SingleM::getEnergy

(

)

const [virtual]

Returns the state specific energy.

Implements ell::State.

Definition at line 139 of file S_RNAfe_SingleM.cc.

int ell::S_RNAfe_SingleM::getFitness

(

)

const [virtual]

Returns the negatived free energy of this RNA state multiplied with 100.

Implements ell::State.

Definition at line 129 of file S_RNAfe_SingleM.cc.

unsigned int ell::S_RNAfe_SingleM::getMinimalDistance

(

const State &

state2

)

const [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 144 of file S_RNAfe_SingleM.cc.

State::NeighborListPtr ell::S_RNAfe_SingleM::getNeighborList

(

)

const [virtual]

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

Implements ell::State.

Definition at line 197 of file S_RNAfe_SingleM.cc.

State * ell::S_RNAfe_SingleM::getRandomNeighbor

(

State *

inPlaceNeigh = NULL

)

const [virtual]

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

Implements ell::State.

Definition at line 368 of file S_RNAfe_SingleM.cc.

State::NeighborListPtr ell::S_RNAfe_SingleM::getRandomNeighborList

(

)

const [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.

Implements ell::State.

Definition at line 202 of file S_RNAfe_SingleM.cc.

S_RNAfe_SingleM::SingleMove ell::S_RNAfe_SingleM::nextValidSingleMove

(

const SingleMove

lastSingleMove

)

const [protected]

Returns the next VALID single move if lastSingleMove was the last single move. Returns SingleMove(0,RNAStructure::INVALID_INDEX) if no next valid single move exits.

lastSingleMove has to be an valid move!

Definition at line 50 of file S_RNAfe_SingleM.cc.

bool ell::S_RNAfe_SingleM::operator!=

(

const State &

state2

)

const [virtual]

Implements ell::State.

Definition at line 123 of file S_RNAfe_SingleM.cc.

bool ell::S_RNAfe_SingleM::operator==

(

const State &

state2

)

const [virtual]

Implements ell::State.

Definition at line 117 of file S_RNAfe_SingleM.cc.

S_RNAfe_SingleM::SingleMove ell::S_RNAfe_SingleM::searchForNextValidSingleMove	(	size_t	pos1,
		size_t	pos2
	)			const [protected]

Searches for the next valid single move and starts the search for the first move position at pos 1 and for the second move position at pos2. If a move was found, it will be returned, otherwise SingleMove(0,RNAStructure::INVALID_INDEX) will be returned.

Definition at line 67 of file S_RNAfe_SingleM.cc.

std::string ell::S_RNAfe_SingleM::toString

(

)

const [virtual]

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

BRACKETNOTATION(SEQUENCE)

Implements ell::State.

Definition at line 191 of file S_RNAfe_SingleM.cc.

State * ell::S_RNAfe_SingleM::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::State.

Definition at line 459 of file S_RNAfe_SingleM.cc.

State * ell::S_RNAfe_SingleM::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::State.

Definition at line 432 of file S_RNAfe_SingleM.cc.

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Field Documentation

biu::Alphabet::AlphElem ell::S_RNAfe_SingleM::close [protected]

Definition at line 144 of file S_RNAfe_SingleM.hh.

biu::Alphabet::AlphElem ell::S_RNAfe_SingleM::none [protected]

Definition at line 143 of file S_RNAfe_SingleM.hh.

biu::Alphabet::AlphElem ell::S_RNAfe_SingleM::open [protected]

Definition at line 142 of file S_RNAfe_SingleM.hh.

RNAFreeEnergy ell::S_RNAfe_SingleM::rnaFreeEnergy [protected]

Definition at line 140 of file S_RNAfe_SingleM.hh.

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

• src/ell/rna/S_RNAfe_SingleM.hh
• src/ell/rna/S_RNAfe_SingleM.cc