ell::S_RNAfe_SingleM Class Reference

#include <S_RNAfe_SingleM.hh>

Inheritance diagram for ell::S_RNAfe_SingleM:

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 (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 NeighborListPtr getNeighborList () const

virtual State * getRandomNeighbor (State *inPlaceNeigh=NULL) const

virtual NeighborListPtr getRandomNeighborList () const

virtual std::string getSequence () const

virtual std::string getStructure () const

virtual bool operator!= (const State &state2) const

virtual bool operator< (const State &rna2) const

virtual bool operator== (const State &state2) const

S_RNAfe_SingleM (const S_RNAfe_SingleM &toCopy)

S_RNAfe_SingleM (const RNAFreeEnergy &rna)

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

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 ~S_RNAfe_SingleM ()

Static Public Member Functions

static bool less (const State *s1, const State *s2)

Static Public Attributes

static const std::string ID

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 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.

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

Definition at line 22 of file S_RNAfe_SingleM.hh.

Constructor & Destructor Documentation

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

Definition at line 21 of file S_RNAfe_SingleM.cc.

ell::S_RNAfe_SingleM::S_RNAfe_SingleM ( const RNAFreeEnergy & rna )

Definition at line 31 of file S_RNAfe_SingleM.cc.

ell::S_RNAfe_SingleM::S_RNAfe_SingleM ( const S_RNAfe_SingleM & toCopy )

copy construction

Parameters:

toCopy

the state to copy

Definition at line 39 of file S_RNAfe_SingleM.cc.

ell::S_RNAfe_SingleM::~S_RNAfe_SingleM ( ) [virtual]

Definition at line 45 of file S_RNAfe_SingleM.cc.

Member Function Documentation

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

Definition at line 200 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 477 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 467 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 59 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 216 of file S_RNAfe_SingleM.cc.

double ell::S_RNAfe_SingleM::getEnergy ( ) const [virtual]

Returns the state specific energy. The energy is calculated via the Vienna RNA package functions. NOTE : The value UNIT is given ( kcal / mol ) !!!

Implements ell::State.

Definition at line 163 of file S_RNAfe_SingleM.cc.

const std::string & ell::S_RNAfe_SingleM::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 53 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 168 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 256 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 427 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 261 of file S_RNAfe_SingleM.cc.

std::string ell::S_RNAfe_SingleM::getSequence ( ) const [virtual]

Access to the nucleotide sequence of this RNA molecule.

Returns:: the RNA sequence

Definition at line 246 of file S_RNAfe_SingleM.cc.

std::string ell::S_RNAfe_SingleM::getStructure ( ) const [virtual]

Access to the structure of this RNA molecule encoded in dot-bracket notation.

Returns:: the RNA structure

Definition at line 251 of file S_RNAfe_SingleM.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.

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 64 of file S_RNAfe_SingleM.cc.

bool ell::S_RNAfe_SingleM::operator!= ( const State & state2 ) const [virtual]

Implements ell::State.

Definition at line 137 of file S_RNAfe_SingleM.cc.

bool ell::S_RNAfe_SingleM::operator< ( const State & rna2 ) const [virtual]

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

Parameters:

rna2

the RNA State object to compare to

Returns:: true if this state is smaller than rna2 according to the unique order of the states

Reimplemented from ell::State.

Definition at line 143 of file S_RNAfe_SingleM.cc.

bool ell::S_RNAfe_SingleM::operator== ( const State & state2 ) const [virtual]

Implements ell::State.

Definition at line 131 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 81 of file S_RNAfe_SingleM.cc.

std::string & ell::S_RNAfe_SingleM::toString ( std::string & toFill ) const [virtual]

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 238 of file S_RNAfe_SingleM.cc.

std::string ell::S_RNAfe_SingleM::toString ( ) const [virtual]

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

Returns:: the dot-bracket-notation of the structure

Implements ell::State.

Definition at line 233 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 518 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 491 of file S_RNAfe_SingleM.cc.

Field Documentation

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

Definition at line 144 of file S_RNAfe_SingleM.hh.

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

the specific ID string of this class

Definition at line 173 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.

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


Public Types
typedef biu::VirtualList< State >	NeighborList
typedef std::auto_ptr< NeighborList >	NeighborListPtr
Public Member Functions
virtual S_RNAfe_SingleM *	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 NeighborListPtr	getNeighborList () const
virtual State *	getRandomNeighbor (State *inPlaceNeigh=NULL) const
virtual NeighborListPtr	getRandomNeighborList () const
virtual std::string	getSequence () const
virtual std::string	getStructure () const
virtual bool	operator!= (const State &state2) const
virtual bool	operator< (const State &rna2) const
virtual bool	operator== (const State &state2) const
	S_RNAfe_SingleM (const S_RNAfe_SingleM &toCopy)
	S_RNAfe_SingleM (const RNAFreeEnergy &rna)
	S_RNAfe_SingleM (const std::string &rnaSeqStr, const std::string &rnaStructBracketNotStr)
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	~S_RNAfe_SingleM ()
Static Public Member Functions
static bool	less (const State s1, const State s2)
Static Public Attributes
static const std::string	ID
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