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ell::S_RNAfe_SingleM_TB

ell::S_RNAfe_SingleM_TB Class Reference

#include <S_RNAfe_SingleM_TB.hh>

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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_TB.hh.

Public Types

typedef biu::VirtualList<
State > 		NeighborList
typedef std::auto_ptr< NeighborList > NeighborListPtr

Public Member Functions

virtual S_RNAfe_SingleM_TB * clone (State *toFill=NULL) const
virtual CSequence & compress (CSequence &toFill) const
virtual CSequence compress (void) const
virtual State * fromString (const std::string &stringRep, const double energy) 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_TB (const S_RNAfe_SingleM_TB &toCopy)
 S_RNAfe_SingleM_TB (const RNAFreeEnergy_TB &rna)
 S_RNAfe_SingleM_TB (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_TB ()

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_TB::SingleMove SingleMove

Protected Member Functions

SingleMove firstValidSingleMove () const
SingleMove nextValidSingleMove (const SingleMove lastSingleMove) const

Protected Attributes

RNAFreeEnergy_TB 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_TB::SingleMove ell::S_RNAfe_SingleM_TB::SingleMove [protected]

Definition at line 22 of file S_RNAfe_SingleM_TB.hh.

Constructor & Destructor Documentation

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

Definition at line 21 of file S_RNAfe_SingleM_TB.cc.

ell::S_RNAfe_SingleM_TB::S_RNAfe_SingleM_TB ( const RNAFreeEnergy_TB &  rna  ) 

Definition at line 31 of file S_RNAfe_SingleM_TB.cc.

ell::S_RNAfe_SingleM_TB::S_RNAfe_SingleM_TB ( const S_RNAfe_SingleM_TB &  toCopy  ) 

copy construction

Parameters:
toCopy the state to copy

Definition at line 39 of file S_RNAfe_SingleM_TB.cc.

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

Definition at line 45 of file S_RNAfe_SingleM_TB.cc.

Member Function Documentation

S_RNAfe_SingleM_TB * ell::S_RNAfe_SingleM_TB::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 221 of file S_RNAfe_SingleM_TB.cc.

CSequence & ell::S_RNAfe_SingleM_TB::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 512 of file S_RNAfe_SingleM_TB.cc.

CSequence ell::S_RNAfe_SingleM_TB::compress ( void   )  const [virtual]

Access to a compressed sequence representation of the state.

Returns:
the compressed sequence representation

Implements ell::State.

Definition at line 502 of file S_RNAfe_SingleM_TB.cc.

S_RNAfe_SingleM_TB::SingleMove ell::S_RNAfe_SingleM_TB::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 60 of file S_RNAfe_SingleM_TB.cc.

State * ell::S_RNAfe_SingleM_TB::fromString ( const std::string &  stringRep,
const double  energy 
) const [virtual]

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

Parameters:
stringRep string encoding of RNA structure
energy energy of the RNA structure (has to be the correct energy as calculated by the Vienna RNA 'energy_of_struct' function)
Returns:
new State object (has to be deleted by the calling function)

Definition at line 255 of file S_RNAfe_SingleM_TB.cc.

State * ell::S_RNAfe_SingleM_TB::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.

Parameters:
stringRep string encoding of RNA structure
Returns:
new State object (has to be deleted by the calling function)

Implements ell::State.

Definition at line 238 of file S_RNAfe_SingleM_TB.cc.

double ell::S_RNAfe_SingleM_TB::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 176 of file S_RNAfe_SingleM_TB.cc.

const std::string & ell::S_RNAfe_SingleM_TB::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 54 of file S_RNAfe_SingleM_TB.cc.

unsigned int ell::S_RNAfe_SingleM_TB::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 181 of file S_RNAfe_SingleM_TB.cc.

State::NeighborListPtr ell::S_RNAfe_SingleM_TB::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 287 of file S_RNAfe_SingleM_TB.cc.

State * ell::S_RNAfe_SingleM_TB::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 461 of file S_RNAfe_SingleM_TB.cc.

State::NeighborListPtr ell::S_RNAfe_SingleM_TB::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 292 of file S_RNAfe_SingleM_TB.cc.

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

Access to the nucleotide sequence of this RNA molecule.

Returns:
the RNA sequence

Definition at line 277 of file S_RNAfe_SingleM_TB.cc.

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

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

Returns:
the RNA structure

Definition at line 282 of file S_RNAfe_SingleM_TB.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_TB::SingleMove ell::S_RNAfe_SingleM_TB::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 71 of file S_RNAfe_SingleM_TB.cc.

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

Implements ell::State.

Definition at line 152 of file S_RNAfe_SingleM_TB.cc.

bool ell::S_RNAfe_SingleM_TB::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 157 of file S_RNAfe_SingleM_TB.cc.

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

Implements ell::State.

Definition at line 144 of file S_RNAfe_SingleM_TB.cc.

std::string & ell::S_RNAfe_SingleM_TB::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 270 of file S_RNAfe_SingleM_TB.cc.

std::string ell::S_RNAfe_SingleM_TB::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 265 of file S_RNAfe_SingleM_TB.cc.

State * ell::S_RNAfe_SingleM_TB::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 556 of file S_RNAfe_SingleM_TB.cc.

State * ell::S_RNAfe_SingleM_TB::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 526 of file S_RNAfe_SingleM_TB.cc.

Field Documentation

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

the specific ID string of this class

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 173 of file S_RNAfe_SingleM_TB.hh.

RNAFreeEnergy_TB ell::S_RNAfe_SingleM_TB::rnaFreeEnergy [protected]

Definition at line 140 of file S_RNAfe_SingleM_TB.hh.

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