IntaRNA::NussinovHandler Class Reference

#include <NussinovHandler.h>

Public Types
typedef UpperTriangularMatrix< Z_type >	Z2dMatrix
	Probability triangular matrix.
typedef UpperTriangularMatrix< E_type >	E2dMatrix
	Energy triangular matrix.
typedef UpperTriangularMatrix< size_t >	IdxMatrix
	Index triangular matrix.

Static Public Member Functions
static Z_type	getQ (const size_t from, const size_t to, const RnaSequence &seq, const Z_type basePairWeight, const size_t minLoopLength, Z2dMatrix &Q, Z2dMatrix &Qb)
static Z_type	getQb (const size_t from, const size_t to, const RnaSequence &seq, const Z_type basePairWeight, const size_t minLoopLength, Z2dMatrix &Q, Z2dMatrix &Qb)
static Z_type	getPbp (const size_t from, const size_t to, const RnaSequence &seq, const Z_type basePairWeight, const size_t minLoopLength, Z2dMatrix &Q, Z2dMatrix &Qb, Z2dMatrix &Ppb)
static Z_type	getPu (const size_t from, const size_t to, const RnaSequence &seq, const Z_type basePairWeight, const size_t minLoopLength, Z2dMatrix &Q, Z2dMatrix &Qb, Z2dMatrix &Ppb, Z2dMatrix &Pu)
static std::string	dotBracket (const size_t from, const size_t to, const RnaSequence &seq, const size_t minLoopLength, const E_type basePairEnergy=Ekcal_2_E(-1.0))
static void	getBasePairs (const size_t from, const size_t to, const IdxMatrix &traceback, Interaction::PairingVec &pairs)
static void	printMatrix (std::ostream &out, const NussinovHandler::E2dMatrix &M)

Member Typedef Documentation

E2dMatrix

typedef UpperTriangularMatrix<E_type> IntaRNA::NussinovHandler::E2dMatrix

Energy triangular matrix.

IdxMatrix

typedef UpperTriangularMatrix<size_t> IntaRNA::NussinovHandler::IdxMatrix

Index triangular matrix.

Z2dMatrix

typedef UpperTriangularMatrix<Z_type> IntaRNA::NussinovHandler::Z2dMatrix

Probability triangular matrix.

Member Function Documentation

dotBracket()

static std::string IntaRNA::NussinovHandler::dotBracket ( const size_t  from, const size_t  to, const RnaSequence &  seq, const size_t  minLoopLength, const E_type  basePairEnergy = Ekcal_2_E(-1.0)  )

static

getBasePairs()

static void IntaRNA::NussinovHandler::getBasePairs ( const size_t  from, const size_t  to, const IdxMatrix &  traceback, Interaction::PairingVec &  pairs  )

static

getPbp()

static Z_type IntaRNA::NussinovHandler::getPbp ( const size_t  from, const size_t  to, const RnaSequence &  seq, const Z_type  basePairWeight, const size_t  minLoopLength, Z2dMatrix &  Q, Z2dMatrix &  Qb, Z2dMatrix &  Ppb  )

static

getPu()

static Z_type IntaRNA::NussinovHandler::getPu ( const size_t  from, const size_t  to, const RnaSequence &  seq, const Z_type  basePairWeight, const size_t  minLoopLength, Z2dMatrix &  Q, Z2dMatrix &  Qb, Z2dMatrix &  Ppb, Z2dMatrix &  Pu  )

static

getQ()

static Z_type IntaRNA::NussinovHandler::getQ ( const size_t  from, const size_t  to, const RnaSequence &  seq, const Z_type  basePairWeight, const size_t  minLoopLength, Z2dMatrix &  Q, Z2dMatrix &  Qb  )

static

getQb()

static Z_type IntaRNA::NussinovHandler::getQb ( const size_t  from, const size_t  to, const RnaSequence &  seq, const Z_type  basePairWeight, const size_t  minLoopLength, Z2dMatrix &  Q, Z2dMatrix &  Qb  )

static

printMatrix()

static void IntaRNA::NussinovHandler::printMatrix ( std::ostream &  out, const NussinovHandler::E2dMatrix &  M  )

static

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

• src/IntaRNA/NussinovHandler.h