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ell Namespace Reference

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Detailed Description

The namespace ell is a shortcut for the Energy Landscape Library, generated on the chair of Bioinformatics at the University of Freiburg. http://www.bioinf.uni-freiburg.de/

It covers a set of classes and methods to model and handle arbitrary types of energy landscapes using the abstract interface class State or derived subclasses.

Author:

Martin Mann, Sebastian Will, Andreas Richter

Data Structures
class	BarrierSampling
class	Basin
class	Basin_F
class	Basin_FME
class	BS_DirectWalk
class	BS_UpDown
class	DirectWalk
class	DW_RNA_MorganHiggs
class	IterableNeighbors
class	LandscapeTopology
class	LT_AutoFlood
class	LT_BarrierTree
class	LT_Funnels
class	LT_MinimaSet
class	LT_SaddleNet
class	LT_SaddleNet_AM
class	MinimumMapping
class	MinimumSelector
class	MM_GradientWalk
class	MS_Boltzmann
class	MS_Uniform
class	NeighborGenerator
class	NG_Random
class	NG_Successive
class	NG_SuccessiveRandom
class	RandomNeighborList
class	RNAFreeEnergy
class	RNAFreeEnergy_TB
class	S_Explicit
class	S_LP
class	S_LP_PullM
class	S_RNAfe_SingleM
class	S_RNAfe_SingleM_TB
class	S_SG_Ising
class	S_SG_NPP
class	SA_All
class	SA_E_Eq
class	SA_E_Gr
class	SA_E_GrEq
class	SA_E_Le
class	SA_E_LeEq
class	SA_Le
class	SA_Max_E
class	SA_Metropolis
class	SAC_MaxIterations
class	SAC_MaxNoChange
class	SAC_NoMinimaChange
class	SamplingAbortionCriterion
class	SC_Counting
class	SC_Listing
class	SC_ListingCompr
class	SC_ListingK
class	SC_Maximum
class	SC_Outstream
class	SC_PartitionFunction
class	SC_PartitionFunction_Shifted
class	SPC_Counting
class	SPC_Listing
class	SPC_MinPair
class	SPC_Outstream
class	State
class	StateAcceptor
class	StateCollector
class	StatePairCollector
class	SuccessiveNeighborList
class	WAC_MaxEnergy
class	WAC_MaxLength
class	WAC_MinEnergy
class	WAC_OpenEnd
class	WAC_OR
class	Walk
class	WalkAbortionCriterion
class	WalkAdaptive
class	WalkGradient
class	WalkMC
class	WalkRandom
Namespaces
namespace	util
Typedefs
typedef biu::Alphabet::CSequence	CSequence
Variables
bool	ViennaFoldParamsSet = false

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Typedef Documentation

typedef biu::Alphabet::CSequence ell::CSequence

A compressed string representation of a state object. The correct en- or decoding is only possible using the same class's object.

Definition at line 26 of file State.hh.

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Variable Documentation

bool ell::ViennaFoldParamsSet = false

Definition at line 35 of file RNAFreeEnergy_TB.cc.