| Cired::graph::adjacency_list< Vertex, Edge > | Graph in adjacency list representation |
| Cired::graph::adjacency_list< vertex_info_t, edge_info_t > | |
| Cired::ArcticEvaluationPolicy< FunValue > | Evaluation Strategy for Optimization (max/+); defining the arctic semiring |
| Cinfrared.libinfrared.Assignment | An assignment (of values to variables) |
| Cired::Assignment | A (partial) assignment of variables to values |
| Cired::AssignmentIterator< FeatureNetwork > | Iterate over the assignments of a subset of variables |
| Cired::Cluster< FunValue > | Cluster (or bag) in the cluster tree |
| Cired::ClusterTree< FunValue, EvaluationPolicy > | A tree of clusters (=variables, functions, constraints) |
| ▼Cinfrared.infrared.ClusterTreeBase | Cluster tree base class |
| Cinfrared.infrared.ArcticClusterTree | Cluster tree for maximization (in arctic semiring) |
| Cinfrared.infrared.PFClusterTree | Cluster tree for partition function calculation and sampling |
| ▼Cinfrared.Constraint | |
| Cinfrared.rna.BPComp | Constrain complementarity of the base pair (i,j) |
| Cinfrared.rna.DifferentComplClassConstraint | Parse RNA structure including pseudoknots |
| Cinfrared.rna.NotBPComp | Function for (position-wise) GC content |
| Cinfrared.rna.SameComplClassConstraint | Constrain nucleotides to be in different complementarity classes |
| ▼Cinfrared.libinfrared.Constraint | A constraint |
| Cinfrared.infrared.ValueIn | Constrain variable to have a value from a specified set |
| Cired::container_selector< FunValue, T > | Switching containers in MaterializedFuntion |
| Cired::container_selector< FunValue, mapS > | Class implementing the specializations to enable instantiation of sparse materialized function classes |
| Cired::container_selector< FunValue, simple_mapS > | Class implementing the specializations to enable space saving instantiation of sparse materialized function classes using the specialized 'map' implementation simple_map |
| Cired::container_selector< FunValue, vecS > | Class implementing the specializations to enable instantiation of non-sparse materialized function classes |
| ▼Cired::Dependency | Dependencies specify a dependency between variables |
| ▼Cired::Function< FunValue > | |
| Cired::MaterializedFunction< FunValue, ContainerS > | A materialized function |
| Cired::Function< FunValue > | Functions evaluate assignments of a subset of variables |
| ▼Cedge_info_t | |
| Cired::graph::adjacency_list< Vertex, Edge >::edge_t | |
| Cired::ClusterTree< FunValue, EvaluationPolicy >::edge_info_t | Information at an edge of the tree |
| ▼CException | |
| Cinfrared.infrared.ConstraintFunctionDefinitionError | |
| Cinfrared.infrared.Feature | Feature in multi-dimensional Boltzmann sampling |
| Cired::FeatureNetwork< FunValue, EvaluationPolicy > | Feature network |
| Cired::FeatureNetwork< double, StdEvaluationPolicy< double > > | |
| Cinfrared.infrared.FeatureStatistics | Keeping statistics on features |
| Cinfrared.libinfrared.FiniteDomain | A finite domain of a variable |
| Cired::FiniteDomain | |
| ▼Cinfrared.libinfrared.Function | A real valued feature function |
| Cinfrared.infrared.PFFunctionAdapter | Adapt function for partition function algebra |
| ▼Cinfrared.libinfrared.IntFunction | An integer valued feature function |
| Cinfrared.infrared.ArcticFunctionAdapter | Adapt function for maximization algebra |
| Cired::mapS | Map selector class |
| Cinfrared.infrared.Model | |
| ▼Cired::PFEvaluationPolicy< FunValue > | The evaluation policy to calculate partition functions |
| Cired::StdEvaluationPolicy< FunValue > | Define PFEvaluationPolicy as standard |
| ▼CRuntimeError | |
| Cinfrared.infrared.ConsistencyError | |
| Cinfrared.rna.ParseError | |
| Cired::ArcticEvaluationPolicy< FunValue >::selector | |
| Cired::PFEvaluationPolicy< FunValue >::selector | |
| Cired::simple_mapS | Simple map selector class |
| Cired::StdEvaluationPolicy< bool > | The evaluation policy to combine constraint values. Here, mul corresponds to &&, plus to ||, one to true, and zero to false |
| Cired::vecS | Vector selector class |
| ▼Cstd::vector | |
| Cired::SimpleMap< key_t, val_t > | Space saving replacement for map |
| Cired::vector_nbv_sel< T > | |
| Cired::vector_nbv_sel< bool > | |
| Cired::vector_nbv_sel< fun_value_t > | |
| Cired::ClusterTree< FunValue, EvaluationPolicy >::vertex_info_t | Information at a vertex (=cluster/bag) of the tree |
| ▼Cinfrared.infrared.WeightedFunction | Function of a constraint network |
| Cinfrared.rna.BPEnergy | Function for Stack Energy model |
| Cinfrared.rna.GCCont | Function for (basepair-wise) BasePair Energy model |
| Cinfrared.rna.StackEnergy | Constrain nucleotides to be in the same complementarity class |
| ▼CABC | |
| ▼Cinfrared.infrared.EngineBase | Abstract base class for samplers and optimizers |
| Cinfrared.infrared.ArcticOptimizer | Maximizing optimizer (based on arctic algebra) |
| ▼Cinfrared.infrared.BoltzmannSampler | Boltzmann sampler |
| Cinfrared.infrared.MultiDimensionalBoltzmannSampler | Multi-dimensional Boltzmann sampler |
| ▼Cinfrared.infrared.EvaluationAlgebra | Algebra for evaluating a constraint network |
| Cinfrared.infrared.ArcticEvaluationAlgebra | Maximization algebra for optimization |
| Cinfrared.infrared.PFEvaluationAlgebra | Partition function algebra for sampling |
1.9.7