| ARFunction | Represents function suitable for the FunctionKernel |
| ARFunctionKernel | Function kernel specialized at solving the kinds of functions involved in ARVineyard construction |
| ARVineyard | Encapsulated filtration, and provides compute_vineyard() functionality |
| AvidaOrganismDetail | Stores organism details stored in a single line of a population detail file in data/ directory of Avida's output |
| AvidaPopulationDetail | Stores entire population details (all organisms in a given time step), i.e., stores an entire population detail file in data/ directory of Avida's ouptut |
| ConeSimplex< S > | Author: Dmitriy Morozov Department of Computer Science, Duke University, 2007 |
| ConsistencyList< T > | ConsistencyList adds consistency order to OrderList which remains unchanged through the lifetime of the list |
| ConsistencyList< T >::ConsistencyComparison | Determines the order of the two elements in the consistency order (that doesn't change during the execution) |
| ConsistencyList< T >::GreaterThanComparison | Determines if the first element is greater than the second one |
| ConsistencyList< T >::LessThanComparison | Determines if the first element is less than the second one |
| ConsistencyList< T >::OrderComparison | Basic comparison that LessThan and GreaterThan derive from |
| ConsistencyListNode< T > | Structure storing auxilliary information requred for each node of ConsistencyList |
| Course_timer | A class of utilities for basic array manipulation |
| Cycle< Itm, OrderCmp, ConsistencyCmp > | Class storing a cycle of simplices |
| EdgeList< SType > | |
| Evaluator< Smplx > | Evaluator is a base class for the structures that are able to return a value given a simplex |
| Filtration< Smplx, FltrSmplx, Vnrd > | |
| FiltrationContainer< FltrSmplx > | FiltrationContainer class |
| FiltrationSimplex< Smplx > | FiltrationSimplex stores information needed for the RU-decomposition: cycle (column of R), trail (row of U), and pair |
| Grid2D | Grid2D stores a grid |
| IndirectComparison< Comparison_ > | Compares elements pointed at by its arguments using the provided Comparison_ (which must not take any arguments during construction) |
| K | Author: Dmitriy Morozov Department of Computer Science, Duke University, 2007 |
| Kernel< NumberType_ > | Geometric Kernel |
| Kernel< NumberType_ >::Point | Point class |
| Kernel< NumberType_ >::Sphere | Sphere class |
| KineticSort< ElementIterator_, TrajectoryExtractor_, Simulator_, Swap_ > | Maintains elements of the given data structure in the sorted order assuming the elements follow trajectories given by TrajectoryExtractor_ |
| Knee< S > | Knee class stores the knee in R^3 as well as the cycle that is associated with the Simplex starting from the Knee |
| List< T > | Singly-linked circular list implementation by Donovan Rebbechi <elflord@pegasus.rutgers.edu> |
| LowerStarFiltration< VI, Smplx, FltrSmplx, Vnrd >::VertexType< IndexType_ > | Helper class that describes lower star vertex type |
| OrderList< T > | OrderList stores a list of objects while maintaining their total order under the operations of insert(), swap(), and delete() |
| OrderList< T >::OrderComparison | Basic comparison that LessThan and GreaterThan derive from |
| OrderListNode< T > | Structure storing auxilliary information requred for each node of OrderList |
| ParallelFiltration< Smplx, FltrSmplx, Vnrd > | Filtration class |
| ParallelFiltration< Smplx, FltrSmplx, Vnrd >::parallel_struct_for_pairing | } |
| ParallelFiltration< Smplx, FltrSmplx, Vnrd >::parallel_struct_for_pairing | } |
| SimplexWithAttachment< V > | SimplexWithAttachment stores the vertex to which the simplex is attached (meant for lower-star filtrations) |
| SimplexWithValue< Vert > | SimplexWithValue explicitly adds a RealType value to the SimplexWithVertices |
| SimplexWithVertices< V > | SimplexWithVertices is a basic simplex class |
| Simulator< FuncKernel_, EventComparison_ > | Simulator class |
| Simulator< FuncKernel_, EventComparison_ >::Event | Base class for events |
| SynapsTraits< T > | < Suitable for double |
| Timer | A class of utilities for basic array manipulation |
| Vine< S > | Vine is a list of Knees |
| Vineyard< FltrSmplx > | Vineyard class |
