Cscaffold::solv::Branch | |
Cscaffold::solv::ilp::callback_statistics | |
Cscaffold::solv::DP::Compare_Instance_Size< Graph, Compare > | |
Cscaffold::filters::contained_filter< Set > | Filter to work with filtered graphs that is based on a set of vertices, passed to the constructor |
Cscaffold::filters::contained_filter< EdgeSet< Graph > > | |
Cscaffold::filters::contained_filter< VertexSet< Graph > > | |
Cscaffold::contig_jump | |
Cdegree_cmp< Graph > | |
Cscaffold::graph_parameters::degree_greater< Graph > | Comparator class, comparing two vertices u,v such that comp(u,v) = true <=> deg(u) > deg(v) |
Cscaffold::graph_parameters::degree_less< Graph > | Comparator class, comparing two vertices u,v such that comp(u,v) = true <=> deg(u) < deg(v) |
Cdiagonal_counter | |
▼Cscaffold::scoring::DistanceScore< Element > | Scoring function returning the distance to a reference score given at construction |
Cscaffold::scoring::PredicatedDistanceScore< Element, Predicate > | Scoring returning the distance to a reference score if a predicate evaluates to true and UINT_MAX otherwise |
Cscaffold::solv::DP::DP_Table< Graph > | |
Cedge_component_t | |
CEdgeHasher< Graph, Pair > | |
▼Cexception | |
Cexcept::info_not_up_to_date | Exception for the case that a graph property is read that is not up to date |
▼Cexcept::invalid_assumption | Exception for the case that some assumption that is made is not true |
Cexcept::invalid_options | Exception for the case that the given program options are not valid |
▼Cexcept::read_error | Exception for the case that a given file could not be read on a low level |
Cexcept::bad_syntax | Exception for the case that a given file does not conform to expected syntax |
Cscaffold::global_list | |
Cscaffold::graph_parameters::graph_parameters | Collection of graph parameters that can be computed |
Cscaffold::graph_infos::GraphInfos< Graph > | Accumulator class for different graph properties |
Cscaffold::io::gviz_property_writer< WhatToWrite > | |
▼Cscaffold::io::gviz_property_writer< RawScaffoldGraph > | |
Cscaffold::io::gviz_simple_graph_writer | |
▼Cscaffold::io::gviz_property_writer< ScafEdge > | |
▼Cscaffold::io::gviz_simple_edge_writer | |
Cscaffold::io::gviz_edge_writer_with_jumps | |
▼Cscaffold::io::gviz_property_writer< ScafVertex > | |
Cscaffold::io::gviz_simple_vertex_writer | |
Cscaffold::scoring::IdentityScore< Element > | Scoring function for a pair of something and unsigned that just returns the unsigned |
Cscaffold::solv::ilp::ilp_options | |
Cscaffold::Instance< Graph > | |
Cscaffold::graph_parameters::interval | Interval consists of a lower & an upper bound |
▼CLazyConstraintCallbackI | |
Cscaffold::solv::ilp::LazyCyclesBlockCallback | |
Cstd::low_priority_queue< Element, Priority > | Low-priority queue of Elements with Priorities |
Cscaffold::filters::map_filter< Map > | Filter to work with filtered graphs that is based on a a mapping of vertices: filter all vertices mapped to some initial X |
Cscaffold::MatrixEntry | |
Cscaffold::normal_distribution | Normal distribution centered with given mean and standard deviation (makes heavy use of std::erf()) |
▼Cscaffold::OrientedSequence | |
Cscaffold::UseCountedOrientedSequence | |
▼Cpair | |
Cstd::unordered_pair< ElementA, ElementB > | Unordered pair |
CPathsAndCycles | |
▼Cscaffold::PCMinMatrix< Compare > | |
Cscaffold::solv::DP::DynProgSolution< Compare > | |
Cscaffold::PermissiveMatching | |
▼Cscaffold::predicates::Predicate< Element > | Prototype predicate |
Cscaffold::predicates::ContainedPredicate< Element, Container > | Predicate that is true iff the given element is (not) contained in a given container |
Cscaffold::predicates::TruePredicate< Element > | Predicate that always evaluates to true |
▼Cscaffold::predicates::Predicate< Edge< Graph > > | |
Cscaffold::predicates::MatchingPredicate< Graph > | Edge predicate that is true iff the given edge is (not) a matching edge |
Cscaffold::predicates::TargetContainedPredicate< Graph, Container > | Edge predicate that is true iff the given edge has its target (not) in a given set |
Cscaffold::Predicated_EdgeIter< Graph, Predicate, EdgeIt > | Edge iterator that skips over all edges for which the predicate evaluates to false |
Cscaffold::solv::pthread_data_block< Graph > | |
Cscaffold::ScafEdgeProperty | |
▼Cscaffold::ScaffoldGraph | Main graph class |
Cscaffold::Instance | Instance is a ScaffoldGraph with given path- & cycle- numbers and a solution to keep track of deleted edges |
Cscaffold::ScafGraphProperty | |
Cscaffold::ScafVertexProperty | |
Cstd::set_queue< T, Priority, Compare > | Priority-queue allowing member queries |
Cscaffold::Solution< Compare > | Solution is a list of edge names with weights; it keeps track of the overall weight for O(1) access |
▼CSolveCallbackI | |
Cscaffold::solv::ilp::RelaxCallback | |
Cscaffold::graph_infos::StructuralInfo< Graph, Information > | Prototype class for structural graph properties |
▼Cscaffold::graph_infos::StructuralInfo< Graph, BridgeMap< Graph > > | |
Cscaffold::graph_infos::BridgeInfo< Graph > | Graph property for the set of bridges in g |
▼Cscaffold::graph_infos::StructuralInfo< Graph, ComponentsAndNum< Graph > > | |
Cscaffold::graph_infos::ComponentInfo< Graph > | Graph property for the number of connected components and a map of vertices to components (represented by unsigneds) |
▼Cscaffold::graph_infos::StructuralInfo< Graph, VertexAndDegree< Graph > > | |
Cscaffold::graph_infos::MaxDegreeInfo< Graph > | Graph property for the maximum degree in g |
Cscaffold::TD_Subgraph< Graph > | |
Ctimer | Simple timer class that can be paused and resumed |
Cscaffold::solv::trees::TreeDPinfos< Compare > | |
▼Cunordered_map | |
Cscaffold::solv::DP::d_to_P_map | |
Cscaffold::solv::DP::P_to_pc_map | |
▼Cscaffold::solv::ilp::var_collection_virt | |
Cscaffold::solv::ilp::var_collection_multi | |
Cscaffold::filters::VP_contained_filter< Graph, Set > | Filter to work with filtered graphs that is based on a set of VertexPairs, passed to the constructor |
Cscaffold::filters::yes_filter< Object > | Dummy filter to always say YES |