Scaffolding  0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 123]
 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_dateException for the case that a graph property is read that is not up to date
 Cexcept::invalid_assumptionException for the case that some assumption that is made is not true
 Cexcept::invalid_optionsException for the case that the given program options are not valid
 Cexcept::read_errorException for the case that a given file could not be read on a low level
 Cexcept::bad_syntaxException for the case that a given file does not conform to expected syntax
 Cscaffold::global_list
 Cscaffold::graph_parameters::graph_parametersCollection 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::intervalInterval 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_distributionNormal 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::ScaffoldGraphMain graph class
 Cscaffold::InstanceInstance 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 >
 CtimerSimple 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