Scaffolding  0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 1234]
 Nexcept
 Cbad_syntaxException for the case that a given file does not conform to expected syntax
 Cinfo_not_up_to_dateException for the case that a graph property is read that is not up to date
 Cinvalid_assumptionException for the case that some assumption that is made is not true
 Cinvalid_optionsException for the case that the given program options are not valid
 Cread_errorException for the case that a given file could not be read on a low level
 Nscaffold
 Nfilters
 Ccontained_filterFilter to work with filtered graphs that is based on a set of vertices, passed to the constructor
 Cmap_filterFilter to work with filtered graphs that is based on a a mapping of vertices: filter all vertices mapped to some initial X
 CVP_contained_filterFilter to work with filtered graphs that is based on a set of VertexPairs, passed to the constructor
 Cyes_filterDummy filter to always say YES
 Ngraph_infos
 CBridgeInfoGraph property for the set of bridges in g
 CComponentInfoGraph property for the number of connected components and a map of vertices to components (represented by unsigneds)
 CGraphInfosAccumulator class for different graph properties
 CMaxDegreeInfoGraph property for the maximum degree in g
 CStructuralInfoPrototype class for structural graph properties
 Ngraph_parameters
 Cdegree_greaterComparator class, comparing two vertices u,v such that comp(u,v) = true <=> deg(u) > deg(v)
 Cdegree_lessComparator class, comparing two vertices u,v such that comp(u,v) = true <=> deg(u) < deg(v)
 Cgraph_parametersCollection of graph parameters that can be computed
 CintervalInterval consists of a lower & an upper bound
 Nio
 Cgviz_edge_writer_with_jumps
 Cgviz_property_writer
 Cgviz_simple_edge_writer
 Cgviz_simple_graph_writer
 Cgviz_simple_vertex_writer
 Npredicates
 CContainedPredicatePredicate that is true iff the given element is (not) contained in a given container
 CMatchingPredicateEdge predicate that is true iff the given edge is (not) a matching edge
 CPredicatePrototype predicate
 CTargetContainedPredicateEdge predicate that is true iff the given edge has its target (not) in a given set
 CTruePredicatePredicate that always evaluates to true
 Nscoring
 CDistanceScoreScoring function returning the distance to a reference score given at construction
 CIdentityScoreScoring function for a pair of something and unsigned that just returns the unsigned
 CPredicatedDistanceScoreScoring returning the distance to a reference score if a predicate evaluates to true and UINT_MAX otherwise
 Nsolv
 NDP
 CCompare_Instance_Size
 Cd_to_P_map
 CDP_Table
 CDynProgSolution
 CP_to_pc_map
 Nilp
 Ccallback_statistics
 Cilp_options
 CLazyCyclesBlockCallback
 CRelaxCallback
 Cvar_collection_multi
 Cvar_collection_virt
 Ntrees
 CTreeDPinfos
 CBranch
 Cpthread_data_block
 Ccontig_jump
 Cglobal_list
 CInstanceInstance is a ScaffoldGraph with given path- & cycle- numbers and a solution to keep track of deleted edges
 CMatrixEntry
 Cnormal_distributionNormal distribution centered with given mean and standard deviation (makes heavy use of std::erf())
 COrientedSequence
 CPCMinMatrix
 CPermissiveMatching
 CPredicated_EdgeIterEdge iterator that skips over all edges for which the predicate evaluates to false
 CScafEdgeProperty
 CScaffoldGraphMain graph class
 CScafGraphProperty
 CScafVertexProperty
 CSolutionSolution is a list of edge names with weights; it keeps track of the overall weight for O(1) access
 CTD_Subgraph
 CUseCountedOrientedSequence
 Nstd
 Clow_priority_queueLow-priority queue of Elements with Priorities
 Cset_queuePriority-queue allowing member queries
 Cunordered_pairUnordered pair
 Cdegree_cmp
 Cdiagonal_counter
 Cedge_component_t
 CEdgeHasher
 CPathsAndCycles
 CtimerSimple timer class that can be paused and resumed