Scaffolding  0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
Public Member Functions | Protected Member Functions | List of all members
scaffold::BridgeInfo< Graph > Class Template Reference
Inheritance diagram for scaffold::BridgeInfo< Graph >:
scaffold::StructuralInfo< Graph, BridgeMap< Graph > >

Public Member Functions

void update (const bool force=false)
 
void read_from_infos (const BridgeInfo< Graph > &infos, const Matching< Graph > &translate)
 
void read_from_split_off_component (const BridgeInfo< Graph > &info, const Matching< Graph > &translate)
 
void update_disjoint_union (const BridgeInfo< Graph > &info, const Matching< Graph > &translate)
 
void add_edge (const Vertex< Graph > &u, const Vertex< Graph > &v)
 
void delete_edge (const VertexPair< Graph > &uv)
 
bool is_bridge (const Vertex< Graph > &u, const Vertex< Graph > &v)
 
bool is_bridge_const (const Vertex< Graph > &u, const Vertex< Graph > &v) const
 
template<class EdgePredicate = TruePredicate<Edge<Graph> >>
void get_non_bridges (std::list< WeightedBridge< Graph >> &non_bridges, const EdgePredicate &predicate=EdgePredicate())
 
template<class EdgePredicate = TruePredicate<Edge<Graph> >>
void get_non_bridges_const (std::list< WeightedBridge< Graph >> &non_bridges, const EdgePredicate &predicate=EdgePredicate()) const
 
template<class EdgePredicate = TruePredicate<Edge<Graph> >>
const WeightedBridge< Graph > get_cheapest_nonbridge (const EdgePredicate &predicate=EdgePredicate())
 
template<class EdgePredicate = TruePredicate<Edge<Graph> >>
const WeightedBridge< Graph > get_cheapest_nonbridge (const EdgePredicate &predicate=EdgePredicate()) const
 
bool has_incident_nonbridge (const Vertex< Graph > &u)
 
bool has_incident_nonbridge_const (const Vertex< Graph > &v) const
 
template<class Scoring = IdentityScore<VertexPair<Graph> >>
const WeightedBridge< Graph > * get_best_bridge (const Scoring &score=Scoring())
 
template<class Scoring = IdentityScore<VertexPair<Graph> >>
const WeightedBridge< Graph > * get_best_bridge (const Scoring &score=Scoring()) const
 
- Public Member Functions inherited from scaffold::StructuralInfo< Graph, BridgeMap< Graph > >
 StructuralInfo (const Graph &_g)
 
 StructuralInfo (const Graph &_g, const BridgeMap< Graph > &_payload)
 
void invalidate ()
 
bool is_valid () const
 
const BridgeMap< Graph > & get ()
 
const BridgeMap< Graph > & get_const () const
 

Protected Member Functions

template<class EdgePredicate = TruePredicate<Edge<Graph> >>
void _get_non_bridges (std::list< WeightedBridge< Graph >> &non_bridges, const EdgePredicate &predicate) const
 
template<class EdgePredicate = TruePredicate<Edge<Graph> >>
const WeightedBridge< Graph > _get_cheapest_nonbridge (const EdgePredicate &predicate) const
 
bool _has_incident_nonbridge (const Vertex< Graph > &u) const
 
template<class Scoring = IdentityScore<VertexPair<Graph> >>
const WeightedBridge< Graph > * _get_best_bridge (const Scoring &score) const
 

Additional Inherited Members

- Protected Attributes inherited from scaffold::StructuralInfo< Graph, BridgeMap< Graph > >
const Graph & g
 
BridgeMap< Graph > payload
 
bool up_to_date
 

The documentation for this class was generated from the following file: