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Scaffolding
0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
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Scaffolding
0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
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a graph property for the set of bridges in g More...
#include <graph_infos.hpp>
Public Member Functions | |
| void | update (const bool force=false) |
| update bridges | |
| void | read_from_infos (const BridgeInfo< Graph > &infos, const Matching< Graph > &translate) |
| read from translated information More... | |
| void | read_from_split_off_component (const BridgeInfo< Graph > &info, const Matching< Graph > &translate) |
| read from given infos, assuming that g is a single connected component that has been split off | |
| void | update_disjoint_union (const BridgeInfo< Graph > &info, const Matching< Graph > &translate) |
| update infos, assuming that g is the disjoint union of a graph with our infos and a graph with the given infos | |
| void | add_edge (const Vertex< Graph > &u, const Vertex< Graph > &v) |
| react to the addition of the edge uv to g | |
| void | delete_edge (const VertexPair< Graph > &uv) |
| react to the deletion of the edge uv | |
| bool | is_bridge (const Vertex< Graph > &u, const Vertex< Graph > &v) |
| return whether the edge uv is a bridge, updating the infos if necessary | |
| bool | is_bridge_const (const Vertex< Graph > &u, const Vertex< Graph > &v) const |
| return whether the edge uv is a bridge, avoiding updating the bridge map | |
| template<class EdgePredicate = TruePredicate<Edge<Graph> >> | |
| void | get_non_bridges (std::list< WeightedBridge< Graph >> &non_bridges, const EdgePredicate &predicate=EdgePredicate()) |
| return the set of non-bridges in g, updating the bridge map if necessary | |
| template<class EdgePredicate = TruePredicate<Edge<Graph> >> | |
| void | get_non_bridges_const (std::list< WeightedBridge< Graph >> &non_bridges, const EdgePredicate &predicate=EdgePredicate()) const |
| return the set of non-bridges without updating the bridge map | |
| template<class EdgePredicate = TruePredicate<Edge<Graph> >> | |
| const WeightedBridge< Graph > | get_cheapest_nonbridge (const EdgePredicate &predicate=EdgePredicate()) |
| return the lightest non-bridge, updating the bridge map if necessary | |
| template<class EdgePredicate = TruePredicate<Edge<Graph> >> | |
| const WeightedBridge< Graph > | get_cheapest_nonbridge (const EdgePredicate &predicate=EdgePredicate()) const |
| return the lightest non-bridge without updating the bridge map | |
| bool | has_incident_nonbridge (const Vertex< Graph > &u) |
| return whether a vertex has an incident nonbridge, updating the bridge map if necessary | |
| bool | has_incident_nonbridge_const (const Vertex< Graph > &v) const |
| return whether a vertex has an incident nonbridge without updating the bridge map | |
| template<class Scoring = IdentityScore<VertexPair<Graph> >> | |
| const WeightedBridge< Graph > * | get_best_bridge (const Scoring &score=Scoring()) |
| get non-matching bridge that minimizes the given scoring function, updating the bridge map if necessary | |
| template<class Scoring = IdentityScore<VertexPair<Graph> >> | |
| const WeightedBridge< Graph > * | get_best_bridge (const Scoring &score=Scoring()) const |
| get non-matching bridge that minimizes the given scoring function without updating the bridge map | |
 Public Member Functions inherited from scaffold::graph_infos::StructuralInfo< Graph, BridgeMap< Graph > > | |
| StructuralInfo (const Graph &_g) | |
| constructor | |
| StructuralInfo (const Graph &_g, const BridgeMap< Graph > &_payload) | |
| constructor | |
| void | invalidate () |
| set the property to "not up-to-date" | |
| bool | is_valid () const |
| return whether the property is up-to-date | |
| const BridgeMap< Graph > & | get () |
| get the current value of the property, updating if necessary | |
| const BridgeMap< Graph > & | get_const () const |
| get the current value of the property without updating More... | |
Protected Member Functions | |
| template<class EdgePredicate = TruePredicate<Edge<Graph> >> | |
| void | _get_non_bridges (std::list< WeightedBridge< Graph >> &non_bridges, const EdgePredicate &predicate) const |
| store all non-bridges with their weights in the parameter More... | |
| template<class EdgePredicate = TruePredicate<Edge<Graph> >> | |
| const WeightedBridge< Graph > | _get_cheapest_nonbridge (const EdgePredicate &predicate) const |
| return the non-bridge of least weight More... | |
| bool | _has_incident_nonbridge (const Vertex< Graph > &u) const |
| return whether a vertex has an incident nonbridge | |
| template<class Scoring = IdentityScore<VertexPair<Graph> >> | |
| const WeightedBridge< Graph > * | _get_best_bridge (const Scoring &score) const |
| get non-matching bridge that minimizes the given scoring function | |
Additional Inherited Members | |
| Protected Attributes inherited from scaffold::graph_infos::StructuralInfo< Graph, BridgeMap< Graph > > | |
| const Graph & | g |
| a reference to the graph | |
| BridgeMap< Graph > | payload |
| the actual graph property | |
| bool | up_to_date |
| indicate whether the property needs to be recomputed due to changes in the graph | |
a graph property for the set of bridges in g
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inlineprotected |
return the non-bridge of least weight
if a predicate is given, consider only non-bridges for which the predicate evaluates to true
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inlineprotected |
store all non-bridges with their weights in the parameter
if a predicate is given, only include the bridges for which the predicate evaluates to true
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inline |
read from translated information
using this function, we can copy the graph property value when copying a graph without having to recompute it.
1.8.10
