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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 number of connected components and a map of vertices to components (represented by unsigneds) More...
#include <graph_infos.hpp>
Public Member Functions | |
| void | update (const bool force=false) |
| update the connected components | |
| void | read_from_infos (const ComponentInfo< Graph > &infos, const Matching< Graph > &translate) |
| read from translated information More... | |
| void | read_from_split_off_component (const ComponentInfo< Graph > &info) |
| react to splitting off a connected component of the graph g More... | |
| void | update_disjoint_union (const ComponentInfo< Graph > &info, const Matching< Graph > &translate) |
| react to forming the disjoint union of g with a graph h, given the corresponding property of h | |
| void | add_vertex (const Vertex< Graph > &u) |
| react to the addition of a single vertex u to g | |
| 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, const bool is_bridge) |
| react to the deletion of the edge uv, depending on whether it was a bridge or not | |
| bool | num_is_valid () const |
| return whether the number of connected components is up to date | |
| const unsigned | get_num () |
| return the number of connected components, updating if necessary | |
| const unsigned | get_num_const () const |
| return the number of connected components without updating | |
Public Member Functions inherited from scaffold::graph_infos::StructuralInfo< Graph, ComponentsAndNum< Graph > > | |
| StructuralInfo (const Graph &_g) | |
| constructor | |
| StructuralInfo (const Graph &_g, const ComponentsAndNum< 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 ComponentsAndNum< Graph > & | get () |
| get the current value of the property, updating if necessary | |
| const ComponentsAndNum< Graph > & | get_const () const |
| get the current value of the property without updating More... | |
Additional Inherited Members | |
Protected Attributes inherited from scaffold::graph_infos::StructuralInfo< Graph, ComponentsAndNum< Graph > > | |
| const Graph & | g |
| a reference to the graph | |
| ComponentsAndNum< 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 number of connected components and a map of vertices to components (represented by unsigneds)
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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.
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inline |
react to splitting off a connected component of the graph g
we just decrease the number of connected components
1.8.10