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 | |
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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 | |
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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