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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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an accumulator class for different graph properties More...
#include <graph_infos.hpp>
Public Member Functions | |
| GraphInfos (const Graph &_g, const bool update_values=false) | |
| constructor: needs a graph to initalize the EdgeHasher of the bridgs; updates all values on construction of the infos | |
| GraphInfos (const Graph &_g, const GraphInfos &infos, const Matching< Graph > &translate) | |
| constructor | |
| void | invalidate_all () |
| invalidate all infos | |
| void | update_all (const bool force=false) |
| update all values | |
| void | add_vertex (const Vertex< Graph > &u) |
| react to addition of vertex u | |
| void | add_edge (const Vertex< Graph > &u, const Vertex< Graph > &v) |
| react to addition of edge uv | |
| void | delete_edge (const VertexPair< Graph > &uv) |
| react to deletion of edge uv | |
| void | read_from_infos (const GraphInfos< Graph > &infos, const Matching< Graph > &translate) |
| update the infos from the graph h of which g has just been copied More... | |
| void | read_from_split_off_component (const GraphInfos< Graph > &infos, const Matching< Graph > &translate) |
| react to splitting off this connected component g from a graph h More... | |
| void | update_disjoint_union (const GraphInfos< Graph > &infos, const Matching< Graph > &translate) |
| react to forming a disjoint union with g with another graph h, given the infos of h and a translate map More... | |
| PathsAndCycles | get_paths_and_cycles () |
| get the number of paths and cycles in the graph, assuming its max degree is 2, updating infos if necessary | |
| PathsAndCycles | get_paths_and_cycles_const () const |
| get the number of paths and cycles in the graph, assuming its max degree is 2, without updating the infos | |
| unsigned | get_FES () |
| return the feedback edge set number of the graph, updating its infos if necessary | |
| unsigned | get_FES_const () const |
| return the feedback edge set number of the graph without updating its infos | |
| bool | is_acyclic () |
| return whether the graph is acyclic, updating its infos if necessary | |
| bool | is_acyclic_const () const |
| return whether the graph is acyclic without updating its infos | |
| bool | is_max_deg_two () |
| return whether the graph has max degree 2, updating its max-degree info if necessary | |
| bool | is_max_deg_two_const () const |
| return whether the graph has max degree 2 without updating infos | |
Public Attributes | |
| const Graph & | g |
| ComponentInfo< Graph > | comps |
| MaxDegreeInfo< Graph > | max_deg |
| BridgeInfo< Graph > | bridges |
Protected Member Functions | |
| PathsAndCycles | _get_paths_and_cycles (const unsigned cc) |
| get the number of paths and cycles in the graph, assuming its max degree is 2 | |
| bool | is_max_deg_two_easy_cases () const |
| return whether g has maximum degree 2 using only queries to |V| and |E| | |
an accumulator class for different graph properties
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inline |
update the infos from the graph h of which g has just been copied
using this function, we can copy the graph property value when copying a graph without having to recompute it.
translate has to contain a map such that, for each vertex u of h, translate[u] is the representation of u in g
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inline |
react to splitting off this connected component g from a graph h
translate has to contain a map such that, for each vertex u of h, translate[u] is the representation of u in g
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inline |
react to forming a disjoint union with g with another graph h, given the infos of h and a translate map
translate has to contain a map such that, for each vertex u of h, translate[u] is the representation of u in g
1.8.10
