Scaffolding  0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
scaffold::ScaffoldGraph Member List

This is the complete list of members for scaffold::ScaffoldGraph, including all inherited members.

_the_graphscaffold::ScaffoldGraphprotected
add_edge(const Vertex &u, const Vertex &v, const EdgeProperty &ep=EdgeProperty(), const bool update_infos=true)scaffold::ScaffoldGraphinline
add_matching_edge(const Vertex &u, const Vertex &v, const EdgeProperty &ep=EdgeProperty(), const bool update_infos=true)scaffold::ScaffoldGraphinline
add_vertex(const VertexProperty &p, const bool update_infos=true)scaffold::ScaffoldGraphinline
add_vertex(const std::string name, const bool update_infos=true, const unsigned index=UINT_MAX)scaffold::ScaffoldGraphinline
add_vertex(const Vertex &u, const bool update_infos=true)scaffold::ScaffoldGraphinline
adjacent(const Vertex &u, const Vertex &v) const scaffold::ScaffoldGraphinline
clear_vertex(const Vertex &u)scaffold::ScaffoldGraphinline
copy_and_init_matching(const ScaffoldGraph &g, Matching< Graph > *const translate, const bool update_infos)scaffold::ScaffoldGraphinlineprotected
cVertexIndexMap typedef (defined in scaffold::ScaffoldGraph)scaffold::ScaffoldGraph
degree(const Vertex &v) const scaffold::ScaffoldGraphinline
delete_edge(const Edge &e, const bool update_infos=true)scaffold::ScaffoldGraphinline
delete_edge(const Vertex &u, const Vertex &v)scaffold::ScaffoldGraphinline
delete_edge(const VertexPair< Graph > &uv)scaffold::ScaffoldGraphinline
delete_matching(const Vertex &u)scaffold::ScaffoldGraphinlineprotected
delete_vertex(const Vertex &u, const bool update_indices=true, const bool update_infos=true)scaffold::ScaffoldGraphinline
disjoint_union(const ScaffoldGraph &g)scaffold::ScaffoldGraphinline
Edge typedef (defined in scaffold::ScaffoldGraph)scaffold::ScaffoldGraph
EdgeProperty typedef (defined in scaffold::ScaffoldGraph)scaffold::ScaffoldGraph
find_edge(const Vertex &u, const Vertex &v) const scaffold::ScaffoldGraphinline
find_edge_by_name(const EdgeName &name) const scaffold::ScaffoldGraphinline
find_vertex_by_name(const VertexName &name) const scaffold::ScaffoldGraphinline
get_edge_name(const VertexPair< Graph > &uv) const scaffold::ScaffoldGraphinline
get_edge_name(const Edge &e) const scaffold::ScaffoldGraphinline
get_edges(const Predicate &pred=Predicate()) const scaffold::ScaffoldGraphinline
get_graph() const scaffold::ScaffoldGraphinline
get_graph_property() const scaffold::ScaffoldGraphinline
get_incident(const Vertex &u, const Predicate &pred=Predicate()) const scaffold::ScaffoldGraphinline
get_incident_non_matching(const Vertex &u) const scaffold::ScaffoldGraphinline
get_index_map() const scaffold::ScaffoldGraphinline
get_infos() const scaffold::ScaffoldGraphinline
get_matching() const scaffold::ScaffoldGraphinline
get_matching_edges() const scaffold::ScaffoldGraphinline
get_max_multiplicity() const scaffold::ScaffoldGraphinline
get_max_non_contig_length() const scaffold::ScaffoldGraphinline
get_neighbors(const Vertex &u, VertexSet &nh) const scaffold::ScaffoldGraphinline
get_non_matching_edges() const scaffold::ScaffoldGraphinline
Graph typedef (defined in scaffold::ScaffoldGraph)scaffold::ScaffoldGraph
GraphProperty typedef (defined in scaffold::ScaffoldGraph)scaffold::ScaffoldGraph
incident_matching_edge(const Vertex &v) const scaffold::ScaffoldGraphinline
infosscaffold::ScaffoldGraphprotected
is_bridge(const ScafVertex &u, const ScafVertex &v)scaffold::ScaffoldGraphinline
is_bridge_const(const ScafVertex &u, const ScafVertex &v) const scaffold::ScaffoldGraphinline
is_matching_edge(const VertexPair< Graph > &uv) const scaffold::ScaffoldGraphinline
is_on_alternating_cycle(const ScafVertex &u, const ScafVertex &v) const scaffold::ScaffoldGraphinline
matchedscaffold::ScaffoldGraphprotected
matched_with(const Vertex &v) const scaffold::ScaffoldGraphinline
operator[](const Vertex &u) const scaffold::ScaffoldGraphinline
operator[](const Vertex &u)scaffold::ScaffoldGraphinline
operator[](const Edge &e) const scaffold::ScaffoldGraphinline
operator[](const Edge &e)scaffold::ScaffoldGraphinline
operator[](const VertexPair< Graph > &uv) const scaffold::ScaffoldGraphinline
operator[](const VertexPair< Graph > &uv)scaffold::ScaffoldGraphinline
parse_matching_from_graph()scaffold::ScaffoldGraphinlineprotected
print_statistics()scaffold::ScaffoldGraphinline
remove_contigs()scaffold::ScaffoldGraphinline
ScaffoldGraph()scaffold::ScaffoldGraphinline
ScaffoldGraph(const Graph &g)scaffold::ScaffoldGraphinline
ScaffoldGraph(Graph *const g)scaffold::ScaffoldGraphinline
ScaffoldGraph(const ScaffoldGraph &g, Matching< Graph > *const translate, const bool update_infos=true)scaffold::ScaffoldGraphinline
source(const Edge &e) const scaffold::ScaffoldGraphinline
split_off_component()scaffold::ScaffoldGraphinline
target(const Edge &e) const scaffold::ScaffoldGraphinline
update_vertex_indices(const unsigned first_index=0)scaffold::ScaffoldGraphinline
Vertex typedef (defined in scaffold::ScaffoldGraph)scaffold::ScaffoldGraph
VertexIndexMap typedef (defined in scaffold::ScaffoldGraph)scaffold::ScaffoldGraph
VertexProperty typedef (defined in scaffold::ScaffoldGraph)scaffold::ScaffoldGraph
VertexSet typedef (defined in scaffold::ScaffoldGraph)scaffold::ScaffoldGraph
weight() const scaffold::ScaffoldGraphinline
~ScaffoldGraph()scaffold::ScaffoldGraphinline