Scaffolding
0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
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This is the complete list of members for scaffold::Instance, including all inherited members.
_the_graph | scaffold::ScaffoldGraph | protected |
add_edge(const Vertex &u, const Vertex &v, const EdgeProperty &ep=EdgeProperty(), const bool update_infos=true) | scaffold::ScaffoldGraph | inline |
add_matching_edge(const Vertex &u, const Vertex &v, const EdgeProperty &ep=EdgeProperty(), const bool update_infos=true) | scaffold::ScaffoldGraph | inline |
add_vertex(const VertexProperty &p, const bool update_infos=true) | scaffold::ScaffoldGraph | inline |
add_vertex(const std::string name, const bool update_infos=true, const unsigned index=UINT_MAX) | scaffold::ScaffoldGraph | inline |
add_vertex(const Vertex &u, const bool update_infos=true) | scaffold::ScaffoldGraph | inline |
adjacent(const Vertex &u, const Vertex &v) const | scaffold::ScaffoldGraph | inline |
clear_vertex(const Vertex &u) | scaffold::ScaffoldGraph | inline |
clear_vertex_except(const ScafVertex &u, const ScafEdge *const e, const bool register_in_solution=false) | scaffold::Instance | inline |
copy_and_init_matching(const ScaffoldGraph &g, Matching< Graph > *const translate, const bool update_infos) | scaffold::ScaffoldGraph | inlineprotected |
cVertexIndexMap typedef (defined in scaffold::ScaffoldGraph) | scaffold::ScaffoldGraph | |
degree(const Vertex &v) const | scaffold::ScaffoldGraph | inline |
delete_edge(const ScafEdge &e, const bool register_in_solution=false) | scaffold::Instance | inline |
delete_edge(const ScafVertex &u, const ScafVertex &v, const bool register_in_solution=false) | scaffold::Instance | inline |
scaffold::ScaffoldGraph::delete_edge(const Edge &e, const bool update_infos=true) | scaffold::ScaffoldGraph | inline |
scaffold::ScaffoldGraph::delete_edge(const Vertex &u, const Vertex &v) | scaffold::ScaffoldGraph | inline |
scaffold::ScaffoldGraph::delete_edge(const VertexPair< Graph > &uv) | scaffold::ScaffoldGraph | inline |
delete_matching(const Vertex &u) | scaffold::ScaffoldGraph | inlineprotected |
delete_vertex(const Vertex &u, const bool update_indices=true, const bool update_infos=true) | scaffold::ScaffoldGraph | inline |
disjoint_union(const Instance &I) | scaffold::Instance | inline |
scaffold::ScaffoldGraph::disjoint_union(const ScaffoldGraph &g) | scaffold::ScaffoldGraph | inline |
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::ScaffoldGraph | inline |
find_edge_by_name(const EdgeName &name) const | scaffold::ScaffoldGraph | inline |
find_vertex_by_name(const VertexName &name) const | scaffold::ScaffoldGraph | inline |
get_edge_name(const VertexPair< Graph > &uv) const | scaffold::ScaffoldGraph | inline |
get_edge_name(const Edge &e) const | scaffold::ScaffoldGraph | inline |
get_edges(const Predicate &pred=Predicate()) const | scaffold::ScaffoldGraph | inline |
get_graph() const | scaffold::ScaffoldGraph | inline |
get_graph_property() const | scaffold::ScaffoldGraph | inline |
get_incident(const Vertex &u, const Predicate &pred=Predicate()) const | scaffold::ScaffoldGraph | inline |
get_incident_non_matching(const Vertex &u) const | scaffold::ScaffoldGraph | inline |
get_index_map() const | scaffold::ScaffoldGraph | inline |
get_infos() const | scaffold::ScaffoldGraph | inline |
get_matching() const | scaffold::ScaffoldGraph | inline |
get_matching_edges() const | scaffold::ScaffoldGraph | inline |
get_max_multiplicity() const | scaffold::ScaffoldGraph | inline |
get_max_non_contig_length() const | scaffold::ScaffoldGraph | inline |
get_neighbors(const Vertex &u, VertexSet &nh) const | scaffold::ScaffoldGraph | inline |
get_non_matching_edges() const | scaffold::ScaffoldGraph | inline |
Graph typedef (defined in scaffold::ScaffoldGraph) | scaffold::ScaffoldGraph | |
GraphProperty typedef (defined in scaffold::ScaffoldGraph) | scaffold::ScaffoldGraph | |
incident_matching_edge(const Vertex &v) const | scaffold::ScaffoldGraph | inline |
infos | scaffold::ScaffoldGraph | protected |
Instance(const unsigned np, const unsigned nc, const unsigned no=UINT_MAX) | scaffold::Instance | inline |
Instance(RawScaffoldGraph *const _g, const unsigned np, const unsigned nc, const unsigned no=UINT_MAX) | scaffold::Instance | inline |
Instance(const ScaffoldGraph &_g, const unsigned np, const unsigned nc, const unsigned no=UINT_MAX, const bool update_infos=false) | scaffold::Instance | inline |
Instance(const Instance &I, ScafMatching *const translate=NULL, const bool update_infos=false) | scaffold::Instance | inline |
is_bridge(const ScafVertex &u, const ScafVertex &v) | scaffold::ScaffoldGraph | inline |
is_bridge_const(const ScafVertex &u, const ScafVertex &v) const | scaffold::ScaffoldGraph | inline |
is_matching_edge(const VertexPair< Graph > &uv) const | scaffold::ScaffoldGraph | inline |
is_on_alternating_cycle(const ScafVertex &u, const ScafVertex &v) const | scaffold::ScaffoldGraph | inline |
matched | scaffold::ScaffoldGraph | protected |
matched_with(const Vertex &v) const | scaffold::ScaffoldGraph | inline |
num_cycles | scaffold::Instance | |
num_objects | scaffold::Instance | |
num_paths | scaffold::Instance | |
operator[](const Vertex &u) const | scaffold::ScaffoldGraph | inline |
operator[](const Vertex &u) | scaffold::ScaffoldGraph | inline |
operator[](const Edge &e) const | scaffold::ScaffoldGraph | inline |
operator[](const Edge &e) | scaffold::ScaffoldGraph | inline |
operator[](const VertexPair< Graph > &uv) const | scaffold::ScaffoldGraph | inline |
operator[](const VertexPair< Graph > &uv) | scaffold::ScaffoldGraph | inline |
parse_matching_from_graph() | scaffold::ScaffoldGraph | inlineprotected |
print_statistics() | scaffold::ScaffoldGraph | inline |
remove_contigs() | scaffold::ScaffoldGraph | inline |
ScaffoldGraph() | scaffold::ScaffoldGraph | inline |
ScaffoldGraph(const Graph &g) | scaffold::ScaffoldGraph | inline |
ScaffoldGraph(Graph *const g) | scaffold::ScaffoldGraph | inline |
ScaffoldGraph(const ScaffoldGraph &g, Matching< Graph > *const translate, const bool update_infos=true) | scaffold::ScaffoldGraph | inline |
solution | scaffold::Instance | |
solution_type typedef (defined in scaffold::Instance) | scaffold::Instance | |
source(const Edge &e) const | scaffold::ScaffoldGraph | inline |
split_off_component() | scaffold::Instance | inline |
target(const Edge &e) const | scaffold::ScaffoldGraph | inline |
update_vertex_indices(const unsigned first_index=0) | scaffold::ScaffoldGraph | inline |
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::ScaffoldGraph | inline |
~ScaffoldGraph() | scaffold::ScaffoldGraph | inline |