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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 instance is a ScaffoldGraph with given path- & cycle- numbers and a solution to keep track of deleted edges More...
#include <instance.hpp>
Public Types | |
| typedef Solution | solution_type |
 Public Types inherited from scaffold::ScaffoldGraph | |
| typedef RawScaffoldGraph | Graph |
| typedef boost::graph_traits< Graph >::vertex_descriptor | Vertex |
| typedef boost::graph_traits< Graph >::edge_descriptor | Edge |
| typedef Graph::vertex_bundled | VertexProperty |
| typedef Graph::edge_bundled | EdgeProperty |
| typedef Graph::graph_bundled | GraphProperty |
| typedef boost::property_map< Graph, unsigned VertexProperty::* >::const_type | cVertexIndexMap |
| typedef boost::property_map< Graph, unsigned VertexProperty::* >::type | VertexIndexMap |
| typedef boost::unordered_set< Vertex > | VertexSet |
Public Member Functions | |
| Instance (const unsigned np, const unsigned nc, const unsigned no=UINT_MAX) | |
| construct an empty solution solution | |
| Instance (RawScaffoldGraph *const _g, const unsigned np, const unsigned nc, const unsigned no=UINT_MAX) | |
| construct an instance using the given pointer _g as graph - no copy is performed | |
| Instance (const ScaffoldGraph &_g, const unsigned np, const unsigned nc, const unsigned no=UINT_MAX, const bool update_infos=false) | |
| construct an instance using the given ScaffoldGraph, which is copied More... | |
| Instance (const Instance &I, ScafMatching *const translate=NULL, const bool update_infos=false) | |
| copy constructor creating a copy of the graph and returning the translate map More... | |
| Instance * | split_off_component () |
| split off one connected component from I and return an instance consisting only of it. If we have just one component, do nothing & return NULL More... | |
| void | disjoint_union (const Instance &I) |
| disjointly merge I into us, merging partial solutions along the way | |
| void | delete_edge (const ScafEdge &e, const bool register_in_solution=false) |
| delete an edge e and add the deletion to the solution if requested | |
| bool | delete_edge (const ScafVertex &u, const ScafVertex &v, const bool register_in_solution=false) |
| delete the edge (u,v) and add this deletion to the solution if requested; return success | |
| void | clear_vertex_except (const ScafVertex &u, const ScafEdge *const e, const bool register_in_solution=false) |
| remove all non-matching edges incident with u, except for e | |
| Public Member Functions inherited from scaffold::ScaffoldGraph | |
| ScaffoldGraph () | |
| constructor initializing an empty graph | |
| ScaffoldGraph (const Graph &g) | |
| constructor initializing a copy of the given graph g | |
| ScaffoldGraph (Graph *const g) | |
| constructor initializing using the given graph pointer; no copy is performed More... | |
| ScaffoldGraph (const ScaffoldGraph &g, Matching< Graph > *const translate, const bool update_infos=true) | |
| constructor initializing a copy of the given graph g and returning the translate map in translate; update infos if requested More... | |
| ~ScaffoldGraph () | |
| destructor deleting _the_graph | |
| void | update_vertex_indices (const unsigned first_index=0) |
| recompute vertex indices; useful after deleting vertices or uniting scaffold graphs | |
| const VertexIndexMap | get_index_map () const |
| get an index map to use in various boost algorithms | |
| std::pair< Edge, bool > | find_edge (const Vertex &u, const Vertex &v) const |
| find an edge in _the_graph, given its endpoints More... | |
| void | clear_vertex (const Vertex &u) |
| remove all non-matching edges incident with u | |
| void | delete_vertex (const Vertex &u, const bool update_indices=true, const bool update_infos=true) |
| remove a vertex and all its incident edges More... | |
| const VertexProperty & | operator[] (const Vertex &u) const |
| get a const reference to the vertex properties of u | |
| VertexProperty & | operator[] (const Vertex &u) |
| get a reference to the vertex properties of u | |
| const EdgeProperty & | operator[] (const Edge &e) const |
| get a const reference to the edge properties of e | |
| EdgeProperty & | operator[] (const Edge &e) |
| get a reference to the edge properties of e | |
| const EdgeProperty & | operator[] (const VertexPair< Graph > &uv) const |
| get a const reference to the edge properties of uv, throwing invalid_assumption if uv does not exist | |
| EdgeProperty & | operator[] (const VertexPair< Graph > &uv) |
| get a reference to the edge properties of uv, throwing invalid_assumption if uv does not exist | |
| const GraphProperty & | get_graph_property () const |
| return a const reference to the graph properties | |
| Vertex | source (const Edge &e) const |
| get a copy of the source vertex of e | |
| Vertex | target (const Edge &e) const |
| get a copy of the target vertex of e | |
| const GraphInfos< Graph > & | get_infos () const |
| get a const reference to the graph infos | |
| const Graph & | get_graph () const |
| get a const reference to the underlying graph | |
| const Matching< Graph > & | get_matching () const |
| get a const reference to the perfect matching in _the_graph | |
| const Vertex & | matched_with (const Vertex &v) const |
| get a const reference to the vertex matched with v | |
| const bool | is_matching_edge (const VertexPair< Graph > &uv) const |
| return whether the given VertexPair is matched More... | |
| const Edge | incident_matching_edge (const Vertex &v) const |
| return the matching edge that is incident with v | |
| const unsigned | degree (const Vertex &v) const |
| return the degree of v | |
| bool | adjacent (const Vertex &u, const Vertex &v) const |
| return whether u & v are adjacent | |
| void | get_neighbors (const Vertex &u, VertexSet &nh) const |
| put all neighbors of u into nh | |
| unsigned | get_max_multiplicity () const |
| compute the maximum multiplicity occuring in g | |
| std::pair< Edge, int > | get_max_non_contig_length () const |
| return a non-contig edge of maximum length in the graph | |
| void | delete_edge (const Edge &e, const bool update_infos=true) |
| delete an edge e and update infos if requested More... | |
| bool | delete_edge (const Vertex &u, const Vertex &v) |
| delete an edge e and update infos if requested; return whether the edge had existed before or not | |
| bool | delete_edge (const VertexPair< Graph > &uv) |
| convenience function to delete pairs of vertices | |
| Vertex const * | find_vertex_by_name (const VertexName &name) const |
| find a vertex given its name More... | |
| Edge const * | find_edge_by_name (const EdgeName &name) const |
| delete edge by name More... | |
| const Vertex | add_vertex (const VertexProperty &p, const bool update_infos=true) |
| add a new vertex and return it | |
| const Vertex | add_vertex (const std::string name, const bool update_infos=true, const unsigned index=UINT_MAX) |
| add a new vertex and return it; use the given name & index More... | |
| const Vertex | add_vertex (const Vertex &u, const bool update_infos=true) |
| add a new vertex and return it; copy the name from vertex u More... | |
| std::pair< Edge, bool > | add_edge (const Vertex &u, const Vertex &v, const EdgeProperty &ep=EdgeProperty(), const bool update_infos=true) |
| add a new edge unless it is already there; return it and whether an insertion took place More... | |
| std::pair< Edge, bool > | add_matching_edge (const Vertex &u, const Vertex &v, const EdgeProperty &ep=EdgeProperty(), const bool update_infos=true) |
| add a matching edge unless the edge already exists; return the edge and whether an insertion took place More... | |
| EdgeName | get_edge_name (const VertexPair< Graph > &uv) const |
| get a copy of the name of the edge uv; independent of its presence | |
| EdgeName | get_edge_name (const Edge &e) const |
| get a copy of the name of an edge | |
| bool | is_bridge (const ScafVertex &u, const ScafVertex &v) |
| return whether the given vertex pair constitutes a bridge, updating infos if necessary | |
| bool | is_bridge_const (const ScafVertex &u, const ScafVertex &v) const |
| return whether the given vertex pair constitutes a bridge without updating the infos | |
| bool | is_on_alternating_cycle (const ScafVertex &u, const ScafVertex &v) const |
| return whether the given edge is on an alternating cycle | |
| unsigned | weight () const |
| return the total weight of the graph | |
| template<class Predicate = TruePredicate<Edge>> | |
| Predicated_EdgeIter< Graph, Predicate, EdgeIter< Graph > > | get_edges (const Predicate &pred=Predicate()) const |
| get all edges satisfying a predicate | |
| Predicated_EdgeIter< Graph, MatchingPredicate< Graph >, EdgeIter< Graph > > | get_matching_edges () const |
| convenience fuction to get all matching edges | |
| Predicated_EdgeIter< Graph, MatchingPredicate< Graph >, EdgeIter< Graph > > | get_non_matching_edges () const |
| convenience fuction to get all non-matching edges | |
| template<class Predicate = TruePredicate<Edge>> | |
| Predicated_EdgeIter< Graph, Predicate > | get_incident (const Vertex &u, const Predicate &pred=Predicate()) const |
| get incident edges of u satisfying a predicate | |
| Predicated_EdgeIter< Graph, MatchingPredicate< Graph > > | get_incident_non_matching (const Vertex &u) const |
| convenience function to get all incident non-matching edges of u | |
| Graph *const | split_off_component () |
| if _the_graph is disconnected, split off & return a connected compoenent, otherwise return NULL | |
| void | disjoint_union (const ScaffoldGraph &g) |
| merge g into our graph | |
| void | print_statistics () |
| print various statistics | |
| void | remove_contigs () |
| remove all contig edges from the graph More... | |
Public Attributes | |
| unsigned | num_paths |
| max number of paths in solutions | |
| unsigned | num_cycles |
| max number of cycles in solutions | |
| unsigned | num_objects |
| max number of objects (sum of paths & cycles) in solutions | |
| solution_type | solution |
| a partial solution | |
Additional Inherited Members | |
| Protected Member Functions inherited from scaffold::ScaffoldGraph | |
| void | copy_and_init_matching (const ScaffoldGraph &g, Matching< Graph > *const translate, const bool update_infos) |
| outsource common constructor work: copy a given graph, construct a matching from the translate map, and update infos if requested | |
| void | parse_matching_from_graph () |
| compute the matching by parsing the properties of all edges | |
| void | delete_matching (const Vertex &u) |
| remove the indication that uv is a matching edge | |
| Protected Attributes inherited from scaffold::ScaffoldGraph | |
| Graph *const | _the_graph |
| the underlying boost graph | |
| Matching< Graph > | matched |
| a perfect matching in _the_graph | |
| GraphInfos< Graph > | infos |
| a set of graph properties of the underlying graph More... | |
an instance is a ScaffoldGraph with given path- & cycle- numbers and a solution to keep track of deleted edges
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inline |
construct an instance using the given ScaffoldGraph, which is copied
update_infos can be used to recompute all graph infos
|
inline |
copy constructor creating a copy of the graph and returning the translate map
update_infos can be used to recompute all graph infos
|
inline |
split off one connected component from I and return an instance consisting only of it. If we have just one component, do nothing & return NULL
NOTE: in case of a split-off, the result is guaranteed connected, while the remainder of the instance might not be
1.8.10
