Scaffolding  0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
Public Types | Public Member Functions | Public Attributes | Protected Attributes | List of all members
phylo::PhyloNet Class Reference

Public Types

typedef adjacency_list< hash_setS, listS, bidirectionalS, property< vertex_index_t, size_t, property< vertex_name_t, std::string > >, no_property > InternalNet
 
typedef Vertex< InternalNet > InternVertex
 
typedef VertexPair< InternalNet > InternVertexPair
 
typedef VertexSet< InternalNet > InternVertexSet
 
typedef VertexList< InternalNet > InternVertexList
 
typedef Edge< InternalNet > Arc
 
typedef boost::graph_traits< InternalNet >::out_edge_iterator OutEdgeIter
 
typedef std::pair< OutEdgeIter, OutEdgeIter > OutEdgeIterRange
 
typedef boost::graph_traits< InternalNet >::in_edge_iterator InEdgeIter
 
typedef std::pair< InEdgeIter, InEdgeIter > InEdgeIterRange
 

Public Member Functions

const InternVertex & get_root () const
 
InternVertexList get_leaves () const
 
std::string get_name (const InternVertex &v) const
 
InternVertexList get_parents (const InternVertex &u) const
 
size_t num_vertices () const
 
size_t num_edges () const
 
const InternalNet get_network () const
 
const InternVertex & set_root (const size_t idx=0)
 
const InternVertex & add_vertex (const InternVertex &parent, const size_t idx=0, const std::string &name="")
 
const InternVertex & add_vertex (const std::list< InternVertex > &parents, const size_t idx=0, const std::string &name="")
 
void make_leaf (const InternVertex &v, const std::string &name)
 
void add_arc (const InternVertexPair &e)
 
void add_arc (const InternVertex &u, const InternVertex &v)
 
void delete_vertex (const InternVertex &v)
 

Public Attributes

InternalNet net
 

Protected Attributes

Vertex< InternalNet > root
 

The documentation for this class was generated from the following file: