Scaffolding  0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
Public Types | Public Member Functions | Public Attributes | Friends | List of all members
scaffold::solv::DP::DP_Table< Graph > Class Template Reference

Public Types

typedef boost::bimap< boost::bimaps::unordered_set_of< Vertex< Graph > >, boost::bimaps::unordered_set_of< byte > > VertexIndex
 
typedef d_to_P_map DP_Entries
 

Public Member Functions

void construct_index (const VertexSet< Graph > &VSet)
 
 DP_Table (const Instance< Graph > &_I, const VertexSet< Graph > &VSet)
 
 DP_Table (const Instance< Graph > &_I, const TOL::GraphVertexSet &VSet, TOL::VTranslateBoostTOL< Graph > *vtranslate)
 
void clear ()
 
bool empty () const
 
void get_VSet (std::list< Vertex< Graph > > &l) const
 
void intro_vertex (const Vertex< Graph > &v)
 
void intro_vertices (const VertexSet< Graph > &V)
 
void forget_vertex_from_table (const byte &v_idx)
 
void forget_vertex (const Vertex< Graph > &v)
 
void forget_vertices (const VertexSet< Graph > &V)
 
void intro_edge_to_table (byte u_idx, byte v_idx, const bool is_matching_edge, const EdgeName &en, const size_t weight)
 
void intro_edge (const Edge< Graph > &e)
 
void intro_edges (const std::list< Edge< Graph > > &E)
 
void unify_indices (const DP_Table &T)
 
void join (DP_Table &T)
 
void init_as_leaf ()
 
size_t size () const
 
void read_solution (DynProgSolution< std::greater< size_t > > &S)
 

Public Attributes

VertexIndex * index
 
DegMap M_adj
 
DP_Entriestable
 

Friends

std::ostream & operator<< (std::ostream &os, const DP_Table &T)
 

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