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

Public Types

typedef PCMinMatrix< Compare >::entries_t entries_t
 
- Public Types inherited from scaffold::PCMinMatrix< Compare >
typedef unordered_map< PathsAndCycles, MatrixEntry * > entries_t
 

Public Member Functions

 DynProgSolution (const PCMinMatrix< Compare > &S)
 
 DynProgSolution (const DynProgSolution &S)
 
bool no_solutions () const
 
void invalidate ()
 
void combine_disjoint_union (const DynProgSolution &S)
 
void combine_min_of_two (const DynProgSolution &S)
 
void destructive_append (DynProgSolution &S)
 
void add_edge_global (const VertexName &u, const VertexName &v, const size_t weight)
 
- Public Member Functions inherited from scaffold::PCMinMatrix< Compare >
 PCMinMatrix (const unsigned paths, const unsigned cycles)
 
 PCMinMatrix (const PathsAndCycles &_max)
 
 PCMinMatrix (const PCMinMatrix &m)
 
bool put (const PathsAndCycles &index, MatrixEntry *ME)
 
bool put_empty (const PathsAndCycles &index)
 
bool put (const PathsAndCycles &index, const EdgeName &e, const size_t weight)
 
template<class Graph >
bool put_all (const PathsAndCycles &index, const Graph &g)
 
bool put (const PathsAndCycles &index, const MatrixEntry &E, const MatrixEntry &cE)
 
void add_to_all (const EdgeName &e, const size_t weight)
 
const MatrixEntryget (const PathsAndCycles &index) const
 
const MatrixEntryget (const unsigned paths, const unsigned cycles) const
 
const MatrixEntryat (const PathsAndCycles &index) const
 
const MatrixEntryat (const unsigned paths, const unsigned cycles) const
 
std::pair< entries_t::const_iterator, entries_t::const_iterator > get_entries () const
 
void destructive_merge (PCMinMatrix< Compare > &pc)
 
bool add_to_key (const PathsAndCycles &key, const PathsAndCycles &pc)
 
void add_to_each_key (const PathsAndCycles &pc)
 
PathsAndCycles find_min_entry_combination_by_iteration (const PathsAndCycles &pc, const PCMinMatrix &m)
 
PathsAndCycles find_min_entry_combination_by_testing (const PathsAndCycles &pc, const PCMinMatrix &m)
 
PathsAndCycles find_min_entry_combination (const PathsAndCycles &pc, const PCMinMatrix &m)
 
const MatrixEntryget_min_entry () const
 
const size_t size () const
 
const PathsAndCycles smallest_index () const
 

Protected Attributes

MatrixEntry global
 
- Protected Attributes inherited from scaffold::PCMinMatrix< Compare >
entries_t * entries
 
const Compare is_better
 

Friends

std::ostream & operator<< (std::ostream &os, const DynProgSolution< Compare > &S)
 

Additional Inherited Members

- Public Attributes inherited from scaffold::PCMinMatrix< Compare >
const PathsAndCycles max
 
PathsAndCycles best_index
 

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