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 | Friends | List of all members
scaffold::PCMinMatrix< Compare > Class Template Reference
Inheritance diagram for scaffold::PCMinMatrix< Compare >:
scaffold::solv::DP::DynProgSolution< Compare >

Public Types

typedef unordered_map< PathsAndCycles, MatrixEntry * > entries_t
 

Public Member Functions

 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
 

Public Attributes

const PathsAndCycles max
 
PathsAndCycles best_index
 

Protected Attributes

entries_t * entries
 
const Compare is_better
 

Friends

std::ostream & operator<< (std::ostream &os, const PCMinMatrix &m)
 

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