Scaffolding  0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
scaffold::solv::DP::DynProgSolution< Compare > Member List

This is the complete list of members for scaffold::solv::DP::DynProgSolution< Compare >, including all inherited members.

add_edge_global(const VertexName &u, const VertexName &v, const size_t weight) (defined in scaffold::solv::DP::DynProgSolution< Compare >)scaffold::solv::DP::DynProgSolution< Compare >inline
add_to_all(const EdgeName &e, const size_t weight) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
add_to_each_key(const PathsAndCycles &pc) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
add_to_key(const PathsAndCycles &key, const PathsAndCycles &pc) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
at(const PathsAndCycles &index) const (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
at(const unsigned paths, const unsigned cycles) const (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
best_index (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >
combine_disjoint_union(const DynProgSolution &S) (defined in scaffold::solv::DP::DynProgSolution< Compare >)scaffold::solv::DP::DynProgSolution< Compare >inline
combine_min_of_two(const DynProgSolution &S) (defined in scaffold::solv::DP::DynProgSolution< Compare >)scaffold::solv::DP::DynProgSolution< Compare >inline
destructive_append(DynProgSolution &S) (defined in scaffold::solv::DP::DynProgSolution< Compare >)scaffold::solv::DP::DynProgSolution< Compare >inline
destructive_merge(PCMinMatrix< Compare > &pc) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
DynProgSolution(const PCMinMatrix< Compare > &S) (defined in scaffold::solv::DP::DynProgSolution< Compare >)scaffold::solv::DP::DynProgSolution< Compare >inline
DynProgSolution(const DynProgSolution &S) (defined in scaffold::solv::DP::DynProgSolution< Compare >)scaffold::solv::DP::DynProgSolution< Compare >inline
entries (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >protected
entries_t typedef (defined in scaffold::solv::DP::DynProgSolution< Compare >)scaffold::solv::DP::DynProgSolution< Compare >
find_min_entry_combination(const PathsAndCycles &pc, const PCMinMatrix &m) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
find_min_entry_combination_by_iteration(const PathsAndCycles &pc, const PCMinMatrix &m) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
find_min_entry_combination_by_testing(const PathsAndCycles &pc, const PCMinMatrix &m) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
get(const PathsAndCycles &index) const (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
get(const unsigned paths, const unsigned cycles) const (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
get_entries() const (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
get_min_entry() const (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
global (defined in scaffold::solv::DP::DynProgSolution< Compare >)scaffold::solv::DP::DynProgSolution< Compare >protected
invalidate() (defined in scaffold::solv::DP::DynProgSolution< Compare >)scaffold::solv::DP::DynProgSolution< Compare >inline
is_better (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >protected
max (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >
no_solutions() const (defined in scaffold::solv::DP::DynProgSolution< Compare >)scaffold::solv::DP::DynProgSolution< Compare >inline
operator<< (defined in scaffold::solv::DP::DynProgSolution< Compare >)scaffold::solv::DP::DynProgSolution< Compare >friend
PCMinMatrix(const unsigned paths, const unsigned cycles) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
PCMinMatrix(const PathsAndCycles &_max) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
PCMinMatrix(const PCMinMatrix &m) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
put(const PathsAndCycles &index, MatrixEntry *ME) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
put(const PathsAndCycles &index, const EdgeName &e, const size_t weight) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
put(const PathsAndCycles &index, const MatrixEntry &E, const MatrixEntry &cE) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
put_all(const PathsAndCycles &index, const Graph &g) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
put_empty(const PathsAndCycles &index) (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
size() const (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
smallest_index() const (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline
~PCMinMatrix() (defined in scaffold::PCMinMatrix< Compare >)scaffold::PCMinMatrix< Compare >inline