#include <algorithm>
#include <stack>

Classes
struct	divsufsortxx::helper::stackinfo3< a_type, b_type, c_type >

struct	divsufsortxx::helper::stackinfo4< a_type, b_type, c_type, d_type >

class	divsufsortxx::substring::substring_wrapper< StringIterator_type, PAIterator_type >

Namespaces
	divsufsortxx

	divsufsortxx::helper

	divsufsortxx::substring

	divsufsortxx::doubling

	divsufsortxx::tandemrepeat

	divsufsortxx::core

Macros
#define	STACK_POP3(_a, _b, _c)

#define	STACK_POP4(_a, _b, _c, _d)

#define	STACK_PUSH3(_a, _b, _c) stack.push(stackinfo_type((_a), (_b), (_c)))

#define	STACK_PUSH4(_a, _b, _c, _d) stack.push(stackinfo_type((_a), (_b), (_c), (_d)))

#define	GETIDX(a) ((0 <= (a)) ? (a) : (~(a)))

#define	MERGE_CHECK(a)

#define	UPDATE_BUDGET(n)

#define	BUCKET_A(c0) bucket_A[(c0)]

#define	BUCKET_B(c0, c1) (bucket_B[((alphabetsize_type)(c1)) * alphabetsize + (alphabetsize_type)(c0)])

#define	BUCKET_BSTAR(c0, c1) (bucket_B[((alphabetsize_type)(c0)) * alphabetsize + (alphabetsize_type)(c1)])

Functions
template<typename ISAIterator_type , typename SAIterator_type >
void	divsufsortxx::helper::insertionsort (const ISAIterator_type ISAd, SAIterator_type first, SAIterator_type last)

template<typename StringIterator_type , typename SAIterator_type , typename pos_type >
void	divsufsortxx::helper::fixdown (const StringIterator_type Td, SAIterator_type SA, pos_type i, pos_type size)

template<typename StringIterator_type , typename SAIterator_type >
void	divsufsortxx::helper::heapsort (const StringIterator_type Td, SAIterator_type SA, typename std::iterator_traits< SAIterator_type >::value_type size)

template<typename numeric_type >
int	divsufsortxx::helper::lg (numeric_type n)

template<typename Iterator1_type , typename Iterator2_type >
void	divsufsortxx::helper::vecswap (Iterator1_type first1, Iterator1_type last1, Iterator2_type first2)

template<typename StringIterator_type , typename SAIterator_type >
SAIterator_type	divsufsortxx::helper::median3 (const StringIterator_type Td, SAIterator_type v1, SAIterator_type v2, SAIterator_type v3)

template<typename StringIterator_type , typename SAIterator_type >
SAIterator_type	divsufsortxx::helper::median5 (const StringIterator_type Td, SAIterator_type v1, SAIterator_type v2, SAIterator_type v3, SAIterator_type v4, SAIterator_type v5)

template<typename StringIterator_type , typename SAIterator_type >
SAIterator_type	divsufsortxx::helper::pivot (const StringIterator_type Td, SAIterator_type first, SAIterator_type last)

template<typename StringIterator_type , typename SAIterator_type >
bool	divsufsortxx::helper::partition (const StringIterator_type Td, SAIterator_type first1, SAIterator_type first2, SAIterator_type last, SAIterator_type &mfirst, SAIterator_type &mlast, const typename std::iterator_traits< StringIterator_type >::value_type &v)

template<typename StringIterator_type , typename SAIterator_type >
int	divsufsortxx::substring::compare (StringIterator_type T, const SAIterator_type p1, const SAIterator_type p2, typename std::iterator_traits< SAIterator_type >::value_type depth)

template<typename StringIterator_type , typename SAIterator_type >
int	divsufsortxx::substring::compare_last (StringIterator_type T, const SAIterator_type p1, const SAIterator_type p2, typename std::iterator_traits< SAIterator_type >::value_type depth, typename std::iterator_traits< SAIterator_type >::value_type size)

template<typename StringIterator_type , typename SAIterator_type >
void	divsufsortxx::substring::insertionsort (StringIterator_type T, const SAIterator_type PA, SAIterator_type first, SAIterator_type last, typename std::iterator_traits< SAIterator_type >::value_type depth)

template<typename SAIterator_type >
SAIterator_type	divsufsortxx::substring::partition (const SAIterator_type PA, SAIterator_type first, SAIterator_type last, typename std::iterator_traits< SAIterator_type >::value_type depth)

template<typename stack_type , typename StringIterator_type , typename SAIterator_type >
void	divsufsortxx::substring::mintrosort (stack_type &stack, const StringIterator_type T, const SAIterator_type PA, SAIterator_type first, SAIterator_type last, typename std::iterator_traits< SAIterator_type >::value_type depth)

template<typename StringIterator_type , typename SAIterator_type , typename BufIterator_type >
void	divsufsortxx::substring::merge_forward (const StringIterator_type T, const SAIterator_type PA, BufIterator_type buf, SAIterator_type first, SAIterator_type middle, SAIterator_type last, typename std::iterator_traits< SAIterator_type >::value_type depth)

template<typename StringIterator_type , typename SAIterator_type , typename BufIterator_type >
void	divsufsortxx::substring::merge_backward (const StringIterator_type T, const SAIterator_type PA, BufIterator_type buf, SAIterator_type first, SAIterator_type middle, SAIterator_type last, typename std::iterator_traits< SAIterator_type >::value_type depth)

template<typename stack_type , typename StringIterator_type , typename SAIterator_type , typename BufIterator_type >
void	divsufsortxx::substring::merge (stack_type &stack, const StringIterator_type T, const SAIterator_type PA, SAIterator_type first, SAIterator_type middle, SAIterator_type last, BufIterator_type buf, typename std::iterator_traits< SAIterator_type >::value_type bufsize, typename std::iterator_traits< SAIterator_type >::value_type depth)

template<typename StringIterator_type , typename SAIterator_type , typename BufIterator_type >
void	divsufsortxx::substring::sort (const StringIterator_type T, const SAIterator_type PA, SAIterator_type first, SAIterator_type last, BufIterator_type buf, typename std::iterator_traits< SAIterator_type >::value_type bufsize, typename std::iterator_traits< SAIterator_type >::value_type depth, typename std::iterator_traits< SAIterator_type >::value_type size, bool lastsuffix, int blocksize=1024)

template<typename ISAIterator_type , typename SAIterator_type >
void	divsufsortxx::doubling::updategroup (ISAIterator_type ISA, const SAIterator_type SA, SAIterator_type first, SAIterator_type last)

template<typename stack_type , typename ISAIterator_type , typename SAIterator_type >
void	divsufsortxx::doubling::introsort (stack_type &stack, ISAIterator_type ISA, const ISAIterator_type ISAd, const SAIterator_type SA, SAIterator_type first, SAIterator_type last)

template<typename ISAIterator_type , typename SAIterator_type >
void	divsufsortxx::doubling::sort (ISAIterator_type ISA, SAIterator_type first, SAIterator_type last)

template<typename stack_type , typename ISAIterator_type , typename SAIterator_type , typename pos_type >
void	divsufsortxx::tandemrepeat::introsort (stack_type &stack, ISAIterator_type ISA, ISAIterator_type ISAd, const SAIterator_type SA, SAIterator_type first, SAIterator_type last, pos_type &budget, int &chance, pos_type size)

template<typename ISAIterator_type , typename SAIterator_type >
bool	divsufsortxx::tandemrepeat::sort (ISAIterator_type ISA, SAIterator_type first, SAIterator_type last)

template<typename StringIterator_type , typename SAIterator_type , typename pos_type , typename alphabetsize_type >
pos_type	divsufsortxx::core::sort_typeBstar (const StringIterator_type T, SAIterator_type SA, pos_type bucket_A, pos_type bucket_B, pos_type n, pos_type SAsize, alphabetsize_type alphabetsize)

template<typename StringIterator_type , typename SAIterator_type , typename pos_type , typename alphabetsize_type >
void	divsufsortxx::core::constructSA_from_typeBstar (const StringIterator_type T, SAIterator_type SA, pos_type bucket_A, pos_type bucket_B, pos_type n, pos_type m, alphabetsize_type alphabetsize)

template<typename StringIterator_type , typename SAIterator_type , typename pos_type , typename alphabetsize_type >
SAIterator_type	divsufsortxx::core::constructBWT_from_typeBstar (const StringIterator_type T, SAIterator_type SA, pos_type bucket_A, pos_type bucket_B, pos_type n, pos_type m, alphabetsize_type alphabetsize)

template<typename StringIterator_type , typename SAIterator_type , typename alphabetsize_type >
int	divsufsortxx::constructSA (const StringIterator_type T, const StringIterator_type T_last, SAIterator_type SA, SAIterator_type SA_last, alphabetsize_type alphabetsize=256)

template<typename StringIterator_type , typename SAIterator_type , typename alphabetsize_type >
int	divsufsortxx::constructSA (const StringIterator_type T, SAIterator_type SA, typename std::iterator_traits< SAIterator_type >::value_type n, alphabetsize_type alphabetsize=256)

template<typename StringIterator1_type , typename StringIterator2_type , typename SAIterator_type , typename alphabetsize_type >
std::iterator_traits < SAIterator_type > ::value_type	divsufsortxx::constructBWT (const StringIterator1_type T, const StringIterator1_type T_last, StringIterator2_type U, StringIterator2_type U_last, SAIterator_type SA, SAIterator_type SA_last, alphabetsize_type alphabetsize=256)

template<typename pos_type , typename StringIterator1_type , typename StringIterator2_type , typename alphabetsize_type >
pos_type	divsufsortxx::constructBWT (const StringIterator1_type T, const StringIterator1_type T_last, StringIterator2_type U, StringIterator2_type U_last, alphabetsize_type alphabetsize=256)

template<typename pos_type , typename StringIterator_type , typename alphabetsize_type >
pos_type	divsufsortxx::constructBWT (StringIterator_type T, StringIterator_type T_last, alphabetsize_type alphabetsize=256)

template<typename StringIterator1_type , typename StringIterator2_type , typename SAIterator_type , typename alphabetsize_type >
std::iterator_traits < SAIterator_type > ::value_type	divsufsortxx::constructBWT (const StringIterator1_type T, StringIterator2_type U, SAIterator_type SA, typename std::iterator_traits< SAIterator_type >::value_type n, alphabetsize_type alphabetsize=256)

template<typename pos_type , typename StringIterator1_type , typename StringIterator2_type , typename alphabetsize_type >
pos_type	divsufsortxx::constructBWT (const StringIterator1_type T, StringIterator2_type U, pos_type n, alphabetsize_type alphabetsize=256)

template<typename pos_type , typename StringIterator_type , typename alphabetsize_type >
pos_type	divsufsortxx::constructBWT (StringIterator_type T, pos_type n, alphabetsize_type alphabetsize=256)

Macro Definition Documentation

#define BUCKET_A ( c0) bucket_A[(c0)]

Definition at line 1107 of file divsufsortxx.h.

#define BUCKET_B	(	c0,
		c1
	)	(bucket_B[((alphabetsize_type)(c1)) * alphabetsize + (alphabetsize_type)(c0)])

Definition at line 1108 of file divsufsortxx.h.

#define BUCKET_BSTAR	(	c0,
		c1
	)	(bucket_B[((alphabetsize_type)(c0)) * alphabetsize + (alphabetsize_type)(c1)])

Definition at line 1109 of file divsufsortxx.h.

#define GETIDX ( a) ((0 <= (a)) ? (a) : (~(a)))

#define MERGE_CHECK ( a)

Value:

{\
    if((0 <= *(a)) &&\
       (compare(T, PA + GETIDX(*((a) - 1)), PA + *(a), depth) == 0)) {\
      *(a) = ~*(a);\
    }\
  }

#define STACK_POP3	(	_a,
		_b,
		_c
	)

Value:

{\
    if(stack.empty()) { return; }\
    stackinfo_type tempinfo = stack.top();\
    (_a) = tempinfo.m_a, (_b) = tempinfo.m_b, (_c) = tempinfo.m_c;\
    stack.pop();\
  }

Definition at line 277 of file divsufsortxx.h.

#define STACK_POP4	(	_a,
		_b,
		_c,
		_d
	)

Value:

{\
    if(stack.empty()) { return; }\
    stackinfo_type tempinfo = stack.top();\
    (_a) = tempinfo.m_a, (_b) = tempinfo.m_b, (_c) = tempinfo.m_c, (_d) = tempinfo.m_d;\
    stack.pop();\
  }

Definition at line 284 of file divsufsortxx.h.

#define STACK_PUSH3	(	_a,
		_b,
		_c
	)	stack.push(stackinfo_type((_a), (_b), (_c)))

Definition at line 291 of file divsufsortxx.h.

#define STACK_PUSH4	(	_a,
		_b,
		_c,
		_d
	)	stack.push(stackinfo_type((_a), (_b), (_c), (_d)))

Definition at line 293 of file divsufsortxx.h.

#define UPDATE_BUDGET ( n)

Value:

{\
    budget -= (n);\
    if(budget <= 0) {\
      budget += size;\
      if(--chance == 0) { break; }\
    }\
  }

Classes

Namespaces

Macros

Functions

Macro Definition Documentation