/* The MIT License

   Copyright (c) 2008, 2012-2013, 2017-2019 Genome Research Ltd (GRL).

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li <lh3@sanger.ac.uk> */

/*
  2012-12-11 (0.1.4):

    * Defined __ks_insertsort_##name as static to compile with C99.

  2008-11-16 (0.1.4):

    * Fixed a bug in introsort() that happens in rare cases.

  2008-11-05 (0.1.3):

    * Fixed a bug in introsort() for complex comparisons.

	* Fixed a bug in mergesort(). The previous version is not stable.

  2008-09-15 (0.1.2):

	* Accelerated introsort. On my Mac (not on another Linux machine),
	  my implementation is as fast as the C++ standard library's sort()
	  on random input.

	* Added combsort and in introsort, switch to combsort if the
	  recursion is too deep.

  2008-09-13 (0.1.1):

	* Added k-small algorithm

  2008-09-05 (0.1.0):

	* Initial version

*/

#ifndef AC_KSORT_H
#define AC_KSORT_H

#include <stdlib.h>
#include <string.h>
#include "hts_defs.h"

#ifndef klib_unused
#if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3)
#define klib_unused __attribute__ ((__unused__))
#else
#define klib_unused
#endif
#endif /* klib_unused */

#ifdef __cplusplus
extern "C" {
#endif

// Use our own drand48() symbol (used by ks_shuffle) to avoid portability
// problems on Windows.  Don't include htslib/hts_os.h for this as it
// may not get on with older attempts to fix this in code that includes
// this file.
HTSLIB_EXPORT
extern double hts_drand48(void);

typedef struct {
	void *left, *right;
	int depth;
} ks_isort_stack_t;

#define KSORT_SWAP(type_t, a, b) { type_t t=(a); (a)=(b); (b)=t; }

#define KSORT_INIT(name, type_t, __sort_lt)	KSORT_INIT_(_ ## name, , type_t, __sort_lt)
#define KSORT_INIT_STATIC(name, type_t, __sort_lt)	KSORT_INIT_(_ ## name, static klib_unused, type_t, __sort_lt)
#define KSORT_INIT2(name, SCOPE, type_t, __sort_lt)	KSORT_INIT_(_ ## name, SCOPE, type_t, __sort_lt)

#define KSORT_INIT_(name, SCOPE, type_t, __sort_lt)						\
	SCOPE int ks_mergesort##name(size_t n, type_t array[], type_t temp[]) \
	{																	\
		type_t *a2[2], *a, *b;											\
		int curr, shift;												\
																		\
		a2[0] = array;													\
		a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n);		\
		for (curr = 0, shift = 0; (1ul<<shift) < n; ++shift) {			\
			a = a2[curr]; b = a2[1-curr];								\
			if (shift == 0) {											\
				type_t *p = b, *i, *eb = a + n;							\
				for (i = a; i < eb; i += 2) {							\
					if (i == eb - 1) *p++ = *i;							\
					else {												\
						if (__sort_lt(*(i+1), *i)) {					\
							*p++ = *(i+1); *p++ = *i;					\
						} else {										\
							*p++ = *i; *p++ = *(i+1);					\
						}												\
					}													\
				}														\
			} else {													\
				size_t i, step = 1ul<<shift;							\
				for (i = 0; i < n; i += step<<1) {						\
					type_t *p, *j, *k, *ea, *eb;						\
					if (n < i + step) {									\
						ea = a + n; eb = a;								\
					} else {											\
						ea = a + i + step;								\
						eb = a + (n < i + (step<<1)? n : i + (step<<1)); \
					}													\
					j = a + i; k = a + i + step; p = b + i;				\
					while (j < ea && k < eb) {							\
						if (__sort_lt(*k, *j)) *p++ = *k++;				\
						else *p++ = *j++;								\
					}													\
					while (j < ea) *p++ = *j++;							\
					while (k < eb) *p++ = *k++;							\
				}														\
			}															\
			curr = 1 - curr;											\
		}																\
		if (curr == 1) {												\
			type_t *p = a2[0], *i = a2[1], *eb = array + n;				\
			for (; p < eb; ++i) *p++ = *i;								\
		}																\
		if (temp == 0) free(a2[1]);										\
		return 0;															\
	}																	\
	SCOPE void ks_heapadjust##name(size_t i, size_t n, type_t l[])		\
	{																	\
		size_t k = i;													\
		type_t tmp = l[i];												\
		while ((k = (k << 1) + 1) < n) {								\
			if (k != n - 1 && __sort_lt(l[k], l[k+1])) ++k;				\
			if (__sort_lt(l[k], tmp)) break;							\
			l[i] = l[k]; i = k;											\
		}																\
		l[i] = tmp;														\
	}																	\
	SCOPE void ks_heapmake##name(size_t lsize, type_t l[])				\
	{																	\
		size_t i;														\
		for (i = (lsize >> 1) - 1; i != (size_t)(-1); --i)				\
			ks_heapadjust##name(i, lsize, l);							\
	}																	\
	SCOPE void ks_heapsort##name(size_t lsize, type_t l[])				\
	{																	\
		size_t i;														\
		for (i = lsize - 1; i > 0; --i) {								\
			type_t tmp;													\
			tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust##name(0, i, l); \
		}																\
	}																	\
	static inline void __ks_insertsort##name(type_t *s, type_t *t)		\
	{																	\
		type_t *i, *j, swap_tmp;										\
		for (i = s + 1; i < t; ++i)										\
			for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) {			\
				swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp;			\
			}															\
	}																	\
	SCOPE void ks_combsort##name(size_t n, type_t a[])					\
	{																	\
		const double shrink_factor = 1.2473309501039786540366528676643; \
		int do_swap;													\
		size_t gap = n;													\
		type_t tmp, *i, *j;												\
		do {															\
			if (gap > 2) {												\
				gap = (size_t)(gap / shrink_factor);					\
				if (gap == 9 || gap == 10) gap = 11;					\
			}															\
			do_swap = 0;												\
			for (i = a; i < a + n - gap; ++i) {							\
				j = i + gap;											\
				if (__sort_lt(*j, *i)) {								\
					tmp = *i; *i = *j; *j = tmp;						\
					do_swap = 1;										\
				}														\
			}															\
		} while (do_swap || gap > 2);									\
		if (gap != 1) __ks_insertsort##name(a, a + n);					\
	}																	\
	SCOPE int ks_introsort##name(size_t n, type_t a[])					\
	{																	\
		int d;															\
		ks_isort_stack_t *top, *stack;									\
		type_t rp, swap_tmp;											\
		type_t *s, *t, *i, *j, *k;										\
																		\
		if (n < 1) return 0;												\
		else if (n == 2) {												\
			if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
			return 0;														\
		}																\
		for (d = 2; 1ul<<d < n; ++d);									\
		stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
		top = stack; s = a; t = a + (n-1); d <<= 1;						\
		while (1) {														\
			if (s < t) {												\
				if (--d == 0) {											\
					ks_combsort##name(t - s + 1, s);					\
					t = s;												\
					continue;											\
				}														\
				i = s; j = t; k = i + ((j-i)>>1) + 1;					\
				if (__sort_lt(*k, *i)) {								\
					if (__sort_lt(*k, *j)) k = j;						\
				} else k = __sort_lt(*j, *i)? i : j;					\
				rp = *k;												\
				if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; }	\
				for (;;) {												\
					do ++i; while (__sort_lt(*i, rp));					\
					do --j; while (i <= j && __sort_lt(rp, *j));		\
					if (j <= i) break;									\
					swap_tmp = *i; *i = *j; *j = swap_tmp;				\
				}														\
				swap_tmp = *i; *i = *t; *t = swap_tmp;					\
				if (i-s > t-i) {										\
					if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \
					s = t-i > 16? i+1 : t;								\
				} else {												\
					if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \
					t = i-s > 16? i-1 : s;								\
				}														\
			} else {													\
				if (top == stack) {										\
					free(stack);										\
					__ks_insertsort##name(a, a+n);						\
					return 0;												\
				} else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \
			}															\
		}																\
		return 0;															\
	}																	\
	/* This function is adapted from: http://ndevilla.free.fr/median/ */ \
	/* 0 <= kk < n */													\
	SCOPE type_t ks_ksmall##name(size_t n, type_t arr[], size_t kk)		\
	{																	\
		type_t *low, *high, *k, *ll, *hh, *mid;							\
		low = arr; high = arr + n - 1; k = arr + kk;					\
		for (;;) {														\
			if (high <= low) return *k;									\
			if (high == low + 1) {										\
				if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
				return *k;												\
			}															\
			mid = low + (high - low) / 2;								\
			if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
			if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
			if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low);	\
			KSORT_SWAP(type_t, *mid, *(low+1));							\
			ll = low + 1; hh = high;									\
			for (;;) {													\
				do ++ll; while (__sort_lt(*ll, *low));					\
				do --hh; while (__sort_lt(*low, *hh));					\
				if (hh < ll) break;										\
				KSORT_SWAP(type_t, *ll, *hh);							\
			}															\
			KSORT_SWAP(type_t, *low, *hh);								\
			if (hh <= k) low = ll;										\
			if (hh >= k) high = hh - 1;									\
		}																\
	}																	\
	SCOPE void ks_shuffle##name(size_t n, type_t a[])					\
	{																	\
		int i, j;														\
		for (i = n; i > 1; --i) {										\
			type_t tmp;													\
			j = (int)(hts_drand48() * i);								\
			tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp;					\
		}																\
	}

#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
#define ks_combsort(name, n, a) ks_combsort_##name(n, a)
#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)
#define ks_shuffle(name, n, a) ks_shuffle_##name(n, a)

#define ks_lt_generic(a, b) ((a) < (b))
#define ks_lt_str(a, b) (strcmp((a), (b)) < 0)

typedef const char *ksstr_t;

#define KSORT_INIT_GENERIC(type_t) KSORT_INIT_(_ ## type_t, , type_t, ks_lt_generic)
#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)

#define KSORT_INIT_STATIC_GENERIC(type_t) KSORT_INIT_(_ ## type_t, static klib_unused, type_t, ks_lt_generic)
#define KSORT_INIT_STATIC_STR KSORT_INIT_STATIC(str, ksstr_t, ks_lt_str)

#define KSORT_INIT2_GENERIC(type_t, SCOPE) KSORT_INIT_(_ ## type_t, SCOPE, type_t, ks_lt_generic)
#define KSORT_INIT2_STR KSORT_INIT2(str, SCOPE, ksstr_t, ks_lt_str)

#ifdef __cplusplus
}
#endif

#endif
