/*****************************************************************************
 IRanges C interface: prototypes
 -------------------------------

   The IRanges C interface is splitted in 2 files:
     1. IRanges_defines.h (in this directory): contains the typedefs and
        defines of the interface.
     2. IRanges_interface.h (this file): contains the prototypes of the
        IRanges C routines that are part of the interface.

 *****************************************************************************/
#include "IRanges_defines.h"


/*
 * Low-level sorting utilities.
 * (see sort_utils.c)
 */

void sort_int_array(
	int *x,
	int nelt,
	int desc
);

void get_order_of_int_array(
	const int *x,
	int nelt,
	int desc,
	int *out,
	int out_shift
);

void get_order_of_two_int_arrays(
	const int *x,
	const int *y,
	int nelt,
	int desc,
	int *out,
	int out_shift
);


/*
 * Low-level manipulation of the Auto-Extending buffers.
 * (see AEbufs.c)
 */

int get_new_buflength(int buflength);

void IntAE_set_val(
	const IntAE *int_ae,
	int val
);

IntAE new_IntAE(
	int buflength,
	int nelt,
	int val
);

void IntAE_insert_at(
	IntAE *int_ae,
	int at,
	int val
);

void IntAE_append(
	IntAE *int_ae,
	const int *newvals,
	int nnewval
);

void IntAE_delete_at(
	IntAE *int_ae,
	int at
);

void IntAE_shift(
	const IntAE *int_ae,
	int shift
);

void IntAE_sum_and_shift(
	const IntAE *int_ae1,
	const IntAE *int_ae2,
	int shift
);

void IntAE_append_shifted_vals(
	IntAE *int_ae,
	const int *newvals,
	int nnewval,
	int shift
);

void IntAE_qsort(
	IntAE *int_ae,
	int desc
);

void IntAE_delete_adjdups(IntAE *int_ae);

SEXP IntAE_asINTEGER(const IntAE *int_ae);

IntAE INTEGER_asIntAE(SEXP x);

IntAE CHARACTER_asIntAE(
	SEXP x,
	int keyshift
);

IntAEAE new_IntAEAE(
	int buflength,
	int nelt
);

void IntAEAE_insert_at(
	IntAEAE *int_aeae,
	int at,
	const IntAE *int_ae
);

void IntAEAE_eltwise_append(
	const IntAEAE *int_aeae1,
	const IntAEAE *int_aeae2
);

void IntAEAE_shift(
	const IntAEAE *int_aeae,
	int shift
);

void IntAEAE_sum_and_shift(
	const IntAEAE *int_aeae1,
	const IntAEAE *int_aeae2,
	int shift
);

SEXP IntAEAE_asLIST(
	const IntAEAE *int_aeae,
	int mode
);

IntAEAE LIST_asIntAEAE(SEXP x);

SEXP IntAEAE_toEnvir(
	const IntAEAE *int_aeae,
	SEXP envir,
	int keyshift
);

RangeAE new_RangeAE(
	int buflength,
	int nelt
);

void RangeAE_insert_at(
	RangeAE *range_ae,
	int at,
	int start,
	int width
);

RangeAEAE new_RangeAEAE(
	int buflength,
	int nelt
);

void RangeAEAE_insert_at(
	RangeAEAE *range_aeae,
	int at,
	const RangeAE *range_ae
);

CharAE new_CharAE(int buflength);

CharAE new_CharAE_from_string(const char *string);

void CharAE_insert_at(
	CharAE *char_ae,
	int at,
	char c
);

void append_string_to_CharAE(
	CharAE *char_ae,
	const char *string
);

SEXP CharAE_asRAW(const CharAE *char_ae);

CharAEAE new_CharAEAE(
	int buflength,
	int nelt
);

void CharAEAE_insert_at(
	CharAEAE *char_aeae,
	int at,
	const CharAE *char_ae
);

void append_string_to_CharAEAE(
	CharAEAE *char_aeae,
	const char *string
);

SEXP CharAEAE_asCHARACTER(const CharAEAE *char_aeae);


/*
 * Ocopy_byteblocks.c
 */

int compare_byteblocks(
	const char *a,
	int ia,
	const char *b,
	int ib,
	int n,
	size_t blocksize
);

void Ocopy_byteblocks_from_i1i2(
	int i1,
	int i2,
	char *dest,
	size_t dest_nblocks,
	const char *src,
	size_t src_nblocks,
	size_t blocksize
);

void Ocopy_byteblocks_from_subscript(
	const int *subset,
	int n,
	char *dest,
	size_t dest_nblocks,
	const char *src,
	size_t src_nblocks,
	size_t blocksize
);

void Ocopy_byteblocks_to_i1i2(
	int i1,
	int i2,
	char *dest,
	size_t dest_nblocks,
	const char *src,
	size_t src_nblocks,
	size_t blocksize
);

void Ocopy_byteblocks_to_subscript(
	const int *subset,
	int n,
	char *dest,
	size_t dest_nblocks,
	const char *src,
	size_t src_nblocks,
	size_t blocksize
);

void Ocopy_bytes_from_i1i2_with_lkup(
	int i1,
	int i2,
	char *dest,
	int dest_nbytes,
	const char *src,
	int src_nbytes,
	const int *lkup,
	int lkup_length
);

void Ocopy_bytes_from_subscript_with_lkup(
	const int *subset,
	int n,
	char *dest,
	int dest_nbytes,
	const char *src,
	int src_nbytes,
	const int *lkup,
	int lkup_length
);

void Ocopy_bytes_to_i1i2_with_lkup(
	int i1,
	int i2,
	char *dest,
	int dest_nbytes,
	const char *src,
	int src_nbytes,
	const int *lkup,
	int lkup_length
);

void Ocopy_bytes_to_subscript_with_lkup(
	const int *subset,
	int n,
	char *dest,
	int dest_nbytes,
	const char *src,
	int src_nbytes,
	const int *lkup,
	int lkup_length
);

void Orevcopy_byteblocks_from_i1i2(
	int i1,
	int i2,
	char *dest,
	size_t dest_nblocks,
	const char *src,
	size_t src_nblocks,
	size_t blocksize
);

void Orevcopy_bytes_from_i1i2_with_lkup(
	int i1,
	int i2,
	char *dest,
	int dest_nbytes,
	const char *src,
	int src_nbytes,
	const int *lkup,
	int lkup_length
);

void Ocopy_bytes_from_i1i2_to_complex(
	int i1,
	int i2,
	Rcomplex *dest,
	int dest_nbytes,
	const char *src,
	int src_nbytes,
	const Rcomplex *lkup,
	int lkup_length
);


/*
 * SEXP_utils.c
 */

const char *get_classname(SEXP x);


/*
 * Low-level manipulation of Sequence objects.
 * (see Sequence_class.c)
 */

const char *get_Sequence_elementType(SEXP x);


/*
 * Low-level manipulation of IRanges objects.
 * (see IRanges_class.c)
 */

SEXP get_IRanges_start(SEXP x);

SEXP get_IRanges_width(SEXP x);

SEXP get_IRanges_names(SEXP x);

int get_IRanges_length(SEXP x);

cachedIRanges cache_IRanges(SEXP x);

int get_cachedIRanges_length(const cachedIRanges *cached_x);

int get_cachedIRanges_elt_width(const cachedIRanges *cached_x, int i);

int get_cachedIRanges_elt_start(const cachedIRanges *cached_x, int i);

int get_cachedIRanges_elt_end(const cachedIRanges *cached_x, int i);

SEXP get_cachedIRanges_elt_name(const cachedIRanges *cached_x, int i);

cachedIRanges sub_cachedIRanges(const cachedIRanges *cached_x, int offset, int length);

void set_IRanges_names(SEXP x, SEXP names);

void copy_IRanges_slots(SEXP x, SEXP x0);

SEXP new_IRanges(const char *classname, SEXP start, SEXP width, SEXP names);

SEXP new_IRanges_from_RangeAE(const char *classname, const RangeAE *range_ae);

SEXP new_list_of_IRanges_from_RangeAEAE(const char *element_type, const RangeAEAE *range_aeae);

SEXP alloc_IRanges(const char *classname, int length);


/*
 * Low-level manipulation of Grouping objects.
 * (see Grouping_class.c)
 */

SEXP get_H2LGrouping_high2low(SEXP x);

SEXP get_H2LGrouping_low2high(SEXP x);

SEXP get_Partitioning_names(SEXP x);

SEXP get_PartitioningByEnd_end(SEXP x);

SEXP new_PartitioningByEnd(const char *classname, SEXP end, SEXP names);

/*
 * Low-level manipulation of SimpleList objects.
 * (see SimpleList_class.c)
 */

SEXP new_SimpleList(const char *className, SEXP listData);

/*
 * Low-level manipulation of DataFrame objects.
 * (see DataFrame_class.c)
 */

SEXP new_DataFrame(const char *className, SEXP vars, SEXP rownames, SEXP nrows);

/*
 * Low-level manipulation of CompressedIRangesList objects.
 * (see CompressedIRangesList_class.c)
 */

cachedCompressedIRangesList cache_CompressedIRangesList(SEXP x);

cachedIRanges get_cachedCompressedIRangesList_elt(const cachedCompressedIRangesList *cached_x, int i);

SEXP new_CompressedIRangesList(const char *classname, SEXP unlistData, SEXP partitioning);

/*
 * Low-level manipulation of RangedData objects.
 * (see RangedData_class.c)
 */

SEXP new_RangedData(const char *className, SEXP ranges, SEXP values);

/*
 * Low-level manipulation of SharedVector objects.
 * (see SharedVector_class.c)
 */

SEXP new_SharedVector(const char *classname, SEXP tag);

SEXP get_SharedVector_tag(SEXP x);

int get_SharedVector_length(SEXP x);


/*
 * Fast SharedRaw utilities.
 * (see SharedRaw_utils.c)
 */

void Ocopy_cachedCharSeq_to_SharedRaw_offset(
	SEXP out,
	int out_offset,
	const cachedCharSeq *in,
	const int *lkup,
	int lkup_length
);


/*
 * Low-level manipulation of XVector objects.
 * (see XVector_class.c)
 */

SEXP get_XVector_shared(SEXP x);

int get_XVector_offset(SEXP x);

int get_XVector_length(SEXP x);

SEXP get_XVector_tag(SEXP x);

cachedCharSeq cache_XRaw(SEXP x);

cachedIntSeq cache_XInteger(SEXP x);

cachedDoubleSeq cache_XDouble(SEXP x);

SEXP new_XVector(const char *classname, SEXP shared, int offset, int length);

SEXP new_XRaw_from_tag(const char *classname, SEXP tag);

SEXP new_XInteger_from_tag(const char *classname, SEXP tag);

SEXP new_XDouble_from_tag(const char *classname, SEXP tag);

SEXP alloc_XRaw(const char *classname, int length);

SEXP alloc_XInteger(const char *classname, int length);

SEXP alloc_XDouble(const char *classname, int length);


/*
 * Low-level manipulation of XVectorList objects.
 * (see XVectorList_class.c)
 */

int get_XVectorList_length(SEXP x);

SEXP get_XVectorList_width(SEXP x);

SEXP get_XVectorList_names(SEXP x);

cachedXVectorList cache_XVectorList(SEXP x);

int get_cachedXVectorList_length(const cachedXVectorList *cached_x);

cachedCharSeq get_cachedXRawList_elt(
	const cachedXVectorList *cached_x,
	int i
);

cachedIntSeq get_cachedXIntegerList_elt(
	const cachedXVectorList *cached_x,
	int i
);

cachedDoubleSeq get_cachedXDoubleList_elt(
	const cachedXVectorList *cached_x,
	int i
);

void set_XVectorList_names(SEXP x, SEXP names);

SEXP new_XVectorList1(const char *classname, SEXP xvector, SEXP ranges);

SEXP alloc_XRawList(
	const char *classname,
	const char *element_type,
	SEXP width
);

SEXP alloc_XIntegerList(
	const char *classname,
	const char *element_type,
	SEXP width
);

SEXP alloc_XDoubleList(
	const char *classname,
	const char *element_type,
	SEXP width
);

SEXP new_XRawList_from_CharAEAE(
	const char *classname,
	const char *element_type,
	const CharAEAE *char_aeae,
	SEXP lkup
);

SEXP new_XIntegerList_from_IntAEAE(
	const char *classname,
	const char *element_type,
	const IntAEAE *int_aeae
);
