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#ifndef __CMPH_COMPRESSED_SEQ_H__
#define __CMPH_COMPRESSED_SEQ_H__
#include"select.h"
struct _compressed_seq_t
{
cmph_uint32 n; // number of values stored in store_table
// The length in bits of each value is decomposed into two compnents: the lg(n) MSBs are stored in rank_select data structure
// the remaining LSBs are stored in a table of n cells, each one of rem_r bits.
cmph_uint32 rem_r;
cmph_uint32 total_length; // total length in bits of stored_table
select_t sel;
cmph_uint32 * length_rems;
cmph_uint32 * store_table;
};
typedef struct _compressed_seq_t compressed_seq_t;
/** \fn void compressed_seq_init(compressed_seq_t * cs);
* \brief Initialize a compressed sequence structure.
* \param cs points to the compressed sequence structure to be initialized
*/
void compressed_seq_init(compressed_seq_t * cs);
/** \fn void compressed_seq_destroy(compressed_seq_t * cs);
* \brief Destroy a compressed sequence given as input.
* \param cs points to the compressed sequence structure to be destroyed
*/
void compressed_seq_destroy(compressed_seq_t * cs);
/** \fn void compressed_seq_generate(compressed_seq_t * cs, cmph_uint32 * vals_table, cmph_uint32 n);
* \brief Generate a compressed sequence from an input array with n values.
* \param cs points to the compressed sequence structure
* \param vals_table poiter to the array given as input
* \param n number of values in @see vals_table
*/
void compressed_seq_generate(compressed_seq_t * cs, cmph_uint32 * vals_table, cmph_uint32 n);
/** \fn cmph_uint32 compressed_seq_query(compressed_seq_t * cs, cmph_uint32 idx);
* \brief Returns the value stored at index @see idx of the compressed sequence structure.
* \param cs points to the compressed sequence structure
* \param idx index to retrieve the value from
* \return the value stored at index @see idx of the compressed sequence structure
*/
cmph_uint32 compressed_seq_query(compressed_seq_t * cs, cmph_uint32 idx);
/** \fn cmph_uint32 compressed_seq_get_space_usage(compressed_seq_t * cs);
* \brief Returns amount of space (in bits) to store the compressed sequence.
* \param cs points to the compressed sequence structure
* \return the amount of space (in bits) to store @see cs
*/
cmph_uint32 compressed_seq_get_space_usage(compressed_seq_t * cs);
void compressed_seq_dump(compressed_seq_t * cs, char ** buf, cmph_uint32 * buflen);
void compressed_seq_load(compressed_seq_t * cs, const char * buf, cmph_uint32 buflen);
/** \fn void compressed_seq_pack(compressed_seq_t *cs, void *cs_packed);
* \brief Support the ability to pack a compressed sequence structure into a preallocated contiguous memory space pointed by cs_packed.
* \param cs points to the compressed sequence structure
* \param cs_packed pointer to the contiguous memory area used to store the compressed sequence structure. The size of cs_packed must be at least @see compressed_seq_packed_size
*/
void compressed_seq_pack(compressed_seq_t *cs, void *cs_packed);
/** \fn cmph_uint32 compressed_seq_packed_size(compressed_seq_t *cs);
* \brief Return the amount of space needed to pack a compressed sequence structure.
* \return the size of the packed compressed sequence structure or zero for failures
*/
cmph_uint32 compressed_seq_packed_size(compressed_seq_t *cs);
/** \fn cmph_uint32 compressed_seq_query_packed(void * cs_packed, cmph_uint32 idx);
* \brief Returns the value stored at index @see idx of the packed compressed sequence structure.
* \param cs_packed is a pointer to a contiguous memory area
* \param idx is the index to retrieve the value from
* \return the value stored at index @see idx of the packed compressed sequence structure
*/
cmph_uint32 compressed_seq_query_packed(void * cs_packed, cmph_uint32 idx);
#endif
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