obitools3/src/obiavl.c

/****************************************************************************
 * OBIDMS AVL tree functions	                                            *
 ****************************************************************************/

/**
 * @file obiavl.c
 * @author Celine Mercier
 * @date December 3rd 2015
 * @brief Functions handling AVL trees for storing and retrieving bit arrays.
 */


#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <string.h>
#include <time.h>
#include <sys/mman.h>
#include <fcntl.h>
#include <math.h>

#include "bloom.h"
#include "crc64.h"
#include "obiavl.h"
#include "obierrno.h"
#include "obitypes.h"
#include "obidebug.h"
#include "private_at_functions.h"
#include "encode.h"


#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)



/**************************************************************************
 *
 * D E C L A R A T I O N   O F   T H E   P R I V A T E   F U N C T I O N S
 *
 **************************************************************************/

/**
 * @brief Internal function building the file name for an AVL tree file.
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @param avl_name The name of the AVL tree.
 *
 * @returns A pointer to the name of the file where the AVL tree is stored.
 * @retval NULL if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
static char* build_avl_file_name(const char* avl_name);


/**
 * @brief Internal function building the file name for an AVL tree file.
 *
 * @warning The returned pointer has to be freed by the caller.
 *
 * @param avl_name The name of the AVL tree.
 *
 * @returns A pointer to the name of the file where the data referred to by the AVL tree is stored.
 * @retval NULL if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
static char* build_avl_data_file_name(const char* avl_name);


/**
 * @brief Internal function returning the size of an AVL tree header on this platform.
 *
 * @returns The size of an AVL tree header in bytes.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
size_t get_avl_header_size();


/**
 * @brief Internal function returning the initial size of an AVL tree on this platform.
 *
 * @returns The initial size of an AVL tree in bytes.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
size_t get_initial_avl_size();


/**
 * @brief Internal function returning the size, on this platform, of the header of the data
 *        referred to by an AVL tree.
 *
 * @returns The size of an AVL data header in bytes.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
size_t get_avl_data_header_size();


/**
 * @brief Internal function returning the initial size, on this platform, of the data
 *        referred to by an AVL tree.
 *
 * @returns The initial size of an AVL data array in bytes.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
size_t get_initial_avl_data_size();


/**
 * @brief Internal function closing an AVL data structure where the data referred to by an AVL tree is stored.
 *
 * @param avl_data A pointer to the data structure referred to by an AVL tree.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int close_avl_data(OBIDMS_avl_data_p avl_data);


/**
 * @brief Internal function enlarging an AVL tree.
 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int grow_avl(OBIDMS_avl_p avl);


/**
 * @brief Internal function enlarging the data array referred to by an AVL tree.
 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @retval 0 if the operation was successfully completed.
 * @retval -1 if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int grow_avl_data(OBIDMS_avl_p avl);


/**
 * @brief Internal function storing a value (byte array) in the data array referred to by an AVL tree.
 *
 * @param avl A pointer to the AVL tree structure.
 * @param value A pointer to the value (byte array).
 *
 * @returns The index of the stored value.
 * @retval -1 if an error occurred.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, byte_t* value);


/**
 * @brief Internal function comparing two byte arrays.
 *
 * The encoding is compared first, then the length of the
 * values, then the values themselves.
 *
 * @param value_1 A pointer to the first byte array.
 * @param value_2 A pointer to the second byte array.
 *
 * @returns A value < 0 if value_1 < value_2,
 * 			a value > 0 if value_1 > value_2,
 * 			and 0 if value_1 == value_2.
 *
 * @since October 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
int byte_array_compare(byte_t* value_1, byte_t* value_2);


/**
 * @brief Internal function calculating the size in bytes of a byte array.
 *
 * @param value A pointer to the byte array.
 *
 * @returns The size of the byte array in bytes.
 *
 * @since October 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
size_t byte_array_sizeof(byte_t* value);


/**
 * @brief Internal function initializing a node in an AVL tree.
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node_idx The index of the node to initialize in the mmapped AVL tree.
 *
 * @returns The node structure initialized.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
AVL_node_p avl_create_node(OBIDMS_avl_p avl, index_t node_idx);


/**
 * @brief Internal function updating the balance factors in an AVL tree
 *        after adding a node, only in the subtree that will have to be balanced.
 *        That subtree is found using the avl->path_idx array and the directions taken
 *        down the tree to add the new node are stored in the avl->path_dir array.
 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
void avl_update_balance_factors(OBIDMS_avl_p avl);


/**
 * @brief Internal function rotating a node with a "left left rotation".
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node that has to be rotated.
 * @param node_idx The index of the node that has to be rotated.
 *
 * @returns The new root of the subtree.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_rotate_leftleft(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx);

/**
 * @brief Internal function rotating a node with a "left right rotation".
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node that has to be rotated.
 * @param node_idx The index of the node that has to be rotated.
 *
 * @returns The new root of the subtree.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_rotate_leftright(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx);


/**
 * @brief Internal function rotating a node with a "right left rotation".
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node that has to be rotated.
 * @param node_idx The index of the node that has to be rotated.
 *
 * @returns The new root of the subtree.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_rotate_rightleft(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx);


/**
 * @brief Internal function rotating a node with a "right right rotation".
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node that has to be rotated.
 * @param node_idx The index of the node that has to be rotated.
 *
 * @returns The new root of the subtree.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_rotate_rightright(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx);


/**
 * @brief Internal function balancing one node.
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node that has to be balanced.
 * @param node_idx The index of the node that has to be balanced.
 *
 * @returns The new root of the subtree.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
index_t avl_balance_node(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx);


/**
 * @brief Internal function balancing the nodes of an AVL tree after adding a node,
 *        only in the subtree that eventually has to be balanced.
 *        That subtree is found using the avl->path_idx array.
 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
void avl_balance(OBIDMS_avl_p avl);


/**
 * @brief Internal function printing a depth first traverse of a node.
 *
 * @param avl A pointer to the AVL tree structure.
 * @param node A pointer to the node.
 * @param node_idx The index of the node.
 * @param depth The depth of the node.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
void avl_print_node(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx, int depth);


/**
 * @brief Internal function printing a depth first traverse of an AVL tree.
 *
 * @param avl A pointer to the AVL tree structure.
 *
 * @since December 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
void avl_print(OBIDMS_avl_p avl);


/************************************************************************
 *
 * D E F I N I T I O N   O F   T H E   P R I V A T E   F U N C T I O N S
 *
 ************************************************************************/

static char* build_avl_file_name(const char* avl_name)
{
	char* file_name;

	// Build the file name
	file_name = (char*) malloc((strlen(avl_name) + 5)*sizeof(char));
	if (sprintf(file_name,"%s.oda", avl_name) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError building an AVL tree file name");
		return NULL;
	}

	// Test if the avl name is not too long
	if (strlen(file_name) >= AVL_MAX_NAME)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError due to AVL tree name too long");
		free(file_name);
		return NULL;
	}

	return file_name;
}


static char* build_avl_data_file_name(const char* avl_name)
{
	char* file_name;

	// Build the file name
	file_name = (char*) malloc((strlen(avl_name) + 5)*sizeof(char));
	if (sprintf(file_name,"%s.odd", avl_name) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError building an AVL tree data file name");
		return NULL;
	}

	return file_name;
}


size_t get_avl_header_size()
{
	size_t header_size;
	size_t rounded_header_size;
	double multiple;

	header_size = sizeof(OBIDMS_avl_header_t);

	multiple = 	ceil((double) header_size / (double) getpagesize());

	rounded_header_size = multiple * getpagesize();

	return rounded_header_size;
}


size_t get_initial_avl_size()
{
	size_t s;
	size_t m;

	m = 1;
	s = getpagesize() * m;

	return s;
}


size_t get_avl_data_header_size()
{
	size_t header_size;
	size_t rounded_header_size;
	double multiple;

	header_size = sizeof(OBIDMS_avl_data_header_t);

	multiple = 	ceil((double) header_size / (double) getpagesize());

	rounded_header_size = multiple * getpagesize();

	return rounded_header_size;
}


size_t get_initial_avl_data_size()
{
	size_t s;
	size_t m;

	m = 1;
	s = getpagesize() * m;

	return s;
}


int close_avl_data(OBIDMS_avl_data_p avl_data)
{
	int ret_val = 0;

	if (munmap(avl_data->data, (avl_data->header)->data_size_max) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError munmapping the data of an AVL tree data file");
		ret_val = -1;
	}

	if (munmap(avl_data->header, (avl_data->header)->header_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError munmapping the header of an AVL tree data file");
		ret_val = -1;
	}

	free(avl_data);

	return ret_val;
}


int grow_avl(OBIDMS_avl_p avl)		// TODO Lock when needed
{
	size_t	file_size;
	size_t 	old_data_size;
	size_t 	new_data_size;
	size_t 	header_size;
	int 	avl_file_descriptor;

	avl_file_descriptor = avl->avl_fd;

	// Calculate the new file size
	old_data_size = (avl->header)->avl_size;
	new_data_size = old_data_size * AVL_GROWTH_FACTOR;
	header_size = (avl->header)->header_size;
	file_size = header_size + new_data_size;

	// Enlarge the file
	if (ftruncate(avl_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError enlarging an AVL tree file");
		close(avl_file_descriptor);
		return -1;
	}

	// Unmap and re-map the data

	if (munmap(avl->tree, old_data_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError munmapping the tree of an AVL tree file before enlarging");
		close(avl_file_descriptor);
		return -1;
	}

	avl->tree = mmap(NULL,
					 new_data_size,
					 PROT_READ | PROT_WRITE,
					 MAP_SHARED,
					 avl_file_descriptor,
					 header_size
					);

	if (avl->tree == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError re-mmapping the tree of an AVL tree file after enlarging the file");
		close(avl_file_descriptor);
		return -1;
	}

	// Set new maximum number of items
	(avl->header)->nb_items_max = floor(((double) new_data_size) / ((double) sizeof(AVL_node_t)));

	// Set the new avl size
	(avl->header)->avl_size = new_data_size;

	//close(avl_file_descriptor);

	return 0;
}


int grow_avl_data(OBIDMS_avl_p avl)		// TODO Lock when needed
{
	size_t 	file_size;
	index_t old_data_size;
	index_t new_data_size;
	size_t 	header_size;
	int 	avl_data_file_descriptor;

	avl_data_file_descriptor = avl->data_fd;

	// Calculate the new file size
	old_data_size = ((avl->data)->header)->data_size_max;
	new_data_size = old_data_size * AVL_GROWTH_FACTOR;
	header_size = ((avl->data)->header)->header_size;
	file_size = header_size + new_data_size;

	// Enlarge the file
	if (ftruncate(avl_data_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError enlarging an AVL tree data file");
		close(avl_data_file_descriptor);
		return -1;
	}

	// Unmap and re-map the data

	if (munmap((avl->data)->data, old_data_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError munmapping the data of an AVL tree data file before enlarging");
		close(avl_data_file_descriptor);
		return -1;
	}

	(avl->data)->data = mmap(NULL,
							   new_data_size,
							   PROT_READ | PROT_WRITE,
							   MAP_SHARED,
							   avl_data_file_descriptor,
							   header_size
							  );

	if ((avl->data)->data == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError re-mmapping the data of an AVL tree data file after enlarging the file");
		close(avl_data_file_descriptor);
		return -1;
	}

	// Set new data size
	((avl->data)->header)->data_size_max = new_data_size;

	//fprintf(stderr, "\nGrowing AVL, new data size = %lld, count = %ld\n", new_data_size, (avl->header)->nb_items);

	// Initialize new data to 0
	memset(((avl->data)->data)+old_data_size, 0, new_data_size - old_data_size);

	//close(avl_data_file_descriptor);

	return 0;
}


index_t avl_add_value_in_data_array(OBIDMS_avl_p avl, byte_t* value)
{
	index_t value_idx;
	size_t value_size;

	value_idx = ((avl->data)->header)->data_size_used;

	// Grow the data if needed
	value_size = byte_array_sizeof(value);
	while (((avl->data)->header)->data_size_max < (value_idx + (int64_t) value_size))
	{
		if (grow_avl_data(avl) < 0)
			return -1;
	}

	// Store the value itself at the end of the data
	memcpy((((avl->data)->data)+value_idx), value, value_size);

	// Update the data size
	((avl->data)->header)->data_size_used = value_idx + value_size;

	// Update the number of items
	(((avl->data)->header)->nb_items)++;

	return value_idx;
}


int byte_array_compare(byte_t* value_1, byte_t* value_2)
{
	int 	comp;
	uint8_t size_1;
	uint8_t size_2;
	int32_t len_1;
	int32_t len_2;
	int32_t ini_len_1;
	int32_t ini_len_2;
	int32_t b;

	size_1 = (uint8_t) *(value_1);
	size_2 = (uint8_t) *(value_2);

	if (size_1 != size_2)
		return (size_1 - size_2);

	len_1 = *((int32_t*)(value_1+1));
	len_2 = *((int32_t*)(value_2+1));

	if (len_1 != len_2)
		return (len_1 - len_2);

	if (size_1 != 8)
	{
		ini_len_1 = *((int32_t*)(value_1+5));
		ini_len_2 = *((int32_t*)(value_2+5));

		if (ini_len_1 != ini_len_2)
			return (ini_len_1 - ini_len_2);
	}

	b = BYTE_ARRAY_HEADER_SIZE;
	comp = 0;
	while (!comp && (b < len_1+BYTE_ARRAY_HEADER_SIZE))
	{
		comp = *(value_1+b) - *(value_2+b);
		b++;
	}
	return comp;
}


size_t byte_array_sizeof(byte_t* value)
{
	return (BYTE_ARRAY_HEADER_SIZE + *((int32_t*)(value+1)));
}


// Initialize a new node
AVL_node_p avl_create_node(OBIDMS_avl_p avl, index_t node_idx)
{
	AVL_node_p node;

	node = (avl->tree)+node_idx;

	node->left_child = -1;
	node->right_child = -1;
	node->balance_factor = 0;
	node->value = -1;
	node->crc64 = 0; 	// TODO

	return node;
}


// Update the balance factors of the nodes from the node that will need balancing
void avl_update_balance_factors(OBIDMS_avl_p avl)
{
	uint8_t n;
	AVL_node_p node;

	// Update balance factors from the node where balancing might be needed
	node=(avl->tree)+((avl->path_idx)[1]);

	for (n=1; (avl->path_dir)[n] != -1; n++)
	{
		if ((avl->path_dir)[n]) // Went right
		{
			(node->balance_factor)--;
			node=RIGHT_CHILD(node);
		}
		else 	// Went left
		{
			(node->balance_factor)++;
			node=LEFT_CHILD(node);
		}
	}
}


// Left Left Rotate
index_t avl_rotate_leftleft(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx)
{
	AVL_node_p left_child = LEFT_CHILD(node);
	index_t left_child_idx = node->left_child;

	node->left_child = left_child->right_child;
	left_child->right_child = node_idx;

	node->balance_factor = 0;
	left_child->balance_factor = 0;

	return left_child_idx;
}


// Left Right Rotate
index_t avl_rotate_leftright(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx)
{
	AVL_node_p left_child = LEFT_CHILD(node);
	index_t left_child_idx = node->left_child;
	AVL_node_p rc_of_lc = RIGHT_CHILD(left_child);
	index_t rc_of_lc_idx = left_child->right_child;

	node->left_child = rc_of_lc->right_child;
	left_child->right_child = rc_of_lc->left_child;
	rc_of_lc->left_child = left_child_idx;
	rc_of_lc->right_child = node_idx;

	if (rc_of_lc->balance_factor == -1)
	{
		left_child->balance_factor = 1;
		node->balance_factor = 0;
	}
	else if (rc_of_lc->balance_factor == 0)
	{
		left_child->balance_factor = 0;
		node->balance_factor = 0;
	}
	else	// if (rc_of_lc->balance_factor == 1)
	{
		left_child->balance_factor = 0;
		node->balance_factor = -1;
	}

	rc_of_lc->balance_factor = 0;

	return rc_of_lc_idx;
}


// Right Left Rotate
index_t avl_rotate_rightleft(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx)
{
	AVL_node_p right_child = RIGHT_CHILD(node);
	index_t right_child_idx = node->right_child;;
	AVL_node_p lc_of_rc = LEFT_CHILD(right_child);
	index_t lc_of_rc_idx = right_child->left_child;

	node->right_child = lc_of_rc->left_child;
	right_child->left_child = lc_of_rc->right_child;
	lc_of_rc->right_child = right_child_idx;
	lc_of_rc->left_child = node_idx;

	if (lc_of_rc->balance_factor == 1)
	{
		right_child->balance_factor = 1;
		node->balance_factor = 0;
	}
	else if (lc_of_rc->balance_factor == 0)
	{
		right_child->balance_factor = 0;
		node->balance_factor = 0;
	}
	else	// if (lc_of_rc->balance_factor == -1)
	{
		right_child->balance_factor = 0;
		node->balance_factor = 1;
	}

	lc_of_rc->balance_factor = 0;

	return lc_of_rc_idx;
}


// Right Right Rotate
index_t avl_rotate_rightright(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx)
{
	AVL_node_p right_child = RIGHT_CHILD(node);
	index_t right_child_idx = node->right_child;

	node->right_child = right_child->left_child;
	right_child->left_child = node_idx;

	node->balance_factor = 0;
	right_child->balance_factor = 0;

	return right_child_idx;
}


// Balance a given node
index_t avl_balance_node(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx)
{
	index_t new_root = 0;

	if (node->balance_factor == 2)
	{ // Left Heavy
		if ((LEFT_CHILD(node))->balance_factor == -1)
			new_root = avl_rotate_leftright(avl, node, node_idx);
		else
			new_root = avl_rotate_leftleft(avl, node, node_idx);
	}
	else if (node->balance_factor == -2)
	{ // Right Heavy
		if ((RIGHT_CHILD(node))->balance_factor == 1)
			new_root = avl_rotate_rightleft(avl, node, node_idx);
		else
			new_root = avl_rotate_rightright(avl, node, node_idx);
	}
	else
	// Node is balanced
		new_root = node_idx;

	return new_root;
}


// Balance a given tree
void avl_balance(OBIDMS_avl_p avl)
{
	index_t new_root;
	index_t node_index;
	AVL_node_p node_to_balance;
	AVL_node_p parent_of_node_to_balance;

	node_index = (avl->path_idx)[1];
	node_to_balance = (avl->tree)+node_index;
	parent_of_node_to_balance = (avl->tree)+((avl->path_idx)[0]);

	// Balance the 2nd node stored in the path (the first is only kept to connect the new root
	// of the subtree if needed).
	new_root = avl_balance_node(avl, node_to_balance, node_index);

	if (new_root != node_index)
	// If the root of the subtree has changed
	{
		// If the subtree's root is the tree's root, store the new root
		if (node_index == (avl->header)->root_idx)
			(avl->header)->root_idx = new_root;
		// Else, connect the new subtree's root to the parent of the subtree
		else if ((avl->path_dir)[0])	   // Subtree is the right child of its parent
			parent_of_node_to_balance->right_child = new_root;
		else	   // Subtree is the left child of its parent
			parent_of_node_to_balance->left_child = new_root;
	}
}


// Print a depth first traverse of a node
void avl_print_node(OBIDMS_avl_p avl, AVL_node_p node, index_t node_idx, int depth)
{
	int i = 0;

	if (node->left_child != -1)
		avl_print_node(avl, LEFT_CHILD(node), node->left_child, depth+2);

	for (i = 0; i < depth; i++)
		putchar(' ');

	fprintf(stderr, "Node idx: %lld, Value idx: %lld, Left child: %lld, Right child: %lld, "
			"Balance factor: %d\n", node_idx, node->value, node->left_child, node->right_child, node->balance_factor);

	if (node->right_child != -1)
		avl_print_node(avl, RIGHT_CHILD(node), node->right_child, depth+2);
}


// Print a depth first traverse of a tree
void avl_print(OBIDMS_avl_p avl)
{
	fprintf(stderr, "\nRoot index: %lld\n", (avl->header)->root_idx);
	avl_print_node(avl, (avl->tree)+((avl->header)->root_idx), (avl->header)->root_idx, 0);
}


/**********************************************************************
 *
 * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
 *
 **********************************************************************/

int obi_avl_exists(OBIDMS_p dms, const char* avl_name)
{
	struct stat buffer;
	char* 	    avl_file_path;
	char* 	    avl_file_name;
	char*		avl_file_relative_path;
	int			relative_path_size;
	int 	    check_dir;

	// Build the AVL tree file path
	avl_file_name = build_avl_file_name(avl_name);
	if (avl_file_name == NULL)
		return -1;
	relative_path_size = strlen(avl_file_name) + strlen(AVL_TREES_DIR_NAME) + 2;
	avl_file_relative_path = (char*) malloc(relative_path_size*sizeof(char));
	strcpy(avl_file_relative_path, AVL_TREES_DIR_NAME);
	strcat(avl_file_relative_path, "/");
	strcat(avl_file_relative_path, avl_file_name);
	avl_file_path = get_full_path(dms, avl_file_relative_path);
	if (avl_file_path == NULL)
	{
		obidebug(1, "\nError getting the file path for an AVL tree file");
		return -1;
	}

	check_dir = stat(avl_file_path, &buffer);

	free(avl_file_path);
	free(avl_file_name);
	free(avl_file_relative_path);

	if (check_dir == 0)
		return 1;
	else
		return 0;
}


OBIDMS_avl_p obi_avl(OBIDMS_p dms, const char* avl_name)
{
	int exists;

	exists = obi_avl_exists(dms, avl_name);

	switch (exists)
	{
		case 0:
			return obi_create_avl(dms, avl_name);
		case 1:
			return obi_open_avl(dms, avl_name);
	};

	obidebug(1, "\nError checking if an AVL tree already exists");
	return NULL;
}


OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name)
{
	OBIDMS_avl_group_p avl_group;
	char* avl_name_with_idx;

	avl_group = (OBIDMS_avl_group_p) malloc(sizeof(OBIDMS_avl_group_t));

	// Create 1st avl
	avl_name_with_idx = malloc((strlen(avl_name) + 3)*sizeof(char));
	if (sprintf(avl_name_with_idx, "%s_%u", avl_name, 0) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError building an AVL tree file name");
		return NULL;
	}
	(avl_group->sub_avls)[0] = obi_create_avl(dms, avl_name_with_idx);
	if ((avl_group->sub_avls)[0] == NULL)
	{
		obidebug(1, "\nError creating the first AVL of an AVL group");
		return NULL;
	}

	avl_group->current_avl_idx = 0;
	strcpy(avl_group->avl_name, avl_name);

	avl_group->dms = dms;

	return avl_group;
}


int unmap_an_avl(OBIDMS_avl_p avl)
{
	if (munmap((avl->data)->data, ((avl->data)->header)->data_size_max) < 0)
		return -1;
	if (munmap(avl->tree, (((avl->header)->nb_items_max) * sizeof(AVL_node_t))) < 0)
		return -1;
	return 0;
}


int remap_an_avl(OBIDMS_avl_p avl)
{
	(avl->data)->data = mmap(NULL,
							 ((avl->data)->header)->data_size_max,
							 PROT_READ,
							 MAP_SHARED,	// TODO test MAP_PRIVATE?
							 avl->data_fd,
							 ((avl->data)->header)->header_size);
	if ((avl->data)->data == NULL)
		return -1;

	avl->tree = mmap(NULL,
				((avl->header)->nb_items_max) * sizeof(AVL_node_t),
				PROT_READ,
				MAP_SHARED,	// TODO test MAP_PRIVATE?
				avl->avl_fd,
				(avl->header)->header_size);
	if (avl->tree == NULL)
		return -1;

	return 0;
}


int obi_add_new_avl_in_group(OBIDMS_avl_group_p avl_group)	// TODO check for errors
{
	char* avl_name_with_idx;
	int avl_idx_length;

	// unmap older
	unmap_an_avl((avl_group->sub_avls)[avl_group->current_avl_idx]);
	(avl_group->current_avl_idx)++;
	avl_idx_length = ((avl_group->current_avl_idx) == 0 ? 1 : (int)(log10(avl_group->current_avl_idx)+1));
	avl_name_with_idx = malloc((strlen(avl_group->avl_name) + avl_idx_length + 2)*sizeof(char));
	if (sprintf(avl_name_with_idx, "%s_%u", avl_group->avl_name, avl_group->current_avl_idx) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError building an AVL tree file name");
		return -1;
	}

	(avl_group->sub_avls)[avl_group->current_avl_idx] = obi_create_avl(avl_group->dms, avl_name_with_idx);
	if ((avl_group->sub_avls)[avl_group->current_avl_idx] == NULL)
	{
		obidebug(1, "\nError creating a new AVL tree in a group");
		return -1;
	}

	return 0;
}


OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name)
{
	char* 				avl_file_name;
	char* 				avl_data_file_name;
	size_t				header_size;
	size_t				data_size;
	size_t				file_size;
	int					avl_file_descriptor;
	int					avl_data_file_descriptor;
	int					avl_dir_file_descriptor;
	OBIDMS_avl_data_p   avl_data;
	OBIDMS_avl_p		avl;

	// Create the data file

		// Build file name
	avl_data_file_name = build_avl_data_file_name(avl_name);
	if (avl_data_file_name == NULL)
		return NULL;

		// Get the file descriptor of the avl directory
	avl_dir_file_descriptor = dms->avl_dir_fd;

		// Create file
	avl_data_file_descriptor = openat(avl_dir_file_descriptor, avl_data_file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
	if (avl_data_file_descriptor < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError creating an AVL tree data file");
		free(avl_data_file_name);
		return NULL;
	}
	free(avl_data_file_name);

		// Calculate the size needed
	header_size = get_avl_data_header_size();
	data_size   = get_initial_avl_data_size();
	file_size   = header_size + data_size;

		// Truncate the AVL tree data file to the right size
	if (ftruncate(avl_data_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError truncating an AVL tree data file to the right size");
		close(avl_data_file_descriptor);
		return NULL;
	}

		// Allocate the memory for the AVL tree data structure
	avl_data = (OBIDMS_avl_data_p) malloc(sizeof(OBIDMS_avl_data_t));
	if (avl_data == NULL)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError allocating the memory for the AVL tree data structure");
		close(avl_data_file_descriptor);
		return NULL;
	}

		// Fill the AVL tree data structure
	avl_data->header = mmap(NULL,
			                header_size,
			                PROT_READ | PROT_WRITE,
			                MAP_SHARED,
			                avl_data_file_descriptor,
			                0
			               );
	if (avl_data->header == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError mmapping the header of an AVL tree data file");
		close(avl_data_file_descriptor);
		free(avl_data);
		return NULL;
	}

	avl_data->data   = mmap(NULL,
			                data_size,
			                PROT_READ | PROT_WRITE,
			                MAP_SHARED,
			                avl_data_file_descriptor,
			                header_size
			               );
	if (avl_data->data == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError mmapping the data of an AVL tree data file");
		munmap(avl_data->header, header_size);
		close(avl_data_file_descriptor);
		free(avl_data);
		return NULL;
	}

	(avl_data->header)->header_size 	 = header_size;
	(avl_data->header)->data_size_max	 = data_size;
	(avl_data->header)->data_size_used   = 0;
	(avl_data->header)->nb_items	 	 = 0;
	(avl_data->header)->creation_date    = time(NULL);
	strcpy((avl_data->header)->avl_name, avl_name);

	// Initialize all bits to 0
	memset(avl_data->data, 0, (avl_data->header)->data_size_max);

	//close(avl_data_file_descriptor);


	// Create the AVL tree file

		// Build file name
	avl_file_name = build_avl_file_name(avl_name);
	if (avl_file_name == NULL)
	{
		close_avl_data(avl_data);
		return NULL;
	}

		// Calculate the size needed
	header_size = get_avl_header_size();
	data_size = get_initial_avl_size();
	file_size = header_size + data_size;

		// Create file
	avl_file_descriptor = openat(avl_dir_file_descriptor, avl_file_name, O_RDWR | O_CREAT | O_EXCL, 0777);
	if (avl_file_descriptor < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError creating an AVL tree file");
		close_avl_data(avl_data);
		free(avl_file_name);
		return NULL;
	}
	free(avl_file_name);

		// Truncate the AVL tree file to the right size
	if (ftruncate(avl_file_descriptor, file_size) < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError truncating an AVL tree file to the right size");
		close_avl_data(avl_data);
		close(avl_file_descriptor);
		return NULL;
	}

		// Allocate the memory for the AVL tree structure
	avl = (OBIDMS_avl_p) malloc(sizeof(OBIDMS_avl_t));
	if (avl == NULL)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError allocating the memory for the AVL tree structure");
		close_avl_data(avl_data);
		close(avl_file_descriptor);
		return NULL;
	}

		// Fill the AVL tree structure
	avl->header = mmap(NULL,
			           header_size,
			           PROT_READ | PROT_WRITE,
			           MAP_SHARED,
			           avl_file_descriptor,
			           0
			          );
	if (avl->header == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError mmapping the header of an AVL tree file");
		close_avl_data(avl_data);
		close(avl_file_descriptor);
		free(avl);
		return NULL;
	}

	avl->tree  = mmap(NULL,
			          data_size,
			          PROT_READ | PROT_WRITE,
			          MAP_SHARED,
			          avl_file_descriptor,
			          header_size
			         );
	if (avl->tree == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError mmapping the data of an AVL tree file");
		close_avl_data(avl_data);
		munmap(avl->header, header_size);
		close(avl_file_descriptor);
		free(avl);
		return NULL;
	}

	avl->dms = dms;
	avl->data = avl_data;
	avl->directory = dms->avl_directory;
	avl->dir_fd = avl_dir_file_descriptor;

	(avl->header)->header_size 	 = header_size;
	(avl->header)->avl_size 	 = data_size;
	(avl->header)->nb_items	 	 = 0;
	(avl->header)->nb_items_max	 = (index_t) floor(((double) get_initial_avl_size()) / ((double) sizeof(AVL_node_t)));
	(avl->header)->root_idx = -1;
	(avl->header)->creation_date = time(NULL);
	strcpy((avl->header)->avl_name, avl_name);

	avl->avl_fd = avl_file_descriptor;
	avl->data_fd = avl_data_file_descriptor;

	// Bloom filter
	bloom_init(&((avl->header)->bloom_filter), NODE_COUNT_PER_AVL, BLOOM_FILTER_ERROR_RATE);

	//close(avl_file_descriptor);

	// Add in the list of opened AVL trees
	*(((dms->opened_avls)->avls)+((dms->opened_avls)->nb_opened_avls)) = avl;
	((dms->opened_avls)->nb_opened_avls)++;
	avl->counter = 1;

	return avl;
}


OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name)
{
	char* 	 			avl_file_name;
	char* 				avl_data_file_name;
	size_t				header_size;
	int					avl_file_descriptor;
	int					avl_data_file_descriptor;
	int					avl_dir_file_descriptor;
	OBIDMS_avl_data_p   avl_data;
	OBIDMS_avl_p		avl;
	size_t i;

	// Check if the AVL tree is already in the list of opened AVL trees
	for (i=0; i < ((dms->opened_avls)->nb_opened_avls); i++)
	{
		if (!strcmp(((*(((dms->opened_avls)->avls)+i))->header)->avl_name, avl_name))
		{	// Found the AVL tree already opened
			((*(((dms->opened_avls)->avls)+i))->counter)++;
			return *(((dms->opened_avls)->avls)+i);
		}
	}

	// Open the data file

		// Get the file descriptor of the AVL trees directory
	avl_dir_file_descriptor = dms->avl_dir_fd;

		// Build file name
	avl_data_file_name = build_avl_data_file_name(avl_name);
	if (avl_data_file_name == NULL)
		return NULL;

		// Open file
	avl_data_file_descriptor = openat(avl_dir_file_descriptor, avl_data_file_name, O_RDWR, 0777);
	if (avl_data_file_descriptor < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError opening an AVL tree data file");
		free(avl_data_file_name);
		return NULL;
	}
	free(avl_data_file_name);

		// Allocate the memory for the AVL tree data structure
	avl_data = (OBIDMS_avl_data_p) malloc(sizeof(OBIDMS_avl_data_t));
	if (avl_data == NULL)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError allocating the memory for the AVL tree data structure");
		close(avl_data_file_descriptor);
		return NULL;
	}

	// Read the header size
	if (read(avl_data_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError reading the header size to open an AVL tree data file");
		close(avl_data_file_descriptor);
		return NULL;
	}

		// Fill the avl data structure
	avl_data->header = mmap(NULL,
			                header_size,
			                PROT_READ | PROT_WRITE,
			                MAP_SHARED,
			                avl_data_file_descriptor,
			                0
			               );
	if (avl_data->header == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError mmapping the header of an AVL tree data file");
		close(avl_data_file_descriptor);
		free(avl_data);
		return NULL;
	}

	avl_data->data   = mmap(NULL,
			                (avl_data->header)->data_size_max,
			                PROT_READ | PROT_WRITE,
			                MAP_SHARED,
			                avl_data_file_descriptor,
			                header_size
			               );
	if (avl_data->data == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError mmapping the data of an AVL tree data file");
		munmap(avl_data->header, header_size);
		close(avl_data_file_descriptor);
		free(avl_data);
		return NULL;
	}

	//close(avl_data_file_descriptor);


	// Open the AVL tree file

		// Build file name
	avl_file_name = build_avl_file_name(avl_name);
	if (avl_file_name == NULL)
	{
		close_avl_data(avl_data);
		return NULL;
	}

		// Open file
	avl_file_descriptor = openat(avl_dir_file_descriptor, avl_file_name, O_RDWR, 0777);
	if (avl_file_descriptor < 0)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError opening an AVL tree file");
		close_avl_data(avl_data);
		free(avl_file_name);
		return NULL;
	}
	free(avl_file_name);

		// Allocate the memory for the AVL tree structure
	avl = (OBIDMS_avl_p) malloc(sizeof(OBIDMS_avl_t));
	if (avl == NULL)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError allocating the memory for the AVL tree structure");
		close_avl_data(avl_data);
		close(avl_file_descriptor);
		return NULL;
	}

		// Read the header size
	if (read(avl_file_descriptor, &header_size, sizeof(size_t)) < ((ssize_t) sizeof(size_t)))
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError reading the header size to open an AVL tree");
		close(avl_file_descriptor);
		return NULL;
	}

		// Fill the avl structure
	avl->header = mmap(NULL,
			           header_size,
			           PROT_READ | PROT_WRITE,
			           MAP_SHARED,
			           avl_file_descriptor,
			           0
			          );
	if (avl->header == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError mmapping the header of an AVL tree file");
		close_avl_data(avl_data);
		close(avl_file_descriptor);
		free(avl);
		return NULL;
	}

	avl->tree = mmap(NULL,
					 (((avl->header)->nb_items_max) * sizeof(AVL_node_t)),
			         PROT_READ | PROT_WRITE,
			         MAP_SHARED,
			         avl_file_descriptor,
			         header_size
			        );
	if (avl->tree == MAP_FAILED)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError mmapping the data of an AVL tree file");
		close_avl_data(avl_data);
		munmap(avl->header, header_size);
		close(avl_file_descriptor);
		free(avl);
		return NULL;
	}

	avl->dms = dms;
	avl->data = avl_data;
	avl->directory = dms->avl_directory;
	avl->dir_fd = avl_dir_file_descriptor;

	avl->avl_fd = avl_file_descriptor;
	avl->data_fd = avl_data_file_descriptor;

	//close(avl_file_descriptor);

	// Add in the list of opened AVL trees
	*(((dms->opened_avls)->avls)+((dms->opened_avls)->nb_opened_avls)) = avl;
	((dms->opened_avls)->nb_opened_avls)++;
	avl->counter = 1;

	return avl;
}


int obi_close_avl(OBIDMS_avl_p avl)
{
	int ret_val = 0;
	size_t i;
	Opened_avls_list_p avls_list;
	OBIDMS_p dms;

	dms = avl->dms;

	avls_list = dms->opened_avls;

	(avl->counter)--;

	if (avl->counter == 0)
	{
		// Delete from the list of opened avls
		for (i=0; i < (avls_list->nb_opened_avls); i++)
		{
			if (!strcmp(((*((avls_list->avls)+i))->header)->avl_name, (avl->header)->avl_name))
			{	// Found the avl. Rearrange list
				(avls_list->nb_opened_avls)--;
				(avls_list->avls)[i] = (avls_list->avls)[avls_list->nb_opened_avls];
			}
		}

		ret_val = close_avl_data(avl->data);

		if (munmap(avl->tree, (((avl->header)->nb_items_max) * sizeof(AVL_node_t))) < 0)
		{
			obi_set_errno(OBI_AVL_ERROR);
			obidebug(1, "\nError munmapping the tree of an AVL tree file");
			ret_val = -1;
		}

		if (munmap(avl->header, (avl->header)->header_size) < 0)
		{
			obi_set_errno(OBI_AVL_ERROR);
			obidebug(1, "\nError munmapping the header of an AVL tree file");
			ret_val = -1;
		}

		free(avl);
	}

	return ret_val;
}


byte_t* obi_avl_group_get(OBIDMS_avl_group_p avl_group, index_t idx)
{
	int32_t avl_idx;
	index_t idx_in_avl;

	avl_idx = (int32_t) (idx >> 32);
	idx_in_avl = idx & 0x00000000FFFFFFFF;

	return obi_avl_get((avl_group->sub_avls)[avl_idx], idx_in_avl);
}


byte_t* obi_avl_get(OBIDMS_avl_p avl, index_t idx)
{
	return (((avl->data)->data)+idx);
}


int maybe_in_avl(OBIDMS_avl_p avl, byte_t* value)
{
	return (bloom_check(&((avl->header)->bloom_filter), value, (BYTE_ARRAY_HEADER_SIZE + *((int32_t*)(value+1)))));
}


int64_t insert_in_avl_group(OBIDMS_avl_group_p avl_group, byte_t* value)	// TODO won't be index_t
{
	int32_t index_in_avl;
	int64_t index_with_avl;
	int     i;

	if (maybe_in_avl((avl_group->sub_avls)[avl_group->current_avl_idx], value))
	{
		index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[avl_group->current_avl_idx], value);
		if (index_in_avl >= 0)
		{
			index_with_avl = avl_group->current_avl_idx;
			index_with_avl = index_with_avl << 32;
			index_with_avl = index_with_avl + index_in_avl;
			return index_with_avl;
		}
	}
	for (i=0; i < (avl_group->current_avl_idx); i++)
	{
		if (maybe_in_avl((avl_group->sub_avls)[i], value))
		{
			if (remap_an_avl((avl_group->sub_avls)[i]) < 0)
				return -1;
			index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[i], value);
			if (unmap_an_avl((avl_group->sub_avls)[i]) < 0)
				return -1;
			if (index_in_avl >= 0)
			{
				index_with_avl = i;
				index_with_avl = index_with_avl << 32;
				index_with_avl = index_with_avl + index_in_avl;
				return index_with_avl;
			}
		}
	}

	// Not found in any AVL: add in current
	// First, check if make new AVL
	if ((((avl_group->sub_avls)[avl_group->current_avl_idx])->header)->nb_items == NODE_COUNT_PER_AVL)		// TODO add condition with data size
		obi_add_new_avl_in_group(avl_group);

	// Add in the current AVL
	bloom_add(&((((avl_group->sub_avls)[avl_group->current_avl_idx])->header)->bloom_filter), value, BYTE_ARRAY_HEADER_SIZE + *((int32_t*)(value+1)));

	// Build the index containing the AVL index
	index_in_avl = (int32_t) obi_avl_add((avl_group->sub_avls)[avl_group->current_avl_idx], value);
	index_with_avl = avl_group->current_avl_idx;
	index_with_avl = index_with_avl << 32;
	index_with_avl = index_with_avl + index_in_avl;

	return index_with_avl;
}


// Insert a new node
index_t obi_avl_add(OBIDMS_avl_p avl, byte_t* value)
{
	AVL_node_p node_to_add = NULL;
	AVL_node_p current_node;
	index_t next, parent;
	index_t value_data_idx;
	index_t node_idx;
	byte_t* to_compare;
	int comp;
	int n = 0;
	int depth = 0;

	uint64_t crc;

	crc = crc64(value, BYTE_ARRAY_HEADER_SIZE + ((uint64_t) (*((int32_t*)(value+1)))));	// TODO warning

	// Check if first node
	if (!((avl->header)->nb_items))
	{
		node_to_add = avl_create_node(avl, 0);

		// Add the value in the data array and store its index
		value_data_idx = avl_add_value_in_data_array(avl, value);
		node_to_add->value = value_data_idx;
		node_to_add->crc64 = crc;

		// Update the number of items
		((avl->header)->nb_items)++;

		// Set the AVL tree root
		(avl->header)->root_idx = 0;

		return 0;
	}

	// Not first node
	next = (avl->header)->root_idx;
	parent = next;
	comp = 0;

	while (next != -1)
	{
		current_node = (avl->tree)+next;

		// Store path from the lowest node with a balance factor different than 0,
		// as it is the node that will have to be balanced.
		if (current_node->balance_factor != 0)
			// New lowest node with a balance factor different than 0
			n=0;
		(avl->path_idx)[n] = parent;	// Store parent
		(avl->path_dir)[n] = comp < 0;	// Store direction (0 if left, 1 if right)
		n++;

		parent = next;

		// Compare value with value of current node
		//to_compare = obi_avl_get(avl, current_node->value);
		//comp = byte_array_compare(to_compare, value);
		comp = (current_node->crc64) - crc;

		if (comp == 0)
		{ // check if really same value
			to_compare = obi_avl_get(avl, current_node->value);
			comp = byte_array_compare(to_compare, value);
		}

		if (comp > 0)
			// Go to left child
			next = current_node->left_child;
		else if (comp < 0)
			// Go to right child
			next = current_node->right_child;
		else if (comp == 0)
			// Value already stored
		{
			fprintf(stderr, "\n>>>ALREADY IN, %s, %lld\n", obi_obibytes_to_seq(value), (avl->header)->nb_items);
			return current_node->value;	// TODO should trigger error if using bloom filters
		}

		depth++;
	}

	// Check if the AVL tree has not become too big
	if (depth == AVL_MAX_DEPTH)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nThis AVL tree has reached the maximum height (%d).", AVL_MAX_DEPTH);
		return -1;
	}

	// Grow the AVL tree if needed
	if ((avl->header)->nb_items == (avl->header)->nb_items_max)
	{
		if (grow_avl(avl) < 0)
			return -1;
	}

	// Initialize node at the end of the tree
	node_idx = (avl->header)->nb_items;
	node_to_add = avl_create_node(avl, node_idx);

	// Add the value in the data array and store its index
	value_data_idx = avl_add_value_in_data_array(avl, value);
	node_to_add->value = value_data_idx;
	node_to_add->crc64 = crc;

	// Update the number of items
	((avl->header)->nb_items)++;

	// Add either as right or left child
	if (comp > 0)	// Add as left child
		((avl->tree)+parent)->left_child = node_idx;
	else		    // Add as right child
		((avl->tree)+parent)->right_child = node_idx;

	// End path
	(avl->path_idx)[n] = parent;
	(avl->path_dir)[n] = comp < 0;	// 0 if went left, 1 if went right
	n++;
	(avl->path_idx)[n] = -1;	// flag path end
	(avl->path_dir)[n] = -1;

	// Update balance factors
	avl_update_balance_factors(avl);

	// Balance tree
	avl_balance(avl);

	// Print tree
	//avl_print(avl);

	return value_data_idx;
}


// Find if a value is already in an AVL tree
index_t obi_avl_find(OBIDMS_avl_p avl, byte_t* value)
{
	int comp;
	index_t next;
	byte_t* to_compare;
	AVL_node_p current_node;

	uint64_t crc;
	crc = crc64(value, BYTE_ARRAY_HEADER_SIZE + ((uint64_t) (*((int32_t*)(value+1)))));	// TODO warning

	next = (avl->header)->root_idx;
	while (next != -1)
	{
		current_node = (avl->tree)+next;

		// Compare value with value of current node
		//to_compare = obi_avl_get(avl, current_node->value);
		//comp = byte_array_compare(to_compare, value);

		comp = (current_node->crc64) - crc;

		if (comp == 0)
		{ // check if really same value
			to_compare = obi_avl_get(avl, current_node->value);
			comp = byte_array_compare(to_compare, value);
		}

		if (comp > 0)
			// Go to left child
			next = current_node->left_child;
		else if (comp < 0)
			// Go to right child
			next = current_node->right_child;
		else if (comp == 0)
		{	// Value found
			fprintf(stderr, "\n>>>ALREADY IN in find, %s, %lld\n", obi_obibytes_to_seq(value), (avl->header)->nb_items);
			return current_node->value;
		}
	}
	// Value not found
	return -1;
}


byte_t* obi_str_to_obibytes(char* value)
{
	byte_t* value_b;
	int32_t length;

	// Compute the number of bytes on which the value will be encoded
	length = strlen(value) + 1;		// +1 to store \0 at the end (makes retrieving faster)

	// Allocate the memory for the encoded value
	value_b = (byte_t*) malloc(BYTE_ARRAY_HEADER_SIZE + length);
	if (value_b == NULL)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError allocating memory for a byte array");
		return NULL;
	}

	// Store the number of bits on which each element is encoded
	*(value_b) = 8;

	// Store the length (in bytes) of the encoded value (same as decoded for character strings)
	*((int32_t*)(value_b+1)) = length;

	// Store the initial length (in bytes) of the decoded value (same as encoded for character strings)
	*((int64_t*)(value_b+5)) = length;

	// Store the character string
	strcpy(value_b+BYTE_ARRAY_HEADER_SIZE, value);

	return value_b;
}


const char* obi_obibytes_to_str(byte_t* value_b)
{
	const char* value;

	value = value_b+BYTE_ARRAY_HEADER_SIZE;

	return value;
}


byte_t* obi_seq_to_obibytes(char* seq)
{
	byte_t*  value_b;
	int32_t  length;	   // length of the value (without the header) in bytes
	uint8_t  size;	  	   // size of one element in bits
	int32_t  seq_length;
	byte_t*  encoded_seq;

	// Check if just ATGC and set size of a nucleotide accordingly (2 bits or 4 bits)
	if (only_ATGC(seq))
		size = 2;
	else
		size = 4;

	// Compute the length (in bytes) of the encoded sequence
	seq_length = strlen(seq);
	if (size == 2)
		length = ceil((double) seq_length / (double) 4.0);
	else	// size == 4
		length = ceil((double) seq_length / (double) 2.0);

	// Encode
	if (size == 2)
		encoded_seq = encode_seq_on_2_bits(seq, seq_length);
	else	// size == 4
		encoded_seq = encode_seq_on_4_bits(seq, seq_length);
	if (encoded_seq == NULL)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError encoding a DNA sequence");
		return NULL;
	}

	// Allocate the memory for the encoded value
	value_b = (byte_t*) malloc(BYTE_ARRAY_HEADER_SIZE + length);
	if (value_b == NULL)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError allocating memory for a byte array");
		return NULL;
	}

	// Store the number of bits on which each nucleotide is encoded
	*(value_b) = size;

	// Store the length (in bytes) of the encoded sequence
	*((int32_t*)(value_b+1)) = length;

	// Store the length (in bytes) of the initial sequence (necessary for decoding)
	*((int32_t*)(value_b+5)) = seq_length;

	// Store the encoded sequence
	memcpy(value_b+BYTE_ARRAY_HEADER_SIZE, encoded_seq, length);

	free(encoded_seq);

	return value_b;
}


const char* obi_obibytes_to_seq(byte_t* value_b)
{
	const char* value;
	uint8_t size;	    // size of one element in bits

	// Check the encoding (each nucleotide on 2 bits or 4 bits)
	size = *(value_b);

	// Decode
	if (size == 2)
		value = decode_seq_on_2_bits(value_b+BYTE_ARRAY_HEADER_SIZE, *((int32_t*)(value_b+5)));
	else
		value = decode_seq_on_4_bits(value_b+BYTE_ARRAY_HEADER_SIZE, *((int32_t*)(value_b+5)));

	if (value == NULL)
	{
		obi_set_errno(OBI_AVL_ERROR);
		obidebug(1, "\nError decoding a DNA sequence");
		return NULL;
	}

	return value;
}