DNA sequences and character strings are now handled using AVL trees.

python/obitools3/obidms/_obidms.cfiles

@@ -12,7 +12,7 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
-../../../src/obiarray.h
+../../../src/obiavl.h
-../../../src/obiarray.c
+../../../src/obiavl.c
 ../../../src/encode.h
 ../../../src/encode.c

python/obitools3/obidms/_obidms.pxd

@@ -25,7 +25,7 @@ cdef class OBIDMS:
                                     index_t nb_lines=*, 
                                     index_t nb_elements_per_line=*, 
                                     list elements_names=*,
-                                    str array_name=*,
+                                    str avl_name=*,
                                     str comments=*)
 
 

python/obitools3/obidms/_obidms.pyx

@@ -133,7 +133,7 @@ cdef class OBIDMS :
                                     index_t nb_lines=0, 
                                     index_t nb_elements_per_line=0, 
                                     list elements_names=None,
-                                    str array_name="default_obiarray",
+                                    str avl_name="default_AVL_tree",
                                     str comments=""):
         
         # Declarations
@@ -263,7 +263,7 @@ cdef class OBIDMS :
                           referring, 
                           version_number, data_type, 
                           nb_lines, nb_elements_per_line, 
-                          elements_names, array_name, 
+                          elements_names, avl_name, 
                           comments)
 
         return column
@@ -284,13 +284,13 @@ cdef class OBIDMS_column :
                  index_t nb_lines, 
                  index_t nb_elements_per_line, 
                  list elements_names,
-                 str array_name,
+                 str avl_name,
                  str comments):
         
         # Declarations
         cdef bytes column_name_b
         cdef bytes dms_name_b
-        cdef bytes array_name_b
+        cdef bytes avl_name_b
         cdef bytes elements_names_b
         cdef bytes comments_b
        
@@ -304,7 +304,7 @@ cdef class OBIDMS_column :
         # Format the character strings to send them to C functions
         column_name_b = str2bytes(column_name)
         dms_name_b = str2bytes(self.dms.dms_name)
-        array_name_b = str2bytes(array_name)
+        avl_name_b = str2bytes(avl_name)
         comments_b = str2bytes(comments)
         
         # Create, clone or open column
@@ -315,7 +315,7 @@ cdef class OBIDMS_column :
                 elements_names_b = str2bytes(";".join(elements_names))
             self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, 
                                              nb_lines, nb_elements_per_line, 
-                                             elements_names_b, array_name_b, comments_b,
+                                             elements_names_b, avl_name_b, comments_b,
                                              referring)
         else :
             if clone :

python/obitools3/obidms/_obidmscolumn_bool.cfiles

@@ -14,5 +14,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
-../../../src/obiarray.h
+../../../src/obiavl.h
-../../../src/obiarray.c
+../../../src/obiavl.c

python/obitools3/obidms/_obidmscolumn_char.cfiles

@@ -14,5 +14,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
-../../../src/obiarray.h
+../../../src/obiavl.h
-../../../src/obiarray.c
+../../../src/obiavl.c

python/obitools3/obidms/_obidmscolumn_float.cfiles

@@ -14,5 +14,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
-../../../src/obiarray.h
+../../../src/obiavl.h
-../../../src/obiarray.c
+../../../src/obiavl.c

python/obitools3/obidms/_obidmscolumn_int.cfiles

@@ -14,5 +14,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
-../../../src/obiarray.h
+../../../src/obiavl.h
-../../../src/obiarray.c
+../../../src/obiavl.c

python/obitools3/obidms/_obidmscolumn_seq.cfiles

@@ -14,5 +14,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
-../../../src/obiarray.h
+../../../src/obiavl.h
-../../../src/obiarray.c
+../../../src/obiavl.c

python/obitools3/obidms/_obidmscolumn_str.cfiles

@@ -14,5 +14,5 @@
 ../../../src/obitypes.c
 ../../../src/private_at_functions.h
 ../../../src/private_at_functions.c
-../../../src/obiarray.h
+../../../src/obiavl.h
-../../../src/obiarray.c
+../../../src/obiavl.c

python/obitools3/obidms/capi/obidmscolumn.pxd

@@ -30,7 +30,7 @@ cdef extern from "obidmscolumn.h" nogil:
         bint            referring
         obiversion_t    referred_column_version
         const_char_p    name
-        const_char_p    array_name
+        const_char_p    avl_name
         const_char_p    comments
     
     ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
@@ -47,7 +47,7 @@ cdef extern from "obidmscolumn.h" nogil:
                                       index_t nb_lines, 
                                       index_t nb_elements_per_line, 
                                       const_char_p elements_names,
-                                      const_char_p array_name,
+                                      const_char_p avl_name,
                                       const_char_p comments,
                                       bint referring)
                 

src/encode.c

@@ -16,7 +16,8 @@
 #include <math.h>
 
 #include "encode.h"
-#include "obiarray.h"
+#include "obierrno.h"
+#include "obitypes.h"	// For byte_t type
 #include "obidebug.h"
 
 

src/encode.h

@@ -15,7 +15,7 @@
 #include <stdint.h>
 #include <stdbool.h>
 
-#include "obiarray.h"
+#include "obitypes.h"
 
 
 #define NUC_MASK_2B 0x3   /**< Binary: 11 to use when decoding 2 bits sequences */

src/obiarray.h

@@ -1,322 +0,0 @@
-/****************************************************************************
- * OBIDMS array header file	                                                *
- ****************************************************************************/
-
-/**
- * @file obiarray.h
- * @author Celine Mercier
- * @date October 19th 2015
- * @brief Header file for handling arrays for storing and retrieving byte arrays (i.e. coding for character strings).
- */
-
-
-#ifndef OBIARRAY_H_
-#define OBIARRAY_H_
-
-
-#include <stdlib.h>
-#include <stdio.h>
-#include <stdint.h>
-#include <time.h>
-#include <sys/types.h>
-#include <dirent.h>
-
-#include "obidms.h"
-#include "obitypes.h"
-
-
-#define ARRAY_MAX_NAME (1024) 		/**< The maximum length of an array name.
-                              	  	 */
-#define ARRAY_GROWTH_FACTOR (2)		/**< The growth factor when an array is enlarged.
-                                	 */
-#define BYTE_ARRAY_HEADER_SIZE (9)  /**< The size of the header of a byte array.
-                              	  	 */
-
-
-typedef char byte_t;		/**< Defining byte type since data is stored in bits
-							 *	 and char (stored on one byte) is the smallest addressable unit.
- 	 	 	 	 	 	 	 */
-
-
-/**
- * @brief OBIDMS array data header structure.
- */
-typedef struct OBIDMS_array_data_header {
-	int			header_size;						/**< Size of the header in bytes.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t		data_size_used;						/**< Size of the data used in bytes.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t		data_size_max;						/**< Max size of the data in bytes.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t		nb_items;							/**< Number of items.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	char    	array_name[ARRAY_MAX_NAME+1];		/**< The array name as a NULL terminated string.
-													 */
-	time_t		creation_date;			    	    /**< Date of creation of the file.
-												     */
-} OBIDMS_array_data_header_t, *OBIDMS_array_data_header_p;
-
-
-/**
- * @brief OBIDMS array data structure.
- */
-typedef struct OBIDMS_array_data {
-	OBIDMS_array_data_header_p	header; 		 	/**< A pointer to the header of the array data.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	byte_t*                   	data;   		 	/**< A pointer to the beginning of the data.
-													 */
-} OBIDMS_array_data_t, *OBIDMS_array_data_p;
-
-
-/**
- * @brief OBIDMS array header structure.
- */
-typedef struct OBIDMS_array_header {
-	int			header_size;						/**< Size of the header in bytes.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	size_t		array_size;							/**< Size of the array in bytes.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t		nb_items;							/**< Number of items in the array.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t		nb_items_max;						/**< Maximum number of items in the array before it has to be enlarged.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	char    	array_name[ARRAY_MAX_NAME+1];		/**< The array name as a NULL terminated string.
-													 */
-	time_t		creation_date;			    	    /**< Date of creation of the file.
-												     */
-} OBIDMS_array_header_t, *OBIDMS_array_header_p;
-
-
-/**
- * @brief OBIDMS array structure.
- */
-typedef struct OBIDMS_array {
-	OBIDMS_p                	dms;			 	/**< A pointer to the OBIDMS structure to which the array belongs.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	OBIDMS_array_header_p		header; 		 	/**< A pointer to the header of the array.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	index_t*                 	first;   		 	/**< A pointer to the beginning of the array itself.
-													 */
-	OBIDMS_array_data_p			data;				/**< A pointer to the structure containing the data
-													 *   that the array references.
-	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	DIR*						directory;			/**< A directory entry usable to
-										 	 	 	 *    refer and scan the array directory.
-										 	 	 	 */
-	int							dir_fd;				/**< The file descriptor of the directory entry
-													 *    usable to refer and scan the array directory.
-													 */
-	size_t						counter;			/**< Indicates by how many threads/programs (TODO) the array is used.
-													 */
-} OBIDMS_array_t, *OBIDMS_array_p;
-
-
-/**
- * @brief Checks if an obiarray already exists or not.
- *
- * @param dms The OBIDMS to which the obiarray belongs.
- * @param array_name The name of the obiarray.
- *
- * @returns A value indicating whether the obiarray exists or not.
- * @retval 1 if the obiarray exists.
- * @retval 0 if the obiarray does not exist.
- * @retval -1 if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_array_exists(OBIDMS_p dms, const char* array_name);
-
-
-/**
- * @brief Opens an obiarray and creates it if it does not already exist.
- *
- * Note: An obiarray is made of two files (referred to by two structures).
- * 		 One file contains the indices referring to the data, and the other
- * 		 file contains the data itself. The obiarray as a whole is referred
- * 		 to via the OBIDMS_array structure.
- *
- * @param dms The OBIDMS to which the obiarray belongs.
- * @param array_name The name of the obiarray.
- *
- * @returns A pointer to the obiarray structure.
- * @retval NULL if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-OBIDMS_array_p obi_array(OBIDMS_p dms, const char* array_name);
-
-
-/**
- * @brief Creates an obiarray. Fails if it already exists.
- *
- * Note: An obiarray is made of two files (referred to by two structures).
- * 		 One file contains the indices referring to the data, and the other
- * 		 file contains the data itself. The obiarray as a whole is referred
- * 		 to via the OBIDMS_array structure.
- *
- * @param dms The OBIDMS to which the obiarray belongs.
- * @param array_name The name of the obiarray.
- *
- * @returns A pointer to the newly created obiarray structure.
- * @retval NULL if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-OBIDMS_array_p obi_create_array(OBIDMS_p dms, const char* array_name);
-
-
-/**
- * @brief Opens an obiarray. Fails if it does not already exist.
- *
- * Note: An obiarray is made of two files (referred to by two structures).
- * 		 One file contains the indices referring to the data, and the other
- * 		 file contains the data itself. The obiarray as a whole is referred
- * 		 to via the OBIDMS_array structure.
- *
- * @param dms The OBIDMS to which the obiarray belongs.
- * @param array_name The name of the obiarray.
- *
- * @returns A pointer to the obiarray structure.
- * @retval NULL if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-OBIDMS_array_p obi_open_array(OBIDMS_p dms, const char* array_name);
-
-
-/**
- * @brief Closes an obiarray.
- *
- * Note: An obiarray is made of two files (referred to by two structures).
- * 		 One file contains the indices referring to the data, and the other
- * 		 file contains the data itself. The obiarray as a whole is referred
- * 		 to via the OBIDMS_array structure.
- *
- * @param array A pointer to the obiarray structure to close and free.
- *
- * @retval 0 if the operation was successfully completed.
- * @retval -1 if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-int obi_close_array(OBIDMS_array_p array);
-
-
-/**
- * @brief Adds a value (byte array) in an obiarray, checking first if it is already in it.
- *
- * @warning The byte array to add must already be encoded and contain its header.
- *
- * @param array A pointer to the obiarray.
- * @param value The byte array to add in the obiarray.
- *
- * @returns The index of the value, whether it was added or already in the obiarray.
- * @retval -1 if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-index_t obi_array_add(OBIDMS_array_p array, byte_t* value);
-
-
-/**
- * @brief Recovers a value (byte array) in an obiarray.
- *
- * @warning The byte array recovered is encoded and contains its header.
- *
- * @param array A pointer to the obiarray.
- * @param index The index of the value in the data array.
- *
- * @returns A pointer to the byte array recovered.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-byte_t* obi_array_get(OBIDMS_array_p array, index_t index);
-
-
-/**
- * @brief Searches a value (byte array) in an obiarray performing a binary search.
- *
- * @warning The byte array to search must already be encoded and contain its header.
- *
- * @param array A pointer to the obiarray.
- * @param value The byte array to add in the obiarray.
- *
- * @returns If the value is found, its data index is returned.
- * 			If the value is not found, the array index indicating where the value's data index
- * 			should be in the array is returned in the form (- (index + 1)), as data indices in an
- * 			obiarray are sorted according to the ascending order of the values (byte arrays) themselves.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-index_t obi_array_search(OBIDMS_array_p array, byte_t* value);
-
-
-/**
- * @brief Converts a character string to a byte array with a header.
- *
- * @warning The byte array must be freed by the caller.
- *
- * @param value The character string to convert.
- *
- * @returns A pointer to the byte array created.
- * @retval NULL if an error occurred.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-byte_t* obi_str_to_obibytes(char* value);
-
-
-/**
- * @brief Converts a byte array to a character string.
- *
- * @param value_b The byte array to convert.
- *
- * @returns A pointer to the character string contained in the byte array.
- *
- * @since October 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-const char* obi_obibytes_to_str(byte_t* value_b);
-
-
-/**
- * @brief Converts a DNA sequence to a byte array with a header.
- *
- * @warning The byte array must be freed by the caller.
- *
- * @param value The DNA sequence to convert.
- *
- * @returns A pointer to the byte array created.
- * @retval NULL if an error occurred.
- *
- * @since November 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-byte_t* obi_seq_to_obibytes(char* seq);
-
-
-/**
- * @brief Converts a byte array to a DNA sequence.
- *
- * @param value_b The byte array to convert.
- *
- * @returns A pointer to the DNA sequence contained in the byte array.
- * @retval NULL if an error occurred.
- *
- * @since November 2015
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-const char* obi_obibytes_to_seq(byte_t* value_b);
-
-
-#endif /* OBIARRAY_H_ */
-

src/obiavl.h

@@ -0,0 +1,344 @@
+/****************************************************************************
+ * OBIDMS AVL tree header file	                                            *
+ ****************************************************************************/
+
+/**
+ * @file obiavl.h
+ * @author Celine Mercier
+ * @date December 3rd 2015
+ * @brief Header file for handling AVL trees for storing and retrieving byte arrays (i.e. coding for character strings).
+ */
+
+
+#ifndef OBIAVL_H_
+#define OBIAVL_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <time.h>
+#include <sys/types.h>
+#include <dirent.h>
+#include <stdbool.h>
+
+#include "obidms.h"
+#include "obitypes.h"
+
+
+#define AVL_MAX_NAME (1024) 								/**< The maximum length of an AVL tree name.
+                              	  	 	 	 	 	 	 	 */
+#define AVL_GROWTH_FACTOR (2)								/**< The growth factor when an AVL tree is enlarged.
+                                	 	 	 	 	 	 	 */
+#define AVL_MAX_DEPTH (50)									/**< The maximum depth of an AVL tree.
+                                	 	 	 	 	 	 	 */
+#define LEFT_CHILD(node)	(avl->tree)+(node->left_child)  /**< Pointer to the left child of a node in an AVL tree.
+															 */
+#define RIGHT_CHILD(node)	(avl->tree)+(node->right_child) /**< Pointer to the right child of a node in an AVL tree.
+															 */
+#define BYTE_ARRAY_HEADER_SIZE (9)  						/**< The size of the header of a byte array.
+                              	  	 	 	 	 	 	 	 */
+
+
+/**
+ * @brief AVL tree node structure.
+ */
+typedef struct AVL_node {
+	index_t left_child;		/**< Index of left less child node.
+	  	 	 	 	 	 	 */
+	index_t right_child; 	/**< Index of right greater child node.
+	 	 	 	 	 	 	 */
+	int8_t balance_factor; /**< Balance factor of the node.
+							 */
+	index_t value;			/**< Index of the value associated with the node in the data array.
+							 */
+} AVL_node_t, *AVL_node_p;
+
+
+/**
+ * @brief OBIDMS AVL tree data header structure.
+ */
+typedef struct OBIDMS_avl_data_header {
+	int			header_size;						/**< Size of the header in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		data_size_used;						/**< Size of the data used in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		data_size_max;						/**< Max size of the data in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items;							/**< Number of items.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char    	avl_name[AVL_MAX_NAME+1];			/**< The AVL tree name as a NULL terminated string.
+													 */
+	time_t		creation_date;			    	    /**< Date of creation of the file.
+												     */
+} OBIDMS_avl_data_header_t, *OBIDMS_avl_data_header_p;
+
+
+/**
+ * @brief OBIDMS AVL tree data structure.
+ */
+typedef struct OBIDMS_avl_data {
+	OBIDMS_avl_data_header_p	header; 		 	/**< A pointer to the header of the AVL tree data.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	byte_t*                   	data;   		 	/**< A pointer to the beginning of the data.
+													 */
+} OBIDMS_avl_data_t, *OBIDMS_avl_data_p;
+
+
+/**
+ * @brief OBIDMS AVL tree header structure.
+ */
+typedef struct OBIDMS_avl_header {
+	int			header_size;						/**< Size of the header in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	size_t		avl_size;							/**< Size of the AVL tree in bytes.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items;							/**< Number of items in the AVL tree.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		nb_items_max;						/**< Maximum number of items in the AVL tree before it has to be enlarged.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	index_t		root_idx;							/**< Index of the root of the AVL tree.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	char    	avl_name[AVL_MAX_NAME+1];			/**< The AVL tree name as a NULL terminated string.
+													 */
+	time_t		creation_date;			    	    /**< Date of creation of the file.
+												     */
+} OBIDMS_avl_header_t, *OBIDMS_avl_header_p;
+
+
+/**
+ * @brief OBIDMS AVL tree structure.
+ */
+typedef struct OBIDMS_avl {
+	OBIDMS_p                	dms;			 	/**< A pointer to the OBIDMS structure to which the AVL tree belongs.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	OBIDMS_avl_header_p			header; 	 		/**< A pointer to the header of the AVL tree.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	struct AVL_node*           	tree;   		 	/**< A pointer to the root of the AVL tree.
+													 */
+	index_t                     path_idx[AVL_MAX_DEPTH];	/**< The path taken to a node from the root as an array of node indices.
+													 	     */
+	int8_t                      path_dir[AVL_MAX_DEPTH];	/**< The path taken to a node from the root as an array of directions
+															 * (0 for left, -1 for right).
+															 */
+	OBIDMS_avl_data_p			data;				/**< A pointer to the structure containing the data
+													 *   that the AVL tree references.
+	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	DIR*						directory;			/**< A directory entry usable to
+										 	 	 	 *    refer and scan the AVL tree directory.
+										 	 	 	 */
+	int							dir_fd;				/**< The file descriptor of the directory entry
+													 *    usable to refer and scan the AVL tree directory.
+													 */
+	size_t						counter;			/**< Indicates by how many threads/programs (TODO) the AVL tree is used.
+													 */
+} OBIDMS_avl_t, *OBIDMS_avl_p;
+
+
+/**
+ * @brief Checks if an AVL tree already exists or not.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ *
+ * @returns A value indicating whether the AVL tree exists or not.
+ * @retval 1 if the AVL tree exists.
+ * @retval 0 if the AVL tree does not exist.
+ * @retval -1 if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_avl_exists(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Opens an AVL tree and creates it if it does not already exist.
+ *
+ * Note: An AVL tree is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The AVL tree as a whole is referred
+ * 		 to via the OBIDMS_avl structure.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ *
+ * @returns A pointer to the AVL tree structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_p obi_avl(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Creates an AVL tree. Fails if it already exists.
+ *
+ * Note: An AVL tree is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The AVL tree as a whole is referred
+ * 		 to via the OBIDMS_avl structure.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ *
+ * @returns A pointer to the newly created AVL tree structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Opens an AVL tree. Fails if it does not already exist.
+ *
+ * Note: An AVL tree is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The AVL tree as a whole is referred
+ * 		 to via the OBIDMS_avl structure.
+ *
+ * @param dms The OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ *
+ * @returns A pointer to the AVL tree structure.
+ * @retval NULL if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name);
+
+
+/**
+ * @brief Closes an AVL tree.
+ *
+ * Note: An AVL tree is made of two files (referred to by two structures).
+ * 		 One file contains the indices referring to the data, and the other
+ * 		 file contains the data itself. The AVL tree as a whole is referred
+ * 		 to via the OBIDMS_avl structure.
+ *
+ * @param avl A pointer to the AVL tree structure to close and free.
+ *
+ * @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 obi_close_avl(OBIDMS_avl_p avl);
+
+
+/**
+ * @brief Adds a value (byte array) in an AVL tree, checking if it is already in it.
+ *
+ * @warning The byte array to add must already be encoded and contain its header.
+ *
+ * @param avl A pointer to the AVL tree.
+ * @param value The byte array to add in the AVL tree.
+ *
+ * @returns The index of the value, whether it was added or already in the AVL tree.
+ * @retval -1 if an error occurred.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_avl_add(OBIDMS_avl_p avl, byte_t* value);
+
+
+/**
+ * @brief Finds a value (byte array) in an AVL tree, checking first if it is already in it.
+ *
+ * @warning The byte array to add must already be encoded and contain its header.
+ *
+ * @param avl A pointer to the AVL tree.
+ * @param value The byte array to add in the AVL tree.
+ *
+ * @returns The data index of the value.
+ * @retval -1 if the value is not in the tree.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+index_t obi_avl_find(OBIDMS_avl_p avl, byte_t* value);
+
+
+/**
+ * @brief Recovers a value (byte array) in an AVL tree.
+ *
+ * @warning The byte array recovered is encoded and contains its header.
+ *
+ * @param avl A pointer to the AVL tree.
+ * @param index The index of the value in the data array.
+ *
+ * @returns A pointer to the byte array recovered.
+ *
+ * @since December 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* obi_avl_get(OBIDMS_avl_p avl, index_t index);
+
+
+/**
+ * @brief Converts a character string to a byte array with a header.
+ *
+ * @warning The byte array must be freed by the caller.
+ *
+ * @param value The character string to convert.
+ *
+ * @returns A pointer to the byte array created.
+ * @retval NULL if an error occurred.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* obi_str_to_obibytes(char* value);
+
+
+/**
+ * @brief Converts a byte array to a character string.
+ *
+ * @param value_b The byte array to convert.
+ *
+ * @returns A pointer to the character string contained in the byte array.
+ *
+ * @since October 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_obibytes_to_str(byte_t* value_b);
+
+
+/**
+ * @brief Converts a DNA sequence to a byte array with a header.
+ *
+ * @warning The byte array must be freed by the caller.
+ *
+ * @param value The DNA sequence to convert.
+ *
+ * @returns A pointer to the byte array created.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+byte_t* obi_seq_to_obibytes(char* seq);
+
+
+/**
+ * @brief Converts a byte array to a DNA sequence.
+ *
+ * @param value_b The byte array to convert.
+ *
+ * @returns A pointer to the DNA sequence contained in the byte array.
+ * @retval NULL if an error occurred.
+ *
+ * @since November 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_obibytes_to_seq(byte_t* value_b);
+
+
+#endif /* OBIAVL_H_ */
+

src/obidms.c

@@ -247,7 +247,7 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 		return NULL;
 	}
 
-	// Get file descriptor of DMS directory to create the arrays directory
+	// Get file descriptor of DMS directory to create the AVL trees directory
 	dms_dir = opendir(directory_name);
 	if (dms_dir == NULL)
 	{
@@ -267,11 +267,11 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 		return NULL;
 	}
 
-	// Create the arrays directory
+	// Create the AVL trees directory
-	if (mkdirat(dms_file_descriptor, ARRAYS_DIR_NAME, 00777) < 0)
+	if (mkdirat(dms_file_descriptor, AVL_TREES_DIR_NAME, 00777) < 0)
 	{
-		obi_set_errno(OBI_ARRAY_ERROR);
+		obi_set_errno(OBI_AVL_ERROR);
-		obidebug(1, "\nProblem creating an arrays directory");
+		obidebug(1, "\nProblem creating an AVL trees directory");
 		return NULL;
 	}
 
@@ -390,24 +390,24 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 
 	dms->little_endian = little_endian_dms;
 
-	// Open the arrays directory
+	// Open the AVL trees directory
-	dms->array_directory = private_opendirat(dms->dir_fd, ARRAYS_DIR_NAME);
+	dms->avl_directory = private_opendirat(dms->dir_fd, AVL_TREES_DIR_NAME);
-	if (dms->array_directory == NULL)
+	if (dms->avl_directory == NULL)
 	{
 		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
-		obidebug(1, "\nError opening the arrays directory");
+		obidebug(1, "\nError opening the AVL trees directory");
 		closedir(dms->directory);
 		free(dms);
 		return NULL;
 	}
 
-	// Store the array directory's file descriptor
+	// Store the AVL trees directory's file descriptor
-	dms->array_dir_fd = dirfd(dms->array_directory);
+	dms->avl_dir_fd = dirfd(dms->avl_directory);
-	if (dms->array_dir_fd < 0)
+	if (dms->avl_dir_fd < 0)
 	{
 		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
-		obidebug(1, "\nError getting the file descriptor of the arrays directory");
+		obidebug(1, "\nError getting the file descriptor of the AVL trees directory");
-		closedir(dms->array_directory);
+		closedir(dms->avl_directory);
 		closedir(dms->directory);
 		free(dms);
 		return NULL;
@@ -418,10 +418,10 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 	(dms->opened_columns)->columns = (OBIDMS_column_p*) malloc(MAX_NB_OPENED_COLUMNS*sizeof(OBIDMS_column_p));
 	(dms->opened_columns)->nb_opened_columns = 0;
 
-	// Initialize the list of opened arrays
+	// Initialize the list of opened AVL trees
-	dms->opened_arrays = (Opened_arrays_list_p) malloc(sizeof(Opened_arrays_list_t));
+	dms->opened_avls = (Opened_avls_list_p) malloc(sizeof(Opened_avls_list_t));
-	(dms->opened_arrays)->arrays = (OBIDMS_array_p*) malloc(MAX_NB_OPENED_ARRAYS*sizeof(OBIDMS_array_p));
+	(dms->opened_avls)->avls = (OBIDMS_avl_p*) malloc(MAX_NB_OPENED_AVL_TREES*sizeof(OBIDMS_avl_p));
-	(dms->opened_arrays)->nb_opened_arrays = 0;
+	(dms->opened_avls)->nb_opened_avls = 0;
 
 	return dms;
 }
@@ -454,7 +454,7 @@ int obi_close_dms(OBIDMS_p dms)
 		while ((dms->opened_columns)->nb_opened_columns > 0)
 			obi_close_column(*((dms->opened_columns)->columns));
 
-		// Close dms and array directories
+		// Close dms and AVL trees directories
 		if (closedir(dms->directory) < 0)
 		{
 			obi_set_errno(OBIDMS_MEMORY_ERROR);
@@ -462,10 +462,10 @@ int obi_close_dms(OBIDMS_p dms)
 			free(dms);
 			return -1;
 		}
-		if (closedir(dms->array_directory) < 0)
+		if (closedir(dms->avl_directory) < 0)
 		{
-			obi_set_errno(OBI_ARRAY_ERROR);
+			obi_set_errno(OBI_AVL_ERROR);
-			obidebug(1, "\nError closing an array directory");
+			obidebug(1, "\nError closing an AVL trees directory");
 			free(dms);
 			return -1;
 		}

src/obidms.h

@@ -25,14 +25,14 @@
 #include "obierrno.h"
 
 
-#define OBIDMS_MAX_NAME (2048) 	    /**< The maximum length of an OBIDMS name.
+#define OBIDMS_MAX_NAME (2048) 	    		/**< The maximum length of an OBIDMS name.
-                                	 */
+                                	 	 	 */
-#define ARRAYS_DIR_NAME "arrays"    /**< The name of the arrays directory.
+#define AVL_TREES_DIR_NAME "AVL_trees"    	/**< The name of the AVL trees directory.
-                                	 */
+                                	 	 	 */
-#define MAX_NB_OPENED_COLUMNS (100) /**< The maximum number of columns open at the same time.
+#define MAX_NB_OPENED_COLUMNS (100) 		/**< The maximum number of columns open at the same time.
-                                	 */
+                                	 	 	 */
-#define MAX_NB_OPENED_ARRAYS (100)  /**< The maximum number of arrays open at the same time.
+#define MAX_NB_OPENED_AVL_TREES (100)  		/**< The maximum number of AVL trees open at the same time.
-                                	 */
+                                	 	 	 */
 
 
 struct OBIDMS_column;		// TODO
@@ -43,12 +43,12 @@ typedef struct Opened_columns_list {
 } Opened_columns_list_t, *Opened_columns_list_p;
 
 
-struct OBIDMS_array;		// TODO
+struct OBIDMS_avl;		// TODO
 
-typedef struct Opened_arrays_list {
+typedef struct Opened_avls_list {
-	size_t	 		 		nb_opened_arrays;
+	size_t	 		 		nb_opened_avls;
-	struct OBIDMS_array** 	arrays;
+	struct OBIDMS_avl** 	avls;
-} Opened_arrays_list_t, *Opened_arrays_list_p;
+} Opened_avls_list_t, *Opened_avls_list_p;
 
 
 /**
@@ -67,17 +67,17 @@ typedef struct OBIDMS {
 	int     				dir_fd;								/**< The file descriptor of the directory entry
 																 *   usable to refer and scan the database directory.
 																 */
-	DIR*					array_directory;					/**< A directory entry usable to
+	DIR*					avl_directory;						/**< A directory entry usable to
-																 *   refer and scan the array directory.
+																 *   refer and scan the AVL trees directory.
 																 */
-	int						array_dir_fd;						/**< The file descriptor of the directory entry
+	int						avl_dir_fd;							/**< The file descriptor of the directory entry
-																 *   usable to refer and scan the array directory.
+																 *   usable to refer and scan the AVL trees directory.
 																 */
 	bool					little_endian;						/**< Endianness of the database.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	Opened_columns_list_p 	opened_columns;						/**< List of opened columns.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	Opened_arrays_list_p 	opened_arrays;						/**< List of opened arrays.
+	Opened_avls_list_p 		opened_avls;						/**< List of opened AVL trees.
 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 } OBIDMS_t, *OBIDMS_p;
 
@@ -105,7 +105,7 @@ int obi_dms_exists(const char* dms_name);
  * if a directory with this name does not already exist
  * before creating the new database.
  *
- * A directory to store obiarrays is also created.
+ * A directory to store AVL trees is also created.
  *
  * @param dms_name A pointer to a C string containing the name of the database.
  *                 The actual directory name used to store the DMS will be

src/obidmscolumn.c

@@ -29,7 +29,7 @@
 #include "obierrno.h"
 #include "obidebug.h"
 #include "obilittlebigman.h"
-#include "obiarray.h"
+#include "obiavl.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -514,14 +514,14 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 								  index_t     nb_lines,
 								  index_t     nb_elements_per_line,
 								  const char* elements_names,
-								  const char* array_name,
+								  const char* avl_name,
 								  const char* comments,
 								  bool        referring)
 {
 	OBIDMS_column_p 			new_column;
 	OBIDMS_column_directory_p	column_directory;
 	OBIDMS_column_header_p 		header;
-	OBIDMS_array_p				array;
+	OBIDMS_avl_p				avl;
 	size_t 						file_size;
 	obiversion_t 				version_number;
 	char* 						column_file_name;
@@ -552,9 +552,9 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 		obidebug(1, "\nCan't create column because of invalid data type");
 		return NULL;
 	}
-	if (((data_type == OBI_STR) || (data_type == OBI_SEQ)) && (array_name == NULL))
+	if (((data_type == OBI_STR) || (data_type == OBI_SEQ)) && (avl_name == NULL))
 	{
-		obidebug(1, "\nCan't create column because of empty array name");
+		obidebug(1, "\nCan't create column because of empty avl name");
 		return NULL;
 	}
 
@@ -732,20 +732,20 @@ OBIDMS_column_p obi_create_column(OBIDMS_p    dms,
 	if (comments != NULL)
 		strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
 
-	// If the data type is OBI_STR or OBI_SEQ, the associated obi_array is opened or created
+	// If the data type is OBI_STR or OBI_SEQ, the associated obi_avl is opened or created
 	if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ))
 	{
-		array = obi_array(dms, array_name);
+		avl = obi_avl(dms, avl_name);
-		if (array == NULL)
+		if (avl == NULL)
 		{
-			obidebug(1, "\nError opening or creating the array associated with a column");
+			obidebug(1, "\nError opening or creating the aVL tree associated with a column");
 			munmap(new_column->header, header_size);
 			close(column_file_descriptor);
 			free(new_column);
 			return NULL;
 		}
-		new_column->array = array;
+		new_column->avl = avl;
-		strncpy(header->array_name, array_name, ARRAY_MAX_NAME);
+		strncpy(header->avl_name, avl_name, AVL_MAX_NAME);
 	}
 
 	// Fill the data with NA values
@@ -768,7 +768,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 {
 	OBIDMS_column_p 		    column;
 	OBIDMS_column_directory_p	column_directory;
-	OBIDMS_array_p				array;
+	OBIDMS_avl_p				avl;
 	char* 						column_file_name;
 	int 						column_file_descriptor;
 	size_t 						header_size;
@@ -886,19 +886,19 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
 
 	column->writable  = false;
 
-	// If the data type is OBI_STR or OBI_SEQ, the associated obi_array is opened
+	// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is opened
 	if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
 	{
-		array = obi_array(dms, (column->header)->array_name);
+		avl = obi_avl(dms, (column->header)->avl_name);
-		if (array == NULL)
+		if (avl == NULL)
 		{
-			obidebug(1, "\nError opening the array associated with a column");
+			obidebug(1, "\nError opening the AVL tree associated with a column");
 			munmap(column->header, header_size);
 			close(column_file_descriptor);
 			free(column);
 			return NULL;
 		}
-		column->array = array;
+		column->avl = avl;
 	}
 
 	if ((column->header)->referring)
@@ -973,7 +973,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p         dms,
 								   nb_lines,
 								   nb_elements_per_line,
 								   (column_to_clone->header)->elements_names,
-								   (column_to_clone->header)->array_name,
+								   (column_to_clone->header)->avl_name,
 								   (column_to_clone->header)->comments,
 								   referring);
 
@@ -1052,10 +1052,10 @@ int obi_close_column(OBIDMS_column_p column)
 		if ((column->header)->referring)
 			obi_close_column(column->referred_column);
 
-		// If the data type is OBI_STR or OBI_SEQ, the associated obi_array is closed
+		// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is closed
 		if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
 		{
-			if (obi_close_array(column->array) < 0)
+			if (obi_close_avl(column->avl) < 0)
 				return -1;
 		}
 

src/obidmscolumn.h

@@ -25,7 +25,7 @@
 #include "obierrno.h"
 #include "obilittlebigman.h"
 #include "obidmscolumndir.h"
-#include "obiarray.h"
+#include "obiavl.h"
 
 
 #define ONE_IF_ZERO(x) (((x)==0)?1:(x))	/**< If x is equal to 0, x takes the value 1.
@@ -86,7 +86,7 @@ typedef struct OBIDMS_column_header {
 															 */
 	char            name[OBIDMS_COLUMN_MAX_NAME+1]; 	    /**< The column name as a NULL terminated string.
 	                                             	 	 	 */
-	char            array_name[ARRAY_MAX_NAME+1]; 	    	/**< If there is one, the obi_array name as a NULL terminated string.
+	char            avl_name[AVL_MAX_NAME+1]; 	    		/**< If there is one, the AVL tree name as a NULL terminated string.
 	                                             	 	 	 */
 	char 			comments[COMMENTS_MAX_LENGTH+1];		/**< Comments stored as a classical zero end C string.
 												 	 	 	 */
@@ -106,7 +106,7 @@ typedef struct OBIDMS_column {
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	OBIDMS_column_header_p		header; 		 	/**< A pointer to the header of the column.
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	OBIDMS_array_p 				array;				/**< A pointer to the array associated with the column if there is one.
+	OBIDMS_avl_p 				avl;				/**< A pointer to the AVL tree associated with the column if there is one.
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 	struct OBIDMS_column*       referred_column;    /**< A pointer to the referred column if the column is referring.
 	 	 	 	 	 	 	 	 	 	 	 	 	 */
@@ -174,7 +174,7 @@ size_t obi_get_platform_header_size();
  * @brief Creates a column.
  *
  * The minimum data size allocated is one memory page, and the data is initialized to the NA value of the OBIType.
- * If there is an array associated with the column, it is opened or created if it does not already exist.
+ * If there is an AVL tree associated with the column, it is opened or created if it does not already exist.
  *
  * @warning If there is one element per line, elements_names should be equal to column_name.	// TODO change this condition?
  *
@@ -182,9 +182,9 @@ size_t obi_get_platform_header_size();
  * @param column_name The name of the new column.
  * @param data_type The OBIType code of the data.
  * @param nb_lines The number of lines to be stored.
- * @param nb_elements_per_line The number of elements per line.
+ * @param nb_elements_per_line The number of elements per line.								// TODO talk about default values
  * @param elements_names The names of the elements with ';' as separator.
- * @param array_name The name of the array if there is one associated with the column.
+ * @param avl_name The name of the AVL tree if there is one associated with the column.
  * @param comments Optional comments associated with the column.
  * @param referring
  *
@@ -200,7 +200,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 								  index_t nb_lines,
 								  index_t nb_elements_per_line,
 								  const char* elements_names,
-								  const char* array_name,
+								  const char* avl_name,
 								  const char* comments,
 								  bool referring);
 

src/obidmscolumn_seq.c

@@ -17,7 +17,7 @@
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
-#include "obiarray.h"
+#include "obiavl.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -67,8 +67,8 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 	if (value_b == NULL)
 		return -1;
 
-	// Add in the obiarray
+	// Add in the AVL tree
-	idx = obi_array_add(column->array, value_b);
+	idx = obi_avl_add(column->avl, value_b);
 	if (idx == -1)
 		return -1;
 
@@ -106,7 +106,7 @@ const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t l
 	if (idx == OBIIdx_NA)
 		return "\0";		// TODO
 
-	value_b = obi_array_get(column->array, idx);
+	value_b = obi_avl_get(column->avl, idx);
 	return obi_obibytes_to_seq(value_b);
 }
 

src/obidmscolumn_seq.h

@@ -23,7 +23,7 @@
 
 /**
  * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
- * to DNA sequences in an obiarray, using the index of the element in the line.
+ * to DNA sequences in an AVL tree, using the index of the element in the line.
  *
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
@@ -44,7 +44,7 @@ int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
- * to DNA sequences in an obiarray, using the index of the element in the line.
+ * to DNA sequences in an AVL tree, using the index of the element in the line.
  *
  * @param column A pointer as returned by obi_create_column().
  * @param line_nb The number of the line where the value should be recovered.
@@ -61,7 +61,7 @@ const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t l
 
 /**
  * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
- * to DNA sequences in an obiarray, using the name of the element in the line.
+ * to DNA sequences in an AVL tree, using the name of the element in the line.
  *
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
@@ -82,7 +82,7 @@ int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb,
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
- * to DNA sequences in an obiarray, using the name of the element in the line.
+ * to DNA sequences in an AVL tree, using the name of the element in the line.
  *
  * @param column A pointer as returned by obi_create_column() or obi_clone_column().
  * @param line_nb The number of the line where the value should be recovered.

src/obidmscolumn_str.c

@@ -17,7 +17,7 @@
 #include "obitypes.h"
 #include "obierrno.h"
 #include "obidebug.h"
-#include "obiarray.h"
+#include "obiavl.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -67,8 +67,8 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 	if (value_b == NULL)
 		return -1;
 
-	// Add in the obiarray
+	// Add in the AVL tree
-	idx = obi_array_add(column->array, value_b);
+	idx = obi_avl_add(column->avl, value_b);
 	if (idx == -1)
 		return -1;
 
@@ -106,7 +106,7 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
 	if (idx == OBIIdx_NA)
 		return "\0";		// TODO
 
-	value_b = obi_array_get(column->array, idx);
+	value_b = obi_avl_get(column->avl, idx);
 	return obi_obibytes_to_str(value_b);
 }
 

src/obidmscolumn_str.h

@@ -23,7 +23,7 @@
 
 /**
  * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
- * to character strings in an obiarray, using the index of the element in the line.
+ * to character strings in an AVL tree, using the index of the element in the line.
  *
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
@@ -44,7 +44,7 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
- * to character strings in an obiarray, using the index of the element in the line.
+ * to character strings in an AVL tree, using the index of the element in the line.
  *
  * @param column A pointer as returned by obi_create_column().
  * @param line_nb The number of the line where the value should be recovered.
@@ -61,7 +61,7 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
 
 /**
  * @brief Sets a value in an OBIDMS column containing data in the form of indices referring
- * to character strings in an obiarray, using the name of the element in the line.
+ * to character strings in an AVL tree, using the name of the element in the line.
  *
  * @warning Pointers returned by obi_open_column() don't allow writing.
  *
@@ -82,7 +82,7 @@ int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb,
 
 /**
  * @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
- * to character strings in an obiarray, using the name of the element in the line.
+ * to character strings in an AVL tree, using the name of the element in the line.
  *
  * @param column A pointer as returned by obi_create_column() or obi_clone_column().
  * @param line_nb The number of the line where the value should be recovered.

src/obierrno.h

@@ -98,7 +98,7 @@ extern int obi_errno;
                                     	 	 */
 #define OBICOL_ACCESS_ERROR    		(19) 	/**< Permission error trying to access an OBIDSM column directory
                                     		 */
-#define OBI_ARRAY_ERROR				(20)    /** Error while handling an array
+#define OBI_AVL_ERROR				(20)    /** Error while handling an AVL tree
 											 */
 /**@}*/
 

src/obitypes.h

@@ -56,6 +56,12 @@ typedef double obifloat_t;
 typedef char obichar_t;
 // TODO same for obistr_t and obiseq_t ?
 
+
+typedef char byte_t;		/**< Defining byte type since the data referred to by AVL trees is stored in bits
+							 *	 and char (stored on one byte) is the smallest addressable unit.
+ 	 	 	 	 	 	 	 */
+
+
 /**
  * @brief Union used to compute the NA value of the OBI_FLOAT OBIType.
  */