obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

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

Browse Source
This commit is contained in:
Celine Mercier
2015-12-11 17:24:44 +01:00
parent 1586956d57
commit c139367555
26 changed files with 2178 additions and 1711 deletions
Download Patch File Download Diff File Expand all files Collapse all files

38
src/obidms.h
View File

@ -25,14 +25,14 @@
#include "obierrno.h"
#define OBIDMS_MAX_NAME (2048) /**< The maximum length of an OBIDMS name.
*/
#define ARRAYS_DIR_NAME "arrays" /**< The name of the arrays directory.
*/
#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 OBIDMS_MAX_NAME (2048) /**< The maximum length of an OBIDMS name.
*/
#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_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 {
size_t nb_opened_arrays;
struct OBIDMS_array** arrays;
} Opened_arrays_list_t, *Opened_arrays_list_p;
typedef struct Opened_avls_list {
size_t nb_opened_avls;
struct OBIDMS_avl** avls;
} 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
* refer and scan the array directory.
DIR* avl_directory; /**< A directory entry usable to
* refer and scan the AVL trees directory.
*/
int array_dir_fd; /**< The file descriptor of the directory entry
* usable to refer and scan the array directory.
int avl_dir_fd; /**< The file descriptor of the directory entry
* 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