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#ifndef DYNAMITEgwquickdbHEADERFILE
#define DYNAMITEgwquickdbHEADERFILE
#ifdef _cplusplus
extern "C" {
#endif
#include "genewisemodeldb.h"
/* Object GeneWiseQuickDB
*
* Descrip: This is a database stream of
* GeneWiseScoreFlat objects, layered
* ontop of a vanilla genewisedb.
*
* The GeneWiseScoreFlat objects give
* around a 10% speed up due to them
* being allocated as a single block
* of memory that then gets accessed
*
* This object is a very thin layer over
* the genewisedb object, which itself handles
* the actual HMM stuff via threestatedb object.
* So if you want to discover how HMMs are
* actually being streamed into the database,
* look in there.
*
*
*/
struct Wise2_GeneWiseQuickDB {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
GeneWiseDB * gwdb;
} ;
/* GeneWiseQuickDB defined */
#ifndef DYNAMITE_DEFINED_GeneWiseQuickDB
typedef struct Wise2_GeneWiseQuickDB Wise2_GeneWiseQuickDB;
#define GeneWiseQuickDB Wise2_GeneWiseQuickDB
#define DYNAMITE_DEFINED_GeneWiseQuickDB
#endif
/***************************************************/
/* Callable functions */
/* These are the functions you are expected to use */
/***************************************************/
/* Function: init_GeneWiseQuickDB(gdb,return_status)
*
* Descrip: inits a genewisequick database.
*
*
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseQuickDB *]
* Arg: return_status [UNKN ] Undocumented argument [int *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScoreFlat *]
*
*/
GeneWiseScoreFlat * Wise2_init_GeneWiseQuickDB(GeneWiseQuickDB * gdb,int * return_status);
#define init_GeneWiseQuickDB Wise2_init_GeneWiseQuickDB
/* Function: reload_GeneWiseQuickDB(prev,gdb,return_status)
*
* Descrip: Reloads a genewisequick database
*
*
*
* Arg: prev [UNKN ] Undocumented argument [GeneWiseScoreFlat *]
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseQuickDB *]
* Arg: return_status [UNKN ] Undocumented argument [int *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScoreFlat *]
*
*/
GeneWiseScoreFlat * Wise2_reload_GeneWiseQuickDB(GeneWiseScoreFlat * prev,GeneWiseQuickDB * gdb,int * return_status);
#define reload_GeneWiseQuickDB Wise2_reload_GeneWiseQuickDB
/* Function: close_GeneWiseQuickDB(gws,gdb)
*
* Descrip: closes a GeneWiseDB
*
*
* Arg: gws [UNKN ] Undocumented argument [GeneWiseScoreFlat *]
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseQuickDB *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_close_GeneWiseQuickDB(GeneWiseScoreFlat * gws,GeneWiseQuickDB * gdb);
#define close_GeneWiseQuickDB Wise2_close_GeneWiseQuickDB
/* Function: dataentry_add_GeneWiseQuickDB(de,gws,gdb)
*
* Descrip: adds dataentry stuff to a query.
*
*
* Arg: de [UNKN ] Undocumented argument [DataEntry *]
* Arg: gws [UNKN ] Undocumented argument [GeneWiseScoreFlat *]
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseQuickDB *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_dataentry_add_GeneWiseQuickDB(DataEntry * de,GeneWiseScoreFlat * gws,GeneWiseQuickDB * gdb);
#define dataentry_add_GeneWiseQuickDB Wise2_dataentry_add_GeneWiseQuickDB
/* Function: GeneWiseQuickDB_from_GeneWiseDB(gwdb)
*
* Descrip: Makes a new genewisequickdb from a genewisemodeldb
*
*
* Arg: gwdb [READ ] genewisedb - hard links as it enters [GeneWiseDB *]
*
* Return [UNKN ] Undocumented return value [GeneWiseQuickDB *]
*
*/
GeneWiseQuickDB * Wise2_GeneWiseQuickDB_from_GeneWiseDB(GeneWiseDB * gwdb);
#define GeneWiseQuickDB_from_GeneWiseDB Wise2_GeneWiseQuickDB_from_GeneWiseDB
/* Function: hard_link_GeneWiseQuickDB(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj [UNKN ] Object to be hard linked [GeneWiseQuickDB *]
*
* Return [UNKN ] Undocumented return value [GeneWiseQuickDB *]
*
*/
GeneWiseQuickDB * Wise2_hard_link_GeneWiseQuickDB(GeneWiseQuickDB * obj);
#define hard_link_GeneWiseQuickDB Wise2_hard_link_GeneWiseQuickDB
/* Function: GeneWiseQuickDB_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [GeneWiseQuickDB *]
*
*/
GeneWiseQuickDB * Wise2_GeneWiseQuickDB_alloc(void);
#define GeneWiseQuickDB_alloc Wise2_GeneWiseQuickDB_alloc
/* Function: free_GeneWiseQuickDB(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [GeneWiseQuickDB *]
*
* Return [UNKN ] Undocumented return value [GeneWiseQuickDB *]
*
*/
GeneWiseQuickDB * Wise2_free_GeneWiseQuickDB(GeneWiseQuickDB * obj);
#define free_GeneWiseQuickDB Wise2_free_GeneWiseQuickDB
/* Unplaced functions */
/* There has been no indication of the use of these functions */
/***************************************************/
/* Internal functions */
/* you are not expected to have to call these */
/***************************************************/
#ifdef _cplusplus
}
#endif
#endif
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