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#ifndef DYNAMITEgenewisemodeldbHEADERFILE
#define DYNAMITEgenewisemodeldbHEADERFILE
#ifdef _cplusplus
extern "C" {
#endif
#include "dyna.h"
#include "genewisemodel.h"
#include "threestatedb.h"
#include "gwlitemodel.h"
/* Object GeneWiseDB
*
* Descrip: This is a database of genewisemodels
* for database searching versions of
* genewise and estwise type algorithms.
*
* The actual HMM database streaming
* happens via the ThreeStateDB (tdb).
* This object holds the necessary conversion
* system for the HMM database as it
* is mapped into the genewisemodel
*
*
*/
struct Wise2_GeneWiseDB {
int dynamite_hard_link;
#ifdef PTHREAD
pthread_mutex_t dynamite_mutex;
#endif
ThreeStateDB * tdb;
double cds_factor;
CodonMapper * cm; /* NB, hard linked. */
RandomModelDNA * rmd; /* NB hard linked */
GeneWiseScore * gws; /* hardlinked, only if single. */
GeneParameter21 * gpara; /* if a genomic model - est models wont use this! */
boolean is_single;
boolean is_syn;
Probability allN;
boolean flat_insert;
GwLiteScore * gwls; /* only if single */
} ;
/* GeneWiseDB defined */
#ifndef DYNAMITE_DEFINED_GeneWiseDB
typedef struct Wise2_GeneWiseDB Wise2_GeneWiseDB;
#define GeneWiseDB Wise2_GeneWiseDB
#define DYNAMITE_DEFINED_GeneWiseDB
#endif
/***************************************************/
/* Callable functions */
/* These are the functions you are expected to use */
/***************************************************/
/* Function: init_GeneWiseDB(gdb,return_status)
*
* Descrip: inits a genewise database. Remember this is used
* for both genomic and cdna searches
*
*
*
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseDB *]
* Arg: return_status [UNKN ] Undocumented argument [int *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScore *]
*
*/
GeneWiseScore * Wise2_init_GeneWiseDB(GeneWiseDB * gdb,int * return_status);
#define init_GeneWiseDB Wise2_init_GeneWiseDB
/* Function: reload_GeneWiseDB(prev,gdb,return_status)
*
* Descrip: Reloads a genewise database
*
*
*
* Arg: prev [UNKN ] Undocumented argument [GeneWiseScore *]
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseDB *]
* Arg: return_status [UNKN ] Undocumented argument [int *]
*
* Return [UNKN ] Undocumented return value [GeneWiseScore *]
*
*/
GeneWiseScore * Wise2_reload_GeneWiseDB(GeneWiseScore * prev,GeneWiseDB * gdb,int * return_status);
#define reload_GeneWiseDB Wise2_reload_GeneWiseDB
/* Function: close_GeneWiseDB(gws,gdb)
*
* Descrip: closes a GeneWiseDB
*
*
* Arg: gws [UNKN ] Undocumented argument [GeneWiseScore *]
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseDB *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_close_GeneWiseDB(GeneWiseScore * gws,GeneWiseDB * gdb);
#define close_GeneWiseDB Wise2_close_GeneWiseDB
/* Function: dataentry_add_GeneWiseDB(de,gws,gdb)
*
* Descrip: adds dataentry stuff to a query. Relies completely
* on threestatedb
*
*
* Arg: de [UNKN ] Undocumented argument [DataEntry *]
* Arg: gws [UNKN ] Undocumented argument [GeneWiseScore *]
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseDB *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_dataentry_add_GeneWiseDB(DataEntry * de,GeneWiseScore * gws,GeneWiseDB * gdb);
#define dataentry_add_GeneWiseDB Wise2_dataentry_add_GeneWiseDB
/* Function: new_GeneWiseDB_cdna(syn,tdb,cp,cm,rmd,use_syn,flat_insert,allN)
*
* Descrip: makes a new GeneWiseDB from its component parts,
* assuming a cDNA db.
*
* All the objects are hard-linked internally, so you can, if you
* wish, free them once passing them into this function
*
*
* Arg: syn [UNKN ] if ture, use a synchronous coding model vs internally stored tdb rm's [NullString]
* Arg: tdb [UNKN ] three state model db to use [ThreeStateDB *]
* Arg: cp [UNKN ] codon parser function to remove from match state [cDNAParser *]
* Arg: cm [UNKN ] Undocumented argument [CodonMapper *]
* Arg: rmd [UNKN ] random model (dna) [RandomModelDNA *]
* Arg: use_syn [UNKN ] Undocumented argument [boolean]
* Arg: flat_insert [UNKN ] Undocumented argument [boolean]
* Arg: allN [UNKN ] Undocumented argument [Probability]
*
* Return [UNKN ] Undocumented return value [GeneWiseDB *]
*
*/
GeneWiseDB * Wise2_new_GeneWiseDB_cdna(ThreeStateDB * tdb,cDNAParser * cp,CodonMapper * cm,RandomModelDNA * rmd,boolean use_syn,boolean flat_insert,Probability allN) ;
#define new_GeneWiseDB_cdna Wise2_new_GeneWiseDB_cdna
/* Function: new_GeneWiseDB(tdb,gp,rmd,use_syn,allN)
*
* Descrip: makes a new GeneWiseDB from its component parts.
* All the objects are hard-linked internally, so you can, if you
* wish, free them once passing them into this function
*
*
* Arg: tdb [UNKN ] Undocumented argument [ThreeStateDB *]
* Arg: gp [UNKN ] Undocumented argument [GeneParameter21 *]
* Arg: rmd [UNKN ] Undocumented argument [RandomModelDNA *]
* Arg: use_syn [UNKN ] Undocumented argument [boolean]
* Arg: allN [UNKN ] Undocumented argument [Probability]
*
* Return [UNKN ] Undocumented return value [GeneWiseDB *]
*
*/
GeneWiseDB * Wise2_new_GeneWiseDB(ThreeStateDB * tdb,GeneParameter21 * gp,RandomModelDNA * rmd,boolean use_syn,Probability allN);
#define new_GeneWiseDB Wise2_new_GeneWiseDB
/* Function: new_single_GeneWiseDB(gws)
*
* Descrip: makes a new GeneWiseDB from a single GeneWiseScore.
* It hard links it, so you should free it afterwards
* in its own scope.
*
*
* Arg: gws [UNKN ] Undocumented argument [GeneWiseScore *]
*
* Return [UNKN ] Undocumented return value [GeneWiseDB *]
*
*/
GeneWiseDB * Wise2_new_single_GeneWiseDB(GeneWiseScore * gws);
#define new_single_GeneWiseDB Wise2_new_single_GeneWiseDB
/* Function: init_GwLite_GeneWiseDB(gdb,return_status)
*
* Descrip: inits a genewise database for gwlite models
*
*
*
*
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseDB *]
* Arg: return_status [UNKN ] Undocumented argument [int *]
*
* Return [UNKN ] Undocumented return value [GwLiteScore *]
*
*/
GwLiteScore * Wise2_init_GwLite_GeneWiseDB(GeneWiseDB * gdb,int * return_status);
#define init_GwLite_GeneWiseDB Wise2_init_GwLite_GeneWiseDB
/* Function: reload_GwLite_GeneWiseDB(prev,gdb,return_status)
*
* Descrip: Reloads a genewise database for a GwLite database
*
*
*
* Arg: prev [UNKN ] Undocumented argument [GwLiteScore *]
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseDB *]
* Arg: return_status [UNKN ] Undocumented argument [int *]
*
* Return [UNKN ] Undocumented return value [GwLiteScore *]
*
*/
GwLiteScore * Wise2_reload_GwLite_GeneWiseDB(GwLiteScore * prev,GeneWiseDB * gdb,int * return_status);
#define reload_GwLite_GeneWiseDB Wise2_reload_GwLite_GeneWiseDB
/* Function: close_GwLite_GeneWiseDB(gws,gdb)
*
* Descrip: closes a GeneWiseDB
*
*
* Arg: gws [UNKN ] Undocumented argument [GwLiteScore *]
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseDB *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_close_GwLite_GeneWiseDB(GwLiteScore * gws,GeneWiseDB * gdb);
#define close_GwLite_GeneWiseDB Wise2_close_GwLite_GeneWiseDB
/* Function: dataentry_add_GwLite_GeneWiseDB(de,gws,gdb)
*
* Descrip: adds dataentry stuff to a query. Relies completely
* on threestatedb
*
*
* Arg: de [UNKN ] Undocumented argument [DataEntry *]
* Arg: gws [UNKN ] Undocumented argument [GwLiteScore *]
* Arg: gdb [UNKN ] Undocumented argument [GeneWiseDB *]
*
* Return [UNKN ] Undocumented return value [boolean]
*
*/
boolean Wise2_dataentry_add_GwLite_GeneWiseDB(DataEntry * de,GwLiteScore * gws,GeneWiseDB * gdb);
#define dataentry_add_GwLite_GeneWiseDB Wise2_dataentry_add_GwLite_GeneWiseDB
/* Function: hard_link_GeneWiseDB(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 [GeneWiseDB *]
*
* Return [UNKN ] Undocumented return value [GeneWiseDB *]
*
*/
GeneWiseDB * Wise2_hard_link_GeneWiseDB(GeneWiseDB * obj);
#define hard_link_GeneWiseDB Wise2_hard_link_GeneWiseDB
/* Function: GeneWiseDB_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Return [UNKN ] Undocumented return value [GeneWiseDB *]
*
*/
GeneWiseDB * Wise2_GeneWiseDB_alloc(void);
#define GeneWiseDB_alloc Wise2_GeneWiseDB_alloc
/* Function: free_GeneWiseDB(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 [GeneWiseDB *]
*
* Return [UNKN ] Undocumented return value [GeneWiseDB *]
*
*/
GeneWiseDB * Wise2_free_GeneWiseDB(GeneWiseDB * obj);
#define free_GeneWiseDB Wise2_free_GeneWiseDB
/* Unplaced functions */
/* There has been no indication of the use of these functions */
/***************************************************/
/* Internal functions */
/* you are not expected to have to call these */
/***************************************************/
GeneWise * Wise2_GeneWise_from_ThreeStateModel_GDB(ThreeStateModel * tsm,GeneWiseDB * gdb);
#define GeneWise_from_ThreeStateModel_GDB Wise2_GeneWise_from_ThreeStateModel_GDB
#ifdef _cplusplus
}
#endif
#endif
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