File: gwquickdb.h

package info (click to toggle)
wise 2.4.1-21
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 27,140 kB
  • sloc: ansic: 276,365; makefile: 1,003; perl: 886; lex: 93; yacc: 81; sh: 24
file content (186 lines) | stat: -rw-r--r-- 5,507 bytes parent folder | download | duplicates (8)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
#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