File: geneparser21.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 (205 lines) | stat: -rw-r--r-- 6,747 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
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
#ifndef DYNAMITEgeneparser21HEADERFILE
#define DYNAMITEgeneparser21HEADERFILE
#ifdef _cplusplus
extern "C" {
#endif
#include "probability.h"
#include "dyna.h"
#include "randommodel.h"
#include "genefrequency.h"

enum {
  GP21_CDS2CENTRAL = 0,
  GP21_CENTRAL2CENTRAL,
  GP21_CENTRAL2PY,
  GP21_PY2PY,
  GP21_PY2SPACER,
  GP21_PY2CDS,
  GP21_SPACER2SPACER,
  GP21_SPACER2CDS,
  GP21_INSERT_1_BASE,
  GP21_INSERT_2_BASE,
  GP21_DELETE_1_BASE,
  GP21_DELETE_2_BASE,
  GP21_CDS2CDS, /* this is for gene parsing outside of the *Wise set */
  GP21_RND2CDS,
  GP21_CDS2RND,
  GP21_RND2RND,
  GP21_RND2MODEL,
  GP21_LINK2MODEL, /* this is for link models */
  GP21_LINK2LINK,
  GP21_LINK2RND,
  GENEPARSER21_TRANSITION_LEN
};


#define GENEPARSER21_EMISSION_LEN 5

#define GeneParser21SetLISTLENGTH 32


struct Wise2_GeneParser21 {  
    int dynamite_hard_link;  
#ifdef PTHREAD   
    pthread_mutex_t dynamite_mutex;  
#endif   
    Probability transition[GENEPARSER21_TRANSITION_LEN];     
    Probability central[GENEPARSER21_EMISSION_LEN];  
    Probability py[GENEPARSER21_EMISSION_LEN];   
    Probability spacer[GENEPARSER21_EMISSION_LEN];   
    } ;  
/* GeneParser21 defined */ 
#ifndef DYNAMITE_DEFINED_GeneParser21
typedef struct Wise2_GeneParser21 Wise2_GeneParser21;
#define GeneParser21 Wise2_GeneParser21
#define DYNAMITE_DEFINED_GeneParser21
#endif


struct Wise2_GeneParser21Score {  
    int dynamite_hard_link;  
#ifdef PTHREAD   
    pthread_mutex_t dynamite_mutex;  
#endif   
    Score transition[GENEPARSER21_TRANSITION_LEN];   
    Score central[GENEPARSER21_EMISSION_LEN];    
    Score py[GENEPARSER21_EMISSION_LEN];     
    Score spacer[GENEPARSER21_EMISSION_LEN];     
    } ;  
/* GeneParser21Score defined */ 
#ifndef DYNAMITE_DEFINED_GeneParser21Score
typedef struct Wise2_GeneParser21Score Wise2_GeneParser21Score;
#define GeneParser21Score Wise2_GeneParser21Score
#define DYNAMITE_DEFINED_GeneParser21Score
#endif




    /***************************************************/
    /* Callable functions                              */
    /* These are the functions you are expected to use */
    /***************************************************/



/* Function:  hard_link_GeneParser21(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 [GeneParser21 *]
 *
 * Return [UNKN ]  Undocumented return value [GeneParser21 *]
 *
 */
GeneParser21 * Wise2_hard_link_GeneParser21(GeneParser21 * obj);
#define hard_link_GeneParser21 Wise2_hard_link_GeneParser21


/* Function:  GeneParser21_alloc(void)
 *
 * Descrip:    Allocates structure: assigns defaults if given 
 *
 *
 *
 * Return [UNKN ]  Undocumented return value [GeneParser21 *]
 *
 */
GeneParser21 * Wise2_GeneParser21_alloc(void);
#define GeneParser21_alloc Wise2_GeneParser21_alloc


/* Function:  free_GeneParser21(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 [GeneParser21 *]
 *
 * Return [UNKN ]  Undocumented return value [GeneParser21 *]
 *
 */
GeneParser21 * Wise2_free_GeneParser21(GeneParser21 * obj);
#define free_GeneParser21 Wise2_free_GeneParser21


/* Function:  hard_link_GeneParser21Score(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 [GeneParser21Score *]
 *
 * Return [UNKN ]  Undocumented return value [GeneParser21Score *]
 *
 */
GeneParser21Score * Wise2_hard_link_GeneParser21Score(GeneParser21Score * obj);
#define hard_link_GeneParser21Score Wise2_hard_link_GeneParser21Score


/* Function:  GeneParser21Score_alloc(void)
 *
 * Descrip:    Allocates structure: assigns defaults if given 
 *
 *
 *
 * Return [UNKN ]  Undocumented return value [GeneParser21Score *]
 *
 */
GeneParser21Score * Wise2_GeneParser21Score_alloc(void);
#define GeneParser21Score_alloc Wise2_GeneParser21Score_alloc


/* Function:  free_GeneParser21Score(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 [GeneParser21Score *]
 *
 * Return [UNKN ]  Undocumented return value [GeneParser21Score *]
 *
 */
GeneParser21Score * Wise2_free_GeneParser21Score(GeneParser21Score * obj);
#define free_GeneParser21Score Wise2_free_GeneParser21Score


  /* Unplaced functions */
  /* There has been no indication of the use of these functions */
RandomModelDNA * Wise2_fudged_mixed_RandomModelDNA_from_GeneParser21(GeneParser21 * gp,RandomModelDNA * rnd);
#define fudged_mixed_RandomModelDNA_from_GeneParser21 Wise2_fudged_mixed_RandomModelDNA_from_GeneParser21
void Wise2_add_flat_error_probabilities_GeneParser21(GeneParser21 * gp21,Probability error);
#define add_flat_error_probabilities_GeneParser21 Wise2_add_flat_error_probabilities_GeneParser21
void Wise2_add_error_probabilities_GeneParser21(GeneParser21 * gp21,Probability insert_1,Probability insert_2,Probability delete_1,Probability delete_2);
#define add_error_probabilities_GeneParser21 Wise2_add_error_probabilities_GeneParser21
GeneParser21 * Wise2_GeneParser21_from_GeneFrequency21_cds(GeneFrequency21 * gf,Probability rnd_loop,Probability cds_loop,Probability rnd_to_model,Probability link_loop,Probability link_to_model);
#define GeneParser21_from_GeneFrequency21_cds Wise2_GeneParser21_from_GeneFrequency21_cds
RandomModelDNA * Wise2_RandomModelDNA_from_central_GeneParser21(GeneParser21 *gp21);
#define RandomModelDNA_from_central_GeneParser21 Wise2_RandomModelDNA_from_central_GeneParser21
void Wise2_show_GeneParser21(GeneParser21 * gp21,FILE * ofp);
#define show_GeneParser21 Wise2_show_GeneParser21
GeneParser21 * Wise2_std_GeneParser21(void);
#define std_GeneParser21 Wise2_std_GeneParser21
Probability Wise2_removed_probability_from_cds(GeneParser21 * gp21);
#define removed_probability_from_cds Wise2_removed_probability_from_cds
void Wise2_GeneParser21_fold_in_RandomModelDNA(GeneParser21 * gp21,RandomModelDNA * rmd);
#define GeneParser21_fold_in_RandomModelDNA Wise2_GeneParser21_fold_in_RandomModelDNA
GeneParser21Score * Wise2_GeneParser21Score_from_GeneParser21(GeneParser21 * gp21);
#define GeneParser21Score_from_GeneParser21 Wise2_GeneParser21Score_from_GeneParser21


    /***************************************************/
    /* Internal functions                              */
    /* you are not expected to have to call these      */
    /***************************************************/

#ifdef _cplusplus
}
#endif

#endif