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
|