1 #ifndef DYNAMITEcomplexevalsetHEADERFILE 2 #define DYNAMITEcomplexevalsetHEADERFILE 3 #ifdef _cplusplus 4 extern "C" { 5 #endif 6 #include "complexsequence.h" 7 #include "genomic.h" 8 9 10 11 /*** ok, some types to works with ***/ 12 13 #define AMINOACID CSEQ_PROTEIN_AMINOACID 14 #define CSEQ_PROTEIN_AMINOACID(cseq,index) (cseq->data[index]) 15 16 17 /*** for genomic ***/ 18 19 #define CSEQ_G_LEN 6 20 21 #define CSEQ_GENOMIC_BASE(cseq,index) (cseq->data[(index)*CSEQ_G_LEN]) 22 #define CSEQ_GENOMIC_CODON(cseq,index) (cseq->data[(index)*CSEQ_G_LEN +1]) 23 #define CSEQ_GENOMIC_5SS(cseq,index) (cseq->data[(index)*CSEQ_G_LEN +2]) 24 #define CSEQ_GENOMIC_3SS(cseq,index) (cseq->data[(index)*CSEQ_G_LEN +3]) 25 #define CSEQ_GENOMIC_REPEAT(cseq,index) (cseq->data[(index)*CSEQ_G_LEN +4]) 26 #define CSEQ_GENOMIC_CDSPOT(cseq,index) (cseq->data[(index)*CSEQ_G_LEN +5]) 27 28 29 /*** for cDNA ***/ 30 31 #define CSEQ_C_LEN 2 32 33 #define CSEQ_CDNA_BASE(cseq,index) (cseq->data[index*CSEQ_C_LEN]) 34 #define CSEQ_CDNA_CODON(cseq,index) (cseq->data[index*CSEQ_C_LEN +1]) 35 36 #define CSEQ_D_LEN 1 37 38 #define CSEQ_DNA_BASE(cseq,index) (cseq->data[index]) 39 40 41 42 /***************************************************/ 43 /* Callable functions */ 44 /* These are the functions you are expected to use */ 45 /***************************************************/ 46 47 48 49 /* Function: evaluate_ComplexSequence_Genomic(gen,cses,score_for_repeat,score_for_cds_in_repeat) 50 * 51 * Descrip: makes a new ComplexSequence from a Genomic 52 * sequence, using the repeat information to 53 * structure the positives and negatives. 54 * 55 * 56 * Arg: gen [UNKN ] Undocumented argument [Genomic *] 57 * Arg: cses [UNKN ] Undocumented argument [ComplexSequenceEvalSet *] 58 * Arg: score_for_repeat [UNKN ] Undocumented argument [int] 59 * Arg: score_for_cds_in_repeat [UNKN ] Undocumented argument [int] 60 * 61 * Return [UNKN ] Undocumented return value [ComplexSequence *] 62 * 63 */ 64 ComplexSequence * Wise2_evaluate_ComplexSequence_Genomic(Genomic * gen,ComplexSequenceEvalSet * cses,int score_for_repeat,int score_for_cds_in_repeat); 65 #define evaluate_ComplexSequence_Genomic Wise2_evaluate_ComplexSequence_Genomic 66 67 68 /* Function: default_genomic_ComplexSequenceEvalSet(void) 69 * 70 * Descrip: Makes a reasonably sensible genomic sequence 71 * eval set. Has base and codon numbers (what 72 * every good genomic sequence should do) and then 73 * /stupid_5SS and /stupid_3SS. Finally the repeat/EST 74 * regions modelled with the /flat_zero 75 * 76 * 77 * 78 * Return [UNKN ] Undocumented return value [ComplexSequenceEvalSet *] 79 * 80 */ 81 ComplexSequenceEvalSet * Wise2_default_genomic_ComplexSequenceEvalSet(void); 82 #define default_genomic_ComplexSequenceEvalSet Wise2_default_genomic_ComplexSequenceEvalSet 83 84 85 /* Function: flat_negi(void) 86 * 87 * Descrip: Makes a ComplexSequenceEval that puts NEGI everywhere 88 * 89 * 90 * 91 * Return [UNKN ] Undocumented return value [ComplexSequenceEval *] 92 * 93 */ 94 ComplexSequenceEval * Wise2_flat_negi(void); 95 #define flat_negi Wise2_flat_negi 96 97 98 /* Function: flat_zero(void) 99 * 100 * Descrip: Makes a ComplexSequenceEval that puts 0 everywhere 101 * 102 * 103 * 104 * Return [UNKN ] Undocumented return value [ComplexSequenceEval *] 105 * 106 */ 107 ComplexSequenceEval * Wise2_flat_zero(void); 108 #define flat_zero Wise2_flat_zero 109 110 111 /* Function: stupid_5SS(void) 112 * 113 * Descrip: Reasonably stupid 5'SS, of 0 at GT's 114 * and NEGI elsewhere. Pretends to have a longer 115 * footprint than it needs to satisify the lookbacks 116 * of more proper genomic models 117 * 118 * 119 * 120 * Return [UNKN ] Undocumented return value [ComplexSequenceEval *] 121 * 122 */ 123 ComplexSequenceEval * Wise2_stupid_5SS(void); 124 #define stupid_5SS Wise2_stupid_5SS 125 126 127 /* Function: stupid_3SS(void) 128 * 129 * Descrip: Reasonably stupid 3'SS, of 0 at AG's 130 * and NEGI elsewhere. Pretends to have a longer 131 * footprint than it needs to satisify the lookbacks 132 * of more proper genomic models 133 * 134 * 135 * 136 * Return [UNKN ] Undocumented return value [ComplexSequenceEval *] 137 * 138 */ 139 ComplexSequenceEval * Wise2_stupid_3SS(void); 140 #define stupid_3SS Wise2_stupid_3SS 141 142 143 /* Function: default_DNA_ComplexSequenceEvalSet(void) 144 * 145 * Descrip: Makes a very sensible DNA sequence 146 * eval set. You shouldn't need your own 147 * 148 * 149 * 150 * Return [UNKN ] Undocumented return value [ComplexSequenceEvalSet *] 151 * 152 */ 153 ComplexSequenceEvalSet * Wise2_default_DNA_ComplexSequenceEvalSet(void); 154 #define default_DNA_ComplexSequenceEvalSet Wise2_default_DNA_ComplexSequenceEvalSet 155 156 157 /* Function: default_cDNA_ComplexSequenceEvalSet(void) 158 * 159 * Descrip: Makes a very sensible cDNA sequence 160 * eval set. You shouldn't need your own 161 * 162 * 163 * 164 * Return [UNKN ] Undocumented return value [ComplexSequenceEvalSet *] 165 * 166 */ 167 ComplexSequenceEvalSet * Wise2_default_cDNA_ComplexSequenceEvalSet(void); 168 #define default_cDNA_ComplexSequenceEvalSet Wise2_default_cDNA_ComplexSequenceEvalSet 169 170 171 /* Function: codon_number_ComplexSequenceEval(void) 172 * 173 * Descrip: ComplexSequenceEval that puts a codon 174 * number in there (0-125 inc, 125 = impossible codon). 175 * 176 * 177 * 178 * Return [UNKN ] Undocumented return value [ComplexSequenceEval *] 179 * 180 */ 181 ComplexSequenceEval * Wise2_codon_number_ComplexSequenceEval(void); 182 #define codon_number_ComplexSequenceEval Wise2_codon_number_ComplexSequenceEval 183 184 185 /* Function: codon64_number_ComplexSequenceEval(void) 186 * 187 * Descrip: Function which puts a 64 base codon... 188 * 189 * 190 * 191 * Return [UNKN ] Undocumented return value [ComplexSequenceEval *] 192 * 193 */ 194 ComplexSequenceEval * Wise2_codon64_number_ComplexSequenceEval(void); 195 #define codon64_number_ComplexSequenceEval Wise2_codon64_number_ComplexSequenceEval 196 197 198 /* Function: base_number_ComplexSequenceEval(void) 199 * 200 * Descrip: ComplexSequenceEval that puts a base 201 * number (0-5 inc) 202 * 203 * 204 * 205 * Return [UNKN ] Undocumented return value [ComplexSequenceEval *] 206 * 207 */ 208 ComplexSequenceEval * Wise2_base_number_ComplexSequenceEval(void); 209 #define base_number_ComplexSequenceEval Wise2_base_number_ComplexSequenceEval 210 211 212 /* Function: default_aminoacid_ComplexSequenceEvalSet(void) 213 * 214 * Descrip: Makes a very sensible protein sequence 215 * eval set. You shouldn't need your own 216 * 217 * 218 * 219 * Return [UNKN ] Undocumented return value [ComplexSequenceEvalSet *] 220 * 221 */ 222 ComplexSequenceEvalSet * Wise2_default_aminoacid_ComplexSequenceEvalSet(void); 223 #define default_aminoacid_ComplexSequenceEvalSet Wise2_default_aminoacid_ComplexSequenceEvalSet 224 225 226 /* Function: aminoacid_number_ComplexSequenceEval(void) 227 * 228 * Descrip: ComplexSequenceEval that puts a amino acid 229 * number in there (0-26) 230 * 231 * 232 * 233 * Return [UNKN ] Undocumented return value [ComplexSequenceEval *] 234 * 235 */ 236 ComplexSequenceEval * Wise2_aminoacid_number_ComplexSequenceEval(void); 237 #define aminoacid_number_ComplexSequenceEval Wise2_aminoacid_number_ComplexSequenceEval 238 239 240 /* Function: default_dna_ComplexSequenceEvalSet(void) 241 * 242 * Descrip: Makes a very sensible dna sequence 243 * eval set. You shouldn't need your own 244 * 245 * 246 * 247 * Return [UNKN ] Undocumented return value [ComplexSequenceEvalSet *] 248 * 249 */ 250 ComplexSequenceEvalSet * Wise2_default_dna_ComplexSequenceEvalSet(void); 251 #define default_dna_ComplexSequenceEvalSet Wise2_default_dna_ComplexSequenceEvalSet 252 253 254 /* Unplaced functions */ 255 /* There has been no indication of the use of these functions */ 256 257 258 /***************************************************/ 259 /* Internal functions */ 260 /* you are not expected to have to call these */ 261 /***************************************************/ 262 int Wise2_flat_negi_eval(int type,void *data,char * seq); 263 #define flat_negi_eval Wise2_flat_negi_eval 264 int Wise2_flat_zero_eval(int type,void *data,char * seq); 265 #define flat_zero_eval Wise2_flat_zero_eval 266 int Wise2_stupid_5SS_eval(int type,void *data,char * seq); 267 #define stupid_5SS_eval Wise2_stupid_5SS_eval 268 int Wise2_stupid_3SS_eval(int type,void *data,char * seq); 269 #define stupid_3SS_eval Wise2_stupid_3SS_eval 270 int Wise2_codon_number_func(int type,void * data,char * seq); 271 #define codon_number_func Wise2_codon_number_func 272 int Wise2_codon64_number_func(int type,void * data,char * seq); 273 #define codon64_number_func Wise2_codon64_number_func 274 int Wise2_base_number_func(int type,void * data,char * seq); 275 #define base_number_func Wise2_base_number_func 276 int Wise2_aminoacid_number_func(int type,void * data,char * seq); 277 #define aminoacid_number_func Wise2_aminoacid_number_func 278 279 #ifdef _cplusplus 280 } 281 #endif 282 283 #endif 284