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/dports/biology/wise/wise2.4.1/src/dynlibsrc/
H A Dcomplexsequence.dy142 out->data = out->datastore + (cses->left_lookback * cses->len);
145 for(j=0;j<cses->len;j++)
146 out->datastore[(i*cses->len)+j] = cses->cse[j]->outside_score;
149 out->depth = cses->len;
155 if( i < cses->cse[j]->right_window || (i + cses->cse[j]->left_window) >= seqlen)
157 …else poi[j] = (*cses->cse[j]->eval_func)(cses->cse[j]->data_type,cses->cse[j]->data,rev->seq+seqle…
212 out->data = out->datastore + (cses->left_lookback * cses->len);
216 out->datastore[(i*cses->len)+j] = cses->cse[j]->outside_score;
219 out->depth = cses->len;
226 … else poi[j] = (*cses->cse[j]->eval_func)(cses->cse[j]->data_type,cses->cse[j]->data,seq->seq+i);
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H A Dcomplexsequence.c58 out->data = out->datastore + (cses->left_lookback * cses->len); in reversed_ComplexSequence()
61 for(j=0;j<cses->len;j++) in reversed_ComplexSequence()
62 out->datastore[(i*cses->len)+j] = cses->cse[j]->outside_score; in reversed_ComplexSequence()
65 out->depth = cses->len; in reversed_ComplexSequence()
71 if( i < cses->cse[j]->right_window || (i + cses->cse[j]->left_window) >= seqlen) in reversed_ComplexSequence()
73 …else poi[j] = (*cses->cse[j]->eval_func)(cses->cse[j]->data_type,cses->cse[j]->data,rev->seq+seqle… in reversed_ComplexSequence()
134 out->data = out->datastore + (cses->left_lookback * cses->len); in new_ComplexSequence()
138 out->datastore[(i*cses->len)+j] = cses->cse[j]->outside_score; in new_ComplexSequence()
141 out->depth = cses->len; in new_ComplexSequence()
148 … else poi[j] = (*cses->cse[j]->eval_func)(cses->cse[j]->data_type,cses->cse[j]->data,seq->seq+i); in new_ComplexSequence()
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H A Dcdnadb.c339 ComplexSequenceEvalSet * cses; in new_cDNADB_from_single_seq() local
345 cs_rev = new_ComplexSequence(temp,cses); in new_cDNADB_from_single_seq()
347 free_ComplexSequenceEvalSet(cses); in new_cDNADB_from_single_seq()
395 ComplexSequenceEvalSet * cses; in new_cDNADB() local
406 if( cses->type != SEQUENCE_CDNA ) { in new_cDNADB()
416 out->cses = hard_link_ComplexSequenceEvalSet(cses); in new_cDNADB()
417 free_ComplexSequenceEvalSet(cses); in new_cDNADB()
476 out->cses = NULL; in cDNADB_alloc()
527 if( obj->cses != NULL) in free_cDNADB()
862 obj->cses = cses; in replace_cses_cDNADB()
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H A Dproteindb.c131 cs = new_ComplexSequence(seq,prodb->cses); in init_ProteinDB()
180 cs = new_ComplexSequence(seq,prodb->cses); in reload_ProteinDB()
228 ComplexSequenceEvalSet * cses; in new_ProteinDB_from_single_seq() local
233 cs = new_ComplexSequence(seq,cses); in new_ProteinDB_from_single_seq()
235 free_ComplexSequenceEvalSet(cses); in new_ProteinDB_from_single_seq()
306 if( cses->type != SEQUENCE_PROTEIN ) { in new_ProteinDB()
315 out->cses = cses; in new_ProteinDB()
371 out->cses = NULL; in ProteinDB_alloc()
418 if( obj->cses != NULL) in free_ProteinDB()
623 obj->cses = cses; in replace_cses_ProteinDB()
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H A Dgenomicdb.c341 cs = evaluate_ComplexSequence_Genomic(gen,cses,0,score_in_repeat_coding); in new_GenomicDB_from_single_seq()
343 cs_rev = evaluate_ComplexSequence_Genomic(temp,cses,0,score_in_repeat_coding); in new_GenomicDB_from_single_seq()
398 if( seqdb == NULL || cses == NULL ) { in new_GenomicDB()
405 if( cses->type != SEQUENCE_GENOMIC ) { in new_GenomicDB()
415 out->cses = hard_link_ComplexSequenceEvalSet(cses); in new_GenomicDB()
475 out->cses = NULL; in GenomicDB_alloc()
529 if( obj->cses != NULL) in free_GenomicDB()
530 free_ComplexSequenceEvalSet(obj->cses); in free_GenomicDB()
818 boolean replace_cses_GenomicDB(GenomicDB * obj,ComplexSequenceEvalSet * cses) in replace_cses_GenomicDB() argument
824 obj->cses = cses; in replace_cses_GenomicDB()
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H A Dgenomicdb.xs174 set_cses(obj,cses)
176 Wise2_ComplexSequenceEvalSet * cses
178 RETVAL = Wise2_replace_cses_GenomicDB(obj,Wise2_hard_link_ComplexSequenceEvalSet(cses));
185 cses(obj)
219 new_GenomicDB_from_single_seq(gen,cses,score_in_repeat_coding)
221 Wise2_ComplexSequenceEvalSet * cses
224 RETVAL = Wise2_new_GenomicDB_from_single_seq(gen,cses,score_in_repeat_coding);
231 new_GenomicDB(seqdb,cses,length_of_N,repeat_in_cds_score)
233 Wise2_ComplexSequenceEvalSet * cses
237 RETVAL = Wise2_new_GenomicDB(seqdb,cses,length_of_N,repeat_in_cds_score);
H A Dproteindb.dy21 ComplexSequenceEvalSet * cses
153 cs = new_ComplexSequence(seq,prodb->cses);
195 cs = new_ComplexSequence(seq,prodb->cses);
231 ComplexSequenceEvalSet * cses;
234 cses = default_aminoacid_ComplexSequenceEvalSet();
236 cs = new_ComplexSequence(seq,cses);
238 free_ComplexSequenceEvalSet(cses);
278 cses protein evaluation set
291 if( cses->type != SEQUENCE_PROTEIN ) {
292 warn("You can't make a protein database with a non SEQUENCE_PROTEIN cses type [%d]",cses->type);
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H A Dcdnadb.dy26 ComplexSequenceEvalSet * cses
196 cs = new_ComplexSequence(seq,cdnadb->cses);
304 cs = new_ComplexSequence(seq,cdnadb->cses);
357 ComplexSequenceEvalSet * cses;
363 cs_rev = new_ComplexSequence(temp,cses);
365 free_ComplexSequenceEvalSet(cses);
402 ComplexSequenceEvalSet * cses;
413 if( cses->type != SEQUENCE_CDNA ) {
414 warn("You can't make a cDNA database with a non SEQUENCE_cDNA cses type [%d]",cses->type);
423 out->cses = hard_link_ComplexSequenceEvalSet(cses);
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H A Dproteindb.xs115 set_cses(obj,cses)
117 Wise2_ComplexSequenceEvalSet * cses
119 RETVAL = Wise2_replace_cses_ProteinDB(obj,Wise2_hard_link_ComplexSequenceEvalSet(cses));
126 cses(obj)
225 new_ProteinDB(seqdb,cses)
227 Wise2_ComplexSequenceEvalSet * cses
229 RETVAL = Wise2_new_ProteinDB(seqdb,cses);
H A Dgenomicdb.pod46 =item cses
306 &Wise2::GenomicDB::set_cses(obj,cses)
308 Replace member variable cses
315 Return [SOFT ] member variable cses [boolean]
318 =item cses
320 &Wise2::GenomicDB::cses(obj)
322 Access member variable cses
328 Return [SOFT ] member variable cses [ComplexSequenceEvalSet *]
337 &Wise2::new_GenomicDB_from_single_seq(gen,cses,score_in_repeat_coding)
345 Argument cses [UNKN ] Undocumented argument [ComplexSequenceEvalSet *]
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H A Dproteindb.pod38 =item cses
209 &Wise2::ProteinDB::set_cses(obj,cses)
211 Replace member variable cses
217 Argument cses [OWNER] New value of the variable [ComplexSequenceEvalSet *]
218 Return [SOFT ] member variable cses [boolean]
221 =item cses
223 &Wise2::ProteinDB::cses(obj)
225 Access member variable cses
231 Return [SOFT ] member variable cses [ComplexSequenceEvalSet *]
320 &Wise2::new_ProteinDB(seqdb,cses)
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H A Dgenomicdb.dy25 ComplexSequenceEvalSet * cses
189 cs = evaluate_ComplexSequence_Genomic(gendb->current,gendb->cses,0,gendb->repeat_in_cds_score);
252 cs = evaluate_ComplexSequence_Genomic(temp,gendb->cses,0,gendb->repeat_in_cds_score);
297 cs = evaluate_ComplexSequence_Genomic(gen,gendb->cses,0,gendb->repeat_in_cds_score);
353 cs = evaluate_ComplexSequence_Genomic(gen,cses,0,score_in_repeat_coding);
355 cs_rev = evaluate_ComplexSequence_Genomic(temp,cses,0,score_in_repeat_coding);
389 cses protein evaluation set
395 if( seqdb == NULL || cses == NULL ) {
402 if( cses->type != SEQUENCE_GENOMIC ) {
403 warn("You can't make a genomic database with a non SEQUENCE_GENOMIC cses type [%d]",cses->type);
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H A Dgenomicdb.tex13 \item[External C] {\tt Wise2_new_GenomicDB_from_single_seq (gen,cses,score_in_repeat_coding)}
14 \item[Perl] {\tt &Wise2::new_GenomicDB_from_single_seq (gen,cses,score_in_repeat_coding)}
20 \item[cses] [UNKN ] Undocumented argument [ComplexSequenceEvalSet *]
30 \item[External C] {\tt Wise2_new_GenomicDB (seqdb,cses,length_of_N,repeat_in_cds_score)}
31 \item[Perl] {\tt &Wise2::new_GenomicDB (seqdb,cses,length_of_N,repeat_in_cds_score)}
37 \item[cses] [UNKN ] protein evaluation set [ComplexSequenceEvalSet *]
65 \item{cses} Type [ComplexSequenceEvalSet * : Scalar] No documentation
H A Dcomplexsequence.h145 ComplexSequence * Wise2_reversed_ComplexSequence(Sequence * forward,ComplexSequenceEvalSet * cses) ;
163 ComplexSequence * Wise2_new_ComplexSequence(Sequence * seq,ComplexSequenceEvalSet * cses);
193 boolean Wise2_prepare_ComplexSequenceEvalSet(ComplexSequenceEvalSet * cses);
210 boolean Wise2_can_evaluate_this_Sequence(ComplexSequenceEvalSet * cses,Sequence * s);
439 boolean Wise2_can_evaluate_this_type(ComplexSequenceEvalSet * cses,int type);
H A Dgenomicdb_api.h248 boolean Wise2_replace_cses_GenomicDB( Wise2_GenomicDB * obj,Wise2_ComplexSequenceEvalSet * cses);
293 …micDB_from_single_seq( Wise2_Genomic * gen,Wise2_ComplexSequenceEvalSet * cses,int score_in_repeat…
308 Wise2_GenomicDB * Wise2_new_GenomicDB( Wise2_SequenceDB * seqdb,Wise2_ComplexSequenceEvalSet * cses…
H A Dgenomicdb.h55 ComplexSequenceEvalSet * cses; member
187 GenomicDB * Wise2_new_GenomicDB_from_single_seq(Genomic * gen,ComplexSequenceEvalSet * cses,int sco…
220 GenomicDB * Wise2_new_GenomicDB(SequenceDB * seqdb,ComplexSequenceEvalSet * cses,int length_of_N,in…
297 boolean Wise2_replace_cses_GenomicDB(GenomicDB * obj,ComplexSequenceEvalSet * cses);
/dports/biology/wise/wise2.4.1/src/models/
H A Dgwrap.c50 out->cses = free_ComplexSequenceEvalSet(out->cses); in GeneParameter21_wrap()
51 out->cses = default_genomic_ComplexSequenceEvalSet(); in GeneParameter21_wrap()
226 ComplexSequenceEvalSet * cses; in AlnBlock_from_TSM_genewise_wrap() local
251 if( prepare_ComplexSequenceEvalSet(gpara->cses) == FALSE ) { in AlnBlock_from_TSM_genewise_wrap()
257 cses = default_cDNA_ComplexSequenceEvalSet(); in AlnBlock_from_TSM_genewise_wrap()
258 cs = new_ComplexSequence(gen->baseseq,cses); in AlnBlock_from_TSM_genewise_wrap()
259 free_ComplexSequenceEvalSet(cses); in AlnBlock_from_TSM_genewise_wrap()
262 tempcse = gpara->cses->cse[1]; in AlnBlock_from_TSM_genewise_wrap()
264 cs = new_ComplexSequence(gen->baseseq,gpara->cses); in AlnBlock_from_TSM_genewise_wrap()
265 free_ComplexSequenceEval(gpara->cses->cse[1]); in AlnBlock_from_TSM_genewise_wrap()
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H A Dgeneparameter.c132 out->cses = new_ComplexSequenceEvalSet_from_GeneModel(gm); in GeneParameter21_from_GeneModel()
180 out->cses = ComplexSequenceEvalSet_alloc_len(6); in GeneParameter21_from_GeneFrequency21()
181 out->cses->type = SEQUENCE_GENOMIC; in GeneParameter21_from_GeneFrequency21()
185 add_ComplexSequenceEvalSet(out->cses,base_number_ComplexSequenceEval()); in GeneParameter21_from_GeneFrequency21()
215 add_ComplexSequenceEvalSet(out->cses,cse); in GeneParameter21_from_GeneFrequency21()
232 add_ComplexSequenceEvalSet(out->cses,cse); in GeneParameter21_from_GeneFrequency21()
250 add_ComplexSequenceEvalSet(out->cses,flat_zero()); in GeneParameter21_from_GeneFrequency21()
251 add_ComplexSequenceEvalSet(out->cses,flat_zero()); in GeneParameter21_from_GeneFrequency21()
607 out->cses = NULL; in GeneParameter21_alloc()
660 if( obj->cses != NULL) in free_GeneParameter21()
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H A Dgeneparameter.dy28 ComplexSequenceEvalSet * cses; !hidden
167 out->cses = new_ComplexSequenceEvalSet_from_GeneModel(gm);
214 out->cses = ComplexSequenceEvalSet_alloc_len(6);
215 out->cses->type = SEQUENCE_GENOMIC;
219 add_ComplexSequenceEvalSet(out->cses,base_number_ComplexSequenceEval());
220 add_ComplexSequenceEvalSet(out->cses,codon_number_ComplexSequenceEval());
247 /** add complexeval to cses **/
249 add_ComplexSequenceEvalSet(out->cses,cse);
266 add_ComplexSequenceEvalSet(out->cses,cse);
284 add_ComplexSequenceEvalSet(out->cses,flat_zero());
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H A Dlba.c65 ComplexSequenceEvalSet *cses; in main() local
98 cses = default_DNA_ComplexSequenceEvalSet(); in main()
99 cone = new_ComplexSequence(one,cses); in main()
100 ctwo = new_ComplexSequence(two,cses); in main()
H A Destwrap.c153 ComplexSequenceEvalSet * cses = NULL ; in AlnBlock_from_TSM_estwise_wrap() local
192 cses = default_cDNA_ComplexSequenceEvalSet(); in AlnBlock_from_TSM_estwise_wrap()
194 cs = new_ComplexSequence(cdna->baseseq,cses); in AlnBlock_from_TSM_estwise_wrap()
196 cses = free_ComplexSequenceEvalSet(cses); in AlnBlock_from_TSM_estwise_wrap()
248 if( cses != NULL) in AlnBlock_from_TSM_estwise_wrap()
249 free_ComplexSequenceEvalSet(cses); in AlnBlock_from_TSM_estwise_wrap()
H A Ddnawise.c40 ComplexSequenceEvalSet * cses; in main() local
64 cses = default_DNA_ComplexSequenceEvalSet(); in main()
67 cseq = new_ComplexSequence(target,cses); in main()
/dports/biology/wise/wise2.4.1/src/dyc/
H A Dkbestsearch.c38 CommonSubExpressionSet * cses; in write_kbest_score_GenericMatrix() local
40 cses = find_CommonSubExpressions(gm,TRUE); in write_kbest_score_GenericMatrix()
41 show_CommonSubExpressionSet(cses,stdout); in write_kbest_score_GenericMatrix()
96 for(i=0;i<cses->len;i++) { in write_kbest_score_GenericMatrix()
154 for(i=0;i<cses->len;i++) { in write_kbest_score_GenericMatrix()
155 if( IS_NON_IJ_DEP_CSE(cses->cse[i]) ) { in write_kbest_score_GenericMatrix()
171 for(i=0;i<cses->len;i++) { in write_kbest_score_GenericMatrix()
172 if( IS_J_DEP_CSE(cses->cse[i]) == TRUE && IS_I_DEP_CSE(cses->cse[i]) == FALSE ) { in write_kbest_score_GenericMatrix()
192 for(i=0;i<cses->len;i++) { in write_kbest_score_GenericMatrix()
193 if( IS_J_DEP_CSE(cses->cse[i]) == TRUE && IS_I_DEP_CSE(cses->cse[i]) == TRUE ) { in write_kbest_score_GenericMatrix()
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H A Doptimiser.dy60 pointer to function that does the magic on the cses placer system
78 Places ids into the cses
81 void id_CommonSubExpressionSet(CommonSubExpressionSet * cses)
85 for(i=0;i<cses->len;i++)
86 cses->cse[i]->id = i;
96 void show_CommonSubExpressionSet(CommonSubExpressionSet * cses,FILE * ofp)
100 for(i=0;i<cses->len;i++) {
101 …p,"Sub Expression %d - Number of times seen %d IJdep %d\n ",i,cses->cse[i]->number,cses->cse[i]-…
102 print_ExprTree(cses->cse[i]->expr,ofp);
H A Dkbestsearch.dy70 CommonSubExpressionSet * cses;
72 cses = find_CommonSubExpressions(gm,TRUE);
73 show_CommonSubExpressionSet(cses,stdout);
128 for(i=0;i<cses->len;i++) {
186 for(i=0;i<cses->len;i++) {
187 if( IS_NON_IJ_DEP_CSE(cses->cse[i]) ) {
203 for(i=0;i<cses->len;i++) {
204 if( IS_J_DEP_CSE(cses->cse[i]) == TRUE && IS_I_DEP_CSE(cses->cse[i]) == FALSE ) {
224 for(i=0;i<cses->len;i++) {
225 if( IS_J_DEP_CSE(cses->cse[i]) == TRUE && IS_I_DEP_CSE(cses->cse[i]) == TRUE ) {
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