| /dports/biology/viennarna/ViennaRNA-2.4.18/src/bin/ |
| H A D | RNALalifold.c | 84 *shape_file_association, verbose, s, tmp_number, in main() local
108 shape_file_association = 0; in main()
219 shape_file_association = (int *)vrna_alloc(sizeof(int *) * (args_info.shape_given + 1)); in main()
234 shape_file_association[s] = tmp_number - 1; in main()
237 shape_file_association[s] = s; in main()
244 shape_file_association[s] + 1); in main()
248 shape_file_association[s] = -1; in main()
479 for (s = 0; shape_file_association[s] != -1; s++); in main()
486 shape_file_association = (int *)vrna_realloc(shape_file_association, in main()
494 shape_file_association, \ in main()
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| H A D | RNAalifold.c | 94 int *shape_file_association; member
268 opt->shape_file_association = NULL; in init_default_options()
484 opt.shape_file_association = (int *)vrna_alloc(sizeof(int) * (args_info.shape_given + 1)); in main()
499 opt.shape_file_association[s] = tmp_number - 1; in main()
502 opt.shape_file_association[s] = s; in main()
509 opt.shape_file_association[s] + 1); in main()
513 opt.shape_file_association[s] = -1; in main()
1406 for (s = 0; opt->shape_file_association[s] != -1; s++); in apply_SHAPE_data()
1418 opt->shape_file_association = (int *)vrna_realloc(opt->shape_file_association, in apply_SHAPE_data()
1424 opt->shape_file_association, in apply_SHAPE_data()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/constraints/ |
| H A D | SHAPE.c | 129 const int *shape_file_association, in vrna_constraints_add_SHAPE_ali() argument
155 vrna_sc_add_SHAPE_deigan_ali(vc, shape_files, shape_file_association, p1, p2, constraint_type); in vrna_constraints_add_SHAPE_ali()
350 const int *shape_file_association, in vrna_sc_add_SHAPE_deigan_ali() argument
371 for (n_data = s = 0; shape_file_association[s] != -1; s++) { in vrna_sc_add_SHAPE_deigan_ali()
372 if (shape_file_association[s] >= n_seq) in vrna_sc_add_SHAPE_deigan_ali()
387 for (s = 0; shape_file_association[s] != -1; s++) { in vrna_sc_add_SHAPE_deigan_ali()
388 int ss = shape_file_association[s]; /* actual sequence number in alignment */ in vrna_sc_add_SHAPE_deigan_ali()
443 char *tmp_seq = vrna_seq_ungapped(vc->sequences[shape_file_association[s]]); in vrna_sc_add_SHAPE_deigan_ali()
446 shape_file_association[s] + 1); in vrna_sc_add_SHAPE_deigan_ali()
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| H A D | SHAPE.h | 33 const int *shape_file_association,
81 const int *shape_file_association,
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| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/ |
| H A D | constraints_SHAPE.i | 28 std::vector<int> shape_file_association,
36 …d_SHAPE_deigan_ali($self, (const char **) &vc[0], (const int *) &shape_file_association[0], m, b, …
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| H A D | constraints_SHAPE.dox | 9 …( vrna_fold_compound_t *vc, const char **shape_files, const int *shape_file_association, double m,…
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| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Perl/ |
| H A D | RNA_wrap.cpp | 7543 … *self,std::vector< std::string > shape_files,std::vector< int > shape_file_association,double m,d… in vrna_fold_compound_t_sc_add_SHAPE_deigan_ali__SWIG_0() argument
7547 …dd_SHAPE_deigan_ali(self, (const char **) &vc[0], (const int *) &shape_file_association[0], m, b, … in vrna_fold_compound_t_sc_add_SHAPE_deigan_ali__SWIG_0()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python/ |
| H A D | RNA_wrap.cpp | 12020 …:string > > shape_files,std::vector< int,std::allocator< int > > shape_file_association,double m,d… in vrna_fold_compound_t_sc_add_SHAPE_deigan_ali() argument
12024 …dd_SHAPE_deigan_ali(self, (const char **) &vc[0], (const int *) &shape_file_association[0], m, b, … in vrna_fold_compound_t_sc_add_SHAPE_deigan_ali()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python3/ |
| H A D | RNA_wrap.cpp | 12157 …:string > > shape_files,std::vector< int,std::allocator< int > > shape_file_association,double m,d… in vrna_fold_compound_t_sc_add_SHAPE_deigan_ali() argument
12161 …dd_SHAPE_deigan_ali(self, (const char **) &vc[0], (const int *) &shape_file_association[0], m, b, … in vrna_fold_compound_t_sc_add_SHAPE_deigan_ali()
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