| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/ |
| H A D | model_details.i | 29 int uniq_ML; member
70 const int uniq_ML = vrna_md_defaults_uniq_ML_get(),
96 md->uniq_ML = uniq_ML;
154 out << ", uniq_ML: " << $self->uniq_ML ; in __str__()
216 extern int uniq_ML;
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| H A D | model_details.dox | 38 | uniq_ML | vrna_md_defaults_uniq_ML_get() | vrna_md_defaults_uniq_ML() |
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| /dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/ |
| H A D | model.c | 58 int uniq_ML = VRNA_MODEL_DEFAULT_UNIQ_ML; variable
322 defaults.uniq_ML = VRNA_MODEL_DEFAULT_UNIQ_ML; in vrna_md_defaults_reset()
356 vrna_md_defaults_uniq_ML(md_p->uniq_ML); in vrna_md_defaults_reset()
388 uniq_ML = defaults.uniq_ML; in vrna_md_defaults_reset()
601 defaults.uniq_ML = flag ? 1 : 0; in vrna_md_defaults_uniq_ML()
603 uniq_ML = defaults.uniq_ML; in vrna_md_defaults_uniq_ML()
611 return defaults.uniq_ML; in vrna_md_defaults_uniq_ML_get()
980 md->uniq_ML = uniq_ML; in set_model_details()
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| H A D | model.h | 215 …int uniq_ML; /**< @brief Flag to ensure unique multi-branch loop de… member
837 extern int uniq_ML;
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| H A D | cofold.c | 195 int uniq_ML; in fill_arrays() local
218 uniq_ML = P->model_details.uniq_ML; in fill_arrays()
254 if (uniq_ML) in fill_arrays()
322 if (uniq_ML) /* compute fM1 for unique decomposition */ in fill_arrays()
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| H A D | mfe.c | 278 int i, j, ij, length, turn, uniq_ML, *indx, *f5, *c, *fML, *fM1; in fill_arrays() local
287 uniq_ML = P->model_details.uniq_ML; in fill_arrays()
310 if (uniq_ML) in fill_arrays()
334 if (uniq_ML) in fill_arrays()
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| H A D | fold_compound.c | 450 md.uniq_ML = 1; in vrna_fold_compound_TwoD()
538 fc->exp_params->model_details.uniq_ML = 1; in vrna_fold_compound_prepare()
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| H A D | subopt.c | 865 if (md->uniq_ML != 1) /* failsafe mechanism to enforce valid fM1 array */ in vrna_subopt_cb()
866 md->uniq_ML = 1; in vrna_subopt_cb()
2394 P->model_details.uniq_ML = uniq_ML = 1; in wrap_subopt()
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| H A D | dp_matrices.c | 679 md_p->uniq_ML = 1; /* we need unique ML arrays for circular folding */ in get_mx_alloc_vector()
684 if (md_p->uniq_ML) in get_mx_alloc_vector()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/examples/Python/ |
| H A D | subopt.py | 6 RNA.cvar.uniq_ML = 1
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| H A D | boltzmann_sampling.py | 22 md.uniq_ML = 1
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| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python3/ |
| H A D | globals-md.i | 119 %typemap(varin) int uniq_ML {
123 %typemap(varout) int uniq_ML {
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| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python/ |
| H A D | globals-md.i | 119 %typemap(varin) int uniq_ML {
123 %typemap(varout) int uniq_ML {
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| /dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Perl/ |
| H A D | globals-md.i | 118 %typemap(varin) int uniq_ML {
122 %typemap(varout) int uniq_ML {
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| /dports/biology/viennarna/ViennaRNA-2.4.18/tests/perl5/ |
| H A D | test-RNA-callbacks.pl | 84 $RNA::uniq_ML = 1; # for subopt calls
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| H A D | test-RNA-boltzmann-sampling.pl | 18 $md->{uniq_ML} = 1;
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| /dports/biology/viennarna/ViennaRNA-2.4.18/tests/ |
| H A D | fold.c | 50 md.uniq_ML = 1; in START_TEST()
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| H A D | fold.ts | 40 md.uniq_ML = 1;
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| /dports/biology/viennarna/ViennaRNA-2.4.18/src/bin/ |
| H A D | RNApvmin.c | 225 md.uniq_ML = 1; in main()
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| H A D | RNAsubopt.c | 102 md.uniq_ML = 1; in main()
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| H A D | RNAalifold.c | 434 opt.md.uniq_ML = 1; in main()
442 opt.md.uniq_ML = 1; in main()
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| H A D | RNAdos.c | 745 md.uniq_ML = 1; in main()
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| H A D | RNAfold.c | 455 opt.md.uniq_ML = opt.lucky = opt.pf = st_back = 1; in main()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/tests/python/ |
| H A D | test-RNA-boltzmann-sampling.py | 17 md.uniq_ML = 1
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| /dports/biology/viennarna/ViennaRNA-2.4.18/tests/python3/ |
| H A D | test-RNA-boltzmann-sampling.py3 | 17 md.uniq_ML = 1
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