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LocARNA-1.9.2
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LocARNA-1.9.2
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00001 #ifndef LOCARNA_EXT_RNA_DATA_IMPL_HH 00002 #define LOCARNA_EXT_RNA_DATA_IMPL_HH 00003 00004 #ifdef HAVE_CONFIG_H 00005 #include <config.h> 00006 #endif 00007 00008 #include <iosfwd> 00009 #include "ext_rna_data.hh" 00010 #include "sequence.hh" 00011 #include "sparse_vector.hh" 00012 00013 namespace LocARNA { 00014 00015 // class Sequence; 00016 // class RnaEnsemble; 00017 // class PFoldParams; 00018 00022 class ExtRnaDataImpl { 00023 public: 00024 // ---------------------------------------- 00025 // TYPES 00026 00028 typedef SparseVector<double> arc_prob_vector_t; 00029 00031 typedef RnaDataImpl::arc_prob_matrix_t arc_prob_matrix_t; 00032 00034 typedef SparseMatrix<arc_prob_vector_t> arc_prob_vector_matrix_t; 00035 00037 typedef SparseMatrix<arc_prob_matrix_t> arc_prob_matrix_matrix_t; 00038 00039 // ---------------------------------------- 00040 // ATTRIBUTES 00041 00042 ExtRnaData *self_; 00043 00045 double p_bpilcut_; 00046 00048 double p_uilcut_; 00049 00051 arc_prob_matrix_matrix_t arc_in_loop_probs_; 00052 00054 arc_prob_vector_matrix_t unpaired_in_loop_probs_; 00055 00058 bool has_in_loop_probs_; 00059 00060 // ---------------------------------------- 00061 // CONSTRUCTORS 00062 00073 ExtRnaDataImpl(ExtRnaData *self, double p_bpilcut, double p_uilcut); 00074 00075 // ---------------------------------------- 00076 // METHODS 00077 00078 private: 00083 void 00084 init_fixed_unpaired_in_loop(size_t i, 00085 size_t j, 00086 const RnaStructure &structure); 00091 void 00092 init_fixed_basepairs_in_loop(size_t i, 00093 size_t j, 00094 const RnaStructure &structure); 00095 00096 public: 00106 void 00107 init_from_fixed_structure(const RnaStructure &structure); 00108 00118 void 00119 init_from_ext_rna_ensemble(const RnaEnsemble &rna_ensemble); 00120 00131 std::istream & 00132 read_pp_in_loop_probabilities(std::istream &in); 00133 00140 void 00141 read_pp_in_loop_probabilities_kwline(const std::string &line); 00142 00149 void 00150 read_pp_in_loop_probabilities_line(const std::string &line); 00151 00162 std::ostream & 00163 write_pp_in_loop_probabilities(std::ostream &out, 00164 double p_outbpcut, 00165 double p_outbpilcut, 00166 double p_outuilcut) const; 00167 00179 std::ostream & 00180 write_pp_in_loop_probability_line(std::ostream &out, 00181 size_t i, 00182 size_t j, 00183 double p_bpcut, 00184 double p_ucut) const; 00194 std::ostream & 00195 write_pp_basepair_in_loop_probabilities(std::ostream &out, 00196 const arc_prob_matrix_t &probs, 00197 double p_cut) const; 00198 00208 std::ostream & 00209 write_pp_unpaired_in_loop_probabilities(std::ostream &out, 00210 const arc_prob_vector_t &probs, 00211 double p_cut) const; 00212 00218 void 00219 drop_worst_bps(size_t keep); 00220 00227 void 00228 drop_worst_uil(size_t keep); 00229 00235 void 00236 drop_worst_bpil(size_t keep); 00237 00245 void 00246 drop_worst_bpil_precise(double ratio); 00247 00248 }; // end ExtRnaDataImpl 00249 00250 } // end namespace LocARNA 00251 00252 #endif // LOCARNA_EXT_RNA_DATA_IMPL_HH
1.7.6.1
