LocARNA-1.9.2: src/LocARNA/ext_rna

00001 #ifndef LOCARNA_EXT_RNA_DATA_HH
00002 #define LOCARNA_EXT_RNA_DATA_HH
00003 
00004 #ifdef HAVE_CONFIG_H
00005 #include <config.h>
00006 #endif
00007 
00008 #include <iosfwd>
00009 #include "aux.hh"
00010 #include "sparse_matrix.hh"
00011 #include "rna_data.hh"
00012 
00013 namespace LocARNA {
00014 
00015     class RnaEnsemble;
00016     class ExtRnaDataImpl;
00017     class PFoldParams;
00018     class RnaStructure;
00019 
00036     class ExtRnaData : public RnaData {
00037     private:
00038         friend class ExtRnaDataImpl;
00039         ExtRnaDataImpl
00040             *ext_pimpl_; 
00041     public:
00054         ExtRnaData(const RnaEnsemble &rna_ensemble,
00055                    double p_bpcut,
00056                    double p_bpilcut,
00057                    double p_uilcut,
00058                    double max_bps_length_ratio,
00059                    double max_uil_length_ratio,
00060                    double max_bpil_length_ratio,
00061                    const PFoldParams &pfoldparams);
00062 
00075         ExtRnaData(const std::string &filename,
00076                    double p_bpcut,
00077                    double p_bpilcut,
00078                    double p_uilcut,
00079                    double max_bps_length_ratio,
00080                    double max_uil_length_ratio,
00081                    double max_bpil_length_ratio,
00082                    const PFoldParams &pfoldparams);
00083 
00084     private:
00088         ExtRnaData(const ExtRnaData &);
00089 
00090     public:
00094         ~ExtRnaData();
00095 
00096     private:
00100         ExtRnaData &
00101         operator=(const ExtRnaData &);
00102 
00103     public:
00108         double
00109         arc_in_loop_cutoff_prob() const;
00110 
00121         double
00122         arc_in_loop_prob(pos_type i, pos_type j, pos_type p, pos_type q) const;
00123 
00132         double
00133         arc_external_prob(pos_type i, pos_type j) const;
00134 
00139         double
00140         unpaired_in_loop_cutoff_prob() const;
00141 
00151         double
00152         unpaired_in_loop_prob(pos_type k, pos_type p, pos_type q) const;
00153 
00161         double
00162         unpaired_external_prob(pos_type k) const;
00163 
00171         std::ostream &
00172         write_size_info(std::ostream &out) const;
00173 
00188         std::ostream &
00189         write_pp(std::ostream &out,
00190                  double p_outbpcut = 0,
00191                  double p_outbpilcut = 0,
00192                  double p_outuilcut = 0) const;
00193 
00194     protected:
00202         virtual std::istream &
00203         read_pp(std::istream &in);
00204 
00214         virtual void
00215         init_from_fixed_structure(const RnaStructure &structure,
00216                                   const PFoldParams &pfoldparams);
00217 
00229         virtual void
00230         init_from_rna_ensemble(const RnaEnsemble &rna_ensemble,
00231                                const PFoldParams &pfoldparams);
00232 
00241         virtual bool
00242         inloopprobs_ok() const;
00243 
00244     }; // end class ExtRnaData
00245 }
00246 
00247 #endif // LOCARNA_EXT_RNA_DATA_HH