--- /dev/null
+#ifndef __VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H__
+#define __VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H__
+
+#include "energy_const.h"
+/**
+ * \file data_structures.h
+ * \brief All datastructures and typedefs shared among the Vienna RNA Package can be found here
+ */
+
+/* to use floats instead of doubles in pf_fold() comment next line */
+#define LARGE_PF
+#ifdef LARGE_PF
+#define FLT_OR_DBL double
+#else
+#define FLT_OR_DBL float
+#endif
+
+#ifndef NBASES
+#define NBASES 8
+#endif
+
+#ifndef MAXALPHA
+/**
+ * \brief Maximal length of alphabet
+ */
+#define MAXALPHA 20
+#endif
+
+/**
+ * \brief Maximum density of states discretization for subopt
+ */
+#define MAXDOS 1000
+
+#define VRNA_GQUAD_MAX_STACK_SIZE 7
+#define VRNA_GQUAD_MIN_STACK_SIZE 2
+#define VRNA_GQUAD_MAX_LINKER_LENGTH 15
+#define VRNA_GQUAD_MIN_LINKER_LENGTH 1
+#define VRNA_GQUAD_MIN_BOX_SIZE ((4*VRNA_GQUAD_MIN_STACK_SIZE)+(3*VRNA_GQUAD_MIN_LINKER_LENGTH))
+#define VRNA_GQUAD_MAX_BOX_SIZE ((4*VRNA_GQUAD_MAX_STACK_SIZE)+(3*VRNA_GQUAD_MAX_LINKER_LENGTH))
+
+
+/*
+* ############################################################
+* Here are the type definitions of various datastructures
+* shared among the Vienna RNA Package
+* ############################################################
+*/
+
+/**
+ * \brief this datastructure is used as input parameter in functions of PS_dot.h and others
+ */
+typedef struct plist {
+ int i;
+ int j;
+ float p;
+ int type;
+} plist;
+
+/**
+ * \brief this datastructure is used as input parameter in functions of PS_dot.c
+ */
+typedef struct cpair {
+ int i,j,mfe;
+ float p, hue, sat;
+} cpair;
+
+/**
+ * \brief this is a workarround for the SWIG Perl Wrapper RNA plot function
+ * that returns an array of type COORDINATE
+ */
+typedef struct {
+ float X; /* X coords */
+ float Y; /* Y coords */
+} COORDINATE;
+
+/**
+ * \brief Stack of partial structures for backtracking
+ */
+typedef struct sect {
+ int i;
+ int j;
+ int ml;
+} sect;
+
+/**
+ * \brief Base pair
+ */
+typedef struct bondT {
+ unsigned int i;
+ unsigned int j;
+} bondT;
+
+/**
+ * \brief Base pair with associated energy
+ */
+typedef struct bondTEn {
+ int i;
+ int j;
+ int energy;
+} bondTEn;
+
+/**
+ * \brief The data structure that contains the complete model details used throughout the calculations
+ *
+ */
+typedef struct{
+ int dangles; /**< \brief Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
+ \note Some function do not implement all dangle model but only a subset of
+ (0,1,2,3). Read the documentaion of the particular recurrences or
+ energy evaluation function for information about the provided dangle
+ model.
+ */
+ int special_hp; /**< \brief Include special hairpin contributions for tri, tetra and hexaloops */
+ int noLP; /**< \brief Only consider canonical structures, i.e. no 'lonely' base pairs */
+ int noGU; /**< \brief Do not allow GU pairs */
+ int noGUclosure; /**< \brief Do not allow loops to be closed by GU pair */
+ int logML; /**< \brief Use logarithmic scaling for multi loops */
+ int circ; /**< \brief Assume molecule to be circular */
+ int gquad; /**< \brief Include G-quadruplexes in structure prediction */
+} model_detailsT;
+
+/**
+ * \brief The datastructure that contains temperature scaled energy parameters.
+ */
+typedef struct{
+ int id;
+ int stack[NBPAIRS+1][NBPAIRS+1];
+ int hairpin[31];
+ int bulge[MAXLOOP+1];
+ int internal_loop[MAXLOOP+1];
+ int mismatchExt[NBPAIRS+1][5][5];
+ int mismatchI[NBPAIRS+1][5][5];
+ int mismatch1nI[NBPAIRS+1][5][5];
+ int mismatch23I[NBPAIRS+1][5][5];
+ int mismatchH[NBPAIRS+1][5][5];
+ int mismatchM[NBPAIRS+1][5][5];
+ int dangle5[NBPAIRS+1][5];
+ int dangle3[NBPAIRS+1][5];
+ int int11[NBPAIRS+1][NBPAIRS+1][5][5];
+ int int21[NBPAIRS+1][NBPAIRS+1][5][5][5];
+ int int22[NBPAIRS+1][NBPAIRS+1][5][5][5][5];
+ int ninio[5];
+ double lxc;
+ int MLbase;
+ int MLintern[NBPAIRS+1];
+ int MLclosing;
+ int TerminalAU;
+ int DuplexInit;
+ int Tetraloop_E[200];
+ char Tetraloops[1401];
+ int Triloop_E[40];
+ char Triloops[241];
+ int Hexaloop_E[40];
+ char Hexaloops[1801];
+ int TripleC;
+ int MultipleCA;
+ int MultipleCB;
+ int gquad [VRNA_GQUAD_MAX_STACK_SIZE + 1]
+ [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
+
+ double temperature; /**< \brief Temperature used for loop contribution scaling */
+
+ model_detailsT model_details; /**< \brief Model details to be used in the recursions */
+
+} paramT;
+
+/**
+ * \brief The datastructure that contains temperature scaled Boltzmann weights of the energy parameters.
+ */
+typedef struct{
+ int id;
+ double expstack[NBPAIRS+1][NBPAIRS+1];
+ double exphairpin[31];
+ double expbulge[MAXLOOP+1];
+ double expinternal[MAXLOOP+1];
+ double expmismatchExt[NBPAIRS+1][5][5];
+ double expmismatchI[NBPAIRS+1][5][5];
+ double expmismatch23I[NBPAIRS+1][5][5];
+ double expmismatch1nI[NBPAIRS+1][5][5];
+ double expmismatchH[NBPAIRS+1][5][5];
+ double expmismatchM[NBPAIRS+1][5][5];
+ double expdangle5[NBPAIRS+1][5];
+ double expdangle3[NBPAIRS+1][5];
+ double expint11[NBPAIRS+1][NBPAIRS+1][5][5];
+ double expint21[NBPAIRS+1][NBPAIRS+1][5][5][5];
+ double expint22[NBPAIRS+1][NBPAIRS+1][5][5][5][5];
+ double expninio[5][MAXLOOP+1];
+ double lxc;
+ double expMLbase;
+ double expMLintern[NBPAIRS+1];
+ double expMLclosing;
+ double expTermAU;
+ double expDuplexInit;
+ double exptetra[40];
+ double exptri[40];
+ double exphex[40];
+ char Tetraloops[1401];
+ double expTriloop[40];
+ char Triloops[241];
+ char Hexaloops[1801];
+ double expTripleC;
+ double expMultipleCA;
+ double expMultipleCB;
+ double expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]
+ [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
+
+ double kT;
+ double pf_scale; /**< \brief Scaling factor to avoid over-/underflows */
+
+ double temperature; /**< \brief Temperature used for loop contribution scaling */
+ double alpha; /**< \brief Scaling factor for the thermodynamic temperature
+ \details This allows for temperature scaling in Boltzmann
+ factors independently from the energy contributions.
+ The resulting Boltzmann factors are then computed by
+ \f$ e^{-E/(\alpha \cdot K \cdot T)} \f$
+ */
+
+ model_detailsT model_details; /**< \brief Model details to be used in the recursions */
+
+} pf_paramT;
+
+
+
+/*
+* ############################################################
+* SUBOPT data structures
+* ############################################################
+*/
+
+
+/**
+ * \brief Base pair data structure used in subopt.c
+ */
+typedef struct {
+ int i;
+ int j;
+} PAIR;
+
+/**
+ * \brief Sequence interval stack element used in subopt.c
+ */
+typedef struct {
+ int i;
+ int j;
+ int array_flag;
+} INTERVAL;
+
+/**
+ * \brief Solution element from subopt.c
+ */
+typedef struct {
+ float energy; /**< \brief Free Energy of structure in kcal/mol */
+ char *structure; /**< \brief Structure in dot-bracket notation */
+} SOLUTION;
+
+/*
+* ############################################################
+* COFOLD data structures
+* ############################################################
+*/
+
+/**
+ * \brief
+ */
+typedef struct cofoldF {
+ /* free energies for: */
+ double F0AB; /**< \brief Null model without DuplexInit */
+ double FAB; /**< \brief all states with DuplexInit correction */
+ double FcAB; /**< \brief true hybrid states only */
+ double FA; /**< \brief monomer A */
+ double FB; /**< \brief monomer B */
+} cofoldF;
+
+/**
+ * \brief
+ */
+typedef struct ConcEnt {
+ double A0; /**< \brief start concentration A */
+ double B0; /**< \brief start concentration B */
+ double ABc; /**< \brief End concentration AB */
+ double AAc;
+ double BBc;
+ double Ac;
+ double Bc;
+} ConcEnt;
+
+/**
+ * \brief
+ */
+typedef struct pairpro{
+ struct plist *AB;
+ struct plist *AA;
+ struct plist *A;
+ struct plist *B;
+ struct plist *BB;
+}pairpro;
+
+/**
+ * \brief A base pair info structure
+ *
+ * For each base pair (i,j) with i,j in [0, n-1] the structure lists:
+ * - its probability 'p'
+ * - an entropy-like measure for its well-definedness 'ent'
+ * - the frequency of each type of pair in 'bp[]'
+ * + 'bp[0]' contains the number of non-compatible sequences
+ * + 'bp[1]' the number of CG pairs, etc.
+ */
+typedef struct {
+ unsigned i; /**< \brief nucleotide position i */
+ unsigned j; /**< \brief nucleotide position j */
+ float p; /**< \brief Probability */
+ float ent; /**< \brief Pseudo entropy for \f$ p(i,j) = S_i + S_j - p_ij*ln(p_ij) \f$ */
+ short bp[8]; /**< \brief Frequencies of pair_types */
+ char comp; /**< \brief 1 iff pair is in mfe structure */
+} pair_info;
+
+
+/*
+* ############################################################
+* FINDPATH data structures
+* ############################################################
+*/
+
+/**
+ * \brief
+ */
+typedef struct move {
+ int i; /* i,j>0 insert; i,j<0 delete */
+ int j;
+ int when; /* 0 if still available, else resulting distance from start */
+ int E;
+} move_t;
+
+/**
+ * \brief
+ */
+typedef struct intermediate {
+ short *pt; /**< \brief pair table */
+ int Sen; /**< \brief saddle energy so far */
+ int curr_en; /**< \brief current energy */
+ move_t *moves; /**< \brief remaining moves to target */
+} intermediate_t;
+
+/**
+ * \brief
+ */
+typedef struct path {
+ double en;
+ char *s;
+} path_t;
+
+/*
+* ############################################################
+* RNAup data structures
+* ############################################################
+*/
+
+/**
+ * \brief contributions to p_u
+ */
+typedef struct pu_contrib {
+ double **H; /**< \brief hairpin loops */
+ double **I; /**< \brief interior loops */
+ double **M; /**< \brief multi loops */
+ double **E; /**< \brief exterior loop */
+ int length; /**< \brief length of the input sequence */
+ int w; /**< \brief longest unpaired region */
+} pu_contrib;
+
+/**
+ * \brief
+ */
+typedef struct interact {
+ double *Pi; /**< \brief probabilities of interaction */
+ double *Gi; /**< \brief free energies of interaction */
+ double Gikjl; /**< \brief full free energy for interaction between [k,i] k<i
+ in longer seq and [j,l] j<l in shorter seq */
+ double Gikjl_wo; /**< \brief Gikjl without contributions for prob_unpaired */
+ int i; /**< \brief k<i in longer seq */
+ int k; /**< \brief k<i in longer seq */
+ int j; /**< \brief j<l in shorter seq */
+ int l; /**< \brief j<l in shorter seq */
+ int length; /**< \brief length of longer sequence */
+} interact;
+
+/**
+ * \brief Collection of all free_energy of beeing unpaired values for output
+ */
+typedef struct pu_out {
+ int len; /**< \brief sequence length */
+ int u_vals; /**< \brief number of different -u values */
+ int contribs; /**< \brief [-c "SHIME"] */
+ char **header; /**< \brief header line */
+ double **u_values; /**< \brief (the -u values * [-c "SHIME"]) * seq len */
+} pu_out;
+
+/**
+ * \brief constraints for cofolding
+ */
+typedef struct constrain{
+ int *indx;
+ char *ptype;
+} constrain;
+
+/*
+* ############################################################
+* RNAduplex data structures
+* ############################################################
+*/
+
+/**
+ * \brief
+ */
+typedef struct {
+ int i;
+ int j;
+ int end;
+ char *structure;
+ double energy;
+ double energy_backtrack;
+ double opening_backtrack_x;
+ double opening_backtrack_y;
+ int offset;
+ double dG1;
+ double dG2;
+ double ddG;
+ int tb;
+ int te;
+ int qb;
+ int qe;
+} duplexT;
+
+/*
+* ############################################################
+* RNAsnoop data structures
+* ############################################################
+*/
+
+/**
+ * \brief
+ */
+typedef struct node {
+ int k;
+ int energy;
+ struct node *next;
+} folden;
+
+/**
+ * \brief
+ */
+typedef struct {
+ int i;
+ int j;
+ int u;
+ char *structure;
+ float energy;
+ float Duplex_El;
+ float Duplex_Er;
+ float Loop_E;
+ float Loop_D;
+ float pscd;
+ float psct;
+ float pscg;
+ float Duplex_Ol;
+ float Duplex_Or;
+ float Duplex_Ot;
+ float fullStemEnergy;
+} snoopT;
+
+
+
+
+
+
+
+/*
+* ############################################################
+* PKplex data structures
+* ############################################################
+*/
+
+/**
+ * \brief
+ */
+typedef struct dupVar{
+ int i;
+ int j;
+ int end;
+ char *pk_helix;
+ char *structure;
+ double energy;
+ int offset;
+ double dG1;
+ double dG2;
+ double ddG;
+ int tb;
+ int te;
+ int qb;
+ int qe;
+ int inactive;
+ int processed;
+} dupVar;
+
+
+
+/*
+* ############################################################
+* 2Dfold data structures
+* ############################################################
+*/
+
+/**
+ * \brief Solution element returned from TwoDfoldList
+ *
+ * This element contains free energy and structure for the appropriate
+ * kappa (k), lambda (l) neighborhood
+ * The datastructure contains two integer attributes 'k' and 'l'
+ * as well as an attribute 'en' of type float representing the free energy
+ * in kcal/mol and an attribute 's' of type char* containg the secondary
+ * structure representative,
+ *
+ * A value of #INF in k denotes the end of a list
+ *
+ * \see TwoDfoldList()
+ */
+typedef struct{
+ int k; /**< \brief Distance to first reference */
+ int l; /**< \brief Distance to second reference */
+ float en; /**< \brief Free energy in kcal/mol */
+ char *s; /**< \brief MFE representative structure in dot-bracket notation */
+} TwoDfold_solution;
+
+/**
+ * \brief Variables compound for 2Dfold MFE folding
+ *
+ * \see get_TwoDfold_variables(), destroy_TwoDfold_variables(), TwoDfoldList()
+ */
+typedef struct{
+ paramT *P; /**< \brief Precomputed energy parameters and model details */
+ int do_backtrack; /**< \brief Flag whether to do backtracing of the structure(s) or not */
+ char *ptype; /**< \brief Precomputed array of pair types */
+ char *sequence; /**< \brief The input sequence */
+ short *S, *S1; /**< \brief The input sequences in numeric form */
+ unsigned int maxD1; /**< \brief Maximum allowed base pair distance to first reference */
+ unsigned int maxD2; /**< \brief Maximum allowed base pair distance to second reference */
+
+
+ unsigned int *mm1; /**< \brief Maximum matching matrix, reference struct 1 disallowed */
+ unsigned int *mm2; /**< \brief Maximum matching matrix, reference struct 2 disallowed */
+
+ int *my_iindx; /**< \brief Index for moving in quadratic distancy dimensions */
+
+ double temperature;
+
+ unsigned int *referenceBPs1; /**< \brief Matrix containing number of basepairs of reference structure1 in interval [i,j] */
+ unsigned int *referenceBPs2; /**< \brief Matrix containing number of basepairs of reference structure2 in interval [i,j] */
+ unsigned int *bpdist; /**< \brief Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j] */
+
+ short *reference_pt1;
+ short *reference_pt2;
+ int circ;
+ int dangles;
+ unsigned int seq_length;
+
+ int ***E_F5;
+ int ***E_F3;
+ int ***E_C;
+ int ***E_M;
+ int ***E_M1;
+ int ***E_M2;
+
+ int **E_Fc;
+ int **E_FcH;
+ int **E_FcI;
+ int **E_FcM;
+
+ int **l_min_values;
+ int **l_max_values;
+ int *k_min_values;
+ int *k_max_values;
+
+ int **l_min_values_m;
+ int **l_max_values_m;
+ int *k_min_values_m;
+ int *k_max_values_m;
+
+ int **l_min_values_m1;
+ int **l_max_values_m1;
+ int *k_min_values_m1;
+ int *k_max_values_m1;
+
+ int **l_min_values_f;
+ int **l_max_values_f;
+ int *k_min_values_f;
+ int *k_max_values_f;
+
+ int **l_min_values_f3;
+ int **l_max_values_f3;
+ int *k_min_values_f3;
+ int *k_max_values_f3;
+
+ int **l_min_values_m2;
+ int **l_max_values_m2;
+ int *k_min_values_m2;
+ int *k_max_values_m2;
+
+ int *l_min_values_fc;
+ int *l_max_values_fc;
+ int k_min_values_fc;
+ int k_max_values_fc;
+
+ int *l_min_values_fcH;
+ int *l_max_values_fcH;
+ int k_min_values_fcH;
+ int k_max_values_fcH;
+
+ int *l_min_values_fcI;
+ int *l_max_values_fcI;
+ int k_min_values_fcI;
+ int k_max_values_fcI;
+
+ int *l_min_values_fcM;
+ int *l_max_values_fcM;
+ int k_min_values_fcM;
+ int k_max_values_fcM;
+
+ /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */
+ int *E_F5_rem;
+ int *E_F3_rem;
+ int *E_C_rem;
+ int *E_M_rem;
+ int *E_M1_rem;
+ int *E_M2_rem;
+
+ int E_Fc_rem;
+ int E_FcH_rem;
+ int E_FcI_rem;
+ int E_FcM_rem;
+
+#ifdef COUNT_STATES
+ unsigned long ***N_F5;
+ unsigned long ***N_C;
+ unsigned long ***N_M;
+ unsigned long ***N_M1;
+#endif
+} TwoDfold_vars;
+
+/**
+ * \brief Solution element returned from TwoDpfoldList
+ *
+ * This element contains the partition function for the appropriate
+ * kappa (k), lambda (l) neighborhood
+ * The datastructure contains two integer attributes 'k' and 'l'
+ * as well as an attribute 'q' of type #FLT_OR_DBL
+ *
+ * A value of #INF in k denotes the end of a list
+ *
+ * \see TwoDpfoldList()
+ */
+typedef struct{
+ int k; /**< \brief Distance to first reference */
+ int l; /**< \brief Distance to second reference */
+ FLT_OR_DBL q; /**< \brief partition function */
+} TwoDpfold_solution;
+
+/**
+ * \brief Variables compound for 2Dfold partition function folding
+ *
+ * \see get_TwoDpfold_variables(), get_TwoDpfold_variables_from_MFE(),
+ * destroy_TwoDpfold_variables(), TwoDpfoldList()
+ */
+typedef struct{
+
+ unsigned int alloc;
+ char *ptype; /**< \brief Precomputed array of pair types */
+ char *sequence; /**< \brief The input sequence */
+ short *S, *S1; /**< \brief The input sequences in numeric form */
+ unsigned int maxD1; /**< \brief Maximum allowed base pair distance to first reference */
+ unsigned int maxD2; /**< \brief Maximum allowed base pair distance to second reference */
+
+ double temperature; /* temperature in last call to scale_pf_params */
+ double init_temp; /* temperature in last call to scale_pf_params */
+ FLT_OR_DBL *scale;
+ FLT_OR_DBL pf_scale;
+ pf_paramT *pf_params; /* holds all [unscaled] pf parameters */
+
+ int *my_iindx; /**< \brief Index for moving in quadratic distancy dimensions */
+ int *jindx; /**< \brief Index for moving in the triangular matrix qm1 */
+
+ short *reference_pt1;
+ short *reference_pt2;
+
+ unsigned int *referenceBPs1; /**< \brief Matrix containing number of basepairs of reference structure1 in interval [i,j] */
+ unsigned int *referenceBPs2; /**< \brief Matrix containing number of basepairs of reference structure2 in interval [i,j] */
+ unsigned int *bpdist; /**< \brief Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j] */
+
+ unsigned int *mm1; /**< \brief Maximum matching matrix, reference struct 1 disallowed */
+ unsigned int *mm2; /**< \brief Maximum matching matrix, reference struct 2 disallowed */
+
+ int circ;
+ int dangles;
+ unsigned int seq_length;
+
+ FLT_OR_DBL ***Q;
+ FLT_OR_DBL ***Q_B;
+ FLT_OR_DBL ***Q_M;
+ FLT_OR_DBL ***Q_M1;
+ FLT_OR_DBL ***Q_M2;
+
+ FLT_OR_DBL **Q_c;
+ FLT_OR_DBL **Q_cH;
+ FLT_OR_DBL **Q_cI;
+ FLT_OR_DBL **Q_cM;
+
+ int **l_min_values;
+ int **l_max_values;
+ int *k_min_values;
+ int *k_max_values;
+
+ int **l_min_values_b;
+ int **l_max_values_b;
+ int *k_min_values_b;
+ int *k_max_values_b;
+
+ int **l_min_values_m;
+ int **l_max_values_m;
+ int *k_min_values_m;
+ int *k_max_values_m;
+
+ int **l_min_values_m1;
+ int **l_max_values_m1;
+ int *k_min_values_m1;
+ int *k_max_values_m1;
+
+ int **l_min_values_m2;
+ int **l_max_values_m2;
+ int *k_min_values_m2;
+ int *k_max_values_m2;
+
+ int *l_min_values_qc;
+ int *l_max_values_qc;
+ int k_min_values_qc;
+ int k_max_values_qc;
+
+ int *l_min_values_qcH;
+ int *l_max_values_qcH;
+ int k_min_values_qcH;
+ int k_max_values_qcH;
+
+ int *l_min_values_qcI;
+ int *l_max_values_qcI;
+ int k_min_values_qcI;
+ int k_max_values_qcI;
+
+ int *l_min_values_qcM;
+ int *l_max_values_qcM;
+ int k_min_values_qcM;
+ int k_max_values_qcM;
+
+ /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */
+ FLT_OR_DBL *Q_rem;
+ FLT_OR_DBL *Q_B_rem;
+ FLT_OR_DBL *Q_M_rem;
+ FLT_OR_DBL *Q_M1_rem;
+ FLT_OR_DBL *Q_M2_rem;
+
+ FLT_OR_DBL Q_c_rem;
+ FLT_OR_DBL Q_cH_rem;
+ FLT_OR_DBL Q_cI_rem;
+ FLT_OR_DBL Q_cM_rem;
+
+} TwoDpfold_vars;
+
+#endif
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