/*
 *                minimum free energy
 *                RNA secondary structure prediction
 *
 *                c Ivo Hofacker, Chrisoph Flamm
 *                original implementation by
 *                Walter Fontana
 *                g-quadruplex support and threadsafety
 *                by Ronny Lorenz
 *
 *                Vienna RNA package
 */

#ifdef HAVE_CONFIG_H
#include "config.h"
#endif

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <ctype.h>
#include <string.h>
#include <limits.h>

#include "ViennaRNA/utils/basic.h"
#include "ViennaRNA/params/default.h"
#include "ViennaRNA/datastructures/basic.h"
#include "ViennaRNA/fold_vars.h"
#include "ViennaRNA/params/basic.h"
#include "ViennaRNA/constraints/hard.h"
#include "ViennaRNA/constraints/soft.h"
#include "ViennaRNA/gquad.h"
#include "ViennaRNA/loops/all.h"
#include "ViennaRNA/fold.h"

#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

#ifdef _OPENMP
#include <omp.h>
#endif

#endif

#define MAXSECTORS        500     /* dimension for a backtrack array */

/*
 #################################
 # GLOBAL VARIABLES              #
 #################################
 */

/*
 #################################
 # PRIVATE VARIABLES             #
 #################################
 */

#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

/* some backward compatibility stuff */
PRIVATE int                   backward_compat           = 0;
PRIVATE vrna_fold_compound_t  *backward_compat_compound = NULL;

#ifdef _OPENMP

#pragma omp threadprivate(backward_compat_compound, backward_compat)

#endif

#endif

/*
 #################################
 # PRIVATE FUNCTION DECLARATIONS #
 #################################
 */

#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

/* wrappers for old API compatibility */
PRIVATE float
wrap_fold(const char    *string,
          char          *structure,
          vrna_param_t  *parameters,
          int           is_constrained,
          int           is_circular);


PRIVATE void
wrap_array_export(int   **f5_p,
                  int   **c_p,
                  int   **fML_p,
                  int   **fM1_p,
                  int   **indx_p,
                  char  **ptype_p);


PRIVATE void
wrap_array_export_circ(int  *Fc_p,
                       int  *FcH_p,
                       int  *FcI_p,
                       int  *FcM_p,
                       int  **fM2_p);


#endif

/*
 #################################
 # BEGIN OF FUNCTION DEFINITIONS #
 #################################
 */

/*
 * ###########################################
 * # deprecated functions below              #
 *###########################################
 */

#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

PRIVATE void
wrap_array_export(int   **f5_p,
                  int   **c_p,
                  int   **fML_p,
                  int   **fM1_p,
                  int   **indx_p,
                  char  **ptype_p)
{
  /* make the DP arrays available to routines such as subopt() */
  if (backward_compat_compound) {
    *f5_p     = backward_compat_compound->matrices->f5;
    *c_p      = backward_compat_compound->matrices->c;
    *fML_p    = backward_compat_compound->matrices->fML;
    *fM1_p    = backward_compat_compound->matrices->fM1;
    *indx_p   = backward_compat_compound->jindx;
    *ptype_p  = backward_compat_compound->ptype;
  }
}


PRIVATE void
wrap_array_export_circ(int  *Fc_p,
                       int  *FcH_p,
                       int  *FcI_p,
                       int  *FcM_p,
                       int  **fM2_p)
{
  /* make the DP arrays available to routines such as subopt() */
  if (backward_compat_compound) {
    *Fc_p   = backward_compat_compound->matrices->Fc;
    *FcH_p  = backward_compat_compound->matrices->FcH;
    *FcI_p  = backward_compat_compound->matrices->FcI;
    *FcM_p  = backward_compat_compound->matrices->FcM;
    *fM2_p  = backward_compat_compound->matrices->fM2;
  }
}


PRIVATE float
wrap_fold(const char    *string,
          char          *structure,
          vrna_param_t  *parameters,
          int           is_constrained,
          int           is_circular)
{
  vrna_fold_compound_t  *vc;
  vrna_param_t          *P;
  float                 mfe;

#ifdef _OPENMP
  /* Explicitly turn off dynamic threads */
  omp_set_dynamic(0);
#endif

  /* we need the parameter structure for hard constraints */
  if (parameters) {
    P = vrna_params_copy(parameters);
  } else {
    vrna_md_t md;
    set_model_details(&md);
    md.temperature  = temperature;
    P               = vrna_params(&md);
  }

  P->model_details.circ = is_circular;

  vc = vrna_fold_compound(string, &(P->model_details), VRNA_OPTION_DEFAULT);

  if (parameters) {
    /* replace params if necessary */
    free(vc->params);
    vc->params = P;
  } else {
    free(P);
  }

  /* handle hard constraints in pseudo dot-bracket format if passed via simple interface */
  if (is_constrained && structure) {
    unsigned int constraint_options = 0;
    constraint_options |= VRNA_CONSTRAINT_DB
                          | VRNA_CONSTRAINT_DB_PIPE
                          | VRNA_CONSTRAINT_DB_DOT
                          | VRNA_CONSTRAINT_DB_X
                          | VRNA_CONSTRAINT_DB_ANG_BRACK
                          | VRNA_CONSTRAINT_DB_RND_BRACK;

    vrna_constraints_add(vc, (const char *)structure, constraint_options);
  }

  if (backward_compat_compound && backward_compat)
    vrna_fold_compound_free(backward_compat_compound);

  backward_compat_compound  = vc;
  backward_compat           = 1;

  /* call mfe() function without backtracking */
  mfe = vrna_mfe(vc, NULL);

  /* backtrack structure */
  if (structure && vc->params->model_details.backtrack) {
    char            *ss;
    int             length;
    sect            bt_stack[MAXSECTORS];
    vrna_bp_stack_t *bp;

    length = vc->length;
    /* add a guess of how many G's may be involved in a G quadruplex */
    bp = (vrna_bp_stack_t *)vrna_alloc(sizeof(vrna_bp_stack_t) * (4 * (1 + length / 2)));

    vrna_backtrack_from_intervals(vc, bp, bt_stack, 0);

    ss = vrna_db_from_bp_stack(bp, length);
    strncpy(structure, ss, length + 1);
    free(ss);

    if (base_pair)
      free(base_pair);

    base_pair = bp;
  }

  return mfe;
}


PUBLIC void
free_arrays(void)
{
  if (backward_compat_compound && backward_compat) {
    vrna_fold_compound_free(backward_compat_compound);
    backward_compat_compound  = NULL;
    backward_compat           = 0;
  }
}


PUBLIC float
fold_par(const char   *string,
         char         *structure,
         vrna_param_t *parameters,
         int          is_constrained,
         int          is_circular)
{
  return wrap_fold(string, structure, parameters, is_constrained, is_circular);
}


PUBLIC float
fold(const char *string,
     char       *structure)
{
  return wrap_fold(string, structure, NULL, fold_constrained, 0);
}


PUBLIC float
circfold(const char *string,
         char       *structure)
{
  return wrap_fold(string, structure, NULL, fold_constrained, 1);
}


PUBLIC void
initialize_fold(int length)
{
  /* DO NOTHING */
}


PUBLIC void
update_fold_params(void)
{
  vrna_md_t md;

  if (backward_compat_compound && backward_compat) {
    set_model_details(&md);
    vrna_params_reset(backward_compat_compound, &md);
  }
}


PUBLIC void
update_fold_params_par(vrna_param_t *parameters)
{
  vrna_md_t md;

  if (backward_compat_compound && backward_compat) {
    if (parameters) {
      vrna_params_subst(backward_compat_compound, parameters);
    } else {
      set_model_details(&md);
      vrna_params_reset(backward_compat_compound, &md);
    }
  }
}


PUBLIC void
export_fold_arrays(int  **f5_p,
                   int  **c_p,
                   int  **fML_p,
                   int  **fM1_p,
                   int  **indx_p,
                   char **ptype_p)
{
  wrap_array_export(f5_p, c_p, fML_p, fM1_p, indx_p, ptype_p);
}


PUBLIC void
export_fold_arrays_par(int          **f5_p,
                       int          **c_p,
                       int          **fML_p,
                       int          **fM1_p,
                       int          **indx_p,
                       char         **ptype_p,
                       vrna_param_t **P_p)
{
  wrap_array_export(f5_p, c_p, fML_p, fM1_p, indx_p, ptype_p);
  if (backward_compat_compound)
    *P_p = backward_compat_compound->params;
}


PUBLIC void
export_circfold_arrays(int  *Fc_p,
                       int  *FcH_p,
                       int  *FcI_p,
                       int  *FcM_p,
                       int  **fM2_p,
                       int  **f5_p,
                       int  **c_p,
                       int  **fML_p,
                       int  **fM1_p,
                       int  **indx_p,
                       char **ptype_p)
{
  wrap_array_export(f5_p, c_p, fML_p, fM1_p, indx_p, ptype_p);
  wrap_array_export_circ(Fc_p, FcH_p, FcI_p, FcM_p, fM2_p);
}


PUBLIC void
export_circfold_arrays_par(int          *Fc_p,
                           int          *FcH_p,
                           int          *FcI_p,
                           int          *FcM_p,
                           int          **fM2_p,
                           int          **f5_p,
                           int          **c_p,
                           int          **fML_p,
                           int          **fM1_p,
                           int          **indx_p,
                           char         **ptype_p,
                           vrna_param_t **P_p)
{
  wrap_array_export(f5_p, c_p, fML_p, fM1_p, indx_p, ptype_p);
  wrap_array_export_circ(Fc_p, FcH_p, FcI_p, FcM_p, fM2_p);
  if (backward_compat_compound)
    *P_p = backward_compat_compound->params;
}


PUBLIC char *
backtrack_fold_from_pair(char *sequence,
                         int  i,
                         int  j)
{
  char            *structure  = NULL;
  unsigned int    length      = 0;
  vrna_bp_stack_t *bp         = NULL;
  sect            bt_stack[MAXSECTORS]; /* stack of partial structures for backtracking */

  if (sequence) {
    length  = strlen(sequence);
    bp      = (vrna_bp_stack_t *)vrna_alloc(sizeof(vrna_bp_stack_t) * (1 + length / 2));
  } else {
    vrna_message_warning("backtrack_fold_from_pair: "
                         "no sequence given");
    return NULL;
  }

  bt_stack[1].i   = i;
  bt_stack[1].j   = j;
  bt_stack[1].ml  = 2;

  bp[0].i = 0; /* ??? this is set by backtrack anyway... */

  vrna_backtrack_from_intervals(backward_compat_compound, bp, bt_stack, 1);
  structure = vrna_db_from_bp_stack(bp, length);

  /* backward compatibitlity stuff */
  if (base_pair)
    free(base_pair);

  base_pair = bp;

  return structure;
}


#define STACK_BULGE1      1       /* stacking energies for bulges of size 1 */
#define NEW_NINIO         1       /* new asymetry penalty */

PUBLIC int
HairpinE(int        size,
         int        type,
         int        si1,
         int        sj1,
         const char *string)
{
  vrna_param_t  *P = backward_compat_compound->params;
  int           energy;

  energy = (size <= 30) ? P->hairpin[size] :
           P->hairpin[30] + (int)(P->lxc * log((size) / 30.));

  if (tetra_loop) {
    if (size == 4) {
      /* check for tetraloop bonus */
      char tl[7] = {
        0
      }, *ts;
      strncpy(tl, string, 6);
      if ((ts = strstr(P->Tetraloops, tl)))
        return P->Tetraloop_E[(ts - P->Tetraloops) / 7];
    }

    if (size == 6) {
      char tl[9] = {
        0
      }, *ts;
      strncpy(tl, string, 8);
      if ((ts = strstr(P->Hexaloops, tl)))
        return energy = P->Hexaloop_E[(ts - P->Hexaloops) / 9];
    }

    if (size == 3) {
      char tl[6] = {
        0, 0, 0, 0, 0, 0
      }, *ts;
      strncpy(tl, string, 5);
      if ((ts = strstr(P->Triloops, tl)))
        return P->Triloop_E[(ts - P->Triloops) / 6];

      if (type > 2)               /* neither CG nor GC */
        energy += P->TerminalAU;  /* penalty for closing AU GU pair IVOO??
                                   * sind dass jetzt beaunuesse oder mahlnuesse (vorzeichen?)*/

      return energy;
    }
  }

  energy += P->mismatchH[type][si1][sj1];

  return energy;
}


/*---------------------------------------------------------------------------*/

PUBLIC int
oldLoopEnergy(int i,
              int j,
              int p,
              int q,
              int type,
              int type_2)
{
  vrna_param_t  *P  = backward_compat_compound->params;
  short         *S1 = backward_compat_compound->sequence_encoding;

  /* compute energy of degree 2 loop (stack bulge or interior) */
  int           n1, n2, m, energy;

  n1  = p - i - 1;
  n2  = j - q - 1;

  if (n1 > n2) {
    m   = n1;
    n1  = n2;
    n2  = m;
  }                                 /* so that n2>=n1 */

  if (n2 == 0) {
    energy = P->stack[type][type_2];   /* stack */
  } else if (n1 == 0) {
    /* bulge */
    energy = (n2 <= MAXLOOP) ? P->bulge[n2] :
             (P->bulge[30] + (int)(P->lxc * log(n2 / 30.)));

#if STACK_BULGE1
    if (n2 == 1)
      energy += P->stack[type][type_2];

#endif
  } else {
    /* interior loop */

    if ((n1 + n2 == 2) && (james_rule)) {
      /* special case for loop size 2 */
      energy = P->int11[type][type_2][S1[i + 1]][S1[j - 1]];
    } else {
      energy = (n1 + n2 <= MAXLOOP) ? (P->internal_loop[n1 + n2]) :
               (P->internal_loop[30] + (int)(P->lxc * log((n1 + n2) / 30.)));

#if NEW_NINIO
      energy += MIN2(MAX_NINIO, (n2 - n1) * P->ninio[2]);
#else
      m       = MIN2(4, n1);
      energy  += MIN2(MAX_NINIO, ((n2 - n1) * P->ninio[m]));
#endif
      energy += P->mismatchI[type][S1[i + 1]][S1[j - 1]] +
                P->mismatchI[type_2][S1[q + 1]][S1[p - 1]];
    }
  }

  return energy;
}


/*--------------------------------------------------------------------------*/

PUBLIC int
LoopEnergy(int  n1,
           int  n2,
           int  type,
           int  type_2,
           int  si1,
           int  sj1,
           int  sp1,
           int  sq1)
{
  vrna_param_t  *P = backward_compat_compound->params;
  /* compute energy of degree 2 loop (stack bulge or interior) */
  int           nl, ns, energy;

  if (n1 > n2) {
    nl  = n1;
    ns  = n2;
  } else {
    nl  = n2;
    ns  = n1;
  }

  if (nl == 0)
    return P->stack[type][type_2];    /* stack */

  if (ns == 0) {
    /* bulge */
    energy = (nl <= MAXLOOP) ? P->bulge[nl] :
             (P->bulge[30] + (int)(P->lxc * log(nl / 30.)));
    if (nl == 1) {
      energy += P->stack[type][type_2];
    } else {
      if (type > 2)
        energy += P->TerminalAU;

      if (type_2 > 2)
        energy += P->TerminalAU;
    }

    return energy;
  } else {
    /* interior loop */
    if (ns == 1) {
      if (nl == 1)                     /* 1x1 loop */
        return P->int11[type][type_2][si1][sj1];

      if (nl == 2) {
        /* 2x1 loop */
        if (n1 == 1)
          energy = P->int21[type][type_2][si1][sq1][sj1];
        else
          energy = P->int21[type_2][type][sq1][si1][sp1];

        return energy;
      } else {
        /* 1xn loop */
        energy = (nl + 1 <= MAXLOOP) ? (P->internal_loop[nl + 1]) :
                 (P->internal_loop[30] + (int)(P->lxc * log((nl + 1) / 30.)));
        energy  += MIN2(MAX_NINIO, (nl - ns) * P->ninio[2]);
        energy  += P->mismatch1nI[type][si1][sj1] +
                   P->mismatch1nI[type_2][sq1][sp1];
        return energy;
      }
    } else if (ns == 2) {
      if (nl == 2) {
        /* 2x2 loop */
        return P->int22[type][type_2][si1][sp1][sq1][sj1];
      } else if (nl == 3) {
        /* 2x3 loop */
        energy  = P->internal_loop[5] + P->ninio[2];
        energy  += P->mismatch23I[type][si1][sj1] +
                   P->mismatch23I[type_2][sq1][sp1];
        return energy;
      }
    }

    {
      /* generic interior loop (no else here!)*/
      energy = (n1 + n2 <= MAXLOOP) ? (P->internal_loop[n1 + n2]) :
               (P->internal_loop[30] + (int)(P->lxc * log((n1 + n2) / 30.)));

      energy += MIN2(MAX_NINIO, (nl - ns) * P->ninio[2]);

      energy += P->mismatchI[type][si1][sj1] +
                P->mismatchI[type_2][sq1][sp1];
    }
  }

  return energy;
}


#endif
