/* Last changed Time-stamp: <2008-06-27 17:21:42 ivo> */

/**
*** \file fold_vars.c
*** global variables to change behaviour of folding routines<BR>
*** Also there are some functions that make the live easier when
*** using functions of the Vienna RNA package
**/
#include <string.h>
#include <stdio.h>
#include "fold_vars.h"

int         circ = 0;

int         noGU = 0;             /* GU not allowed at all */

int         no_closingGU = 0;     /* GU allowed only inside stacks */

int         tetra_loop = 1;       /* Fold with specially stable 4-loops */

int         energy_set = 0;       /* 0 = BP; 1=any with GC; 2=any with AU parameters */

int         dangles = 2;          /* use dangling end energies */

char        *nonstandards = (char *)0;  /* contains allowed non standard bases */

double      temperature = 37.0;

int         james_rule = 1;       /* interior loops of size 2 get energy 0.8Kcal and
                                    no mismatches (no longer used) */

int         oldAliEn = 0;         /* use old alifold-energies (without removing gaps) */

int         ribo = 0;             /* use ribosum instead of classic covariance term */

char        *RibosumFile = NULL;  /* TODO: compile ribosums into program
                                    Warning: this variable will vanish */

int         csv = 0;              /*generate comma seperated output*/

bondT       *base_pair = NULL;

FLT_OR_DBL  *pr = NULL;           /* base pairing prob. matrix */

int         *iindx = NULL;        /* pr[i,j] -> pr[iindx[i]-j] */

double      pf_scale = -1;        /* scaling factor to avoid floating point overflows */

int         fold_constrained = 0; /* fold with constraints */

int         do_backtrack = 1;     /* calculate pair prob matrix in part_func() */

int         noLonelyPairs = 0;    /* avoid helices of length 1 */

char        backtrack_type = 'F'; /* 'C' require (1,N) to be bonded;
                                    'M' seq is part of s multi loop */

int         *cut_points;

int         *strand;

int         gquad = 0;            /* consider g-qudruplexes in the calculations */

PUBLIC char * option_string(void){
  static char options[100];
  *options = '\0';
  if (noGU) strcat(options, "-noGU ");
  if (no_closingGU) strcat(options, "-noCloseGU ");
  if (!tetra_loop) strcat(options, "-4 ");
  if (noLonelyPairs) strcat(options, "-noLP ");
  if (fold_constrained) strcat(options, "-C ");
  if (dangles!=1) sprintf(options+strlen(options), "-d%d ", dangles);
  if (temperature!=37.0)
    sprintf(options+strlen(options), "-T %f ", temperature);
  return options;
}

PUBLIC void set_model_details(model_detailsT *md){
  if(md){
    md->dangles     = dangles;
    md->special_hp  = tetra_loop;
    md->noLP        = noLonelyPairs;
    md->noGU        = noGU;
    md->noGUclosure = no_closingGU;
    md->logML       = logML;
    md->gquad       = gquad;
  }
}