/*
###################################
# Access to RNAlib routines to    #
# convert energy parameter files  #
# from ViennaRNAPackage 1.8.4 to  #
# 2.0 format                      #
#                                 #
# Ronny Lorenz                    #
###################################
*/

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <ctype.h>
#include <unistd.h>
#include <string.h>
#include "utils.h"
#include "convert_epars.h"
#include "RNAparconv_cmdl.h"

int main(int argc, char *argv[]){
  struct  RNAparconv_args_info  args_info;
  char                          *ifileName, *ofileName;
  int                           i, silent;
  unsigned int                  options;

  ifileName = ofileName = NULL;
  silent    = 0;
  options   = VRNA_CONVERT_OUTPUT_ALL;

  /*
  #############################################
  # check the command line parameters
  #############################################
  */
  if(RNAparconv_cmdline_parser (argc, argv, &args_info) != 0) exit(1);

  /* use input file */
  if(args_info.input_given)             ifileName = strdup(args_info.input_arg);
  /* use output file */
  if(args_info.output_given)            ofileName = strdup(args_info.output_arg);
  /* output without (special) hairpin energies + enthalpies */
  if(args_info.without_HairpinE_given)  options &= ~(VRNA_CONVERT_OUTPUT_HP
                                                    |VRNA_CONVERT_OUTPUT_SPECIAL_HP);
  /* output without stacking energies + enthalpies */
  if(args_info.without_StackE_given)    options &= ~VRNA_CONVERT_OUTPUT_STACK;
  /* output without 5' dangle energies + enthalpies */
  if(args_info.without_Dangle5_given)   options &= ~VRNA_CONVERT_OUTPUT_DANGLE5;
  /* output without 3' dangle energies + enthalpies */
  if(args_info.without_Dangle3_given)   options &= ~VRNA_CONVERT_OUTPUT_DANGLE3;
  /* output without interior loop energies + enthalpies */
  if(args_info.without_IntE_given)      options &= ~(VRNA_CONVERT_OUTPUT_NINIO
                                                    |VRNA_CONVERT_OUTPUT_INT
                                                    |VRNA_CONVERT_OUTPUT_INT_11
                                                    |VRNA_CONVERT_OUTPUT_INT_21
                                                    |VRNA_CONVERT_OUTPUT_INT_22);
  /* output without bulge loop energies + enthalpies */
  if(args_info.without_BulgeE_given)    options &= ~VRNA_CONVERT_OUTPUT_BULGE;
  /* output without multi loop energies + enthalpies */
  if(args_info.without_MultiE_given)    options &= ~VRNA_CONVERT_OUTPUT_ML;
  /* output without misc energies + enthalpies */
  if(args_info.without_Misc_given)      options &= ~VRNA_CONVERT_OUTPUT_MISC;
  /* output without hairpin mismatch energies + enthalpies */
  if(args_info.without_MismatchH_given) options &= ~VRNA_CONVERT_OUTPUT_MM_HP;
  /* output without interior loop mismatch energies + enthalpies */
  if(args_info.without_MismatchI_given) options &= ~(VRNA_CONVERT_OUTPUT_MM_INT
                                                    |VRNA_CONVERT_OUTPUT_MM_INT_1N
                                                    |VRNA_CONVERT_OUTPUT_MM_INT_23);
  /* output without multi loop mismatch energies + enthalpies */
  if(args_info.without_MismatchM_given) options &= ~VRNA_CONVERT_OUTPUT_MM_MULTI;
  /* output without exterior loop mismatch energies + enthalpies */
  if(args_info.without_MismatchE_given) options &= ~VRNA_CONVERT_OUTPUT_MM_EXT;

  /* output given energy parameters only */
  if(args_info.vanilla_given)           options |= VRNA_CONVERT_OUTPUT_VANILLA;

  /* just dump Vienna 1.8.4 parameters in new format */
  if(args_info.dump_given)              options |= VRNA_CONVERT_OUTPUT_DUMP;

  /* file names given as unnamed option? */
  for(i = 0; i < args_info.inputs_num; i++){
    if(ifileName == NULL)       ifileName = strdup(args_info.inputs[i]);
    else if(ofileName == NULL)  ofileName = strdup(args_info.inputs[i]);
    else{
      RNAparconv_cmdline_parser_print_help();
      nrerror("unrecognized or too many parameter options given!");
    }
  }

  /* be silent */
  if(args_info.silent_given) silent = 1;

  /* free allocated memory of command line data structure */
  RNAparconv_cmdline_parser_free (&args_info);

  /*
  #############################################
  # do something
  #############################################
  */

  if(ifileName == NULL)
    if(!(silent || (options & VRNA_CONVERT_OUTPUT_DUMP)))
      fprintf(stdout, "Enter parameters:\n(Indicate last line of input parameters by typing \"# END\" or EOF\n\n");

  convert_parameter_file(ifileName, ofileName, options);

  return EXIT_SUCCESS;
}