/* See {pz_mismatch.h}. */
/* Last edited on 2008-02-08 11:44:29 by stolfi */

#include <argparser.h>

#include <pz_types.h>
#include <pz_mismatch.h>

#define pz_mismatch_C_copyright "Copyright © 2001 Universidade Estadual de Campinas (UNICAMP)"
#define pz_mismatch_C_authors "Helena C. G. Leitão and Jorge Stolfi, 2001--2008"

Options  ParseOptions(
    arparser_t pp 
  )
  RAISES {ParseParams.Error} =
  VAR o: Options;
  {
    argparser_get_keyword(pp, "-maxDist");

    { /* with */
      ??? d = argparser_get_next_double(pp, 0.0e0);
      /* do */ o.maxDistSqr := d*d END;

    argparser_get_keyword(pp, "-critDist");

    { /* with */
      ??? d = argparser_get_next_double(pp, 0.0e0);
      /* do */ o.critDistSqr := d*d END;

    argparser_get_keyword(pp, "-skipDist");

    { /* with */
      ??? d = argparser_get_next_double(pp, 0.0e0);
      /* do */ o.skipDistSqr := d*d END;
    
    return o
  } /* ParseOptions */


double  Eval(
    double length         /* Total length of pairing. */
    double intgDistSqr,   /* Integral of the curve distance squared and clipped. */
    double totAsymm,      /* Total step asymmetry. */
    Options *o, /* Mismatch parameters. */
  )
  {
    return intgDistSqr - length * o.critDistSqr + totAsymm * o.skipDistSqr
  } /* Eval */

{