/*
  Copyright (c) 2008 Stefan Kurtz <kurtz@zbh.uni-hamburg.de>
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef DIST_SHORT_H
#define DIST_SHORT_H
#include "core/defined-types.h"
#include "core/encseq_api.h"
#include "core/types_api.h"

unsigned long gt_distanceofshortstringsbytearray(unsigned long *eqsvector,
                                     unsigned int alphasize,
                                     const GtUchar *useq,
                                     unsigned long ulen,
                                     const GtUchar *vseq,
                                     unsigned long vlen);

unsigned long gt_distanceofshortstringsencseq(unsigned long *eqsvector,
                                           unsigned int alphasize,
                                           const GtUchar *useq,
                                           unsigned long ulen,
                                           const GtEncseq *encseq,
                                           unsigned long vstartpos,
                                           unsigned long vlen);

unsigned long gt_reversesuffixmatch(unsigned long *eqsvector,
                                 unsigned int alphasize,
                                 const GtUchar *useq,
                                 unsigned long ulen,
                                 const GtUchar *vseq,
                                 unsigned long vlen,
                                 unsigned long maxdistance);

Definedunsignedlong gt_forwardprefixmatch(const GtEncseq *encseq,
                                       unsigned int alphasize,
                                       unsigned long startpos,
                                       bool nowildcards,
                                       unsigned long *eqsvector,
                                       const GtUchar *useq,
                                       unsigned long ulen,
                                       unsigned long maxdistance);

#endif
