text: /*
    Copyright (c) 2010-2011 Giorgio Gonnella <gonnella@zbh.uni-hamburg.de>
    Copyright (c) 2010-2011 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 RDJ_OVLFIND_BF_H
  #define RDJ_OVLFIND_BF_H
  
  #include "core/error_api.h"               /* GtError       */
  #include "match/rdj-contfind-def.h"       /* GtContfind    */
  #include "match/rdj-pairwise.h"           /* GtOvlfindMode */
  
  /* brute force overlap finder */
  
  /*
    known issues:
    - case sensitive (a != A)
    - no notion of wildcards (i.e. n == n)
  */
  
  GtContfind gt_ovlfind_bf(const char *u, unsigned long u_length,
                           const char *v, /* NULL for u vs. u */
                           unsigned long v_length,
                           GtOvlfindMode m, unsigned long min_length,
                           bool find_nonmaximal,
                           void(*spmproc)
                             (unsigned long /* overlap length */,
                              bool /* true if suffix of u == prefix of v
                                      false if prefix of u == suffix of v */,
                              void* /* spmprocdata */),
                           void* spmprocdata);
  
  int gt_ovlfind_bf_unit_test(GtError *err);
  
  #endif
  