blast_seg.h

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: blast_seg.h,v $
 * PRODUCTION Revision 1000.1  2004/06/01 18:03:44  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.11
 * PRODUCTION
 * ===========================================================================
 */

/* $Id: blast_seg.h,v 1000.1 2004/06/01 18:03:44 gouriano Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's offical duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Author:  Ilya Dondoshansky
 *
 */

/** @file blast_seg.h
 * SEG filtering functions. @todo FIXME: should this be combined with
 * blast_filter/dust? Needs doxygen documentation and comments
 */

#ifndef __BLAST_SEG__
#define __BLAST_SEG__

#ifdef __cplusplus
extern "C" {
#endif

#include <algo/blast/core/blast_def.h>

/*--------------------------------------------------------------(structs)---*/

typedef struct Alpha
  {
   Int4 alphabet;
   Int4 alphasize;
   double lnalphasize;
   Int4* alphaindex;
   unsigned char* alphaflag;
   char* alphachar;
  } Alpha;

typedef struct SegParameters
  {
   Int4 window;
   double locut;
   double hicut;
   Int4 period;
   Int4 hilenmin;
   Boolean overlaps;	/* merge overlapping pieces if TRUE. */
   Int4 maxtrim;
   Int4 maxbogus;
   Alpha* palpha;
  } SegParameters;

SegParameters* SegParametersNewAa (void);
void SegParametersFree(SegParameters* sparamsp);

Int2 SeqBufferSeg (Uint1* sequence, Int4 length, Int4 offset,
                   SegParameters* sparamsp, BlastSeqLoc** seg_locs);

#ifdef __cplusplus
}
#endif
#endif /* !__BLAST_FILTER__ */