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/* $Id: blast_seg.h,v 1.17 2006/11/21 16:45:08 papadopo 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 official 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__
#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_def.h>
#ifdef __cplusplus
extern "C" {
#endif
/** Structure to hold parameters for seg search.
*/
typedef struct SegParameters
{
Int4 window; /**< initial window size to trigger further work. */
double locut;
double hicut;
Int4 period;
Int4 hilenmin;
Boolean overlaps; /* merge overlapping pieces if TRUE. */
Int4 maxtrim;
Int4 maxbogus;
} SegParameters;
/** Allocated SeqParameter struct for proteins and fills with default values.
* @return pointer to SegParameters
*/
SegParameters* SegParametersNewAa (void);
/** Free SegParameters structure
* @param sparamsp object to be freed [in]
*/
void SegParametersFree(SegParameters* sparamsp);
/** Runs seg on a protein sequence in ncbistdaa.
* @param sequence the protein residues in ncbistdaa [in]
* @param length number of redidues [in]
* @param offset amount to shift over resulting locations
* (if full sequence not passed in) [in]
* @param sparamsp the seg parameters created with SegParametersNewAa [in]
* @param seg_locs resulting locations for filtering [out]
* @return zero on success
*/
Int2 SeqBufferSeg (Uint1* sequence, Int4 length, Int4 offset,
SegParameters* sparamsp, BlastSeqLoc** seg_locs);
#ifdef __cplusplus
}
#endif
#endif /* !__BLAST_FILTER__ */
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