NCBI C Toolkit Cross Reference

C/tools/blast_dust.h

  1 /* $Id: blast_dust.h,v 1.16 2007/01/23 15:25:22 madden Exp $
  2  * ===========================================================================
  3  *
  4  *                            PUBLIC DOMAIN NOTICE
  5  *               National Center for Biotechnology Information
  6  *
  7  *  This software/database is a "United States Government Work" under the
  8  *  terms of the United States Copyright Act.  It was written as part of
  9  *  the author's official duties as a United States Government employee and
 10  *  thus cannot be copyrighted.  This software/database is freely available
 11  *  to the public for use. The National Library of Medicine and the U.S.
 12  *  Government have not placed any restriction on its use or reproduction.
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 25  * 
 26  * Author: Tom Madden
 27  *
 28  */
 29 
 30 /** @file blast_dust.h
 31  * DUST filtering functions. (shouldn't this be merged with blast_filter?)
 32  * @todo FIXME: include reference?
 33  */
 34 
 35 #ifndef ALGO_BLAST_CORE__BLAST_DUST__H
 36 #define ALGO_BLAST_CORE__BLAST_DUST__H
 37 
 38 
 39 #ifdef __cplusplus
 40 extern "C" {
 41 #endif
 42 
 43 
 44 /** endpoints
 45  * linked list of low-complexity offsets.
 46  */
 47 typedef struct DREGION {
 48         struct  DREGION*        next;
 49         Int4    from, to;
 50 } DREGION;
 51 
 52 
 53 Int4 DustSegs (Uint1* sequence, Int4 length, Int4 start,
 54                        DREGION* reg,
 55                        Int4 level, Int4 windowsize, Int4 linker);
 56 
 57 SeqLocPtr BioseqDustEx (BioseqPtr bsp, Int4 level, Int4 windowsize, Int4 linker);
 58 SeqLocPtr SeqLocDustEx (SeqLocPtr this_slp, Int4 level, Int4 window, Int4 linker);
 59 
 60 
 61 #ifdef __cplusplus
 62 }
 63 #endif
 64 #endif /* !ALGO_BLAST_CORE__BLAST_DUST__H */
 65
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