NCBI C Toolkit Cross Reference

C/tools/blastconcat.h

  1 /* ===========================================================================
  2 *
  3 *                            PUBLIC DOMAIN NOTICE
  4 *               National Center for Biotechnology Information
  5 *
  6 *  This software/database is a "United States Government Work" under the
  7 *  terms of the United States Copyright Act.  It was written as part of
  8 *  the author's official duties as a United States Government employee and
  9 *  thus cannot be copyrighted.  This software/database is freely available
 10 *  to the public for use. The National Library of Medicine and the U.S.
 11 *  Government have not placed any restriction on its use or reproduction.
 12 *
 13 *  Although all reasonable efforts have been taken to ensure the accuracy
 14 *  and reliability of the software and data, the NLM and the U.S.
 15 *  Government do not and cannot warrant the performance or results that
 16 *  may be obtained by using this software or data. The NLM and the U.S.
 17 *  Government disclaim all warranties, express or implied, including
 18 *  warranties of performance, merchantability or fitness for any particular
 19 *  purpose.
 20 *
 21 *  Please cite the author in any work or product based on this material.
 22 *
 23 * ===========================================================================*/
 24 /*****************************************************************************
 25 
 26 File name: blastconcat.h
 27 
 28 Author: Karolina Maciag, Aleksandr Morgulis
 29 
 30 Contents: type declarations for query multiplexing code.
 31 
 32 ******************************************************************************/
 33 /* $Revision: 1.2 $ 
 34 *  $Log: blastconcat.h,v $
 35 *  Revision 1.2  2004/04/20 14:55:47  morgulis
 36 *  1. Fixed query offsets in results when -B option is used.
 37 *  2. Fixes for lower case masking handling with -B option.
 38 *
 39 *  Revision 1.1  2003/03/24 20:47:28  madden
 40 *  Utilities for concatenation of blastn/tblastn queries
 41 *
 42 * */
 43 
 44 
 45 #ifndef _BLASTCONCAT_
 46 #define _BLASTCONCAT_
 47 
 48 #include <ncbi.h>
 49 
 50 #define LAST_N                          15
 51 #define TWO_N                           (LAST_N*16 + LAST_N)
 52 #define SPACER_POS              -1
 53 #define DROPOFF_NUMBER_OF_BITS 10.0
 54 
 55 typedef SeqAlignPtr *SeqAlignPtrArray;
 56 typedef SeqAlignPtrArray *SeqAlignPtrArrayPtr;
 57 typedef SeqAnnotPtr *SeqAnnotPtrArray;
 58 
 59 /* --KM types necessary when the -B option is used for query concatenation */
 60 
 61 /* array to store the fake_bsps corresponding to indiv. queries */
 62 typedef BioseqPtr PNTR BspArray; 
 63 /* integer arrays for indiv. query bounds */
 64 typedef Int4 PNTR IntArray;
 65 
 66 /* AM: float and Int8 arrays for effective search spaces and effective
 67        database lengths. */
 68 typedef Int8 PNTR Int8Array;
 69 typedef Uint1 PNTR Uint1Array;
 70 typedef Nlm_FloatHi PNTR FloatArray;
 71 
 72 struct queries; /* Forward declaration of Queries type */
 73 
 74 #endif  /* _BLASTCONCAT_ */
 75 
 76
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