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/* ===========================================================================
*
* 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.
*
* ===========================================================================*/
/*****************************************************************************
File name: blastconcat.h
Author: Karolina Maciag, Aleksandr Morgulis
Contents: type declarations for query multiplexing code.
******************************************************************************/
/* $Revision: 1.2 $
* $Log: blastconcat.h,v $
* Revision 1.2 2004/04/20 14:55:47 morgulis
* 1. Fixed query offsets in results when -B option is used.
* 2. Fixes for lower case masking handling with -B option.
*
* Revision 1.1 2003/03/24 20:47:28 madden
* Utilities for concatenation of blastn/tblastn queries
*
* */
#ifndef _BLASTCONCAT_
#define _BLASTCONCAT_
#include <ncbi.h>
#define LAST_N 15
#define TWO_N (LAST_N*16 + LAST_N)
#define SPACER_POS -1
#define DROPOFF_NUMBER_OF_BITS 10.0
typedef SeqAlignPtr *SeqAlignPtrArray;
typedef SeqAlignPtrArray *SeqAlignPtrArrayPtr;
typedef SeqAnnotPtr *SeqAnnotPtrArray;
/* --KM types necessary when the -B option is used for query concatenation */
/* array to store the fake_bsps corresponding to indiv. queries */
typedef BioseqPtr PNTR BspArray;
/* integer arrays for indiv. query bounds */
typedef Int4 PNTR IntArray;
/* AM: float and Int8 arrays for effective search spaces and effective
database lengths. */
typedef Int8 PNTR Int8Array;
typedef Uint1 PNTR Uint1Array;
typedef Nlm_FloatHi PNTR FloatArray;
struct queries; /* Forward declaration of Queries type */
#endif /* _BLASTCONCAT_ */
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