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/* (C) Copyright 1993, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */
/* blastapp.h: set up defines for aabet.h, alphabet.h, and gcode.h */
/* Modified by: Bill Alford */
/* Change log information is at the end of the file. */
/**************************************************************************
* *
* National Center for Biotechnology Information *
* Bldg. 38A, NIH, 8600 Rockville Pike, Bethesda, MD 20894 *
* *
* COPYRIGHT NOTICE *
* *
* This software/database is categorized as "United States Government *
* Work" under the terms of the United States Copyright Act. It was *
* produced as part of the author's official duties as a Government *
* employee and thus can not be copyrighted. This software/database is *
* freely available to the public for use without a copyright notice. *
* Restrictions can not be placed on its present or future use. *
* *
* Although all reasonable efforts have been taken to ensure the accuracy *
* and reliability of the software and data, the National Library of *
* Medicine (NLM) and the U.S. Government do not and can not warrant the *
* performance or results that may be obtained by using this software, *
* data, or derivative works thereof. The NLM and the U.S. Government *
* disclaim any and all warranties, expressed or implied, as to the *
* performance, merchantability or fitness for any particular purpose or *
* use. *
* *
* In any work or product derived from this material, proper attribution *
* of the author(s) as the source of the software or data would be *
* appreciated. *
* *
Karlin, Samuel and Stephen F. Altschul (1990). Methods for assessing
the statistical significance of molecular sequence features by using
general scoring schemes. Proc. Natl. Acad. Sci. USA 87:2264-2268.
Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and
David J. Lipman (1990). A basic local alignment search tool.
J. Mol. Biol. 215:403-410.
**************************************************************************/
/* (For a better look, set tabstops every 4 columns) */
#ifndef __BLAST_H__
#define __BLAST_H__
/*
#include <signal.h>
#include <gish.h>
*/
#include <limits.h> /* defines CHAR_BIT for aabet.h and ntbet.h */
/* EXTERN should be defined in the main program module only */
#ifndef EXTERN
#define EXTERN extern
#ifndef INITIAL
#define INITIAL(x)
#endif
#else
#ifndef INITIAL
#define INITIAL(x) = x
#endif
#ifndef INIT
#define INIT
#endif
#endif
/* much deleted here */
/* added */
#define PROTO(x) ()
#endif /* __BLAST_H__ */
/* Change log information follows. */
/* $Log: blastapp.h,v $
* Revision 2.2010 1995/07/28 23:47:14 billa
* Added new convert method and pattern matching and minor updates merged.
*
* Revision 2.2001 1994/05/18 19:17:57 billa
* Removed global.c and moved Buffer variable to strutil.[ch].
*
* Revision 2.2000 1994/05/10 18:39:13 billa
* System version 2.2 A [2.2000]
* Goofed on dev. version.
*
* Revision 2.1100 1994/05/10 18:27:07 billa
* System version 2.2 A [2.1100].
* Created blimps library and fixed up minor bugs. No major changes to the
* program.
*
* Revision 2.1025 1994/05/10 00:51:47 billa
* Added SCCS patterns to trick the what command into printing out the RCS
* identifying patterns.
*
* Revision 2.1020 1994/04/27 21:59:11 billa
* After library creation. In testing phase.
*
* Revision 2.1015 1994/04/26 03:15:34 billa
* Pre-library checkin.
*
* Revision 2.1011 1994/04/26 03:14:16 billa
* Pre-library checkin.
*
* Revision 2.1010 1994/04/26 00:28:18 billa
* Cleaned up warnings from gcc switches.
*
* Revision 2.1000 1994/03/09 22:23:59 billa
* System version 2.1 A [2.1000]
* Added reading and scoring of precomputed site specific scoring matricies.
* Reconfigured files.[ch] into files.[ch] and config.[ch].
*
* Revision 2.0 1993/12/06 19:31:18 billa
* System version 2.0 A [2.0000].
* Changed source to remove some warnings. Added sequence weights to the
* blocks. Added a conversion method to use the weights. Made the method
* the default. Added some ifndef's in preparation of creating a library
* of functions. Added the ability to choose the genetic code to use for
* translation. Added the ability to read a flat file as a sequence if the
* other types sequences fail to match. Added some defines for strdup().
*
* Revision 1.1120 1993/12/02 03:44:22 billa
* Development version 1.1120. Right after copyright/license info added.
*
* Revision 1.1101 1993/12/02 03:37:12 billa
* Added the copyright notice to the top of the file.
*
* Revision 1.1100 1993/09/09 17:23:19 billa
* System version 1.1 B [1.1100].
*
* Revision 1.1000 1993/08/27 17:01:31 billa
* System version 1.1 A, development version 1.1000.
* Added the function reclaim_space() and the macro CheckMem(A) to handle
* the situation when there is no more memory to allocate.
*
* Revision 1.0 1993/08/14 00:50:52 billa
* System version 1.00
*
* Revision 0.110 1993/08/10 02:50:53 billa
* System version update. Added convert.[ch], scoring.[ch] and version.[ch].
*
* Revision 0.105 1993/08/04 19:53:40 billa
* System version 0.105. Post file structure reorganization.
*
* Revision 0.100 1993/08/03 00:48:46 billa
* System version 0.100. Pre file structure reorganization.
*
* Revision 0.11 1993/07/16 22:16:00 billa
* Added RCS information. Added PROTO definition.
*
*/
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