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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. */
/* alphabet.h: Definitions for the nucleotide and amino acid alphabets in */
/* aabet.h and ntbet.h */
/* Modified by: Bill Alford */
/* Change log information is at the end of the file. */
#ifndef _ALPHABET_
#define _ALPHABET_
/*
For better performance on most platforms, ALPHASIZE_MAX and ALPHAVAL_MAX
should have values of 2**N and (2**N - 1), respectively, for some N.
Choose an N that is just large enough for the job, to avoid needlessly
thrashing in small CPU caches.
*/
#define ALPHASIZE_MAX 128 /* Max. no. of letters permitted in an alphabet */
#define ALPHAVAL_MAX 127 /* Max. numerical value permitted for a letter */
/* Ambiguous residues are defined using this structure */
typedef struct degen {
char residue; /* ASCII letter for this residue */
int ndegen; /* no. of residues this ASCII letter matches */
char *list; /* null-terminated list of matching letters */
} Degen, DegenPtr;
/* Use DEGENLIST macro to more easily manage data initialization */
#define DEGENLIST(Chr, List) { Chr, (sizeof(List)-1), (List) }
#endif /* !_ALPHABET_ */
/* Change log information follows. */
/*
* Revision 2.2010 1995/07/28 23:47:14 billa
*
*/
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