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* HMMER - Biological sequence analysis with profile HMMs
* Copyright (C) 1992-2003 Washington University School of Medicine
* All Rights Reserved
*
* This source code is distributed under the terms of the
* GNU General Public License. See the files COPYING and LICENSE
* for details.
************************************************************/
/* globals.h
* Mon Nov 18 13:05:03 1996
*
* Global variable definitions.
* This file may only be included in a main() .c file.
*
* Alphabet[] is usually treated as an array, but may be treated as
* strings w/ strchr() calls to find index of a particular character,
* so they must be null terminated. Hence the +1.
* [bug #h25. xref STL7 p121]
*/
char Alphabet[MAXCODE+1]; /* ACGT, for instance */
int Alphabet_type; /* hmmNUCLEIC or hmmAMINO */
int Alphabet_size; /* uniq alphabet size: 4 or 20 */
int Alphabet_iupac; /* total size of alphabet + IUPAC degen. */
char Degenerate[MAXCODE][MAXABET]; /* 1/0 arrays, for whether IUPAC code includes a residue */
int DegenCount[MAXCODE];
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