1 /* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
3 /*********************************************************************
4 * Clustal Omega - Multiple sequence alignment
6 * Copyright (C) 2010 University College Dublin
8 * Clustal-Omega is free software; you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License as
10 * published by the Free Software Foundation; either version 2 of the
11 * License, or (at your option) any later version.
13 * This file is part of Clustal-Omega.
15 ********************************************************************/
18 * RCS $Id: general.h 247 2011-06-16 11:41:15Z fabian $
26 #include "../clustal/log.h"
29 ***** Omega definitions************************************
34 enum {AMINOACIDS = 20, STATE_TRANSITIONS = 7};
35 enum {MAXWORD = 100, MAXLEN = 10000};
36 enum {OVER_ALLOCATE = 2};
37 enum {FAILURE = -1, OK};
38 enum {RETURN_OK = 0, RETURN_FROM_MAC, RETURN_FROM_VITERBI, RETURN_FROM_PRINT_ALI, RETURN_FROM_RNP, RETURN_UNKNOWN};
39 enum {REALLY_BIG_MEMORY_MB = 64000};
41 enum {INTERN_ALN_2_HMM = 0, READ_ALN_2_HMM, READ_HMM_2_HMM, INTERN_HMM_2_HMM};
44 /*#define MIN(a,b) ((a)<(b)?(a):(b))*/
47 /* parameters passed from Clustal-Omega to hhalign; FS, r240 -> */
50 int iMacRamMB; /* dedicated amount of RAM for Maximum Accuracy (in MB) */