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// Copyright (C) 1999-2003 Paul O. Lewis
//
// This file is part of NCL (Nexus Class Library) version 2.0.
//
// NCL is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// NCL is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with NCL; if not, write to the Free Software Foundation, Inc.,
// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
#ifndef NCL_NXSDEFS_H
#define NCL_NXSDEFS_H
#define NCL_NAME_AND_VERSION "NCL version 2.0"
#define NCL_COPYRIGHT "Copyright (c) 1999-2003 by Paul O. Lewis"
#define NCL_HOMEPAGEURL "http://lewis.eeb.uconn.edu/ncl/"
// Maximum number of states that can be stored; the only limitation is that this
// number be less than the maximum size of an int (not likely to be a problem).
// A good number for this is 76, which is 96 (the number of distinct symbols
// able to be input from a standard keyboard) less 20 (the number of symbols
// symbols disallowed by the NEXUS standard for use as state symbols)
//
#define NCL_MAX_STATES 76
#if defined(__MWERKS__) || defined(__DECCXX) || defined(_MSC_VER)
typedef long file_pos;
#else
typedef streampos file_pos;
#endif
#define SUPPORT_OLD_NCL_NAMES
class NxsString;
typedef vector<bool> NxsBoolVector;
typedef vector<char> NxsCharVector;
typedef vector<unsigned> NxsUnsignedVector;
typedef vector<NxsString> NxsStringVector;
typedef vector<NxsStringVector> NxsAllelesVector;
typedef set< unsigned, less<unsigned> > NxsUnsignedSet;
typedef map< unsigned, NxsStringVector, less<unsigned> > NxsStringVectorMap;
typedef map< NxsString, NxsString, less<NxsString> > NxsStringMap;
typedef map< NxsString, NxsUnsignedSet, less<NxsString> > NxsUnsignedSetMap;
// The following typedefs are simply for maintaining compatibility with existing code.
// The names on the right are deprecated and should not be used.
//
typedef NxsBoolVector BoolVect;
typedef NxsUnsignedSet IntSet;
typedef NxsUnsignedSetMap IntSetMap;
typedef NxsAllelesVector AllelesVect;
typedef NxsStringVector LabelList;
typedef NxsStringVector StrVec;
typedef NxsStringVector vecStr;
typedef NxsStringVectorMap LabelListBag;
typedef NxsStringMap AssocList;
//class NxsTreesBlock;
//class NxsTaxaBlock;
//class NxsAllelesBlock;
//class NxsAssumptionsBlock;
//class NxsCharactersBlock;
//class NxsDistancesBlock;
//class NxsAssumptionsBlock;
//class NxsDiscreteDatum;
//class NxsDiscreteMatrix;
#endif
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