nxscdiscretematrix.h

//  Copyright (C) 2008 Mark Holder
//
//  This file is part of NCL (Nexus Class Library) version 2.1
//
//  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

// This code is based on code developed by Mark Holder for the CIPRES project

#if !defined(NXS_C_DISCRETE_MATRIX_H)
#define NXS_C_DISCRETE_MATRIX_H


#if defined (HAVE_CONFIG_H)
#   include <config.h>
#endif

#if defined(_MSC_VER)
#   undef   HAVE_COMPILE_TIME_DISPATCH
#else
#   define HAVE_COMPILE_TIME_DISPATCH
#endif

/* For typedefs like uint8_t */
#if HAVE_INTTYPES_H
#   include <inttypes.h>
#elif HAVE_STDINT_H
#   include <stdint.h>
#elif defined(_MSC_VER) && _MSC_VER >= 1200
#   include <basetsd.h>
    typedef   INT8 int8_t;
    typedef  UINT8 uint8_t;
    typedef  INT64 int64_t;
    typedef UINT64 uint64_t;
#elif defined(_MSC_VER)
    typedef signed char int8_t;
    typedef unsigned char uint8_t;
    typedef long long int64_t;
    typedef unsigned long long uint64_t;
#elif defined(_WIN32)
#   include <stdint.h>
#endif

    /* For size_t */
#if defined(HAVE_STDDEF_H)
#   include <stddef.h>
#endif


#ifdef __cplusplus
extern "C"
{
#endif


typedef int8_t NxsCDiscreteState_t; 
typedef int8_t NxsCDiscreteStateSet; 
/*
The following enum is a cropping of the NxsCharactersBlock::DataTypesEnum
which includes all of the datatypes (and only those) that can be expressed
in a NxsCDiscreteMatrix. Each of the enum facets will have the same
value as in  NxsCharactersBlock::DataTypesEnum.

This enum is also handy because it is accessible via C.
*/
typedef enum {
              NxsAltGeneric_Datatype = 1,
              NxsAltDNA_Datatype = 2,
              NxsAltRNA_Datatype = 3,
              NxsAltNuc_Datatype = 4,
              NxsAltAA_Datatype = 5,
              NxsAltCodon_Datatype = 6
              } NxsAltDatatypes;
const int LowestNxsCDatatype = 1;
const int HighestNxsCDatatype = 6;

typedef struct NxsCDiscreteMatrixStruct
    {
    NxsCDiscreteState_t       *stateList;       
    unsigned * stateListPos;    
    NxsCDiscreteStateSet ** matrix;         
    const char * symbolsList;   
    unsigned nStates;
    unsigned nChar;
    unsigned nTax;
    unsigned nObservedStateSets; /* the length of stateListPos */
    NxsAltDatatypes datatype;
    } NxsCDiscreteMatrix;


#ifdef __cplusplus
}
#endif

#endif /* __TREEINFER_HELPER_H */

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