/usr/include/ncl/nxscdiscretematrix.h is in libncl-dev 2.1.18+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 | // 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; /** type used to enumerate possible states.
-1 is used for gaps, other negative flags may be added later.
This size limits the maximum number of states allowed. */
typedef int8_t NxsCDiscreteStateSet; /** type used to refer to unique combinations of states (the "fundamental" states and ambiguity codes)
-1 is used for gaps. To handle all possible data sets, this must be large enough to hold
2^(nStates + 1) values if the datatype allows gaps. Thus using int8_t limits us to 8 states */
/*
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; /** Flattened array of array of observed states. If more than one state was observed, then the first element is the number of states observed.
Exceptions: -1 is for gaps, nStates is for missing. */
unsigned * stateListPos; /** Maps a state set code (the elements of the matrix) to the index in stateList where the states are listed */
NxsCDiscreteStateSet ** matrix; /** taxa x characters matrix of indices of state sets */
const char * symbolsList; /** array of the characters used to stand for each state ("ACGT?NRY" for example) //@temp paup depends on all symbols being unique (even ambiguity codes)*/
unsigned nStates;
unsigned nChar;
unsigned nTax;
unsigned nObservedStateSets; /* the length of stateListPos */
NxsAltDatatypes datatype;
} NxsCDiscreteMatrix;
#ifdef __cplusplus
}
#endif
#endif /* __TREEINFER_HELPER_H */
|