/usr/include/libMUSCLE-3.7/libMUSCLE/types.h is in libmuscle-3.7-dev 3.7+4565-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 | #ifndef types_h
#define types_h
namespace muscle {
typedef unsigned char byte;
typedef unsigned short ushort;
typedef float SCOREMATRIX[32][32];
typedef SCOREMATRIX *PTR_SCOREMATRIX;
typedef SCOREMATRIX *DYN_PTR_SCOREMATRIX;
class MSA;
class Seq;
class ClusterTree;
class DistFunc;
class TextFile;
class PWPath;
class Tree;
class SeqVect;
class DistCalc;
struct ProgNode;
struct ProfPos;
#if SINGLE_AFFINE
// Compress M, D and I trace-back matrices into 4 bits
enum
{
BIT_MM = 0x00,
BIT_DM = 0x01,
BIT_IM = 0x02,
BIT_xM = 0x03,
BIT_DD = 0x00,
BIT_MD = 0x04,
// ID not allowed
BIT_xD = 0x04,
BIT_II = 0x00,
BIT_MI = 0x08,
// DI not allowed
BIT_xI = 0x08,
};
#endif
#if DOUBLE_AFFINE
// Compress M, D, E, I and J trace-back matrices into 7 bits
enum
{
BIT_MM = 0x00,
BIT_DM = 0x01,
BIT_EM = 0x02,
BIT_IM = 0x03,
BIT_JM = 0x04,
BIT_xM = 0x07,
BIT_DD = 0x00,
BIT_MD = 0x08,
// [EIJ]D not sallowed
BIT_xD = 0x08,
BIT_EE = 0x00,
BIT_ME = 0x10,
// [DDJ]E not allowed
BIT_xE = 0x10,
BIT_II = 0x00,
BIT_MI = 0x20,
// [EDJ]I not allowed
BIT_xI = 0x20,
BIT_JJ = 0x00,
BIT_MJ = 0x40,
// [EDI]J not allowed
BIT_xJ = 0x40,
};
#endif
enum EXIT
{
EXIT_Success = 0,
EXIT_NotStarted = 1,
EXIT_FatalError = 2,
EXIT_Except = 3,
};
enum NODECMP
{
NODECMP_Undefined = 0,
NODECMP_Same = 0, // equivalent to node in old tree
NODECMP_Diff = 1, // equivalent & parent is changed
NODECMP_Changed = 2 // no equivalent node in old tree
};
// Declare enums using macro hacks (see libMUSCLE/enums.h).
#define s(t) enum t { t##_Undefined = 0,
#define c(t, x) t##_##x,
#define e(t) };
#include "libMUSCLE/enums.h"
// Declare conversion function XXXToStr(XXX x)
// for each enum type XXX.
#define s(t) const char *t##ToStr(t x);
#define c(t, x) /* empty */
#define e(t) /* empty */
#include "libMUSCLE/enums.h"
// Declare conversion function StrToXXX(const char *Str)
// for each enum type XXX.
#define s(t) t StrTo##t(const char *Str);
#define c(t, x) /* empty */
#define e(t) /* empty */
#include "libMUSCLE/enums.h"
const char *BoolToStr(bool b);
const char *SecsToStr(unsigned long Secs);
} // namespace muscle
#endif // types_h
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