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#ifndef types_h
#define types_h
typedef unsigned char byte;
typedef unsigned short ushort;
typedef float SCOREMATRIX[32][32];
typedef SCOREMATRIX *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 enums.h).
#define s(t) enum t { t##_Undefined = 0,
#define c(t, x) t##_##x,
#define e(t) };
#include "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 "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 "enums.h"
const char *BoolToStr(bool b);
const char *SecsToStr(unsigned long Secs);
#endif // types_h
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