source: branches/lib/GDE/MUSCLE/src/types.h

#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