#ifndef PRD_GLOBALS_HXX
#define PRD_GLOBALS_HXX

#ifndef _GLIBCXX_CLIMITS
#include <climits>
#endif
#ifndef ARB_ASSERT_H
#include <arb_assert.h>
#endif
#ifndef ARBTOOLS_H
#include <arbtools.h>
#endif

#define prd_assert(cond) arb_assert(cond)

#ifndef MAX_LONG
#define MAX_LONG LONG_MAX
#endif

#define PRD_MAX_SEQUENCE_POS MAX_LONG
typedef long int PRD_Sequence_Pos;


//
// BaseInverter is used to invert bases while matching sequence
// backwards vs. the primertrees
//
struct BaseInverter {
    char BASE[128];

    BaseInverter() {
        for (int i=0; i < 128; i++)
            BASE[i] = '\x00';

        BASE[(unsigned char)'A'] = 'T';
        BASE[(unsigned char)'T'] = 'A';
        BASE[(unsigned char)'U'] = 'A';
        BASE[(unsigned char)'C'] = 'G';
        BASE[(unsigned char)'G'] = 'C';

        BASE[(unsigned char)'R'] = 'Y';
        BASE[(unsigned char)'M'] = 'K';
        BASE[(unsigned char)'S'] = 'S';
        BASE[(unsigned char)'Y'] = 'R';
        BASE[(unsigned char)'K'] = 'M';
        BASE[(unsigned char)'W'] = 'W';
        BASE[(unsigned char)'V'] = 'B';
        BASE[(unsigned char)'B'] = 'V';
        BASE[(unsigned char)'D'] = 'H';
        BASE[(unsigned char)'H'] = 'D';
        BASE[(unsigned char)'N'] = 'N';
    }
};

static BaseInverter INVERT;


struct ChildLookupTable {
    int INDEX[128];

    ChildLookupTable() {
        for (int i=0; i < 128; i++) INDEX[i] = -1;

        INDEX[(unsigned char)'C'] = 0;
        INDEX[(unsigned char)'G'] = 1;
        INDEX[(unsigned char)'A'] = 2;
        INDEX[(unsigned char)'T'] = 3;
        INDEX[(unsigned char)'U'] = 3;
    }
};

static ChildLookupTable CHAR2CHILD;


class BitField {
    // Meaning of single bits:
    //  2^0 = 1 = A
    //  2^1 = 2 = T/U
    //  2^2 = 4 = C
    //  2^3 = 8 = G
public:
    unsigned int FIELD[128]; // bitoperations are done as unsigned int :(

    BitField() {
        for (int i=0; i < 128; i++)
            FIELD[i] = 0;

        FIELD[(unsigned char)'A'] =  1;
        FIELD[(unsigned char)'T'] =  2;
        FIELD[(unsigned char)'U'] =  2;
        FIELD[(unsigned char)'C'] =  4;
        FIELD[(unsigned char)'G'] =  8;

        FIELD[(unsigned char)'R'] =  9; // A  G
        FIELD[(unsigned char)'M'] =  5; // A C
        FIELD[(unsigned char)'S'] = 12; //   CG
        FIELD[(unsigned char)'Y'] =  6; //  TC
        FIELD[(unsigned char)'K'] = 10; //  T G
        FIELD[(unsigned char)'W'] =  3; // AT
        FIELD[(unsigned char)'V'] = 13; // A CG
        FIELD[(unsigned char)'B'] = 14; //  TCG
        FIELD[(unsigned char)'D'] = 11; // AT G
        FIELD[(unsigned char)'H'] =  7; // ATC
        FIELD[(unsigned char)'N'] = 15; // ATCG
    }
};

static BitField CHAR2BIT;

#else
#error PRD_Globals.hxx included twice
#endif // PRD_GLOBALS_HXX