sequtil_tables.cpp

ncbi源码

    0x57,0x47,    0x57,0x52,    0x57,0x53,    0x57,0x56,
    0x57,0x54,    0x57,0x57,    0x57,0x59,    0x57,0x48,
    0x57,0x4b,    0x57,0x44,    0x57,0x42,    0x57,0x4e,
    0x59,0x4e,    0x59,0x41,    0x59,0x43,    0x59,0x4d,
    0x59,0x47,    0x59,0x52,    0x59,0x53,    0x59,0x56,
    0x59,0x54,    0x59,0x57,    0x59,0x59,    0x59,0x48,
    0x59,0x4b,    0x59,0x44,    0x59,0x42,    0x59,0x4e,
    0x48,0x4e,    0x48,0x41,    0x48,0x43,    0x48,0x4d,
    0x48,0x47,    0x48,0x52,    0x48,0x53,    0x48,0x56,
    0x48,0x54,    0x48,0x57,    0x48,0x59,    0x48,0x48,
    0x48,0x4b,    0x48,0x44,    0x48,0x42,    0x48,0x4e,
    0x4b,0x4e,    0x4b,0x41,    0x4b,0x43,    0x4b,0x4d,
    0x4b,0x47,    0x4b,0x52,    0x4b,0x53,    0x4b,0x56,
    0x4b,0x54,    0x4b,0x57,    0x4b,0x59,    0x4b,0x48,
    0x4b,0x4b,    0x4b,0x44,    0x4b,0x42,    0x4b,0x4e,
    0x44,0x4e,    0x44,0x41,    0x44,0x43,    0x44,0x4d,
    0x44,0x47,    0x44,0x52,    0x44,0x53,    0x44,0x56,
    0x44,0x54,    0x44,0x57,    0x44,0x59,    0x44,0x48,
    0x44,0x4b,    0x44,0x44,    0x44,0x42,    0x44,0x4e,
    0x42,0x4e,    0x42,0x41,    0x42,0x43,    0x42,0x4d,
    0x42,0x47,    0x42,0x52,    0x42,0x53,    0x42,0x56,
    0x42,0x54,    0x42,0x57,    0x42,0x59,    0x42,0x48,
    0x42,0x4b,    0x42,0x44,    0x42,0x42,    0x42,0x4e,
    0x4e,0x4e,    0x4e,0x41,    0x4e,0x43,    0x4e,0x4d,
    0x4e,0x47,    0x4e,0x52,    0x4e,0x53,    0x4e,0x56,
    0x4e,0x54,    0x4e,0x57,    0x4e,0x59,    0x4e,0x48,
    0x4e,0x4b,    0x4e,0x44,    0x4e,0x42,    0x4e,0x4e
};


// NCBI4na to NCBI2na
// 0  -> 3  (gap -> T)
// 1  -> 0  (A -> A)
// 2  -> 1  (C -> C)
// 3  -> 1  (M -> C)
// 4  -> 2  (G -> G)
// 5  -> 2  (R -> G)
// 6  -> 1  (S -> C)
// 7  -> 0  (V -> A)
// 8  -> 3  (T -> T)
// 9  -> 3  (W -> T)
// 10 -> 3  (Y -> T)
// 11 -> 0  (H -> A)
// 12 -> 2  (K -> G)
// 13 -> 2  (D -> G)
// 14 -> 1  (B -> C)
// 15 -> 0  (N -> A)
/*
    for ( base[0] = 0; base[0] < 16; ++base[0] ) {
        for ( base[1] = 0; base[1] < 16; ++base[1] ) {
            Uint1 index = base[0] << 4 | base[1];
            sm_TableOffset0[index * 2] = 
                (convert[base[0]] << 6) | (convert[base[1]] << 4);
            sm_TableOffset0[index * 2 + 1] = 
                (convert[base[0]] << 2) | convert[base[1]];
        }
    }
*/
const Uint1 C4naTo2na::scm_Table0[512] = {
    0xf0,0xf,    0xc0,0xc,    0xd0,0xd,    0xd0,0xd,
    0xe0,0xe,    0xe0,0xe,    0xd0,0xd,    0xc0,0xc,
    0xf0,0xf,    0xf0,0xf,    0xf0,0xf,    0xc0,0xc,
    0xe0,0xe,    0xe0,0xe,    0xd0,0xd,    0xc0,0xc,
    0x30,0x3,    0x0,0x0,    0x10,0x1,    0x10,0x1,
    0x20,0x2,    0x20,0x2,    0x10,0x1,    0x0,0x0,
    0x30,0x3,    0x30,0x3,    0x30,0x3,    0x0,0x0,
    0x20,0x2,    0x20,0x2,    0x10,0x1,    0x0,0x0,
    0x70,0x7,    0x40,0x4,    0x50,0x5,    0x50,0x5,
    0x60,0x6,    0x60,0x6,    0x50,0x5,    0x40,0x4,
    0x70,0x7,    0x70,0x7,    0x70,0x7,    0x40,0x4,
    0x60,0x6,    0x60,0x6,    0x50,0x5,    0x40,0x4,
    0x70,0x7,    0x40,0x4,    0x50,0x5,    0x50,0x5,
    0x60,0x6,    0x60,0x6,    0x50,0x5,    0x40,0x4,
    0x70,0x7,    0x70,0x7,    0x70,0x7,    0x40,0x4,
    0x60,0x6,    0x60,0x6,    0x50,0x5,    0x40,0x4,
    0xb0,0xb,    0x80,0x8,    0x90,0x9,    0x90,0x9,
    0xa0,0xa,    0xa0,0xa,    0x90,0x9,    0x80,0x8,
    0xb0,0xb,    0xb0,0xb,    0xb0,0xb,    0x80,0x8,
    0xa0,0xa,    0xa0,0xa,    0x90,0x9,    0x80,0x8,
    0xb0,0xb,    0x80,0x8,    0x90,0x9,    0x90,0x9,
    0xa0,0xa,    0xa0,0xa,    0x90,0x9,    0x80,0x8,
    0xb0,0xb,    0xb0,0xb,    0xb0,0xb,    0x80,0x8,
    0xa0,0xa,    0xa0,0xa,    0x90,0x9,    0x80,0x8,
    0x70,0x7,    0x40,0x4,    0x50,0x5,    0x50,0x5,
    0x60,0x6,    0x60,0x6,    0x50,0x5,    0x40,0x4,
    0x70,0x7,    0x70,0x7,    0x70,0x7,    0x40,0x4,
    0x60,0x6,    0x60,0x6,    0x50,0x5,    0x40,0x4,
    0x30,0x3,    0x0,0x0,    0x10,0x1,    0x10,0x1,
    0x20,0x2,    0x20,0x2,    0x10,0x1,    0x0,0x0,
    0x30,0x3,    0x30,0x3,    0x30,0x3,    0x0,0x0,
    0x20,0x2,    0x20,0x2,    0x10,0x1,    0x0,0x0,
    0xf0,0xf,    0xc0,0xc,    0xd0,0xd,    0xd0,0xd,
    0xe0,0xe,    0xe0,0xe,    0xd0,0xd,    0xc0,0xc,
    0xf0,0xf,    0xf0,0xf,    0xf0,0xf,    0xc0,0xc,
    0xe0,0xe,    0xe0,0xe,    0xd0,0xd,    0xc0,0xc,
    0xf0,0xf,    0xc0,0xc,    0xd0,0xd,    0xd0,0xd,
    0xe0,0xe,    0xe0,0xe,    0xd0,0xd,    0xc0,0xc,
    0xf0,0xf,    0xf0,0xf,    0xf0,0xf,    0xc0,0xc,
    0xe0,0xe,    0xe0,0xe,    0xd0,0xd,    0xc0,0xc,
    0xf0,0xf,    0xc0,0xc,    0xd0,0xd,    0xd0,0xd,
    0xe0,0xe,    0xe0,0xe,    0xd0,0xd,    0xc0,0xc,
    0xf0,0xf,    0xf0,0xf,    0xf0,0xf,    0xc0,0xc,
    0xe0,0xe,    0xe0,0xe,    0xd0,0xd,    0xc0,0xc,
    0x30,0x3,    0x0,0x0,    0x10,0x1,    0x10,0x1,
    0x20,0x2,    0x20,0x2,    0x10,0x1,    0x0,0x0,
    0x30,0x3,    0x30,0x3,    0x30,0x3,    0x0,0x0,
    0x20,0x2,    0x20,0x2,    0x10,0x1,    0x0,0x0,
    0xb0,0xb,    0x80,0x8,    0x90,0x9,    0x90,0x9,
    0xa0,0xa,    0xa0,0xa,    0x90,0x9,    0x80,0x8,
    0xb0,0xb,    0xb0,0xb,    0xb0,0xb,    0x80,0x8,
    0xa0,0xa,    0xa0,0xa,    0x90,0x9,    0x80,0x8,
    0xb0,0xb,    0x80,0x8,    0x90,0x9,    0x90,0x9,
    0xa0,0xa,    0xa0,0xa,    0x90,0x9,    0x80,0x8,
    0xb0,0xb,    0xb0,0xb,    0xb0,0xb,    0x80,0x8,
    0xa0,0xa,    0xa0,0xa,    0x90,0x9,    0x80,0x8,
    0x70,0x7,    0x40,0x4,    0x50,0x5,    0x50,0x5,
    0x60,0x6,    0x60,0x6,    0x50,0x5,    0x40,0x4,
    0x70,0x7,    0x70,0x7,    0x70,0x7,    0x40,0x4,
    0x60,0x6,    0x60,0x6,    0x50,0x5,    0x40,0x4,
    0x30,0x3,    0x0,0x0,    0x10,0x1,    0x10,0x1,
    0x20,0x2,    0x20,0x2,    0x10,0x1,    0x0,0x0,
    0x30,0x3,    0x30,0x3,    0x30,0x3,    0x0,0x0,
    0x20,0x2,    0x20,0x2,    0x10,0x1,    0x0,0x0
};

/*
    for ( base[0] = 0; base[0] < 16; ++base[0] ) {
        for ( base[1] = 0; base[1] < 16; ++base[1] ) {
            Uint1 index = base[0] << 4 | base[1];
            sm_TableOffset1[index * 3] = 
                convert[base[1]] << 6;
            sm_TableOffset1[index * 3 + 1] = 
                (convert[base[0]] << 4) | (convert[base[1]] << 2);
            sm_TableOffset1[index * 3 + 2] = 
                convert[base[0]];
        }
    }
*/
const Uint1 C4naTo2na::scm_Table1[768] = {
    0xc0,0x3c,0x3,    0x0,0x30,0x3,    0x40,0x34,0x3,    0x40,0x34,0x3,
    0x80,0x38,0x3,    0x80,0x38,0x3,    0x40,0x34,0x3,    0x0,0x30,0x3,
    0xc0,0x3c,0x3,    0xc0,0x3c,0x3,    0xc0,0x3c,0x3,    0x0,0x30,0x3,
    0x80,0x38,0x3,    0x80,0x38,0x3,    0x40,0x34,0x3,    0x0,0x30,0x3,
    0xc0,0xc,0x0,    0x0,0x0,0x0,    0x40,0x4,0x0,    0x40,0x4,0x0,
    0x80,0x8,0x0,    0x80,0x8,0x0,    0x40,0x4,0x0,    0x0,0x0,0x0,
    0xc0,0xc,0x0,    0xc0,0xc,0x0,    0xc0,0xc,0x0,    0x0,0x0,0x0,
    0x80,0x8,0x0,    0x80,0x8,0x0,    0x40,0x4,0x0,    0x0,0x0,0x0,
    0xc0,0x1c,0x1,    0x0,0x10,0x1,    0x40,0x14,0x1,    0x40,0x14,0x1,
    0x80,0x18,0x1,    0x80,0x18,0x1,    0x40,0x14,0x1,    0x0,0x10,0x1,
    0xc0,0x1c,0x1,    0xc0,0x1c,0x1,    0xc0,0x1c,0x1,    0x0,0x10,0x1,
    0x80,0x18,0x1,    0x80,0x18,0x1,    0x40,0x14,0x1,    0x0,0x10,0x1,
    0xc0,0x1c,0x1,    0x0,0x10,0x1,    0x40,0x14,0x1,    0x40,0x14,0x1,
    0x80,0x18,0x1,    0x80,0x18,0x1,    0x40,0x14,0x1,    0x0,0x10,0x1,
    0xc0,0x1c,0x1,    0xc0,0x1c,0x1,    0xc0,0x1c,0x1,    0x0,0x10,0x1,
    0x80,0x18,0x1,    0x80,0x18,0x1,    0x40,0x14,0x1,    0x0,0x10,0x1,
    0xc0,0x2c,0x2,    0x0,0x20,0x2,    0x40,0x24,0x2,    0x40,0x24,0x2,
    0x80,0x28,0x2,    0x80,0x28,0x2,    0x40,0x24,0x2,    0x0,0x20,0x2,
    0xc0,0x2c,0x2,    0xc0,0x2c,0x2,    0xc0,0x2c,0x2,    0x0,0x20,0x2,
    0x80,0x28,0x2,    0x80,0x28,0x2,    0x40,0x24,0x2,    0x0,0x20,0x2,
    0xc0,0x2c,0x2,    0x0,0x20,0x2,    0x40,0x24,0x2,    0x40,0x24,0x2,
    0x80,0x28,0x2,    0x80,0x28,0x2,    0x40,0x24,0x2,    0x0,0x20,0x2,
    0xc0,0x2c,0x2,    0xc0,0x2c,0x2,    0xc0,0x2c,0x2,    0x0,0x20,0x2,
    0x80,0x28,0x2,    0x80,0x28,0x2,    0x40,0x24,0x2,    0x0,0x20,0x2,
    0xc0,0x1c,0x1,    0x0,0x10,0x1,    0x40,0x14,0x1,    0x40,0x14,0x1,
    0x80,0x18,0x1,    0x80,0x18,0x1,    0x40,0x14,0x1,    0x0,0x10,0x1,
    0xc0,0x1c,0x1,    0xc0,0x1c,0x1,    0xc0,0x1c,0x1,    0x0,0x10,0x1,
    0x80,0x18,0x1,    0x80,0x18,0x1,    0x40,0x14,0x1,    0x0,0x10,0x1,
    0xc0,0xc,0x0,    0x0,0x0,0x0,    0x40,0x4,0x0,    0x40,0x4,0x0,
    0x80,0x8,0x0,    0x80,0x8,0x0,    0x40,0x4,0x0,    0x0,0x0,0x0,
    0xc0,0xc,0x0,    0xc0,0xc,0x0,    0xc0,0xc,0x0,    0x0,0x0,0x0,
    0x80,0x8,0x0,    0x80,0x8,0x0,    0x40,0x4,0x0,    0x0,0x0,0x0,
    0xc0,0x3c,0x3,    0x0,0x30,0x3,    0x40,0x34,0x3,    0x40,0x34,0x3,
    0x80,0x38,0x3,    0x80,0x38,0x3,    0x40,0x34,0x3,    0x0,0x30,0x3,
    0xc0,0x3c,0x3,    0xc0,0x3c,0x3,    0xc0,0x3c,0x3,    0x0,0x30,0x3,
    0x80,0x38,0x3,    0x80,0x38,0x3,    0x40,0x34,0x3,    0x0,0x30,0x3,
    0xc0,0x3c,0x3,    0x0,0x30,0x3,    0x40,0x34,0x3,    0x40,0x34,0x3,
    0x80,0x38,0x3,    0x80,0x38,0x3,    0x40,0x34,0x3,    0x0,0x30,0x3,
    0xc0,0x3c,0x3,    0xc0,0x3c,0x3,    0xc0,0x3c,0x3,    0x0,0x30,0x3,
    0x80,0x38,0x3,    0x80,0x38,0x3,    0x40,0x34,0x3,    0x0,0x30,0x3,
    0xc0,0x3c,0x3,    0x0,0x30,0x3,    0x40,0x34,0x3,    0x40,0x34,0x3,
    0x80,0x38,0x3,    0x80,0x38,0x3,    0x40,0x34,0x3,    0x0,0x30,0x3,
    0xc0,0x3c,0x3,    0xc0,0x3c,0x3,    0xc0,0x3c,0x3,    0x0,0x30,0x3,
    0x80,0x38,0x3,    0x80,0x38,0x3,    0x40,0x34,0x3,    0x0,0x30,0x3,
    0xc0,0xc,0x0,    0x0,0x0,0x0,    0x40,0x4,0x0,    0x40,0x4,0x0,
    0x80,0x8,0x0,    0x80,0x8,0x0,    0x40,0x4,0x0,    0x0,0x0,0x0,
    0xc0,0xc,0x0,    0xc0,0xc,0x0,    0xc0,0xc,0x0,    0x0,0x0,0x0,
    0x80,0x8,0x0,    0x80,0x8,0x0,    0x40,0x4,0x0,    0x0,0x0,0x0,
    0xc0,0x2c,0x2,    0x0,0x20,0x2,    0x40,0x24,0x2,    0x40,0x24,0x2,
    0x80,0x28,0x2,    0x80,0x28,0x2,    0x40,0x24,0x2,    0x0,0x20,0x2,
    0xc0,0x2c,0x2,    0xc0,0x2c,0x2,    0xc0,0x2c,0x2,    0x0,0x20,0x2,
    0x80,0x28,0x2,    0x80,0x28,0x2,    0x40,0x24,0x2,    0x0,0x20,0x2,
    0xc0,0x2c,0x2,    0x0,0x20,0x2,    0x40,0x24,0x2,    0x40,0x24,0x2,
    0x80,0x28,0x2,    0x80,0x28,0x2,    0x40,0x24,0x2,    0x0,0x20,0x2,
    0xc0,0x2c,0x2,    0xc0,0x2c,0x2,    0xc0,0x2c,0x2,    0x0,0x20,0x2,
    0x80,0x28,0x2,    0x80,0x28,0x2,    0x40,0x24,0x2,    0x0,0x20,0x2,
    0xc0,0x1c,0x1,    0x0,0x10,0x1,    0x40,0x14,0x1,    0x40,0x14,0x1,
    0x80,0x18,0x1,    0x80,0x18,0x1,    0x40,0x14,0x1,    0x0,0x10,0x1,
    0xc0,0x1c,0x1,    0xc0,0x1c,0x1,    0xc0,0x1c,0x1,    0x0,0x10,0x1,
    0x80,0x18,0x1,    0x80,0x18,0x1,    0x40,0x14,0x1,    0x0,0x10,0x1,
    0xc0,0xc,0x0,    0x0,0x0,0x0,    0x40,0x4,0x0,    0x40,0x4,0x0,
    0x80,0x8,0x0,    0x80,0x8,0x0,    0x40,0x4,0x0,    0x0,0x0,0x0,
    0xc0,0xc,0x0,    0xc0,0xc,0x0,    0xc0,0xc,0x0,    0x0,0x0,0x0,
    0x80,0x8,0x0,    0x80,0x8,0x0,    0x40,0x4,0x0,    0x0,0x0,0x0
};


// NCBI4na to NCBI2na_expand
// gap -> 3 T
// A   -> 0 A
// C   -> 1 C
// M   -> 1 C
// G   -> 2 G
// R   -> 2 G
// S   -> 1 C
// V   -> 0 A
// T   -> 3 T
// W   -> 3 T
// Y   -> 3 T
// H   -> 0 A
// K   -> 2 G
// D   -> 2 G
// B   -> 1 C
// N   -> 0 A

const Uint1 C4naTo2naExpand::scm_Table[512] = {
    0x3,0x3,    0x3,0x0,    0x3,0x1,    0x3,0x1,
    0x3,0x2,    0x3,0x2,    0x3,0x1,    0x3,0x0,
    0x3,0x3,    0x3,0x3,    0x3,0x3,    0x3,0x0,
    0x3,0x2,    0x3,0x2,    0x3,0x1,    0x3,0x0,
    0x0,0x3,    0x0,0x0,    0x0,0x1,    0x0,0x1,
    0x0,0x2,    0x0,0x2,    0x0,0x1,    0x0,0x0,
    0x0,0x3,    0x0,0x3,    0x0,0x3,    0x0,0x0,
    0x0,0x2,    0x0,0x2,    0x0,0x1,    0x0,0x0,
    0x1,0x3,    0x1,0x0,    0x1,0x1,    0x1,0x1,
    0x1,0x2,    0x1,0x2,    0x1,0x1,    0x1,0x0,
    0x1,0x3,    0x1,0x3,    0x1,0x3,    0x1,0x0,
    0x1,0x2,    0x1,0x2,    0x1,0x1,    0x1,0x0,
    0x1,0x3,    0x1,0x0,    0x1,0x1,    0x1,0x1,
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