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BioD import
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268 changes: 268 additions & 0 deletions BioD/bio/core/base.d
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/*
This file is part of BioD.
Copyright (C) 2012 Artem Tarasov <lomereiter@gmail.com>
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
*/
module bio.core.base;

import bio.core.tinymap;
import std.traits;

/// Code common to both Base5 and Base16
mixin template CommonBaseOperations() {
/// Convert to char
char asCharacter() @property const { return _code2char[_code]; }
///
alias asCharacter this;

}

/// Base representation supporting full set of IUPAC codes
struct Base {
mixin TinyMapInterface!16;

private enum ubyte[256] _char2code = [
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0,15,15,

15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,
15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,

15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,

15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
];

// = 0000
//
// A 0001
// C 0010
// G 0100
// T 1000
//
// W 1001 (A T) Weak
// S 0110 (C G) Strong
//
// M 0011 (A C) aMino
// K 1100 (G T) Keto
// R 0101 (A G) puRine
// Y 1010 (A G) pYrimidine
//
// B 1110 (not A)
// D 1101 (not C)
// H 1011 (not G)
// V 0111 (not T)
//
// N 1111 (aNy base)
private enum _code2char = "=ACMGRSVTWYHKDBN";

private enum ubyte[16] _complement_table = [0x0, 0x8, 0x4, 0xC,
0x2, 0xA, 0x6, 0xE,
0x1, 0x9, 0x5, 0xD,
0x3, 0xB, 0x7, 0xF];
/// Complementary base
Base complement() @property const {
// take the code, reverse the bits, and return the base
return Base.fromInternalCode(_complement_table[_code]);
}

unittest {
import std.ascii;

foreach (i, c; _code2char) {
assert(_char2code[c] == i);
}

foreach (c; 0 .. 256) {
auto c2 = _code2char[_char2code[c]];
if (c2 != 'N') {
if ('0' <= c && c <= '9') {
assert(c2 == "ACGT"[c - '0']);
} else {
assert(c2 == toUpper(c));
}
}
}
}

mixin CommonBaseOperations;
/// Construct from IUPAC code
this(char c) {
_code = _char2code[cast(ubyte)c];
}

/// ditto
this(dchar c) {
_code = _char2code[cast(ubyte)c];
}

private enum ubyte[5] nt5_to_nt16 = [1, 2, 4, 8, 15];
private static Base fromBase5(Base5 base) {
Base b = void;
b._code = nt5_to_nt16[base.internal_code];
return b;
}

/// Conversion to Base5
Base5 opCast(T)() const
if (is(T == Base5))
{
return Base5.fromBase16(this);
}

T opCast(T)() const
if (is(Unqual!T == char) || is(Unqual!T == dchar))
{
return asCharacter;
}
}

unittest {
Base b = 'W';
assert(b == 'W');

b = Base.fromInternalCode(0);
assert(b == '=');
}

alias Base Base16;

/// Base representation supporting only 'A', 'C', 'G', 'T', and 'N'
/// (internal codes are 0, 1, 2, 3, and 4 correspondingly)
struct Base5 {
mixin TinyMapInterface!5;

private enum ubyte[256] _char2code = [
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,

4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,

4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,

4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
];

private enum _code2char = "ACGTN";
private enum ubyte[16] nt16_to_nt5 = [4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4];

mixin CommonBaseOperations;

/// Complementary base
Base5 complement() @property const {
return Base5.fromInternalCode(cast(ubyte)(_code == 4 ? 4 : (3 - _code)));
}

/// Construct base from one of "acgtACGT" symbols.
/// Every other character is converted to 'N'
this(char c) {
_code = _char2code[cast(ubyte)c];
}

/// ditto
this(dchar c) {
_code = _char2code[cast(ubyte)c];
}

private static Base5 fromBase16(Base16 base) {
Base5 b = void;
b._code = nt16_to_nt5[base.internal_code];
return b;
}

/// Conversion to Base16
Base16 opCast(T)() const
if(is(T == Base16))
{
return Base16.fromBase5(this);
}

T opCast(T)() const
if (is(Unqual!T == char) || is(Unqual!T == dchar))
{
return asCharacter;
}
}

unittest {
auto b5 = Base5('C');
assert(b5.internal_code == 1);
b5 = Base5.fromInternalCode(3);
assert(b5 == 'T');

// doesn't work with std.conv.to
//
//import std.conv;
//assert(to!Base16(b5).internal_code == 8);

assert((cast(Base16)b5).internal_code == 8);
}

/// Complement base, which might be Base5, Base16, char, or dchar.
B complementBase(B)(B base) {
static if(is(Unqual!B == dchar) || is(Unqual!B == char))
{
return cast(B)(Base16(base).complement);
}
else
return base.complement;
}

/// Convert character to base
template charToBase(B=Base16)
{
B charToBase(C)(C c)
if(is(Unqual!C == char) || is(Unqual!C == dchar))
{
return B(c);
}
}

unittest {
assert(complementBase('T') == 'A');
assert(complementBase('G') == 'C');

assert(complementBase(Base5('A')) == Base5('T'));
assert(complementBase(Base16('C')) == Base16('G'));

assert(charToBase!Base16('A').complement == Base16('T'));
}
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