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BioD import
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‎BioD/bio/core/base.d

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/*
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This file is part of BioD.
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Copyright (C) 2012 Artem Tarasov <lomereiter@gmail.com>
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Permission is hereby granted, free of charge, to any person obtaining a
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copy of this software and associated documentation files (the "Software"),
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to deal in the Software without restriction, including without limitation
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the rights to use, copy, modify, merge, publish, distribute, sublicense,
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and/or sell copies of the Software, and to permit persons to whom the
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Software is furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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DEALINGS IN THE SOFTWARE.
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*/
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module bio.core.base;
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import bio.core.tinymap;
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import std.traits;
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/// Code common to both Base5 and Base16
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mixin template CommonBaseOperations() {
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/// Convert to char
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char asCharacter() @property const { return _code2char[_code]; }
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///
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alias asCharacter this;
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}
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/// Base representation supporting full set of IUPAC codes
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struct Base {
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mixin TinyMapInterface!16;
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private enum ubyte[256] _char2code = [
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15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0,15,15,
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15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
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15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,
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15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
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15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15,
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15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
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15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
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];
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// = 0000
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//
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// A 0001
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// C 0010
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// G 0100
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// T 1000
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//
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// W 1001 (A T) Weak
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// S 0110 (C G) Strong
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//
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// M 0011 (A C) aMino
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// K 1100 (G T) Keto
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// R 0101 (A G) puRine
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// Y 1010 (A G) pYrimidine
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//
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// B 1110 (not A)
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// D 1101 (not C)
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// H 1011 (not G)
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// V 0111 (not T)
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//
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// N 1111 (aNy base)
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private enum _code2char = "=ACMGRSVTWYHKDBN";
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private enum ubyte[16] _complement_table = [0x0, 0x8, 0x4, 0xC,
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0x2, 0xA, 0x6, 0xE,
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0x1, 0x9, 0x5, 0xD,
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0x3, 0xB, 0x7, 0xF];
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/// Complementary base
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Base complement() @property const {
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// take the code, reverse the bits, and return the base
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return Base.fromInternalCode(_complement_table[_code]);
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}
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unittest {
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import std.ascii;
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foreach (i, c; _code2char) {
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assert(_char2code[c] == i);
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}
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foreach (c; 0 .. 256) {
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auto c2 = _code2char[_char2code[c]];
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if (c2 != 'N') {
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if ('0' <= c && c <= '9') {
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assert(c2 == "ACGT"[c - '0']);
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} else {
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assert(c2 == toUpper(c));
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}
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}
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}
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}
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mixin CommonBaseOperations;
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/// Construct from IUPAC code
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this(char c) {
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_code = _char2code[cast(ubyte)c];
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}
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/// ditto
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this(dchar c) {
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_code = _char2code[cast(ubyte)c];
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}
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private enum ubyte[5] nt5_to_nt16 = [1, 2, 4, 8, 15];
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private static Base fromBase5(Base5 base) {
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Base b = void;
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b._code = nt5_to_nt16[base.internal_code];
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return b;
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}
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/// Conversion to Base5
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Base5 opCast(T)() const
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if (is(T == Base5))
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{
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return Base5.fromBase16(this);
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}
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T opCast(T)() const
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if (is(Unqual!T == char) || is(Unqual!T == dchar))
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{
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return asCharacter;
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}
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}
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unittest {
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Base b = 'W';
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assert(b == 'W');
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b = Base.fromInternalCode(0);
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assert(b == '=');
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}
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alias Base Base16;
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/// Base representation supporting only 'A', 'C', 'G', 'T', and 'N'
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/// (internal codes are 0, 1, 2, 3, and 4 correspondingly)
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struct Base5 {
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mixin TinyMapInterface!5;
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private enum ubyte[256] _char2code = [
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
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];
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private enum _code2char = "ACGTN";
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private enum ubyte[16] nt16_to_nt5 = [4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4];
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mixin CommonBaseOperations;
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/// Complementary base
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Base5 complement() @property const {
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return Base5.fromInternalCode(cast(ubyte)(_code == 4 ? 4 : (3 - _code)));
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}
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/// Construct base from one of "acgtACGT" symbols.
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/// Every other character is converted to 'N'
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this(char c) {
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_code = _char2code[cast(ubyte)c];
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}
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/// ditto
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this(dchar c) {
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_code = _char2code[cast(ubyte)c];
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}
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private static Base5 fromBase16(Base16 base) {
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Base5 b = void;
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b._code = nt16_to_nt5[base.internal_code];
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return b;
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}
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/// Conversion to Base16
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Base16 opCast(T)() const
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if(is(T == Base16))
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{
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return Base16.fromBase5(this);
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}
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T opCast(T)() const
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if (is(Unqual!T == char) || is(Unqual!T == dchar))
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{
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return asCharacter;
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}
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}
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unittest {
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auto b5 = Base5('C');
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assert(b5.internal_code == 1);
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b5 = Base5.fromInternalCode(3);
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assert(b5 == 'T');
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// doesn't work with std.conv.to
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//
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//import std.conv;
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//assert(to!Base16(b5).internal_code == 8);
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assert((cast(Base16)b5).internal_code == 8);
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}
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/// Complement base, which might be Base5, Base16, char, or dchar.
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B complementBase(B)(B base) {
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static if(is(Unqual!B == dchar) || is(Unqual!B == char))
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{
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return cast(B)(Base16(base).complement);
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}
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else
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return base.complement;
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}
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/// Convert character to base
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template charToBase(B=Base16)
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{
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B charToBase(C)(C c)
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if(is(Unqual!C == char) || is(Unqual!C == dchar))
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{
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return B(c);
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}
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}
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unittest {
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assert(complementBase('T') == 'A');
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assert(complementBase('G') == 'C');
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assert(complementBase(Base5('A')) == Base5('T'));
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assert(complementBase(Base16('C')) == Base16('G'));
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assert(charToBase!Base16('A').complement == Base16('T'));
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}

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