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/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "BaseAsciiMap.h"
//
// Map ASCII values to a 2 (or 3) bit encoding for the base pair value for
// both base and color space.
// class 0 -> 'A' (Adenine - 0x41 and 0x61)
// class 1 -> 'C' (Cytosine - 0x43 and 0x63)
// class 2 -> 'G' (Guanine - 0x47 and 0x67)
// class 3 -> 'T' (Thymine - 0x54 and 0x74)
// class 4 -> 'N' (Unknown - read error or incomplete data - 0x4E and 0x6E)
// class 5 -> not a valid DNA base pair character
//
// Note: The +1 array size is for the terminating NUL character
//
// NB: This table also maps 0, 1, 2, and 3 to the corresponding integers,
// and '.' to class 4. This allows ABI SOLiD reads to be converted
// to integers via ReadIndexer::Word2Integer.
//
unsigned char BaseAsciiMap::baseColor2int[256+1] =
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x00-0x0F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x10-0x1F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\004\005" // 0x20-0x2F
"\000\001\002\003\005\005\005\005\005\005\005\005\005\005\005\005" // 0x30-0x3F
"\005\000\005\001\005\005\005\002\005\005\005\005\005\005\004\005" // 0x40-0x4F
"\005\005\005\005\003\005\005\005\005\005\005\005\005\005\005\005" // 0x50-0x5F
"\005\000\005\001\005\005\005\002\005\005\005\005\005\005\004\005" // 0x60-0x6F
"\005\005\005\005\003\005\005\005\005\005\005\005\005\005\005\005" // 0x70-0x7F
// not used, but included for completeness:
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x80-0x8F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x90-0x9F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xA0-0xAF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xB0-0xBF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xC0-0xCF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xD0-0xDF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xE0-0xEF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xF0-0xFF
;
// Map ASCII values to a 2 (or 3) bit encoding for the base pair value for
// just base space (ACTGNactgn).
unsigned char BaseAsciiMap::base2int[256+1] =
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x00-0x0F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x10-0x1F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x20-0x2F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x30-0x3F
"\005\000\005\001\005\005\005\002\005\005\005\005\005\005\004\005" // 0x40-0x4F
"\005\005\005\005\003\005\005\005\005\005\005\005\005\005\005\005" // 0x50-0x5F
"\005\000\005\001\005\005\005\002\005\005\005\005\005\005\004\005" // 0x60-0x6F
"\005\005\005\005\003\005\005\005\005\005\005\005\005\005\005\005" // 0x70-0x7F
// not used, but included for completeness:
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x80-0x8F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x90-0x9F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xA0-0xAF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xB0-0xBF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xC0-0xCF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xD0-0xDF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xE0-0xEF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xF0-0xFF
;
// Map ASCII values to a 2 (or 3) bit encoding for the base pair value for
// just color space (0123).
unsigned char BaseAsciiMap::color2int[256+1] =
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x00-0x0F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x10-0x1F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\004\005" // 0x20-0x2F
"\000\001\002\003\005\005\005\005\005\005\005\005\005\005\005\005" // 0x30-0x3F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x40-0x4F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x50-0x5F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x60-0x6F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x70-0x7F
// not used, but included for completeness:
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x80-0x8F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0x90-0x9F
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xA0-0xAF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xB0-0xBF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xC0-0xCF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xD0-0xDF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xE0-0xEF
"\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005\005" // 0xF0-0xFF
;
//
// This is obviously for base space use only:
//
const char BaseAsciiMap::int2base[] = "ACGTNMXXXXXXXXXX";
//
// convert int to color space value
//
const char BaseAsciiMap::int2colorSpace[] = "0123NXXXXXXXXXXX";
/// This table maps 5' base space to the 3' complement base space
/// values, as well as 5' color space values to the corresponding
/// 3' complement color space values.
///
/// In both cases, invalids are mapped to 'N', which isn't accurate
/// for ABI SOLiD, but internally it shouldn't matter (on output it
/// will).
unsigned char BaseAsciiMap::base2complement[256+1 /* for NUL char */] =
"NNNNNNNNNNNNNNNN" // 0x00-0x0F
"NNNNNNNNNNNNNNNN" // 0x10-0x1F
"NNNNNNNNNNNNNNNN" // 0x20-0x2F
"0123NNNNNNNNNNNN" // 0x30-0x3F
"NTNGNNNCNNNNNNNN" // 0x40-0x4F
"NNNNANNNNNNNNNNN" // 0x50-0x5F
"NTNGNNNCNNNNNNNN" // 0x60-0x6F
"NNNNANNNNNNNNNNN" // 0x70-0x7F
// not used, but included for completeness:
"NNNNNNNNNNNNNNNN" // 0x80-0x8F
"NNNNNNNNNNNNNNNN" // 0x90-0x9F
"NNNNNNNNNNNNNNNN" // 0xA0-0xAF
"NNNNNNNNNNNNNNNN" // 0xB0-0xBF
"NNNNNNNNNNNNNNNN" // 0xC0-0xCF
"NNNNNNNNNNNNNNNN" // 0xD0-0xDF
"NNNNNNNNNNNNNNNN" // 0xE0-0xEF
"NNNNNNNNNNNNNNNN" // 0xF0-0xFF
;
BaseAsciiMap::BaseAsciiMap()
: myNumPrimerBases(1)
{
myBase2IntMapPtr = NULL;
}
BaseAsciiMap::~BaseAsciiMap()
{
}
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