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sequence_model.cpp
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sequence_model.cpp
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/*
* Copyright (C) 2009-2012 Simon A. Berger
*
* This file is part of papara.
*
* papara 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.
*
* papara 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 papara. If not, see <http://www.gnu.org/licenses/>.
*/
#include "sequence_model.h"
using sequence_model::model;
using sequence_model::tag_aa;
using sequence_model::tag_dna;
using sequence_model::tag_dna4;
namespace raxml_aa_meaning {
// is it officially legal to initialize const static members in the header? I guess c++ removes redundant definitions during linking...
const static char inverse[23] = {'A','R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', 'B', 'Z', '-'};
const static unsigned int bitVector[23] = {1, 2, 4, 8, 16, 32, 64, 128,
256, 512, 1024, 2048, 4096,
8192, 16384, 32768, 65536, 131072, 262144,
524288, 12 /* N | D */, 96 /*Q | E*/, 1048575 /* - */ };
}
const std::vector<char> model<tag_aa>::inverse_meaning(raxml_aa_meaning::inverse, raxml_aa_meaning::inverse + ivy_mike::arrlen(raxml_aa_meaning::inverse));
const std::vector<unsigned int> model<tag_aa>::bit_vector(raxml_aa_meaning::bitVector, raxml_aa_meaning::bitVector + ivy_mike::arrlen(raxml_aa_meaning::bitVector));
namespace raxml_dna_meaning {
const char inverse[16] = {'_', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', '-' };
//const char bitvector[17] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 15 };
}
const std::vector<char> model<tag_dna>::inverse_meaning(raxml_dna_meaning::inverse, raxml_dna_meaning::inverse + ivy_mike::arrlen(raxml_dna_meaning::inverse));
//const std::vector<uint8_t> model<tag_dna>::bit_vector(raxml_dna_meaning::bitvector, raxml_dna_meaning::bitvector + ivy_mike::arrlen(raxml_dna_meaning::bitvector));
namespace raxml_dna4_meaning {
const char inverse[5] = {'A', 'C', 'G', 'T', '-' };
//const char bitvector[17] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 15 };
}
const std::vector<char> model<tag_dna4>::inverse_meaning(raxml_dna4_meaning::inverse, raxml_dna4_meaning::inverse + ivy_mike::arrlen(raxml_dna4_meaning::inverse));