81 lines
2.8 KiB
C++
81 lines
2.8 KiB
C++
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/*
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* Copyright 2021, Yun (Leo) Zhang <imzhangyun@gmail.com>
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*
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* This file is part of HISAT-3N.
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*
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* HISAT-3N is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* HISAT-3N is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with HISAT-3N. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include <unistd.h>
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#include "utility_3n.h"
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#include "alphabet.h"
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void getConversion(char usrInputFrom, char usrInputTo, char& convertFrom, char& convertTo) {
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if ((usrInputFrom == 'A' && usrInputTo == 'T') ||
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(usrInputFrom == 'A' && usrInputTo == 'C') ||
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(usrInputFrom == 'C' && usrInputTo == 'G') ||
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(usrInputFrom == 'C' && usrInputTo == 'T') ||
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(usrInputFrom == 'G' && usrInputTo == 'A') ||
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(usrInputFrom == 'T' && usrInputTo == 'G')) {
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convertFrom = usrInputFrom;
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convertTo = usrInputTo;
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return;
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}
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if ((usrInputFrom == 'C' && usrInputTo == 'A') ||
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(usrInputFrom == 'G' && usrInputTo == 'C') ||
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(usrInputFrom == 'T' && usrInputTo == 'A') ||
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(usrInputFrom == 'T' && usrInputTo == 'C') ||
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(usrInputFrom == 'A' && usrInputTo == 'G') ||
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(usrInputFrom == 'G' && usrInputTo == 'T')) {
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convertFrom = usrInputTo;
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convertTo = usrInputFrom;
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return;
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}
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cerr << "Un-identified --base-change type: " << usrInputFrom << "," << usrInputTo << endl;
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throw 1;
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}
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bool fileExist (string name) {
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return ( access( name.c_str(), F_OK ) != -1 );
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}
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void ConvertMatrix3N:: convertMatrix() {
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restoreNormal();
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for (int i = 0; i < 4; i++) {
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char base = allBase[i];
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char lowerBase = allBaseLower[i];
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if (convertFrom == base) {
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asc2dna[base] = charToInt(convertTo);
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asc2dna[lowerBase] = charToInt(convertTo);
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} else if (complement(convertFrom) == base) {
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asc2dnacomp[base] = convertTo;
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asc2dnacomp[lowerBase] = convertTo;
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dnacomp[i] = charToInt(convertTo);
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}
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}
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}
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void ConvertMatrix3N::restoreNormal() {
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for (int i = 0; i < 4; i++) {
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char base = allBase[i];
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char lowerBase = allBaseLower[i];
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asc2dna[base] = charToInt(base);
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asc2dna[lowerBase] = charToInt(base);
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asc2dnacomp[base] = complement(base);
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asc2dnacomp[lowerBase] = complement(base);
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dnacomp[i] = charToInt(complement(base));
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}
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}
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