1 /** 2 * UGENE - Integrated Bioinformatics Tools. 3 * Copyright (C) 2008-2021 UniPro <ugene@unipro.ru> 4 * http://ugene.net 5 * 6 * This program is free software; you can redistribute it and/or 7 * modify it under the terms of the GNU General Public License 8 * as published by the Free Software Foundation; either version 2 9 * of the License, or (at your option) any later version. 10 * 11 * This program is distributed in the hope that it will be useful, 12 * but WITHOUT ANY WARRANTY; without even the implied warranty of 13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 * GNU General Public License for more details. 15 * 16 * You should have received a copy of the GNU General Public License 17 * along with this program; if not, write to the Free Software 18 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, 19 * MA 02110-1301, USA. 20 */ 21 22 #ifndef PAIRALIGNMENTSTRINGS_H 23 #define PAIRALIGNMENTSTRINGS_H 24 25 #include <U2Core/U2Region.h> 26 27 namespace U2 { 28 29 class PairAlignSequences { 30 public: 31 PairAlignSequences(); 32 void setValues(int _score, const U2Region &_refSubseqInterval, const U2Region &_ptrnSubseqInterval, QByteArray _pairAlignment); 33 34 U2Region refSubseqInterval; 35 U2Region ptrnSubseqInterval; 36 int score; 37 QByteArray pairAlignment; 38 39 bool isAminoTranslated; 40 bool isDNAComplemented; 41 42 static const char UP = 'u'; 43 static const char LEFT = 'l'; 44 static const char DIAG = 'd'; 45 }; 46 47 } // namespace U2 48 49 #endif 50