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 _U2_SMITH_WATERMAN_RESULT_H_ 23 #define _U2_SMITH_WATERMAN_RESULT_H_ 24 25 #include <U2Core/AnnotationData.h> 26 27 namespace U2 { 28 29 struct U2ALGORITHM_EXPORT SmithWatermanResult { 30 SharedAnnotationData toAnnotation(const QString &name) const; 31 bool operator<(const SmithWatermanResult &op1) const; 32 33 U2Strand strand; 34 bool trans; 35 float score; 36 U2Region refSubseq; 37 bool isJoined; 38 U2Region refJoinedSubseq; 39 40 U2Region ptrnSubseq; 41 QByteArray pairAlignment; 42 43 static const char UP = 'u'; 44 static const char LEFT = 'l'; 45 static const char DIAG = 'd'; 46 }; 47 48 class U2ALGORITHM_EXPORT SmithWatermanResultListener { 49 public: 50 virtual ~SmithWatermanResultListener(); 51 52 virtual void pushResult(const SmithWatermanResult &r); 53 virtual void pushResult(const QList<SmithWatermanResult> &r); 54 virtual QList<SmithWatermanResult> popResults(); 55 virtual QList<SmithWatermanResult> getResults() const; 56 57 private: 58 QList<SmithWatermanResult> result; 59 }; 60 61 } // namespace U2 62 63 #endif 64