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_UTIL_H_ 23 #define _U2_SMITH_WATERMAN_UTIL_H_ 24 25 #include "SmithWatermanResult.h" 26 27 namespace U2 { 28 29 class SMatrix; 30 31 class U2ALGORITHM_EXPORT SmithWatermanUtil { 32 public: 33 static float calcScoreItSelf(const SMatrix &m, 34 const char *pattern, 35 int patternLen); 36 37 static int calcWindowLen(bool transl, 38 int sequenceLen, 39 int patternLen, 40 float scoreItSelf, 41 float thresholdScore, 42 float scoreGapOpen, 43 float scoreGapExtd); 44 45 static float calcScoreThreshold(float percent, 46 float scoreItSelf); 47 48 static int calcOverlapSize(bool transl, 49 int windowLen, 50 float scoreItSelf, 51 float scoreGapOpen, 52 float scoreGapExtd); 53 54 static bool removeIdenticalResults(QList<SmithWatermanResult> *lst); 55 }; 56 57 } // namespace U2 58 59 #endif 60