MASA-Core: SequenceModifiers.hpp Source File

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00001 /*******************************************************************************
00002  *
00003  * Copyright (c) 2010-2015   Edans Sandes
00004  *
00005  * This file is part of MASA-Core.
00006  * 
00007  * MASA-Core is free software: you can redistribute it and/or modify
00008  * it under the terms of the GNU General Public License as published by
00009  * the Free Software Foundation, either version 3 of the License, or
00010  * (at your option) any later version.
00011  * 
00012  * MASA-Core is distributed in the hope that it will be useful,
00013  * but WITHOUT ANY WARRANTY; without even the implied warranty of
00014  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00015  * GNU General Public License for more details.
00016  * 
00017  * You should have received a copy of the GNU General Public License
00018  * along with MASA-Core.  If not, see <http://www.gnu.org/licenses/>.
00019  *
00020  ******************************************************************************/
00021 
00022 #ifndef SEQUENCEMODIFIERS_HPP_
00023 #define SEQUENCEMODIFIERS_HPP_
00024 
00025 class SequenceModifiers {
00026 public:
00027         bool isCompatible(const SequenceModifiers* other) const;
00028 
00029         int getTrimEnd() const;
00030         void setTrimEnd(int trimEnd);
00031         int getTrimStart() const;
00032         void setTrimStart(int trimStart);
00033         bool isClearN() const;
00034         void setClearN(bool clearN);
00035         bool isComplement() const;
00036         void setComplement(bool complement);
00037         bool isReverse() const;
00038         void setReverse(bool reverse);
00039 
00040 private:
00041         bool clear_n;
00042         bool complement;
00043         bool reverse;
00044 
00045         int trimStart;
00046         int trimEnd;
00047 };
00048 
00049 #endif /* SEQUENCEMODIFIERS_HPP_ */