MASA-Core: AlignmentParams.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 ALIGNMENTPARAMS_H_
00023 #define ALIGNMENTPARAMS_H_
00024 
00025 #include "Sequence.hpp"
00026 
00027 class AlignmentParams {
00028 public:
00029         AlignmentParams();
00030         virtual ~AlignmentParams();
00031 
00032         Sequence* getSequence(int id);
00033         vector<Sequence*> getSequences();
00034         void addSequence(Sequence* sequence);
00035         void swapSequences();
00036 
00037         int getAlignmentMethod() const;
00038         void setAlignmentMethod(int alignmentMethod);
00039 
00040         int getGapOpen() const;
00041         int getGapExtension() const;
00042         void setAffineGapPenalties(int gapOpen, int gapExtension);
00043 
00044         int getMatch() const;
00045         int getMismatch() const;
00046         void setMatchMismatchScores(int match, int mismatch);
00047 
00048         int getPenaltySystem() const;
00049         void setPenaltySystem(int penaltySystem);
00050 
00051         int getScoreSystem() const;
00052         void setScoreSystem(int scoreSystem);
00053 
00054         int getSequencesCount() const;
00055 
00056         void printParams(FILE* file);
00057 private:
00058         vector<Sequence*> sequences;
00059 
00060         int alignmentMethod;
00061         int penaltySystem;
00062         int scoreSystem;
00063 
00064         int match;
00065         int mismatch;
00066 
00067         int gapOpen;
00068         int gapExtension;
00069 
00070 };
00071 
00072 #endif /* ALIGNMENTPARAMS_H_ */