MASA-Core: Constants.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 CONSTANTS_HPP_
00023 #define CONSTANTS_HPP_
00024 
00025 
00026 #define FLAG_CLEAR_N    0x0004
00027 #define FLAG_COMPLEMENT 0x0002
00028 #define FLAG_REVERSE    0x0001
00029 
00030 #define SEQUENCE_TYPE_DNA                               (1)
00031 #define SEQUENCE_TYPE_RNA                               (2)
00032 #define SEQUENCE_TYPE_PROTEIN                   (3)
00033 #define SEQUENCE_TYPE_UNKNOWN                   (255)
00034 
00035 
00036 #define ALIGNMENT_METHOD_GLOBAL         (1)
00037 #define ALIGNMENT_METHOD_LOCAL          (2)
00038 
00039 #define PENALTY_LINEAR_GAP                      (1)
00040 #define PENALTY_AFFINE_GAP                      (2)
00041 
00042 #define SCORE_MATCH_MISMATCH            (1)
00043 #define SCORE_SIMILARITY_MATRIX         (2)
00044 
00045 
00046 #endif /* CONSTANTS_HPP_ */